cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4563685
title: Jones et al - Pavlovian influences on rat and mouse learning

description: Data accompanying paper by Jones et al. which investigates learning during a counterbalanced Go/NoGo judgement bias task in both rats and mice. There are 5 separate excel files. All files contain a sheet with data and another sheet containing descriptions of the variables. The files are:<br>1) Jones et al - rat and mice learning criterion data: contains data for number of sessions required to achieve learning criterion (as defined in the paper) for different phases of training on the Go/NoGo judgement bias task.<br>2) Jones et al - rat and mice percentage correct responses data: contains data on the percentage of correct responses made by rats to positive and negative tones during the discrimination training phase of the task.<br>3) Jones et al - rat and mice proportion positive responses during ambiguity tests data: contains data on the proportion of positive responses made during ambiguity tests.<br>4) Jones et al - rat and mice latency to escape air puff data: contains data on escape latencies following receipt of air puffs during the first 6 sessions of the negative tone and discrimination training phases.<br>5) Jones et al - rat and mice shuttle rate data: contains data on the shuttle rates / min during the ITIs of the last 5 discrimination training sessions.
DOI: 10.6084/m9.figshare.4563928.v3
title: Model code, data, and output

description: Saved R files containing model outputs for the manuscript "Detecting the impact of temperature on transmission of Zika, dengue and chikungunya using mechanistic models."<br>
DOI: 10.6084/m9.figshare.4563685.v2
title: Jones et al - Pavlovian influences on rat and mouse learning

description: Data accompanying paper by Jones et al. which investigates learning during a counterbalanced Go/NoGo judgement bias task in both rats and mice. There are 5 separate excel files. All files contain a sheet with data and another sheet containing descriptions of the variables. The files are:<br>1) Jones et al - rat and mice learning criterion data: contains data for number of sessions required to achieve learning criterion (as defined in the paper) for different phases of training on the Go/NoGo judgement bias task.<br>2) Jones et al - rat and mice percentage correct responses data: contains data on the percentage of correct responses made by rats to positive and negative tones during the discrimination training phase of the task.<br>3) Jones et al - rat and mice proportion positive responses during ambiguity tests data: contains data on the proportion of positive responses made during ambiguity tests.<br>4) Jones et al - rat and mice latency to escape air puff data: contains data on escape latencies following receipt of air puffs during the first 6 sessions of the negative tone and discrimination training phases.<br>5) Jones et al - rat and mice shuttle rate data: contains data on the shuttle rates / min during the ITIs of the last 5 discrimination training sessions.
DOI: 10.6084/m9.figshare.4563574
title: Supplementary files for the bryozoan cell lineage project

description: Supplementary files for the bryozoan <i>Membranipora membranacea</i> cell lineage project. Contains:- Simi BioCell source files containing the cell lineages of four wild type embryos.- Cleaned Simi BioCell files used for cell lineage analyses.- MaMuT cell lineage files converted from the Simi files.- Data and code to generate plots for the cell lineage analyses.- Additional MAPK data.- Image processing commands.- Source scripts for establishing the orthology of <i>M. membranacea</i> genes.- Sequences submitted to the NCBI.
DOI: 10.6084/m9.figshare.4563685.v1
title: Jones et al - Pavlovian influences on rat and mouse learning

description: Data accompanying paper by Jones et al. which investigates learning during a counterbalanced Go/NoGo judgement bias task in both rats and mice. There are 5 separate excel files. All files contain a sheet with data and another sheet containing descriptions of the variables. The files are:<br>1) Jones et al - rat and mice learning criterion data: contains data for number of sessions required to achieve learning criterion (as defined in the paper) for different phases of training on the Go/NoGo judgement bias task.<br>2) Jones et al - rat and mice percentage correct responses data: contains data on the percentage of correct responses made by rats to positive and negative tones during the discrimination training phase of the task.<br>3) Jones et al - rat and mice proportion positive responses during ambiguity tests data: contains data on the proportion of positive responses made during ambiguity tests.<br>4) Jones et al - rat and mice latency to escape air puff data: contains data on escape latencies following receipt of air puffs during the first 6 sessions of the negative tone and discrimination training phases.<br>5) Jones et al - rat and mice shuttle rate data: contains data on the shuttle rates / min during the ITIs of the last 5 discrimination training sessions.
DOI: 10.6084/m9.figshare.4563928.v4
title: Model code, data, and output

