cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17632/5fbp62w77x.1
title: Aberrant gut microbiota alters host bile acid metabolism and contributes to intrahepatic cholestasis of pregnancy

description: Intrahepatic cholestasis of pregnancy (ICP) is a pregnancy-specific disorder, which is associated with an increased risk of adverse perinatal outcomes. The etiology and mechanism of ICP are complicated and poorly understood, thus therapies have been largely empiric. Currently, the mainstay of treatment for ICP has been ursodeoxycholic acid (UDCA). However, the largest randomized controlled clinical trial (PITCHES trial) and several Cochrane database meta-analyses found that there was no evidence in reducing adverse perinatal outcomes using UDCA versus placebo, raising controversy in the treatment of ICP. As such, there is an urgent unmet clinical need for this serious disease. In this study, we demonstrated that the abundance of Bacteroides fragilis (B. fragilis) was substantially increased in individuals with ICP. B. fragilis colonization could suppress FXR signaling through mediating bile acid metabolism and result in excessive bile acid synthesis and disrupted bile acid excretion, highlighting the role of bile acids and FXR in gut microbiota-mediated ICP development. Most importantly, our finding revealed that GDCA was identified as a novel FXR agonist and might be of potential value in the prevention and treatment of ICP.
DOI: 10.17632/yfmn2yc238.1
title: MATLAB codes - Thermally triggered multimodal and asymmetric deformations of a single mesostructure with reverse stiffness and localized prestress

description: The MATLAB codes, ABAQUS simulation input files, and materials characterization data are on the figures in the manuscript titled "Thermally triggered multimodal and asymmetric deformations of a single mesostructure with reverse stiffness and localized prestress."
DOI: 10.5066/p9xm4elb
title: Cyanobacterial toxin effects on inflammatory response of human toll-like receptors (TLRs)

description: Various stressors including temperature, environmental chemicals and toxins can have profound impacts on immunity to pathogens. It is believed that increased eutrophication near rivers and lakes coupled with climate change are predicted to lead to increased algal blooms. Currently, the effects of cyanobacterial toxins on disease resistance in mammals is a largely unexplored area of research. Importantly, recent studies have suggested that freshwater cyanotoxins can elicit immunomodulation through interaction with specific components of innate immunity thus potentially altering disease susceptibility parameters for fish, wildlife and human health owing to the conserved nature of the vertebrate immune system. In this study, we investigated the effects of three microcystin congeners (LR, LA and RR), nodularin-R and cylindrospermopsin for their ability to directly interact with 9 different human toll-like receptors-key pathogen recognition receptors for innate immunity. Toxin concentrations were verified by LC/MS/MS prior to use. Using an established HEK293-hTLR NF-&#954;B reporter assay, we concluded that none of the tested toxins (26-78 nM final concentration) directly interacted with human TLRs in either an agonistic or antagonistic manner. These results suggest that earlier reports of cyanotoxin-induced NF-&#954;B responses likely occur through different surface receptors to mediate inflammation.
DOI: 10.17632/xndcmbn6wd.2
title: Glyphosate and Melanization

description: Melanin is a black-brown pigment found throughout all kingdoms of life playing diverse roles including: UV protection, thermoregulation, oxidant scavenging, arthropod immunity, and microbial virulence. Given melanin’s broad functions in the biosphere, particularly in insect immune defenses, it is important to understand how environmental conditions affect melanization. Glyphosate, the most widely used herbicide, inhibits melanin production. Here we elucidate the mechanism underlying glyphosate’s inhibition of melanization demonstrate the herbicide’s multifactorial effects on insects. Glyphosate acts as an antioxidant and disrupts the oxidation-reduction balance of melanization. The drug reduced wax moth larvae survival after infection, increased parasite burden in malaria-transmitting mosquitoes, and altered midgut microbiome composition in adult mosquitoes. These findings suggest that glyphosate’s environmental accumulation could contribute to the so called insect apocalypse, characterized by species declines, by rendering them more susceptible to microbial pathogens due to melanization inhibition, immune impairment, and perturbations in microbiota composition.
DOI: 10.5066/p95s9rfv
title: Inputs and Selected Outputs Used to Assess Spatial and Temporal Patterns in Streamflow, Water-Chemistry, and Aquatic Macroinvertebrates of Selected Streams in Fairfax County, Virginia, 2007-2018

