Publications
The ‘Ike Wai project publications section provides a list sorted by year of publications produced as a result of this research.
2020
Dudley, B D; Hughes, R F; Asner, G P; Baldwin, J A; Miyazawa, Y; Dulai, H; Waters, C; Bishop, J; Vaughn, N R; Yeh, J; Kettwich, S; MacKenzie, R A; Ostertag, R; Giambelluca, T
Hydrological effects of tree invasion on a dry coastal Hawaiian
ecosystem Journal Article
For. Ecol. Manage., 458 , pp. 117653, 2020.
@article{Dudley2020-sj,
title = {Hydrological effects of tree invasion on a dry coastal Hawaiian
ecosystem},
author = {B D Dudley and R F Hughes and G P Asner and J A Baldwin and Y Miyazawa and H Dulai and C Waters and J Bishop and N R Vaughn and J Yeh and S Kettwich and R A MacKenzie and R Ostertag and T Giambelluca},
year = {2020},
date = {2020-02-01},
journal = {For. Ecol. Manage.},
volume = {458},
pages = {117653},
abstract = {In ecosystems invaded by non-native plants invasion effects are
often spatially variable, and this variability is difficult to
capture via plot-scale sampling. We used airborne high-resolution
LiDAR (Light Detection and Ranging) to generate spatially
explicit and contiguous information on hydrological effects of
invasive trees (Prosopis pallida (Humb. & Bonpl. ex Willd.)
Kunth). We developed regression relationships between LiDAR
metrics (i.e., ground elevation and tree canopy height) and
plot-scale measurements of vegetation stem water $delta$18O, to
assess groundwater use, and transpiration rates. We used
electrical resistivity imaging to assess subsurface geology and
hydrology and their relationships to P. pallida stand structure.
P. pallida biomass and transpiration varied greatly across the
study area; both were controlled by depth to groundwater. Stem
water $delta$18O values (-8.6 to 3.7‰) indicated a threshold
ground elevation of ca. 15 m above sea level, above which P.
pallida could not access groundwater; this threshold corresponded
to declines in tree biomass and height. Transpiration modelled
across the study area was 0.034 $pm$ 0.017 mm day−1, but over
98% of transpiration came from the ca. 25% of the total study
area where groundwater depths were less than 15 m. Our
combination of methods offers a new way to incorporate fine-scale
spatial variation into estimation of plant invasion effects on
hydrology, increase our understanding of interactions of geology,
hydrology, and biology in such invasions, and prioritise areas
for control in well-advanced invasions.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
In ecosystems invaded by non-native plants invasion effects are
often spatially variable, and this variability is difficult to
capture via plot-scale sampling. We used airborne high-resolution
LiDAR (Light Detection and Ranging) to generate spatially
explicit and contiguous information on hydrological effects of
invasive trees (Prosopis pallida (Humb. & Bonpl. ex Willd.)
Kunth). We developed regression relationships between LiDAR
metrics (i.e., ground elevation and tree canopy height) and
plot-scale measurements of vegetation stem water $delta$18O, to
assess groundwater use, and transpiration rates. We used
electrical resistivity imaging to assess subsurface geology and
hydrology and their relationships to P. pallida stand structure.
P. pallida biomass and transpiration varied greatly across the
study area; both were controlled by depth to groundwater. Stem
water $delta$18O values (-8.6 to 3.7‰) indicated a threshold
ground elevation of ca. 15 m above sea level, above which P.
pallida could not access groundwater; this threshold corresponded
to declines in tree biomass and height. Transpiration modelled
across the study area was 0.034 $pm$ 0.017 mm day−1, but over
98% of transpiration came from the ca. 25% of the total study
area where groundwater depths were less than 15 m. Our
combination of methods offers a new way to incorporate fine-scale
spatial variation into estimation of plant invasion effects on
hydrology, increase our understanding of interactions of geology,
hydrology, and biology in such invasions, and prioritise areas
for control in well-advanced invasions. Regnery, Julia; Li, Dong; Lee, Jonghyun; Smits, Kathleen M; Sharp, Jonathan O
Hydrogeochemical and microbiological effects of simulated
recharge and drying within a 2D meso-scale aquifer Journal Article
Chemosphere, 241 , pp. 125116, 2020.
@article{Regnery2020-hd,
title = {Hydrogeochemical and microbiological effects of simulated
recharge and drying within a 2D meso-scale aquifer},
author = {Julia Regnery and Dong Li and Jonghyun Lee and Kathleen M Smits and Jonathan O Sharp},
year = {2020},
date = {2020-02-01},
journal = {Chemosphere},
volume = {241},
pages = {125116},
abstract = {Oscillating cycles of dewatering (termed drying) and rewetting
during managed aquifer recharge (MAR) are used to maintain
infiltration rates and could also exert an influence on
subsurface microbial structure and respiratory processes.
Despite this practice, little knowledge is available about
changes to microbial community structure and trace organic
chemical biodegradation potential in MAR systems under these
conditions. A biologically active two-dimensional (2D)
synthetic MAR system equipped with automated sensors
(temperature, water pressure, conductivity, soil moisture,
oxidation-reduction potential) and embedded water and soil
sampling ports was used to test and model these important
subsurface processes at the meso-scale. The fate and transport
of the antiepileptic drug carbamazepine, the antibiotics
sulfamethoxazole and trimethoprim, and the flame retardant
tris (2-chloroethyl) phosphate were simulated using the finite
element analysis model, FEFLOW. All of these compounds exhibit
moderate to poor biodegradability in MAR systems. Within the
operational MAR scenario tested, three episodic drying cycles
spanning between 18 and 24 days were conducted over a period
of 184 days. Notably, cessation of flow and partial dewatering
of the 2D synthetic aquifer during dry cycles caused no
measurable decrease in soil moisture content beyond the
near-surface layer. The episodic flow introduction and
dewatering cycles in turn had little impact on overall trace
organic chemical biotransformation behavior and soil microbial
community structure. However, spatial differences in
oxidation-reduction potential and soil moisture were both
identified as significant environmental predictors for
microbial community structure in the 2D synthetic aquifer.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Oscillating cycles of dewatering (termed drying) and rewetting
during managed aquifer recharge (MAR) are used to maintain
infiltration rates and could also exert an influence on
subsurface microbial structure and respiratory processes.
Despite this practice, little knowledge is available about
changes to microbial community structure and trace organic
chemical biodegradation potential in MAR systems under these
conditions. A biologically active two-dimensional (2D)
synthetic MAR system equipped with automated sensors
(temperature, water pressure, conductivity, soil moisture,
oxidation-reduction potential) and embedded water and soil
sampling ports was used to test and model these important
subsurface processes at the meso-scale. The fate and transport
of the antiepileptic drug carbamazepine, the antibiotics
sulfamethoxazole and trimethoprim, and the flame retardant
tris (2-chloroethyl) phosphate were simulated using the finite
element analysis model, FEFLOW. All of these compounds exhibit
moderate to poor biodegradability in MAR systems. Within the
operational MAR scenario tested, three episodic drying cycles
spanning between 18 and 24 days were conducted over a period
of 184 days. Notably, cessation of flow and partial dewatering
of the 2D synthetic aquifer during dry cycles caused no
measurable decrease in soil moisture content beyond the
near-surface layer. The episodic flow introduction and
dewatering cycles in turn had little impact on overall trace
organic chemical biotransformation behavior and soil microbial
community structure. However, spatial differences in
oxidation-reduction potential and soil moisture were both
identified as significant environmental predictors for
microbial community structure in the 2D synthetic aquifer. Dores, Daniel; Lautze, Nicole
Preliminary assessment of ground-source heat exchangers for
cooling in Hawai`i Journal Article
Sustainable Energy Technologies and Assessments, 37 , pp. 100579, 2020.
@article{Dores2020-mg,
title = {Preliminary assessment of ground-source heat exchangers for
cooling in Hawai`i},
author = {Daniel Dores and Nicole Lautze},
year = {2020},
date = {2020-02-01},
journal = {Sustainable Energy Technologies and Assessments},
volume = {37},
pages = {100579},
abstract = {This study provides a preliminary assessment of ground source
heat exchangers (GSHE) for cooling applications in the
tropical environment of Hawai`i. Recent demonstrations proved
GSHE capacity for space cooling in tropical southeast Asia. We
present multiple engineering scenarios in which GSHE could be
feasible across Hawai`i, highlighting regions of interest.
Limestone and basalt provide the best host geology, feasible
when air-ground temperature differences are >4 C and cooling
is only required for Hawai`i's five summer months. This work
investigates the effect of varying input parameters such as
energy efficiency ratio, rock thermal conductivity, piping
thermal resistance, temperature gradient, and fraction of time
operating on the length of cooling loop required to
successfully operate a GSHE. Maps of depth to water are
provided, as well as calculations of Peclet numbers for
basalt, limestone, and alluvium. Basalt's Peclet number shows
advection is a more dominant process than conduction in heat
exchange; limestone has equivalent advective and conductive
processes; alluvium is dominated by conduction. Thus, both
basalt and limestone may have an increased capacity to
efficiently act as heat sinks in Hawaiian environments as
groundwater flow could additionally transfer heat through
advection, not relying solely on the calculated capacity of
conductive heat exchange.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
This study provides a preliminary assessment of ground source
heat exchangers (GSHE) for cooling applications in the
tropical environment of Hawai`i. Recent demonstrations proved
GSHE capacity for space cooling in tropical southeast Asia. We
present multiple engineering scenarios in which GSHE could be
feasible across Hawai`i, highlighting regions of interest.
Limestone and basalt provide the best host geology, feasible
when air-ground temperature differences are >4 C and cooling
is only required for Hawai`i's five summer months. This work
investigates the effect of varying input parameters such as
energy efficiency ratio, rock thermal conductivity, piping
thermal resistance, temperature gradient, and fraction of time
operating on the length of cooling loop required to
successfully operate a GSHE. Maps of depth to water are
provided, as well as calculations of Peclet numbers for
basalt, limestone, and alluvium. Basalt's Peclet number shows
advection is a more dominant process than conduction in heat
exchange; limestone has equivalent advective and conductive
processes; alluvium is dominated by conduction. Thus, both
basalt and limestone may have an increased capacity to
efficiently act as heat sinks in Hawaiian environments as
groundwater flow could additionally transfer heat through
advection, not relying solely on the calculated capacity of
conductive heat exchange. Nelson, Sara H; Bremer, Leah L; Prado, Kelly Meza; Brauman, Kate A
The Political Life of Natural Infrastructure: Water Funds and
Alternative Histories of Payments for Ecosystem Services in
Valle del Cauca, Colombia Journal Article
Development & Change, 51 (1), pp. 26–50, 2020.
@article{Nelson2020-jk,
title = {The Political Life of Natural Infrastructure: Water Funds and
Alternative Histories of Payments for Ecosystem Services in
Valle del Cauca, Colombia},
author = {Sara H Nelson and Leah L Bremer and Kelly Meza Prado and Kate A Brauman},
year = {2020},
date = {2020-01-01},
journal = {Development & Change},
volume = {51},
number = {1},
pages = {26--50},
publisher = {Wiley-Blackwell},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Amato, Daniel W; Whittier, Robert B; Dulai, Henrietta; Smith, Celia M
Algal bioassays detect modeled loading of wastewater-derived
nitrogen in coastal waters of O'AHU, HAWAI'I Journal Article
Mar. Pollut. Bull., 150 , pp. 110668, 2020.
@article{Amato2020-in,
title = {Algal bioassays detect modeled loading of wastewater-derived
nitrogen in coastal waters of O'AHU, HAWAI'I},
author = {Daniel W Amato and Robert B Whittier and Henrietta Dulai and Celia M Smith},
year = {2020},
date = {2020-01-01},
journal = {Mar. Pollut. Bull.},
volume = {150},
pages = {110668},
abstract = {Previous studies indicate coastlines are at risk of wastewater
contamination from injection wells, cesspools, and septic
systems. In this study, common marine algae were used to
ground-truth modeled loading of wastewater-derived N to
coastlines of O'ahu, Hawai'i. Macroalgae were collected and/or
deployed at 118 sites and analyzed for tissue $delta$15N and N
%. Wastewater source locations were used to estimate
wastewater-derived N in groundwater with the modeling software
MT3DMS/MODFLOW. Algal bioassays identified six coastal regions
subjected to elevated wastewater-derived N loading. In a case
study, submarine groundwater discharge (estimated by 222Rn mass
balance) was related to wastewater loading from onsite sewage
disposal systems (OSDS) and municipal wastewater injection wells in Waim=analo. The highest 222Rn-derived SGD rate and N flux
were 21.4 m3/m/d and 62.6 g/m/d, respectively. The results of
this study suggest that OSDS and injection wells discharge
substantial volumes of wastewater and N across broad regions of
coastal O'ahu.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Previous studies indicate coastlines are at risk of wastewater
contamination from injection wells, cesspools, and septic
systems. In this study, common marine algae were used to
ground-truth modeled loading of wastewater-derived N to
coastlines of O'ahu, Hawai'i. Macroalgae were collected and/or
deployed at 118 sites and analyzed for tissue $delta$15N and N
%. Wastewater source locations were used to estimate
wastewater-derived N in groundwater with the modeling software
MT3DMS/MODFLOW. Algal bioassays identified six coastal regions
subjected to elevated wastewater-derived N loading. In a case
study, submarine groundwater discharge (estimated by 222Rn mass
balance) was related to wastewater loading from onsite sewage
disposal systems (OSDS) and municipal wastewater injection wells in Waim=analo. The highest 222Rn-derived SGD rate and N flux
were 21.4 m3/m/d and 62.6 g/m/d, respectively. The results of
this study suggest that OSDS and injection wells discharge
substantial volumes of wastewater and N across broad regions of
coastal O'ahu. Endress, Lee H; Roumasset, James A; Wada, Christopher A
Do Natural Disasters Make Sustainable Growth Impossible? Journal Article
Economics of Disasters and Climate Change, 2020.
@article{Endress2020-xv,
title = {Do Natural Disasters Make Sustainable Growth Impossible?},
author = {Lee H Endress and James A Roumasset and Christopher A Wada},
year = {2020},
date = {2020-01-01},
journal = {Economics of Disasters and Climate Change},
abstract = {We consider the prospects for sustainable growth using expected
utility models of optimal investment under threat from natural
disasters. Adoption of a continuous time, stochastic Ramsey
growth model over an infinite time horizon permits the analysis
of sustainability under uncertainty regarding adverse events,
including both one-time and recurrent disasters. As appropriate
to small economies, we consider adaptation to the risk of
disaster. Natural disasters reduce capital stocks and disrupt the
optimal consumption and felicity paths. While the time path of
inter-temporal welfare might consequently shift downward, the
path may still be non-decreasing over time, even without adding
strong or weak sustainability constraints. Prudent disaster
preparedness includes precautionary investment in productive
capital, programs of adaptation to disaster risk, and avoiding
distortionary policies undermining the prospects of optimality
and sustainability.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
We consider the prospects for sustainable growth using expected
utility models of optimal investment under threat from natural
disasters. Adoption of a continuous time, stochastic Ramsey
growth model over an infinite time horizon permits the analysis
of sustainability under uncertainty regarding adverse events,
including both one-time and recurrent disasters. As appropriate
to small economies, we consider adaptation to the risk of
disaster. Natural disasters reduce capital stocks and disrupt the
optimal consumption and felicity paths. While the time path of
inter-temporal welfare might consequently shift downward, the
path may still be non-decreasing over time, even without adding
strong or weak sustainability constraints. Prudent disaster
preparedness includes precautionary investment in productive
capital, programs of adaptation to disaster risk, and avoiding
distortionary policies undermining the prospects of optimality
and sustainability.
2019
Attias, Eric; Amalokwu, Kelvin; Watts, Millie; Falcon-Suarez, Ismael Himar; North, Laurence; Hu, Gao Wei; Best, Angus I; Weitemeyer, Karen; Minshull, Tim A
Gas hydrate quantification at a pockmark offshore Norway from
joint effective medium modelling of resistivity and seismic
velocity Journal Article
Mar. Pet. Geol., pp. 104151, 2019.
@article{Attias2019-bw,
title = {Gas hydrate quantification at a pockmark offshore Norway from
joint effective medium modelling of resistivity and seismic
velocity},
author = {Eric Attias and Kelvin Amalokwu and Millie Watts and Ismael Himar Falcon-Suarez and Laurence North and Gao Wei Hu and Angus I Best and Karen Weitemeyer and Tim A Minshull},
year = {2019},
date = {2019-12-01},
journal = {Mar. Pet. Geol.},
pages = {104151},
abstract = {Methane emissions from gas hydrate deposits along continental
margins may alter the biogeophysical properties of marine
environments, both on local and regional scales. The saturation
of a gas hydrate deposit is commonly calculated using the elastic
or electrical properties measured remotely or in-situ at the site
of interest. Here, we used a combination of controlled-source
electromagnetic (CSEM), seismic and sediment core data obtained
in the Nyegga region, offshore Norway, in a joint
elastic-electrical approach to quantify marine gas hydrates found
within the CNE03 pockmark. Multiscale analysis of two sediment
cores reveals significant differences between the CNE03 pockmark
and a reference site located approximately 150 m northwest of
CNE03. Gas hydrates and chemosynthetic bivalves were observed in
the CNE03 sediments collected. The seismic velocity and
electrical resistivity measured in the CNE03 sediment core are
consistent with the P-wave velocity (VP) and resistivity values
derived from seismic and CSEM remote sensing datasets,
respectively. The VP gradually increases (∼1.75--1.9 km/s) with
depth within the CNE03 pipe-like structure, whereas the
resistivity anomaly remains ∼3 $Ømega$m. A joint interpretation
of the collocated seismic and CSEM data using a joint
elastic-electrical effective medium model suggests that for the
porosity range 0.55--0.65, the gas hydrate saturation within the
CNE03 hydrate stability zone varies with depth between ∼20 and
48%. At 0.6 porosity, the hydrate saturation within CNE03 varies
between ∼23 and 37%, whereas the weighted mean saturation is
∼30%. Our results demonstrate that a well-constrained gas
hydrate quantification can be accomplished by coupling P-wave
velocity and CSEM resistivity data through joint
elastic-electrical effective medium modelling. The approach
applied in this study can be used as a framework to quantify
hydrate in various marine sediments.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Methane emissions from gas hydrate deposits along continental
margins may alter the biogeophysical properties of marine
environments, both on local and regional scales. The saturation
of a gas hydrate deposit is commonly calculated using the elastic
or electrical properties measured remotely or in-situ at the site
of interest. Here, we used a combination of controlled-source
electromagnetic (CSEM), seismic and sediment core data obtained
in the Nyegga region, offshore Norway, in a joint
elastic-electrical approach to quantify marine gas hydrates found
within the CNE03 pockmark. Multiscale analysis of two sediment
cores reveals significant differences between the CNE03 pockmark
and a reference site located approximately 150 m northwest of
CNE03. Gas hydrates and chemosynthetic bivalves were observed in
the CNE03 sediments collected. The seismic velocity and
electrical resistivity measured in the CNE03 sediment core are
consistent with the P-wave velocity (VP) and resistivity values
derived from seismic and CSEM remote sensing datasets,
respectively. The VP gradually increases (∼1.75--1.9 km/s) with
depth within the CNE03 pipe-like structure, whereas the
resistivity anomaly remains ∼3 $Ømega$m. A joint interpretation
of the collocated seismic and CSEM data using a joint
elastic-electrical effective medium model suggests that for the
porosity range 0.55--0.65, the gas hydrate saturation within the
CNE03 hydrate stability zone varies with depth between ∼20 and
48%. At 0.6 porosity, the hydrate saturation within CNE03 varies
between ∼23 and 37%, whereas the weighted mean saturation is
∼30%. Our results demonstrate that a well-constrained gas
hydrate quantification can be accomplished by coupling P-wave
velocity and CSEM resistivity data through joint
elastic-electrical effective medium modelling. The approach
applied in this study can be used as a framework to quantify
hydrate in various marine sediments. Jansen, C; Shimoda, L M N; Kawakami, J K; Ang, L; Bacani, A J; Baker, J D; Badowski, C; Speck, M; Stokes, A J; Small-Howard, A L; Turner, H
Myrcene and terpene regulation of TRPV1 Journal Article
Channels, 13 (1), pp. 344–366, 2019.
@article{Jansen2019-ce,
title = {Myrcene and terpene regulation of TRPV1},
author = {C Jansen and L M N Shimoda and J K Kawakami and L Ang and A J Bacani and J D Baker and C Badowski and M Speck and A J Stokes and A L Small-Howard and H Turner},
year = {2019},
date = {2019-12-01},
journal = {Channels},
volume = {13},
number = {1},
pages = {344--366},
abstract = {Nociceptive Transient Receptor Potential channels such as TRPV1
are targets for treating pain. Both antagonism and agonism of TRP
channels can promote analgesia, through inactivation and chronic
desensitization. Since plant-derived mixtures of cannabinoids and
the Cannabis component myrcene have been suggested as pain
therapeutics, we screened terpenes found in Cannabis for activity
at TRPV1. We used inducible expression of TRPV1 to examine
TRPV1-dependency of terpene-induced calcium flux responses.
Terpenes contribute differentially to calcium fluxes via TRPV1
induced by Cannabis-mimetic cannabinoid/terpenoid mixtures.
Myrcene dominates the TRPV1-mediated calcium responses seen with
terpenoid mixtures. Myrcene-induced calcium influx is inhibited
by the TRPV1 inhibitor capsazepine and Myrcene elicits TRPV1
currents in the whole-cell patch-clamp configuration. TRPV1
currents are highly sensitive to internal calcium. When Myrcene
currents are evoked, they are distinct from capsaicin responses
on the basis of Imax and their lack of shift to a pore-dilated
state. Myrcene pre-application and residency at TRPV1 appears to
negatively impact subsequent responses to TRPV1 ligands such as
Cannabidiol, indicating allosteric modulation and possible
competition by Myrcene. Molecular docking studies suggest a
non-covalent interaction site for Myrcene in TRPV1 and identifies
key residues that form partially overlapping Myrcene and
Cannabidiol binding sites. We identify several non-Cannabis
plant-derived sources of Myrcene and other compounds targeting
nociceptive TRPs using a data mining approach focused on
analgesics suggested by non-Western Traditional Medical Systems.
These data establish TRPV1 as a target of Myrcene and suggest the
therapeutic potential of analgesic formulations containing
Myrcene.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Nociceptive Transient Receptor Potential channels such as TRPV1
are targets for treating pain. Both antagonism and agonism of TRP
channels can promote analgesia, through inactivation and chronic
desensitization. Since plant-derived mixtures of cannabinoids and
the Cannabis component myrcene have been suggested as pain
therapeutics, we screened terpenes found in Cannabis for activity
at TRPV1. We used inducible expression of TRPV1 to examine
TRPV1-dependency of terpene-induced calcium flux responses.
Terpenes contribute differentially to calcium fluxes via TRPV1
induced by Cannabis-mimetic cannabinoid/terpenoid mixtures.
Myrcene dominates the TRPV1-mediated calcium responses seen with
terpenoid mixtures. Myrcene-induced calcium influx is inhibited
by the TRPV1 inhibitor capsazepine and Myrcene elicits TRPV1
currents in the whole-cell patch-clamp configuration. TRPV1
currents are highly sensitive to internal calcium. When Myrcene
currents are evoked, they are distinct from capsaicin responses
on the basis of Imax and their lack of shift to a pore-dilated
state. Myrcene pre-application and residency at TRPV1 appears to
negatively impact subsequent responses to TRPV1 ligands such as
Cannabidiol, indicating allosteric modulation and possible
competition by Myrcene. Molecular docking studies suggest a
non-covalent interaction site for Myrcene in TRPV1 and identifies
key residues that form partially overlapping Myrcene and
Cannabidiol binding sites. We identify several non-Cannabis
plant-derived sources of Myrcene and other compounds targeting
nociceptive TRPs using a data mining approach focused on
analgesics suggested by non-Western Traditional Medical Systems.
These data establish TRPV1 as a target of Myrcene and suggest the
therapeutic potential of analgesic formulations containing
Myrcene. Wada, Christopher A; Pongkijvorasin, Sittidaj; Burnett, Kimberly M
Mountain-to-sea ecological-resource management: forested
watersheds, coastal aquifers, and groundwater dependent
ecosystems Journal Article
Res. Energy Econ., pp. 101146, 2019.
@article{Wada2019-iy,
title = {Mountain-to-sea ecological-resource management: forested
watersheds, coastal aquifers, and groundwater dependent
ecosystems},
author = {Christopher A Wada and Sittidaj Pongkijvorasin and Kimberly M Burnett},
year = {2019},
date = {2019-12-01},
journal = {Res. Energy Econ.},
pages = {101146},
abstract = {Improving the understanding of connections spanning from mountain
to sea and integrating those connections into decision models
have been increasingly recognized as key to effective coastal
resource management. In this paper, we aim to improve our
understanding of the relative importance of linkages between a
forested watershed, a coastal groundwater aquifer, and a
nearshore marine groundwater-dependent ecosystem (GDE) using a
dynamic groundwater optimization framework and simple ecosystem equations. Data from the K=iholo aquifer on the Kona Coast of
Hawai`i Island are used to numerically illustrate optimal joint
management strategies and test the sensitivity of those
strategies to variations in physical and behavioral parameter
values. We find that for a plausible range of watershed
management costs, protecting part of the recharge capture area is
always optimal. Without watershed protection, maintaining a safe
minimum standard growth rate for a GDE-dependent marine indicator
species, reduces net present value non-trivially, but optimal
investment in watershed conservation offsets that potential
reduction by 75%. In general, we find that optimal watershed
management and groundwater pumping are most sensitive to changes
in water demand growth and parameters that describe nearshore
salinity.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Improving the understanding of connections spanning from mountain
to sea and integrating those connections into decision models
have been increasingly recognized as key to effective coastal
resource management. In this paper, we aim to improve our
understanding of the relative importance of linkages between a
forested watershed, a coastal groundwater aquifer, and a
nearshore marine groundwater-dependent ecosystem (GDE) using a
dynamic groundwater optimization framework and simple ecosystem equations. Data from the K=iholo aquifer on the Kona Coast of
Hawai`i Island are used to numerically illustrate optimal joint
management strategies and test the sensitivity of those
strategies to variations in physical and behavioral parameter
values. We find that for a plausible range of watershed
management costs, protecting part of the recharge capture area is
always optimal. Without watershed protection, maintaining a safe
minimum standard growth rate for a GDE-dependent marine indicator
species, reduces net present value non-trivially, but optimal
investment in watershed conservation offsets that potential
reduction by 75%. In general, we find that optimal watershed
management and groundwater pumping are most sensitive to changes
in water demand growth and parameters that describe nearshore
salinity. Jansen, C; Shimoda, L M N; Starkus, J; Lange, I; Rysavy, N; Maaetoft-Udsen, K; Tobita, C; Stokes, A J; Turner, H
In vitro exposure to Hymenoptera venom and constituents activates
discrete ionotropic pathways in mast cells Journal Article
Channels, 13 (1), pp. 264–286, 2019.
@article{Jansen2019-hu,
title = {In vitro exposure to Hymenoptera venom and constituents activates
discrete ionotropic pathways in mast cells},
author = {C Jansen and L M N Shimoda and J Starkus and I Lange and N Rysavy and K Maaetoft-Udsen and C Tobita and A J Stokes and H Turner},
year = {2019},
date = {2019-12-01},
journal = {Channels},
volume = {13},
number = {1},
pages = {264--286},
abstract = {Calcium entry is central to the functional processes in mast
cells and basophils that contribute to the induction and
maintenance of inflammatory responses. Mast cells and basophils
express an array of calcium channels, which mediate responses to
diverse stimuli triggered by small bioactive molecules,
physicochemical stimuli and immunological inputs including
antigens and direct immune cell interactions. These cells are
also highly responsive to certain venoms (such as Hymenoptera
envenomations), which cause histamine secretion, cytokine release
and an array of pro-inflammatory functional responses. There are
gaps in our understanding of the coupling of venom exposure to
specific signaling pathways such as activation of calcium
channels. In the present study, we performed a current survey of
a model mast cell line selected for its pleiotropic
responsiveness to multiple pro-inflammatory inputs. As a
heterogenous stimulus, Hymenoptera venom activates multiple
classes of conductance at the population level but tend to lead
to the measurement of only one type of conductance per cell,
despite the cell co-expressing multiple channel types. The data
show that ICRAC, IARC, and TRPV-like currents are present in the
model mast cell populations and respond to venom exposure. We
further assessed individual venom components, specifically
secretagogues and arachidonic acid, and identified the
conductances associated with these stimuli in mast cells.
Single-cell calcium assays and immunofluorescence analysis show
that there is heterogeneity of channel expression across the cell
population, but this heterogeneity does not explain the apparent
selectivity for specific channels in response to exposure to
venom as a composite stimulus.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Calcium entry is central to the functional processes in mast
cells and basophils that contribute to the induction and
maintenance of inflammatory responses. Mast cells and basophils
express an array of calcium channels, which mediate responses to
diverse stimuli triggered by small bioactive molecules,
physicochemical stimuli and immunological inputs including
antigens and direct immune cell interactions. These cells are
also highly responsive to certain venoms (such as Hymenoptera
envenomations), which cause histamine secretion, cytokine release
and an array of pro-inflammatory functional responses. There are
gaps in our understanding of the coupling of venom exposure to
specific signaling pathways such as activation of calcium
channels. In the present study, we performed a current survey of
a model mast cell line selected for its pleiotropic
responsiveness to multiple pro-inflammatory inputs. As a
heterogenous stimulus, Hymenoptera venom activates multiple
classes of conductance at the population level but tend to lead
to the measurement of only one type of conductance per cell,
despite the cell co-expressing multiple channel types. The data
show that ICRAC, IARC, and TRPV-like currents are present in the
model mast cell populations and respond to venom exposure. We
further assessed individual venom components, specifically
secretagogues and arachidonic acid, and identified the
conductances associated with these stimuli in mast cells.
Single-cell calcium assays and immunofluorescence analysis show
that there is heterogeneity of channel expression across the cell
population, but this heterogeneity does not explain the apparent
selectivity for specific channels in response to exposure to
venom as a composite stimulus. Aldan, Johnny T; Jansen, Chad; Speck, Mark; Maaetoft-Udsen, Kristina; Cordasco, Edward A; Faiai, Mata'uitafa; Shimoda, Lori M N; Greineisen, William E; Turner, Helen; Stokes, Alexander J
Insulin-induced lipid body accumulation is accompanied by lipid
remodelling in model mast cells Journal Article
Adipocyte, 8 (1), pp. 265–279, 2019.
@article{Aldan2019-np,
title = {Insulin-induced lipid body accumulation is accompanied by lipid
remodelling in model mast cells},
author = {Johnny T Aldan and Chad Jansen and Mark Speck and Kristina Maaetoft-Udsen and Edward A Cordasco and Mata'uitafa Faiai and Lori M N Shimoda and William E Greineisen and Helen Turner and Alexander J Stokes},
year = {2019},
date = {2019-12-01},
journal = {Adipocyte},
volume = {8},
number = {1},
pages = {265--279},
abstract = {Mast cell lipid bodies are key to initiation, maintenance and
resolution of inflammatory responses in tissue. Mast cell lines,
primary bone marrow-derived mast cells and peripheral blood
basophils present a 'steatotic' phenotype in response to chronic
insulin exposure, where cells become loaded with lipid bodies.
Here we show this state is associated with reduced histamine
release, but increased capacity to release bioactive lipids. We
describe the overall lipid phenotype of mast cells in this
insulin-induced steatotic state and the consequences for critical
cellular lipid classes involved in stages of inflammation. We
show significant insulin-induced shifts in specific lipid
classes, especially arachidonic acid derivatives, MUFA and PUFA,
the EPA/DHA ratio, and in cardiolipins, especially those
conjugated to certain DHA and EPAs. Functionally, insulin
exposure markedly alters the Fc$epsilon$RI-induced release of
Series 4 leukotriene LTC4, Series 2 prostaglandin PGD2,
Resolvin-D1, Resolvin-D2 and Resolvin-1, reflecting the expanded
precursor pools and impact on both the pro-inflammation and
pro-resolution bioactive lipids that are released during mast
cell activation. Chronic hyperinsulinemia is a feature of obesity
and progression to Type 2 Diabetes, these data suggest that mast
cell release of key lipid mediators is altered in patients with
metabolic syndrome.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Mast cell lipid bodies are key to initiation, maintenance and
resolution of inflammatory responses in tissue. Mast cell lines,
primary bone marrow-derived mast cells and peripheral blood
basophils present a 'steatotic' phenotype in response to chronic
insulin exposure, where cells become loaded with lipid bodies.
Here we show this state is associated with reduced histamine
release, but increased capacity to release bioactive lipids. We
describe the overall lipid phenotype of mast cells in this
insulin-induced steatotic state and the consequences for critical
cellular lipid classes involved in stages of inflammation. We
show significant insulin-induced shifts in specific lipid
classes, especially arachidonic acid derivatives, MUFA and PUFA,
the EPA/DHA ratio, and in cardiolipins, especially those
conjugated to certain DHA and EPAs. Functionally, insulin
exposure markedly alters the Fc$epsilon$RI-induced release of
Series 4 leukotriene LTC4, Series 2 prostaglandin PGD2,
Resolvin-D1, Resolvin-D2 and Resolvin-1, reflecting the expanded
precursor pools and impact on both the pro-inflammation and
pro-resolution bioactive lipids that are released during mast
cell activation. Chronic hyperinsulinemia is a feature of obesity
and progression to Type 2 Diabetes, these data suggest that mast
cell release of key lipid mediators is altered in patients with
metabolic syndrome. Hayes, Tanya; Grillos, Tara; Bremer, Leah L; Murtinho, Felipe; Shapiro, Elizabeth
Collective PES: More than the sum of individual incentives Journal Article
Environ. Sci. Policy, 102 , pp. 1–8, 2019.
@article{Hayes2019-an,
title = {Collective PES: More than the sum of individual incentives},
author = {Tanya Hayes and Tara Grillos and Leah L Bremer and Felipe Murtinho and Elizabeth Shapiro},
year = {2019},
date = {2019-12-01},
journal = {Environ. Sci. Policy},
volume = {102},
pages = {1--8},
abstract = {This study synthesizes findings from studies of the social and
behavioral outcomes of collective payment for ecosystem
services (PES) programs. The collective PES model is distinct
from the conventional PES model in that by working with
groups, not individuals, it breaks the direct relationship
between an individual's consent to participate, the economic
incentive and the expected conservation behavior. In doing so,
it raises concerns about whether the collective model is
effective and socially just. Here, we assess these concerns by
synthesizing findings on four distinct challenges for
collective PES: (i) voluntary and informed participation; (ii)
household compliance with PES restrictions; (iii) the balance
of costs and benefits across community members; and (iv) the
interaction with local governance conditions to address the
second-order collective action problem inherent in collective
PES. Through a review of 41 studies covering 16 collective PES
programs located in 12 countries, we find that collective PES
can change behavior and provide socioeconomic and ecological
benefits, but institutional context matters. Our review points
to how program design and local governance dynamics can
influence the ability of collective PES to attain desired
social and behavioral outcomes.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
This study synthesizes findings from studies of the social and
behavioral outcomes of collective payment for ecosystem
services (PES) programs. The collective PES model is distinct
from the conventional PES model in that by working with
groups, not individuals, it breaks the direct relationship
between an individual's consent to participate, the economic
incentive and the expected conservation behavior. In doing so,
it raises concerns about whether the collective model is
effective and socially just. Here, we assess these concerns by
synthesizing findings on four distinct challenges for
collective PES: (i) voluntary and informed participation; (ii)
household compliance with PES restrictions; (iii) the balance
of costs and benefits across community members; and (iv) the
interaction with local governance conditions to address the
second-order collective action problem inherent in collective
PES. Through a review of 41 studies covering 16 collective PES
programs located in 12 countries, we find that collective PES
can change behavior and provide socioeconomic and ecological
benefits, but institutional context matters. Our review points
to how program design and local governance dynamics can
influence the ability of collective PES to attain desired
social and behavioral outcomes. Horton, Jaime S; Shiraishi, Takuya; Alfulaij, Naghum; Small-Howard, Andrea L; Turner, Helen C; Kurokawa, Tatsuki; Mori, Yasuo; Stokes, Alexander J
``TRPV1 is a component of the atrial natriuretic signaling
complex, and using orally delivered antagonists, presents a valid
therapeutic target in the longitudinal reversal and treatment of
cardiac hypertrophy and heart failure'' Journal Article
Channels, 13 (1), pp. 1–16, 2019.
