cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7856711
title: Changes in platelet function with inflammation in patients undergoing vascular surgery

description: The role of platelets in ischaemic events is well established. Aspirin represents the default antiplatelet and blocks the metabolism of arachidonic acid (AA) at the cyclo-oxygenase enzyme (COX). AA is commonly used as a test of response to aspirin, but recent data raise uncertainty about the validity of this approach. Specifically, in some patients AA-induced clotting is not suppressed, but the level of COX-dependent AA metabolite, thromboxane B2 (TXB<sub>2</sub>) is negligible. Furthermore, AA-induced whole blood clotting varies dynamically in individuals, who are aspirin responsive according to TXB<sub>2</sub> levels. The aim of this study was to assess the level of AA-, ADP- and thrombin-mediated platelet reactivity in patients on aspirin before, during, and after major vascular surgery, which represents a model of on/off vascular inflammation. Firstly, we hypothesized, that in association with this inflammatory episode AA-, ADP- and thrombin-induced clotting would change in a dynamic manner. Secondly, that AA-induced clotting will be modified despite complete suppression of platelet TXB<sub>2</sub> production by aspirin throughout the periprocedural period, possibly via a lipoxygenase-mediated mechanism. Fourty patients underwent major vascular surgery (open abdominal aortic aneurysm operation, infrainguinal bypass for subcritical limb ischaemia or peripheral aneurysm repair with bypass). They were all on 75 mg of aspirin prior to and throughout the perioperative period and received 5000 units of unfractionated heparin intraoperatively. AA-, ADP-, and thrombin-induced clotting, AA metabolites (TXB<sub>2</sub> and 12-Hyroxyeicosatetraenoic acid (12-HETE)) and inflammatory markers (CRP, IL-6, TNF-α and CD40) were measured pre-procedure and at 2, 24, 48 hours, 3 to 5 days and 3 months after surgery. AA-, ADP- and thrombin-induced platelet reactivity was assessed using thrombelastography. TXB<sub>2</sub>, 12-HETE, IL-6, TNF-α, CD40 were determined using the sequential competitive binding Enzyme-Linked ImmunoAssay technique and CRP was determined using an immune-turbidimetric test on human serum. There was a transient rise in inflammatory markers in the early perioperative period (CRP at 24, 48 hours and 3 to 5 days <i>p</i> p 2 throughout, confirming a consistent therapeutic response to aspirin. There was a transient rise in thrombin-mediated clotting (MA<sub>Thrombin</sub> at 48 hours <i>p</i> = 0.001 and 3 to 5 days <i>p</i> AA and MA<sub>ADP</sub> <i>p</i> = 0.001 at 2 hours). At 3 months, the level of AA- and ADP-induced clotting was significantly higher than at baseline (<i>p</i> = 0.008 for MA<sub>AA</sub> and <i>p</i> = 0.002 for MA<sub>ADP</sub>), hence demonstrating a rebound effect. These data demonstrate a novel dynamic variation in platelet aggregation with acute vascular inflammation, including AA-induced whole blood clotting which is apparently COX-1 independent.
DOI: 10.6084/m9.figshare.7856708
title: Development of the cephalopod-specific universal primer set and its application for the metabarcoding analysis of planktonic cephalopods in Korean waters

description: The NGS raw data files generated by Illumina MiSeq system to analyze the biodiversity of planktonic cephalopods in Korean waters, 2016.
DOI: 10.6084/m9.figshare.7856711.v1
title: Changes in platelet function with inflammation in patients undergoing vascular surgery

