cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3826290.v1
title: Loto E. coli: Suspension Vs Biofilm network files

description: EXAMPLE FILES FOR LOTO (Condition specific networks and gold standard)<br><br>The contents of this folder (tgz) are:<br><br><br>- ReguloDB_8.7.tsv gold standard network generated from RegulonDB, it includes both true and false edges.<br><br>- ReguloDB_8.7_TP.tsv gold standard network, it only includes true edges.<br><br>- B4h_TP.tsv dynamic network corresponding to Biofilm at 4 hours, it only includes true edges.<br><br>- B7h_TP.tsv dynamic network corresponding to Biofilm at 7 hours, it only includes true edges.<br><br>- B15h_TP.tsv dynamic network corresponding to Biofilm at 15 hours, it only includes true edges.<br><br>- B24h_TP.tsv dynamic network corresponding to Biofilm at 24 hours, it only includes true edges.<br><br>- S4h_TP.tsv dynamic network corresponding to Suspension at 4 hours, it only includes true edges.<br><br>- S7h_TP.tsv dynamic network corresponding to Suspension at 7 hours, it only includes true edges.<br><br>- S15h_TP.tsv dynamic network corresponding to Suspension at 15 hours, it only includes true edges.<br><br>- S24h_TP.tsv dynamic network corresponding to Suspension at 24 hours, it only includes true edges.<br><br><br><br>
DOI: 10.7910/dvn/v1rjpf/uok3l9
title: iqa20160730_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3826284
title: NegDDI-Drugbank.zip

description: NegDDI-DrugBank
DOI: 10.6084/m9.figshare.3824451
title: Simulation data

description: Simulation data for a calcium adatom on doped graphene.<br>
DOI: 10.7910/dvn/v1rjpf/gqseg0
title: iqa20151114_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/k3boyz
title: iqa20160523_03.txt.gz

description: :unav
DOI: 10.6073/pasta/c1890a7b3e2c6ffa45e5dbb9326d32e2
title: Jornada Basin LTER Cross-scale Interactions Study (CSIS) Block 13 meteorological station: 5-minute summary wind and air temperature data: 2013 - ongoing

description: This data package contains 5-minute air temperature and wind summary data from Jornada Basin LTER Cross Scale Interactions Study (CSIS) Block-13 met station. Average air temperature, wind speed, and wind direction are measured and calculated at an automated meteorological station connected to a 900 MHz spread spectrum wireless network. Wind speed is measured at 37cm, 75 cm, 150 cm, and 300 cm, wind direction at approximately 3m, and air temperature and relative humidity at approximate 2.5m. This is a subset of baseline weather data collected at the 15 Jornada Basin LTER CSIS study blocks, New Mexico. Measurements are aggregated at intervals of 5, 30, 60 minutes and daily, with precipitation additionally provided with 1 second aggregation during precipitation events. The met station variables measured include air temperature, precipitation, relative humidity, wind direction, wind speed. Precipitation is not measured at Block 1 and Block 12 because of proximity to Block 2 and Block 13, respectively . This is an ONGOING dataset.
DOI: 10.6084/m9.figshare.3824451.v1
title: A first-principles theory of Coulomb impurities on doped graphene: Application to calcium adatoms

description: Simulation data for the paper: A first-principles theory of Coulomb impurities on doped graphene: Application to calcium adatoms<br>
DOI: 10.7910/dvn/v1rjpf/7vooto
title: iqa20150527_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/pfrmri
title: iqa20151009_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3824451.v2
title: Calcium adatom on doped graphene

description: Simulation data for a calcium adatom on doped graphene.<br>
DOI: 10.7910/dvn/v1rjpf/cxnyrj
title: iqa20161211_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3824448
title: The diversity of arthropods in homes across the United States determined by environmental DNA analyses

description: See manuscript for information on methods, including processing pipeline for sequences. Abbreviated information on files provided in the associated .pdf file "Abbreviated_Processing_Pipeline_Co1"<br>
DOI: 10.7910/dvn/v1rjpf/vz4mer
title: iqa20151221_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3824448.v2
title: The diversity of arthropods in homes across the United States determined by environmental DNA analyses

description: See manuscript for information on methods, including processing pipeline for sequences. Abbreviated information on files provided in the associated .pdf file "Abbreviated_Processing_Pipeline_Co1"<br>
DOI: 10.7910/dvn/v1rjpf/srszgk
title: iqa20150420_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3824448.v1
title: The diversity of arthropods in homes across the United States determined by environmental DNA analyses

description: See manuscript for information on methods, including processing pipeline for sequences. Abbreviated information on files provided in the associated .pdf file "Abbreviated_Processing_Pipeline_Co1"<br>
DOI: 10.7910/dvn/v1rjpf/i1pylr
title: iqa20150920_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/xukf8m
title: iqa20160727_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3824412
title: CC_dataset

