cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17632/bkh2h24jh3.1
title: Images from Meso- and Bathypelagic Surveys in the Gully Marine Protected Area: III: Fish of the 2009 Survey

description: During 2007–10, Canada’s Department of Fisheries and Oceans conducted four midwater-trawl surveys, at meso- and bathypelagic depths, in The Gully – a large submarine canyon incised into the Scotian Shelf, east of Sable Island, the core of which has been within a Marine Protected Area since 2004. The surveys followed a fixed-station, depth-stratified design, with replicate sets both in daylight and at night. Most sampling used International Young Gadoid Pelagic Trawls (IYGPTs) –open nets with 60 m² mouth area– worked on double-oblique profiles. From the 2008 survey, the trawls were fitted with rigid (“aquarium”) codends and successfully took a number of delicate specimens in exceptional condition. Full details of the field methodologies have been presented by Kenchington et al. (2009, 2014). Catches of the abundance- or biomass-dominant fish species have been published by Thompson and Kenchington (2016) and Kenchington et al. (2018, 2020a). The ceratioid anglerfishes have been published by Kenchington et al. (2020b) and DNA barcodes derived from selected specimens by Kenchington et al. (2017). 

Identification of fish specimens is ongoing (in 2022), while damage in the nets means that not all can be identified to species. It is, nevertheless, sure that specimens from in excess of 240 fish species were captured. Many of those have rarely been seen and most had never been photographed in fresh condition. Thus, a variety of camera systems were taken to sea on the surveys and an attempt made to create images of every species captured. The resulting collection has been catalogued and lightly edited, while erring on the side of retaining any image that might prove useful in the future. Almost all of those retained are in their original formats and resolutions, though some copies subsequently edited for publication have been added. Because of file-size limits, the present collection includes only the 498 catalogued images of fish specimens from the 2009 survey, together with a copy of the entire catalogue of fish images. Individual files are uniquely numbered (from F09001 to F09498), with corresponding entries in the catalogue. The latter presents the contents of each image (typically only a species name, though some entries have more details) and such other image-specific details as are available. Not all images can be linked to particular specimens but, for those which can be, catalogue entries include cross-references to the survey-program’s catch database, which provides further details on the specimens concerned.

All images © His Majesty the King in Right of Canada, 2022.

Amongst the named authors, the surveys were led by Trevor Kenchington, who also catalogued the images and, working with Cam Lirette, presented them here. Specimen identifications at sea and most of those ashore were by Daphne Themelis, while Merlin Best and Andrew Cogswell captured the images at sea.
DOI: 10.5066/f71v5c4s
title: DNA Microsatellite and Sex Identification Markers for Emperor Goose (Chen canagica) and Cross-Species Amplification of Microsatellites in Select Goose Species, Alaska 2016

description: This data set contains allele sizes for 30 individuals of 9 previously published and 20 novel microsatellite loci and the molecular sex verification (n = 31) of Emperor Geese (Chen canagica) from various locations across Alaska. The allele sizes for the 20 microsatellite loci developed in this study are included for 10 White-fronted Geese (Anser albifrons) from Selawik, 11 Black Brant (Branta bernicla nigricans) from Kigigak Island, 10 Canada Geese (Branta canadensis) from Copper River Delta, and 9 Cackling Geese (Branta hutchinsii) from lower Kashunuk River (Hock Slough) and Tutakoke River.
DOI: 10.5281/zenodo.11236177
title: Data for Legay et al. "A framework for assessing ocean mixed layer depth evolution"

description: This repository contains all the "npz" Python archives and the netCDF files needed for realizing the figures presented in Legay et al. "A framework for assessing ocean mixed layer depth evolution".
DOI: 10.5281/zenodo.4297693
title: PaleoMAP PaleoCoastlines data