description: Saved R files containing model outputs for the manuscript "Detecting the impact of temperature on transmission of Zika, dengue and chikungunya using mechanistic models."<br>
DOI: 10.6084/m9.figshare.4563928.v5
title: Model code, data, and output

description: Saved R files containing model outputs for the manuscript "Detecting the impact of temperature on transmission of Zika, dengue and chikungunya using mechanistic models."<br>
DOI: 10.6084/m9.figshare.4561015
title: Table S2. Biological Process Ontology (BP-GO) term enrichment in genes showing their expression affected by pico and mrtf. from Transcriptional responses to hyperplastic MRL signalling in <i>Drosophila</i>

description: Biological Process Ontology (BP-GO) term enrichment in genes showing their expression affected by pico and mrtf. Gene Ontology (GO) enrichment was determined using DAVID (Huang et al., 2009). Biological process categories from GO analysis that are significantly overrepresented among the genes for which the expression were either decreased (downregulated worksheet) or increased (upregulated worksheet) in response to pico overexpression or mrtf overexpression. BP-GO were grouped into categories sharing similar function and used to produce the pie chart (Figure 1A). Only the categories with a minimum of 5 genes per category and an EASE score ≤0.05 were considered.
DOI: 10.6084/m9.figshare.4561006
title: Table S1 from The Notch pathway in the annelid <i>Platynereis</i>: insights into chaetogenesis and neurogenesis processes

description: Notch is a key signalling pathway playing multiple and varied functions during development. Notch regulates the selection of cells with a neurogenic fate and maintains a pool of yet uncommitted precursors through lateral inhibition, both in insects and in vertebrates. Here, we explore the functions of Notch in the annelid <i>Platynereis dumerilii</i> (Lophotrochozoa). Conserved components of the pathway are identified and a scenario for their evolution in metazoans is proposed. Unexpectedly, neither <i>Notch</i> nor its ligands are expressed in the neurogenic epithelia of the larva at the time when massive neurogenesis begins. Using chemical inhibitors and neural markers, we demonstrate that Notch plays no major role in the general neurogenesis of larvae. Instead, we find Notch components expressed in nascent chaetal sacs, the organs that produce the annelid bristles. Impairing Notch signalling induces defects in chaetal sac formation, abnormalities in chaetae producing cells and a change of identity of chaeta growth accessory cells. This is the first bilaterian species in which the early neurogenesis processes appear to occur without a major involvement of the Notch pathway. Instead, Notch is co-opted to pattern annelid-specific organs, likely through a lateral inhibition process. These features reinforce the view that Notch signalling has been recruited multiple times in evolution due to its remarkable ‘toolkit’ nature.
DOI: 10.6084/m9.figshare.4561015.v1
title: Table S2. Biological Process Ontology (BP-GO) term enrichment in genes showing their expression affected by pico and mrtf. from Transcriptional responses to hyperplastic MRL signalling in <i>Drosophila</i>

description: Biological Process Ontology (BP-GO) term enrichment in genes showing their expression affected by pico and mrtf. Gene Ontology (GO) enrichment was determined using DAVID (Huang et al., 2009). Biological process categories from GO analysis that are significantly overrepresented among the genes for which the expression were either decreased (downregulated worksheet) or increased (upregulated worksheet) in response to pico overexpression or mrtf overexpression. BP-GO were grouped into categories sharing similar function and used to produce the pie chart (Figure 1A). Only the categories with a minimum of 5 genes per category and an EASE score ≤0.05 were considered.
DOI: 10.6084/m9.figshare.4561006.v1
title: Table S1 from The Notch pathway in the annelid <i>Platynereis</i>: insights into chaetogenesis and neurogenesis processes