@article{Horton2019-cs,
title = {``TRPV1 is a component of the atrial natriuretic signaling
complex, and using orally delivered antagonists, presents a valid
therapeutic target in the longitudinal reversal and treatment of
cardiac hypertrophy and heart failure''},
author = {Jaime S Horton and Takuya Shiraishi and Naghum Alfulaij and Andrea L Small-Howard and Helen C Turner and Tatsuki Kurokawa and Yasuo Mori and Alexander J Stokes},
year = {2019},
date = {2019-12-01},
journal = {Channels},
volume = {13},
number = {1},
pages = {1--16},
abstract = {Activation of the atrial natriuretic signaling pathway is
intrinsic to the pathological responses associated with a range
of cardiovascular diseases that stress the heart, especially
those involved in sustained cardiac pressure overload which
induces hypertrophy and the pathological remodeling that
frequently leads to heart failure. We identify transient receptor
potential cation channel, subfamily V, member 1, as a regulated
molecular component, and therapeutic target of this signaling
system. Data show that TRPV1 is a physical component of the
natriuretic peptide A, cGMP, PKG signaling complex, interacting
with the Natriuretic Peptide Receptor 1 (NPR1), and upon binding
its ligand, Natriuretic Peptide A (NPPA, ANP) TRPV1 activation is
subsequently suppressed through production of cGMP and PKG
mediated phosphorylation of the TRPV1 channel. Further,
inhibition of TRPV1, with orally delivered drugs, suppresses
chamber and myocyte hypertrophy, and can longitudinally improve
in vivo heart function in mice exposed to chronic pressure
overload induced by transverse aortic constriction, reversing
pre-established hypertrophy induced by pressure load while
restoring chamber function. TRPV1 is a physical and regulated
component of the natriuretic peptide signaling system, and TRPV1
inhibition may provide a new treatment strategy for treating, and
reversing the loss of function associated with cardiac
hypertrophy and heart failure.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Activation of the atrial natriuretic signaling pathway is
intrinsic to the pathological responses associated with a range
of cardiovascular diseases that stress the heart, especially
those involved in sustained cardiac pressure overload which
induces hypertrophy and the pathological remodeling that
frequently leads to heart failure. We identify transient receptor
potential cation channel, subfamily V, member 1, as a regulated
molecular component, and therapeutic target of this signaling
system. Data show that TRPV1 is a physical component of the
natriuretic peptide A, cGMP, PKG signaling complex, interacting
with the Natriuretic Peptide Receptor 1 (NPR1), and upon binding
its ligand, Natriuretic Peptide A (NPPA, ANP) TRPV1 activation is
subsequently suppressed through production of cGMP and PKG
mediated phosphorylation of the TRPV1 channel. Further,
inhibition of TRPV1, with orally delivered drugs, suppresses
chamber and myocyte hypertrophy, and can longitudinally improve
in vivo heart function in mice exposed to chronic pressure
overload induced by transverse aortic constriction, reversing
pre-established hypertrophy induced by pressure load while
restoring chamber function. TRPV1 is a physical and regulated
component of the natriuretic peptide signaling system, and TRPV1
inhibition may provide a new treatment strategy for treating, and
reversing the loss of function associated with cardiac
hypertrophy and heart failure. Bruno, Barbara C; Wallace, Anne
Interpretive Panels for Geoheritage Sites: Guidelines for Design
and Evaluation Journal Article
Geoheritage, 2019.
@article{Bruno2019-ga,
title = {Interpretive Panels for Geoheritage Sites: Guidelines for Design
and Evaluation},
author = {Barbara C Bruno and Anne Wallace},
year = {2019},
date = {2019-11-01},
journal = {Geoheritage},
abstract = {Effective interpretive panels go far beyond conveying
information: they are highly engaging, instill passion, and
inspire visitors to engage in environmental stewardship. This
review paper on designing and evaluating interpretive panels at
geoheritage sites shares recommendations gleaned from experts in
conservation science, neuroscience, pedagogy, psychology, visual
arts, and communication. It emphasizes the importance of
developing a communication plan, knowing your audience, using
strong visuals, invoking storytelling and active learning
techniques, layering your message, being inclusive, choosing an
appropriate panel location, integrating evaluation throughout the
design process, and budgeting appropriately. An extensive
reference list is provided for further reading.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Effective interpretive panels go far beyond conveying
information: they are highly engaging, instill passion, and
inspire visitors to engage in environmental stewardship. This
review paper on designing and evaluating interpretive panels at
geoheritage sites shares recommendations gleaned from experts in
conservation science, neuroscience, pedagogy, psychology, visual
arts, and communication. It emphasizes the importance of
developing a communication plan, knowing your audience, using
strong visuals, invoking storytelling and active learning
techniques, layering your message, being inclusive, choosing an
appropriate panel location, integrating evaluation throughout the
design process, and budgeting appropriately. An extensive
reference list is provided for further reading. Bremer, Leah L; Wada, Christopher A; Medoff, Sarah; Page, Jonathan; Falinski, Kim; Burnett, Kimberly M
Contributions of native forest protection to local water supplies
in East Maui Journal Article
Sci. Total Environ., 688 , pp. 1422–1432, 2019.
@article{Bremer2019-eq,
title = {Contributions of native forest protection to local water supplies
in East Maui},
author = {Leah L Bremer and Christopher A Wada and Sarah Medoff and Jonathan Page and Kim Falinski and Kimberly M Burnett},
year = {2019},
date = {2019-10-01},
journal = {Sci. Total Environ.},
volume = {688},
pages = {1422--1432},
abstract = {Tropical forests provide a suite of benefits including
biodiversity, cultural value, and a range of ecosystem services.
Globally, there is increasing interest in incentivizing native
forest protection as a multi-benefit natural infrastructure
strategy to secure clean and ample water supplies. In addition to
conversion to agriculture and other non-forest land uses,
non-native species invasion represents a major threat to these
systems, particularly on islands. Whereas several recent efforts
have quantified the benefits of reforestation or avoided
agricultural expansion in tropical forest areas, the hydrologic
and associated economic benefits of avoided invasion have
received less attention. To address this gap, we quantified the
benefits of protecting native forest from conversion to
non-native forest in East Maui, Hawai'i in terms of groundwater
recharge, a highly valued hydrologic ecosystem service that water
utilities increasingly seek to co-finance. Compared with two
counterfactual invasion scenarios, the groundwater recharge
benefits of planned conservation activities reached 40.9 to 146.3
million cubic meters over 100 years depending on invasion rate
assumptions. This translated to 2.70 to 137.6 million dollars of
cost savings to the water utility in present value terms
(achieved through reducing reliance on more expensive water
alternatives) under a range of discount rates and water scarcity
assumptions. Our results suggest that investing in native forest
conservation provides an important hydrologic ecosystem service
benefit that complements the range of benefits provided by these
ecosystems. These findings demonstrate that co-financing native
forest conservation represents an important supply side option in
water resources planning.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Tropical forests provide a suite of benefits including
biodiversity, cultural value, and a range of ecosystem services.
Globally, there is increasing interest in incentivizing native
forest protection as a multi-benefit natural infrastructure
strategy to secure clean and ample water supplies. In addition to
conversion to agriculture and other non-forest land uses,
non-native species invasion represents a major threat to these
systems, particularly on islands. Whereas several recent efforts
have quantified the benefits of reforestation or avoided
agricultural expansion in tropical forest areas, the hydrologic
and associated economic benefits of avoided invasion have
received less attention. To address this gap, we quantified the
benefits of protecting native forest from conversion to
non-native forest in East Maui, Hawai'i in terms of groundwater
recharge, a highly valued hydrologic ecosystem service that water
utilities increasingly seek to co-finance. Compared with two
counterfactual invasion scenarios, the groundwater recharge
benefits of planned conservation activities reached 40.9 to 146.3
million cubic meters over 100 years depending on invasion rate
assumptions. This translated to 2.70 to 137.6 million dollars of
cost savings to the water utility in present value terms
(achieved through reducing reliance on more expensive water
alternatives) under a range of discount rates and water scarcity
assumptions. Our results suggest that investing in native forest
conservation provides an important hydrologic ecosystem service
benefit that complements the range of benefits provided by these
ecosystems. These findings demonstrate that co-financing native
forest conservation represents an important supply side option in
water resources planning. McKenzie, Trista; Dulai, Henrietta; Chang, Jennet
Parallels between stream and coastal water quality associated
with groundwater discharge Journal Article
PLoS One, 14 (10), pp. e0224513, 2019.
@article{McKenzie2019-ob,
title = {Parallels between stream and coastal water quality associated
with groundwater discharge},
author = {Trista McKenzie and Henrietta Dulai and Jennet Chang},
year = {2019},
date = {2019-10-01},
journal = {PLoS One},
volume = {14},
number = {10},
pages = {e0224513},
abstract = {Groundwater-surface water interactions drive water quality in
both streams and the coastal ocean, where groundwater discharge
occurs in streams as baseflow and along the coastline as
submarine groundwater discharge (SGD). Groundwater contributions
to streams and to the coastal ocean were quantified in three urban streams in K=ane'ohe Watershed, Hawai'i. We used radon
as a groundwater tracer to show that baseflow contributions to
streams ranged from 22 to 68% along their reaches leading to the coast of K=ane'ohe Bay. Total SGD was 4,500, 18,000, and
23,000 m3/day for the northwest, central, and southern sectors of
the bay, respectively. Total groundwater (stream baseflow + SGD)
dissolved nutrient fluxes were significantly greater than those
sourced from stream surface runoff. The studied streams exhibited
increasing nutrient levels downstream from groundwater inputs
with high nutrient concentrations, negatively impacting coastal
water quality. SGD dynamics were also assessed during the
anomalously high perigean spring tides in 2017, where SGD was
four times greater during the perigean spring tide compared to a
spring tide and resulted in strong shifts in N:P ratios,
suggesting that rising sea level stands may disrupt primary
productivity with greater frequency. This study demonstrates the
importance of considering baseflow inputs to streams to coastal
groundwater budgets and suggests that coastal water quality may
be improved through management and reduction of groundwater
contaminants.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Groundwater-surface water interactions drive water quality in
both streams and the coastal ocean, where groundwater discharge
occurs in streams as baseflow and along the coastline as
submarine groundwater discharge (SGD). Groundwater contributions
to streams and to the coastal ocean were quantified in three urban streams in K=ane'ohe Watershed, Hawai'i. We used radon
as a groundwater tracer to show that baseflow contributions to
streams ranged from 22 to 68% along their reaches leading to the coast of K=ane'ohe Bay. Total SGD was 4,500, 18,000, and
23,000 m3/day for the northwest, central, and southern sectors of
the bay, respectively. Total groundwater (stream baseflow + SGD)
dissolved nutrient fluxes were significantly greater than those
sourced from stream surface runoff. The studied streams exhibited
increasing nutrient levels downstream from groundwater inputs
with high nutrient concentrations, negatively impacting coastal
water quality. SGD dynamics were also assessed during the
anomalously high perigean spring tides in 2017, where SGD was
four times greater during the perigean spring tide compared to a
spring tide and resulted in strong shifts in N:P ratios,
suggesting that rising sea level stands may disrupt primary
productivity with greater frequency. This study demonstrates the
importance of considering baseflow inputs to streams to coastal
groundwater budgets and suggests that coastal water quality may
be improved through management and reduction of groundwater
contaminants. Arisdakessian, Cédric; Poirion, Olivier; Yunits, Breck; Zhu, Xun; Garmire, Lana X
DeepImpute: an accurate, fast, and scalable deep neural network
method to impute single-cell RNA-seq data Journal Article
Genome Biol., 20 (1), pp. 211, 2019.
@article{Arisdakessian2019-sc,
title = {DeepImpute: an accurate, fast, and scalable deep neural network
method to impute single-cell RNA-seq data},
author = {Cédric Arisdakessian and Olivier Poirion and Breck Yunits and Xun Zhu and Lana X Garmire},
year = {2019},
date = {2019-10-01},
journal = {Genome Biol.},
volume = {20},
number = {1},
pages = {211},
abstract = {Single-cell RNA sequencing (scRNA-seq) offers new opportunities
to study gene expression of tens of thousands of single cells
simultaneously. We present DeepImpute, a deep neural
network-based imputation algorithm that uses dropout layers and
loss functions to learn patterns in the data, allowing for
accurate imputation. Overall, DeepImpute yields better accuracy
than other six publicly available scRNA-seq imputation methods on
experimental data, as measured by the mean squared error or
Pearson's correlation coefficient. DeepImpute is an accurate,
fast, and scalable imputation tool that is suited to handle the
ever-increasing volume of scRNA-seq data, and is freely available
at https://github.com/lanagarmire/DeepImpute .},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Single-cell RNA sequencing (scRNA-seq) offers new opportunities
to study gene expression of tens of thousands of single cells
simultaneously. We present DeepImpute, a deep neural
network-based imputation algorithm that uses dropout layers and
loss functions to learn patterns in the data, allowing for
accurate imputation. Overall, DeepImpute yields better accuracy
than other six publicly available scRNA-seq imputation methods on
experimental data, as measured by the mean squared error or
Pearson's correlation coefficient. DeepImpute is an accurate,
fast, and scalable imputation tool that is suited to handle the
ever-increasing volume of scRNA-seq data, and is freely available
at https://github.com/lanagarmire/DeepImpute . McKenzie, Marie M; Giambelluca, Thomas W; Diaz, Henry F
Temperature trends in Hawaiʻi: A century of change, 1917--2016 Journal Article
Int. J. Climatol., 39 (10), pp. 3987–4001, 2019.
@article{McKenzie2019-ad,
title = {Temperature trends in Hawaiʻi: A century of change, 1917--2016},
author = {Marie M McKenzie and Thomas W Giambelluca and Henry F Diaz},
year = {2019},
date = {2019-08-01},
journal = {Int. J. Climatol.},
volume = {39},
number = {10},
pages = {3987--4001},
abstract = {Based on a revised and extended multi-station Hawai?i
Temperature Index (HTI), the mean air temperature in the
Hawaiian Islands has warmed significantly at 0.052°C/decade
(p?
was the warmest year on record at 0.924°C above the 100-year
mean (0.202°C). During each of the last four decades, mean
state-wide positive air temperature anomalies were greater
than those of any of the previous decades. Significant warming
trends for the last 100?years are evident at low-
(0.056°C/decade, p
(0.047°C/decade, p?
attributed to significant increases in minimum temperature
(0.072°C/decade, p?
downward trend in diurnal temperature range (?0.055°C/decade,
p?
correlations were found between HTI, the Pacific Decadal
Oscillation, and the Multivariate ENSO Index, indicating that
natural climate variability has a significant impact on
temperature in Hawai?i. Analysis of surface air temperatures
from NCEP/NCAR reanalysis data for the region of Hawai?i over
the last 69?years (1948?2016) and a mean atmospheric layer
temperature time series calculated from radiosonde-measured
thickness (distance between constant pressure surfaces) data
over the last 40?years (1977?2016) give results consistent
with the HTI. Finally, we compare temperature trends for
Hawaii's highest elevation station, Mauna Loa Observatory
(3,397?m), to those on another mountainous subtropical island
station in the Atlantic, Mt. Iza~na Observatory (2,373?m),
Tenerife, Canary Islands. Both stations sit above the local
temperature inversion layer and have virtually identical
significant warming trends of 0.19°C/decade (p?
between 1955 and 2016.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Based on a revised and extended multi-station Hawai?i
Temperature Index (HTI), the mean air temperature in the
Hawaiian Islands has warmed significantly at 0.052°C/decade
(p?<?0.01) over the past 100?years (1917?2016). The year 2016
was the warmest year on record at 0.924°C above the 100-year
mean (0.202°C). During each of the last four decades, mean
state-wide positive air temperature anomalies were greater
than those of any of the previous decades. Significant warming
trends for the last 100?years are evident at low-
(0.056°C/decade, p <?0.001) and high-elevations
(0.047°C/decade, p?<?0.01). Warming in Hawai?i is largely
attributed to significant increases in minimum temperature
(0.072°C/decade, p?<?0.001) resulting in a corresponding
downward trend in diurnal temperature range (?0.055°C/decade,
p?<?0.001) over the 100-year period. Significant positive
correlations were found between HTI, the Pacific Decadal
Oscillation, and the Multivariate ENSO Index, indicating that
natural climate variability has a significant impact on
temperature in Hawai?i. Analysis of surface air temperatures
from NCEP/NCAR reanalysis data for the region of Hawai?i over
the last 69?years (1948?2016) and a mean atmospheric layer
temperature time series calculated from radiosonde-measured
thickness (distance between constant pressure surfaces) data
over the last 40?years (1977?2016) give results consistent
with the HTI. Finally, we compare temperature trends for
Hawaii's highest elevation station, Mauna Loa Observatory
(3,397?m), to those on another mountainous subtropical island
station in the Atlantic, Mt. Iza~na Observatory (2,373?m),
Tenerife, Canary Islands. Both stations sit above the local
temperature inversion layer and have virtually identical
significant warming trends of 0.19°C/decade (p?<?0.001)
between 1955 and 2016. Elshall, Ahmed S; Ye, Ming
Making Steppingstones out of Stumbling Blocks: A Bayesian
Model Evidence Estimator with Application to Groundwater
Transport Model Selection Journal Article
Water, 11 (8), pp. 1579, 2019.
@article{Elshall2019-bc,
title = {Making Steppingstones out of Stumbling Blocks: A Bayesian
Model Evidence Estimator with Application to Groundwater
Transport Model Selection},
author = {Ahmed S Elshall and Ming Ye},
year = {2019},
date = {2019-07-01},
journal = {Water},
volume = {11},
number = {8},
pages = {1579},
publisher = {Multidisciplinary Digital Publishing Institute},
abstract = {Bayesian model evidence (BME) is a measure of the average fit
of a model to observation data given all the parameter values
that the model can assume. By accounting for the trade-off
between goodness-of-fit and model complexity, BME is used for
model selection and model averaging purposes. For strict
Bayesian computation, the theoretically unbiased Monte Carlo
based numerical estimators are preferred over semi-analytical
solutions. This study examines five BME numerical estimators
and asks how accurate estimation of the BME is important for
penalizing model complexity. The limiting cases for numerical
BME estimators are the prior sampling arithmetic mean
estimator (AM) and the posterior sampling harmonic mean (HM)
estimator, which are straightforward to implement, yet they
result in underestimation and overestimation, respectively. We
also consider the path sampling methods of thermodynamic
integration (TI) and steppingstone sampling (SS) that sample
multiple intermediate distributions that link the prior and
the posterior. Although TI and SS are theoretically unbiased
estimators, they could have a bias in practice arising from
numerical implementation. For example, sampling errors of some
intermediate distributions can introduce bias. We propose a
variant of SS, namely the multiple one-steppingstone sampling
(MOSS) that is less sensitive to sampling errors. We evaluate
these five estimators using a groundwater transport model
selection problem. SS and MOSS give the least biased BME
estimation at an efficient computational cost. If the
estimated BME has a bias that covariates with the true BME,
this would not be a problem because we are interested in BME
ratios and not their absolute values. On the contrary, the
results show that BME estimation bias can be a function of
model complexity. Thus, biased BME estimation results in
inaccurate penalization of more complex models, which changes
the model ranking. This was less observed with SS and MOSS as
with the three other methods.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Bayesian model evidence (BME) is a measure of the average fit
of a model to observation data given all the parameter values
that the model can assume. By accounting for the trade-off
between goodness-of-fit and model complexity, BME is used for
model selection and model averaging purposes. For strict
Bayesian computation, the theoretically unbiased Monte Carlo
based numerical estimators are preferred over semi-analytical
solutions. This study examines five BME numerical estimators
and asks how accurate estimation of the BME is important for
penalizing model complexity. The limiting cases for numerical
BME estimators are the prior sampling arithmetic mean
estimator (AM) and the posterior sampling harmonic mean (HM)
estimator, which are straightforward to implement, yet they
result in underestimation and overestimation, respectively. We
also consider the path sampling methods of thermodynamic
integration (TI) and steppingstone sampling (SS) that sample
multiple intermediate distributions that link the prior and
the posterior. Although TI and SS are theoretically unbiased
estimators, they could have a bias in practice arising from
numerical implementation. For example, sampling errors of some
intermediate distributions can introduce bias. We propose a
variant of SS, namely the multiple one-steppingstone sampling
(MOSS) that is less sensitive to sampling errors. We evaluate
these five estimators using a groundwater transport model
selection problem. SS and MOSS give the least biased BME
estimation at an efficient computational cost. If the
estimated BME has a bias that covariates with the true BME,
this would not be a problem because we are interested in BME
ratios and not their absolute values. On the contrary, the
results show that BME estimation bias can be a function of
model complexity. Thus, biased BME estimation results in
inaccurate penalization of more complex models, which changes
the model ranking. This was less observed with SS and MOSS as
with the three other methods. Cleveland, Sean B; McLean, Jared H; Rotzoll, Kolja; Izuka, Scot K; Jacobs, Gwen A
Enabling Real-Time User Interaction For Decision Support:
Experiences Extending A Local Agave Platform Metadata Service Inproceedings
Proceedings of the Practice and Experience in Advanced
Research Computing on Rise of the Machines (learning), pp. 8, ACM, 2019.
@inproceedings{Cleveland2019-ux,
title = {Enabling Real-Time User Interaction For Decision Support:
Experiences Extending A Local Agave Platform Metadata Service},
author = {Sean B Cleveland and Jared H McLean and Kolja Rotzoll and Scot K Izuka and Gwen A Jacobs},
year = {2019},
date = {2019-07-01},
booktitle = {Proceedings of the Practice and Experience in Advanced
Research Computing on Rise of the Machines (learning)},
pages = {8},
publisher = {ACM},
keywords = {},
pubstate = {published},
tppubtype = {inproceedings}
}
Delevaux, Jade M S; Stamoulis, Kostantinos A; Whittier, Robert; Jupiter, Stacy D; Bremer, Leah L; Friedlander, Alan; Kurashima, Natalie; Giddens, Jonatha; Winter, Kawika B; Blaich-Vaughan, Mehana; Burnett, Kimberly M; Geslani, Cheryl; Ticktin, Tamara
Place-based management can reduce human impacts on coral reefs in
a changing climate Journal Article
Ecol. Appl., 29 (4), pp. e01891, 2019.
@article{Delevaux2019-px,
title = {Place-based management can reduce human impacts on coral reefs in
a changing climate},
author = {Jade M S Delevaux and Kostantinos A Stamoulis and Robert Whittier and Stacy D Jupiter and Leah L Bremer and Alan Friedlander and Natalie Kurashima and Jonatha Giddens and Kawika B Winter and Mehana Blaich-Vaughan and Kimberly M Burnett and Cheryl Geslani and Tamara Ticktin},
year = {2019},
date = {2019-06-01},
journal = {Ecol. Appl.},
volume = {29},
number = {4},
pages = {e01891},
abstract = {Declining natural resources have contributed to a cultural
renaissance across the Pacific that seeks to revive customary
ridge-to-reef management approaches to protect freshwater and
restore abundant coral reef fisheries. We applied a linked
land-sea modeling framework based on remote sensing and empirical
data, which couples groundwater nutrient export and coral reef
models at fine spatial resolution. This spatially explicit (60
$times$ 60 m) framework simultaneously tracks changes in
multiple benthic and fish indicators as a function of
community-led marine closures, land-use and climate change scenarios. We applied this framework in H=a'ena and Ka'=up=ulehu, located at opposite ends of the Hawaiian
Archipelago to investigate the effects of coastal development and
marine closures on coral reefs in the face of climate change. Our
results indicated that projected coastal development and
bleaching can result in a significant decrease in benthic habitat
quality and community-led marine closures can result in a
significant increase in fish biomass. In general, Ka'=up=ulehu is more vulnerable to land-based nutrients and coral bleaching than H=a'ena due to high coral cover and
limited dilution and mixing from low rainfall and wave power,
except for the shallow and wave-sheltered back-reef areas of H=a'ena, which support high coral cover and act as nursery
habitat for fishes. By coupling spatially explicit land-sea
models with scenario planning, we identified priority areas on
land where upgrading cesspools can reduce human impacts on coral
reefs in the face of projected climate change impacts.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Declining natural resources have contributed to a cultural
renaissance across the Pacific that seeks to revive customary
ridge-to-reef management approaches to protect freshwater and
restore abundant coral reef fisheries. We applied a linked
land-sea modeling framework based on remote sensing and empirical
data, which couples groundwater nutrient export and coral reef
models at fine spatial resolution. This spatially explicit (60
$times$ 60 m) framework simultaneously tracks changes in
multiple benthic and fish indicators as a function of
community-led marine closures, land-use and climate change scenarios. We applied this framework in H=a'ena and Ka'=up=ulehu, located at opposite ends of the Hawaiian
Archipelago to investigate the effects of coastal development and
marine closures on coral reefs in the face of climate change. Our
results indicated that projected coastal development and
bleaching can result in a significant decrease in benthic habitat
quality and community-led marine closures can result in a
significant increase in fish biomass. In general, Ka'=up=ulehu is more vulnerable to land-based nutrients and coral bleaching than H=a'ena due to high coral cover and
limited dilution and mixing from low rainfall and wave power,
except for the shallow and wave-sheltered back-reef areas of H=a'ena, which support high coral cover and act as nursery
habitat for fishes. By coupling spatially explicit land-sea
models with scenario planning, we identified priority areas on
land where upgrading cesspools can reduce human impacts on coral
reefs in the face of projected climate change impacts. Levia, Delphis F; Nanko, Kazuki; Amasaki, Hiromasa; Giambelluca, Thomas W; Hotta, Norifumi; Iida, Shin'ichi; Mudd, Ryan G; Nullet, Michael A; Sakai, Naoki; Shinohara, Yoshinori; Sun, Xinchao; Suzuki, Masakazu; Tanaka, Nobuaki; Tantasirin, Chatchai; Yamada, Kozo
Throughfall partitioning by trees Journal Article
Hydrol. Process., 33 (12), pp. 1698–1708, 2019.
@article{Levia2019-ik,
title = {Throughfall partitioning by trees},
author = {Delphis F Levia and Kazuki Nanko and Hiromasa Amasaki and Thomas W Giambelluca and Norifumi Hotta and Shin'ichi Iida and Ryan G Mudd and Michael A Nullet and Naoki Sakai and Yoshinori Shinohara and Xinchao Sun and Masakazu Suzuki and Nobuaki Tanaka and Chatchai Tantasirin and Kozo Yamada},
year = {2019},
date = {2019-06-01},
journal = {Hydrol. Process.},
volume = {33},
number = {12},
pages = {1698--1708},
abstract = {Abstract Although we know that rainfall interception (the rain
caught, stored, and evaporated from aboveground vegetative
surfaces and ground litter) is affected by rain and
throughfall drop size, what was unknown until now is the
relative proportion of each throughfall type (free
throughfall, splash throughfall, canopy drip) beneath
coniferous and broadleaved trees. Based on a multinational
data set of >120 million throughfall drops, we found that the
type, number, and volume of throughfall drops are different
between coniferous and broadleaved tree species, leaf states,
and timing within rain events. Compared with leafed
broadleaved trees, conifers had a lower percentage of canopy
drip (51% vs. 69% with respect to total throughfall volume)
and slightly smaller diameter splash throughfall and canopy
drip. Canopy drip from leafless broadleaved trees consisted of
fewer and smaller diameter drops (D50_DR, 50th cumulative
drop volume percentile for canopy drip, of 2.24 mm) than
leafed broadleaved trees (D50_DR of 4.32 mm). Canopy drip was
much larger in diameter under woody drip points (D50_DR of
5.92 mm) than leafed broadleaved trees. Based on throughfall
volume, the percentage of canopy drip was significantly
different between conifers, leafed broadleaved trees, leafless
broadleaved trees, and woody surface drip points (p ranged
from <0.001 to 0.005). These findings are partly attributable
to differences in canopy structure and plant surface
characteristics between plant functional types and canopy
state (leaf, leafless), among other factors. Hence, our
results demonstrating the importance of drop-size-dependent
partitioning between coniferous and broadleaved tree species
could be useful to those requiring more detailed information
on throughfall fluxes to the forest floor.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Abstract Although we know that rainfall interception (the rain
caught, stored, and evaporated from aboveground vegetative
surfaces and ground litter) is affected by rain and
throughfall drop size, what was unknown until now is the
relative proportion of each throughfall type (free
throughfall, splash throughfall, canopy drip) beneath
coniferous and broadleaved trees. Based on a multinational
data set of >120 million throughfall drops, we found that the
type, number, and volume of throughfall drops are different
between coniferous and broadleaved tree species, leaf states,
and timing within rain events. Compared with leafed
broadleaved trees, conifers had a lower percentage of canopy
drip (51% vs. 69% with respect to total throughfall volume)
and slightly smaller diameter splash throughfall and canopy
drip. Canopy drip from leafless broadleaved trees consisted of
fewer and smaller diameter drops (D50_DR, 50th cumulative
drop volume percentile for canopy drip, of 2.24 mm) than
leafed broadleaved trees (D50_DR of 4.32 mm). Canopy drip was
much larger in diameter under woody drip points (D50_DR of
5.92 mm) than leafed broadleaved trees. Based on throughfall
volume, the percentage of canopy drip was significantly
different between conifers, leafed broadleaved trees, leafless
broadleaved trees, and woody surface drip points (p ranged
from <0.001 to 0.005). These findings are partly attributable
to differences in canopy structure and plant surface
characteristics between plant functional types and canopy
state (leaf, leafless), among other factors. Hence, our
results demonstrating the importance of drop-size-dependent
partitioning between coniferous and broadleaved tree species
could be useful to those requiring more detailed information
on throughfall fluxes to the forest floor. Ghazal, Kariem A; Leta, Olkeba Tolessa; El-Kadi, Aly I; Dulai, Henrietta
Assessment of Wetland Restoration and Climate Change Impacts
on Water Balance Components of the Heeia Coastal Wetland in
Hawaii Journal Article
Hydrology, 6 (2), pp. 37, 2019.
@article{Ghazal2019-oc,
title = {Assessment of Wetland Restoration and Climate Change Impacts
on Water Balance Components of the Heeia Coastal Wetland in
Hawaii},
author = {Kariem A Ghazal and Olkeba Tolessa Leta and Aly I El-Kadi and Henrietta Dulai},
year = {2019},
date = {2019-05-01},
journal = {Hydrology},
volume = {6},
number = {2},
pages = {37},
publisher = {Multidisciplinary Digital Publishing Institute},
abstract = {Hydrological modeling is an important tool that can be used to
assess water resources' availability and sustainability that
are necessary for food security and ecological health of
coastal regions. In this study, we assessed the impacts of
land use and climate changes on water balance components
(WBCs) of the Heeia coastal wetland. We developed a Soil and
Water Assessment Tool (SWAT) model to capture the unique
characteristics of the Hawaiian Islands, including its
volcanic soil's nature and high initial infiltration rates. We
used the sequential uncertainty fitting algorithm to assess
the sensitivity and uncertainty of WBCs under different
climate change scenarios. Results of the statistical analysis
of daily streamflow simulations showed that the model
performance was within the generally acceptable criteria.
Under future climate scenarios, rainfall change was the
determinant factor most negatively impacting WBCs. Recharge
and baseflow components had the highest sensitivity to the
combined effects of land use and climate changes, especially
during dry season. The uncertainty analysis indicated that the
streamflow is projected to slightly increase by the middle of
21st century, but expected to decline by 40% during the late
21st century of Representative Concentration Pathways (RCP)
8.5.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Hydrological modeling is an important tool that can be used to
assess water resources' availability and sustainability that
are necessary for food security and ecological health of
coastal regions. In this study, we assessed the impacts of
land use and climate changes on water balance components
(WBCs) of the Heeia coastal wetland. We developed a Soil and
Water Assessment Tool (SWAT) model to capture the unique
characteristics of the Hawaiian Islands, including its
volcanic soil's nature and high initial infiltration rates. We
used the sequential uncertainty fitting algorithm to assess
the sensitivity and uncertainty of WBCs under different
climate change scenarios. Results of the statistical analysis
of daily streamflow simulations showed that the model
performance was within the generally acceptable criteria.
Under future climate scenarios, rainfall change was the
determinant factor most negatively impacting WBCs. Recharge
and baseflow components had the highest sensitivity to the
combined effects of land use and climate changes, especially
during dry season. The uncertainty analysis indicated that the
streamflow is projected to slightly increase by the middle of
21st century, but expected to decline by 40% during the late
21st century of Representative Concentration Pathways (RCP)
8.5. Elshall, Ahmed S; Ye, Ming; Niu, Guo-Yue; Barron-Gafford, Greg A
Bayesian inference and predictive performance of soil
respiration models in the presence of model discrepancy Journal Article
Geoscientific Model Development, 12 (5), pp. 2009–2032, 2019.
@article{Elshall2019-ts,
title = {Bayesian inference and predictive performance of soil
respiration models in the presence of model discrepancy},
author = {Ahmed S Elshall and Ming Ye and Guo-Yue Niu and Greg A Barron-Gafford},
year = {2019},
date = {2019-05-01},
journal = {Geoscientific Model Development},
volume = {12},
number = {5},
pages = {2009--2032},
publisher = {Copernicus GmbH},
abstract = {Abstract. Bayesian inference of microbial soil respiration
models is often based on the assumptions that the residuals
are independent (i.e., no temporal or spatial correlation),
identically distributed (i.e., Gaussian noise), and have
constant variance (i.e., homoscedastic). In the presence of
model discrepancy, as no model is perfect, this study shows
that these assumptions are generally invalid in soil
respiration modeling such that residuals have high temporal
correlation, an increasing variance with increasing magnitude
of CO2 efflux, and non-Gaussian distribution. Relaxing these
three assumptions stepwise results in eight data models. Data
models are the basis of formulating likelihood functions of
Bayesian inference. This study presents a systematic and
comprehensive investigation of the impacts of data model
selection on Bayesian inference and predictive performance. We
use three mechanistic soil respiration models with different
levels of model fidelity (i.e., model discrepancy) with
respect to the number of carbon pools and the explicit
representations of soil moisture controls on carbon
degradation; therefore, we have different levels of model
complexity with respect to the number of model parameters. The
study shows that data models have substantial impacts on
Bayesian inference and predictive performance of the soil
respiration models such that the following points are true:
(i) the level of complexity of the best model is generally
justified by the cross-validation results for different data
models; (ii) not accounting for heteroscedasticity and
autocorrelation might not necessarily result in biased
parameter estimates or predictions, but will definitely
underestimate uncertainty; (iii) using a non-Gaussian data
model improves the parameter estimates and the predictive
performance; and (iv) accounting for autocorrelation only or
joint inversion of correlation and heteroscedasticity can be
problematic and requires special treatment. Although the
conclusions of this study are empirical, the analysis may
provide insights for selecting appropriate data models for
soil respiration modeling.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Abstract. Bayesian inference of microbial soil respiration
models is often based on the assumptions that the residuals
are independent (i.e., no temporal or spatial correlation),
identically distributed (i.e., Gaussian noise), and have
constant variance (i.e., homoscedastic). In the presence of
model discrepancy, as no model is perfect, this study shows
that these assumptions are generally invalid in soil
respiration modeling such that residuals have high temporal
correlation, an increasing variance with increasing magnitude
of CO2 efflux, and non-Gaussian distribution. Relaxing these
three assumptions stepwise results in eight data models. Data
models are the basis of formulating likelihood functions of
Bayesian inference. This study presents a systematic and
comprehensive investigation of the impacts of data model
selection on Bayesian inference and predictive performance. We
use three mechanistic soil respiration models with different
levels of model fidelity (i.e., model discrepancy) with
respect to the number of carbon pools and the explicit
representations of soil moisture controls on carbon
degradation; therefore, we have different levels of model
complexity with respect to the number of model parameters. The
study shows that data models have substantial impacts on
Bayesian inference and predictive performance of the soil
respiration models such that the following points are true:
(i) the level of complexity of the best model is generally
justified by the cross-validation results for different data
models; (ii) not accounting for heteroscedasticity and
autocorrelation might not necessarily result in biased
parameter estimates or predictions, but will definitely
underestimate uncertainty; (iii) using a non-Gaussian data
model improves the parameter estimates and the predictive
performance; and (iv) accounting for autocorrelation only or
joint inversion of correlation and heteroscedasticity can be
problematic and requires special treatment. Although the
conclusions of this study are empirical, the analysis may
provide insights for selecting appropriate data models for
soil respiration modeling. Engels, Jennifer; Bruno, Barbara; Dasalla, Noelle; Böttjer-Wilson, Daniela
Class observations from the University of Hawai`i at M=anoa
highlight the need for active learning strategies to support
diverse students in large classes Inproceedings
Fifth International Conference on Higher Education Advances, 2019.
