cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8080907.v2
title: Data from Gopko et al.: Parasite transmission in aquatic ecosystems under temperature change: effects of host activity and elimination of parasite larvae by filter-feeders.

description: Three data files (csv) with full and abridged datasets, and one text file with the description of the variables.<br>Our research concerned the transmission of parasites in a freshwater ecosystem in relation to temperature, host behavior and the presence of predators feeding on free-living larvae of parasites in the environment. We used rainbow trout as a host, common trematode Diplostomum pseudospathaceum as a parasite and freshwater mussel Anodonta anatina as a predator eliminating cercariae (free-living stage of the trematode) from the environment. Temperatures of our study ranged from the mean summer temperature in the temperate lakes to those predicted by moderate scenarios of global warming. We found that both the presence of filter-feeders in the test tanks and temperature substantially influence the infection intensities in fish. Temperature increase led to higher infection intensities, while the presence of mussels strongly decreased parasitic loads. Importantly these two factors did not interact with each other implying that an increased filter activity of mussels is unlikely to compensate for the increased fish vulnerability to trematodes with temperature raise. Host activity before the exposure to parasites positively correlated with infection intensities, however, its correlation with temperature was rather weak.<br>After exposure to parasites, fish strongly decreased their activity. This decrease was temperature-dependent and more pronounced in bolder (more active) fish, which leads to lower variability in the activity of fish exposed to parasites compared with the safe environment. Post-exposure activity did not influence the infection intensity. In general, we showed that the elimination of trematode larvae by filter-feeders is unlikely to deter the potential effects of global warming on host-parasite interactions in temperate freshwater ecosystems.
DOI: 10.6084/m9.figshare.8080790
title: Killer shrimp preferences

description: Data for Experiments 1-3Experiment 1. Choice of zebra mussel density Experiment 2. Preference for zebra mussel over an artificial substrate<br> Experiment 3. Chemical attraction to zebra mussel <br>
DOI: 10.6084/m9.figshare.8080766
title: Data A.1. Concatenated matrix.fasta

description: This dataset includes the concatenated alignment of five genes (18S, 28S, rbcL, psbA and COI) and 100 strains belonging to the marine diatom family Chaetocerotaceae. It is linked to the paper by De Luca D, Sarno D, Piredda R, Kooistra WHCF. "A multigene phylogeny to infer the evolutionary history of Chaetocerotaceae (Bacillariophyta)".<b></b>
DOI: 10.6084/m9.figshare.8080733
title: AZ.fa

description: This is the version 2 of the azadirachta indica genome assembly used in Krishnan et al. 2016.<br>Krishnan NM, Jain P, Gupta S, Hariharan AK, Panda B. An Improved Genome Assembly of Azadirachta indica A. Juss. G3: Genes, Genomes, Genetics. 2016 Jul 1;6(7):1835-40.<br>
DOI: 10.6084/m9.figshare.8080664
title: Lake McConaughy Lake Dynamic Tracking Data

description: This data is long-term lake dynamic (surface elevation, area, and volume) derived from topographic datasets and Landsat imagery in Google Earth Engine.
DOI: 10.6084/m9.figshare.8080613
title: MOESM9 of Ezh2-dCas9 and KRAB-dCas9 enable engineering of epigenetic memory in a context-dependent manner

description: Additional file 9: Table S3. Lists of hypermethylated CpG probes and hypermethylated gene promoters (&gt;3 probes).
DOI: 10.6084/m9.figshare.8080613.v1
title: MOESM9 of Ezh2-dCas9 and KRAB-dCas9 enable engineering of epigenetic memory in a context-dependent manner

description: Additional file 9: Table S3. Lists of hypermethylated CpG probes and hypermethylated gene promoters (&gt;3 probes).
DOI: 10.6084/m9.figshare.8080592
title: MOESM6 of Ezh2-dCas9 and KRAB-dCas9 enable engineering of epigenetic memory in a context-dependent manner

description: Additional file 6: Table S2. Lists of H3K27ac ChIP-seq peaks.
DOI: 10.6084/m9.figshare.8080592.v1
title: MOESM6 of Ezh2-dCas9 and KRAB-dCas9 enable engineering of epigenetic memory in a context-dependent manner

