cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.23729/d841cfd5-eef9-4ae4-a820-50becf91ec97
title: Atomistic and coarse grained simulations reveal increased ice nucleation activity on silver iodide surfaces in slit and wedge geometries - Simulation data

description: Outputs of molecular dynamics simulation of TIP4P/ice water and mW model on wedge and slit structures of silver iodide. This data is used to create the snapshots and plots of the following paper: Roudsari, G., Pakarinen, O. H., Reischl, B., Vehkamäki, H. (2022). Atomistic and coarse grained simulations reveal increased ice nucleation activity on silver iodide surfaces in slit and wedge geometries, Atmos. Chem. Phys. Discuss. [preprint], https://doi.org/10.5194/acp-2021-1054, in review.
DOI: 10.5066/f7b56h72
title: Air-water temperature data for the study of groundwater influence on stream thermal regimes in Shenandoah National Park, Virginia (ver. 2.0, May 3, 2018)

description: USGS Leetown Science Center scientists collected hourly air and water temperature data at 79 site locations within nine watersheds in Shenandoah National Park, Virginia over four water years (2012-2015). Data were collected using HOBO Pro V2 thermographs (accuracy = 0.2 degrees Celsius, drift = less than 0.1 degrees Celsius per year per year).
DOI: 10.5066/f7hh6j8x
title: Digital products from a hydrogeologic framework for Quaternary sediments within the glaciated conterminous United States

description: This data release is a compilation of the digital products from a hydrogeologic framework of the glaciated conterminous United States that were constructed to portray sediment and aquifer characteristics within this area. These digital products are described in Yager, R.M., Kauffman, L.J., Soller, D.R., Haj, A.E., Heisig, P.M., Buchwald, C.A., Westenbroek, S.M., and Reddy, J.E., 2018, Characterization and occurrence of confined and unconfined aquifers in Quaternary sediments in the glaciated conterminous United States: U.S. Geological Survey Scientific Investigations Report 2018-5091, 90 p., https://doi.org/10.3133/sir20185091.
DOI: 10.5066/p9ijmgib
title: Passive seismic data collected along headwater stream corridors in Shenandoah National Park in 2016 - 2020

description: In July 2016, July 2019, and March 2020, 318 seismic recordings were acquired at locations within Shenandoah National Park, Virginia, using MOHO Tromino Model TEP-3C three-component seismometers to assess depth to bedrock using the HVSR method. This method requires a measurement of estimate of shear wave velocity, which depends on the regolith sediment composition and density, for the conversion of measured resonance frequency to a depth to bedrock. Shear wave velocities were calculated for sediment in Shenandoah NP at locations where regolith thickness is known (e.g. at documented boreholes). The locations in this study were generally selected to characterize the depths to bedrock adjacent to streams monitored for coupled temperature and flow dynamics related to several ongoing USGS projects.
DOI: 10.5281/zenodo.5792882
title: Dataset for 'Intraocular scatter compensation with spatial light amplitude modulation for improved vision in simulated cataractous eyes'

description: Dataset for the manuscript entitled: Intraocular scatter compensation with spatial light amplitude modulation for improved vision in simulated cataractous eyes includes: 1) PSF from numerical simulations 2) CSF measured in subjects 3) Michelson contrast from numerical simulations
DOI: 10.5281/zenodo.6322881
title: A Daily Highest Air Temperature dataset in China from 1979 to 2018

description: The DHAT dataset is a daily highest air temperature data during the period of 1979-2018, in Celsius, in daily temporal and 0.1° spatial resolution. It is produced by using meteorological station data and near-surface air temperature reanalysis data (CMFD and ERA5) combined with diurnal variation model of air temperature to establish daily highest air temperature data, and then a correction model is constructed to further correct the data to improve the data accuracy according to different geographic partitions. The accuracy assessments indicate that the dataset exhibits high accuracy and can be used for climate change analysis in China.
DOI: 10.5287/bodleian:jbdxrnqn1
title: Measuring Laser Beams with a Neural Network (Data)
DOI: 10.6084/m9.figshare.20448174
title: Supplementary Material for: Ex vivo and in vitro Monocyte Responses Do Not Reflect in vivo Immune Responses and Tolerance