description: The dataset is intended to supplement the journal article describing it (Kocsis and Scotese, Mapping paleocoastlines and continental flooding during the Phanerozoic. Earth-Science Reviews, https://doi.org/10.1016/j.earscirev.2020.103463). Please cite this study if you use the dataset. ESRI vector shapefiles of continental margins and coastlines are included. Continental margins are -1400m isobaths of the PaleoMAP PaleoDEMs (https://www.earthbyte.org/paleodem-resource-scotese-and-wright-2018/). Coastlines from the PaleoDEMs are adjusted to represent maximum transgressive surfaces, as indicated by the stage-level fossil occurrences of the Paleobiology Database (https://paleobiodb.org). This is version 7.1.
DOI: 10.5281/zenodo.7838110
title: Modern Human Articular Landmarks

description: Skeletal elements of interest were segmented from CT image stacks using Avizo 2021.1 or an automated custom routine in Matlab 2021b. Landmarks were placed on the resulting surface models of these bones using Stratovan Checkpoint. Landmarks follow published definitions (Arias-Martorell, Tallman, Potau, Bello-Hellegouarch, & Perez-Perez, 2015; San Millán, Kaliontzopoulou, Rissech, & Turbón, 2015; Tallman, 2013, 2016); novel landmarks were defined by the author. This dataset contains the raw landmarks exported into excel spreadsheets; landmark figures and definitions are included in Supplemental Information.
DOI: 10.5281/zenodo.8343505
title: Deepurify: a multi-modal deep language model to remove contamination from metagenome-assembled genomes

description: The SIM2 testing set.
DOI: 10.57707/fmi-b2share.5b37722cc31d4b8c9edfeca6a8dd88f6
title: Data and code for the manuscript "Can pollen affect precipitation?" by Prank et al.

description: This dataset consists of UCLALES-SALSA model output of the experiments presented in the manuscript "Can pollen affect precipitation?" by Prank et al. and the model code used for making these simulations. Simulations were made for two cases, one for warm cumulus (RICO) and one for mixed-phase stratocumulus (Puijo) with a range of pollen emission fluxes.
description: UCLALES-SALSA combines the widely used UCLA Large Eddy Simulator with a detailed aerosol-cloud microphysics model SALSA, that includes sectional representations of aerosols, liquid cloud droplets, raindrops and ice and simulates their interactions. The model was amended with parameterizations for pollen emission and humidity dependent rupture.
DOI: 10.6084/m9.figshare.27179109
title: Supplementary Material for: Effect of frail phenotype on cardiorenal risk and healthcare utilization in older patients with chronic kidney disease

description: Introduction
Limited data have addressed frailty’s role in cardiorenal risk among older adult patients with chronic kidney disease (CKD). We investigated whether frailty could predict major renal and cardiovascular events, healthcare utilization, and mortality in these patients.
Methods
We conducted a prospective cohort enrolling patients ≥ 75 years with a stable estimated glomerular filtration rate (eGFR) &lt; 60 mL/min/1.73 m2. Frailty phenotype consists of shrinking, low activity, exhaustion, weakness, and slowness, scored 0 to 5. The primary composite renal outcome was a ≥ 25 % decrease in eGFR concurrent with CKD stage progression or dialysis initiation. Secondary outcomes included major adverse cardiovascular events (MACE), emergency room (ER) visits, all-cause mortality, and hospitalization. Using multivariate Cox models with/without competing risk analyses, we explored frailty’s impact on these outcomes.
Results
Among 203 older CKD patients (mean age 81.6 ± 5.0 years, female 40.9 %, diabetes 33.0 %, body mass index 24.9 ± 3.7 kg/m2), 67.9% were frail. Over 3.47 years, 38.9% faced composite renal outcomes, 13.3% MACE, 15.3% mortality, and more than half utilized healthcare. Every one-point frailty elevated composite renal outcome risk by 28.0 % (HR: 1.28, 95% CI:1.03–1.59) and significantly increased secondary outcomes (hospitalization [HR: 1.24, 95% CI: 1.06–1.46], unexpected ER visit [HR: 1.20, [95% CI:1.03–1.39], and mortality [HR: 1.51, 95% CI: 1.06–2.16]) but not for MACE [HR: 1.43, 95% CI: 0.99–2.08]. Results were consistent across subgroups and competing risk analysis.
Conclusion
In CKD patients ≥ 75 years, frailty was associated with progressive kidney disease, increased mortality and healthcare utilization.
DOI: 10.7910/dvn/tddmib/4sxlfj
title: SSI Negative PID .tab