description: Additional file 6: Table S2. Lists of H3K27ac ChIP-seq peaks.
DOI: 10.6084/m9.figshare.8080568
title: MOESM2 of Ezh2-dCas9 and KRAB-dCas9 enable engineering of epigenetic memory in a context-dependent manner

description: Additional file 2: Table S1. gRNA target sequences, predicted off-target sites and oligonucleotide sequences of RT-qPCR primers.
DOI: 10.6084/m9.figshare.8080568.v1
title: MOESM2 of Ezh2-dCas9 and KRAB-dCas9 enable engineering of epigenetic memory in a context-dependent manner

description: Additional file 2: Table S1. gRNA target sequences, predicted off-target sites and oligonucleotide sequences of RT-qPCR primers.
DOI: 10.6084/m9.figshare.8080550
title: Additional file 2: of Absence of evidence is not evidence of absence: Nanopore sequencing and complete assembly of the European lobster (Homarus gammarus) mitogenome uncovers the missing nad2 and a new major gene cluster duplication

description: DataÂ 1. Mitogenome assemblies in fasta format of 5 additional Homarus gammarus sampled from distant location in Europe (See Fig.Â 2c for details) (TXT 99 kb)
DOI: 10.6084/m9.figshare.8080550.v1
title: Additional file 2: of Absence of evidence is not evidence of absence: Nanopore sequencing and complete assembly of the European lobster (Homarus gammarus) mitogenome uncovers the missing nad2 and a new major gene cluster duplication

description: DataÂ 1. Mitogenome assemblies in fasta format of 5 additional Homarus gammarus sampled from distant location in Europe (See Fig.Â 2c for details) (TXT 99 kb)
DOI: 10.6084/m9.figshare.8080517
title: MOESM2 of Progress and perspectives in the discovery of polychaete worms (Annelida) of the world

description: Additional file 2: Table S3. The cleaned dataset of valid polychaete species names.
DOI: 10.6084/m9.figshare.8080517.v1
title: MOESM2 of Progress and perspectives in the discovery of polychaete worms (Annelida) of the world

description: Additional file 2: Table S3. The cleaned dataset of valid polychaete species names.
DOI: 10.6084/m9.figshare.8080475
title: Additional file 2 of FastqPuri: high-performance preprocessing of RNA-seq data

description: Archive of FastqPuri. Archive containing all files needed to install and run FastqPuri v1.0.6. Date stamp March 22, 2019. (GZ 47,819 kb)
DOI: 10.6084/m9.figshare.8080475.v1
title: Additional file 2 of FastqPuri: high-performance preprocessing of RNA-seq data

description: Archive of FastqPuri. Archive containing all files needed to install and run FastqPuri v1.0.6. Date stamp March 22, 2019. (GZ 47,819 kb)
DOI: 10.6084/m9.figshare.8080445
title: Additional file 6: of Systematic characterization of germline variants from the DiscovEHR study endometrial carcinoma population

description: Difference of proportions test. After binning variants into genes, a difference of proportions test was performed across all genes between variants in the EMCA and the control or OHRM cohort. P-values were adjusted for multiple tests using FDR. (XLSX 16 kb)
DOI: 10.6084/m9.figshare.8080445.v1
title: Additional file 6: of Systematic characterization of germline variants from the DiscovEHR study endometrial carcinoma population

description: Difference of proportions test. After binning variants into genes, a difference of proportions test was performed across all genes between variants in the EMCA and the control or OHRM cohort. P-values were adjusted for multiple tests using FDR. (XLSX 16 kb)
DOI: 10.6084/m9.figshare.8080388
title: Additional file 2: of Characterization of a relaxase belonging to the MOBT family, a widespread family in Firmicutes mediating the transfer of ICEs

description: Figure S2. Sequence alignment of MOBT relaxase and Rep_trans RCR initiators. This larger alignment with more MOBT and Rep_trans initiator sequences illustrates the conservation of the motifs through very distant proteins. See complete legend in Additional file 4. (RTF 1402 kb)
DOI: 10.6084/m9.figshare.8080385
title: Additional file 1: of Characterization of a relaxase belonging to the MOBT family, a widespread family in Firmicutes mediating the transfer of ICEs