description: Notch is a key signalling pathway playing multiple and varied functions during development. Notch regulates the selection of cells with a neurogenic fate and maintains a pool of yet uncommitted precursors through lateral inhibition, both in insects and in vertebrates. Here, we explore the functions of Notch in the annelid <i>Platynereis dumerilii</i> (Lophotrochozoa). Conserved components of the pathway are identified and a scenario for their evolution in metazoans is proposed. Unexpectedly, neither <i>Notch</i> nor its ligands are expressed in the neurogenic epithelia of the larva at the time when massive neurogenesis begins. Using chemical inhibitors and neural markers, we demonstrate that Notch plays no major role in the general neurogenesis of larvae. Instead, we find Notch components expressed in nascent chaetal sacs, the organs that produce the annelid bristles. Impairing Notch signalling induces defects in chaetal sac formation, abnormalities in chaetae producing cells and a change of identity of chaeta growth accessory cells. This is the first bilaterian species in which the early neurogenesis processes appear to occur without a major involvement of the Notch pathway. Instead, Notch is co-opted to pattern annelid-specific organs, likely through a lateral inhibition process. These features reinforce the view that Notch signalling has been recruited multiple times in evolution due to its remarkable ‘toolkit’ nature.
DOI: 10.6084/m9.figshare.4561000
title: Table S1. Comparison of gene level expression in wings imaginal disks of pico and mrtf to control by RNA-sequencing. from Transcriptional responses to hyperplastic MRL signalling in <i>Drosophila</i>

description: Comparison of gene level expression in wings imaginal disks of pico and mrtf to control by RNA-sequencing. mRNA from wings imaginal disks of MS1096&gt;pico MS1096&gt;mrft and MS1096-GAL4 alone were sequenced on illumina Hi-seq 2000 (40 M reads each repeat) and statistically compared by t-test where P value were adjusted by Benjamini-Hochberg (FDR&lt;0.05; (Benjamini and Hochberg, 1995)) multiple testing procedure (allDataset worksheet). Genes significantly under- or over-expressed in pico and mrtf are displayed in separated worksheets.
DOI: 10.6084/m9.figshare.4561000.v1
title: Table S1. Comparison of gene level expression in wings imaginal disks of pico and mrtf to control by RNA-sequencing. from Transcriptional responses to hyperplastic MRL signalling in <i>Drosophila</i>

description: Comparison of gene level expression in wings imaginal disks of pico and mrtf to control by RNA-sequencing. mRNA from wings imaginal disks of MS1096&gt;pico MS1096&gt;mrft and MS1096-GAL4 alone were sequenced on illumina Hi-seq 2000 (40 M reads each repeat) and statistically compared by t-test where P value were adjusted by Benjamini-Hochberg (FDR&lt;0.05; (Benjamini and Hochberg, 1995)) multiple testing procedure (allDataset worksheet). Genes significantly under- or over-expressed in pico and mrtf are displayed in separated worksheets.
DOI: 10.6084/m9.figshare.4560862
title: Transcriptome - Nutomonas longa CCAP 1958/5

description: <i>Nutomonas longa</i>'s transcriptome<i> </i>(formerly known as <i>Planomonas carolina)</i><br><br>Reads are deposited in NCBI: https://www.ncbi.nlm.nih.gov/sra/SRX736986<br><br>- Assembly in-home BGI to obtain Unigene (contigs)- ORF prediction using TransDecoder (Trinity plugin) and PfamScan to obtain coding sequences (CDS files) from transcripts (mRNA)- Protein translations are included (pep)<br>- clean.fasta: Assembly cleaned from cross-contamination of other species multiplexed (Corallochytrium limacisporum India, Ichthyophonus hoferi and Sphaerothecum destruens) after applying CroCo V0.1.1 (Simion et al. in prep). It may contain bacterial contamination.<br><br><br><strong>Guifré Torruella, Alex de Mendoza, Xavier Grau-Bové, Meritxell Antó, </strong>Mark A. Chaplin<strong>, Javier del Campo, </strong>Laura Eme, Gregorio Pérez-Cordón, Christopher M. Whipps, Krista M. Nichols, Richard Paley, Andrew J. Roger, Ariadna Sitjà-Bobadilla, Stuart Donachie,<strong> and Iñaki Ruiz-Trillo. </strong>(2015)<br><em>Phylogenomics reveals convergent evolution of lifestyles in close relatives of animals and fungi.</em><br><strong><em>Current Biology </em></strong>25(18):2404-10.<br><br>www.multicellgenome.com
DOI: 10.6084/m9.figshare.4560790
title: Supplementary Material for: Hepatitis C Virus of Subtype 2l in Marseille, Southeastern France