description: Dataset
DOI: 10.25625/h3an3a
title: Replication Data for: "Sparsity comparison of polytopal finite element methods"

description: Replication python script that generates the tables for the publication "Sparsity comparison of polytopal finite element methods"
DOI: 10.5281/zenodo.10394580
title: Biochar production paramters and physico-chemical characteristics

description: Data on biochar production parameters and physico-chemical characteristics collected from the scientific, peer-reviewed literature. Articles published up to June 2021 were found via the Scopus electronic database using search terms "biochar properties" AND "biochar characteristics" in titles, abstracts and keywords. Data were manually extracted from text and tables, but not from figures. Data were curated as follows:



deletion of implossible entries: H:C > 3 and sum of C, O, N, H, S and ash content > 110 weigth%

deletion of entries that do not meet criteria to be considered as biochar (HTT < 350 °C)

conversion to the unit reported in the database when needed and possible


In addition to the main data table, in order to ease re-use of this dataset for other purposes, a bibliography table is provided with analytical field allowing to sort studies by biochar use case, and production parameter sutdied. Both tables are accompanied by a text read me file that describes each variable.
DOI: 10.5281/zenodo.5003976
title: LANID-US: Landsat-based Irrigation Dataset for the United States

description: <strong>Annual 30-m resolution irrigation maps, derivative products, and ground reference locations for the United States, 1997-2017</strong>, including: (1) lanidYYYY (binary): Annual irrigation layer for the year YYYY (ranging from 1997 to 2017), e.g., lanid2017 is the irrigation map for the year 2017. (2) irrFreq (1-21): The number of years irrigated during 1997-2017. (3) irrFreqPasture_West: irrFreq of pasture/hay for the western CONUS. (4) maxIrrExt (binary): Croplands that have been irrigated at least once during 1997-2017. (5) irrFreqChange (1-21): The difference of number of years irrigated between 1998-2007 and that of between 2008-2017 (i.e., irrFreq<sub>2008-2017</sub> - irrFreq<sub>1998-2007</sub>). (6) irrAreaGain (-1684-2333): LANID-derived irrigation gain (in hectare) from 1998-2007 to 2008-2017 at the 6km×6km scale. (7) formerIrr (binary): Not irrigated anytime in 2015-2017, but irrigated at least 3 times prior. (8) irrWholePeriod (binary): Irrigated at least once for both 1997-1999 and 2015-2017. (9) intermittentIrr (binary): Irrigated at least once for both 1997-1999 and 2015-2017, and irrigation frequency ≤ 18. (10) irrSamples_eastCONUS: Sample locations of center pivot fields in the eastern CONUS (4976 sample locations). (11) rainfedSamples_eastCONUS: Sample locations of stable rainfed fields in the eastern CONUS (4978 sample locations). <strong>For technical details that used to create the dataset, please refer to <em>https://doi.org/10.1016/j.rse.2021.112445</em>; Data description details are available via <em>https://essd.copernicus.org/preprints/essd-2021-207/</em>.</strong>
DOI: 10.5281/zenodo.7159104
title: TAIR functional annotation data