description: aaaa
DOI: 10.6084/m9.figshare.3824412.v1
title: CC_dataset

description: aaaa
DOI: 10.7910/dvn/v1rjpf/3urkuw
title: iqa20150407_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/sv1gh2
title: iqa20161212_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/bkpgjt
title: iqa20160101_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3824379
title: Cell-contact-dependent activation of CD4<sup>+</sup> T cells by adhesion molecules on synovial fibroblasts

description: <i>Objective</i>: To determine how cell–cell contact with synovial fibroblasts (SF) influence on the proliferation and cytokine production of CD4<sup>+ </sup>T cells. <i>Methods</i>: Naïve CD4<sup>+ </sup>T cells were cultured with SF from rheumatoid arthritis patients, stimulated by anti-CD3/28 antibody, and CD4<sup>+ </sup>T cell proliferation and IFN-γ/IL-17 production were analyzed. To study the role of adhesion molecules, cell contact was blocked by transwell plate or anti-intracellular adhesion molecule-1 (ICAM-1)/vascular cell adhesion molecule-1(VCAM-1) antibody. To study the direct role of adhesion molecules for CD4<sup>+ </sup>T cells, CD161<sup>+ </sup>or CD161<sup>-</sup> naïve CD4<sup>+ </sup>T cells were stimulated on plastic plates coated by recombinant ICAM-1 or VCAM-1, and the source of IFN-γ/IL-17 were analyzed. <i>Results</i>: SF enhanced naïve CD4<sup>+ </sup>T cell proliferation and IFN-γ/IL-17 production in cell-contact and in part ICAM-1-/VCAM-1-dependent manner. Plate-coated ICAM-1 and VCAM-1 enhanced naïve CD4<sup>+ </sup>T cell proliferation and IFN-γ production, while VCAM-1 efficiently promoting IL-17 production. CD161<sup>+ </sup>naïve T cells upregulating LFA-1 and VLA-4 were the major source of IFN-γ/IL-17 upon interaction with ICAM-1/VCAM-1. <i>Conclusion</i>: CD4<sup>+ </sup>T cells rapidly expand and secrete IFN-γ/IL-17 upon cell-contact with SF via adhesion molecules. Interfering with ICAM-1-/VCAM-1 may be beneficial for inhibiting RA synovitis.
DOI: 10.7910/dvn/v1rjpf/pxnqhw
title: iqa20160717_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/lv4wnw
title: iqa20160918_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/t9lpmq
title: iqa20161118_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/haj6bo
title: iqa20161218_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/oxpygb
title: iqa20161114_03.txt.gz

description: :unav
DOI: 10.5281/zenodo.4013854
title: Supplementary data to *Benchmarking of numerical integration methods for ODE models of biological systems*

description: This archive contains supplementary data and code for the manuscript <strong>Benchmarking of numerical integration methods for ODE models of biological systems </strong>by<strong> Städter et al. 2020</strong>. It contains scripts to automatically download and install all required packages and models, scripts to compile the models and to perform the study, value files containing all data underlying the analyses in the manuscript, scripts to generate the manuscript figures. There is a <strong>README.md </strong>file with further information, in particular on what scripts to execute to reproduce the study.
DOI: 10.6084/m9.figshare.3824373
title: Mirounga angustirostris blubber transcriptome (single ACTH challenge)

description: Juvenile northern elephant seal (Mirounga angustirostris) blubber transcriptome assemblies and annotation. Blubber biopsies were collected during an acute stress challenge induced by administration of a single 30-U dose of adrenocorticotropic hormone (ACTH; Oct-Nov 2014). Blubber samples were collected immediately prior to ("baseline") and 2 and 24 hours following ACTH administration ("acute response" and "recovery", respectively). Mean RNA integrity value for samples was 8.04. Library preparation and Illumina HiSeq 2500 sequencing were conducted at UC Davis DNA Technologies Core Facility using standard protocols. <br>Four baseline, four acute response, and two recovery samples were 100-bp paired-end sequenced on a single Illumina lane, generating mean 32 million reads per sample (SRA Accession: SRP045540). Reads were quality trimmed and abundance normalized using one round of diginorm (khmer v0.8.4; coverage: 20X, k-mer: 20). The raw assembly was produced de novo using Trinity v2.0.6 with default settings. The overall TransRate (v1.0.1) quality score for the assembly was 0.42. The assembly contained 80% of highly conserved vertebrate orthologs (BUSCOs). The filtered assembly was produced using TransDecoder v2.0.1. The annotation report was produced using Trinotate v3.0.0. (SwissProt database downloaded on 3/15/16).<br>
DOI: 10.6084/m9.figshare.3824373.v1
title: Mirounga angustirostris blubber transcriptome