description: Cytokine production by ex vivo (EV)-stimulated leukocytes is commonly used to gauge immune function and frequently proposed to guide immunomodulatory therapy. However, whether EV cytokine production capacity accurately reflects the in vivo (IV) immune status is largely unknown. We investigated relationships between EV monocyte cytokine responses and IV cytokine responses in a large cohort of healthy volunteers using a highly standardized IV model of short-lived LPS-induced systemic inflammation, which captures hallmarks of both hyperinflammation and immunological tolerance. Therefore, 110 healthy volunteers were intravenously challenged with 1 ng/kg LPS twice: on day 0 to determine the extent of the IV (hyper)inflammatory response and on day 7 to determine the degree of IV endotoxin tolerance. Baseline EV monocyte cytokine production capacity was assessed prior to LPS administration. Short-term and long-term EV tolerance was assessed in monocytes isolated 4 h and 7 days after LPS administration, respectively. No robust correlations were observed between baseline EV cytokine production capacity and IV cytokine responses following LPS administration. However, highly robust inverse correlations were observed between IV cytokine responses and EV cytokine responses of monocytes isolated 4 h after IV LPS administration. No correlations between IV and EV tolerance were found. In conclusion, attenuated EV cytokine production capacity reflects ongoing IV inflammation rather than immune suppression. Results of EV assays should be interpreted with caution at the risk of improper use of immuno­stimulatory drugs.
DOI: 10.5281/zenodo.1035402
title: Pseudoproxies For The Paper  "A Pseudoproxy Assessment Of Data Assimilation For Reconstructing The Atmosphere–Ocean Dynamics Of Hydroclimate Extremes"

description: Pseudoproxies for the paper “A pseudoproxy assessment of data assimilation for reconstructing the atmosphere–ocean dynamics of hydroclimate extremes” by Steiger and Smerdon 2017.

If you have further questions, address them to the author Nathan J. Steiger.
DOI: 10.6084/m9.figshare.19769218.v2
title: Raw Data of Viral Load and Gastrointestinal Inflammation Research in COVID-19 Patients.xlsx

description: The raw material data contain much information about general biodata patients, the observational result of vital signs, head/neck, thoracal, abdominal, and extremity. In addition, the data include Peripheral Complete Blood Count, Inflammation markers, CT value to see the viral load, and the fecal calprotectin
DOI: 10.15482/usda.adc/1173142
title: Oncopeltus fasciatus Official Gene set v1.1

description: The Oncopeltus fasciatus genome was recently sequenced and annotated as part of the i5k pilot project by the Baylor College of Medicine. The O. fasciatus research community has manually reviewed and curated the computational gene predictions and generated an official gene set, OGSv1.1. Oncopeltus fasciatus has been an established lab organism for over 60 years, and has been used for a wide range of studies from physiology to development and evolution. As a relatively conservative and generalized species, it affords a baseline against which other species can be compared. For example, this species has the same piercing and sucking type mouthparts as its less benign relatives, including the blood-sucking kissing bug, Rhodnius prolixus, and the brown marmorated stink bug, Halyomorpha halys, which are disease vector and agricultural pest species, respectively. Unlike the pest species, the benign, seed-feeding Oncopeltus can be functionally investigated in the lab by RNA interference (RNAi). Comparing the genomes, and conducting experimental lab work in Oncopeltus, will help to identify unique features of the pest species, and thus inform management strategies for them. More generally, Oncopeltus is a key species for comparisons across the insects. It is one of the few experimentally tractable hemimetabolous species that can ground comparisons with the completely metamorphosing species of the Holometabola (e.g., flies, beetles, wasps). Topics investigated in this framework include reproductive biology and development of the legs, wings, body segments, extraembryonic membranes, and overall establishment of the body plan. This dataset presents the Oncopeltus fasciatus Official Gene Set (OGS) v1.1. The OGS is an integration of automatic gene predictions from Maker (done by Dan Hughes at Baylor) with manual annotations by the research community (done via Web Apollo). If you wish to use this dataset, please follow the Baylor College of Medicine's conditions for data use: https://www.hgsc.bcm.edu/bcm-hgsc-conditions-use
DOI: 10.5291/ill-data.3-14-374
title: Measurement of the mean free path of UCN in liguid and solid hydrogen and deuterium at various temperatures
DOI: 10.5063/f1c24tnh
title: Mya arenaria and Mercenaria mercenaria predator-prey dynamics