@inproceedings{Engels2019-cb,
title = {Class observations from the University of Hawai`i at M=anoa
highlight the need for active learning strategies to support
diverse students in large classes},
author = {Jennifer Engels and Barbara Bruno and Noelle Dasalla and Daniela Böttjer-Wilson},
year = {2019},
date = {2019-05-01},
booktitle = {Fifth International Conference on Higher Education Advances},
abstract = {Compelling evidence indicates that ``active learning'' (learning
by doing) is an effective pedagogy regardless of discipline or
class size, and can be particularly effective with diverse
students. This study investigated active learning practices in 64 classes at the University of Hawai`i at M=anoa, a US
university with a highly diverse student body, using a
``Passivity Indicator'' (PI: ratio of class time spent in
passive activities to total class time). For all classes, the
mean PI was 43%. Statistical analysis reveals no significant
differences in the PI of classes taught in STEM vs. non-STEM
disciplines, or between upper vs. lower division courses.
However, the PI in larger classes was found to be significantly
greater than in small classes (64% vs. 39%, respectively; p=0.02). Moreover, classroom activities aligned with an active
learning standard in Language and Literacy Development (e.g.,
students answering questions) occurred twice as often in small (24%) vs. large classes (12%, with p=0.02). Altogether, these
findings indicate an opportunity for more active learning in
large classes. We present a range of research-based pedagogical
strategies that can be readily implemented in large classrooms,
and encourage instructors to use their implementation as
research opportunities to gather data on student success.},
keywords = {},
pubstate = {published},
tppubtype = {inproceedings}
}
Compelling evidence indicates that ``active learning'' (learning
by doing) is an effective pedagogy regardless of discipline or
class size, and can be particularly effective with diverse
students. This study investigated active learning practices in 64 classes at the University of Hawai`i at M=anoa, a US
university with a highly diverse student body, using a
``Passivity Indicator'' (PI: ratio of class time spent in
passive activities to total class time). For all classes, the
mean PI was 43%. Statistical analysis reveals no significant
differences in the PI of classes taught in STEM vs. non-STEM
disciplines, or between upper vs. lower division courses.
However, the PI in larger classes was found to be significantly
greater than in small classes (64% vs. 39%, respectively; p=0.02). Moreover, classroom activities aligned with an active
learning standard in Language and Literacy Development (e.g.,
students answering questions) occurred twice as often in small (24%) vs. large classes (12%, with p=0.02). Altogether, these
findings indicate an opportunity for more active learning in
large classes. We present a range of research-based pedagogical
strategies that can be readily implemented in large classrooms,
and encourage instructors to use their implementation as
research opportunities to gather data on student success. Ghorbanidehno, Hojat; Lee, Jonghyun; Farthing, Matthew; Hesser, Tyler; Kitanidis, Peter K; Darve, Eric F
Novel Data Assimilation Algorithm for Nearshore Bathymetry Journal Article
J. Atmos. Ocean. Technol., 36 (4), pp. 699–715, 2019.
@article{Ghorbanidehno2019-ni,
title = {Novel Data Assimilation Algorithm for Nearshore Bathymetry},
author = {Hojat Ghorbanidehno and Jonghyun Lee and Matthew Farthing and Tyler Hesser and Peter K Kitanidis and Eric F Darve},
year = {2019},
date = {2019-04-01},
journal = {J. Atmos. Ocean. Technol.},
volume = {36},
number = {4},
pages = {699--715},
publisher = {American Meteorological Society},
abstract = {AbstractIt can be expensive and difficult to collect direct
bathymetry data for nearshore regions, especially in
high-energy locations where there are temporally and spatially
varying bathymetric features like sandbars. As a result, there
has been increasing interest in remote assessment techniques
for estimating bathymetry. Recent efforts have combined Kalman
filter?based techniques with indirect video-based observations
for bathymetry inversion. Here, we estimate nearshore
bathymetry by utilizing observed wave celerity and wave
height, which are related to bathymetry through phase-averaged
wave dynamics. We present a modified compressed-state Kalman
filter (CSKF) method, a fast and scalable Kalman filter method
for linear and nonlinear problems with large numbers of
unknowns and measurements, and apply it to two nearshore
bathymetry estimation problems. To illustrate the robustness
and accuracy of our method, we compare its performance with
that of two ensemble-based approaches on twin bathymetry
estimation problems with profiles based on surveys taken by
the U.S. Army Corps of Engineer Field Research Facility (FRF)
in Duck, North Carolina. We first consider an estimation
problem for a temporally constant bathymetry profile. Then we
estimate bathymetry as it evolves in time. Our results
indicate that the CSKF method is more accurate and robust than
the ensemble-based methods with the same computational cost.
The superior performance is due to the optimal low-rank
representation of the covariance matrices.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
AbstractIt can be expensive and difficult to collect direct
bathymetry data for nearshore regions, especially in
high-energy locations where there are temporally and spatially
varying bathymetric features like sandbars. As a result, there
has been increasing interest in remote assessment techniques
for estimating bathymetry. Recent efforts have combined Kalman
filter?based techniques with indirect video-based observations
for bathymetry inversion. Here, we estimate nearshore
bathymetry by utilizing observed wave celerity and wave
height, which are related to bathymetry through phase-averaged
wave dynamics. We present a modified compressed-state Kalman
filter (CSKF) method, a fast and scalable Kalman filter method
for linear and nonlinear problems with large numbers of
unknowns and measurements, and apply it to two nearshore
bathymetry estimation problems. To illustrate the robustness
and accuracy of our method, we compare its performance with
that of two ensemble-based approaches on twin bathymetry
estimation problems with profiles based on surveys taken by
the U.S. Army Corps of Engineer Field Research Facility (FRF)
in Duck, North Carolina. We first consider an estimation
problem for a temporally constant bathymetry profile. Then we
estimate bathymetry as it evolves in time. Our results
indicate that the CSKF method is more accurate and robust than
the ensemble-based methods with the same computational cost.
The superior performance is due to the optimal low-rank
representation of the covariance matrices. Watson, Sheree J; Needoba, Joseph A; Peterson, Tawnya D
Widespread detection of Candidatus Accumulibacter phosphatis, a
polyphosphate-accumulating organism, in sediments of the Columbia
River estuary Journal Article
Environ. Microbiol., 21 (4), pp. 1369–1382, 2019.
@article{Watson2019-ej,
title = {Widespread detection of Candidatus Accumulibacter phosphatis, a
polyphosphate-accumulating organism, in sediments of the Columbia
River estuary},
author = {Sheree J Watson and Joseph A Needoba and Tawnya D Peterson},
year = {2019},
date = {2019-04-01},
journal = {Environ. Microbiol.},
volume = {21},
number = {4},
pages = {1369--1382},
abstract = {Enhanced biological phosphorus removal (EBPR) exploits the
metabolism of polyphosphate-accumulating organisms (PAOs) to
remove excess phosphorus (P) from wastewater treatment.
Candidatus Accumulibacter phosphatis (Accumulibacter) is the most
abundant and well-studied PAO in EBPR systems. In a previous
study, we detected polyphosphates throughout peripheral bay
sediments, and hypothesized that an estuary is an ideal setting
to evaluate PAOs in a natural system, given that estuaries are
characterized by dynamic dissolved oxygen fluctuations that
potentially favour PAO metabolism. We detected nucleotide
sequences attributable to Accumulibacter (16S rRNA, ppk1) in
sediments within three peripheral bays of the Columbia River
estuary at abundances rivalling those observed in conventional
wastewater treatment plants (0.01%-2.6%). Most of the sequences
attributable to Accumulibacter were Type I rather than Type II,
despite the fact that the estuary does not have particularly high
nutrient concentrations. The highest diversity of Accumulibacter
was observed in oligohaline peripheral bays, while the greatest
abundances were observed at the mouth of the estuary in
mesohaline sediments in the spring and summer. In addition, an
approximately 70% increase in polyphosphate concentrations
observed at one of the sites between dawn and dusk suggests that
PAOs may play an important role in P cycling in estuary
sediments.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Enhanced biological phosphorus removal (EBPR) exploits the
metabolism of polyphosphate-accumulating organisms (PAOs) to
remove excess phosphorus (P) from wastewater treatment.
Candidatus Accumulibacter phosphatis (Accumulibacter) is the most
abundant and well-studied PAO in EBPR systems. In a previous
study, we detected polyphosphates throughout peripheral bay
sediments, and hypothesized that an estuary is an ideal setting
to evaluate PAOs in a natural system, given that estuaries are
characterized by dynamic dissolved oxygen fluctuations that
potentially favour PAO metabolism. We detected nucleotide
sequences attributable to Accumulibacter (16S rRNA, ppk1) in
sediments within three peripheral bays of the Columbia River
estuary at abundances rivalling those observed in conventional
wastewater treatment plants (0.01%-2.6%). Most of the sequences
attributable to Accumulibacter were Type I rather than Type II,
despite the fact that the estuary does not have particularly high
nutrient concentrations. The highest diversity of Accumulibacter
was observed in oligohaline peripheral bays, while the greatest
abundances were observed at the mouth of the estuary in
mesohaline sediments in the spring and summer. In addition, an
approximately 70% increase in polyphosphate concentrations
observed at one of the sites between dawn and dusk suggests that
PAOs may play an important role in P cycling in estuary
sediments. Newman, Andrew J; Clark, Martyn P; Longman, Ryan J; Gilleland, Eric; Giambelluca, Thomas W; Arnold, Jeffrey R
Use of Daily Station Observations to Produce High-Resolution
Gridded Probabilistic Precipitation and Temperature Time
Series for the Hawaiian Islands Journal Article
J. Hydrometeorol., 20 (3), pp. 509–529, 2019.
@article{Newman2019-cp,
title = {Use of Daily Station Observations to Produce High-Resolution
Gridded Probabilistic Precipitation and Temperature Time
Series for the Hawaiian Islands},
author = {Andrew J Newman and Martyn P Clark and Ryan J Longman and Eric Gilleland and Thomas W Giambelluca and Jeffrey R Arnold},
year = {2019},
date = {2019-03-01},
journal = {J. Hydrometeorol.},
volume = {20},
number = {3},
pages = {509--529},
publisher = {American Meteorological Society},
abstract = {AbstractIt is a major challenge to develop gridded
precipitation and temperature estimates that adequately
resolve the extreme spatial gradients present in the Hawaiian
Islands. The challenge is particularly pronounced because the
available station networks are irregularly spaced and sparse,
creating large uncertainties in gridded spatial meteorological
estimates. Here a 100-member, daily ensemble of precipitation
and temperature estimates over the Hawaiian Islands for the
period 1990?2014 at 1-km grid resolution is developed. First,
an intermediary ensemble estimate of the monthly
climatological precipitation and temperature is created, and
those climatological surfaces are used to inform daily anomaly
interpolation. This climatologically aided interpolation (CAI)
method extends our initial ensemble system developed for the
continental United States. This study demonstrates that direct
interpolation of daily precipitation values is inferior to the
CAI methodology, particularly over longer time periods (from
years to decades). Daily interpolation performs better for
short time periods (e.g., 1 month or less) or when the
precipitation distribution substantially diverges from
climatology. The CAI ensemble is able to reproduce observed
precipitation and temperature patterns, including
precipitation occurrence. Leave-one-out cross-validation
results illustrate that the ensemble has 1) minimal bias for
precipitation and temperature; 2) a mean absolute error of 2.5
mm day?1, 1.0 K, and 2.2 K for precipitation and mean and
diurnal temperature, respectively; 3) a mean absolute error of
3.3 mm day?1 for the standard deviation of precipitation; and
4) nearly unbiased probability distributions across multiple
thresholds of precipitation intensity. Additionally, the
ensemble provides estimates of uncertainty across the
distributions with increasing uncertainty for higher
percentiles.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
AbstractIt is a major challenge to develop gridded
precipitation and temperature estimates that adequately
resolve the extreme spatial gradients present in the Hawaiian
Islands. The challenge is particularly pronounced because the
available station networks are irregularly spaced and sparse,
creating large uncertainties in gridded spatial meteorological
estimates. Here a 100-member, daily ensemble of precipitation
and temperature estimates over the Hawaiian Islands for the
period 1990?2014 at 1-km grid resolution is developed. First,
an intermediary ensemble estimate of the monthly
climatological precipitation and temperature is created, and
those climatological surfaces are used to inform daily anomaly
interpolation. This climatologically aided interpolation (CAI)
method extends our initial ensemble system developed for the
continental United States. This study demonstrates that direct
interpolation of daily precipitation values is inferior to the
CAI methodology, particularly over longer time periods (from
years to decades). Daily interpolation performs better for
short time periods (e.g., 1 month or less) or when the
precipitation distribution substantially diverges from
climatology. The CAI ensemble is able to reproduce observed
precipitation and temperature patterns, including
precipitation occurrence. Leave-one-out cross-validation
results illustrate that the ensemble has 1) minimal bias for
precipitation and temperature; 2) a mean absolute error of 2.5
mm day?1, 1.0 K, and 2.2 K for precipitation and mean and
diurnal temperature, respectively; 3) a mean absolute error of
3.3 mm day?1 for the standard deviation of precipitation; and
4) nearly unbiased probability distributions across multiple
thresholds of precipitation intensity. Additionally, the
ensemble provides estimates of uncertainty across the
distributions with increasing uncertainty for higher
percentiles. Longman, Ryan J; Frazier, Abby G; Newman, Andrew J; Giambelluca, Thomas W; Schanzenbach, David; Kagawa-Viviani, Aurora; Needham, Heidi; Arnold, Jeffrey R; Clark, Martyn P
High-Resolution Gridded Daily Rainfall and Temperature for
the Hawaiian Islands (1990--2014) Journal Article
J. Hydrometeorol., 20 (3), pp. 489–508, 2019.
@article{Longman2019-mn,
title = {High-Resolution Gridded Daily Rainfall and Temperature for
the Hawaiian Islands (1990--2014)},
author = {Ryan J Longman and Abby G Frazier and Andrew J Newman and Thomas W Giambelluca and David Schanzenbach and Aurora Kagawa-Viviani and Heidi Needham and Jeffrey R Arnold and Martyn P Clark},
year = {2019},
date = {2019-03-01},
journal = {J. Hydrometeorol.},
volume = {20},
number = {3},
pages = {489--508},
publisher = {American Meteorological Society},
abstract = {AbstractSpatially continuous data products are essential for a
number of applications including climate and hydrologic
modeling, weather prediction, and water resource management.
In this work, a distance-weighted interpolation method used to
map daily rainfall and temperature in Hawaii is described and
assessed. New high-resolution (250 m) maps were developed for
daily rainfall and daily maximum (Tmax) and minimum (Tmin)
near-surface air temperature for the period 1990?2014. Maps
were produced using climatologically aided interpolation, in
which station anomalies were interpolated using an optimized
inverse distance weighting approach and then combined with
long-term means to produce daily gridded estimates.
Leave-one-out cross validation was performed to assess the
quality of the final daily grids. The median absolute
prediction error for rainfall was 0.1 mm with an average
overprediction (+0.6 mm) on days when total rainfall was less
than 1 mm. On days with total rainfall greater than 1 mm,
median absolute prediction errors were 2 mm and rainfall was
typically underpredicted above the 10-mm threshold. For daily
temperature, median absolute prediction errors were 3.1° and
2.8°C for Tmax and Tmin, respectively. On average, this method
overpredicted Tmax (+1.1°C) and Tmin (+1.5°C), and errors
varied considerably among stations. Errors for all variables
exhibited significant seasonal variations. However, the annual
range of errors was small. The methods presented here provide
an effective approach for mapping daily weather fields in a
topographically diverse region and improve on previous
products in their spatial resolution, time period of coverage,
and use of data.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
AbstractSpatially continuous data products are essential for a
number of applications including climate and hydrologic
modeling, weather prediction, and water resource management.
In this work, a distance-weighted interpolation method used to
map daily rainfall and temperature in Hawaii is described and
assessed. New high-resolution (250 m) maps were developed for
daily rainfall and daily maximum (Tmax) and minimum (Tmin)
near-surface air temperature for the period 1990?2014. Maps
were produced using climatologically aided interpolation, in
which station anomalies were interpolated using an optimized
inverse distance weighting approach and then combined with
long-term means to produce daily gridded estimates.
Leave-one-out cross validation was performed to assess the
quality of the final daily grids. The median absolute
prediction error for rainfall was 0.1 mm with an average
overprediction (+0.6 mm) on days when total rainfall was less
than 1 mm. On days with total rainfall greater than 1 mm,
median absolute prediction errors were 2 mm and rainfall was
typically underpredicted above the 10-mm threshold. For daily
temperature, median absolute prediction errors were 3.1° and
2.8°C for Tmax and Tmin, respectively. On average, this method
overpredicted Tmax (+1.1°C) and Tmin (+1.5°C), and errors
varied considerably among stations. Errors for all variables
exhibited significant seasonal variations. However, the annual
range of errors was small. The methods presented here provide
an effective approach for mapping daily weather fields in a
topographically diverse region and improve on previous
products in their spatial resolution, time period of coverage,
and use of data. Newman, Andrew J; Clark, Martyn P; Longman, Ryan J; Giambelluca, Thomas W
Methodological Intercomparisons of Station-Based Gridded
Meteorological Products: Utility, Limitations, and Paths
Forward Journal Article
J. Hydrometeorol., 20 (3), pp. 531–547, 2019.
@article{Newman2019-vb,
title = {Methodological Intercomparisons of Station-Based Gridded
Meteorological Products: Utility, Limitations, and Paths
Forward},
author = {Andrew J Newman and Martyn P Clark and Ryan J Longman and Thomas W Giambelluca},
year = {2019},
date = {2019-03-01},
journal = {J. Hydrometeorol.},
volume = {20},
number = {3},
pages = {531--547},
publisher = {American Meteorological Society},
abstract = {AbstractThis study presents a gridded meteorology
intercomparison using the State of Hawaii as a testbed. This
is motivated by the goal to provide the broad user community
with knowledge of interproduct differences and the reasons
differences exist. More generally, the challenge of generating
station-based gridded meteorological surfaces and the
difficulties in attributing interproduct differences to
specific methodological decisions are demonstrated. Hawaii is
a useful testbed because it is traditionally underserved, yet
meteorologically interesting and complex. In addition, several
climatological and daily gridded meteorology datasets are now
available, which are used extensively by the applications
modeling community, thus an intercomparison enhances Hawaiian
specific capabilities. We compare PRISM climatology and three
daily datasets: new datasets from the University of Hawai?i
and the National Center for Atmospheric Research, and Daymet
version 3 for precipitation and temperature variables only.
General conclusions that have emerged are 1) differences in
input station data significantly influence the product
differences, 2) explicit prediction of precipitation
occurrence is crucial across multiple metrics, and 3)
attribution of differences to specific methodological choices
is difficult and limits the usefulness of intercomparisons.
Because generating gridded meteorological fields is an
elaborate process with many methodological choices interacting
in complex ways, future work should 1) develop modular
frameworks that allows users to easily examine the breadth of
methodological choices, 2) collate available nontraditional
high-quality observational datasets for true out-of-sample
validation and make them publicly available, and 3) define
benchmarks of acceptable performance for methodological
components and products.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
AbstractThis study presents a gridded meteorology
intercomparison using the State of Hawaii as a testbed. This
is motivated by the goal to provide the broad user community
with knowledge of interproduct differences and the reasons
differences exist. More generally, the challenge of generating
station-based gridded meteorological surfaces and the
difficulties in attributing interproduct differences to
specific methodological decisions are demonstrated. Hawaii is
a useful testbed because it is traditionally underserved, yet
meteorologically interesting and complex. In addition, several
climatological and daily gridded meteorology datasets are now
available, which are used extensively by the applications
modeling community, thus an intercomparison enhances Hawaiian
specific capabilities. We compare PRISM climatology and three
daily datasets: new datasets from the University of Hawai?i
and the National Center for Atmospheric Research, and Daymet
version 3 for precipitation and temperature variables only.
General conclusions that have emerged are 1) differences in
input station data significantly influence the product
differences, 2) explicit prediction of precipitation
occurrence is crucial across multiple metrics, and 3)
attribution of differences to specific methodological choices
is difficult and limits the usefulness of intercomparisons.
Because generating gridded meteorological fields is an
elaborate process with many methodological choices interacting
in complex ways, future work should 1) develop modular
frameworks that allows users to easily examine the breadth of
methodological choices, 2) collate available nontraditional
high-quality observational datasets for true out-of-sample
validation and make them publicly available, and 3) define
benchmarks of acceptable performance for methodological
components and products. Shuler, Christopher K; Amato, Daniel W; Gibson, Veronica; Baker, Lydia; Olguin, Ashley N; Dulai, Henrietta; Smith, Celia M; Alegado, Rosanna A
Assessment of Terrigenous Nutrient Loading to Coastal
Ecosystems along a Human Land-Use Gradient, Tutuila,
American Samoa Journal Article
Hydrology, 6 (1), pp. 18, 2019.
@article{Shuler2019-ys,
title = {Assessment of Terrigenous Nutrient Loading to Coastal
Ecosystems along a Human Land-Use Gradient, Tutuila,
American Samoa},
author = {Christopher K Shuler and Daniel W Amato and Veronica Gibson and Lydia Baker and Ashley N Olguin and Henrietta Dulai and Celia M Smith and Rosanna A Alegado},
year = {2019},
date = {2019-02-01},
journal = {Hydrology},
volume = {6},
number = {1},
pages = {18},
publisher = {Multidisciplinary Digital Publishing Institute},
abstract = {Anthropogenic nutrient loading is well recognized as a
stressor to coastal ecosystem health. However, resource
managers are often focused on addressing point source or
surface water discharge, whereas the impact of submarine
groundwater discharge (SGD) as a nutrient vector is often
unappreciated. This study examines connections between land
use and nutrient loading through comparison of four watersheds
and embayments spanning a gradient of human use impact on
Tutuila, a high tropical oceanic island in American Samoa. In
each study location, coastal radon-222 measurements, dissolved
nutrient concentrations, and nitrogen isotope values
($delta$15N) in water and in situ macroalgal tissue were used
to explore SGD and baseflow derived nutrient impacts, and to
determine probable nutrient sources. In addition to sampling
in situ macroalgae, pre-treated macroalgal specimens were
deployed throughout each embayment to uptake ambient nutrients
and provide a standardized assessment of differences between
locations. Results show SGD-derived nutrient flux was more
significant than baseflow nutrient flux in all watersheds, and
$delta$15N values in water and algae suggested wastewater or
manure are likely sources of elevated nutrient levels. While
nutrient loading correlated well with expected anthropogenic
impact, other factors such as differences in hydrogeology,
distribution of development, and wastewater infrastructure
also likely play a role in the visibility of impacts in each
watershed.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Anthropogenic nutrient loading is well recognized as a
stressor to coastal ecosystem health. However, resource
managers are often focused on addressing point source or
surface water discharge, whereas the impact of submarine
groundwater discharge (SGD) as a nutrient vector is often
unappreciated. This study examines connections between land
use and nutrient loading through comparison of four watersheds
and embayments spanning a gradient of human use impact on
Tutuila, a high tropical oceanic island in American Samoa. In
each study location, coastal radon-222 measurements, dissolved
nutrient concentrations, and nitrogen isotope values
($delta$15N) in water and in situ macroalgal tissue were used
to explore SGD and baseflow derived nutrient impacts, and to
determine probable nutrient sources. In addition to sampling
in situ macroalgae, pre-treated macroalgal specimens were
deployed throughout each embayment to uptake ambient nutrients
and provide a standardized assessment of differences between
locations. Results show SGD-derived nutrient flux was more
significant than baseflow nutrient flux in all watersheds, and
$delta$15N values in water and algae suggested wastewater or
manure are likely sources of elevated nutrient levels. While
nutrient loading correlated well with expected anthropogenic
impact, other factors such as differences in hydrogeology,
distribution of development, and wastewater infrastructure
also likely play a role in the visibility of impacts in each
watershed. Leigh, Jason; Belcaid, Mahdi; Kobayashi, Dylan; Kirshenbaum, Nurit; Wooton, Troy; Gonzalez, Alberto; Renambot, Luc; Johnson, Andrew; Brown, Maxine; Burks, Andrew; Others,
Usage Patterns of Wideband Display Environments In e-Science
Research, Development and Training Inproceedings
15th IEEE International Conference on e-Science,(eScience
2019), evl.uic.edu, 2019.
@inproceedings{Leigh2019-yr,
title = {Usage Patterns of Wideband Display Environments In e-Science
Research, Development and Training},
author = {Jason Leigh and Mahdi Belcaid and Dylan Kobayashi and Nurit Kirshenbaum and Troy Wooton and Alberto Gonzalez and Luc Renambot and Andrew Johnson and Maxine Brown and Andrew Burks and Others},
year = {2019},
date = {2019-01-01},
booktitle = {15th IEEE International Conference on e-Science,(eScience
2019)},
publisher = {evl.uic.edu},
abstract = {Group Environment) are operating systems for managing content
across wideband display environments. This paper documents the
prevalent usage patterns of SAGE-enabled display walls in
support of the e-Science enterprise, based on nearly 15 years of
observations of the SAGE community. These patterns will help
guide e-Science users and cyberinfrastructure developers on how
best to leverage large tiled display walls, and the types of
software services that could be provided in the future.},
keywords = {},
pubstate = {published},
tppubtype = {inproceedings}
}
Group Environment) are operating systems for managing content
across wideband display environments. This paper documents the
prevalent usage patterns of SAGE-enabled display walls in
support of the e-Science enterprise, based on nearly 15 years of
observations of the SAGE community. These patterns will help
guide e-Science users and cyberinfrastructure developers on how
best to leverage large tiled display walls, and the types of
software services that could be provided in the future. Burnett, Kimberly M; Ticktin, Tamara; Bremer, Leah L; Quazi, Shimona A; Geslani, Cheryl; Wada, Christopher A; Kurashima, Natalie; Mandle, Lisa; Pascua, Pua`ala; Depraetere, Taina; Wolkis, Dustin; Edmonds, Merlin; Giambelluca, Thomas; Falinski, Kim; Winter, Kawika B
Restoring to the future: Environmental, cultural, and management
trade-offs in historical versus hybrid restoration of a highly
modified ecosystem Journal Article
CONSERVATION LETTERS, 12 (1), pp. e12606, 2019.
@article{Burnett2019-wz,
title = {Restoring to the future: Environmental, cultural, and management
trade-offs in historical versus hybrid restoration of a highly
modified ecosystem},
author = {Kimberly M Burnett and Tamara Ticktin and Leah L Bremer and Shimona A Quazi and Cheryl Geslani and Christopher A Wada and Natalie Kurashima and Lisa Mandle and Pua`ala Pascua and Taina Depraetere and Dustin Wolkis and Merlin Edmonds and Thomas Giambelluca and Kim Falinski and Kawika B Winter},
year = {2019},
date = {2019-01-01},
journal = {CONSERVATION LETTERS},
volume = {12},
number = {1},
pages = {e12606},
abstract = {Abstract With growing calls to scale up reforestation efforts
worldwide, conservation managers increasingly must decide whether
and how to restore highly altered ecosystems. However, empirical
research on potential trade-offs remains scarce. We use a Hawai'i
watershed to demonstrate a collaborative, interdisciplinary
approach to identifying synergies and trade-offs associated with
maintaining an unrestored forest, versus restoration to a
historical or hybrid (native and non-native plant species) state.
We focused on restoration scenarios designed by conservation
managers and measured ecological, hydrologic, and cultural
outcomes they identified as important metrics of success. The
hybrid restoration scenario maximized potential outcomes at
moderate cost, and increased two rarely measured but often
critical metrics to managers and communities: cultural value and
resilience to disturbance. Hybrid restoration approaches
developed collaboratively can provide a viable option for scaling
up restoration in island ecosystems and other contexts where
invasive species pose significant challenges and/or where
community support is important.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Abstract With growing calls to scale up reforestation efforts
worldwide, conservation managers increasingly must decide whether
and how to restore highly altered ecosystems. However, empirical
research on potential trade-offs remains scarce. We use a Hawai'i
watershed to demonstrate a collaborative, interdisciplinary
approach to identifying synergies and trade-offs associated with
maintaining an unrestored forest, versus restoration to a
historical or hybrid (native and non-native plant species) state.
We focused on restoration scenarios designed by conservation
managers and measured ecological, hydrologic, and cultural
outcomes they identified as important metrics of success. The
hybrid restoration scenario maximized potential outcomes at
moderate cost, and increased two rarely measured but often
critical metrics to managers and communities: cultural value and
resilience to disturbance. Hybrid restoration approaches
developed collaboratively can provide a viable option for scaling
up restoration in island ecosystems and other contexts where
invasive species pose significant challenges and/or where
community support is important. Ginsberg, Alexandra Daisy; Chieza, Natsai; Frank, Kiana; Rands, Ahilapalapa; Vilutis, Justinas
Piko A, Piko O, Piko I: Those That Came Before, Those That are
Here Now, and Those That Will Come After Journal Article
Journal of Design and Science, 2019.
@article{Ginsberg2019-bs,
title = {Piko A, Piko O, Piko I: Those That Came Before, Those That are
Here Now, and Those That Will Come After},
author = {Alexandra Daisy Ginsberg and Natsai Chieza and Kiana Frank and Ahilapalapa Rands and Justinas Vilutis},
year = {2019},
date = {2019-01-01},
journal = {Journal of Design and Science},
publisher = {PubPub},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Welch, Eric M; Dulai, Henrietta; El-Kadi, Aly; Shuler, Christopher K
Submarine Groundwater Discharge and Stream Baseflow Sustain
Pesticide and Nutrient Fluxes in Faga'alu Bay, American Samoa Journal Article
Front. Environ. Sci. Eng. China, 7 , pp. 577, 2019.
@article{Welch2019-dc,
title = {Submarine Groundwater Discharge and Stream Baseflow Sustain
Pesticide and Nutrient Fluxes in Faga'alu Bay, American Samoa},
author = {Eric M Welch and Henrietta Dulai and Aly El-Kadi and Christopher K Shuler},
year = {2019},
date = {2019-01-01},
journal = {Front. Environ. Sci. Eng. China},
volume = {7},
pages = {577},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Bremer, Leah L; Farley, Kathleen A; DeMaagd, Nathan; Suárez, Esteban; Tandalla, Daisy Cárate; Tapia, Sebastián Vasco; Vásconez, Patricio Mena
Biodiversity outcomes of payment for ecosystem services: lessons
from páramo grasslands Journal Article
Biodivers. Conserv., 28 (4), pp. 885–908, 2019.
@article{Bremer2019-xh,
title = {Biodiversity outcomes of payment for ecosystem services: lessons
from páramo grasslands},
author = {Leah L Bremer and Kathleen A Farley and Nathan DeMaagd and Esteban Suárez and Daisy Cárate Tandalla and Sebastián Vasco Tapia and Patricio Mena Vásconez},
year = {2019},
date = {2019-01-01},
journal = {Biodivers. Conserv.},
volume = {28},
number = {4},
pages = {885--908},
abstract = {As payment for ecosystem services (PES) programs grow around the
world, so have concerns over whether a focus on ecosystem
services will also protect biodiversity. Biodiverse Ecuadorian
páramo grasslands have become a hotspot for PES in an effort
to protect water supplies, sequester carbon, conserve
biodiversity, and improve rural livelihoods. However, the
outcomes of PES-incentivized land management, particularly burn
exclusion, on plant communities and their associated ecosystem
services remain poorly understood. To address this science-policy
gap, we evaluated plant richness and number and cover of the ten
major páramo growth forms in two study areas with
chronosequences of burn exclusion. Both species richness and
number of growth forms was highest in sites with intermediate
times-since-last burn and the cover of tussock grasses---critical
to protecting soils and maintaining hydrologic
function---recovered within 3--6 years after fire at both study
areas, suggesting that PES programs targeting hydrologic services
do not need to exclude burning to ensure adequate vegetation
cover over the long-term. However, shrub growth forms were slower
to recover, indicating that conserving the plant composition
characteristic of less disturbed páramos requires some
protection from burning. Findings provide broad lessons for PES
programs focused on both biodiversity and ecosystem services and
point to the importance of clearly defining PES ecological goals
since land-use prescriptions may differ depending on the
management objective.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
As payment for ecosystem services (PES) programs grow around the
world, so have concerns over whether a focus on ecosystem
services will also protect biodiversity. Biodiverse Ecuadorian
páramo grasslands have become a hotspot for PES in an effort
to protect water supplies, sequester carbon, conserve
biodiversity, and improve rural livelihoods. However, the
outcomes of PES-incentivized land management, particularly burn
exclusion, on plant communities and their associated ecosystem
services remain poorly understood. To address this science-policy
gap, we evaluated plant richness and number and cover of the ten
major páramo growth forms in two study areas with
chronosequences of burn exclusion. Both species richness and
number of growth forms was highest in sites with intermediate
times-since-last burn and the cover of tussock grasses---critical
to protecting soils and maintaining hydrologic
function---recovered within 3--6 years after fire at both study
areas, suggesting that PES programs targeting hydrologic services
do not need to exclude burning to ensure adequate vegetation
cover over the long-term. However, shrub growth forms were slower
to recover, indicating that conserving the plant composition
characteristic of less disturbed páramos requires some
protection from burning. Findings provide broad lessons for PES
programs focused on both biodiversity and ecosystem services and
point to the importance of clearly defining PES ecological goals
since land-use prescriptions may differ depending on the
management objective. Beck, Hannah N; Cohen, Ashley; McKenzie, Trista; Weisend, Rachel; Wilkins, Keiko W; Woodstock, Matthew S
Broadening Horizons: Graduate Students Participating in
International Collaborations through the Limnology and
Oceanography Research Exchange (LOREX) Program Journal Article
Limnol. Oceanog. Bull., 28 (3), pp. 85–89, 2019.
@article{Beck2019-xa,
title = {Broadening Horizons: Graduate Students Participating in
International Collaborations through the Limnology and
Oceanography Research Exchange (LOREX) Program},
author = {Hannah N Beck and Ashley Cohen and Trista McKenzie and Rachel Weisend and Keiko W Wilkins and Matthew S Woodstock},
year = {2019},
date = {2019-01-01},
journal = {Limnol. Oceanog. Bull.},
volume = {28},
number = {3},
pages = {85--89},
abstract = {Abstract International research is necessary in aquatic sciences
because water moves across borders. Historically, international
collaborations have been useful in conducting oceanographic
research programs, which span large distances and require several
funding sources. Although valuable, international research can
have unforeseen challenges to the unprepared researcher.
Communication with an international collaborator and professional
development training can mitigate these pitfalls. The Limnology
and Oceanography Research Exchange Program (LOREX) is an
opportunity for graduate students to gain experience developing
international collaborations. The LOREX program aims to help
graduate students develop connections and gain experience in
international research. During the summer of 2019 and spring of
2020, 26 graduate students from 24 U.S. institutions will travel
to one of six different host institutions to conduct a research
project that they developed with an international collaborator.
To prepare for their research experience, LOREX participants
participated in training programs during the 2019 Aquatic
Sciences Meeting in San Juan, Puerto Rico. The first group of
LOREX graduate students will share their experience through
social media and blog posts throughout their journey.
Applications are now open for the second cohort of LOREX
participants, and potential applicants are encouraged to contact
potential collaborators to develop a research project.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Abstract International research is necessary in aquatic sciences
because water moves across borders. Historically, international
collaborations have been useful in conducting oceanographic
research programs, which span large distances and require several
funding sources. Although valuable, international research can
have unforeseen challenges to the unprepared researcher.
Communication with an international collaborator and professional
development training can mitigate these pitfalls. The Limnology
and Oceanography Research Exchange Program (LOREX) is an
opportunity for graduate students to gain experience developing
international collaborations. The LOREX program aims to help
graduate students develop connections and gain experience in
international research. During the summer of 2019 and spring of
2020, 26 graduate students from 24 U.S. institutions will travel
to one of six different host institutions to conduct a research
project that they developed with an international collaborator.
To prepare for their research experience, LOREX participants
participated in training programs during the 2019 Aquatic
Sciences Meeting in San Juan, Puerto Rico. The first group of
LOREX graduate students will share their experience through
social media and blog posts throughout their journey.