description: Juvenile northern elephant seal (Mirounga angustirostris) blubber transcriptome assemblies and annotation. Blubber biopsies were collected during an acute stress challenge induced by administration of a single 30-U dose of adrenocorticotropic hormone (ACTH; Oct-Nov 2014). Blubber samples were collected immediately prior to ("baseline") and 2 and 24 hours following ACTH administration ("acute response" and "recovery", respectively). Mean RNA integrity value for samples was 8.04. Library preparation and Illumina HiSeq 2500 sequencing were conducted at UC Davis DNA Technologies Core Facility using standard protocols. <br>Four baseline, four acute response, and two recovery samples were 100-bp paired-end sequenced on a single Illumina lane, generating mean 32 million reads per sample (SRA Accession: SRP045540). Reads were quality trimmed and abundance normalized using one round of diginorm (khmer v0.8.4; coverage: 20X, k-mer: 20). The raw assembly was produced de novo using Trinity v2.0.6 with default settings. The overall TransRate (v1.0.1) quality score for the assembly was 0.42. The assembly contained 80% of highly conserved vertebrate orthologs (BUSCOs). The filtered assembly was produced using TransDecoder v2.0.1. The annotation report was produced using Trinotate v3.0.0. (SwissProt database downloaded on 3/15/16).<br>
DOI: 10.7910/dvn/v1rjpf/xwbpvg
title: iqa20160520_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/nagag9
title: iqa20150702_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/u3mkpv
title: iqa20160911_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/iqycir
title: iqa20151008_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/m6efxe
title: iqa20150720_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/z5oxgv
title: iqa20150626_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/vygsdh
title: iqa20161013_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/hgkkat
title: iqa20151001_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/a6cbf9
title: iqa20160510_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/xbc4io
title: iqa20150521_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/lbx1ra
title: iqa20150712_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/4m88rb
title: iqa20160830_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/fcechg
title: iqa20151004_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/76mhtp
title: iqa20150519_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/reqbmt
title: iqa20150328_03.txt.gz

description: :unav
DOI: 10.5281/zenodo.4013863
title: Replication package for «Business disruptions from social distancing»

description: Replication package for Koren, Miklós and Rita Pető. Business disruptions from social distancing; PLoS ONE 2020. https://doi.org/10.1371/journal.pone.0239113
description: {"references": ["National Center for O* NET Development. O* NET OnLine [dataset]; 2020. https://www.onetonline.org/", "U S Bureau of the Census. County Business Patterns [dataset]; 2017. https://www.census.gov/data/datasets/2017/econ/cbp/2017-cbp.html", "SafeGraph. Patterns [dataset]; 2020. https://www.safegraph.com/covid-19-data-consortium", "U S Bureau of Labor Statistics. American Time Use Survey [dataset]; 2018. https://www.bls.gov/tus/#data", "U S Bureau of Labor Statistics. Current Employment Statistics [dataset]; 2020. https://www.bls.gov/ces/", "U S Bureau of Labor Statistics. National Employment Matrix [dataset]; 2020. https://www.bls.gov/emp/tables/industry-occupation-matrix-industry.htm"]}
DOI: 10.7910/dvn/v1rjpf/myzr5p
title: iqa20151101_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/vtolly
title: iqa20160603_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/octzls
title: iqa20160714_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/rvkbaz
title: iqa20160104_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/uvuel8
title: iqa20150706_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/n16dyx
title: iqa20160816_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/jqoa2g
title: iqa20150711_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/oudutn
title: iqa20151011_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/agqn9i
title: iqa20151204_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/1xebh8
title: iqa20160508_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/ckysno
title: iqa20160622_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/jdvpfd
title: iqa20150417_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/bjfoxd
title: iqa20150907_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/smgmya
title: iqa20160517_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/v13ddj
title: iqa20161110_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/zif3pa
title: iqa20151014_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/8km3mo
title: iqa20150430_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/rxqnpm
title: iqa20150611_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3824259
title: Desvenlafaxine overdose and the occurrence of serotonin toxicity, seizures and cardiovascular effects