description: R code and data sets support/recreate all analysis in the following manuscript: Glaspie, C.N. and Seitz, R.D. Habitat complexity and benthic predator-prey interactions in Chesapeake Bay. Submitted to PLOS ONE. We examined the potential for habitat and predators to drive densities and distributions of bivalves in a field caging experiment (Mya arenaria) and laboratory mesocosm experiments (Mya arenaria and Mercenaria mercenaria). A caging study was conducted with juvenile Mya in patchy seagrass, sand, and mud near-shore habitats (1.5-2 m depth mean high water) in May 2014 near the mouth of the York River, VA (between 37.258323, -76.428047 and 37.275197, -76.370150). Cages were designed to elucidate the impacts of major predators, including blue crabs Callinectes sapidus and cownose rays Rhinoptera bonasus. Mya (thin-shelled deep infaunal) and Mercenaria (armored shallow infaunal) were exposed to blue crab C. sapidus predation in mesocosm tanks of 0.87 m diameter and 0.59 m height. For half of the trials (n = 3 for each treatment) predator behavior was recorded using an infrared-sensitive camera system. Metadata for all files in this data package can be found in the metadata.txt file.
DOI: 10.5063/f1n29v34
title: Mya arenaria population and disease survey

description: R code and data sets support/recreate all analysis in the following manuscript: Glaspie, CN, RD Seitz, MB Ogburn, CF Dungan, and AH Hines. Impacts of predators, habitat, recruitment, and disease on soft-shell clams Mya arenaria and stout razor clams Tagelus plebeius in Chesapeake Bay. Submitted to Marine Ecology Progress Series. A bivalve survey was conducted in Chesapeake Bay to examine influential factors on bivalve populations, focusing on predation (crab, fish, and cownose rays), habitat type (mud, sand, gravel, shell, or seagrass), environment (temperature, salinity, and dissolved oxygen), recruitment, and disease. M. arenaria and T. plebeius were found more often in more-complex habitats such as seagrass or shell than any other habitat. Clams were collected from three river systems of lower Chesapeake Bay (Lynnhaven River, York River, Mobjack Bay), and three river systems of upper Chesapeake Bay (Western Shore, Eastern Bay, Chester River) in fall 2011; spring/summer/fall 2012; and either spring/summer 2013 (for lower Bay) or summer/fall 2013. Each sampling season, four to nine sites within each subestuary were sampled, with three to four replicate samples from each site. The long-term trend of M. arenaria recruitment in Maryland was evaluated using data from surveys conducted by SERC in the Rhode River, Maryland. Benthic core samples were collected approximately quarterly (typically March/April, June, October, December) at two sandy subtidal sites from 1981-2016. Spring/summer temperature (April-August) obtained from the Chesapeake Bay Program Water Quality Database (http://www.chesapeakebay.net/data) for all tidal mainstem Chesapeake Bay stations, and annually averaged Susquehanna River discharge obtained from the USGS water quality monitoring station at Harrisburg, PA (National Water Information System at https://waterdata.usgs.gov/usa/nwis).
DOI: 10.5063/f1wm1bjd
title: Mya arenaria population and disease survey

description: R code and data sets support/recreate all analysis in the following manuscript: Glaspie, CN, RD Seitz, MB Ogburn, CF Dungan, and AH Hines. Impacts of predators, habitat, recruitment, and disease on soft-shell clams Mya arenaria and stout razor clams Tagelus plebeius in Chesapeake Bay. Submitted to Marine Ecology Progress Series. A bivalve survey was conducted in Chesapeake Bay to examine influential factors on bivalve populations, focusing on predation (crab, fish, and cownose rays), habitat type (mud, sand, gravel, shell, or seagrass), environment (temperature, salinity, and dissolved oxygen), recruitment, and disease. M. arenaria and T. plebeius were found more often in more-complex habitats such as seagrass or shell than any other habitat. Clams were collected from three river systems of lower Chesapeake Bay (Lynnhaven River, York River, Mobjack Bay), and three river systems of upper Chesapeake Bay (Western Shore, Eastern Bay, Chester River) in fall 2011; spring/summer/fall 2012; and either spring/summer 2013 (for lower Bay) or summer/fall 2013. Each sampling season, four to nine sites within each subestuary were sampled, with three to four replicate samples from each site. The long-term trend of M. arenaria recruitment in Maryland was evaluated using data from surveys conducted by SERC in the Rhode River, Maryland. Benthic core samples were collected approximately quarterly (typically March/April, June, October, December) at two sandy subtidal sites from 1981-2016. Spring/summer temperature (April-August) obtained from the Chesapeake Bay Program Water Quality Database (http://www.chesapeakebay.net/data) for all tidal mainstem Chesapeake Bay stations, and annually averaged Susquehanna River discharge obtained from the USGS water quality monitoring station at Harrisburg, PA (National Water Information System at https://waterdata.usgs.gov/usa/nwis).
DOI: 10.6084/m9.figshare.20431167
title: Supplementary Material for: Usefulness of Liver Uptake Rate Constant in <sup>99m</sup>Tc-GSA Scintigraphy for the Risk Stratification of Patients Undergoing Hepatectomy: A New Method for Calculation