description: The role of platelets in ischaemic events is well established. Aspirin represents the default antiplatelet and blocks the metabolism of arachidonic acid (AA) at the cyclo-oxygenase enzyme (COX). AA is commonly used as a test of response to aspirin, but recent data raise uncertainty about the validity of this approach. Specifically, in some patients AA-induced clotting is not suppressed, but the level of COX-dependent AA metabolite, thromboxane B2 (TXB<sub>2</sub>) is negligible. Furthermore, AA-induced whole blood clotting varies dynamically in individuals, who are aspirin responsive according to TXB<sub>2</sub> levels. The aim of this study was to assess the level of AA-, ADP- and thrombin-mediated platelet reactivity in patients on aspirin before, during, and after major vascular surgery, which represents a model of on/off vascular inflammation. Firstly, we hypothesized, that in association with this inflammatory episode AA-, ADP- and thrombin-induced clotting would change in a dynamic manner. Secondly, that AA-induced clotting will be modified despite complete suppression of platelet TXB<sub>2</sub> production by aspirin throughout the periprocedural period, possibly via a lipoxygenase-mediated mechanism. Fourty patients underwent major vascular surgery (open abdominal aortic aneurysm operation, infrainguinal bypass for subcritical limb ischaemia or peripheral aneurysm repair with bypass). They were all on 75 mg of aspirin prior to and throughout the perioperative period and received 5000 units of unfractionated heparin intraoperatively. AA-, ADP-, and thrombin-induced clotting, AA metabolites (TXB<sub>2</sub> and 12-Hyroxyeicosatetraenoic acid (12-HETE)) and inflammatory markers (CRP, IL-6, TNF-α and CD40) were measured pre-procedure and at 2, 24, 48 hours, 3 to 5 days and 3 months after surgery. AA-, ADP- and thrombin-induced platelet reactivity was assessed using thrombelastography. TXB<sub>2</sub>, 12-HETE, IL-6, TNF-α, CD40 were determined using the sequential competitive binding Enzyme-Linked ImmunoAssay technique and CRP was determined using an immune-turbidimetric test on human serum. There was a transient rise in inflammatory markers in the early perioperative period (CRP at 24, 48 hours and 3 to 5 days <i>p</i> p 2 throughout, confirming a consistent therapeutic response to aspirin. There was a transient rise in thrombin-mediated clotting (MA<sub>Thrombin</sub> at 48 hours <i>p</i> = 0.001 and 3 to 5 days <i>p</i> AA and MA<sub>ADP</sub> <i>p</i> = 0.001 at 2 hours). At 3 months, the level of AA- and ADP-induced clotting was significantly higher than at baseline (<i>p</i> = 0.008 for MA<sub>AA</sub> and <i>p</i> = 0.002 for MA<sub>ADP</sub>), hence demonstrating a rebound effect. These data demonstrate a novel dynamic variation in platelet aggregation with acute vascular inflammation, including AA-induced whole blood clotting which is apparently COX-1 independent.
DOI: 10.6084/m9.figshare.7856720.v1
title: Characteristics of platelet count and size and diagnostic accuracy of mean platelet volume in patients with venous thromboembolism. A systematic review and meta-analysis

description: The purpose of this study was to evaluate the association between platelet (PLT) count and mean platelet volume (MPV) and venous thromboembolism (VTE). Thus, this study reviewed and performed a quantitative synthesis on data from the literature. This meta-analysis was conducted in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. 18 studies were included in this paper. A random-effect meta-analysis was conducted for the assessment of heterogeneity using thrombosis place, type of analyzer, type of anticoagulant and incubation time of samples as covariates. A mixed-effect meta-regression was performed based on the subgroup for the whole samples using thrombosis place and method of measurement as moderators for MPV and PLT, respectively. The cumulative estimates and 95% confidence interval (95%CI) of specificity, sensitivity, area under the receiver operator characteristic curve (AUC) and diagnostic odds ratio (DOR) for MPV were calculated using a random effect model. The quality assessments were evaluated according to the quality assessment and diagnostic accuracy tool-2 (QUADAS-2). The primary outcome was the occurrence of VTE. Secondary outcomes included PLT and MPV. Patient with deep vein thrombosis is likely to have a higher value of MPV than control group (<i>P</i> P
DOI: 10.6084/m9.figshare.7856660
title: Analysis scripts and supplementary files: Incidence of symptomatic and asymptomatic HIV-associated sensory neuropathy in tenofovir-exposed individuals