description: Nitrogen (N), phosphorus (P), and suspended-sediment (SS) loads, in Fairfax County, Virginia streams have been calculated using monitoring data from five intensively monitored watersheds for the period from water year (October - September) 2008-2017. Nutrient and suspended-sediment loads were computed using a surrogate (multiple-linear regression) approach with lab analyzed N, P, and SS samples as the response variable and basic water-quality parameters (e.g. turbidity, specific conductance, pH, water temperature), streamflow, and time and seasonal terms that could be measured continuously as predictor (surrogate) variables. The load results represent the total mass of N, P, and SS that was exported from each of the Fairfax County watersheds. Trends in N, P, SS concentrations, as well as basic water-quality parameters including turbidity, water temperature, dissolved oxygen, specific conductance, and pH have been calculated using both non-flow-normalized and flow-normalized Seasonal Kendall tests at 14 monitoring stations in Fairfax County, Virginia for the period beginning April 2008 and ending March 2018. Flow-normalized trends were used to integrate out the effect of annual streamflow variability on concentration (or unit value). Streamflow is an important driver of water-quality conditions; therefore, several datasets are provided describing a suite of annual streamflow metrics: streamflow volume/yield, flashiness, peak stage, baseflow index, stormflow index, and runoff ratio. Depending on the metric, data are provided from the 5 intensively monitored Fairfax County, VA watersheds, the entire 20-station Fairfax County monitoring network (5 intensively monitored + 15 trend only monitoring stations), and/or 3 reference stations that are part of the USGS Chesapeake Bay Non-Tidal Network (USGS Station IDs 01646000, 01654000, 01658500). Streamflow analyses were conducted on data collected in water years 2008-2017 for all Fairfax County monitoring stations as well as station ID 01658500, 1948-2017 for station ID 01654000, and 1946-2017 for 01646000. Benthic macroinvertebrate data were collected annually (waters years 2008 - 2017) by Fairfax County staff from each of the 20 monitoring stations. These data were used to explore trends in 20 biological metrics; the data used to calculate these trends are provided.
DOI: 10.5066/p90ejl2e
title: Depth to Groundwater Measured from Wells Completed in the Chicot, Evangeline, and Jasper Aquifers, Houston-Galveston Region, Texas, 2020

description: This dataset documents the depth to groundwater measured in wells screened in the Chicot, Evangeline, and Jasper aquifers in the Houston?Galveston region, Texas for 2020. The U.S. Geological Survey prepared this dataset in cooperation with the Harris?Galveston Subsidence District, City of Houston, Fort Bend Subsidence District, Lone Star Groundwater Conservation District, and Brazoria County Groundwater Conservation District. This dataset was created to provide resource managers, public officials, researchers, and the general public with ready access to information regarding depths to groundwater in the region. All of the data in this dataset were collected from December 2019 through March 2020 and are stored in the National Water Information System (NWIS), a publicly available, searchable, online database of water information (http://dx.doi.org/10.5066/F7P55KJN). These digital data accompany a U.S. Geological Survey Scientific Investigation Report by Braun and Ramage (2020).
DOI: 10.5066/p9lth0ro
title: Survey and Bathymetric Data of Deadmans Lake; Golf Course Reservoir 9; Ice Lake; Kettle Lakes 1-3; and Non-Potable Reservoirs 1-4 at the U.S. Air Force Academy, Colorado, 2019 (ver. 1.1, June 2020)