description: <b>Context:</b> Desvenlafaxine is used to treat major depression. Desvenlafaxine is also the active metabolite of venlafaxine. Venlafaxine overdose can cause serotonin toxicity, seizures and cardiovascular effects, but there is limited information on desvenlafaxine overdose. <b>Objective:</b> We aimed at investigating the clinical effects and complications from desvenlafaxine overdose. <b>Materials and methods:</b> This was a retrospective observational study of desvenlafaxine overdoses over a six-year period. Demographic details, dose and timing of the overdose, together with clinical effects, treatment and complications were extracted from a local hospital network database or the medical records of patients following hospital admission with a desvenlafaxine overdose. <b>Results:</b> There were 182 cases of desvenlafaxine overdose included in the study. From the 182 cases, 75 were desvenlafaxine (± alcohol) only ingestions and 107 included one or more co-ingested drugs. In single-agent desvenlafaxine ingestions, median age was 25 years (range: 13–68 years) with a median ingested dose of 800 mg (range: 250–3500 mg; interquartile range (IQR): 600–1400 mg), and 54/75 (72%) were female. The Glasgow Coma Score (GCS) was 15 in 68/74 (92%) patients, 13–14 in 5/74 (7%), and was seven in one patient following aspiration. Mild hypertension (systolic blood pressure [BP] &gt; 140–180 mmHg) occurred in 23/71 patients (32%), and tachycardia occurred in 29/74 (39%) patients. There were no abnormal QT intervals and no QRS &gt;120 m s. Serotonin toxicity was diagnosed by the treating physician in 7/75 (9%) patients, but only one of these met the Hunter Serotonin Toxicity Criteria. None of the 75 patients who took desvenlafaxine only (± alcohol) had seizures, were admitted to intensive care or died. In comparison, the 107 patients taking desvenlafaxine in overdose with other medications developed more pronounced toxicity. Generalised seizures occurred in 5/107 (5%), but in three of these cases co-ingestants were possible proconvulsants. Fifteen patients had a GCS ≤9 and none had an abnormal QT or QRS. Severe effects appeared to be associated with coingestants. <b>Conclusion:</b> Desvenlafaxine overdose causes minor effects with mild hypertension and tachycardia. The risk of seizures or serotonin toxicity is low.
DOI: 10.7910/dvn/v1rjpf/tnldfu
title: iqa20150908_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3824259.v1
title: Desvenlafaxine overdose and the occurrence of serotonin toxicity, seizures and cardiovascular effects

description: <b>Context:</b> Desvenlafaxine is used to treat major depression. Desvenlafaxine is also the active metabolite of venlafaxine. Venlafaxine overdose can cause serotonin toxicity, seizures and cardiovascular effects, but there is limited information on desvenlafaxine overdose. <b>Objective:</b> We aimed at investigating the clinical effects and complications from desvenlafaxine overdose. <b>Materials and methods:</b> This was a retrospective observational study of desvenlafaxine overdoses over a six-year period. Demographic details, dose and timing of the overdose, together with clinical effects, treatment and complications were extracted from a local hospital network database or the medical records of patients following hospital admission with a desvenlafaxine overdose. <b>Results:</b> There were 182 cases of desvenlafaxine overdose included in the study. From the 182 cases, 75 were desvenlafaxine (± alcohol) only ingestions and 107 included one or more co-ingested drugs. In single-agent desvenlafaxine ingestions, median age was 25 years (range: 13–68 years) with a median ingested dose of 800 mg (range: 250–3500 mg; interquartile range (IQR): 600–1400 mg), and 54/75 (72%) were female. The Glasgow Coma Score (GCS) was 15 in 68/74 (92%) patients, 13–14 in 5/74 (7%), and was seven in one patient following aspiration. Mild hypertension (systolic blood pressure [BP] &gt; 140–180 mmHg) occurred in 23/71 patients (32%), and tachycardia occurred in 29/74 (39%) patients. There were no abnormal QT intervals and no QRS &gt;120 m s. Serotonin toxicity was diagnosed by the treating physician in 7/75 (9%) patients, but only one of these met the Hunter Serotonin Toxicity Criteria. None of the 75 patients who took desvenlafaxine only (± alcohol) had seizures, were admitted to intensive care or died. In comparison, the 107 patients taking desvenlafaxine in overdose with other medications developed more pronounced toxicity. Generalised seizures occurred in 5/107 (5%), but in three of these cases co-ingestants were possible proconvulsants. Fifteen patients had a GCS ≤9 and none had an abnormal QT or QRS. Severe effects appeared to be associated with coingestants. <b>Conclusion:</b> Desvenlafaxine overdose causes minor effects with mild hypertension and tachycardia. The risk of seizures or serotonin toxicity is low.
DOI: 10.6084/m9.figshare.3824250
title: Data summary for paper "Individual differences in internal noise are consistent across two measurement techniques"

description: The data used in the 'Individual differences in internal noise are consistent across two measurement techniques' paper by Vilidaite & Baker (Vision Research).
DOI: 10.7910/dvn/v1rjpf/w8fuum
title: iqa20160623_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/qvpfhy
title: iqa20160729_03.txt.gz

description: :unav
DOI: 10.15156/bio/sh1284949.08fu
title: SH1284949.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1284950.08fu
title: SH1284950.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1284951.08fu
title: SH1284951.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.