description: Quarterly release of curated gene function data for Arabidopsis thaliana from The Arabidopsis Information Resource (www.arabidopsis.org) The contents of the compressed archive include the following files which are described in detail in the included README file. <br> 1.ATH_GO_GOSLIM.txt.gz<br> This document is a tab-delimited file containing GO annotations for Arabidopsis genes annotated by TAIR and TIGR with terms from the Gene Ontology Consortium controlled vocabularies (see www.geneontology.org). This file includes an updated set of literature based annotations and &gt;40,000 electronic annotations based upon matches to INTERPRO domains supplied by Nicola Mulder from SWISS PROT/INTERPRO. Please cite this paper when using TAIR's GO annotations in your research: Berardini, TZ, Mundodi, S, Reiser, L, Huala, E, Garcia-Hernandez, M, Zhang, P, Mueller, LM, Yoon, J, Doyle, A, Lander, G, Moseyko, N, Yoo, D, Xu, I, Zoeckler, B, Montoya, M, Miller, N, Weems, D, and Rhee, SY (2004) Functional annotation of the Arabidopsis genome using controlled vocabularies. Plant Physiol. 135(2):1-11. <br> 2.gene_aliases_yyyymmdd.txt(.gz)<br> This file lists alternative names for each gene. <br> 3.Locus_Germplasm_Phenotype_yyyymmdd.txt.gz<br> This file contains links between loci, germplasms, and phenotypes. <br> <br> 4.Locus_Published_yyyymmdd.txt.gz<br> This file contains links between loci and publications. <br> <br> 5.po_temporal_gene_arabidopsis_tair.assoc.gz<br> po_anatomy_gene_arabidopsis_tair.assoc.gz<br> These two files are tab-delimited files. Each contains the <br> set of literature-based annotations of Arabidopsis genes and loci annotated at TAIR to the terms from the Plant Ontology developed by the Plant Ontology Consortium (POC, www.plantontology.org). <br> 6.TAIR10 or ARAPORT11_functional_descriptions_yyyymmdd.txt(.gz)<br> This file contains functional descriptions for gene models included in either the TAIR 10 or as of 20170630 the Araport11 genome release. TAIR10/Araport11 refers to the version of the genome annotation.<br>
description: {"references": ["Berardini, TZ, Mundodi, S, Reiser, L, Huala, E, Garcia-Hernandez, M, Zhang, P, Mueller, LM, Yoon, J, Doyle, A, Lander, G, Moseyko, N, Yoo, D, Xu, I, Zoeckler, B, Montoya, M, Miller, N, Weems, D, and Rhee, SY (2004) Functional annotation of the Arabidopsis genome using controlled vocabularies. Plant Physiol. 135(2):1-11. DOI:10.1104/pp.104.040071", "Huala E, Dickerman AW, Garcia-Hernandez M, Weems D, Reiser L, LaFond F, Hanley D, Kiphart D, Zhuang M, Huang W, Mueller LA, Bhattacharyya D, Bhaya D, Sobral BW, Beavis W, Meinke DW, Town CD, Somerville C, Rhee SY. The Arabidopsis Information Resource (TAIR): a comprehensive database and web-based information retrieval, analysis, and visualization system for a model plant. Nucleic Acids Res. 2001 Jan 1;29(1):102-5. PubMed PMID: 11125061; PubMed Central PMCID: PMC29827."]}
DOI: 10.6084/m9.figshare.156386
title: EVALUATION AND COMPARISON OF VO2MAX ASSESSMENT MODELS IN HIGH SCHOOL STUDENTS

description: The purpose of this study was to evaluation and comparison of VO2max assessment models in students. Thirty students from high schools of Ardabil city were selected randomly and served as subjects in this study (age: 15.73±0.69 year, height: 169.46±8.1 cm, weight: 61.70±9.32 Kg). Subjects were divided into two groups. In one group Rockport test was used to estimate their VO2 max and in other group Balk test was used for the same purpose. Also, the VO2max of both groups were examined by a standard treadmill test and the results were compared with the results of field tests. The one way of ANOVA and Tukey's post-hoc tests were used for data analysis (p&gt;0/05). The results showed that there were significant differences between the results of the field tests and standard treadmill test (Bruce: 40.93±5.83 vs. Rockport: 58.71±2.73 and Balke: 52.09± 6.18). As a result of these findings it was concluded that the regression equations used in this study used is not suitable for 15-17 (yr) boys and does not estimate their aerobic power correctly.
DOI: 10.6084/m9.figshare.25814881
title: Dataset for Nearshore Propagation and Amplification of the Tsunami Following the 2024 Noto Peninsula Earthquake, Japan