description: The rate of eradication of chronic hepatitis C considerably increases with direct-acting antiviral agents, particularly hepatitis C virus (HCV) polymerase inhibitors. While implementing full-length HCV NS5B polymerase sequencing in our clinical microbiology laboratory, we identified atypical HCV sequences, classified as subtype 2l, from 2 patients. HCV-2l NS5B polymerase sequences were detected from 5 and 14 additional patients by screening our laboratory hepatitis virus sequence database and the NCBI GenBank sequence database. Phylogenetic analyses show unambiguously that all HCV-2l sequences are clustered apart from HCV 2 non-l sequences, which compose a second cluster. Mean (±SD) nucleotide identity between near full-length NS5B fragments of subtype 2l was 93.4 ± 0.8% (range: 92.4-95.1). Of note, all HCV-2l sequences obtained in our laboratory and in other centers were from serum samples collected in France. Analysis of the HCV-2l NS5B polymerase amino acid sequences at 30 positions critical for interaction with or resistance to HCV polymerase inhibitors showed specific patterns.
DOI: 10.6084/m9.figshare.4560772
title: Myosins dataset - Sebé-Pedrós et al. (2014)

description: Arnau Sebé-Pedrós, Xavier Grau-Bové, Thomas A. Richards & Iñaki Ruiz-Trillo. (2014)<br>Evolution and classification of myosins, a paneukaryotic whole genome approach.<br>Genome Biology and Evolution 6(2):290-305.
DOI: 10.6084/m9.figshare.4560766
title: Supplementary Material for: Risk of Intracranial Hemorrhage after Endovascular Treatment for Acute Ischemic Stroke: Systematic Review and Meta-Analysis

description: <b><i>Background:</i></b> Intracranial hemorrhage is a major complication of endovascular treatment in patients with acute ischemic stroke. Controlled clinical trials reported varied incidences of intracranial hemorrhage after endovascular treatment. This meta-analysis aimed to estimate whether endovascular treatment, compared with medical treatment, increases the risk of intracranial hemorrhage in patients with acute ischemic stroke. <b><i>Methods:</i></b> The current publications on endovascular treatment for acute ischemic stroke were systematically reviewed. Rates of intracranial hemorrhage after endovascular treatment for acute ischemic stroke reported in controlled clinical trials were pooled and analyzed. Random and fixed-effect models were used to pool the outcomes. For analyzing their individual risks, intracranial hemorrhages after endovascular treatment were classified as symptomatic and asymptomatic. <b><i>Results:</i></b> Eleven studies involving 1,499 patients with endovascular treatment and 1,320 patients with medical treatment were included. After pooling the data, the risk of any intracranial hemorrhage was significantly higher in patients with endovascular treatment than in patients with medical treatment (35.0 vs. 19.0%, OR = 2.55, 95% CI: 1.64-3.97, <i>p &lt; </i>0.00001). The risk of asymptomatic intracranial hemorrhage was also significantly higher in patients with endovascular treatment than in those with medical treatment (28 vs. 12%, OR = 3.16, 95% CI: 1.62-6.16, <i>p </i>&lt; 0.001). However, the risks of symptomatic intracranial hemorrhage were similar in patients with endovascular treatment and in those with medical treatment (5.6 vs. 5.2%, OR = 1.09, 95% CI: 0.79-1.50, <i>p</i> = 0.61). <b><i>Conclusion:</i></b> Although the risk of any intracranial hemorrhage may increase after endovascular treatment, the risk of symptomatic intracranial hemorrhage may remain similar as compared with medical treatment.
DOI: 10.6084/m9.figshare.4560772.v2
title: Myosins dataset - Sebé-Pedrós et al. (2014)

description: Arnau Sebé-Pedrós, Xavier Grau-Bové, Thomas A. Richards & Iñaki Ruiz-Trillo. (2014)<br>Evolution and classification of myosins, a paneukaryotic whole genome approach.<br>Genome Biology and Evolution 6(2):290-305.
DOI: 10.6084/m9.figshare.4560772.v1
title: Myosins dataset

description: Dataset of myosins. <br>Arnau Sebé-Pedrós, Xavier Grau-Bové, Thomas A. Richards & Iñaki Ruiz-Trillo. (2014)<br>Evolution and classification of myosins, a paneukaryotic whole genome approach.<br>Genome Biology and Evolution 6(2):290-305.
DOI: 10.6084/m9.figshare.4560760
title: Supplementary Material for: Quality of Life after Intestinal Resection in Patients with Crohn Disease: A Systematic Review