description: The U.S. Geological Survey (USGS), in cooperation with the U.S. Air Force Academy, carried out bathymetry surveys to characterize the water-supply capacity of Deadmans Lake; Golf Course Reservoir 9; Ice Lake; Kettle Lakes 1, 2, and 3; and Non-Potable reservoirs 1, 2, 3, and 4 at the U.S. Air Force Academy, Colorado in 2019. This data release includes: the elevation and volumes at specified elevations for each lake or reservoir, combined terrestrial and bathymetry real-time kinematic (RTK) Global Navigation Satellite Systems (GNSS) survey points, and digital elevation models (DEMs) of the lakes and reservoirs. Bathymetric data were collected between October 15, 2019, and December 12, 2019, using a man-operated, boat-mounted, single-beam echo sounder integrated with RTK GNSS . Terrestrial surveys were carried out during the same time period using RTK GNSS and covered the dry shorelines of lakes and reservoirs. The terrestrial and bathymetric datasets were merged and imported into geographic information system software. The data points were then interpolated to create bathymetric DEMs, which were in turn used to generate elevation-volume curves of each lake or reservoir. These data provide water-resource managers with a better understanding of current water supply in the lakes and reservoirs and could also be used to determine sedimentation infill rates and estimates of the lifespan of the lakes and reservoir when compared with future surveys.
DOI: 10.5066/p941biys
title: Chemistry of water, stream sediment, wildfire ash, soil, dust, and mine waste for Fourmile Creek Watershed, Colorado, 2010-2019

description: In response to the 2010 Fourmile Canyon fire near Boulder, Colorado, the U.S. Geological Survey collected data to support investigations into the magnitude and critical drivers of water-quality impairment after wildfire. We analyzed chemistry of stream water, sediment, wildfire ash, soil, dust, and mine waste for metals and other parameters in order to evaluate the effects of legacy mining and wildfire on stream chemistry in the Colorado Front Range, USA. This data release includes data that were published earlier (McCleskey et al., 2012; Murphy et al., 2018).
DOI: 10.5066/p98irljf
title: Water-Quality, Bed-Sediment, and Invertebrate Tissue Trace Element Concentrations for Tributaries in the Clark Fork Basin, Montana, October 2017 - September 2018

description: Water, bed sediment, and biota were sampled in selected streams from Butte to near Missoula, Montana, as part of a monitoring program in the upper Clark Fork Basin of western Montana. The sampling program was led by the U.S. Geological Survey (USGS), in cooperation with the U.S. Environmental Protection Agency.
DOI: 10.5066/p9ujoyvr
title: Dependence of sedimentation behavior on pore-fluid chemistry for sediment collected offshore South Korea during the Second Ulleung Basin Gas Hydrate Expedition, UBGH2

description: One goal of Korea?s second Ulleung Basin Gas Hydrate Expedition, UBGH2, is to examine geotechnical properties of the marine sediment associated with methane gas hydrate occurrences found offshore eastern Korea in the Ulleung Basin, East Sea. Methane gas hydrate is a naturally occurring crystalline solid that sequesters methane in individual molecular cages formed by a lattice of water molecules. Offshore Korea, gas hydrate is found in thin, coarse-grained sediment layers that are interbedded with fine-grained sediment. Methane gas hydrate is a potential energy resource, but whether extracting methane from gas hydrate in these layered marine environments is technically and economically viable remains an open research topic as of 2019. This data release provides insight about a poorly quantified aspect of this process: the reaction of fine-grained sediment particles (fines) to the change in pore water chemistry that occurs when methane is extracted from gas hydrate. Fines are an issue for production because they can get resuspended in the flow of fluid and gas toward an extraction well. As fines move, they can cluster and subsequently clog pore throats in the sediment, reducing permeability (which controls how easily methane can flow toward the extraction well). The type of fine-grained particle and the chemistry of the surrounding pore water are the two main factors in determining the cluster structure (the size and fabric of the cluster) and the cluster formation and settling rates. Data in this study provide insight into both factors. Fine particles interact with each other primarily in response to electrical forces, and changes in pore water chemistry can significantly alter how those forces are communicated between particles. In marine systems, in situ pore water is an electrically conductive brine. As gas hydrate dissociates, however, fresh water is released along with the methane, making the pore water less conductive. Depending on the type of fine-grained particles involved, the pore water chemistry change enhances or diminishes the clustering and changes the rates at which the clusters form and settle. For this data release, specimens from the UBGH2 expedition were observed during sedimentation (settling) tests in pore fluids of differing chemistry. The results included in this data release can (1) provide insight into the types of fines present, which can be difficult to quantify if using the more standard x-ray diffraction method for identifying fines and (2) indicate whether the in situ fines are likely to increase or decrease their capacity to clog pore throats as the pore water transitions from higher to lower salinity during gas hydrate dissociation.
DOI: 10.5066/p9214iqu
title: Walleye (Sander vitreus) egg deposition and spawning habitat suitability in the Maumee River, OH (2014-2015)