description: The dataset is used in the following article.Yamanaka et al. Nearshore Propagation and Amplification of the Tsunami Following the 2024 Noto Peninsula Earthquake, Japan. <i>Geophysical Research Letters</i>
DOI: 10.6084/m9.figshare.26954659
title: Supplementary Material for: Causal Relationships between Gut Microbiotas, Blood Metabolites, and Neuroendocrine Tumors: A Mediated Mendelian Randomization Study

description: Introduction Neuroendocrine tumors (NETs) are a heterogeneous group of epithelial tumors originating from different anatomical sites, identifying the gut microbiota and metabolic mechanisms involved in the onset of NETs may help to develop appropriate disease prevention and monitoring strategies.
Methods We employed a mediated two-sample Mendelian Randomization (MR) approach, analyzing gut microbiota from German studies and NET datasets from the 10th round of the FinnGen project. Mediation analyses were conducted using the metabolites dataset from the Canadian Longitudinal Study of Aging (CLSA) and the TwinsUK study. Instrumental variables (IVs) chosen according to established MR criteria and analyzed using the Wald ratio, inverse-variance weighted (IVW), MR-Egger, and weighted median methods. To ensure robustness, sensitivity analyses were performed using Cochrane’s Q, Egger’s intercept, MR-PRESSO, and leave-one-out (LOO) methods. 
Results Causal relationships were identified between the genetic determinants of 6, 5, 2, 1, 2, 3 gut microbiotas and the risk of colorectal, lung, pancreatic, rectum, small intestine and stomach NETs. Similarly, the genetic determinants of 4, 6, 1, 5, 10 and 7 metabolites were found to be causally related to the risk of colorectal, lung, pancreatic, rectum, small intestine and stomach NETs, respectively. Through Wald ratio and IVW methods, we preliminarily identified 957 microbiota-metabolite pairs with significant causal associations, and formed 13 mediated relationships between the impact of gut microbiotas on NETs.
Conclusion Our study suggests that gut microbiotas and its derived metabolites may contribute to the onset of NET, offering a novel insight into the disease's pathogenesis.
DOI: 10.7910/dvn/wvzc90/4adqtq
title: CollectiveLaborRightsDataset.tab
DOI: 10.15468/dl.65fabt
title: Occurrence Download

description: A dataset listing the 10467 species recorded in GBIF matching the query:
{
 "GadmGid" : [
 "is AUT.3.2_2"
 ]
}

 The dataset's 10467 records were derived from 173 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011093-230918134249559/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.4231/r7xs5sjj
title: Automatic Vehicle Location Data Set

description: These data consist of a unique identifier and the times the vehicles were identified as passing through virtual detection zones at mile markers 2.5 and 10.5 in the eastbound and westbound directions of I-80/94.
DOI: 10.5066/f7rv0kwr
title: 2017 One-Year Seismic Hazard Forecast for the Central and Eastern United States from Induced and Natural Earthquakes