description: <b><i>Introduction:</i></b> The use of technetium 99m diethylenetriaminepentaacetic acid-galactosyl human serum albumin (<sup>99m</sup>Tc-GSA) scintigraphy parameters, HH15 and LHL15, in assessing the future liver remnant function is not expedient because of their nonlinear behaviour against liver volume. Uptake rate constant for the binding of <sup>99m</sup>Tc-GSA to asialoglycoprotein receptors is probably more favourable, but the reported calculation methods are complex. We devised a simple method to calculate the uptake rate constant, K<i>r</i>GSA. <b><i>Methods:</i></b> Radioactivity counts for the entire liver and heart regions were extracted at 10, 20, and 30 min. Using whole liver and heart volumes measured from single-photon emission computed tomography images, free radioactivity corresponding to the liver blood pool was subtracted. The time activity curve was fitted to the equation <i>L</i>(<i>t</i>) = <i>L</i>(∞) × [1 − Exp (−<i>kt</i>)] using Microsoft Office Excel (add-in free programme Solver)®, where <i>L</i>(∞) is the count at plateau level and <i>k</i> denotes K<i>r</i>GSA. <b><i>Results:</i></b> K<i>r</i>GSA values accurately identified liver cirrhosis and were similar to the KICG. The areas under the curve for K<i>r</i>GSA and KICG in the receiver operating characteristic analysis were 0.808 and 0.795, respectively, and a good correlation was seen between K<i>r</i>GSA and KICG. <b><i>Discussion/Conclusion:</i></b> K<i>r</i>GSA can be utilized as an alternative to KICG in assessing the future liver remnant function.
DOI: 10.5066/p9teyrnc
title: Liquid Chromatography Triple Quadrupole Mass Spectrometry (LC/MS/MS) analysis of cyanotoxins and algal toxins in estuary samples collected from California, USA, in 2016-17

description: Cyanobacteria are primary producers present in many water bodies, certain types of which may produce potent toxins (known as cyanotoxins). They are known to impact human and animal health when exposed through recreational activities, consumption, and inhalation. In an effort to understand the presence of toxin-producing cyanobacteria in California water bodies, cyanobacteria samples were collected from 19 California water bodies. These data document the liquid chromatography triple quadrupole mass spectrometry (LC/MS/MS) results for 21 cyanotoxins and algal toxins in 41 cyanobacteria samples collected from California water bodies in 2015-2016.
DOI: 10.34740/kaggle/ds/1933301
title: SA-UNet for The Recovery of Ionograms
DOI: 10.6084/m9.figshare.1466782
title: Women's preferences for penis size: A new research method using selection among 3D models

description: Women’s preferences for penis size may affect men’s comfort with their own bodies and may have implications for sexual health. Studies of women’s penis size preferences typically have relied on their abstract ratings or selecting amongst 2D, flaccid images. This study used haptic stimuli to allow assessment of women’s size recall accuracy for the first time, as well as examine their preferences for erect penis sizes in different relationship contexts. Women (N = 75) selected amongst 33, 3D models. Women recalled model size accurately using this method, although they made more errors with respect to penis length than circumference. Women preferred a penis of slightly larger circumference and length for one-time (length = 6.4 inches/16.3 cm, circumference = 5.0 inches/12.7 cm) versus long-term (length = 6.3 inches/16.0 cm, circumference = 4.8 inches/12.2 cm) sexual partners. These first estimates of erect penis size preferences using 3D models suggest women accurately recall size and prefer penises only slightly larger than average.
DOI: 10.11583/dtu.8204711.v2
title: ALEX17 surface flux measurements: gradient turbulent fluxes over complex terrain