Applications are now open for the second cohort of LOREX
participants, and potential applicants are encouraged to contact
potential collaborators to develop a research project. Starkus, J; Jansen, C; Shimoda, L M N; Stokes, A J; Small-Howard, A L; Turner, H
Diverse TRPV1 responses to cannabinoids Journal Article
Channels, 13 (1), pp. 172–191, 2019.
@article{Starkus2019-mr,
title = {Diverse TRPV1 responses to cannabinoids},
author = {J Starkus and C Jansen and L M N Shimoda and A J Stokes and A L Small-Howard and H Turner},
year = {2019},
date = {2019-01-01},
journal = {Channels},
volume = {13},
number = {1},
pages = {172--191},
publisher = {Taylor & Francis},
abstract = {ABSTRACTCannabinoid compounds are potential analgesics. Users of
medicinal Cannabis report efficacy for pain control, clinical
studies show that cannabis can be effective and opioid sparing
in chronic pain, and some constituent cannabinoids have been
shown to target nociceptive ion channels. Here, we explore and
compare a suite of cannabinoids for their impact upon the
physiology of TRPV1. The cannabinoids tested evoke differential
responses in terms of kinetics of activation and inactivation.
Cannabinoid activation of TRPV1 displays significant dependence
on internal and external calcium levels. Cannabinoid activation
of TRPV1 does not appear to induce the highly permeant,
pore-dilated channel state seen with Capsaicin, even at high
current amplitudes. Finally, we analyzed cannabinoid responses
at nociceptive channels other than TRPV1 (TRPV2, TRPM8, and
TRPA1), and report that cannabinoids differentially activate
these channels. On the basis of response activation and
kinetics, state-selectivity and receptor selectivity, it may be
possible to rationally design approaches to pain using single or
multiple cannabinoids.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
ABSTRACTCannabinoid compounds are potential analgesics. Users of
medicinal Cannabis report efficacy for pain control, clinical
studies show that cannabis can be effective and opioid sparing
in chronic pain, and some constituent cannabinoids have been
shown to target nociceptive ion channels. Here, we explore and
compare a suite of cannabinoids for their impact upon the
physiology of TRPV1. The cannabinoids tested evoke differential
responses in terms of kinetics of activation and inactivation.
Cannabinoid activation of TRPV1 displays significant dependence
on internal and external calcium levels. Cannabinoid activation
of TRPV1 does not appear to induce the highly permeant,
pore-dilated channel state seen with Capsaicin, even at high
current amplitudes. Finally, we analyzed cannabinoid responses
at nociceptive channels other than TRPV1 (TRPV2, TRPM8, and
TRPA1), and report that cannabinoids differentially activate
these channels. On the basis of response activation and
kinetics, state-selectivity and receptor selectivity, it may be
possible to rationally design approaches to pain using single or
multiple cannabinoids. Reimann-Philipp, Ulrich; Speck, Mark; Orser, Cindy; Johnson, Steve; Hilyard, Aaron; Turner, Helen; Stokes, Alexander J; Small-Howard, Andrea L
Cannabis Chemovar Nomenclature Misrepresents Chemical and
Genetic Diversity; Survey of Variations in Chemical Profiles and
Genetic Markers in Nevada Medical Cannabis Samples Journal Article
Cannabis and Cannabinoid Research, 2019.
@article{Reimann-Philipp2019-tm,
title = {Cannabis Chemovar Nomenclature Misrepresents Chemical and
Genetic Diversity; Survey of Variations in Chemical Profiles and
Genetic Markers in Nevada Medical Cannabis Samples},
author = {Ulrich Reimann-Philipp and Mark Speck and Cindy Orser and Steve Johnson and Aaron Hilyard and Helen Turner and Alexander J Stokes and Andrea L Small-Howard},
year = {2019},
date = {2019-01-01},
journal = {Cannabis and Cannabinoid Research},
publisher = {Mary Ann Liebert, Inc., publishers 140 Huguenot Street, 3rd
Floor New …},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Adolf, Jason E; Burns, John; Walker, Judy K; Gamiao, Sydney
Near shore distributions of phytoplankton and bacteria in
relation to submarine groundwater discharge-fed fishponds, Kona
coast, Hawai`i, USA Journal Article
Estuar. Coast. Shelf Sci., 219 , pp. 341–353, 2019.
@article{Adolf2019-ci,
title = {Near shore distributions of phytoplankton and bacteria in
relation to submarine groundwater discharge-fed fishponds, Kona
coast, Hawai`i, USA},
author = {Jason E Adolf and John Burns and Judy K Walker and Sydney Gamiao},
year = {2019},
date = {2019-01-01},
journal = {Estuar. Coast. Shelf Sci.},
volume = {219},
pages = {341--353},
abstract = {Phytoplankton are important components of coastal marine
ecosystems that are strongly influenced by freshwater inputs from
land, including submarine groundwater discharge (SGD). Although
SGD generates sharp onshore -- offshore gradients in physical and
chemical conditions at several locations around Hawaii Island
little is known about the biotic responses of water column
microbes to these conditions. We studied the distributions of
phytoplankton and bacteria at two contrasting sites with SGD-fed
fishponds, Kiholo and Kaloko Bay, including the full range of
salinity extending from the fishponds to the coastal ocean. We
addressed the hypotheses that (1) SGD-fed fishponds support a
higher biomass and different composition of phytoplankton than
the adjacent ocean, and (2) phytoplankton biomass and composition
are related to SGD-driven salinity gradients in the coastal
ocean. Phytoplankton biomass in fishponds was elevated
(10--100-fold) and accompanied by higher average cell size pico-
and nano-phytoplankton (2--6 $mu$m) relative to sites outside
the fishpond. General additive models (GAMs) showed elevated
biomass and average cell size at mid-range salinities and
declining biomass at salinity < 20 outside the fishponds.
Multivariate RDA showed significant, site-specific relationships
between surface phytoplankton biomass (Chl a), cell counts, and
environmental parameters. Analysis of surface vs. deep samples
from outside the fishponds showed elevated phytoplankton biomass
at the surface, except in Kiholo lagoon where phytoplankton was
elevated beneath the SGD-driven pycnocline. This study shows
structuring of coastal phytoplankton through SGD inputs and
suggest that changes in SGD due to coastal development or climate
change can impact coastal marine ecosystems through effects on
phytoplankton communities.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Phytoplankton are important components of coastal marine
ecosystems that are strongly influenced by freshwater inputs from
land, including submarine groundwater discharge (SGD). Although
SGD generates sharp onshore -- offshore gradients in physical and
chemical conditions at several locations around Hawaii Island
little is known about the biotic responses of water column
microbes to these conditions. We studied the distributions of
phytoplankton and bacteria at two contrasting sites with SGD-fed
fishponds, Kiholo and Kaloko Bay, including the full range of
salinity extending from the fishponds to the coastal ocean. We
addressed the hypotheses that (1) SGD-fed fishponds support a
higher biomass and different composition of phytoplankton than
the adjacent ocean, and (2) phytoplankton biomass and composition
are related to SGD-driven salinity gradients in the coastal
ocean. Phytoplankton biomass in fishponds was elevated
(10--100-fold) and accompanied by higher average cell size pico-
and nano-phytoplankton (2--6 $mu$m) relative to sites outside
the fishpond. General additive models (GAMs) showed elevated
biomass and average cell size at mid-range salinities and
declining biomass at salinity < 20 outside the fishponds.
Multivariate RDA showed significant, site-specific relationships
between surface phytoplankton biomass (Chl a), cell counts, and
environmental parameters. Analysis of surface vs. deep samples
from outside the fishponds showed elevated phytoplankton biomass
at the surface, except in Kiholo lagoon where phytoplankton was
elevated beneath the SGD-driven pycnocline. This study shows
structuring of coastal phytoplankton through SGD inputs and
suggest that changes in SGD due to coastal development or climate
change can impact coastal marine ecosystems through effects on
phytoplankton communities. Fukunaga, Atsuko; Burns, John H R; Craig, Brianna K; Kosaki, Randall K
Integrating Three-Dimensional Benthic Habitat Characterization
Techniques into Ecological Monitoring of Coral Reefs Journal Article
J. Mar. Sci. Eng., 7 (2), pp. 27, 2019.
@article{Fukunaga2019-ep,
title = {Integrating Three-Dimensional Benthic Habitat Characterization
Techniques into Ecological Monitoring of Coral Reefs},
author = {Atsuko Fukunaga and John H R Burns and Brianna K Craig and Randall K Kosaki},
year = {2019},
date = {2019-01-01},
journal = {J. Mar. Sci. Eng.},
volume = {7},
number = {2},
pages = {27},
publisher = {Multidisciplinary Digital Publishing Institute},
abstract = {Long-term ecological monitoring of reef fish populations often
requires the simultaneous collection of data on benthic habitats
in order to account for the effects of these variables on fish
assemblage structure. Here, we described an approach to benthic
surveys that uses photogrammetric techniques to facilitate the
extraction of quantitative metrics for characterization of
benthic habitats from the resulting three-dimensional (3D)
reconstruction of coral reefs. Out of 92 sites surveyed in the
Northwestern Hawaiian Islands, photographs from 85 sites
achieved complete alignment and successfully produced 3D
reconstructions and digital elevation models (DEMs). Habitat
metrics extracted from the DEMs were generally correlated with
one another, with the exception of curvature measures,
indicating that complexity and curvature measures should be
treated separately when quantifying the habitat structure.
Fractal dimension D64, calculated by changing resolutions of the
DEMs from 1 cm to 64 cm, had the best correlations with other
habitat metrics. Fractal dimension was also less affected by
changes in orientations of the models compared to surface
complexity or slope. These results showed that fractal dimension
can be used as a single measure of complexity for the
characterization of coral reef habitats. Further investigations
into metrics for 3D characterization of habitats should consider
relevant spatial scales and focus on obtaining variables that
can complement fractal dimension in the characterization of reef
habitats.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Long-term ecological monitoring of reef fish populations often
requires the simultaneous collection of data on benthic habitats
in order to account for the effects of these variables on fish
assemblage structure. Here, we described an approach to benthic
surveys that uses photogrammetric techniques to facilitate the
extraction of quantitative metrics for characterization of
benthic habitats from the resulting three-dimensional (3D)
reconstruction of coral reefs. Out of 92 sites surveyed in the
Northwestern Hawaiian Islands, photographs from 85 sites
achieved complete alignment and successfully produced 3D
reconstructions and digital elevation models (DEMs). Habitat
metrics extracted from the DEMs were generally correlated with
one another, with the exception of curvature measures,
indicating that complexity and curvature measures should be
treated separately when quantifying the habitat structure.
Fractal dimension D64, calculated by changing resolutions of the
DEMs from 1 cm to 64 cm, had the best correlations with other
habitat metrics. Fractal dimension was also less affected by
changes in orientations of the models compared to surface
complexity or slope. These results showed that fractal dimension
can be used as a single measure of complexity for the
characterization of coral reef habitats. Further investigations
into metrics for 3D characterization of habitats should consider
relevant spatial scales and focus on obtaining variables that
can complement fractal dimension in the characterization of reef
habitats. Jerram, Dougal A; Millett, John M; Kück, Jochem; Thomas, Donald; Planke, Sverre; Haskins, Eric; Lautze, Nicole; Pierdominici, Simona
Understanding volcanic facies in the subsurface: a combined
core, wireline logging and image log data set from the PTA2
and KMA1 boreholes, Big Island, Hawai`i Journal Article
Sci. Drill., 25 , pp. 15–33, 2019.
@article{Jerram2019-tn,
title = {Understanding volcanic facies in the subsurface: a combined
core, wireline logging and image log data set from the PTA2
and KMA1 boreholes, Big Island, Hawai`i},
author = {Dougal A Jerram and John M Millett and Jochem Kück and Donald Thomas and Sverre Planke and Eric Haskins and Nicole Lautze and Simona Pierdominici},
year = {2019},
date = {2019-01-01},
journal = {Sci. Drill.},
volume = {25},
pages = {15--33},
publisher = {Copernicus GmbH},
abstract = {Abstract. To help understand volcanic facies in the subsurface,
data sets that enable detailed comparisons between down-hole
geophysical data and cored volcanic intervals are critical.
However, in many cases, the collection of extended core
intervals within volcanic sequences is rare and often incomplete
due to challenging coring conditions. In this contribution we
outline and provide initial results from borehole logging
operations within two fully cored lava-dominated borehole
sequences, PTA2 and KMA1, on the Big Island of Hawai`i. Data for
spectral gamma, magnetic susceptibility, dipmeter resistivity,
sonic, total magnetic field, temperature and televiewer wireline
logs were successfully acquired for the open hole interval ca.
889 m to 1567 m within the PTA2 borehole. Spectral gamma was
also collected from inside the casing of both wells, extending
the coverage for PTA2 to the surface and covering the interval
from ca. 300 to 1200 m for KMA1. High-quality core material was
available for both boreholes with almost complete recovery which
enabled high-resolution core-to-log integration. Gamma data are
generally low commonly in the range ca. 7--20 gAPI but are shown
to increase up to API of ca. 60 with some intrusions and with
increases in hawaiite compositions in the upper part of PTA2.
Velocity data are more variable due to alteration within porous
volcanic facies than with burial depth, with a general degrease
down-hole. The high-resolution televiewer data have been
compared directly to the core, enabling a comprehensive analysis
of the variations in the televiewer responses. This has enabled
the identification of key features including individual
vesicles, vesicle segregations, strained vesicles, chilled margins, rubble zones, intrusive contacts and p=ahoehoe lobe
morphologies, which can be confidently matched between the
televiewer data and the full diameter core. The data set and
results of this study include findings which should enable
improved borehole facies analysis through volcanic sequences in
the future, especially where down-borehole data and images but
no core are available.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Abstract. To help understand volcanic facies in the subsurface,
data sets that enable detailed comparisons between down-hole
geophysical data and cored volcanic intervals are critical.
However, in many cases, the collection of extended core
intervals within volcanic sequences is rare and often incomplete
due to challenging coring conditions. In this contribution we
outline and provide initial results from borehole logging
operations within two fully cored lava-dominated borehole
sequences, PTA2 and KMA1, on the Big Island of Hawai`i. Data for
spectral gamma, magnetic susceptibility, dipmeter resistivity,
sonic, total magnetic field, temperature and televiewer wireline
logs were successfully acquired for the open hole interval ca.
889 m to 1567 m within the PTA2 borehole. Spectral gamma was
also collected from inside the casing of both wells, extending
the coverage for PTA2 to the surface and covering the interval
from ca. 300 to 1200 m for KMA1. High-quality core material was
available for both boreholes with almost complete recovery which
enabled high-resolution core-to-log integration. Gamma data are
generally low commonly in the range ca. 7--20 gAPI but are shown
to increase up to API of ca. 60 with some intrusions and with
increases in hawaiite compositions in the upper part of PTA2.
Velocity data are more variable due to alteration within porous
volcanic facies than with burial depth, with a general degrease
down-hole. The high-resolution televiewer data have been
compared directly to the core, enabling a comprehensive analysis
of the variations in the televiewer responses. This has enabled
the identification of key features including individual
vesicles, vesicle segregations, strained vesicles, chilled margins, rubble zones, intrusive contacts and p=ahoehoe lobe
morphologies, which can be confidently matched between the
televiewer data and the full diameter core. The data set and
results of this study include findings which should enable
improved borehole facies analysis through volcanic sequences in
the future, especially where down-borehole data and images but
no core are available. Battistel, Maria; Muniruzzaman, Muhammad; Onses, Felix; Lee, Jonghyun; Rolle, Massimo
Reactive fronts in chemically heterogeneous porous media:
Experimental and modeling investigation of pyrite oxidation Journal Article
Appl. Geochem., 100 , pp. 77–89, 2019.
@article{Battistel2019-zf,
title = {Reactive fronts in chemically heterogeneous porous media:
Experimental and modeling investigation of pyrite oxidation},
author = {Maria Battistel and Muhammad Muniruzzaman and Felix Onses and Jonghyun Lee and Massimo Rolle},
year = {2019},
date = {2019-01-01},
journal = {Appl. Geochem.},
volume = {100},
pages = {77--89},
abstract = {The spatial distribution of reactive minerals in subsurface
porous media is an important control for groundwater quality. In
this study we investigate pyrite oxidation reactive fronts in
chemically heterogeneous porous media by combining laboratory
experiments and reactive transport modeling. We performed
experiments in different setups including batch, 1-D column, and
2-D flow-through systems. The flow-through experiments were
performed in physically homogenous but chemically heterogeneous
domains with embedded reactive pyrite inclusions at different
spatial locations and with different concentrations. The setups
were initially maintained under anoxic conditions and
subsequently flushed with an inflowing oxic solution. A
non-invasive optode technique was used for high-resolution
monitoring of oxygen. This allowed us to capture the dynamics of
the reactive oxygen fronts in the 1-D columns and in the 2-D
flow-through chamber. Water quality analyses of the products of
pyrite oxidation, iron (Fe) and sulfur (S), were also carried out
in the different setups. The concentration of these species
released in the 1-D columns (up to 6.2 $times$ 10−5 mol/L Fe and
13.7 $times$ 10−5 mol/L S) and in the 2-D setup (up to 3
$times$ 10−6 mol/L Fe and 9 $times$ 10−6 mol/L S) could be
quantitatively related to the consumption of oxygen (up to 1.9
$times$ 10−4 mol/L consumed in the 1-D and 2-D setups). The
reaction rates were found to be different between the setups and
dependent on the spatial location and concentration of the pyrite
inclusions. A modeling approach coupling 1-D and 2-D transport
codes with the geochemical simulator PHREEQC is proposed to
simulate the spatial and temporal dynamics of oxygen transport,
the kinetics of pyrite oxidative dissolution, and the changes in
water quality in the chemically heterogeneous flow-through
setups. The model allowed the quantitative interpretation of the
experimental results and represents a valuable tool to capture
the coupling between multidimensional transport and geochemical
reactions both in laboratory and in field scale applications.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The spatial distribution of reactive minerals in subsurface
porous media is an important control for groundwater quality. In
this study we investigate pyrite oxidation reactive fronts in
chemically heterogeneous porous media by combining laboratory
experiments and reactive transport modeling. We performed
experiments in different setups including batch, 1-D column, and
2-D flow-through systems. The flow-through experiments were
performed in physically homogenous but chemically heterogeneous
domains with embedded reactive pyrite inclusions at different
spatial locations and with different concentrations. The setups
were initially maintained under anoxic conditions and
subsequently flushed with an inflowing oxic solution. A
non-invasive optode technique was used for high-resolution
monitoring of oxygen. This allowed us to capture the dynamics of
the reactive oxygen fronts in the 1-D columns and in the 2-D
flow-through chamber. Water quality analyses of the products of
pyrite oxidation, iron (Fe) and sulfur (S), were also carried out
in the different setups. The concentration of these species
released in the 1-D columns (up to 6.2 $times$ 10−5 mol/L Fe and
13.7 $times$ 10−5 mol/L S) and in the 2-D setup (up to 3
$times$ 10−6 mol/L Fe and 9 $times$ 10−6 mol/L S) could be
quantitatively related to the consumption of oxygen (up to 1.9
$times$ 10−4 mol/L consumed in the 1-D and 2-D setups). The
reaction rates were found to be different between the setups and
dependent on the spatial location and concentration of the pyrite
inclusions. A modeling approach coupling 1-D and 2-D transport
codes with the geochemical simulator PHREEQC is proposed to
simulate the spatial and temporal dynamics of oxygen transport,
the kinetics of pyrite oxidative dissolution, and the changes in
water quality in the chemically heterogeneous flow-through
setups. The model allowed the quantitative interpretation of the
experimental results and represents a valuable tool to capture
the coupling between multidimensional transport and geochemical
reactions both in laboratory and in field scale applications. Taniguchi, Makoto; Burnett, Kimberly M; Shimada, Jun; Hosono, Takahiro; Wada, Christopher A; Ide, Kiyoshi
Recovery of Lost Nexus Synergy via Payment for Environmental
Services in Kumamoto, Japan Journal Article
Front. Environ. Sci. Eng. China, 7 , pp. 28, 2019.
@article{Taniguchi2019-xv,
title = {Recovery of Lost Nexus Synergy via Payment for Environmental
Services in Kumamoto, Japan},
author = {Makoto Taniguchi and Kimberly M Burnett and Jun Shimada and Takahiro Hosono and Christopher A Wada and Kiyoshi Ide},
year = {2019},
date = {2019-01-01},
journal = {Front. Environ. Sci. Eng. China},
volume = {7},
pages = {28},
abstract = {The objective of this study is to characterize and quantify the
``trans-spatial nexus synergy'' benefit of subsidized water
ponding in the water-energy-food nexus in Kumamoto, Japan. After
years of decreased rice production in upstream areas and
associated declines in groundwater levels, the Kumamoto city
government implemented a subsidy program whereby farmers in the
Shira River basin receive payments to water their fields, which
provides valuable groundwater recharge to downstream Kumamoto
city. We quantify the economic benefits of this subsidy program,
which include avoided additional energy costs to obtain scarcer
levels of groundwater, as well as net revenue from the crops in
the Shira River basin that would otherwise not be grown in the
absence of the subsidy. These annual benefits can be combined and
compared to the annual cost of the government subsidy. We also
calculate potential historical losses that may have occurred in
the region as a result of land use transitions from rice farming
to urban use, which disrupted the nexus synergy between the
watered fields and the groundwater table.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The objective of this study is to characterize and quantify the
``trans-spatial nexus synergy'' benefit of subsidized water
ponding in the water-energy-food nexus in Kumamoto, Japan. After
years of decreased rice production in upstream areas and
associated declines in groundwater levels, the Kumamoto city
government implemented a subsidy program whereby farmers in the
Shira River basin receive payments to water their fields, which
provides valuable groundwater recharge to downstream Kumamoto
city. We quantify the economic benefits of this subsidy program,
which include avoided additional energy costs to obtain scarcer
levels of groundwater, as well as net revenue from the crops in
the Shira River basin that would otherwise not be grown in the
absence of the subsidy. These annual benefits can be combined and
compared to the annual cost of the government subsidy. We also
calculate potential historical losses that may have occurred in
the region as a result of land use transitions from rice farming
to urban use, which disrupted the nexus synergy between the
watered fields and the groundwater table. Magel, Jennifer M T; Burns, John H R; Gates, Ruth D; Baum, Julia K
Effects of bleaching-associated mass coral mortality on reef
structural complexity across a gradient of local disturbance Journal Article
Sci. Rep., 9 (1), pp. 2512, 2019.
@article{Magel2019-zm,
title = {Effects of bleaching-associated mass coral mortality on reef
structural complexity across a gradient of local disturbance},
author = {Jennifer M T Magel and John H R Burns and Ruth D Gates and Julia K Baum},
year = {2019},
date = {2019-01-01},
journal = {Sci. Rep.},
volume = {9},
number = {1},
pages = {2512},
abstract = {Structural complexity underpins the ecological functioning of
coral reefs. However, rising ocean temperatures and associated
coral bleaching threaten the structural integrity of these
important ecosystems. Despite the increased frequency of coral
bleaching events, few studies to date have examined changes in
three-dimensional (3D) reef structural complexity following
severe bleaching. The influence of local stressors on reef
complexity also remains poorly understood. In the wake of the
2015-2016 El Ni~no-induced mass coral bleaching event, we
quantified the effects of severe heat stress on 3D reef
structural complexity across a gradient of local human
disturbance. Using Structure-from-Motion photogrammetry we
created 3D reconstructions of permanent reef plots and observed
substantial declines in reef structural complexity, measured as
surface rugosity and terrain ruggedness, and a detectable loss of
habitat volume one year after the bleaching event. 3D reef
complexity also declined with increasing levels of human
disturbance, and with decreasing densities of branching and
massive corals. These findings improve our understanding of the
effects of local and global stressors on the structural
foundation of coral reef ecosystems. In the face of accelerating
climate change, mitigating local stressors may increase reef
structural complexity, thereby heightening reef resilience to
future bleaching events.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Structural complexity underpins the ecological functioning of
coral reefs. However, rising ocean temperatures and associated
coral bleaching threaten the structural integrity of these
important ecosystems. Despite the increased frequency of coral
bleaching events, few studies to date have examined changes in
three-dimensional (3D) reef structural complexity following
severe bleaching. The influence of local stressors on reef
complexity also remains poorly understood. In the wake of the
2015-2016 El Ni~no-induced mass coral bleaching event, we
quantified the effects of severe heat stress on 3D reef
structural complexity across a gradient of local human
disturbance. Using Structure-from-Motion photogrammetry we
created 3D reconstructions of permanent reef plots and observed
substantial declines in reef structural complexity, measured as
surface rugosity and terrain ruggedness, and a detectable loss of
habitat volume one year after the bleaching event. 3D reef
complexity also declined with increasing levels of human
disturbance, and with decreasing densities of branching and
massive corals. These findings improve our understanding of the
effects of local and global stressors on the structural
foundation of coral reef ecosystems. In the face of accelerating
climate change, mitigating local stressors may increase reef
structural complexity, thereby heightening reef resilience to
future bleaching events. Bottjer-Wilson, Daniela; Bruno, Barbara C
Place Matters! Fostering place-based geoscience teaching at the University of Hawai`i at M=anoa Inproceedings
Fifth International Conference on Higher Education Advances, 2019.
@inproceedings{Bottjer-Wilson2019-ap,
title = {Place Matters! Fostering place-based geoscience teaching at the University of Hawai`i at M=anoa},
author = {Daniela Bottjer-Wilson and Barbara C Bruno},
year = {2019},
date = {2019-01-01},
booktitle = {Fifth International Conference on Higher Education Advances},
abstract = {Drawing on the importance of place has been shown to be a
powerful tool in education. This paper explores place-based
teaching (PBT) in geoscience courses at the University of Hawai`i at M=anoa's School of Ocean and Earth Science and
Technology, where faculty and student demographics sharply
differ. Despite these differences, survey results from geoscience faculty (n=59) and students (n=83) revealed a strong
consensus: 78% of students and 83% of faculty reported that
PBT is an important and effective practice to reach all
students. Most faculty (91%) indicated that they currently
incorporate at least some PBT practices in their geoscience
classes and would like to incorporate additional ones in the
future. However, many faculty expressed concern about lack of
knowledge or resources, particularly regarding PBT strategies
that require a high level of cultural competency. We therefore
propose a three-layered PBT framework, where faculty can start
with more accessible PBT strategies (the base layer) and
progress upwards as their cultural competency deepens. Through
providing geoscience resources and professional development
opportunities, we can empower faculty to include more diverse
and culturally meaningful practices as their experience and
knowledge deepens.},
keywords = {},
pubstate = {published},
tppubtype = {inproceedings}
}
Drawing on the importance of place has been shown to be a
powerful tool in education. This paper explores place-based
teaching (PBT) in geoscience courses at the University of Hawai`i at M=anoa's School of Ocean and Earth Science and
Technology, where faculty and student demographics sharply
differ. Despite these differences, survey results from geoscience faculty (n=59) and students (n=83) revealed a strong
consensus: 78% of students and 83% of faculty reported that
PBT is an important and effective practice to reach all
students. Most faculty (91%) indicated that they currently
incorporate at least some PBT practices in their geoscience
classes and would like to incorporate additional ones in the
future. However, many faculty expressed concern about lack of
knowledge or resources, particularly regarding PBT strategies
that require a high level of cultural competency. We therefore
propose a three-layered PBT framework, where faculty can start
with more accessible PBT strategies (the base layer) and
progress upwards as their cultural competency deepens. Through
providing geoscience resources and professional development
opportunities, we can empower faculty to include more diverse
and culturally meaningful practices as their experience and
knowledge deepens. Goldberg, David M; Hong, Sukhwa
Minimizing the Risks of Highway Transport of Hazardous Materials Journal Article
Sustain. Sci. Pract. Policy, 11 (22), pp. 6300, 2019.
@article{Goldberg2019-yz,
title = {Minimizing the Risks of Highway Transport of Hazardous Materials},
author = {David M Goldberg and Sukhwa Hong},
year = {2019},
date = {2019-01-01},
journal = {Sustain. Sci. Pract. Policy},
volume = {11},
number = {22},
pages = {6300},
publisher = {Multidisciplinary Digital Publishing Institute},
abstract = {Many key industrial and scientific processes, such as the
generation of nuclear energy, are of enormous social benefit as
energy demand and consumption grow over time. However, a
drawback of several such processes is the production of
hazardous waste materials, which often requires transportation
along highway networks to treatment or disposal facilities. This
waste can represent a safety hazard to civilians located along
the transportation route. Most prior literature in this domain
considers risk within only a single facet, and thus several
important risk factors may not be considered. In our paper, we
propose a multi-objective program to allow for the analysis and
selection of minimally risky routes for hazardous materials
transportation. The model assesses risk factors including the
length of the selected route, the total population in areas
surrounding the selected route, and the likelihood of an
accident occurring along the selected route. Our paper uniquely
uses geographic information systems (GIS) technology to model
this optimization problem. This approach allows us to model risk
along multiple dimensions simultaneously. We collect empirical
data to test the model and present a case study for risk
mitigation using a study area located in California. We show
that our multi-objective approach is effective in presenting the
decision-maker with a portfolio of solutions that perform well
via each factor.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Many key industrial and scientific processes, such as the
generation of nuclear energy, are of enormous social benefit as
energy demand and consumption grow over time. However, a
drawback of several such processes is the production of
hazardous waste materials, which often requires transportation
along highway networks to treatment or disposal facilities. This
waste can represent a safety hazard to civilians located along
the transportation route. Most prior literature in this domain
considers risk within only a single facet, and thus several
important risk factors may not be considered. In our paper, we
propose a multi-objective program to allow for the analysis and
selection of minimally risky routes for hazardous materials
transportation. The model assesses risk factors including the
length of the selected route, the total population in areas
surrounding the selected route, and the likelihood of an
accident occurring along the selected route. Our paper uniquely
uses geographic information systems (GIS) technology to model
this optimization problem. This approach allows us to model risk
along multiple dimensions simultaneously. We collect empirical
data to test the model and present a case study for risk
mitigation using a study area located in California. We show
that our multi-objective approach is effective in presenting the
decision-maker with a portfolio of solutions that perform well
via each factor. Misra, Anupam K; Acosta-Maeda, Tayro E; Porter, John N; Egan, Miles J; Sandford, Macey W; Oyama, Tamra; Zhou, Jie
Remote Raman Detection of Chemicals from 1752 m During Afternoon
Daylight Journal Article
Appl. Spectrosc., pp. 3702819875437, 2019.
@article{Misra2019-aj,
title = {Remote Raman Detection of Chemicals from 1752 m During Afternoon
Daylight},
author = {Anupam K Misra and Tayro E Acosta-Maeda and John N Porter and Miles J Egan and Macey W Sandford and Tamra Oyama and Jie Zhou},
year = {2019},
date = {2019-01-01},
journal = {Appl. Spectrosc.},
pages = {3702819875437},
abstract = {The detection and identification of materials from a distance is
highly desirable for applications where accessibility is limited
or there are safety concerns. Raman spectroscopy can be performed
remotely and provides a very high level of confidence in
detection of chemicals through vibrational modes. However, the
remote Raman detection of chemicals is challenging because of the
very weak nature of Raman signals. Using a remote Raman system,
we performed fast remote detection of various solid and liquid
chemicals from 1752 m during afternoon hours on a sunny day in
Hawaii. Remote Raman systems with kilometer target range could be
useful for chemical detection of volcanic gases, methane
clathrate icebergs or fire ice, toxic gas clouds and toxic waste,
explosives, and hazardous chemicals. With this successful test,
we demonstrate the feasibility of developing future mid-size
remote Raman systems suitable for long range chemical detection
using helicopters and light airplanes.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The detection and identification of materials from a distance is
highly desirable for applications where accessibility is limited
or there are safety concerns. Raman spectroscopy can be performed
remotely and provides a very high level of confidence in
detection of chemicals through vibrational modes. However, the
remote Raman detection of chemicals is challenging because of the
very weak nature of Raman signals. Using a remote Raman system,
we performed fast remote detection of various solid and liquid
chemicals from 1752 m during afternoon hours on a sunny day in
Hawaii. Remote Raman systems with kilometer target range could be
useful for chemical detection of volcanic gases, methane
clathrate icebergs or fire ice, toxic gas clouds and toxic waste,
explosives, and hazardous chemicals. With this successful test,
we demonstrate the feasibility of developing future mid-size
remote Raman systems suitable for long range chemical detection
using helicopters and light airplanes.
2018
Bremer, Leah L; Brauman, Kate A; Nelson, Sara; Prado, Kelly Meza; Wilburn, Eric; Fiorini, Ana Carolina O
Relational values in evaluations of upstream social outcomes of
watershed Payment for Ecosystem Services: a review Journal Article
Current Opinion in Environmental Sustainability, 35 , pp. 116–123, 2018.
@article{Bremer2018-hx,
title = {Relational values in evaluations of upstream social outcomes of
watershed Payment for Ecosystem Services: a review},
author = {Leah L Bremer and Kate A Brauman and Sara Nelson and Kelly Meza Prado and Eric Wilburn and Ana Carolina O Fiorini},
year = {2018},
date = {2018-12-01},
journal = {Current Opinion in Environmental Sustainability},
volume = {35},
pages = {116--123},
abstract = {Relational values associated with meaningful and just
human--environment relationships (e.g. care and responsibility)
have been proposed as motivating `upstream' participation in
Payments for Watershed Services (PWS). However, the way
relational values are affected by and interact with PWS remains
poorly understood. We reviewed 50 studies of social outcomes of
PWS and found that approximately half assessed or discussed
relational values. This included changes in relational values
presented positively, such as amplifying values and norms around
care for land; negatively, such as undermining traditional
practices and intergenerational learning; and influencing other
outcomes, such as links between land ties and human health. To
improve understanding of the full suite of outcomes linked to the
effectiveness, durability, and equity of PWS, we propose a
research agenda based on locally-based relational value systems
that include, for example, place-based conceptualizations of
responsibility, care, and relation to the natural world.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Relational values associated with meaningful and just
human--environment relationships (e.g. care and responsibility)
have been proposed as motivating `upstream' participation in
Payments for Watershed Services (PWS). However, the way
relational values are affected by and interact with PWS remains
poorly understood. We reviewed 50 studies of social outcomes of
PWS and found that approximately half assessed or discussed
relational values. This included changes in relational values
presented positively, such as amplifying values and norms around
care for land; negatively, such as undermining traditional
practices and intergenerational learning; and influencing other
outcomes, such as links between land ties and human health. To
improve understanding of the full suite of outcomes linked to the
effectiveness, durability, and equity of PWS, we propose a
research agenda based on locally-based relational value systems
that include, for example, place-based conceptualizations of
responsibility, care, and relation to the natural world. Leary, James; Mahnken, Brooke; Wada, Christopher; Burnett, Kimberly
Interpreting Life-History Traits of Miconia (Miconia
calvescens) through Management over Space and Time in the East
Maui Watershed, Hawaii (USA) Journal Article
Invasive Plant Sci. Manage., 11 (4), pp. 191–200, 2018.
@article{Leary2018-xt,
title = {Interpreting Life-History Traits of Miconia (Miconia
calvescens) through Management over Space and Time in the East
Maui Watershed, Hawaii (USA)},
author = {James Leary and Brooke Mahnken and Christopher Wada and Kimberly Burnett},
year = {2018},
date = {2018-12-01},
journal = {Invasive Plant Sci. Manage.},
volume = {11},
number = {4},
pages = {191--200},
publisher = {Cambridge University Press},
abstract = {Miconia (Miconia calvescens DC) was introduced to the East Maui
Watershed (EMW) a half-century ago with more than 25 yr of
management recorded. Using a historical spatiotemporal data set,
we constructed a leptokurtic dispersal kernel with 99% of
progeny confined to within 549 m of the nearest maternal source
and the remaining 1% dispersed out to 1,636 m. Seedbank
persistence, based on postdated recruitment, displayed an
exponential decay projecting extinction beyond 20 yr. These
parameters are highly congruent to independent interpretations
of M. calvescens in Australia and Tahiti. In a simulated stage
matrix model, we projected management efforts to locally
eradicate a small incipient propagule bank wherein optimal
management was achieved with an annual harvest rate that
eliminated all juvenile recruits before reaching maturity, until
extinction. Based on current pricing for helicopter herbicide
ballistic technology (HBT) operations, the optimal, variable
cost to locally eradicate this incipient propagule bank was
estimated to be less than US$42,000, with ~90% of the effort
searching for the most distant 1% of the progeny expended
within the first 9 yr after the mature discovery. This variable
cost was sensitive to seedbank size, recruitment rate, and
dispersal range, but was most sensitive to harvest rates between
suboptimal and excess. In a scenario prioritizing the upper
region of EMW, we retroactively analyzed past HBT efforts
eliminating satellite M. calvescens and determined that 27% of
the total effort resulted in 87% of the total protection to
this priority asset, with every US$1 invested potentially
avoiding US$184 in future costs. Management outside the
priority area was less economical, with returns in protection
diminishing with distance from the priority upper region.