description: Tributaries support spawning habitats for three of the four major sub-stocks of Lake Erie walleye (Sander vitreus). Despite a history of anthropogenic degradation and the extirpation of other potamodromous species, the Maumee River, OH continues to support one of the largest fish migrations in the Laurentian Great Lakes. To determine if spawning habitat availability and quality could limit production of Maumee River walleye, a habitat suitability model based on river bottom substrates and water depth was created for the lower 51 km of the Maumee River, and the distribution and relative abundance of walleye eggs deposited in a 25-km stretch of river were assessed. Walleye eggs were collected using a diaphragm pump at 7-10 sites two to three times per week from 1 April?7 May 2014 and from 24 March?5 May 2015, beginning shortly after ice out and continuing until early May when spawning ceased. To quantify spawning habitat within the Maumee River, a side-scan sonar unit and a bow-mounted transducer were used to identify river bottom substrate types. Substrate composition was visually delineated by drawing polygons around substrate patches and assigning the dominant substrate classification to each polygon in GIS software. Visual substrate surveys were conducted throughout the study area during June and September 2014?2016 and were used to inform the substrate classifications made by the side-scan sonar. Water depth and water velocity were modeled in the hydraulic modeling program HEC-RAS based on topographic data and water level gage data. Known walleye spawning habitat preferences from peer-reviewed literature were used to assign habitat suitability index (HSI) values from two different HSI models to substrate, modeled water depth, and modeled water velocity for spawning adult walleye, and habitat suitability maps were generated.
DOI: 10.15468/sswdxn
title: Life histories of Paucispinigera Freeman, Paraborniella Freeman and Paratendipes Kieffer (Diptera: Chironomidae) with phylogenetic considerations

description: This dataset contains the digitized treatments in Plazi based on the original journal article Cranston, Peter S. (2020): Life histories of Paucispinigera Freeman, Paraborniella Freeman and Paratendipes Kieffer (Diptera: Chironomidae) with phylogenetic considerations. Zootaxa 4853 (4): 527-547, DOI: https://doi.org/10.11646/zootaxa.4853.4.3
DOI: 10.5281/zenodo.4463389
title: FAMAZOA v3.0

description: The largest publicy available dataset of Open-source applications written in Kotlin. <strong>The source code of all applications from FAMAZOA v3.</strong> <strong>More info available at: </strong>https://uphf.github.io/FAMAZOA/
DOI: 10.5281/zenodo.4463388
title: FAMAZOA v3.0

description: The largest publicy available dataset of Open-source applications written in Kotlin. <strong>The source code of all applications from FAMAZOA v3.</strong> <strong>More info available at: </strong>https://uphf.github.io/FAMAZOA/
DOI: 10.34740/kaggle/ds/1059356
title: ANTM.JK Stock Market 2005 to Jan 2021
DOI: 10.17033/data.00000089
title: Formation of the giant Aynak copper deposit, Afghanistan: evidence from mineralogy, lithogeochemistry and sulfur isotopes