description: The present dataset is part of the Alaiz Experiment-2017 (ALEX17) which consists of measurements of nine surface-layer stations (SLS) distributed over the Elorz valley bottom and mountain slopes (geographical coordinates are indicated in the experimental report). The stations were deployed in several phases along Autumn 2017 and Spring 2018 and were in operation until December 2018, providing 8 months of measurements from the entire SLS network. These 2-m high stations monitor both atmospheric and soil parameters to characterize their variability along the valley. Measurements of wind at 2 m above the ground and air temperature and humidity at two different levels are used to estimate the surface turbulent fluxes through the flux-gradient approach, together with the atmospheric stability within the surface layer. Both raw data with a sampling period of 5 minutes, as well as 30-min averages of quality-controlled flux data are available.
DOI: 10.25318/3210041101-eng
title: Land practices and land features, Census of Agriculture, inactive

description: Census of Agriculture, 2011 and 2016. Farms reporting selected land practices and land features.
DOI: 10.5066/f7cf9n9t
title: Biological and physical data for zebra mussel (Dreissena polymorpha) veligers collected from a coupled lake-stream ecosystem in north Texas, 2012-2014

description: Dispersal, establishment, and spread of aquatic invasive species such as the zebra mussel (Dreissena polymorpha) can be influenced by riverine velocities and volumetric flows in invaded lake-stream ecosystems. Zebra mussels, which have a planktonic larval form (veliger), disperse rapidly downstream from a source population. Concentrations, dispersal, and body conditions of zebra mussel veligers were studied under different volumetric flow, or discharge, conditions in a coupled lake-stream ecosystem in northern Texas, USA. Veliger densities in lotic environments were strongly related to population dynamics in upstream lentic source populations. A strong exponential decrease in veliger density was observed through a 28-km downstream study reach. Increased water releases from the source reservoir increased veliger flux and dispersal potential, concomitantly increasing veliger flux and decreasing transit time. However, passage through release gates in the dam and increased turbulence in the river during high-discharge events could negatively affect body condition of veligers, and veliger body condition generally decreased from the source population to the farthest downstream site and was lower for veligers during periods of high discharge. Thus increased discharge appears to reduce the proportion of viable veligers because of increased turbulence-induced mortality. Colonization of distant downstream reservoirs can occur if discharge and propagule pressure are sufficient or if interim habitats are suitable for establishment of in-stream populations.
DOI: 10.5281/zenodo.5908381
title: Replication Package for "Trust Enhancement Issues in Program Repair"

description: This is the replication artifact for our work on "Trust Enhancement Issues in Program Repair". The corresponding paper has been published at the International Conference of Software Engineering (ICSE) 2022, and is available under the following URL: https://doi.org/10.1145/3510003.3510040. A pre-print of our work is available on arXiv: https://arxiv.org/pdf/2108.13064.pdf. The artifacts is organized in two parts: the artifacts for our <strong>developer survey</strong>, and the artifacts for our <strong>empirical assessment</strong> of state-of-the-art automated program repair (APR) techniques. <strong>1. Survey Artifacts</strong> The <code>survey</code> folder includes: <code>Survey_Form.pdf</code> -- It shows the PDF version of the web form of our survey. <code>Study_Results.pdf</code> -- It shows a summary of the questions and responses. <code>Codebooks.xlsx</code> -- It shows all created codebooks. <code>CodedResults.xlsx</code> -- It shows the responses for all questions, the corresponding coding, and statistics we applied during our analysis. Additionally, it includes plots for all responses and also the plots that are included in our paper. <strong>2. Experiment Artifacts</strong> The <code>experiments</code> folder includes: <code>tools.md</code> -- It lists and describes the APR techniques that we used in our experiments. <code>Results.xlsx</code> -- Contains the results of the experiments for each tool we considered, configuration details, and all the data from the ManyBugs benchmark. <code>protocols/</code> -- This folder includes the analysis protocols, which describe for each tool "how" we extracted the values for our evaluation metrics (see Table 3 in our paper). <code>results/</code> -- Contains the log files and relevant outputs for all tools and configurations. In particular, it includes the generated patches. <code>subjects/</code> -- Contains the subjects taken from the ManyBugs benchmark. For our experiments, we made some changes to the instrumentations, test-ids, etc. The file <code>meta-data.json</code> states the configurations, relevant test cases, etc.
DOI: 10.5281/zenodo.6109803
title: Functional Ultrasound Localization Microscopy reveals brain-wide neurovascular activity on a microscopic scale

description: Matlab script to process fULM dynamic maps and compute activation maps. Two dataset are provided : one from a whiskers stimulation experiment in rats and one from a visual stimulation experiment in rats.