Miconia calvescens is currently not eradicable in the EMW, and
full containment of the invasion would require a substantial
increase in stable, long-term funding. With limited resources,
local eradication of satellite M. calvescens could be the most
cost-effective alternative to protecting uninvaded areas
prioritized for critical ecosystem functions.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Miconia (Miconia calvescens DC) was introduced to the East Maui
Watershed (EMW) a half-century ago with more than 25 yr of
management recorded. Using a historical spatiotemporal data set,
we constructed a leptokurtic dispersal kernel with 99% of
progeny confined to within 549 m of the nearest maternal source
and the remaining 1% dispersed out to 1,636 m. Seedbank
persistence, based on postdated recruitment, displayed an
exponential decay projecting extinction beyond 20 yr. These
parameters are highly congruent to independent interpretations
of M. calvescens in Australia and Tahiti. In a simulated stage
matrix model, we projected management efforts to locally
eradicate a small incipient propagule bank wherein optimal
management was achieved with an annual harvest rate that
eliminated all juvenile recruits before reaching maturity, until
extinction. Based on current pricing for helicopter herbicide
ballistic technology (HBT) operations, the optimal, variable
cost to locally eradicate this incipient propagule bank was
estimated to be less than US$42,000, with ~90% of the effort
searching for the most distant 1% of the progeny expended
within the first 9 yr after the mature discovery. This variable
cost was sensitive to seedbank size, recruitment rate, and
dispersal range, but was most sensitive to harvest rates between
suboptimal and excess. In a scenario prioritizing the upper
region of EMW, we retroactively analyzed past HBT efforts
eliminating satellite M. calvescens and determined that 27% of
the total effort resulted in 87% of the total protection to
this priority asset, with every US$1 invested potentially
avoiding US$184 in future costs. Management outside the
priority area was less economical, with returns in protection
diminishing with distance from the priority upper region.
Miconia calvescens is currently not eradicable in the EMW, and
full containment of the invasion would require a substantial
increase in stable, long-term funding. With limited resources,
local eradication of satellite M. calvescens could be the most
cost-effective alternative to protecting uninvaded areas
prioritized for critical ecosystem functions.
2020 |
Dudley, B D; Hughes, R F; Asner, G P; Baldwin, J A; Miyazawa, Y; Dulai, H; Waters, C; Bishop, J; Vaughn, N R; Yeh, J; Kettwich, S; MacKenzie, R A; Ostertag, R; Giambelluca, T Hydrological effects of tree invasion on a dry coastal Hawaiian ecosystem Journal Article For. Ecol. Manage., 458 , pp. 117653, 2020. @article{Dudley2020-sj, title = {Hydrological effects of tree invasion on a dry coastal Hawaiian ecosystem}, author = {B D Dudley and R F Hughes and G P Asner and J A Baldwin and Y Miyazawa and H Dulai and C Waters and J Bishop and N R Vaughn and J Yeh and S Kettwich and R A MacKenzie and R Ostertag and T Giambelluca}, year = {2020}, date = {2020-02-01}, journal = {For. Ecol. Manage.}, volume = {458}, pages = {117653}, abstract = {In ecosystems invaded by non-native plants invasion effects are often spatially variable, and this variability is difficult to capture via plot-scale sampling. We used airborne high-resolution LiDAR (Light Detection and Ranging) to generate spatially explicit and contiguous information on hydrological effects of invasive trees (Prosopis pallida (Humb. & Bonpl. ex Willd.) Kunth). We developed regression relationships between LiDAR metrics (i.e., ground elevation and tree canopy height) and plot-scale measurements of vegetation stem water $delta$18O, to assess groundwater use, and transpiration rates. We used electrical resistivity imaging to assess subsurface geology and hydrology and their relationships to P. pallida stand structure. P. pallida biomass and transpiration varied greatly across the study area; both were controlled by depth to groundwater. Stem water $delta$18O values (-8.6 to 3.7‰) indicated a threshold ground elevation of ca. 15 m above sea level, above which P. pallida could not access groundwater; this threshold corresponded to declines in tree biomass and height. Transpiration modelled across the study area was 0.034 $pm$ 0.017 mm day−1, but over 98% of transpiration came from the ca. 25% of the total study area where groundwater depths were less than 15 m. Our combination of methods offers a new way to incorporate fine-scale spatial variation into estimation of plant invasion effects on hydrology, increase our understanding of interactions of geology, hydrology, and biology in such invasions, and prioritise areas for control in well-advanced invasions.}, keywords = {}, pubstate = {published}, tppubtype = {article} } In ecosystems invaded by non-native plants invasion effects are often spatially variable, and this variability is difficult to capture via plot-scale sampling. We used airborne high-resolution LiDAR (Light Detection and Ranging) to generate spatially explicit and contiguous information on hydrological effects of invasive trees (Prosopis pallida (Humb. & Bonpl. ex Willd.) Kunth). We developed regression relationships between LiDAR metrics (i.e., ground elevation and tree canopy height) and plot-scale measurements of vegetation stem water $delta$18O, to assess groundwater use, and transpiration rates. We used electrical resistivity imaging to assess subsurface geology and hydrology and their relationships to P. pallida stand structure. P. pallida biomass and transpiration varied greatly across the study area; both were controlled by depth to groundwater. Stem water $delta$18O values (-8.6 to 3.7‰) indicated a threshold ground elevation of ca. 15 m above sea level, above which P. pallida could not access groundwater; this threshold corresponded to declines in tree biomass and height. Transpiration modelled across the study area was 0.034 $pm$ 0.017 mm day−1, but over 98% of transpiration came from the ca. 25% of the total study area where groundwater depths were less than 15 m. Our combination of methods offers a new way to incorporate fine-scale spatial variation into estimation of plant invasion effects on hydrology, increase our understanding of interactions of geology, hydrology, and biology in such invasions, and prioritise areas for control in well-advanced invasions. |
Regnery, Julia; Li, Dong; Lee, Jonghyun; Smits, Kathleen M; Sharp, Jonathan O Hydrogeochemical and microbiological effects of simulated recharge and drying within a 2D meso-scale aquifer Journal Article Chemosphere, 241 , pp. 125116, 2020. @article{Regnery2020-hd, title = {Hydrogeochemical and microbiological effects of simulated recharge and drying within a 2D meso-scale aquifer}, author = {Julia Regnery and Dong Li and Jonghyun Lee and Kathleen M Smits and Jonathan O Sharp}, year = {2020}, date = {2020-02-01}, journal = {Chemosphere}, volume = {241}, pages = {125116}, abstract = {Oscillating cycles of dewatering (termed drying) and rewetting during managed aquifer recharge (MAR) are used to maintain infiltration rates and could also exert an influence on subsurface microbial structure and respiratory processes. Despite this practice, little knowledge is available about changes to microbial community structure and trace organic chemical biodegradation potential in MAR systems under these conditions. A biologically active two-dimensional (2D) synthetic MAR system equipped with automated sensors (temperature, water pressure, conductivity, soil moisture, oxidation-reduction potential) and embedded water and soil sampling ports was used to test and model these important subsurface processes at the meso-scale. The fate and transport of the antiepileptic drug carbamazepine, the antibiotics sulfamethoxazole and trimethoprim, and the flame retardant tris (2-chloroethyl) phosphate were simulated using the finite element analysis model, FEFLOW. All of these compounds exhibit moderate to poor biodegradability in MAR systems. Within the operational MAR scenario tested, three episodic drying cycles spanning between 18 and 24 days were conducted over a period of 184 days. Notably, cessation of flow and partial dewatering of the 2D synthetic aquifer during dry cycles caused no measurable decrease in soil moisture content beyond the near-surface layer. The episodic flow introduction and dewatering cycles in turn had little impact on overall trace organic chemical biotransformation behavior and soil microbial community structure. However, spatial differences in oxidation-reduction potential and soil moisture were both identified as significant environmental predictors for microbial community structure in the 2D synthetic aquifer.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Oscillating cycles of dewatering (termed drying) and rewetting during managed aquifer recharge (MAR) are used to maintain infiltration rates and could also exert an influence on subsurface microbial structure and respiratory processes. Despite this practice, little knowledge is available about changes to microbial community structure and trace organic chemical biodegradation potential in MAR systems under these conditions. A biologically active two-dimensional (2D) synthetic MAR system equipped with automated sensors (temperature, water pressure, conductivity, soil moisture, oxidation-reduction potential) and embedded water and soil sampling ports was used to test and model these important subsurface processes at the meso-scale. The fate and transport of the antiepileptic drug carbamazepine, the antibiotics sulfamethoxazole and trimethoprim, and the flame retardant tris (2-chloroethyl) phosphate were simulated using the finite element analysis model, FEFLOW. All of these compounds exhibit moderate to poor biodegradability in MAR systems. Within the operational MAR scenario tested, three episodic drying cycles spanning between 18 and 24 days were conducted over a period of 184 days. Notably, cessation of flow and partial dewatering of the 2D synthetic aquifer during dry cycles caused no measurable decrease in soil moisture content beyond the near-surface layer. The episodic flow introduction and dewatering cycles in turn had little impact on overall trace organic chemical biotransformation behavior and soil microbial community structure. However, spatial differences in oxidation-reduction potential and soil moisture were both identified as significant environmental predictors for microbial community structure in the 2D synthetic aquifer. |
Dores, Daniel; Lautze, Nicole Preliminary assessment of ground-source heat exchangers for cooling in Hawai`i Journal Article Sustainable Energy Technologies and Assessments, 37 , pp. 100579, 2020. @article{Dores2020-mg, title = {Preliminary assessment of ground-source heat exchangers for cooling in Hawai`i}, author = {Daniel Dores and Nicole Lautze}, year = {2020}, date = {2020-02-01}, journal = {Sustainable Energy Technologies and Assessments}, volume = {37}, pages = {100579}, abstract = {This study provides a preliminary assessment of ground source heat exchangers (GSHE) for cooling applications in the tropical environment of Hawai`i. Recent demonstrations proved GSHE capacity for space cooling in tropical southeast Asia. We present multiple engineering scenarios in which GSHE could be feasible across Hawai`i, highlighting regions of interest. Limestone and basalt provide the best host geology, feasible when air-ground temperature differences are >4 C and cooling is only required for Hawai`i's five summer months. This work investigates the effect of varying input parameters such as energy efficiency ratio, rock thermal conductivity, piping thermal resistance, temperature gradient, and fraction of time operating on the length of cooling loop required to successfully operate a GSHE. Maps of depth to water are provided, as well as calculations of Peclet numbers for basalt, limestone, and alluvium. Basalt's Peclet number shows advection is a more dominant process than conduction in heat exchange; limestone has equivalent advective and conductive processes; alluvium is dominated by conduction. Thus, both basalt and limestone may have an increased capacity to efficiently act as heat sinks in Hawaiian environments as groundwater flow could additionally transfer heat through advection, not relying solely on the calculated capacity of conductive heat exchange.}, keywords = {}, pubstate = {published}, tppubtype = {article} } This study provides a preliminary assessment of ground source heat exchangers (GSHE) for cooling applications in the tropical environment of Hawai`i. Recent demonstrations proved GSHE capacity for space cooling in tropical southeast Asia. We present multiple engineering scenarios in which GSHE could be feasible across Hawai`i, highlighting regions of interest. Limestone and basalt provide the best host geology, feasible when air-ground temperature differences are >4 C and cooling is only required for Hawai`i's five summer months. This work investigates the effect of varying input parameters such as energy efficiency ratio, rock thermal conductivity, piping thermal resistance, temperature gradient, and fraction of time operating on the length of cooling loop required to successfully operate a GSHE. Maps of depth to water are provided, as well as calculations of Peclet numbers for basalt, limestone, and alluvium. Basalt's Peclet number shows advection is a more dominant process than conduction in heat exchange; limestone has equivalent advective and conductive processes; alluvium is dominated by conduction. Thus, both basalt and limestone may have an increased capacity to efficiently act as heat sinks in Hawaiian environments as groundwater flow could additionally transfer heat through advection, not relying solely on the calculated capacity of conductive heat exchange. |
Nelson, Sara H; Bremer, Leah L; Prado, Kelly Meza; Brauman, Kate A The Political Life of Natural Infrastructure: Water Funds and Alternative Histories of Payments for Ecosystem Services in Valle del Cauca, Colombia Journal Article Development & Change, 51 (1), pp. 26–50, 2020. @article{Nelson2020-jk, title = {The Political Life of Natural Infrastructure: Water Funds and Alternative Histories of Payments for Ecosystem Services in Valle del Cauca, Colombia}, author = {Sara H Nelson and Leah L Bremer and Kelly Meza Prado and Kate A Brauman}, year = {2020}, date = {2020-01-01}, journal = {Development & Change}, volume = {51}, number = {1}, pages = {26--50}, publisher = {Wiley-Blackwell}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Amato, Daniel W; Whittier, Robert B; Dulai, Henrietta; Smith, Celia M Algal bioassays detect modeled loading of wastewater-derived nitrogen in coastal waters of O'AHU, HAWAI'I Journal Article Mar. Pollut. Bull., 150 , pp. 110668, 2020. @article{Amato2020-in, title = {Algal bioassays detect modeled loading of wastewater-derived nitrogen in coastal waters of O'AHU, HAWAI'I}, author = {Daniel W Amato and Robert B Whittier and Henrietta Dulai and Celia M Smith}, year = {2020}, date = {2020-01-01}, journal = {Mar. Pollut. Bull.}, volume = {150}, pages = {110668}, abstract = {Previous studies indicate coastlines are at risk of wastewater contamination from injection wells, cesspools, and septic systems. In this study, common marine algae were used to ground-truth modeled loading of wastewater-derived N to coastlines of O'ahu, Hawai'i. Macroalgae were collected and/or deployed at 118 sites and analyzed for tissue $delta$15N and N %. Wastewater source locations were used to estimate wastewater-derived N in groundwater with the modeling software MT3DMS/MODFLOW. Algal bioassays identified six coastal regions subjected to elevated wastewater-derived N loading. In a case study, submarine groundwater discharge (estimated by 222Rn mass balance) was related to wastewater loading from onsite sewage disposal systems (OSDS) and municipal wastewater injection wells in Waim=analo. The highest 222Rn-derived SGD rate and N flux were 21.4 m3/m/d and 62.6 g/m/d, respectively. The results of this study suggest that OSDS and injection wells discharge substantial volumes of wastewater and N across broad regions of coastal O'ahu.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Previous studies indicate coastlines are at risk of wastewater contamination from injection wells, cesspools, and septic systems. In this study, common marine algae were used to ground-truth modeled loading of wastewater-derived N to coastlines of O'ahu, Hawai'i. Macroalgae were collected and/or deployed at 118 sites and analyzed for tissue $delta$15N and N %. Wastewater source locations were used to estimate wastewater-derived N in groundwater with the modeling software MT3DMS/MODFLOW. Algal bioassays identified six coastal regions subjected to elevated wastewater-derived N loading. In a case study, submarine groundwater discharge (estimated by 222Rn mass balance) was related to wastewater loading from onsite sewage disposal systems (OSDS) and municipal wastewater injection wells in Waim=analo. The highest 222Rn-derived SGD rate and N flux were 21.4 m3/m/d and 62.6 g/m/d, respectively. The results of this study suggest that OSDS and injection wells discharge substantial volumes of wastewater and N across broad regions of coastal O'ahu. |
Endress, Lee H; Roumasset, James A; Wada, Christopher A Do Natural Disasters Make Sustainable Growth Impossible? Journal Article Economics of Disasters and Climate Change, 2020. @article{Endress2020-xv, title = {Do Natural Disasters Make Sustainable Growth Impossible?}, author = {Lee H Endress and James A Roumasset and Christopher A Wada}, year = {2020}, date = {2020-01-01}, journal = {Economics of Disasters and Climate Change}, abstract = {We consider the prospects for sustainable growth using expected utility models of optimal investment under threat from natural disasters. Adoption of a continuous time, stochastic Ramsey growth model over an infinite time horizon permits the analysis of sustainability under uncertainty regarding adverse events, including both one-time and recurrent disasters. As appropriate to small economies, we consider adaptation to the risk of disaster. Natural disasters reduce capital stocks and disrupt the optimal consumption and felicity paths. While the time path of inter-temporal welfare might consequently shift downward, the path may still be non-decreasing over time, even without adding strong or weak sustainability constraints. Prudent disaster preparedness includes precautionary investment in productive capital, programs of adaptation to disaster risk, and avoiding distortionary policies undermining the prospects of optimality and sustainability.}, keywords = {}, pubstate = {published}, tppubtype = {article} } We consider the prospects for sustainable growth using expected utility models of optimal investment under threat from natural disasters. Adoption of a continuous time, stochastic Ramsey growth model over an infinite time horizon permits the analysis of sustainability under uncertainty regarding adverse events, including both one-time and recurrent disasters. As appropriate to small economies, we consider adaptation to the risk of disaster. Natural disasters reduce capital stocks and disrupt the optimal consumption and felicity paths. While the time path of inter-temporal welfare might consequently shift downward, the path may still be non-decreasing over time, even without adding strong or weak sustainability constraints. Prudent disaster preparedness includes precautionary investment in productive capital, programs of adaptation to disaster risk, and avoiding distortionary policies undermining the prospects of optimality and sustainability. |
2019 |
Attias, Eric; Amalokwu, Kelvin; Watts, Millie; Falcon-Suarez, Ismael Himar; North, Laurence; Hu, Gao Wei; Best, Angus I; Weitemeyer, Karen; Minshull, Tim A Gas hydrate quantification at a pockmark offshore Norway from joint effective medium modelling of resistivity and seismic velocity Journal Article Mar. Pet. Geol., pp. 104151, 2019. @article{Attias2019-bw, title = {Gas hydrate quantification at a pockmark offshore Norway from joint effective medium modelling of resistivity and seismic velocity}, author = {Eric Attias and Kelvin Amalokwu and Millie Watts and Ismael Himar Falcon-Suarez and Laurence North and Gao Wei Hu and Angus I Best and Karen Weitemeyer and Tim A Minshull}, year = {2019}, date = {2019-12-01}, journal = {Mar. Pet. Geol.}, pages = {104151}, abstract = {Methane emissions from gas hydrate deposits along continental margins may alter the biogeophysical properties of marine environments, both on local and regional scales. The saturation of a gas hydrate deposit is commonly calculated using the elastic or electrical properties measured remotely or in-situ at the site of interest. Here, we used a combination of controlled-source electromagnetic (CSEM), seismic and sediment core data obtained in the Nyegga region, offshore Norway, in a joint elastic-electrical approach to quantify marine gas hydrates found within the CNE03 pockmark. Multiscale analysis of two sediment cores reveals significant differences between the CNE03 pockmark and a reference site located approximately 150 m northwest of CNE03. Gas hydrates and chemosynthetic bivalves were observed in the CNE03 sediments collected. The seismic velocity and electrical resistivity measured in the CNE03 sediment core are consistent with the P-wave velocity (VP) and resistivity values derived from seismic and CSEM remote sensing datasets, respectively. The VP gradually increases (∼1.75--1.9 km/s) with depth within the CNE03 pipe-like structure, whereas the resistivity anomaly remains ∼3 $Ømega$m. A joint interpretation of the collocated seismic and CSEM data using a joint elastic-electrical effective medium model suggests that for the porosity range 0.55--0.65, the gas hydrate saturation within the CNE03 hydrate stability zone varies with depth between ∼20 and 48%. At 0.6 porosity, the hydrate saturation within CNE03 varies between ∼23 and 37%, whereas the weighted mean saturation is ∼30%. Our results demonstrate that a well-constrained gas hydrate quantification can be accomplished by coupling P-wave velocity and CSEM resistivity data through joint elastic-electrical effective medium modelling. The approach applied in this study can be used as a framework to quantify hydrate in various marine sediments.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Methane emissions from gas hydrate deposits along continental margins may alter the biogeophysical properties of marine environments, both on local and regional scales. The saturation of a gas hydrate deposit is commonly calculated using the elastic or electrical properties measured remotely or in-situ at the site of interest. Here, we used a combination of controlled-source electromagnetic (CSEM), seismic and sediment core data obtained in the Nyegga region, offshore Norway, in a joint elastic-electrical approach to quantify marine gas hydrates found within the CNE03 pockmark. Multiscale analysis of two sediment cores reveals significant differences between the CNE03 pockmark and a reference site located approximately 150 m northwest of CNE03. Gas hydrates and chemosynthetic bivalves were observed in the CNE03 sediments collected. The seismic velocity and electrical resistivity measured in the CNE03 sediment core are consistent with the P-wave velocity (VP) and resistivity values derived from seismic and CSEM remote sensing datasets, respectively. The VP gradually increases (∼1.75--1.9 km/s) with depth within the CNE03 pipe-like structure, whereas the resistivity anomaly remains ∼3 $Ømega$m. A joint interpretation of the collocated seismic and CSEM data using a joint elastic-electrical effective medium model suggests that for the porosity range 0.55--0.65, the gas hydrate saturation within the CNE03 hydrate stability zone varies with depth between ∼20 and 48%. At 0.6 porosity, the hydrate saturation within CNE03 varies between ∼23 and 37%, whereas the weighted mean saturation is ∼30%. Our results demonstrate that a well-constrained gas hydrate quantification can be accomplished by coupling P-wave velocity and CSEM resistivity data through joint elastic-electrical effective medium modelling. The approach applied in this study can be used as a framework to quantify hydrate in various marine sediments. |
Jansen, C; Shimoda, L M N; Kawakami, J K; Ang, L; Bacani, A J; Baker, J D; Badowski, C; Speck, M; Stokes, A J; Small-Howard, A L; Turner, H Myrcene and terpene regulation of TRPV1 Journal Article Channels, 13 (1), pp. 344–366, 2019. @article{Jansen2019-ce, title = {Myrcene and terpene regulation of TRPV1}, author = {C Jansen and L M N Shimoda and J K Kawakami and L Ang and A J Bacani and J D Baker and C Badowski and M Speck and A J Stokes and A L Small-Howard and H Turner}, year = {2019}, date = {2019-12-01}, journal = {Channels}, volume = {13}, number = {1}, pages = {344--366}, abstract = {Nociceptive Transient Receptor Potential channels such as TRPV1 are targets for treating pain. Both antagonism and agonism of TRP channels can promote analgesia, through inactivation and chronic desensitization. Since plant-derived mixtures of cannabinoids and the Cannabis component myrcene have been suggested as pain therapeutics, we screened terpenes found in Cannabis for activity at TRPV1. We used inducible expression of TRPV1 to examine TRPV1-dependency of terpene-induced calcium flux responses. Terpenes contribute differentially to calcium fluxes via TRPV1 induced by Cannabis-mimetic cannabinoid/terpenoid mixtures. Myrcene dominates the TRPV1-mediated calcium responses seen with terpenoid mixtures. Myrcene-induced calcium influx is inhibited by the TRPV1 inhibitor capsazepine and Myrcene elicits TRPV1 currents in the whole-cell patch-clamp configuration. TRPV1 currents are highly sensitive to internal calcium. When Myrcene currents are evoked, they are distinct from capsaicin responses on the basis of Imax and their lack of shift to a pore-dilated state. Myrcene pre-application and residency at TRPV1 appears to negatively impact subsequent responses to TRPV1 ligands such as Cannabidiol, indicating allosteric modulation and possible competition by Myrcene. Molecular docking studies suggest a non-covalent interaction site for Myrcene in TRPV1 and identifies key residues that form partially overlapping Myrcene and Cannabidiol binding sites. We identify several non-Cannabis plant-derived sources of Myrcene and other compounds targeting nociceptive TRPs using a data mining approach focused on analgesics suggested by non-Western Traditional Medical Systems. These data establish TRPV1 as a target of Myrcene and suggest the therapeutic potential of analgesic formulations containing Myrcene.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Nociceptive Transient Receptor Potential channels such as TRPV1 are targets for treating pain. Both antagonism and agonism of TRP channels can promote analgesia, through inactivation and chronic desensitization. Since plant-derived mixtures of cannabinoids and the Cannabis component myrcene have been suggested as pain therapeutics, we screened terpenes found in Cannabis for activity at TRPV1. We used inducible expression of TRPV1 to examine TRPV1-dependency of terpene-induced calcium flux responses. Terpenes contribute differentially to calcium fluxes via TRPV1 induced by Cannabis-mimetic cannabinoid/terpenoid mixtures. Myrcene dominates the TRPV1-mediated calcium responses seen with terpenoid mixtures. Myrcene-induced calcium influx is inhibited by the TRPV1 inhibitor capsazepine and Myrcene elicits TRPV1 currents in the whole-cell patch-clamp configuration. TRPV1 currents are highly sensitive to internal calcium. When Myrcene currents are evoked, they are distinct from capsaicin responses on the basis of Imax and their lack of shift to a pore-dilated state. Myrcene pre-application and residency at TRPV1 appears to negatively impact subsequent responses to TRPV1 ligands such as Cannabidiol, indicating allosteric modulation and possible competition by Myrcene. Molecular docking studies suggest a non-covalent interaction site for Myrcene in TRPV1 and identifies key residues that form partially overlapping Myrcene and Cannabidiol binding sites. We identify several non-Cannabis plant-derived sources of Myrcene and other compounds targeting nociceptive TRPs using a data mining approach focused on analgesics suggested by non-Western Traditional Medical Systems. These data establish TRPV1 as a target of Myrcene and suggest the therapeutic potential of analgesic formulations containing Myrcene. |
Wada, Christopher A; Pongkijvorasin, Sittidaj; Burnett, Kimberly M Mountain-to-sea ecological-resource management: forested watersheds, coastal aquifers, and groundwater dependent ecosystems Journal Article Res. Energy Econ., pp. 101146, 2019. @article{Wada2019-iy, title = {Mountain-to-sea ecological-resource management: forested watersheds, coastal aquifers, and groundwater dependent ecosystems}, author = {Christopher A Wada and Sittidaj Pongkijvorasin and Kimberly M Burnett}, year = {2019}, date = {2019-12-01}, journal = {Res. Energy Econ.}, pages = {101146}, abstract = {Improving the understanding of connections spanning from mountain to sea and integrating those connections into decision models have been increasingly recognized as key to effective coastal resource management. In this paper, we aim to improve our understanding of the relative importance of linkages between a forested watershed, a coastal groundwater aquifer, and a nearshore marine groundwater-dependent ecosystem (GDE) using a dynamic groundwater optimization framework and simple ecosystem equations. Data from the K=iholo aquifer on the Kona Coast of Hawai`i Island are used to numerically illustrate optimal joint management strategies and test the sensitivity of those strategies to variations in physical and behavioral parameter values. We find that for a plausible range of watershed management costs, protecting part of the recharge capture area is always optimal. Without watershed protection, maintaining a safe minimum standard growth rate for a GDE-dependent marine indicator species, reduces net present value non-trivially, but optimal investment in watershed conservation offsets that potential reduction by 75%. In general, we find that optimal watershed management and groundwater pumping are most sensitive to changes in water demand growth and parameters that describe nearshore salinity.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Improving the understanding of connections spanning from mountain to sea and integrating those connections into decision models have been increasingly recognized as key to effective coastal resource management. In this paper, we aim to improve our understanding of the relative importance of linkages between a forested watershed, a coastal groundwater aquifer, and a nearshore marine groundwater-dependent ecosystem (GDE) using a dynamic groundwater optimization framework and simple ecosystem equations. Data from the K=iholo aquifer on the Kona Coast of Hawai`i Island are used to numerically illustrate optimal joint management strategies and test the sensitivity of those strategies to variations in physical and behavioral parameter values. We find that for a plausible range of watershed management costs, protecting part of the recharge capture area is always optimal. Without watershed protection, maintaining a safe minimum standard growth rate for a GDE-dependent marine indicator species, reduces net present value non-trivially, but optimal investment in watershed conservation offsets that potential reduction by 75%. In general, we find that optimal watershed management and groundwater pumping are most sensitive to changes in water demand growth and parameters that describe nearshore salinity. |
Jansen, C; Shimoda, L M N; Starkus, J; Lange, I; Rysavy, N; Maaetoft-Udsen, K; Tobita, C; Stokes, A J; Turner, H In vitro exposure to Hymenoptera venom and constituents activates discrete ionotropic pathways in mast cells Journal Article Channels, 13 (1), pp. 264–286, 2019. @article{Jansen2019-hu, title = {In vitro exposure to Hymenoptera venom and constituents activates discrete ionotropic pathways in mast cells}, author = {C Jansen and L M N Shimoda and J Starkus and I Lange and N Rysavy and K Maaetoft-Udsen and C Tobita and A J Stokes and H Turner}, year = {2019}, date = {2019-12-01}, journal = {Channels}, volume = {13}, number = {1}, pages = {264--286}, abstract = {Calcium entry is central to the functional processes in mast cells and basophils that contribute to the induction and maintenance of inflammatory responses. Mast cells and basophils express an array of calcium channels, which mediate responses to diverse stimuli triggered by small bioactive molecules, physicochemical stimuli and immunological inputs including antigens and direct immune cell interactions. These cells are also highly responsive to certain venoms (such as Hymenoptera envenomations), which cause histamine secretion, cytokine release and an array of pro-inflammatory functional responses. There are gaps in our understanding of the coupling of venom exposure to specific signaling pathways such as activation of calcium channels. In the present study, we performed a current survey of a model mast cell line selected for its pleiotropic responsiveness to multiple pro-inflammatory inputs. As a heterogenous stimulus, Hymenoptera venom activates multiple classes of conductance at the population level but tend to lead to the measurement of only one type of conductance per cell, despite the cell co-expressing multiple channel types. The data show that ICRAC, IARC, and TRPV-like currents are present in the model mast cell populations and respond to venom exposure. We further assessed individual venom components, specifically secretagogues and arachidonic acid, and identified the conductances associated with these stimuli in mast cells. Single-cell calcium assays and immunofluorescence analysis show that there is heterogeneity of channel expression across the cell population, but this heterogeneity does not explain the apparent selectivity for specific channels in response to exposure to venom as a composite stimulus.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Calcium entry is central to the functional processes in mast cells and basophils that contribute to the induction and maintenance of inflammatory responses. Mast cells and basophils express an array of calcium channels, which mediate responses to diverse stimuli triggered by small bioactive molecules, physicochemical stimuli and immunological inputs including antigens and direct immune cell interactions. These cells are also highly responsive to certain venoms (such as Hymenoptera envenomations), which cause histamine secretion, cytokine release and an array of pro-inflammatory functional responses. There are gaps in our understanding of the coupling of venom exposure to specific signaling pathways such as activation of calcium channels. In the present study, we performed a current survey of a model mast cell line selected for its pleiotropic responsiveness to multiple pro-inflammatory inputs. As a heterogenous stimulus, Hymenoptera venom activates multiple classes of conductance at the population level but tend to lead to the measurement of only one type of conductance per cell, despite the cell co-expressing multiple channel types. The data show that ICRAC, IARC, and TRPV-like currents are present in the model mast cell populations and respond to venom exposure. We further assessed individual venom components, specifically secretagogues and arachidonic acid, and identified the conductances associated with these stimuli in mast cells. Single-cell calcium assays and immunofluorescence analysis show that there is heterogeneity of channel expression across the cell population, but this heterogeneity does not explain the apparent selectivity for specific channels in response to exposure to venom as a composite stimulus. |
Aldan, Johnny T; Jansen, Chad; Speck, Mark; Maaetoft-Udsen, Kristina; Cordasco, Edward A; Faiai, Mata'uitafa; Shimoda, Lori M N; Greineisen, William E; Turner, Helen; Stokes, Alexander J Insulin-induced lipid body accumulation is accompanied by lipid remodelling in model mast cells Journal Article Adipocyte, 8 (1), pp. 265–279, 2019. @article{Aldan2019-np, title = {Insulin-induced lipid body accumulation is accompanied by lipid remodelling in model mast cells}, author = {Johnny T Aldan and Chad Jansen and Mark Speck and Kristina Maaetoft-Udsen and Edward A Cordasco and Mata'uitafa Faiai and Lori M N Shimoda and William E Greineisen and Helen Turner and Alexander J Stokes}, year = {2019}, date = {2019-12-01}, journal = {Adipocyte}, volume = {8}, number = {1}, pages = {265--279}, abstract = {Mast cell lipid bodies are key to initiation, maintenance and resolution of inflammatory responses in tissue. Mast cell lines, primary bone marrow-derived mast cells and peripheral blood basophils present a 'steatotic' phenotype in response to chronic insulin exposure, where cells become loaded with lipid bodies. Here we show this state is associated with reduced histamine release, but increased capacity to release bioactive lipids. We describe the overall lipid phenotype of mast cells in this insulin-induced steatotic state and the consequences for critical cellular lipid classes involved in stages of inflammation. We show significant insulin-induced shifts in specific lipid classes, especially arachidonic acid derivatives, MUFA and PUFA, the EPA/DHA ratio, and in cardiolipins, especially those conjugated to certain DHA and EPAs. Functionally, insulin exposure markedly alters the Fc$epsilon$RI-induced release of Series 4 leukotriene LTC4, Series 2 prostaglandin PGD2, Resolvin-D1, Resolvin-D2 and Resolvin-1, reflecting the expanded precursor pools and impact on both the pro-inflammation and pro-resolution bioactive lipids that are released during mast cell activation. Chronic hyperinsulinemia is a feature of obesity and progression to Type 2 Diabetes, these data suggest that mast cell release of key lipid mediators is altered in patients with metabolic syndrome.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Mast cell lipid bodies are key to initiation, maintenance and resolution of inflammatory responses in tissue. Mast cell lines, primary bone marrow-derived mast cells and peripheral blood basophils present a 'steatotic' phenotype in response to chronic insulin exposure, where cells become loaded with lipid bodies. Here we show this state is associated with reduced histamine release, but increased capacity to release bioactive lipids. We describe the overall lipid phenotype of mast cells in this insulin-induced steatotic state and the consequences for critical cellular lipid classes involved in stages of inflammation. We show significant insulin-induced shifts in specific lipid classes, especially arachidonic acid derivatives, MUFA and PUFA, the EPA/DHA ratio, and in cardiolipins, especially those conjugated to certain DHA and EPAs. Functionally, insulin exposure markedly alters the Fc$epsilon$RI-induced release of Series 4 leukotriene LTC4, Series 2 prostaglandin PGD2, Resolvin-D1, Resolvin-D2 and Resolvin-1, reflecting the expanded precursor pools and impact on both the pro-inflammation and pro-resolution bioactive lipids that are released during mast cell activation. Chronic hyperinsulinemia is a feature of obesity and progression to Type 2 Diabetes, these data suggest that mast cell release of key lipid mediators is altered in patients with metabolic syndrome. |
Hayes, Tanya; Grillos, Tara; Bremer, Leah L; Murtinho, Felipe; Shapiro, Elizabeth Collective PES: More than the sum of individual incentives Journal Article Environ. Sci. Policy, 102 , pp. 1–8, 2019. @article{Hayes2019-an, title = {Collective PES: More than the sum of individual incentives}, author = {Tanya Hayes and Tara Grillos and Leah L Bremer and Felipe Murtinho and Elizabeth Shapiro}, year = {2019}, date = {2019-12-01}, journal = {Environ. Sci. Policy}, volume = {102}, pages = {1--8}, abstract = {This study synthesizes findings from studies of the social and behavioral outcomes of collective payment for ecosystem services (PES) programs. The collective PES model is distinct from the conventional PES model in that by working with groups, not individuals, it breaks the direct relationship between an individual's consent to participate, the economic incentive and the expected conservation behavior. In doing so, it raises concerns about whether the collective model is effective and socially just. Here, we assess these concerns by synthesizing findings on four distinct challenges for collective PES: (i) voluntary and informed participation; (ii) household compliance with PES restrictions; (iii) the balance of costs and benefits across community members; and (iv) the interaction with local governance conditions to address the second-order collective action problem inherent in collective PES. Through a review of 41 studies covering 16 collective PES programs located in 12 countries, we find that collective PES can change behavior and provide socioeconomic and ecological benefits, but institutional context matters. Our review points to how program design and local governance dynamics can influence the ability of collective PES to attain desired social and behavioral outcomes.}, keywords = {}, pubstate = {published}, tppubtype = {article} } This study synthesizes findings from studies of the social and behavioral outcomes of collective payment for ecosystem services (PES) programs. The collective PES model is distinct from the conventional PES model in that by working with groups, not individuals, it breaks the direct relationship between an individual's consent to participate, the economic incentive and the expected conservation behavior. In doing so, it raises concerns about whether the collective model is effective and socially just. Here, we assess these concerns by synthesizing findings on four distinct challenges for collective PES: (i) voluntary and informed participation; (ii) household compliance with PES restrictions; (iii) the balance of costs and benefits across community members; and (iv) the interaction with local governance conditions to address the second-order collective action problem inherent in collective PES. Through a review of 41 studies covering 16 collective PES programs located in 12 countries, we find that collective PES can change behavior and provide socioeconomic and ecological benefits, but institutional context matters. Our review points to how program design and local governance dynamics can influence the ability of collective PES to attain desired social and behavioral outcomes. |