description: <b><i>Background/Aims:</i></b> Most patients with Crohn disease (CD) require surgery within 10 years of diagnosis. Intestinal resection is the most commonly performed operation although the effects on health-related quality of life (HRQOL), particularly long-term, are contentious. <b><i>Methods:</i></b> We conducted a systematic review evaluating the impact of intestinal resection on the HRQOL of CD patients, predictors of postoperative HRQOL, and patient satisfaction with surgery. <b><i>Results:</i></b> Nine studies including 1,108 CD patients undergoing intestinal resection were identified as eligible for inclusion. The median age at surgery was 29-41 years with varying follow-up period (range 30 days-5 years). Ileocolic resection was the most commonly performed operation on an elective basis (range 95-100%). HRQOL improved as early as 2 weeks postoperatively and lasted up to 5 years across both generic and gastrointestinal domains. Gender, smoking, and disease recurrence were potential predictors of postoperative HRQOL. Patient satisfaction is high with regard to surgery, with preference for a laparoscopic approach. <b><i>Conclusion:</i></b> Intestinal resection in CD patients improved HRQOL in the short- and long-term and patients describe high satisfaction about their surgery. Further studies are needed to validate potential predictors of postoperative HRQOL in this cohort.
DOI: 10.6084/m9.figshare.4560691
title: OCC dataset of all the identifiers, as of December 24, 2016

description: <pre>This archive contains the dump of the OpenCitation Corpus (OCC, http://opencitations.net) dataset about identifiers, created regularly every month.<br><br>After unzipping the archive, Disk ARchive (DAR, http://dar.linux.free.fr/, a multi-platform archive tool for managing huge amount of data) is needed for recreating the whole structure. For extracting the DAR archive, please run the command<br><br>dar -x [archive-name]<br><br>Where "[archive-name"] is the name of the DAR file without final package number and extension. E.g.:<br><br>dar -x 2016-09-23-corpus_re<br><br>For further questions, comments, and suggestions please don't hesitate to contact Silvio Peroni at essepuntato@opencitations.net.</pre>
DOI: 10.6084/m9.figshare.4560658
title: OCC dataset of all the bibliographic resources, as of December 24, 2016

description: <pre>This archive contains the dump of the OpenCitation Corpus (OCC, http://opencitations.net) dataset about bibliographic resources, created regularly every month.<br><br>After unzipping the archive, Disk ARchive (DAR, http://dar.linux.free.fr/, a multi-platform archive tool for managing huge amount of data) is needed for recreating the whole structure. For extracting the DAR archive, please run the command<br><br>dar -x [archive-name]<br><br>Where "[archive-name"] is the name of the DAR file without final package number and extension. E.g.:<br><br>dar -x 2016-09-23-corpus_re<br><br>For further questions, comments, and suggestions please don't hesitate to contact Silvio Peroni at essepuntato@opencitations.net.</pre>
DOI: 10.6084/m9.figshare.4560691.v1
title: OCC dataset of all the identifiers, as of December 24, 2016

description: <pre>This archive contains the dump of the OpenCitation Corpus (OCC, http://opencitations.net) dataset about identifiers, created regularly every month.<br><br>After unzipping the archive, Disk ARchive (DAR, http://dar.linux.free.fr/, a multi-platform archive tool for managing huge amount of data) is needed for recreating the whole structure. For extracting the DAR archive, please run the command<br><br>dar -x [archive-name]<br><br>Where "[archive-name"] is the name of the DAR file without final package number and extension. E.g.:<br><br>dar -x 2016-09-23-corpus_re<br><br>For further questions, comments, and suggestions please don't hesitate to contact Silvio Peroni at essepuntato@opencitations.net.</pre>
DOI: 10.6084/m9.figshare.4560649
title: Impact of predator diversity treatments on aphid prey density

description: Predator density and diversity were manipulated in a field cage experiment. <br><br>The data uploaded is the mean numbers and standard deviation of aphids (<i>R. padi</i>) at predator introduction and at the end of experiment 12 days later. <br><br>we had:<br>- Three low diversity treatments: carabid <i>P. melanariu</i>s, ladybird larvae <i>(C. septempunctata)</i>, lacewing larvae (<i>C. carnea</i>)<br>- A high diversity treatment using a subsitutive design <br>