description: We produced a one-year 2017 seismic hazard forecast for the central and eastern United States from induced and natural earthquakes that replaces the one-year 2016 forecast, and evaluated the 2016 seismic hazard forecast to improve future assessments. The 2016 forecast indicated high seismic hazard (greater than 1% probability of damaging ground shaking in 1 year) in portions of Oklahoma/Kansas, the Raton Basin (Colorado/New Mexico border), northern Texas, northern Arkansas, and the New Madrid Seismic Zone (NSMZ). During 2016, several damaging induced earthquakes occurred in Oklahoma within the highest hazard region of the 2016 forecast; all of the 15 magnitude (M) &gt; 4 and 3 M &gt; 5 earthquakes occurred within the highest 5%-12% per year probability-of-damage contours shown in the 2016 forecast. Outside Oklahoma a moderate earthquake with M ≥ 4 occurred near Trinidad, Colorado, but no earthquakes with magnitudes M ≥ 2.7 were observed in northern Texas or Arkansas. Several observations of damaging ground shaking levels were also recorded in the highest hazard region of Oklahoma. The 2017 hazard model applies the same methodology and input logic tree as the 2016 forecast, but with an updated earthquake catalog. The 2017 seismic rates are lower in almost all regions of induced activity due to lower rates of earthquakes in 2016 compared to 2015, which may be related to decreased wastewater injection, caused by regulatory actions or by a decrease in unconventional oil and gas production. Nevertheless, the 2017 forecasted hazard is still hundreds of times higher than hazard calculated before induced seismicity rates rapidly increased about 2008.
DOI: 10.5066/p1y9gbjk
title: Abundance, Biomass, and Density Data for Fishes and Amphipods in Prairie Pothole Region Wetlands in 2019 and 2020

description: This dataset includes information from 59 prairie pothole wetlands in Minnesota, collected in 2019 and 2020. The data includes wetland characteristics (e.g., size, depth, plant biomass, and water quality), multiple fish metrics, and multiple amphipod metrics. The amphipod species include Gammarus lacustris and Hyalella azteca. There are 22 species of fish recorded.
DOI: 10.5281/zenodo.10810230
title: Floristic survey of vascular plants of the Parque Estadual da Pedra Selada, Rio de Janeiro, Brazil

description: The Atlantic Forest is one of the most diverse and threatened phytogeographical domains of the world. Despite that, it includes regions of poor floristic knowledge, even in protected areas. Although the importance of protected areas in conserving the Atlantic Forest hotspot is undisputed, it is necessary to recognize the floristic richness of these areas to propose effective conservation actions. In this sense, online databases have proved to be a promising tool for compiling species lists with relevant biodiversity information. This study is based on the list of vascular plants of the “Parque Estadual da Pedra Selada”, published in the “Catálogo de Plantas das Unidades de Conservação do Brasil’. It summarizes species richness, endemism, and conservation status of this protected area.
DOI: 10.7910/dvn/4gt3u3/ga7vxr
title: auxiliary.do

description: :unav
DOI: 10.7910/dvn/4gt3u3/ozip5v
title: cleaneneu_web.do

description: :unav
DOI: 10.7488/ds/2716
title: Brain Network Measures and Spatial Lesion Distribution in a Sample of 47 Patients with Systemic Lupus Erythematosus (SLE)
title: Brain Network Measures and Spatial Lesion Distribution in Systemic Lupus Erythematosus

description: This dataset corresponds to a research on network organisation of brain structural connectivity in systemic lupus erythematosus (SLE) and its putative association with lesion distribution and disease indicators. White matter hyperintensity (WMH) segmentation and connectomics were performed in 47 patients with SLE from structural and diffusion magnetic resonance imaging (MRI) data. Network nodes were divided into hierarchical tiers based on numbers of connections. From each tier, and globally, brain network metrics were extracted for each patient. Voxel-based analyses of the spatial distribution of WMH in relation to disease indicators and network measures were also conducted. The data comprise all lesion distribution maps from the sample, the raw results (in nifti-1 format) of the voxel-based analyses of the WMH distribution in relation to disease indicators and network parameters, the MATLAB code to process the data, and the excel spreadsheets with the brain network metrics.
description: This dataset and the methods used to generate it are described in details in the file Brain_Network_in_SLE_Data_Summary.pdf that is part of this submission. A graphical overview of the dataset and the processing methods used to generate it are in Overview_SLE_data_processing.pdf , which is also part of this submission.
DOI: 10.7910/dvn/4gt3u3/7y46xv
title: figs.do

description: :unav
DOI: 10.7910/dvn/4gt3u3/h4fwdl
title: housekeeping.do

description: :unav