Horton, Jaime S; Shiraishi, Takuya; Alfulaij, Naghum; Small-Howard, Andrea L; Turner, Helen C; Kurokawa, Tatsuki; Mori, Yasuo; Stokes, Alexander J ``TRPV1 is a component of the atrial natriuretic signaling complex, and using orally delivered antagonists, presents a valid therapeutic target in the longitudinal reversal and treatment of cardiac hypertrophy and heart failure'' Journal Article Channels, 13 (1), pp. 1–16, 2019. @article{Horton2019-cs, title = {``TRPV1 is a component of the atrial natriuretic signaling complex, and using orally delivered antagonists, presents a valid therapeutic target in the longitudinal reversal and treatment of cardiac hypertrophy and heart failure''}, author = {Jaime S Horton and Takuya Shiraishi and Naghum Alfulaij and Andrea L Small-Howard and Helen C Turner and Tatsuki Kurokawa and Yasuo Mori and Alexander J Stokes}, year = {2019}, date = {2019-12-01}, journal = {Channels}, volume = {13}, number = {1}, pages = {1--16}, abstract = {Activation of the atrial natriuretic signaling pathway is intrinsic to the pathological responses associated with a range of cardiovascular diseases that stress the heart, especially those involved in sustained cardiac pressure overload which induces hypertrophy and the pathological remodeling that frequently leads to heart failure. We identify transient receptor potential cation channel, subfamily V, member 1, as a regulated molecular component, and therapeutic target of this signaling system. Data show that TRPV1 is a physical component of the natriuretic peptide A, cGMP, PKG signaling complex, interacting with the Natriuretic Peptide Receptor 1 (NPR1), and upon binding its ligand, Natriuretic Peptide A (NPPA, ANP) TRPV1 activation is subsequently suppressed through production of cGMP and PKG mediated phosphorylation of the TRPV1 channel. Further, inhibition of TRPV1, with orally delivered drugs, suppresses chamber and myocyte hypertrophy, and can longitudinally improve in vivo heart function in mice exposed to chronic pressure overload induced by transverse aortic constriction, reversing pre-established hypertrophy induced by pressure load while restoring chamber function. TRPV1 is a physical and regulated component of the natriuretic peptide signaling system, and TRPV1 inhibition may provide a new treatment strategy for treating, and reversing the loss of function associated with cardiac hypertrophy and heart failure.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Activation of the atrial natriuretic signaling pathway is intrinsic to the pathological responses associated with a range of cardiovascular diseases that stress the heart, especially those involved in sustained cardiac pressure overload which induces hypertrophy and the pathological remodeling that frequently leads to heart failure. We identify transient receptor potential cation channel, subfamily V, member 1, as a regulated molecular component, and therapeutic target of this signaling system. Data show that TRPV1 is a physical component of the natriuretic peptide A, cGMP, PKG signaling complex, interacting with the Natriuretic Peptide Receptor 1 (NPR1), and upon binding its ligand, Natriuretic Peptide A (NPPA, ANP) TRPV1 activation is subsequently suppressed through production of cGMP and PKG mediated phosphorylation of the TRPV1 channel. Further, inhibition of TRPV1, with orally delivered drugs, suppresses chamber and myocyte hypertrophy, and can longitudinally improve in vivo heart function in mice exposed to chronic pressure overload induced by transverse aortic constriction, reversing pre-established hypertrophy induced by pressure load while restoring chamber function. TRPV1 is a physical and regulated component of the natriuretic peptide signaling system, and TRPV1 inhibition may provide a new treatment strategy for treating, and reversing the loss of function associated with cardiac hypertrophy and heart failure. |
Bruno, Barbara C; Wallace, Anne Interpretive Panels for Geoheritage Sites: Guidelines for Design and Evaluation Journal Article Geoheritage, 2019. @article{Bruno2019-ga, title = {Interpretive Panels for Geoheritage Sites: Guidelines for Design and Evaluation}, author = {Barbara C Bruno and Anne Wallace}, year = {2019}, date = {2019-11-01}, journal = {Geoheritage}, abstract = {Effective interpretive panels go far beyond conveying information: they are highly engaging, instill passion, and inspire visitors to engage in environmental stewardship. This review paper on designing and evaluating interpretive panels at geoheritage sites shares recommendations gleaned from experts in conservation science, neuroscience, pedagogy, psychology, visual arts, and communication. It emphasizes the importance of developing a communication plan, knowing your audience, using strong visuals, invoking storytelling and active learning techniques, layering your message, being inclusive, choosing an appropriate panel location, integrating evaluation throughout the design process, and budgeting appropriately. An extensive reference list is provided for further reading.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Effective interpretive panels go far beyond conveying information: they are highly engaging, instill passion, and inspire visitors to engage in environmental stewardship. This review paper on designing and evaluating interpretive panels at geoheritage sites shares recommendations gleaned from experts in conservation science, neuroscience, pedagogy, psychology, visual arts, and communication. It emphasizes the importance of developing a communication plan, knowing your audience, using strong visuals, invoking storytelling and active learning techniques, layering your message, being inclusive, choosing an appropriate panel location, integrating evaluation throughout the design process, and budgeting appropriately. An extensive reference list is provided for further reading. |
Bremer, Leah L; Wada, Christopher A; Medoff, Sarah; Page, Jonathan; Falinski, Kim; Burnett, Kimberly M Contributions of native forest protection to local water supplies in East Maui Journal Article Sci. Total Environ., 688 , pp. 1422–1432, 2019. @article{Bremer2019-eq, title = {Contributions of native forest protection to local water supplies in East Maui}, author = {Leah L Bremer and Christopher A Wada and Sarah Medoff and Jonathan Page and Kim Falinski and Kimberly M Burnett}, year = {2019}, date = {2019-10-01}, journal = {Sci. Total Environ.}, volume = {688}, pages = {1422--1432}, abstract = {Tropical forests provide a suite of benefits including biodiversity, cultural value, and a range of ecosystem services. Globally, there is increasing interest in incentivizing native forest protection as a multi-benefit natural infrastructure strategy to secure clean and ample water supplies. In addition to conversion to agriculture and other non-forest land uses, non-native species invasion represents a major threat to these systems, particularly on islands. Whereas several recent efforts have quantified the benefits of reforestation or avoided agricultural expansion in tropical forest areas, the hydrologic and associated economic benefits of avoided invasion have received less attention. To address this gap, we quantified the benefits of protecting native forest from conversion to non-native forest in East Maui, Hawai'i in terms of groundwater recharge, a highly valued hydrologic ecosystem service that water utilities increasingly seek to co-finance. Compared with two counterfactual invasion scenarios, the groundwater recharge benefits of planned conservation activities reached 40.9 to 146.3 million cubic meters over 100 years depending on invasion rate assumptions. This translated to 2.70 to 137.6 million dollars of cost savings to the water utility in present value terms (achieved through reducing reliance on more expensive water alternatives) under a range of discount rates and water scarcity assumptions. Our results suggest that investing in native forest conservation provides an important hydrologic ecosystem service benefit that complements the range of benefits provided by these ecosystems. These findings demonstrate that co-financing native forest conservation represents an important supply side option in water resources planning.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Tropical forests provide a suite of benefits including biodiversity, cultural value, and a range of ecosystem services. Globally, there is increasing interest in incentivizing native forest protection as a multi-benefit natural infrastructure strategy to secure clean and ample water supplies. In addition to conversion to agriculture and other non-forest land uses, non-native species invasion represents a major threat to these systems, particularly on islands. Whereas several recent efforts have quantified the benefits of reforestation or avoided agricultural expansion in tropical forest areas, the hydrologic and associated economic benefits of avoided invasion have received less attention. To address this gap, we quantified the benefits of protecting native forest from conversion to non-native forest in East Maui, Hawai'i in terms of groundwater recharge, a highly valued hydrologic ecosystem service that water utilities increasingly seek to co-finance. Compared with two counterfactual invasion scenarios, the groundwater recharge benefits of planned conservation activities reached 40.9 to 146.3 million cubic meters over 100 years depending on invasion rate assumptions. This translated to 2.70 to 137.6 million dollars of cost savings to the water utility in present value terms (achieved through reducing reliance on more expensive water alternatives) under a range of discount rates and water scarcity assumptions. Our results suggest that investing in native forest conservation provides an important hydrologic ecosystem service benefit that complements the range of benefits provided by these ecosystems. These findings demonstrate that co-financing native forest conservation represents an important supply side option in water resources planning. |
McKenzie, Trista; Dulai, Henrietta; Chang, Jennet Parallels between stream and coastal water quality associated with groundwater discharge Journal Article PLoS One, 14 (10), pp. e0224513, 2019. @article{McKenzie2019-ob, title = {Parallels between stream and coastal water quality associated with groundwater discharge}, author = {Trista McKenzie and Henrietta Dulai and Jennet Chang}, year = {2019}, date = {2019-10-01}, journal = {PLoS One}, volume = {14}, number = {10}, pages = {e0224513}, abstract = {Groundwater-surface water interactions drive water quality in both streams and the coastal ocean, where groundwater discharge occurs in streams as baseflow and along the coastline as submarine groundwater discharge (SGD). Groundwater contributions to streams and to the coastal ocean were quantified in three urban streams in K=ane'ohe Watershed, Hawai'i. We used radon as a groundwater tracer to show that baseflow contributions to streams ranged from 22 to 68% along their reaches leading to the coast of K=ane'ohe Bay. Total SGD was 4,500, 18,000, and 23,000 m3/day for the northwest, central, and southern sectors of the bay, respectively. Total groundwater (stream baseflow + SGD) dissolved nutrient fluxes were significantly greater than those sourced from stream surface runoff. The studied streams exhibited increasing nutrient levels downstream from groundwater inputs with high nutrient concentrations, negatively impacting coastal water quality. SGD dynamics were also assessed during the anomalously high perigean spring tides in 2017, where SGD was four times greater during the perigean spring tide compared to a spring tide and resulted in strong shifts in N:P ratios, suggesting that rising sea level stands may disrupt primary productivity with greater frequency. This study demonstrates the importance of considering baseflow inputs to streams to coastal groundwater budgets and suggests that coastal water quality may be improved through management and reduction of groundwater contaminants.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Groundwater-surface water interactions drive water quality in both streams and the coastal ocean, where groundwater discharge occurs in streams as baseflow and along the coastline as submarine groundwater discharge (SGD). Groundwater contributions to streams and to the coastal ocean were quantified in three urban streams in K=ane'ohe Watershed, Hawai'i. We used radon as a groundwater tracer to show that baseflow contributions to streams ranged from 22 to 68% along their reaches leading to the coast of K=ane'ohe Bay. Total SGD was 4,500, 18,000, and 23,000 m3/day for the northwest, central, and southern sectors of the bay, respectively. Total groundwater (stream baseflow + SGD) dissolved nutrient fluxes were significantly greater than those sourced from stream surface runoff. The studied streams exhibited increasing nutrient levels downstream from groundwater inputs with high nutrient concentrations, negatively impacting coastal water quality. SGD dynamics were also assessed during the anomalously high perigean spring tides in 2017, where SGD was four times greater during the perigean spring tide compared to a spring tide and resulted in strong shifts in N:P ratios, suggesting that rising sea level stands may disrupt primary productivity with greater frequency. This study demonstrates the importance of considering baseflow inputs to streams to coastal groundwater budgets and suggests that coastal water quality may be improved through management and reduction of groundwater contaminants. |
Arisdakessian, Cédric; Poirion, Olivier; Yunits, Breck; Zhu, Xun; Garmire, Lana X DeepImpute: an accurate, fast, and scalable deep neural network method to impute single-cell RNA-seq data Journal Article Genome Biol., 20 (1), pp. 211, 2019. @article{Arisdakessian2019-sc, title = {DeepImpute: an accurate, fast, and scalable deep neural network method to impute single-cell RNA-seq data}, author = {Cédric Arisdakessian and Olivier Poirion and Breck Yunits and Xun Zhu and Lana X Garmire}, year = {2019}, date = {2019-10-01}, journal = {Genome Biol.}, volume = {20}, number = {1}, pages = {211}, abstract = {Single-cell RNA sequencing (scRNA-seq) offers new opportunities to study gene expression of tens of thousands of single cells simultaneously. We present DeepImpute, a deep neural network-based imputation algorithm that uses dropout layers and loss functions to learn patterns in the data, allowing for accurate imputation. Overall, DeepImpute yields better accuracy than other six publicly available scRNA-seq imputation methods on experimental data, as measured by the mean squared error or Pearson's correlation coefficient. DeepImpute is an accurate, fast, and scalable imputation tool that is suited to handle the ever-increasing volume of scRNA-seq data, and is freely available at https://github.com/lanagarmire/DeepImpute .}, keywords = {}, pubstate = {published}, tppubtype = {article} } Single-cell RNA sequencing (scRNA-seq) offers new opportunities to study gene expression of tens of thousands of single cells simultaneously. We present DeepImpute, a deep neural network-based imputation algorithm that uses dropout layers and loss functions to learn patterns in the data, allowing for accurate imputation. Overall, DeepImpute yields better accuracy than other six publicly available scRNA-seq imputation methods on experimental data, as measured by the mean squared error or Pearson's correlation coefficient. DeepImpute is an accurate, fast, and scalable imputation tool that is suited to handle the ever-increasing volume of scRNA-seq data, and is freely available at https://github.com/lanagarmire/DeepImpute . |
McKenzie, Marie M; Giambelluca, Thomas W; Diaz, Henry F Temperature trends in Hawaiʻi: A century of change, 1917--2016 Journal Article Int. J. Climatol., 39 (10), pp. 3987–4001, 2019. @article{McKenzie2019-ad, title = {Temperature trends in Hawaiʻi: A century of change, 1917--2016}, author = {Marie M McKenzie and Thomas W Giambelluca and Henry F Diaz}, year = {2019}, date = {2019-08-01}, journal = {Int. J. Climatol.}, volume = {39}, number = {10}, pages = {3987--4001}, abstract = {Based on a revised and extended multi-station Hawai?i Temperature Index (HTI), the mean air temperature in the Hawaiian Islands has warmed significantly at 0.052°C/decade (p? was the warmest year on record at 0.924°C above the 100-year mean (0.202°C). During each of the last four decades, mean state-wide positive air temperature anomalies were greater than those of any of the previous decades. Significant warming trends for the last 100?years are evident at low- (0.056°C/decade, p (0.047°C/decade, p? attributed to significant increases in minimum temperature (0.072°C/decade, p? downward trend in diurnal temperature range (?0.055°C/decade, p? correlations were found between HTI, the Pacific Decadal Oscillation, and the Multivariate ENSO Index, indicating that natural climate variability has a significant impact on temperature in Hawai?i. Analysis of surface air temperatures from NCEP/NCAR reanalysis data for the region of Hawai?i over the last 69?years (1948?2016) and a mean atmospheric layer temperature time series calculated from radiosonde-measured thickness (distance between constant pressure surfaces) data over the last 40?years (1977?2016) give results consistent with the HTI. Finally, we compare temperature trends for Hawaii's highest elevation station, Mauna Loa Observatory (3,397?m), to those on another mountainous subtropical island station in the Atlantic, Mt. Iza~na Observatory (2,373?m), Tenerife, Canary Islands. Both stations sit above the local temperature inversion layer and have virtually identical significant warming trends of 0.19°C/decade (p? between 1955 and 2016.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Based on a revised and extended multi-station Hawai?i Temperature Index (HTI), the mean air temperature in the Hawaiian Islands has warmed significantly at 0.052°C/decade (p?<?0.01) over the past 100?years (1917?2016). The year 2016 was the warmest year on record at 0.924°C above the 100-year mean (0.202°C). During each of the last four decades, mean state-wide positive air temperature anomalies were greater than those of any of the previous decades. Significant warming trends for the last 100?years are evident at low- (0.056°C/decade, p <?0.001) and high-elevations (0.047°C/decade, p?<?0.01). Warming in Hawai?i is largely attributed to significant increases in minimum temperature (0.072°C/decade, p?<?0.001) resulting in a corresponding downward trend in diurnal temperature range (?0.055°C/decade, p?<?0.001) over the 100-year period. Significant positive correlations were found between HTI, the Pacific Decadal Oscillation, and the Multivariate ENSO Index, indicating that natural climate variability has a significant impact on temperature in Hawai?i. Analysis of surface air temperatures from NCEP/NCAR reanalysis data for the region of Hawai?i over the last 69?years (1948?2016) and a mean atmospheric layer temperature time series calculated from radiosonde-measured thickness (distance between constant pressure surfaces) data over the last 40?years (1977?2016) give results consistent with the HTI. Finally, we compare temperature trends for Hawaii's highest elevation station, Mauna Loa Observatory (3,397?m), to those on another mountainous subtropical island station in the Atlantic, Mt. Iza~na Observatory (2,373?m), Tenerife, Canary Islands. Both stations sit above the local temperature inversion layer and have virtually identical significant warming trends of 0.19°C/decade (p?<?0.001) between 1955 and 2016. |
Elshall, Ahmed S; Ye, Ming Making Steppingstones out of Stumbling Blocks: A Bayesian Model Evidence Estimator with Application to Groundwater Transport Model Selection Journal Article Water, 11 (8), pp. 1579, 2019. @article{Elshall2019-bc, title = {Making Steppingstones out of Stumbling Blocks: A Bayesian Model Evidence Estimator with Application to Groundwater Transport Model Selection}, author = {Ahmed S Elshall and Ming Ye}, year = {2019}, date = {2019-07-01}, journal = {Water}, volume = {11}, number = {8}, pages = {1579}, publisher = {Multidisciplinary Digital Publishing Institute}, abstract = {Bayesian model evidence (BME) is a measure of the average fit of a model to observation data given all the parameter values that the model can assume. By accounting for the trade-off between goodness-of-fit and model complexity, BME is used for model selection and model averaging purposes. For strict Bayesian computation, the theoretically unbiased Monte Carlo based numerical estimators are preferred over semi-analytical solutions. This study examines five BME numerical estimators and asks how accurate estimation of the BME is important for penalizing model complexity. The limiting cases for numerical BME estimators are the prior sampling arithmetic mean estimator (AM) and the posterior sampling harmonic mean (HM) estimator, which are straightforward to implement, yet they result in underestimation and overestimation, respectively. We also consider the path sampling methods of thermodynamic integration (TI) and steppingstone sampling (SS) that sample multiple intermediate distributions that link the prior and the posterior. Although TI and SS are theoretically unbiased estimators, they could have a bias in practice arising from numerical implementation. For example, sampling errors of some intermediate distributions can introduce bias. We propose a variant of SS, namely the multiple one-steppingstone sampling (MOSS) that is less sensitive to sampling errors. We evaluate these five estimators using a groundwater transport model selection problem. SS and MOSS give the least biased BME estimation at an efficient computational cost. If the estimated BME has a bias that covariates with the true BME, this would not be a problem because we are interested in BME ratios and not their absolute values. On the contrary, the results show that BME estimation bias can be a function of model complexity. Thus, biased BME estimation results in inaccurate penalization of more complex models, which changes the model ranking. This was less observed with SS and MOSS as with the three other methods.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Bayesian model evidence (BME) is a measure of the average fit of a model to observation data given all the parameter values that the model can assume. By accounting for the trade-off between goodness-of-fit and model complexity, BME is used for model selection and model averaging purposes. For strict Bayesian computation, the theoretically unbiased Monte Carlo based numerical estimators are preferred over semi-analytical solutions. This study examines five BME numerical estimators and asks how accurate estimation of the BME is important for penalizing model complexity. The limiting cases for numerical BME estimators are the prior sampling arithmetic mean estimator (AM) and the posterior sampling harmonic mean (HM) estimator, which are straightforward to implement, yet they result in underestimation and overestimation, respectively. We also consider the path sampling methods of thermodynamic integration (TI) and steppingstone sampling (SS) that sample multiple intermediate distributions that link the prior and the posterior. Although TI and SS are theoretically unbiased estimators, they could have a bias in practice arising from numerical implementation. For example, sampling errors of some intermediate distributions can introduce bias. We propose a variant of SS, namely the multiple one-steppingstone sampling (MOSS) that is less sensitive to sampling errors. We evaluate these five estimators using a groundwater transport model selection problem. SS and MOSS give the least biased BME estimation at an efficient computational cost. If the estimated BME has a bias that covariates with the true BME, this would not be a problem because we are interested in BME ratios and not their absolute values. On the contrary, the results show that BME estimation bias can be a function of model complexity. Thus, biased BME estimation results in inaccurate penalization of more complex models, which changes the model ranking. This was less observed with SS and MOSS as with the three other methods. |
Cleveland, Sean B; McLean, Jared H; Rotzoll, Kolja; Izuka, Scot K; Jacobs, Gwen A Enabling Real-Time User Interaction For Decision Support: Experiences Extending A Local Agave Platform Metadata Service Inproceedings Proceedings of the Practice and Experience in Advanced Research Computing on Rise of the Machines (learning), pp. 8, ACM, 2019. @inproceedings{Cleveland2019-ux, title = {Enabling Real-Time User Interaction For Decision Support: Experiences Extending A Local Agave Platform Metadata Service}, author = {Sean B Cleveland and Jared H McLean and Kolja Rotzoll and Scot K Izuka and Gwen A Jacobs}, year = {2019}, date = {2019-07-01}, booktitle = {Proceedings of the Practice and Experience in Advanced Research Computing on Rise of the Machines (learning)}, pages = {8}, publisher = {ACM}, keywords = {}, pubstate = {published}, tppubtype = {inproceedings} } |
Delevaux, Jade M S; Stamoulis, Kostantinos A; Whittier, Robert; Jupiter, Stacy D; Bremer, Leah L; Friedlander, Alan; Kurashima, Natalie; Giddens, Jonatha; Winter, Kawika B; Blaich-Vaughan, Mehana; Burnett, Kimberly M; Geslani, Cheryl; Ticktin, Tamara Place-based management can reduce human impacts on coral reefs in a changing climate Journal Article Ecol. Appl., 29 (4), pp. e01891, 2019. @article{Delevaux2019-px, title = {Place-based management can reduce human impacts on coral reefs in a changing climate}, author = {Jade M S Delevaux and Kostantinos A Stamoulis and Robert Whittier and Stacy D Jupiter and Leah L Bremer and Alan Friedlander and Natalie Kurashima and Jonatha Giddens and Kawika B Winter and Mehana Blaich-Vaughan and Kimberly M Burnett and Cheryl Geslani and Tamara Ticktin}, year = {2019}, date = {2019-06-01}, journal = {Ecol. Appl.}, volume = {29}, number = {4}, pages = {e01891}, abstract = {Declining natural resources have contributed to a cultural renaissance across the Pacific that seeks to revive customary ridge-to-reef management approaches to protect freshwater and restore abundant coral reef fisheries. We applied a linked land-sea modeling framework based on remote sensing and empirical data, which couples groundwater nutrient export and coral reef models at fine spatial resolution. This spatially explicit (60 $times$ 60 m) framework simultaneously tracks changes in multiple benthic and fish indicators as a function of community-led marine closures, land-use and climate change scenarios. We applied this framework in H=a'ena and Ka'=up=ulehu, located at opposite ends of the Hawaiian Archipelago to investigate the effects of coastal development and marine closures on coral reefs in the face of climate change. Our results indicated that projected coastal development and bleaching can result in a significant decrease in benthic habitat quality and community-led marine closures can result in a significant increase in fish biomass. In general, Ka'=up=ulehu is more vulnerable to land-based nutrients and coral bleaching than H=a'ena due to high coral cover and limited dilution and mixing from low rainfall and wave power, except for the shallow and wave-sheltered back-reef areas of H=a'ena, which support high coral cover and act as nursery habitat for fishes. By coupling spatially explicit land-sea models with scenario planning, we identified priority areas on land where upgrading cesspools can reduce human impacts on coral reefs in the face of projected climate change impacts.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Declining natural resources have contributed to a cultural renaissance across the Pacific that seeks to revive customary ridge-to-reef management approaches to protect freshwater and restore abundant coral reef fisheries. We applied a linked land-sea modeling framework based on remote sensing and empirical data, which couples groundwater nutrient export and coral reef models at fine spatial resolution. This spatially explicit (60 $times$ 60 m) framework simultaneously tracks changes in multiple benthic and fish indicators as a function of community-led marine closures, land-use and climate change scenarios. We applied this framework in H=a'ena and Ka'=up=ulehu, located at opposite ends of the Hawaiian Archipelago to investigate the effects of coastal development and marine closures on coral reefs in the face of climate change. Our results indicated that projected coastal development and bleaching can result in a significant decrease in benthic habitat quality and community-led marine closures can result in a significant increase in fish biomass. In general, Ka'=up=ulehu is more vulnerable to land-based nutrients and coral bleaching than H=a'ena due to high coral cover and limited dilution and mixing from low rainfall and wave power, except for the shallow and wave-sheltered back-reef areas of H=a'ena, which support high coral cover and act as nursery habitat for fishes. By coupling spatially explicit land-sea models with scenario planning, we identified priority areas on land where upgrading cesspools can reduce human impacts on coral reefs in the face of projected climate change impacts. |
Levia, Delphis F; Nanko, Kazuki; Amasaki, Hiromasa; Giambelluca, Thomas W; Hotta, Norifumi; Iida, Shin'ichi; Mudd, Ryan G; Nullet, Michael A; Sakai, Naoki; Shinohara, Yoshinori; Sun, Xinchao; Suzuki, Masakazu; Tanaka, Nobuaki; Tantasirin, Chatchai; Yamada, Kozo Throughfall partitioning by trees Journal Article Hydrol. Process., 33 (12), pp. 1698–1708, 2019. @article{Levia2019-ik, title = {Throughfall partitioning by trees}, author = {Delphis F Levia and Kazuki Nanko and Hiromasa Amasaki and Thomas W Giambelluca and Norifumi Hotta and Shin'ichi Iida and Ryan G Mudd and Michael A Nullet and Naoki Sakai and Yoshinori Shinohara and Xinchao Sun and Masakazu Suzuki and Nobuaki Tanaka and Chatchai Tantasirin and Kozo Yamada}, year = {2019}, date = {2019-06-01}, journal = {Hydrol. Process.}, volume = {33}, number = {12}, pages = {1698--1708}, abstract = {Abstract Although we know that rainfall interception (the rain caught, stored, and evaporated from aboveground vegetative surfaces and ground litter) is affected by rain and throughfall drop size, what was unknown until now is the relative proportion of each throughfall type (free throughfall, splash throughfall, canopy drip) beneath coniferous and broadleaved trees. Based on a multinational data set of >120 million throughfall drops, we found that the type, number, and volume of throughfall drops are different between coniferous and broadleaved tree species, leaf states, and timing within rain events. Compared with leafed broadleaved trees, conifers had a lower percentage of canopy drip (51% vs. 69% with respect to total throughfall volume) and slightly smaller diameter splash throughfall and canopy drip. Canopy drip from leafless broadleaved trees consisted of fewer and smaller diameter drops (D50_DR, 50th cumulative drop volume percentile for canopy drip, of 2.24 mm) than leafed broadleaved trees (D50_DR of 4.32 mm). Canopy drip was much larger in diameter under woody drip points (D50_DR of 5.92 mm) than leafed broadleaved trees. Based on throughfall volume, the percentage of canopy drip was significantly different between conifers, leafed broadleaved trees, leafless broadleaved trees, and woody surface drip points (p ranged from <0.001 to 0.005). These findings are partly attributable to differences in canopy structure and plant surface characteristics between plant functional types and canopy state (leaf, leafless), among other factors. Hence, our results demonstrating the importance of drop-size-dependent partitioning between coniferous and broadleaved tree species could be useful to those requiring more detailed information on throughfall fluxes to the forest floor.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Abstract Although we know that rainfall interception (the rain caught, stored, and evaporated from aboveground vegetative surfaces and ground litter) is affected by rain and throughfall drop size, what was unknown until now is the relative proportion of each throughfall type (free throughfall, splash throughfall, canopy drip) beneath coniferous and broadleaved trees. Based on a multinational data set of >120 million throughfall drops, we found that the type, number, and volume of throughfall drops are different between coniferous and broadleaved tree species, leaf states, and timing within rain events. Compared with leafed broadleaved trees, conifers had a lower percentage of canopy drip (51% vs. 69% with respect to total throughfall volume) and slightly smaller diameter splash throughfall and canopy drip. Canopy drip from leafless broadleaved trees consisted of fewer and smaller diameter drops (D50_DR, 50th cumulative drop volume percentile for canopy drip, of 2.24 mm) than leafed broadleaved trees (D50_DR of 4.32 mm). Canopy drip was much larger in diameter under woody drip points (D50_DR of 5.92 mm) than leafed broadleaved trees. Based on throughfall volume, the percentage of canopy drip was significantly different between conifers, leafed broadleaved trees, leafless broadleaved trees, and woody surface drip points (p ranged from <0.001 to 0.005). These findings are partly attributable to differences in canopy structure and plant surface characteristics between plant functional types and canopy state (leaf, leafless), among other factors. Hence, our results demonstrating the importance of drop-size-dependent partitioning between coniferous and broadleaved tree species could be useful to those requiring more detailed information on throughfall fluxes to the forest floor. |
Ghazal, Kariem A; Leta, Olkeba Tolessa; El-Kadi, Aly I; Dulai, Henrietta Assessment of Wetland Restoration and Climate Change Impacts on Water Balance Components of the Heeia Coastal Wetland in Hawaii Journal Article Hydrology, 6 (2), pp. 37, 2019. @article{Ghazal2019-oc, title = {Assessment of Wetland Restoration and Climate Change Impacts on Water Balance Components of the Heeia Coastal Wetland in Hawaii}, author = {Kariem A Ghazal and Olkeba Tolessa Leta and Aly I El-Kadi and Henrietta Dulai}, year = {2019}, date = {2019-05-01}, journal = {Hydrology}, volume = {6}, number = {2}, pages = {37}, publisher = {Multidisciplinary Digital Publishing Institute}, abstract = {Hydrological modeling is an important tool that can be used to assess water resources' availability and sustainability that are necessary for food security and ecological health of coastal regions. In this study, we assessed the impacts of land use and climate changes on water balance components (WBCs) of the Heeia coastal wetland. We developed a Soil and Water Assessment Tool (SWAT) model to capture the unique characteristics of the Hawaiian Islands, including its volcanic soil's nature and high initial infiltration rates. We used the sequential uncertainty fitting algorithm to assess the sensitivity and uncertainty of WBCs under different climate change scenarios. Results of the statistical analysis of daily streamflow simulations showed that the model performance was within the generally acceptable criteria. Under future climate scenarios, rainfall change was the determinant factor most negatively impacting WBCs. Recharge and baseflow components had the highest sensitivity to the combined effects of land use and climate changes, especially during dry season. The uncertainty analysis indicated that the streamflow is projected to slightly increase by the middle of 21st century, but expected to decline by 40% during the late 21st century of Representative Concentration Pathways (RCP) 8.5.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Hydrological modeling is an important tool that can be used to assess water resources' availability and sustainability that are necessary for food security and ecological health of coastal regions. In this study, we assessed the impacts of land use and climate changes on water balance components (WBCs) of the Heeia coastal wetland. We developed a Soil and Water Assessment Tool (SWAT) model to capture the unique characteristics of the Hawaiian Islands, including its volcanic soil's nature and high initial infiltration rates. We used the sequential uncertainty fitting algorithm to assess the sensitivity and uncertainty of WBCs under different climate change scenarios. Results of the statistical analysis of daily streamflow simulations showed that the model performance was within the generally acceptable criteria. Under future climate scenarios, rainfall change was the determinant factor most negatively impacting WBCs. Recharge and baseflow components had the highest sensitivity to the combined effects of land use and climate changes, especially during dry season. The uncertainty analysis indicated that the streamflow is projected to slightly increase by the middle of 21st century, but expected to decline by 40% during the late 21st century of Representative Concentration Pathways (RCP) 8.5. |
Elshall, Ahmed S; Ye, Ming; Niu, Guo-Yue; Barron-Gafford, Greg A Bayesian inference and predictive performance of soil respiration models in the presence of model discrepancy Journal Article Geoscientific Model Development, 12 (5), pp. 2009–2032, 2019. @article{Elshall2019-ts, title = {Bayesian inference and predictive performance of soil respiration models in the presence of model discrepancy}, author = {Ahmed S Elshall and Ming Ye and Guo-Yue Niu and Greg A Barron-Gafford}, year = {2019}, date = {2019-05-01}, journal = {Geoscientific Model Development}, volume = {12}, number = {5}, pages = {2009--2032}, publisher = {Copernicus GmbH}, abstract = {Abstract. Bayesian inference of microbial soil respiration models is often based on the assumptions that the residuals are independent (i.e., no temporal or spatial correlation), identically distributed (i.e., Gaussian noise), and have constant variance (i.e., homoscedastic). In the presence of model discrepancy, as no model is perfect, this study shows that these assumptions are generally invalid in soil respiration modeling such that residuals have high temporal correlation, an increasing variance with increasing magnitude of CO2 efflux, and non-Gaussian distribution. Relaxing these three assumptions stepwise results in eight data models. Data models are the basis of formulating likelihood functions of Bayesian inference. This study presents a systematic and comprehensive investigation of the impacts of data model selection on Bayesian inference and predictive performance. We use three mechanistic soil respiration models with different levels of model fidelity (i.e., model discrepancy) with respect to the number of carbon pools and the explicit representations of soil moisture controls on carbon degradation; therefore, we have different levels of model complexity with respect to the number of model parameters. The study shows that data models have substantial impacts on Bayesian inference and predictive performance of the soil respiration models such that the following points are true: (i) the level of complexity of the best model is generally justified by the cross-validation results for different data models; (ii) not accounting for heteroscedasticity and autocorrelation might not necessarily result in biased parameter estimates or predictions, but will definitely underestimate uncertainty; (iii) using a non-Gaussian data model improves the parameter estimates and the predictive performance; and (iv) accounting for autocorrelation only or joint inversion of correlation and heteroscedasticity can be problematic and requires special treatment. Although the conclusions of this study are empirical, the analysis may provide insights for selecting appropriate data models for soil respiration modeling.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Abstract. Bayesian inference of microbial soil respiration models is often based on the assumptions that the residuals are independent (i.e., no temporal or spatial correlation), identically distributed (i.e., Gaussian noise), and have constant variance (i.e., homoscedastic). In the presence of model discrepancy, as no model is perfect, this study shows that these assumptions are generally invalid in soil respiration modeling such that residuals have high temporal correlation, an increasing variance with increasing magnitude of CO2 efflux, and non-Gaussian distribution. Relaxing these three assumptions stepwise results in eight data models. Data models are the basis of formulating likelihood functions of Bayesian inference. This study presents a systematic and comprehensive investigation of the impacts of data model selection on Bayesian inference and predictive performance. We use three mechanistic soil respiration models with different levels of model fidelity (i.e., model discrepancy) with respect to the number of carbon pools and the explicit representations of soil moisture controls on carbon degradation; therefore, we have different levels of model complexity with respect to the number of model parameters. The study shows that data models have substantial impacts on Bayesian inference and predictive performance of the soil respiration models such that the following points are true: (i) the level of complexity of the best model is generally justified by the cross-validation results for different data models; (ii) not accounting for heteroscedasticity and autocorrelation might not necessarily result in biased parameter estimates or predictions, but will definitely underestimate uncertainty; (iii) using a non-Gaussian data model improves the parameter estimates and the predictive performance; and (iv) accounting for autocorrelation only or joint inversion of correlation and heteroscedasticity can be problematic and requires special treatment. Although the conclusions of this study are empirical, the analysis may provide insights for selecting appropriate data models for soil respiration modeling. |