description: This project is based on PhD research undertaken by Hamidullah Waizy at the University of Brighton, 2014-2018. The files are linked to an article published on 4th October 2020 in 'International Geology Review', doi: 10.1080/00206814.2020.1824129 Abstract: Aynak is the largest known copper deposit in Afghanistan, with indicated resources of 240 Mt grading 2.3% Cu placing it in the ‘giant’ category. Host rocks are Neoproterozoic metasediments comprising dolomitic marble, carbonaceous quartz schist and quartz-biotite-dolomite schist containing garnet, scapolite and apatite. Chalcopyrite and bornite dominate the hypogene ore with lesser pyrite, pyrrhotite, cobaltite and chalcocite, and rare sphalerite, molybdenite, uraninite and barite. Sulfides occur as bedding-parallel laminae, disseminations, metamorphic segregations and crosscutting veins. Sulfide δ34S ratios range –14.5 to +17.3‰ in bedded and disseminated sulfides (n=34). This broad range favours biogenic reduction of seawater sulfate as a major source of sulfur, although thermochemical reduction processes are not precluded. The narrower δ34S range of –6 to +12.2‰ in vein and segregation sulfides (n=21) suggests localised redistribution and partial homogenization during metamorphism. Geochemical associations suggest that Al, P, Ca, Ti and Fe were primary sedimentary constituents whereas Cu, Mg, S, Se, As, Co and Bi were introduced subsequently. We infer that Aynak originated as a shale- and carbonate-hosted stratabound replacement deposit, resembling orebodies of the Central African Copperbelt, although underlying red-beds are absent at Aynak and mafic volcanics were the probable copper source. These giant deposits formed worldwide in the Cryogenian probably due to marine enrichment in copper, magnesium and sulfate coincident with profuse basaltic volcanism and ocean oxidation.
description: 1. Mineral chemistry analyses by scanning electron microscope, PABS, University of Brighton 2. Rock geochemistry analyses by Portable X-Ray Fluorescence, SET, University of Brighton 3. Sulphur isotope analyses at Scottish Universities Environmental Research Centre, East Kilbride
DOI: 10.17033/data.00000087
title: CHORUS

description: Characterisation of River Bed Surface Structure - Funded by NERC. (2012 – ongoing) Changes to the sediment bed surface in gravel rivers to accommodate both the overlying fluid flow regime and the upstream sediment supply fundamentally changes the overall stability of the river. To date, being able to describe changes to river stability in response to changing ‘bed structure’ and explicitly linking this development with changes to the overlying hydraulic signatures and sediment transport characteristics has been severely limited. This project aims to address this deficiency specifically examining how sediment grade, sediment supply characteristics and hydrograph shape affect the development of surface structures in gravel-bed rivers.
description: Data was collected in a series of runs in a hydraulic flume.
DOI: 10.5281/zenodo.4501530
title: COVID-19: Self-Reported Reductions in Physical Activity and Increases in Sedentary Behaviour During the First National Lockdown in the United Kingdom

description: Data set relating to the publication 'COVID-19: Self-Reported Reductions in Physical Activity and Increases in Sedentary Behaviour During the First National Lockdown in the United Kingdom'.
DOI: 10.5281/zenodo.4501529
title: COVID-19: Self-Reported Reductions in Physical Activity and Increases in Sedentary Behaviour During the First National Lockdown in the United Kingdom

description: Data set relating to the publication 'COVID-19: Self-Reported Reductions in Physical Activity and Increases in Sedentary Behaviour During the First National Lockdown in the United Kingdom'.
DOI: 10.17632/c3yxbgx8yw.1
title: Supplementary Tables

description: Table S1. Related to Figure 5. Gene lists associated with GO analysis. Lists of up-regulated and down-regulated genes comparing Isotype control mAb versus COV2-2050 D+1, COV2-2050 D+1 versus COV2-2050 LALA-PG D+1, Isotype control mAb versus COV2-2050 D+2, and COV2-2050 D+2 versus COV2-2050 LALA-PG D+2 in the top pathways identified through Gene Ontology analysis. Associated q-value and fold-change values are shown. Table S2. Related to Figure 5. Gene lists associated with CompBio analysis. Lists of up-regulated and down-regulated genes comparing Isotype control mAb versus COV2-2050 D+1, COV2-2050 D+1 versus COV2-2050 LALA-PG D+1, Isotype control mAb versus COV2-2050 D+2, and COV2-2050 D+2 versus COV2-2050 LALA-PG D+2 in the top pathways identified through CompBio analysis. Associated q-value and fold-change values are shown.
DOI: 10.17632/b4cvrb7f8g.1
title: A 3D road surface topography dataset of an entire route

description: This dataset represents the 3D topography of the road surface in the entire route of 27 km long located in the UK. The first purpose of the dataset is to test numerical programs that need the road surface topography as input. The dataset is composed of 2658 text files and each representing a section of that route.