description: <b>Bibliometric information</b>Pillay P, Wadley AL, Cherry CL, Karstaedt AS, Kamerman PR. HIV-associated sensory neuropathy continues to be a problem in South Africans starting tenofovir-based antiretroviral treatment.<br><b>Abstract</b><i>Objectives:</i> HIV-associated sensory neuropathy (HIV-SN) is a common and often painful neurological condition associated with HIV-infection and its treatment. However, data on the incidence of HIV-SN in neuropathy-free individuals initiating combination antiretroviral therapies (cART) that do not contain the neurotoxic agent stavudine are lacking.<br><i>Design: </i>We investigated the six-month incidence of HIV-SN in ART naïve individuals initiating tenofovir (TDF)-based cART, and the clinical factors associated with the development of HIV-SN.<br><i>Methods:</i> 120 neuropathy-free and ART naïve individuals initiating cART at a single centre in Johannesburg, South Africa were enrolled. Participants were screened for HIV-SN at study enrolment and then approximately every two-months for a period of approximately six-months. Symptomatic HIV-SN was defined by the presence of at least one symptom (pain/burning, numbness, paraesthesias) and at least two clinical signs (reduced vibration sense, absent ankle reflexes or pin-prick hypoaesthesia). Asymptomatic HIV-SN required at least two clinical signs only.<br><i>Results: </i>Approximately 80% of the cohort completed three or more visits with the six-mopnth period. Eleven individuals developed asymptomatic HIV-SN and nine developed symptomatic HIV-SN, giving a six-month cumulative incidence of neuropathy of 140 cases per 1000 patients (95% CI: 80 - 210) at an incidence rate of 0.37 (95% CI: 0.2 - 0.5) per person year. Increasing height and a current tuberculosis (TB) infection were independently associated with the risk of developing HIV-SN (p &lt; 0.05).<br><i>Conclusions: </i>We found that within the first six months of starting cART, incident SN persists in the post-stavudine era, but tends to be asymptomatic.<b><br></b><b>Analysis outputs</b>The data required to run the scripts have not been included in the repo because study participants did not consent to public release of their data. However, the data are available on request from Peter Kamerman (peter.kamerman@gmail.com), or by submitting an issue at: https://github.com/kamermanpr/hivsn-incidence/issues.<br>The outputs from all analysis scripts are located in the /outputs directory. The outputs are formatted as markdown and html. The markdown documents are intermediate outputs generated during the production of the html documents, and while they allow quick browsing of the analysis outputs on GitHub, MathJax formulae and tables are not formatted. <br>
DOI: 10.6084/m9.figshare.7856708.v1
title: Development of the cephalopod-specific universal primer set and its application for the metabarcoding analysis of planktonic cephalopods in Korean waters

description: The NGS raw data files generated by Illumina MiSeq system to analyze the biodiversity of planktonic cephalopods in Korean waters, 2016.
DOI: 10.6084/m9.figshare.7856657
title: Raw Data Saliva Japanese Children.xlsx

description: Veillonella isolation in the saliva of Japanese children
DOI: 10.6084/m9.figshare.7856648
title: Table Veillonella.xlsx

description: Veillonella isolation in the saliva of Japanese children
DOI: 10.6084/m9.figshare.7856648.v1
title: Table Veillonella.xlsx

description: Veillonella isolation in the saliva of Japanese children
DOI: 10.6084/m9.figshare.7856180
title: R_Script for estimation of minimum and maximum error.