Engels, Jennifer; Bruno, Barbara; Dasalla, Noelle; Böttjer-Wilson, Daniela Class observations from the University of Hawai`i at M=anoa highlight the need for active learning strategies to support diverse students in large classes Inproceedings Fifth International Conference on Higher Education Advances, 2019. @inproceedings{Engels2019-cb, title = {Class observations from the University of Hawai`i at M=anoa highlight the need for active learning strategies to support diverse students in large classes}, author = {Jennifer Engels and Barbara Bruno and Noelle Dasalla and Daniela Böttjer-Wilson}, year = {2019}, date = {2019-05-01}, booktitle = {Fifth International Conference on Higher Education Advances}, abstract = {Compelling evidence indicates that ``active learning'' (learning by doing) is an effective pedagogy regardless of discipline or class size, and can be particularly effective with diverse students. This study investigated active learning practices in 64 classes at the University of Hawai`i at M=anoa, a US university with a highly diverse student body, using a ``Passivity Indicator'' (PI: ratio of class time spent in passive activities to total class time). For all classes, the mean PI was 43%. Statistical analysis reveals no significant differences in the PI of classes taught in STEM vs. non-STEM disciplines, or between upper vs. lower division courses. However, the PI in larger classes was found to be significantly greater than in small classes (64% vs. 39%, respectively; p=0.02). Moreover, classroom activities aligned with an active learning standard in Language and Literacy Development (e.g., students answering questions) occurred twice as often in small (24%) vs. large classes (12%, with p=0.02). Altogether, these findings indicate an opportunity for more active learning in large classes. We present a range of research-based pedagogical strategies that can be readily implemented in large classrooms, and encourage instructors to use their implementation as research opportunities to gather data on student success.}, keywords = {}, pubstate = {published}, tppubtype = {inproceedings} } Compelling evidence indicates that ``active learning'' (learning by doing) is an effective pedagogy regardless of discipline or class size, and can be particularly effective with diverse students. This study investigated active learning practices in 64 classes at the University of Hawai`i at M=anoa, a US university with a highly diverse student body, using a ``Passivity Indicator'' (PI: ratio of class time spent in passive activities to total class time). For all classes, the mean PI was 43%. Statistical analysis reveals no significant differences in the PI of classes taught in STEM vs. non-STEM disciplines, or between upper vs. lower division courses. However, the PI in larger classes was found to be significantly greater than in small classes (64% vs. 39%, respectively; p=0.02). Moreover, classroom activities aligned with an active learning standard in Language and Literacy Development (e.g., students answering questions) occurred twice as often in small (24%) vs. large classes (12%, with p=0.02). Altogether, these findings indicate an opportunity for more active learning in large classes. We present a range of research-based pedagogical strategies that can be readily implemented in large classrooms, and encourage instructors to use their implementation as research opportunities to gather data on student success. |
Ghorbanidehno, Hojat; Lee, Jonghyun; Farthing, Matthew; Hesser, Tyler; Kitanidis, Peter K; Darve, Eric F Novel Data Assimilation Algorithm for Nearshore Bathymetry Journal Article J. Atmos. Ocean. Technol., 36 (4), pp. 699–715, 2019. @article{Ghorbanidehno2019-ni, title = {Novel Data Assimilation Algorithm for Nearshore Bathymetry}, author = {Hojat Ghorbanidehno and Jonghyun Lee and Matthew Farthing and Tyler Hesser and Peter K Kitanidis and Eric F Darve}, year = {2019}, date = {2019-04-01}, journal = {J. Atmos. Ocean. Technol.}, volume = {36}, number = {4}, pages = {699--715}, publisher = {American Meteorological Society}, abstract = {AbstractIt can be expensive and difficult to collect direct bathymetry data for nearshore regions, especially in high-energy locations where there are temporally and spatially varying bathymetric features like sandbars. As a result, there has been increasing interest in remote assessment techniques for estimating bathymetry. Recent efforts have combined Kalman filter?based techniques with indirect video-based observations for bathymetry inversion. Here, we estimate nearshore bathymetry by utilizing observed wave celerity and wave height, which are related to bathymetry through phase-averaged wave dynamics. We present a modified compressed-state Kalman filter (CSKF) method, a fast and scalable Kalman filter method for linear and nonlinear problems with large numbers of unknowns and measurements, and apply it to two nearshore bathymetry estimation problems. To illustrate the robustness and accuracy of our method, we compare its performance with that of two ensemble-based approaches on twin bathymetry estimation problems with profiles based on surveys taken by the U.S. Army Corps of Engineer Field Research Facility (FRF) in Duck, North Carolina. We first consider an estimation problem for a temporally constant bathymetry profile. Then we estimate bathymetry as it evolves in time. Our results indicate that the CSKF method is more accurate and robust than the ensemble-based methods with the same computational cost. The superior performance is due to the optimal low-rank representation of the covariance matrices.}, keywords = {}, pubstate = {published}, tppubtype = {article} } AbstractIt can be expensive and difficult to collect direct bathymetry data for nearshore regions, especially in high-energy locations where there are temporally and spatially varying bathymetric features like sandbars. As a result, there has been increasing interest in remote assessment techniques for estimating bathymetry. Recent efforts have combined Kalman filter?based techniques with indirect video-based observations for bathymetry inversion. Here, we estimate nearshore bathymetry by utilizing observed wave celerity and wave height, which are related to bathymetry through phase-averaged wave dynamics. We present a modified compressed-state Kalman filter (CSKF) method, a fast and scalable Kalman filter method for linear and nonlinear problems with large numbers of unknowns and measurements, and apply it to two nearshore bathymetry estimation problems. To illustrate the robustness and accuracy of our method, we compare its performance with that of two ensemble-based approaches on twin bathymetry estimation problems with profiles based on surveys taken by the U.S. Army Corps of Engineer Field Research Facility (FRF) in Duck, North Carolina. We first consider an estimation problem for a temporally constant bathymetry profile. Then we estimate bathymetry as it evolves in time. Our results indicate that the CSKF method is more accurate and robust than the ensemble-based methods with the same computational cost. The superior performance is due to the optimal low-rank representation of the covariance matrices. |
Watson, Sheree J; Needoba, Joseph A; Peterson, Tawnya D Widespread detection of Candidatus Accumulibacter phosphatis, a polyphosphate-accumulating organism, in sediments of the Columbia River estuary Journal Article Environ. Microbiol., 21 (4), pp. 1369–1382, 2019. @article{Watson2019-ej, title = {Widespread detection of Candidatus Accumulibacter phosphatis, a polyphosphate-accumulating organism, in sediments of the Columbia River estuary}, author = {Sheree J Watson and Joseph A Needoba and Tawnya D Peterson}, year = {2019}, date = {2019-04-01}, journal = {Environ. Microbiol.}, volume = {21}, number = {4}, pages = {1369--1382}, abstract = {Enhanced biological phosphorus removal (EBPR) exploits the metabolism of polyphosphate-accumulating organisms (PAOs) to remove excess phosphorus (P) from wastewater treatment. Candidatus Accumulibacter phosphatis (Accumulibacter) is the most abundant and well-studied PAO in EBPR systems. In a previous study, we detected polyphosphates throughout peripheral bay sediments, and hypothesized that an estuary is an ideal setting to evaluate PAOs in a natural system, given that estuaries are characterized by dynamic dissolved oxygen fluctuations that potentially favour PAO metabolism. We detected nucleotide sequences attributable to Accumulibacter (16S rRNA, ppk1) in sediments within three peripheral bays of the Columbia River estuary at abundances rivalling those observed in conventional wastewater treatment plants (0.01%-2.6%). Most of the sequences attributable to Accumulibacter were Type I rather than Type II, despite the fact that the estuary does not have particularly high nutrient concentrations. The highest diversity of Accumulibacter was observed in oligohaline peripheral bays, while the greatest abundances were observed at the mouth of the estuary in mesohaline sediments in the spring and summer. In addition, an approximately 70% increase in polyphosphate concentrations observed at one of the sites between dawn and dusk suggests that PAOs may play an important role in P cycling in estuary sediments.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Enhanced biological phosphorus removal (EBPR) exploits the metabolism of polyphosphate-accumulating organisms (PAOs) to remove excess phosphorus (P) from wastewater treatment. Candidatus Accumulibacter phosphatis (Accumulibacter) is the most abundant and well-studied PAO in EBPR systems. In a previous study, we detected polyphosphates throughout peripheral bay sediments, and hypothesized that an estuary is an ideal setting to evaluate PAOs in a natural system, given that estuaries are characterized by dynamic dissolved oxygen fluctuations that potentially favour PAO metabolism. We detected nucleotide sequences attributable to Accumulibacter (16S rRNA, ppk1) in sediments within three peripheral bays of the Columbia River estuary at abundances rivalling those observed in conventional wastewater treatment plants (0.01%-2.6%). Most of the sequences attributable to Accumulibacter were Type I rather than Type II, despite the fact that the estuary does not have particularly high nutrient concentrations. The highest diversity of Accumulibacter was observed in oligohaline peripheral bays, while the greatest abundances were observed at the mouth of the estuary in mesohaline sediments in the spring and summer. In addition, an approximately 70% increase in polyphosphate concentrations observed at one of the sites between dawn and dusk suggests that PAOs may play an important role in P cycling in estuary sediments. |
Newman, Andrew J; Clark, Martyn P; Longman, Ryan J; Gilleland, Eric; Giambelluca, Thomas W; Arnold, Jeffrey R Use of Daily Station Observations to Produce High-Resolution Gridded Probabilistic Precipitation and Temperature Time Series for the Hawaiian Islands Journal Article J. Hydrometeorol., 20 (3), pp. 509–529, 2019. @article{Newman2019-cp, title = {Use of Daily Station Observations to Produce High-Resolution Gridded Probabilistic Precipitation and Temperature Time Series for the Hawaiian Islands}, author = {Andrew J Newman and Martyn P Clark and Ryan J Longman and Eric Gilleland and Thomas W Giambelluca and Jeffrey R Arnold}, year = {2019}, date = {2019-03-01}, journal = {J. Hydrometeorol.}, volume = {20}, number = {3}, pages = {509--529}, publisher = {American Meteorological Society}, abstract = {AbstractIt is a major challenge to develop gridded precipitation and temperature estimates that adequately resolve the extreme spatial gradients present in the Hawaiian Islands. The challenge is particularly pronounced because the available station networks are irregularly spaced and sparse, creating large uncertainties in gridded spatial meteorological estimates. Here a 100-member, daily ensemble of precipitation and temperature estimates over the Hawaiian Islands for the period 1990?2014 at 1-km grid resolution is developed. First, an intermediary ensemble estimate of the monthly climatological precipitation and temperature is created, and those climatological surfaces are used to inform daily anomaly interpolation. This climatologically aided interpolation (CAI) method extends our initial ensemble system developed for the continental United States. This study demonstrates that direct interpolation of daily precipitation values is inferior to the CAI methodology, particularly over longer time periods (from years to decades). Daily interpolation performs better for short time periods (e.g., 1 month or less) or when the precipitation distribution substantially diverges from climatology. The CAI ensemble is able to reproduce observed precipitation and temperature patterns, including precipitation occurrence. Leave-one-out cross-validation results illustrate that the ensemble has 1) minimal bias for precipitation and temperature; 2) a mean absolute error of 2.5 mm day?1, 1.0 K, and 2.2 K for precipitation and mean and diurnal temperature, respectively; 3) a mean absolute error of 3.3 mm day?1 for the standard deviation of precipitation; and 4) nearly unbiased probability distributions across multiple thresholds of precipitation intensity. Additionally, the ensemble provides estimates of uncertainty across the distributions with increasing uncertainty for higher percentiles.}, keywords = {}, pubstate = {published}, tppubtype = {article} } AbstractIt is a major challenge to develop gridded precipitation and temperature estimates that adequately resolve the extreme spatial gradients present in the Hawaiian Islands. The challenge is particularly pronounced because the available station networks are irregularly spaced and sparse, creating large uncertainties in gridded spatial meteorological estimates. Here a 100-member, daily ensemble of precipitation and temperature estimates over the Hawaiian Islands for the period 1990?2014 at 1-km grid resolution is developed. First, an intermediary ensemble estimate of the monthly climatological precipitation and temperature is created, and those climatological surfaces are used to inform daily anomaly interpolation. This climatologically aided interpolation (CAI) method extends our initial ensemble system developed for the continental United States. This study demonstrates that direct interpolation of daily precipitation values is inferior to the CAI methodology, particularly over longer time periods (from years to decades). Daily interpolation performs better for short time periods (e.g., 1 month or less) or when the precipitation distribution substantially diverges from climatology. The CAI ensemble is able to reproduce observed precipitation and temperature patterns, including precipitation occurrence. Leave-one-out cross-validation results illustrate that the ensemble has 1) minimal bias for precipitation and temperature; 2) a mean absolute error of 2.5 mm day?1, 1.0 K, and 2.2 K for precipitation and mean and diurnal temperature, respectively; 3) a mean absolute error of 3.3 mm day?1 for the standard deviation of precipitation; and 4) nearly unbiased probability distributions across multiple thresholds of precipitation intensity. Additionally, the ensemble provides estimates of uncertainty across the distributions with increasing uncertainty for higher percentiles. |
Longman, Ryan J; Frazier, Abby G; Newman, Andrew J; Giambelluca, Thomas W; Schanzenbach, David; Kagawa-Viviani, Aurora; Needham, Heidi; Arnold, Jeffrey R; Clark, Martyn P High-Resolution Gridded Daily Rainfall and Temperature for the Hawaiian Islands (1990--2014) Journal Article J. Hydrometeorol., 20 (3), pp. 489–508, 2019. @article{Longman2019-mn, title = {High-Resolution Gridded Daily Rainfall and Temperature for the Hawaiian Islands (1990--2014)}, author = {Ryan J Longman and Abby G Frazier and Andrew J Newman and Thomas W Giambelluca and David Schanzenbach and Aurora Kagawa-Viviani and Heidi Needham and Jeffrey R Arnold and Martyn P Clark}, year = {2019}, date = {2019-03-01}, journal = {J. Hydrometeorol.}, volume = {20}, number = {3}, pages = {489--508}, publisher = {American Meteorological Society}, abstract = {AbstractSpatially continuous data products are essential for a number of applications including climate and hydrologic modeling, weather prediction, and water resource management. In this work, a distance-weighted interpolation method used to map daily rainfall and temperature in Hawaii is described and assessed. New high-resolution (250 m) maps were developed for daily rainfall and daily maximum (Tmax) and minimum (Tmin) near-surface air temperature for the period 1990?2014. Maps were produced using climatologically aided interpolation, in which station anomalies were interpolated using an optimized inverse distance weighting approach and then combined with long-term means to produce daily gridded estimates. Leave-one-out cross validation was performed to assess the quality of the final daily grids. The median absolute prediction error for rainfall was 0.1 mm with an average overprediction (+0.6 mm) on days when total rainfall was less than 1 mm. On days with total rainfall greater than 1 mm, median absolute prediction errors were 2 mm and rainfall was typically underpredicted above the 10-mm threshold. For daily temperature, median absolute prediction errors were 3.1° and 2.8°C for Tmax and Tmin, respectively. On average, this method overpredicted Tmax (+1.1°C) and Tmin (+1.5°C), and errors varied considerably among stations. Errors for all variables exhibited significant seasonal variations. However, the annual range of errors was small. The methods presented here provide an effective approach for mapping daily weather fields in a topographically diverse region and improve on previous products in their spatial resolution, time period of coverage, and use of data.}, keywords = {}, pubstate = {published}, tppubtype = {article} } AbstractSpatially continuous data products are essential for a number of applications including climate and hydrologic modeling, weather prediction, and water resource management. In this work, a distance-weighted interpolation method used to map daily rainfall and temperature in Hawaii is described and assessed. New high-resolution (250 m) maps were developed for daily rainfall and daily maximum (Tmax) and minimum (Tmin) near-surface air temperature for the period 1990?2014. Maps were produced using climatologically aided interpolation, in which station anomalies were interpolated using an optimized inverse distance weighting approach and then combined with long-term means to produce daily gridded estimates. Leave-one-out cross validation was performed to assess the quality of the final daily grids. The median absolute prediction error for rainfall was 0.1 mm with an average overprediction (+0.6 mm) on days when total rainfall was less than 1 mm. On days with total rainfall greater than 1 mm, median absolute prediction errors were 2 mm and rainfall was typically underpredicted above the 10-mm threshold. For daily temperature, median absolute prediction errors were 3.1° and 2.8°C for Tmax and Tmin, respectively. On average, this method overpredicted Tmax (+1.1°C) and Tmin (+1.5°C), and errors varied considerably among stations. Errors for all variables exhibited significant seasonal variations. However, the annual range of errors was small. The methods presented here provide an effective approach for mapping daily weather fields in a topographically diverse region and improve on previous products in their spatial resolution, time period of coverage, and use of data. |
Newman, Andrew J; Clark, Martyn P; Longman, Ryan J; Giambelluca, Thomas W Methodological Intercomparisons of Station-Based Gridded Meteorological Products: Utility, Limitations, and Paths Forward Journal Article J. Hydrometeorol., 20 (3), pp. 531–547, 2019. @article{Newman2019-vb, title = {Methodological Intercomparisons of Station-Based Gridded Meteorological Products: Utility, Limitations, and Paths Forward}, author = {Andrew J Newman and Martyn P Clark and Ryan J Longman and Thomas W Giambelluca}, year = {2019}, date = {2019-03-01}, journal = {J. Hydrometeorol.}, volume = {20}, number = {3}, pages = {531--547}, publisher = {American Meteorological Society}, abstract = {AbstractThis study presents a gridded meteorology intercomparison using the State of Hawaii as a testbed. This is motivated by the goal to provide the broad user community with knowledge of interproduct differences and the reasons differences exist. More generally, the challenge of generating station-based gridded meteorological surfaces and the difficulties in attributing interproduct differences to specific methodological decisions are demonstrated. Hawaii is a useful testbed because it is traditionally underserved, yet meteorologically interesting and complex. In addition, several climatological and daily gridded meteorology datasets are now available, which are used extensively by the applications modeling community, thus an intercomparison enhances Hawaiian specific capabilities. We compare PRISM climatology and three daily datasets: new datasets from the University of Hawai?i and the National Center for Atmospheric Research, and Daymet version 3 for precipitation and temperature variables only. General conclusions that have emerged are 1) differences in input station data significantly influence the product differences, 2) explicit prediction of precipitation occurrence is crucial across multiple metrics, and 3) attribution of differences to specific methodological choices is difficult and limits the usefulness of intercomparisons. Because generating gridded meteorological fields is an elaborate process with many methodological choices interacting in complex ways, future work should 1) develop modular frameworks that allows users to easily examine the breadth of methodological choices, 2) collate available nontraditional high-quality observational datasets for true out-of-sample validation and make them publicly available, and 3) define benchmarks of acceptable performance for methodological components and products.}, keywords = {}, pubstate = {published}, tppubtype = {article} } AbstractThis study presents a gridded meteorology intercomparison using the State of Hawaii as a testbed. This is motivated by the goal to provide the broad user community with knowledge of interproduct differences and the reasons differences exist. More generally, the challenge of generating station-based gridded meteorological surfaces and the difficulties in attributing interproduct differences to specific methodological decisions are demonstrated. Hawaii is a useful testbed because it is traditionally underserved, yet meteorologically interesting and complex. In addition, several climatological and daily gridded meteorology datasets are now available, which are used extensively by the applications modeling community, thus an intercomparison enhances Hawaiian specific capabilities. We compare PRISM climatology and three daily datasets: new datasets from the University of Hawai?i and the National Center for Atmospheric Research, and Daymet version 3 for precipitation and temperature variables only. General conclusions that have emerged are 1) differences in input station data significantly influence the product differences, 2) explicit prediction of precipitation occurrence is crucial across multiple metrics, and 3) attribution of differences to specific methodological choices is difficult and limits the usefulness of intercomparisons. Because generating gridded meteorological fields is an elaborate process with many methodological choices interacting in complex ways, future work should 1) develop modular frameworks that allows users to easily examine the breadth of methodological choices, 2) collate available nontraditional high-quality observational datasets for true out-of-sample validation and make them publicly available, and 3) define benchmarks of acceptable performance for methodological components and products. |
Shuler, Christopher K; Amato, Daniel W; Gibson, Veronica; Baker, Lydia; Olguin, Ashley N; Dulai, Henrietta; Smith, Celia M; Alegado, Rosanna A Assessment of Terrigenous Nutrient Loading to Coastal Ecosystems along a Human Land-Use Gradient, Tutuila, American Samoa Journal Article Hydrology, 6 (1), pp. 18, 2019. @article{Shuler2019-ys, title = {Assessment of Terrigenous Nutrient Loading to Coastal Ecosystems along a Human Land-Use Gradient, Tutuila, American Samoa}, author = {Christopher K Shuler and Daniel W Amato and Veronica Gibson and Lydia Baker and Ashley N Olguin and Henrietta Dulai and Celia M Smith and Rosanna A Alegado}, year = {2019}, date = {2019-02-01}, journal = {Hydrology}, volume = {6}, number = {1}, pages = {18}, publisher = {Multidisciplinary Digital Publishing Institute}, abstract = {Anthropogenic nutrient loading is well recognized as a stressor to coastal ecosystem health. However, resource managers are often focused on addressing point source or surface water discharge, whereas the impact of submarine groundwater discharge (SGD) as a nutrient vector is often unappreciated. This study examines connections between land use and nutrient loading through comparison of four watersheds and embayments spanning a gradient of human use impact on Tutuila, a high tropical oceanic island in American Samoa. In each study location, coastal radon-222 measurements, dissolved nutrient concentrations, and nitrogen isotope values ($delta$15N) in water and in situ macroalgal tissue were used to explore SGD and baseflow derived nutrient impacts, and to determine probable nutrient sources. In addition to sampling in situ macroalgae, pre-treated macroalgal specimens were deployed throughout each embayment to uptake ambient nutrients and provide a standardized assessment of differences between locations. Results show SGD-derived nutrient flux was more significant than baseflow nutrient flux in all watersheds, and $delta$15N values in water and algae suggested wastewater or manure are likely sources of elevated nutrient levels. While nutrient loading correlated well with expected anthropogenic impact, other factors such as differences in hydrogeology, distribution of development, and wastewater infrastructure also likely play a role in the visibility of impacts in each watershed.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Anthropogenic nutrient loading is well recognized as a stressor to coastal ecosystem health. However, resource managers are often focused on addressing point source or surface water discharge, whereas the impact of submarine groundwater discharge (SGD) as a nutrient vector is often unappreciated. This study examines connections between land use and nutrient loading through comparison of four watersheds and embayments spanning a gradient of human use impact on Tutuila, a high tropical oceanic island in American Samoa. In each study location, coastal radon-222 measurements, dissolved nutrient concentrations, and nitrogen isotope values ($delta$15N) in water and in situ macroalgal tissue were used to explore SGD and baseflow derived nutrient impacts, and to determine probable nutrient sources. In addition to sampling in situ macroalgae, pre-treated macroalgal specimens were deployed throughout each embayment to uptake ambient nutrients and provide a standardized assessment of differences between locations. Results show SGD-derived nutrient flux was more significant than baseflow nutrient flux in all watersheds, and $delta$15N values in water and algae suggested wastewater or manure are likely sources of elevated nutrient levels. While nutrient loading correlated well with expected anthropogenic impact, other factors such as differences in hydrogeology, distribution of development, and wastewater infrastructure also likely play a role in the visibility of impacts in each watershed. |
Leigh, Jason; Belcaid, Mahdi; Kobayashi, Dylan; Kirshenbaum, Nurit; Wooton, Troy; Gonzalez, Alberto; Renambot, Luc; Johnson, Andrew; Brown, Maxine; Burks, Andrew; Others, Usage Patterns of Wideband Display Environments In e-Science Research, Development and Training Inproceedings 15th IEEE International Conference on e-Science,(eScience 2019), evl.uic.edu, 2019. @inproceedings{Leigh2019-yr, title = {Usage Patterns of Wideband Display Environments In e-Science Research, Development and Training}, author = {Jason Leigh and Mahdi Belcaid and Dylan Kobayashi and Nurit Kirshenbaum and Troy Wooton and Alberto Gonzalez and Luc Renambot and Andrew Johnson and Maxine Brown and Andrew Burks and Others}, year = {2019}, date = {2019-01-01}, booktitle = {15th IEEE International Conference on e-Science,(eScience 2019)}, publisher = {evl.uic.edu}, abstract = {Group Environment) are operating systems for managing content across wideband display environments. This paper documents the prevalent usage patterns of SAGE-enabled display walls in support of the e-Science enterprise, based on nearly 15 years of observations of the SAGE community. These patterns will help guide e-Science users and cyberinfrastructure developers on how best to leverage large tiled display walls, and the types of software services that could be provided in the future.}, keywords = {}, pubstate = {published}, tppubtype = {inproceedings} } Group Environment) are operating systems for managing content across wideband display environments. This paper documents the prevalent usage patterns of SAGE-enabled display walls in support of the e-Science enterprise, based on nearly 15 years of observations of the SAGE community. These patterns will help guide e-Science users and cyberinfrastructure developers on how best to leverage large tiled display walls, and the types of software services that could be provided in the future. |
Burnett, Kimberly M; Ticktin, Tamara; Bremer, Leah L; Quazi, Shimona A; Geslani, Cheryl; Wada, Christopher A; Kurashima, Natalie; Mandle, Lisa; Pascua, Pua`ala; Depraetere, Taina; Wolkis, Dustin; Edmonds, Merlin; Giambelluca, Thomas; Falinski, Kim; Winter, Kawika B Restoring to the future: Environmental, cultural, and management trade-offs in historical versus hybrid restoration of a highly modified ecosystem Journal Article CONSERVATION LETTERS, 12 (1), pp. e12606, 2019. @article{Burnett2019-wz, title = {Restoring to the future: Environmental, cultural, and management trade-offs in historical versus hybrid restoration of a highly modified ecosystem}, author = {Kimberly M Burnett and Tamara Ticktin and Leah L Bremer and Shimona A Quazi and Cheryl Geslani and Christopher A Wada and Natalie Kurashima and Lisa Mandle and Pua`ala Pascua and Taina Depraetere and Dustin Wolkis and Merlin Edmonds and Thomas Giambelluca and Kim Falinski and Kawika B Winter}, year = {2019}, date = {2019-01-01}, journal = {CONSERVATION LETTERS}, volume = {12}, number = {1}, pages = {e12606}, abstract = {Abstract With growing calls to scale up reforestation efforts worldwide, conservation managers increasingly must decide whether and how to restore highly altered ecosystems. However, empirical research on potential trade-offs remains scarce. We use a Hawai'i watershed to demonstrate a collaborative, interdisciplinary approach to identifying synergies and trade-offs associated with maintaining an unrestored forest, versus restoration to a historical or hybrid (native and non-native plant species) state. We focused on restoration scenarios designed by conservation managers and measured ecological, hydrologic, and cultural outcomes they identified as important metrics of success. The hybrid restoration scenario maximized potential outcomes at moderate cost, and increased two rarely measured but often critical metrics to managers and communities: cultural value and resilience to disturbance. Hybrid restoration approaches developed collaboratively can provide a viable option for scaling up restoration in island ecosystems and other contexts where invasive species pose significant challenges and/or where community support is important.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Abstract With growing calls to scale up reforestation efforts worldwide, conservation managers increasingly must decide whether and how to restore highly altered ecosystems. However, empirical research on potential trade-offs remains scarce. We use a Hawai'i watershed to demonstrate a collaborative, interdisciplinary approach to identifying synergies and trade-offs associated with maintaining an unrestored forest, versus restoration to a historical or hybrid (native and non-native plant species) state. We focused on restoration scenarios designed by conservation managers and measured ecological, hydrologic, and cultural outcomes they identified as important metrics of success. The hybrid restoration scenario maximized potential outcomes at moderate cost, and increased two rarely measured but often critical metrics to managers and communities: cultural value and resilience to disturbance. Hybrid restoration approaches developed collaboratively can provide a viable option for scaling up restoration in island ecosystems and other contexts where invasive species pose significant challenges and/or where community support is important. |
Ginsberg, Alexandra Daisy; Chieza, Natsai; Frank, Kiana; Rands, Ahilapalapa; Vilutis, Justinas Piko A, Piko O, Piko I: Those That Came Before, Those That are Here Now, and Those That Will Come After Journal Article Journal of Design and Science, 2019. @article{Ginsberg2019-bs, title = {Piko A, Piko O, Piko I: Those That Came Before, Those That are Here Now, and Those That Will Come After}, author = {Alexandra Daisy Ginsberg and Natsai Chieza and Kiana Frank and Ahilapalapa Rands and Justinas Vilutis}, year = {2019}, date = {2019-01-01}, journal = {Journal of Design and Science}, publisher = {PubPub}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Welch, Eric M; Dulai, Henrietta; El-Kadi, Aly; Shuler, Christopher K Submarine Groundwater Discharge and Stream Baseflow Sustain Pesticide and Nutrient Fluxes in Faga'alu Bay, American Samoa Journal Article Front. Environ. Sci. Eng. China, 7 , pp. 577, 2019. @article{Welch2019-dc, title = {Submarine Groundwater Discharge and Stream Baseflow Sustain Pesticide and Nutrient Fluxes in Faga'alu Bay, American Samoa}, author = {Eric M Welch and Henrietta Dulai and Aly El-Kadi and Christopher K Shuler}, year = {2019}, date = {2019-01-01}, journal = {Front. Environ. Sci. Eng. China}, volume = {7}, pages = {577}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Bremer, Leah L; Farley, Kathleen A; DeMaagd, Nathan; Suárez, Esteban; Tandalla, Daisy Cárate; Tapia, Sebastián Vasco; Vásconez, Patricio Mena Biodiversity outcomes of payment for ecosystem services: lessons from páramo grasslands Journal Article Biodivers. Conserv., 28 (4), pp. 885–908, 2019. @article{Bremer2019-xh, title = {Biodiversity outcomes of payment for ecosystem services: lessons from páramo grasslands}, author = {Leah L Bremer and Kathleen A Farley and Nathan DeMaagd and Esteban Suárez and Daisy Cárate Tandalla and Sebastián Vasco Tapia and Patricio Mena Vásconez}, year = {2019}, date = {2019-01-01}, journal = {Biodivers. Conserv.}, volume = {28}, number = {4}, pages = {885--908}, abstract = {As payment for ecosystem services (PES) programs grow around the world, so have concerns over whether a focus on ecosystem services will also protect biodiversity. Biodiverse Ecuadorian páramo grasslands have become a hotspot for PES in an effort to protect water supplies, sequester carbon, conserve biodiversity, and improve rural livelihoods. However, the outcomes of PES-incentivized land management, particularly burn exclusion, on plant communities and their associated ecosystem services remain poorly understood. To address this science-policy gap, we evaluated plant richness and number and cover of the ten major páramo growth forms in two study areas with chronosequences of burn exclusion. Both species richness and number of growth forms was highest in sites with intermediate times-since-last burn and the cover of tussock grasses---critical to protecting soils and maintaining hydrologic function---recovered within 3--6 years after fire at both study areas, suggesting that PES programs targeting hydrologic services do not need to exclude burning to ensure adequate vegetation cover over the long-term. However, shrub growth forms were slower to recover, indicating that conserving the plant composition characteristic of less disturbed páramos requires some protection from burning. Findings provide broad lessons for PES programs focused on both biodiversity and ecosystem services and point to the importance of clearly defining PES ecological goals since land-use prescriptions may differ depending on the management objective.}, keywords = {}, pubstate = {published}, tppubtype = {article} } As payment for ecosystem services (PES) programs grow around the world, so have concerns over whether a focus on ecosystem services will also protect biodiversity. Biodiverse Ecuadorian páramo grasslands have become a hotspot for PES in an effort to protect water supplies, sequester carbon, conserve biodiversity, and improve rural livelihoods. However, the outcomes of PES-incentivized land management, particularly burn exclusion, on plant communities and their associated ecosystem services remain poorly understood. To address this science-policy gap, we evaluated plant richness and number and cover of the ten major páramo growth forms in two study areas with chronosequences of burn exclusion. Both species richness and number of growth forms was highest in sites with intermediate times-since-last burn and the cover of tussock grasses---critical to protecting soils and maintaining hydrologic function---recovered within 3--6 years after fire at both study areas, suggesting that PES programs targeting hydrologic services do not need to exclude burning to ensure adequate vegetation cover over the long-term. However, shrub growth forms were slower to recover, indicating that conserving the plant composition characteristic of less disturbed páramos requires some protection from burning. Findings provide broad lessons for PES programs focused on both biodiversity and ecosystem services and point to the importance of clearly defining PES ecological goals since land-use prescriptions may differ depending on the management objective. |
Beck, Hannah N; Cohen, Ashley; McKenzie, Trista; Weisend, Rachel; Wilkins, Keiko W; Woodstock, Matthew S Broadening Horizons: Graduate Students Participating in International Collaborations through the Limnology and Oceanography Research Exchange (LOREX) Program Journal Article Limnol. Oceanog. Bull., 28 (3), pp. 85–89, 2019. @article{Beck2019-xa, title = {Broadening Horizons: Graduate Students Participating in International Collaborations through the Limnology and Oceanography Research Exchange (LOREX) Program}, author = {Hannah N Beck and Ashley Cohen and Trista McKenzie and Rachel Weisend and Keiko W Wilkins and Matthew S Woodstock}, year = {2019}, date = {2019-01-01}, journal = {Limnol. Oceanog. Bull.}, volume = {28}, number = {3}, pages = {85--89}, abstract = {Abstract International research is necessary in aquatic sciences because water moves across borders. Historically, international collaborations have been useful in conducting oceanographic research programs, which span large distances and require several funding sources. Although valuable, international research can have unforeseen challenges to the unprepared researcher. Communication with an international collaborator and professional development training can mitigate these pitfalls. The Limnology and Oceanography Research Exchange Program (LOREX) is an opportunity for graduate students to gain experience developing international collaborations. The LOREX program aims to help graduate students develop connections and gain experience in international research. During the summer of 2019 and spring of 2020, 26 graduate students from 24 U.S. institutions will travel to one of six different host institutions to conduct a research project that they developed with an international collaborator. To prepare for their research experience, LOREX participants participated in training programs during the 2019 Aquatic Sciences Meeting in San Juan, Puerto Rico. The first group of LOREX graduate students will share their experience through social media and blog posts throughout their journey. Applications are now open for the second cohort of LOREX participants, and potential applicants are encouraged to contact potential collaborators to develop a research project.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Abstract International research is necessary in aquatic sciences because water moves across borders. Historically, international collaborations have been useful in conducting oceanographic research programs, which span large distances and require several funding sources. Although valuable, international research can have unforeseen challenges to the unprepared researcher. Communication with an international collaborator and professional development training can mitigate these pitfalls. The Limnology and Oceanography Research Exchange Program (LOREX) is an opportunity for graduate students to gain experience developing international collaborations. The LOREX program aims to help graduate students develop connections and gain experience in international research. During the summer of 2019 and spring of 2020, 26 graduate students from 24 U.S. institutions will travel to one of six different host institutions to conduct a research project that they developed with an international collaborator. To prepare for their research experience, LOREX participants participated in training programs during the 2019 Aquatic Sciences Meeting in San Juan, Puerto Rico. The first group of LOREX graduate students will share their experience through social media and blog posts throughout their journey. Applications are now open for the second cohort of LOREX participants, and potential applicants are encouraged to contact potential collaborators to develop a research project. |
Starkus, J; Jansen, C; Shimoda, L M N; Stokes, A J; Small-Howard, A L; Turner, H Diverse TRPV1 responses to cannabinoids Journal Article Channels, 13 (1), pp. 172–191, 2019. @article{Starkus2019-mr, title = {Diverse TRPV1 responses to cannabinoids}, author = {J Starkus and C Jansen and L M N Shimoda and A J Stokes and A L Small-Howard and H Turner}, year = {2019}, date = {2019-01-01}, journal = {Channels}, volume = {13}, number = {1}, pages = {172--191}, publisher = {Taylor & Francis}, abstract = {ABSTRACTCannabinoid compounds are potential analgesics. Users of medicinal Cannabis report efficacy for pain control, clinical studies show that cannabis can be effective and opioid sparing in chronic pain, and some constituent cannabinoids have been shown to target nociceptive ion channels. Here, we explore and compare a suite of cannabinoids for their impact upon the physiology of TRPV1. The cannabinoids tested evoke differential responses in terms of kinetics of activation and inactivation. Cannabinoid activation of TRPV1 displays significant dependence on internal and external calcium levels. Cannabinoid activation of TRPV1 does not appear to induce the highly permeant, pore-dilated channel state seen with Capsaicin, even at high current amplitudes. Finally, we analyzed cannabinoid responses at nociceptive channels other than TRPV1 (TRPV2, TRPM8, and TRPA1), and report that cannabinoids differentially activate these channels. On the basis of response activation and kinetics, state-selectivity and receptor selectivity, it may be possible to rationally design approaches to pain using single or multiple cannabinoids.}, keywords = {}, pubstate = {published}, tppubtype = {article} } ABSTRACTCannabinoid compounds are potential analgesics. Users of medicinal Cannabis report efficacy for pain control, clinical studies show that cannabis can be effective and opioid sparing in chronic pain, and some constituent cannabinoids have been shown to target nociceptive ion channels. Here, we explore and compare a suite of cannabinoids for their impact upon the physiology of TRPV1. The cannabinoids tested evoke differential responses in terms of kinetics of activation and inactivation. Cannabinoid activation of TRPV1 displays significant dependence on internal and external calcium levels. Cannabinoid activation of TRPV1 does not appear to induce the highly permeant, pore-dilated channel state seen with Capsaicin, even at high current amplitudes. Finally, we analyzed cannabinoid responses at nociceptive channels other than TRPV1 (TRPV2, TRPM8, and TRPA1), and report that cannabinoids differentially activate these channels. On the basis of response activation and kinetics, state-selectivity and receptor selectivity, it may be possible to rationally design approaches to pain using single or multiple cannabinoids. |