description: R script used for the estimation of minimum and maximum error rate from the clustering results. <br>
DOI: 10.6084/m9.figshare.7856171
title: Niche-desert facilitation studies synthesis

description: Studies that examined niche and facilitation in deserts used in a systematic review and synthesis.
DOI: 10.6084/m9.figshare.7856156
title: Summarized Table

description: A table summarizing the estimated minimum and maximum numbers of mislabeled sequences per phylum and per gene.
DOI: 10.6084/m9.figshare.7856141
title: Jumping model with foot

description: Matlab codes for simulating vertical jumping with a 6-DoF musculoskeletal model
DOI: 10.6084/m9.figshare.7856171.v1
title: Niche-desert facilitation studies synthesis

description: Studies that examined niche and facilitation in deserts used in a systematic review and synthesis.
DOI: 10.6084/m9.figshare.7855850
title: Han_etal_Data.tsv.gz

description: Table of functional inference for genetic variants in <i>Pan </i>species (chimpanzees and bonobos), from 69 individuals, with gene names, annotation of deleterious alleles, and individual genotypes (0 = homozygous reference, 1 = heterozygous, 2 = homozygous alternative).<br>This study is published in Genome Biology and Evolution: https://doi.org/10.1093/gbe/evz047<br>Genetic variation in Pan species is shaped by demographic history and harbors lineage-specific functions Sojung Han, Aida M Andrés, Tomas Marques-Bonet, Martin Kuhlwilm
DOI: 10.6084/m9.figshare.7855853
title: Kremlin transcripts 1999–February 2019, Russian

description: Document collection scraped from the Russian governmental website kremlin.ru, where all content is licensed under Creative Commons Attribution 4.0.<br>Downloaded on 17 March 2019. Includes all items listed at http://kremlin.ru/events/president/transcripts up to the end of February 2019 (10221 documents).<br>Format:1) Kremlin_transcripts_ru_corpus.rds: a 'corporaexplorerobject' intended to be used with the corporaexplorer R package (https://github.com/kgjerde/corporaexplorer).2) Kremlin_transcripts_ru_df.rds: A regular R data frame with the documents and some metadata.<br>Version 3. Edited 1 November 2019: utf8 encoding fix.
DOI: 10.6084/m9.figshare.7855853.v1
title: Kremlin transcripts 1999–February 2019, Russian

description: Document collection scraped from the Russian governmental website kremlin.ru, where all content is licensed under Creative Commons Attribution 4.0.<br>Downloaded on 17 March 2019. Includes all items listed at http://kremlin.ru/events/president/transcripts up to the end of February 2019 (10221 documents).<br>Format:1) Kremlin_transcripts_ru_corpus.rds: a 'corporaexplorerobject' intended to be used with the corporaexplorer R package (https://github.com/kgjerde/corporaexplorer).2) Kremlin_transcripts_ru_df.rds: A regular R data frame with the documents and some metadata.
DOI: 10.6084/m9.figshare.7855853.v2
title: Kremlin transcripts 1999–February 2019, Russian

description: Document collection scraped from the Russian governmental website kremlin.ru, where all content is licensed under Creative Commons Attribution 4.0.<br>Downloaded on 17 March 2019. Includes all items listed at http://kremlin.ru/events/president/transcripts up to the end of February 2019 (10221 documents).<br>Format:1) Kremlin_transcripts_ru_corpus.rds: a 'corporaexplorerobject' intended to be used with the corporaexplorer R package (https://github.com/kgjerde/corporaexplorer).2) Kremlin_transcripts_ru_df.rds: A regular R data frame with the documents and some metadata.
DOI: 10.5519/qd.1csnq44g
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (6 records)
DOI: 10.6084/m9.figshare.7855736
title: Vitamin D Intake Research

description: Contains the data set available for the research completed assessing the relationship between vitamin D intake to mood and vitamin D-related knowledge in college students. Also available is the survey used to better assess data.
DOI: 10.6084/m9.figshare.7855736.v2
title: Vitamin D Intake Research

description: Contains the data set available for the research completed assessing the relationship between vitamin D intake to mood and vitamin D-related knowledge in college students. Also available is the survey used to better assess data.
DOI: 10.6084/m9.figshare.7855736.v1
title: Vitamin D Intake Research

description: Contains the data set available for the research completed assessing the relationship between vitamin D intake to mood and vitamin D-related knowledge in college students.
DOI: 10.6084/m9.figshare.7855673
title: Jumping model

description: Matlab files for running a 2D simulation of vertical jumping
DOI: 10.6084/m9.figshare.7855670
title: Wild Australia Cane Toad Skin Microbe Raw Data

description: Fastq data from MiSeq microbiome sequencing of swab samples from wild cane toads in Australia. Zipped file includes one .fastq.gz file per toad/negative control and .xlsx file of toad IDs and their sampling locations.<br>Data are associated with:Weitzman, C. L., M. Kaestli, K. Gibb, G. P. Brown, R. Shine, and K. Christian. 2019. Disease exposure and antifungal bacteria on skin of invasive cane toads, Australia. Emerging Infectious Diseases 25(9):1770-1771. https://doi.org/10.3201/eid2509.190386
DOI: 10.6084/m9.figshare.7855670.v1
title: Wild Australia Cane Toad Skin Microbe Raw Data

description: Fastq data from MiSeq microbiome sequencing of swab samples from wild cane toads in Australia. Zipped file includes one .fastq.gz file per toad/negative control and .xlsx file of toad IDs and their sampling locations.<br>Data are associated with:Weitzman, C. L., M. Kaestli, K. Gibb, G. P. Brown, R. Shine, and K. Christian. 2019. Disease exposure and antifungal bacteria on skin of invasive cane toads, Australia. Emerging Infectious Diseases 25(9):1770-1771. https://doi.org/10.3201/eid2509.190386
DOI: 10.6084/m9.figshare.7855673.v1
title: Jumping model

description: Matlab files for running a 2D simulation of vertical jumping
DOI: 10.6084/m9.figshare.7855673.v2
title: Jumping model

description: Matlab files for running a 2D simulation of vertical jumping
DOI: 10.6084/m9.figshare.7855592
title: Knowledge and attitudes among life scientists towards reproducibility within journal articles_survey_datafile_raw_data

description: Raw datafile of the survey data collected from the survey distributed to collect knowledge and attitudes among life scientists towards reproducibility within journal articles.
DOI: 10.6084/m9.figshare.7855580
title: Supplementary Section 2. Free text answers: Knowledge and attitudes among life scientists towards reproducibility within journal articles: a research survey.

description: Supplementary Section 2. Free text answers. <br><br>Free text answers: Knowledge and attitudes among life scientists towards reproducibility within journal articles.<br><br><br>
DOI: 10.6084/m9.figshare.7855673.v3
title: Jumping model

description: Matlab files for running a 2D simulation of vertical jumping
DOI: 10.6084/m9.figshare.7855577
title: Social Interaction test videos registered on day 1 in adult Japanese quail

description: Social Interaction test videos of the first day of testing. Japanese quail test birds were placed in a novel test environment and after an adaptation period were exposed to a photocastrated (non-aggressive) opponent. All birds were tested only once over a 5 day period. Video file names provide the ID of the animal testes.
DOI: 10.6084/m9.figshare.7855583
title: T lymphocytes migrate upstream after completing the leukocyte adhesion cascade

description: The leukocyte adhesion cascade is of critical importance for both the maintenance of immune homeostasis and the ability of immune cells to perform effector functions. Here, we present data showing CD4<sup>+</sup> T cells migrate upstream (against the direction of flow) after completing the leukocyte adhesion cascade on surfaces displaying either ICAM-1 or ICAM-1 and VCAM-1, but migrate downstream on surfaces displaying only VCAM-1. Cells completing the cascade on HUVECs initially migrate upstream before reverting to more random migration, partly caused by transmigration of cells migrating against the flow. Furthermore, cells migrating upstream transmigrate faster than cells migrating downstream. On HUVECs, blocking interactions between LFA-1 and ICAM-1 resulted in downstream migration and slower transmigration. These results further suggest a possible physiological role for upstream migration <i>in vivo</i>.
DOI: 10.6084/m9.figshare.7855577.v1
title: Social Interaction test videos registered on day 1 in adult Japanese quail