Reimann-Philipp, Ulrich; Speck, Mark; Orser, Cindy; Johnson, Steve; Hilyard, Aaron; Turner, Helen; Stokes, Alexander J; Small-Howard, Andrea L Cannabis Chemovar Nomenclature Misrepresents Chemical and Genetic Diversity; Survey of Variations in Chemical Profiles and Genetic Markers in Nevada Medical Cannabis Samples Journal Article Cannabis and Cannabinoid Research, 2019. @article{Reimann-Philipp2019-tm, title = {Cannabis Chemovar Nomenclature Misrepresents Chemical and Genetic Diversity; Survey of Variations in Chemical Profiles and Genetic Markers in Nevada Medical Cannabis Samples}, author = {Ulrich Reimann-Philipp and Mark Speck and Cindy Orser and Steve Johnson and Aaron Hilyard and Helen Turner and Alexander J Stokes and Andrea L Small-Howard}, year = {2019}, date = {2019-01-01}, journal = {Cannabis and Cannabinoid Research}, publisher = {Mary Ann Liebert, Inc., publishers 140 Huguenot Street, 3rd Floor New …}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Adolf, Jason E; Burns, John; Walker, Judy K; Gamiao, Sydney Near shore distributions of phytoplankton and bacteria in relation to submarine groundwater discharge-fed fishponds, Kona coast, Hawai`i, USA Journal Article Estuar. Coast. Shelf Sci., 219 , pp. 341–353, 2019. @article{Adolf2019-ci, title = {Near shore distributions of phytoplankton and bacteria in relation to submarine groundwater discharge-fed fishponds, Kona coast, Hawai`i, USA}, author = {Jason E Adolf and John Burns and Judy K Walker and Sydney Gamiao}, year = {2019}, date = {2019-01-01}, journal = {Estuar. Coast. Shelf Sci.}, volume = {219}, pages = {341--353}, abstract = {Phytoplankton are important components of coastal marine ecosystems that are strongly influenced by freshwater inputs from land, including submarine groundwater discharge (SGD). Although SGD generates sharp onshore -- offshore gradients in physical and chemical conditions at several locations around Hawaii Island little is known about the biotic responses of water column microbes to these conditions. We studied the distributions of phytoplankton and bacteria at two contrasting sites with SGD-fed fishponds, Kiholo and Kaloko Bay, including the full range of salinity extending from the fishponds to the coastal ocean. We addressed the hypotheses that (1) SGD-fed fishponds support a higher biomass and different composition of phytoplankton than the adjacent ocean, and (2) phytoplankton biomass and composition are related to SGD-driven salinity gradients in the coastal ocean. Phytoplankton biomass in fishponds was elevated (10--100-fold) and accompanied by higher average cell size pico- and nano-phytoplankton (2--6 $mu$m) relative to sites outside the fishpond. General additive models (GAMs) showed elevated biomass and average cell size at mid-range salinities and declining biomass at salinity < 20 outside the fishponds. Multivariate RDA showed significant, site-specific relationships between surface phytoplankton biomass (Chl a), cell counts, and environmental parameters. Analysis of surface vs. deep samples from outside the fishponds showed elevated phytoplankton biomass at the surface, except in Kiholo lagoon where phytoplankton was elevated beneath the SGD-driven pycnocline. This study shows structuring of coastal phytoplankton through SGD inputs and suggest that changes in SGD due to coastal development or climate change can impact coastal marine ecosystems through effects on phytoplankton communities.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Phytoplankton are important components of coastal marine ecosystems that are strongly influenced by freshwater inputs from land, including submarine groundwater discharge (SGD). Although SGD generates sharp onshore -- offshore gradients in physical and chemical conditions at several locations around Hawaii Island little is known about the biotic responses of water column microbes to these conditions. We studied the distributions of phytoplankton and bacteria at two contrasting sites with SGD-fed fishponds, Kiholo and Kaloko Bay, including the full range of salinity extending from the fishponds to the coastal ocean. We addressed the hypotheses that (1) SGD-fed fishponds support a higher biomass and different composition of phytoplankton than the adjacent ocean, and (2) phytoplankton biomass and composition are related to SGD-driven salinity gradients in the coastal ocean. Phytoplankton biomass in fishponds was elevated (10--100-fold) and accompanied by higher average cell size pico- and nano-phytoplankton (2--6 $mu$m) relative to sites outside the fishpond. General additive models (GAMs) showed elevated biomass and average cell size at mid-range salinities and declining biomass at salinity < 20 outside the fishponds. Multivariate RDA showed significant, site-specific relationships between surface phytoplankton biomass (Chl a), cell counts, and environmental parameters. Analysis of surface vs. deep samples from outside the fishponds showed elevated phytoplankton biomass at the surface, except in Kiholo lagoon where phytoplankton was elevated beneath the SGD-driven pycnocline. This study shows structuring of coastal phytoplankton through SGD inputs and suggest that changes in SGD due to coastal development or climate change can impact coastal marine ecosystems through effects on phytoplankton communities. |
Fukunaga, Atsuko; Burns, John H R; Craig, Brianna K; Kosaki, Randall K Integrating Three-Dimensional Benthic Habitat Characterization Techniques into Ecological Monitoring of Coral Reefs Journal Article J. Mar. Sci. Eng., 7 (2), pp. 27, 2019. @article{Fukunaga2019-ep, title = {Integrating Three-Dimensional Benthic Habitat Characterization Techniques into Ecological Monitoring of Coral Reefs}, author = {Atsuko Fukunaga and John H R Burns and Brianna K Craig and Randall K Kosaki}, year = {2019}, date = {2019-01-01}, journal = {J. Mar. Sci. Eng.}, volume = {7}, number = {2}, pages = {27}, publisher = {Multidisciplinary Digital Publishing Institute}, abstract = {Long-term ecological monitoring of reef fish populations often requires the simultaneous collection of data on benthic habitats in order to account for the effects of these variables on fish assemblage structure. Here, we described an approach to benthic surveys that uses photogrammetric techniques to facilitate the extraction of quantitative metrics for characterization of benthic habitats from the resulting three-dimensional (3D) reconstruction of coral reefs. Out of 92 sites surveyed in the Northwestern Hawaiian Islands, photographs from 85 sites achieved complete alignment and successfully produced 3D reconstructions and digital elevation models (DEMs). Habitat metrics extracted from the DEMs were generally correlated with one another, with the exception of curvature measures, indicating that complexity and curvature measures should be treated separately when quantifying the habitat structure. Fractal dimension D64, calculated by changing resolutions of the DEMs from 1 cm to 64 cm, had the best correlations with other habitat metrics. Fractal dimension was also less affected by changes in orientations of the models compared to surface complexity or slope. These results showed that fractal dimension can be used as a single measure of complexity for the characterization of coral reef habitats. Further investigations into metrics for 3D characterization of habitats should consider relevant spatial scales and focus on obtaining variables that can complement fractal dimension in the characterization of reef habitats.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Long-term ecological monitoring of reef fish populations often requires the simultaneous collection of data on benthic habitats in order to account for the effects of these variables on fish assemblage structure. Here, we described an approach to benthic surveys that uses photogrammetric techniques to facilitate the extraction of quantitative metrics for characterization of benthic habitats from the resulting three-dimensional (3D) reconstruction of coral reefs. Out of 92 sites surveyed in the Northwestern Hawaiian Islands, photographs from 85 sites achieved complete alignment and successfully produced 3D reconstructions and digital elevation models (DEMs). Habitat metrics extracted from the DEMs were generally correlated with one another, with the exception of curvature measures, indicating that complexity and curvature measures should be treated separately when quantifying the habitat structure. Fractal dimension D64, calculated by changing resolutions of the DEMs from 1 cm to 64 cm, had the best correlations with other habitat metrics. Fractal dimension was also less affected by changes in orientations of the models compared to surface complexity or slope. These results showed that fractal dimension can be used as a single measure of complexity for the characterization of coral reef habitats. Further investigations into metrics for 3D characterization of habitats should consider relevant spatial scales and focus on obtaining variables that can complement fractal dimension in the characterization of reef habitats. |
Jerram, Dougal A; Millett, John M; Kück, Jochem; Thomas, Donald; Planke, Sverre; Haskins, Eric; Lautze, Nicole; Pierdominici, Simona Understanding volcanic facies in the subsurface: a combined core, wireline logging and image log data set from the PTA2 and KMA1 boreholes, Big Island, Hawai`i Journal Article Sci. Drill., 25 , pp. 15–33, 2019. @article{Jerram2019-tn, title = {Understanding volcanic facies in the subsurface: a combined core, wireline logging and image log data set from the PTA2 and KMA1 boreholes, Big Island, Hawai`i}, author = {Dougal A Jerram and John M Millett and Jochem Kück and Donald Thomas and Sverre Planke and Eric Haskins and Nicole Lautze and Simona Pierdominici}, year = {2019}, date = {2019-01-01}, journal = {Sci. Drill.}, volume = {25}, pages = {15--33}, publisher = {Copernicus GmbH}, abstract = {Abstract. To help understand volcanic facies in the subsurface, data sets that enable detailed comparisons between down-hole geophysical data and cored volcanic intervals are critical. However, in many cases, the collection of extended core intervals within volcanic sequences is rare and often incomplete due to challenging coring conditions. In this contribution we outline and provide initial results from borehole logging operations within two fully cored lava-dominated borehole sequences, PTA2 and KMA1, on the Big Island of Hawai`i. Data for spectral gamma, magnetic susceptibility, dipmeter resistivity, sonic, total magnetic field, temperature and televiewer wireline logs were successfully acquired for the open hole interval ca. 889 m to 1567 m within the PTA2 borehole. Spectral gamma was also collected from inside the casing of both wells, extending the coverage for PTA2 to the surface and covering the interval from ca. 300 to 1200 m for KMA1. High-quality core material was available for both boreholes with almost complete recovery which enabled high-resolution core-to-log integration. Gamma data are generally low commonly in the range ca. 7--20 gAPI but are shown to increase up to API of ca. 60 with some intrusions and with increases in hawaiite compositions in the upper part of PTA2. Velocity data are more variable due to alteration within porous volcanic facies than with burial depth, with a general degrease down-hole. The high-resolution televiewer data have been compared directly to the core, enabling a comprehensive analysis of the variations in the televiewer responses. This has enabled the identification of key features including individual vesicles, vesicle segregations, strained vesicles, chilled margins, rubble zones, intrusive contacts and p=ahoehoe lobe morphologies, which can be confidently matched between the televiewer data and the full diameter core. The data set and results of this study include findings which should enable improved borehole facies analysis through volcanic sequences in the future, especially where down-borehole data and images but no core are available.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Abstract. To help understand volcanic facies in the subsurface, data sets that enable detailed comparisons between down-hole geophysical data and cored volcanic intervals are critical. However, in many cases, the collection of extended core intervals within volcanic sequences is rare and often incomplete due to challenging coring conditions. In this contribution we outline and provide initial results from borehole logging operations within two fully cored lava-dominated borehole sequences, PTA2 and KMA1, on the Big Island of Hawai`i. Data for spectral gamma, magnetic susceptibility, dipmeter resistivity, sonic, total magnetic field, temperature and televiewer wireline logs were successfully acquired for the open hole interval ca. 889 m to 1567 m within the PTA2 borehole. Spectral gamma was also collected from inside the casing of both wells, extending the coverage for PTA2 to the surface and covering the interval from ca. 300 to 1200 m for KMA1. High-quality core material was available for both boreholes with almost complete recovery which enabled high-resolution core-to-log integration. Gamma data are generally low commonly in the range ca. 7--20 gAPI but are shown to increase up to API of ca. 60 with some intrusions and with increases in hawaiite compositions in the upper part of PTA2. Velocity data are more variable due to alteration within porous volcanic facies than with burial depth, with a general degrease down-hole. The high-resolution televiewer data have been compared directly to the core, enabling a comprehensive analysis of the variations in the televiewer responses. This has enabled the identification of key features including individual vesicles, vesicle segregations, strained vesicles, chilled margins, rubble zones, intrusive contacts and p=ahoehoe lobe morphologies, which can be confidently matched between the televiewer data and the full diameter core. The data set and results of this study include findings which should enable improved borehole facies analysis through volcanic sequences in the future, especially where down-borehole data and images but no core are available. |
Battistel, Maria; Muniruzzaman, Muhammad; Onses, Felix; Lee, Jonghyun; Rolle, Massimo Reactive fronts in chemically heterogeneous porous media: Experimental and modeling investigation of pyrite oxidation Journal Article Appl. Geochem., 100 , pp. 77–89, 2019. @article{Battistel2019-zf, title = {Reactive fronts in chemically heterogeneous porous media: Experimental and modeling investigation of pyrite oxidation}, author = {Maria Battistel and Muhammad Muniruzzaman and Felix Onses and Jonghyun Lee and Massimo Rolle}, year = {2019}, date = {2019-01-01}, journal = {Appl. Geochem.}, volume = {100}, pages = {77--89}, abstract = {The spatial distribution of reactive minerals in subsurface porous media is an important control for groundwater quality. In this study we investigate pyrite oxidation reactive fronts in chemically heterogeneous porous media by combining laboratory experiments and reactive transport modeling. We performed experiments in different setups including batch, 1-D column, and 2-D flow-through systems. The flow-through experiments were performed in physically homogenous but chemically heterogeneous domains with embedded reactive pyrite inclusions at different spatial locations and with different concentrations. The setups were initially maintained under anoxic conditions and subsequently flushed with an inflowing oxic solution. A non-invasive optode technique was used for high-resolution monitoring of oxygen. This allowed us to capture the dynamics of the reactive oxygen fronts in the 1-D columns and in the 2-D flow-through chamber. Water quality analyses of the products of pyrite oxidation, iron (Fe) and sulfur (S), were also carried out in the different setups. The concentration of these species released in the 1-D columns (up to 6.2 $times$ 10−5 mol/L Fe and 13.7 $times$ 10−5 mol/L S) and in the 2-D setup (up to 3 $times$ 10−6 mol/L Fe and 9 $times$ 10−6 mol/L S) could be quantitatively related to the consumption of oxygen (up to 1.9 $times$ 10−4 mol/L consumed in the 1-D and 2-D setups). The reaction rates were found to be different between the setups and dependent on the spatial location and concentration of the pyrite inclusions. A modeling approach coupling 1-D and 2-D transport codes with the geochemical simulator PHREEQC is proposed to simulate the spatial and temporal dynamics of oxygen transport, the kinetics of pyrite oxidative dissolution, and the changes in water quality in the chemically heterogeneous flow-through setups. The model allowed the quantitative interpretation of the experimental results and represents a valuable tool to capture the coupling between multidimensional transport and geochemical reactions both in laboratory and in field scale applications.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The spatial distribution of reactive minerals in subsurface porous media is an important control for groundwater quality. In this study we investigate pyrite oxidation reactive fronts in chemically heterogeneous porous media by combining laboratory experiments and reactive transport modeling. We performed experiments in different setups including batch, 1-D column, and 2-D flow-through systems. The flow-through experiments were performed in physically homogenous but chemically heterogeneous domains with embedded reactive pyrite inclusions at different spatial locations and with different concentrations. The setups were initially maintained under anoxic conditions and subsequently flushed with an inflowing oxic solution. A non-invasive optode technique was used for high-resolution monitoring of oxygen. This allowed us to capture the dynamics of the reactive oxygen fronts in the 1-D columns and in the 2-D flow-through chamber. Water quality analyses of the products of pyrite oxidation, iron (Fe) and sulfur (S), were also carried out in the different setups. The concentration of these species released in the 1-D columns (up to 6.2 $times$ 10−5 mol/L Fe and 13.7 $times$ 10−5 mol/L S) and in the 2-D setup (up to 3 $times$ 10−6 mol/L Fe and 9 $times$ 10−6 mol/L S) could be quantitatively related to the consumption of oxygen (up to 1.9 $times$ 10−4 mol/L consumed in the 1-D and 2-D setups). The reaction rates were found to be different between the setups and dependent on the spatial location and concentration of the pyrite inclusions. A modeling approach coupling 1-D and 2-D transport codes with the geochemical simulator PHREEQC is proposed to simulate the spatial and temporal dynamics of oxygen transport, the kinetics of pyrite oxidative dissolution, and the changes in water quality in the chemically heterogeneous flow-through setups. The model allowed the quantitative interpretation of the experimental results and represents a valuable tool to capture the coupling between multidimensional transport and geochemical reactions both in laboratory and in field scale applications. |
Taniguchi, Makoto; Burnett, Kimberly M; Shimada, Jun; Hosono, Takahiro; Wada, Christopher A; Ide, Kiyoshi Recovery of Lost Nexus Synergy via Payment for Environmental Services in Kumamoto, Japan Journal Article Front. Environ. Sci. Eng. China, 7 , pp. 28, 2019. @article{Taniguchi2019-xv, title = {Recovery of Lost Nexus Synergy via Payment for Environmental Services in Kumamoto, Japan}, author = {Makoto Taniguchi and Kimberly M Burnett and Jun Shimada and Takahiro Hosono and Christopher A Wada and Kiyoshi Ide}, year = {2019}, date = {2019-01-01}, journal = {Front. Environ. Sci. Eng. China}, volume = {7}, pages = {28}, abstract = {The objective of this study is to characterize and quantify the ``trans-spatial nexus synergy'' benefit of subsidized water ponding in the water-energy-food nexus in Kumamoto, Japan. After years of decreased rice production in upstream areas and associated declines in groundwater levels, the Kumamoto city government implemented a subsidy program whereby farmers in the Shira River basin receive payments to water their fields, which provides valuable groundwater recharge to downstream Kumamoto city. We quantify the economic benefits of this subsidy program, which include avoided additional energy costs to obtain scarcer levels of groundwater, as well as net revenue from the crops in the Shira River basin that would otherwise not be grown in the absence of the subsidy. These annual benefits can be combined and compared to the annual cost of the government subsidy. We also calculate potential historical losses that may have occurred in the region as a result of land use transitions from rice farming to urban use, which disrupted the nexus synergy between the watered fields and the groundwater table.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The objective of this study is to characterize and quantify the ``trans-spatial nexus synergy'' benefit of subsidized water ponding in the water-energy-food nexus in Kumamoto, Japan. After years of decreased rice production in upstream areas and associated declines in groundwater levels, the Kumamoto city government implemented a subsidy program whereby farmers in the Shira River basin receive payments to water their fields, which provides valuable groundwater recharge to downstream Kumamoto city. We quantify the economic benefits of this subsidy program, which include avoided additional energy costs to obtain scarcer levels of groundwater, as well as net revenue from the crops in the Shira River basin that would otherwise not be grown in the absence of the subsidy. These annual benefits can be combined and compared to the annual cost of the government subsidy. We also calculate potential historical losses that may have occurred in the region as a result of land use transitions from rice farming to urban use, which disrupted the nexus synergy between the watered fields and the groundwater table. |
Magel, Jennifer M T; Burns, John H R; Gates, Ruth D; Baum, Julia K Effects of bleaching-associated mass coral mortality on reef structural complexity across a gradient of local disturbance Journal Article Sci. Rep., 9 (1), pp. 2512, 2019. @article{Magel2019-zm, title = {Effects of bleaching-associated mass coral mortality on reef structural complexity across a gradient of local disturbance}, author = {Jennifer M T Magel and John H R Burns and Ruth D Gates and Julia K Baum}, year = {2019}, date = {2019-01-01}, journal = {Sci. Rep.}, volume = {9}, number = {1}, pages = {2512}, abstract = {Structural complexity underpins the ecological functioning of coral reefs. However, rising ocean temperatures and associated coral bleaching threaten the structural integrity of these important ecosystems. Despite the increased frequency of coral bleaching events, few studies to date have examined changes in three-dimensional (3D) reef structural complexity following severe bleaching. The influence of local stressors on reef complexity also remains poorly understood. In the wake of the 2015-2016 El Ni~no-induced mass coral bleaching event, we quantified the effects of severe heat stress on 3D reef structural complexity across a gradient of local human disturbance. Using Structure-from-Motion photogrammetry we created 3D reconstructions of permanent reef plots and observed substantial declines in reef structural complexity, measured as surface rugosity and terrain ruggedness, and a detectable loss of habitat volume one year after the bleaching event. 3D reef complexity also declined with increasing levels of human disturbance, and with decreasing densities of branching and massive corals. These findings improve our understanding of the effects of local and global stressors on the structural foundation of coral reef ecosystems. In the face of accelerating climate change, mitigating local stressors may increase reef structural complexity, thereby heightening reef resilience to future bleaching events.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Structural complexity underpins the ecological functioning of coral reefs. However, rising ocean temperatures and associated coral bleaching threaten the structural integrity of these important ecosystems. Despite the increased frequency of coral bleaching events, few studies to date have examined changes in three-dimensional (3D) reef structural complexity following severe bleaching. The influence of local stressors on reef complexity also remains poorly understood. In the wake of the 2015-2016 El Ni~no-induced mass coral bleaching event, we quantified the effects of severe heat stress on 3D reef structural complexity across a gradient of local human disturbance. Using Structure-from-Motion photogrammetry we created 3D reconstructions of permanent reef plots and observed substantial declines in reef structural complexity, measured as surface rugosity and terrain ruggedness, and a detectable loss of habitat volume one year after the bleaching event. 3D reef complexity also declined with increasing levels of human disturbance, and with decreasing densities of branching and massive corals. These findings improve our understanding of the effects of local and global stressors on the structural foundation of coral reef ecosystems. In the face of accelerating climate change, mitigating local stressors may increase reef structural complexity, thereby heightening reef resilience to future bleaching events. |
Bottjer-Wilson, Daniela; Bruno, Barbara C Place Matters! Fostering place-based geoscience teaching at the University of Hawai`i at M=anoa Inproceedings Fifth International Conference on Higher Education Advances, 2019. @inproceedings{Bottjer-Wilson2019-ap, title = {Place Matters! Fostering place-based geoscience teaching at the University of Hawai`i at M=anoa}, author = {Daniela Bottjer-Wilson and Barbara C Bruno}, year = {2019}, date = {2019-01-01}, booktitle = {Fifth International Conference on Higher Education Advances}, abstract = {Drawing on the importance of place has been shown to be a powerful tool in education. This paper explores place-based teaching (PBT) in geoscience courses at the University of Hawai`i at M=anoa's School of Ocean and Earth Science and Technology, where faculty and student demographics sharply differ. Despite these differences, survey results from geoscience faculty (n=59) and students (n=83) revealed a strong consensus: 78% of students and 83% of faculty reported that PBT is an important and effective practice to reach all students. Most faculty (91%) indicated that they currently incorporate at least some PBT practices in their geoscience classes and would like to incorporate additional ones in the future. However, many faculty expressed concern about lack of knowledge or resources, particularly regarding PBT strategies that require a high level of cultural competency. We therefore propose a three-layered PBT framework, where faculty can start with more accessible PBT strategies (the base layer) and progress upwards as their cultural competency deepens. Through providing geoscience resources and professional development opportunities, we can empower faculty to include more diverse and culturally meaningful practices as their experience and knowledge deepens.}, keywords = {}, pubstate = {published}, tppubtype = {inproceedings} } Drawing on the importance of place has been shown to be a powerful tool in education. This paper explores place-based teaching (PBT) in geoscience courses at the University of Hawai`i at M=anoa's School of Ocean and Earth Science and Technology, where faculty and student demographics sharply differ. Despite these differences, survey results from geoscience faculty (n=59) and students (n=83) revealed a strong consensus: 78% of students and 83% of faculty reported that PBT is an important and effective practice to reach all students. Most faculty (91%) indicated that they currently incorporate at least some PBT practices in their geoscience classes and would like to incorporate additional ones in the future. However, many faculty expressed concern about lack of knowledge or resources, particularly regarding PBT strategies that require a high level of cultural competency. We therefore propose a three-layered PBT framework, where faculty can start with more accessible PBT strategies (the base layer) and progress upwards as their cultural competency deepens. Through providing geoscience resources and professional development opportunities, we can empower faculty to include more diverse and culturally meaningful practices as their experience and knowledge deepens. |
Goldberg, David M; Hong, Sukhwa Minimizing the Risks of Highway Transport of Hazardous Materials Journal Article Sustain. Sci. Pract. Policy, 11 (22), pp. 6300, 2019. @article{Goldberg2019-yz, title = {Minimizing the Risks of Highway Transport of Hazardous Materials}, author = {David M Goldberg and Sukhwa Hong}, year = {2019}, date = {2019-01-01}, journal = {Sustain. Sci. Pract. Policy}, volume = {11}, number = {22}, pages = {6300}, publisher = {Multidisciplinary Digital Publishing Institute}, abstract = {Many key industrial and scientific processes, such as the generation of nuclear energy, are of enormous social benefit as energy demand and consumption grow over time. However, a drawback of several such processes is the production of hazardous waste materials, which often requires transportation along highway networks to treatment or disposal facilities. This waste can represent a safety hazard to civilians located along the transportation route. Most prior literature in this domain considers risk within only a single facet, and thus several important risk factors may not be considered. In our paper, we propose a multi-objective program to allow for the analysis and selection of minimally risky routes for hazardous materials transportation. The model assesses risk factors including the length of the selected route, the total population in areas surrounding the selected route, and the likelihood of an accident occurring along the selected route. Our paper uniquely uses geographic information systems (GIS) technology to model this optimization problem. This approach allows us to model risk along multiple dimensions simultaneously. We collect empirical data to test the model and present a case study for risk mitigation using a study area located in California. We show that our multi-objective approach is effective in presenting the decision-maker with a portfolio of solutions that perform well via each factor.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Many key industrial and scientific processes, such as the generation of nuclear energy, are of enormous social benefit as energy demand and consumption grow over time. However, a drawback of several such processes is the production of hazardous waste materials, which often requires transportation along highway networks to treatment or disposal facilities. This waste can represent a safety hazard to civilians located along the transportation route. Most prior literature in this domain considers risk within only a single facet, and thus several important risk factors may not be considered. In our paper, we propose a multi-objective program to allow for the analysis and selection of minimally risky routes for hazardous materials transportation. The model assesses risk factors including the length of the selected route, the total population in areas surrounding the selected route, and the likelihood of an accident occurring along the selected route. Our paper uniquely uses geographic information systems (GIS) technology to model this optimization problem. This approach allows us to model risk along multiple dimensions simultaneously. We collect empirical data to test the model and present a case study for risk mitigation using a study area located in California. We show that our multi-objective approach is effective in presenting the decision-maker with a portfolio of solutions that perform well via each factor. |
Misra, Anupam K; Acosta-Maeda, Tayro E; Porter, John N; Egan, Miles J; Sandford, Macey W; Oyama, Tamra; Zhou, Jie Remote Raman Detection of Chemicals from 1752 m During Afternoon Daylight Journal Article Appl. Spectrosc., pp. 3702819875437, 2019. @article{Misra2019-aj, title = {Remote Raman Detection of Chemicals from 1752 m During Afternoon Daylight}, author = {Anupam K Misra and Tayro E Acosta-Maeda and John N Porter and Miles J Egan and Macey W Sandford and Tamra Oyama and Jie Zhou}, year = {2019}, date = {2019-01-01}, journal = {Appl. Spectrosc.}, pages = {3702819875437}, abstract = {The detection and identification of materials from a distance is highly desirable for applications where accessibility is limited or there are safety concerns. Raman spectroscopy can be performed remotely and provides a very high level of confidence in detection of chemicals through vibrational modes. However, the remote Raman detection of chemicals is challenging because of the very weak nature of Raman signals. Using a remote Raman system, we performed fast remote detection of various solid and liquid chemicals from 1752 m during afternoon hours on a sunny day in Hawaii. Remote Raman systems with kilometer target range could be useful for chemical detection of volcanic gases, methane clathrate icebergs or fire ice, toxic gas clouds and toxic waste, explosives, and hazardous chemicals. With this successful test, we demonstrate the feasibility of developing future mid-size remote Raman systems suitable for long range chemical detection using helicopters and light airplanes.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The detection and identification of materials from a distance is highly desirable for applications where accessibility is limited or there are safety concerns. Raman spectroscopy can be performed remotely and provides a very high level of confidence in detection of chemicals through vibrational modes. However, the remote Raman detection of chemicals is challenging because of the very weak nature of Raman signals. Using a remote Raman system, we performed fast remote detection of various solid and liquid chemicals from 1752 m during afternoon hours on a sunny day in Hawaii. Remote Raman systems with kilometer target range could be useful for chemical detection of volcanic gases, methane clathrate icebergs or fire ice, toxic gas clouds and toxic waste, explosives, and hazardous chemicals. With this successful test, we demonstrate the feasibility of developing future mid-size remote Raman systems suitable for long range chemical detection using helicopters and light airplanes. |
2018 |
Bremer, Leah L; Brauman, Kate A; Nelson, Sara; Prado, Kelly Meza; Wilburn, Eric; Fiorini, Ana Carolina O Relational values in evaluations of upstream social outcomes of watershed Payment for Ecosystem Services: a review Journal Article Current Opinion in Environmental Sustainability, 35 , pp. 116–123, 2018. @article{Bremer2018-hx, title = {Relational values in evaluations of upstream social outcomes of watershed Payment for Ecosystem Services: a review}, author = {Leah L Bremer and Kate A Brauman and Sara Nelson and Kelly Meza Prado and Eric Wilburn and Ana Carolina O Fiorini}, year = {2018}, date = {2018-12-01}, journal = {Current Opinion in Environmental Sustainability}, volume = {35}, pages = {116--123}, abstract = {Relational values associated with meaningful and just human--environment relationships (e.g. care and responsibility) have been proposed as motivating `upstream' participation in Payments for Watershed Services (PWS). However, the way relational values are affected by and interact with PWS remains poorly understood. We reviewed 50 studies of social outcomes of PWS and found that approximately half assessed or discussed relational values. This included changes in relational values presented positively, such as amplifying values and norms around care for land; negatively, such as undermining traditional practices and intergenerational learning; and influencing other outcomes, such as links between land ties and human health. To improve understanding of the full suite of outcomes linked to the effectiveness, durability, and equity of PWS, we propose a research agenda based on locally-based relational value systems that include, for example, place-based conceptualizations of responsibility, care, and relation to the natural world.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Relational values associated with meaningful and just human--environment relationships (e.g. care and responsibility) have been proposed as motivating `upstream' participation in Payments for Watershed Services (PWS). However, the way relational values are affected by and interact with PWS remains poorly understood. We reviewed 50 studies of social outcomes of PWS and found that approximately half assessed or discussed relational values. This included changes in relational values presented positively, such as amplifying values and norms around care for land; negatively, such as undermining traditional practices and intergenerational learning; and influencing other outcomes, such as links between land ties and human health. To improve understanding of the full suite of outcomes linked to the effectiveness, durability, and equity of PWS, we propose a research agenda based on locally-based relational value systems that include, for example, place-based conceptualizations of responsibility, care, and relation to the natural world. |
Leary, James; Mahnken, Brooke; Wada, Christopher; Burnett, Kimberly Interpreting Life-History Traits of Miconia (Miconia calvescens) through Management over Space and Time in the East Maui Watershed, Hawaii (USA) Journal Article Invasive Plant Sci. Manage., 11 (4), pp. 191–200, 2018. @article{Leary2018-xt, title = {Interpreting Life-History Traits of Miconia (Miconia calvescens) through Management over Space and Time in the East Maui Watershed, Hawaii (USA)}, author = {James Leary and Brooke Mahnken and Christopher Wada and Kimberly Burnett}, year = {2018}, date = {2018-12-01}, journal = {Invasive Plant Sci. Manage.}, volume = {11}, number = {4}, pages = {191--200}, publisher = {Cambridge University Press}, abstract = {Miconia (Miconia calvescens DC) was introduced to the East Maui Watershed (EMW) a half-century ago with more than 25 yr of management recorded. Using a historical spatiotemporal data set, we constructed a leptokurtic dispersal kernel with 99% of progeny confined to within 549 m of the nearest maternal source and the remaining 1% dispersed out to 1,636 m. Seedbank persistence, based on postdated recruitment, displayed an exponential decay projecting extinction beyond 20 yr. These parameters are highly congruent to independent interpretations of M. calvescens in Australia and Tahiti. In a simulated stage matrix model, we projected management efforts to locally eradicate a small incipient propagule bank wherein optimal management was achieved with an annual harvest rate that eliminated all juvenile recruits before reaching maturity, until extinction. Based on current pricing for helicopter herbicide ballistic technology (HBT) operations, the optimal, variable cost to locally eradicate this incipient propagule bank was estimated to be less than US$42,000, with ~90% of the effort searching for the most distant 1% of the progeny expended within the first 9 yr after the mature discovery. This variable cost was sensitive to seedbank size, recruitment rate, and dispersal range, but was most sensitive to harvest rates between suboptimal and excess. In a scenario prioritizing the upper region of EMW, we retroactively analyzed past HBT efforts eliminating satellite M. calvescens and determined that 27% of the total effort resulted in 87% of the total protection to this priority asset, with every US$1 invested potentially avoiding US$184 in future costs. Management outside the priority area was less economical, with returns in protection diminishing with distance from the priority upper region. Miconia calvescens is currently not eradicable in the EMW, and full containment of the invasion would require a substantial increase in stable, long-term funding. With limited resources, local eradication of satellite M. calvescens could be the most cost-effective alternative to protecting uninvaded areas prioritized for critical ecosystem functions.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Miconia (Miconia calvescens DC) was introduced to the East Maui Watershed (EMW) a half-century ago with more than 25 yr of management recorded. Using a historical spatiotemporal data set, we constructed a leptokurtic dispersal kernel with 99% of progeny confined to within 549 m of the nearest maternal source and the remaining 1% dispersed out to 1,636 m. Seedbank persistence, based on postdated recruitment, displayed an exponential decay projecting extinction beyond 20 yr. These parameters are highly congruent to independent interpretations of M. calvescens in Australia and Tahiti. In a simulated stage matrix model, we projected management efforts to locally eradicate a small incipient propagule bank wherein optimal management was achieved with an annual harvest rate that eliminated all juvenile recruits before reaching maturity, until extinction. Based on current pricing for helicopter herbicide ballistic technology (HBT) operations, the optimal, variable cost to locally eradicate this incipient propagule bank was estimated to be less than US$42,000, with ~90% of the effort searching for the most distant 1% of the progeny expended within the first 9 yr after the mature discovery. This variable cost was sensitive to seedbank size, recruitment rate, and dispersal range, but was most sensitive to harvest rates between suboptimal and excess. In a scenario prioritizing the upper region of EMW, we retroactively analyzed past HBT efforts eliminating satellite M. calvescens and determined that 27% of the total effort resulted in 87% of the total protection to this priority asset, with every US$1 invested potentially avoiding US$184 in future costs. Management outside the priority area was less economical, with returns in protection diminishing with distance from the priority upper region. Miconia calvescens is currently not eradicable in the EMW, and full containment of the invasion would require a substantial increase in stable, long-term funding. With limited resources, local eradication of satellite M. calvescens could be the most cost-effective alternative to protecting uninvaded areas prioritized for critical ecosystem functions. |