description: Social Interaction test videos of the first day of testing. Japanese quail test birds were placed in a novel test environment and after an adaptation period were exposed to a photocastrated (non-aggressive) opponent. All birds were tested only once over a 5 day period. Video file names provide the ID of the animal testes.
DOI: 10.6084/m9.figshare.7855571
title: A fuzzy optimization model for the electric vehicle routing problem with time windows and recharging stations

description: This is the experimental data of the manuscript entitled "A fuzzy optimization model for the electric vehicle routing problem with time windows and recharging stations". All data are saved in the file with txt format.
DOI: 10.6084/m9.figshare.7855574
title: Splitting the spotlight? Evidence from attentional capture by successive events

description: Please refer to the manuscript attached to this project
DOI: 10.6084/m9.figshare.7855583.v1
title: T lymphocytes migrate upstream after completing the leukocyte adhesion cascade

description: The leukocyte adhesion cascade is of critical importance for both the maintenance of immune homeostasis and the ability of immune cells to perform effector functions. Here, we present data showing CD4<sup>+</sup> T cells migrate upstream (against the direction of flow) after completing the leukocyte adhesion cascade on surfaces displaying either ICAM-1 or ICAM-1 and VCAM-1, but migrate downstream on surfaces displaying only VCAM-1. Cells completing the cascade on HUVECs initially migrate upstream before reverting to more random migration, partly caused by transmigration of cells migrating against the flow. Furthermore, cells migrating upstream transmigrate faster than cells migrating downstream. On HUVECs, blocking interactions between LFA-1 and ICAM-1 resulted in downstream migration and slower transmigration. These results further suggest a possible physiological role for upstream migration <i>in vivo</i>.
DOI: 10.6084/m9.figshare.7855478
title: gVCF_HG00122

description: 1000 Genomes gVCF mapped to hs37d5 for HG00122.
DOI: 10.6084/m9.figshare.7855580.v1
title: Free text answers: Knowledge and attitudes among life scientists towards reproducibility within journal articles.

description: Free text answers. <br>
DOI: 10.6084/m9.figshare.7855478.v1
title: gVCF_HG00122

description: 1000 Genomes gVCF mapped to hs37d5 for HG00122.
DOI: 10.6084/m9.figshare.7855472
title: gVCF_HG00120

description: 1000 Genomes gVCF mapped to hs37d5 for HG00120.
DOI: 10.6084/m9.figshare.7855475
title: gVCF_HG00121

description: 1000 Genomes gVCF mapped to hs37d5 for HG00121.
DOI: 10.6084/m9.figshare.7855472.v1
title: gVCF_HG00120

description: 1000 Genomes gVCF mapped to hs37d5 for HG00120.
DOI: 10.6084/m9.figshare.7855475.v1
title: gVCF_HG00121

description: 1000 Genomes gVCF mapped to hs37d5 for HG00121.
DOI: 10.6084/m9.figshare.7855571.v1
title: A fuzzy optimization model for the electric vehicle routing problem with time windows

description: This is the experimental data of the manuscript entitled "A fuzzy optimization model for the electric vehicle routing problem with time windows". All data are saved in the file with txt format.
DOI: 10.6084/m9.figshare.7855580.v3
title: Supplementary Section 2. Free text answers: Knowledge and attitudes among life scientists towards reproducibility within journal articles: a research survey.

description: Supplementary Section 2. Free text answers. <br><br>Free text answers: Knowledge and attitudes among life scientists towards reproducibility within journal articles.<br><br><br>
DOI: 10.6084/m9.figshare.7855463
title: gVCF_HG00117

description: 1000 Genomes gVCF mapped to hs37d5 for HG00117.
DOI: 10.6084/m9.figshare.7855466
title: gVCF_HG00118

description: 1000 Genomes gVCF mapped to hs37d5 for HG00118.
DOI: 10.6084/m9.figshare.7855469
title: gVCF_HG00119

description: 1000 Genomes gVCF mapped to hs37d5 for HG00119.