description: Figure S1. Alignment of MOBT relaxase representatives with Rep_trans RCR initiator representatives. This alignment with reduced number of sequences allows the identification of the different motifs cited in this study. See complete legend in Additional file 4. (RTF 194 kb)
DOI: 10.6084/m9.figshare.8080385.v1
title: Additional file 1: of Characterization of a relaxase belonging to the MOBT family, a widespread family in Firmicutes mediating the transfer of ICEs

description: Figure S1. Alignment of MOBT relaxase representatives with Rep_trans RCR initiator representatives. This alignment with reduced number of sequences allows the identification of the different motifs cited in this study. See complete legend in Additional file 4. (RTF 194 kb)
DOI: 10.6084/m9.figshare.8080388.v1
title: Additional file 2: of Characterization of a relaxase belonging to the MOBT family, a widespread family in Firmicutes mediating the transfer of ICEs

description: Figure S2. Sequence alignment of MOBT relaxase and Rep_trans RCR initiators. This larger alignment with more MOBT and Rep_trans initiator sequences illustrates the conservation of the motifs through very distant proteins. See complete legend in Additional file 4. (RTF 1402 kb)
DOI: 10.6084/m9.figshare.8080343
title: Additional file 1: of Brain transcriptome analysis of a familial Alzheimer’s disease-like mutation in the zebrafish presenilin 1 gene implies effects on energy production

description: Genes differentially expressed between heterozygous mutant and wild type brains at 6 months. Lists the genes identified as differentially expressed between the brains of heterozygous psen1Q96_K97del mutant fish and the brains of their wild type siblings at an age of 6 months. Genes are ranked according to FDR-corrected p-value. Only genes with a FDR-corrected p-value less than 0.05 are shown. “FC” denotes fold change. “DE” denotes differential expression. For DE_Direction, “1” denotes increased expression in the mutant and “-1” denotes decreased expression in the mutant. (XLSX 39 kb)
DOI: 10.6084/m9.figshare.8080343.v1
title: Additional file 1: of Brain transcriptome analysis of a familial Alzheimer’s disease-like mutation in the zebrafish presenilin 1 gene implies effects on energy production

description: Genes differentially expressed between heterozygous mutant and wild type brains at 6 months. Lists the genes identified as differentially expressed between the brains of heterozygous psen1Q96_K97del mutant fish and the brains of their wild type siblings at an age of 6 months. Genes are ranked according to FDR-corrected p-value. Only genes with a FDR-corrected p-value less than 0.05 are shown. “FC” denotes fold change. “DE” denotes differential expression. For DE_Direction, “1” denotes increased expression in the mutant and “-1” denotes decreased expression in the mutant. (XLSX 39 kb)
DOI: 10.6084/m9.figshare.8080202
title: Additional file 1: of Comparing access to orphan medicinal products in Europe

description: Presents a table with the list of 143 OMPs with relevant EC authorisation data matched with a reimbursement binary indicator for each country. (XLSX 28 kb)
DOI: 10.6084/m9.figshare.8080202.v1
title: Additional file 1: of Comparing access to orphan medicinal products in Europe

description: Presents a table with the list of 143 OMPs with relevant EC authorisation data matched with a reimbursement binary indicator for each country. (XLSX 28 kb)
DOI: 10.6084/m9.figshare.8080157
title: Additional file 2: of Effect of triploidy on liver gene expression in coho salmon (Oncorhynchus kisutch) under different metabolic states

description: Supporting Information. This is a spreadsheet file with information on RNA-seq alignments, significant differentially expressed genes for the various comparisons, growth hormone (GH and GH2) gene expression, principal component analyses results, enriched GO categories, the REVIGO reduced GO categories, and summary information. (ZIP 4703 kb)
DOI: 10.6084/m9.figshare.8080157.v1
title: Additional file 2: of Effect of triploidy on liver gene expression in coho salmon (Oncorhynchus kisutch) under different metabolic states

description: Supporting Information. This is a spreadsheet file with information on RNA-seq alignments, significant differentially expressed genes for the various comparisons, growth hormone (GH and GH2) gene expression, principal component analyses results, enriched GO categories, the REVIGO reduced GO categories, and summary information. (ZIP 4703 kb)
DOI: 10.6084/m9.figshare.8080145
title: Additional file 10: of Effect of triploidy on liver gene expression in coho salmon (Oncorhynchus kisutch) under different metabolic states

description: Python Scripts. This is a compressed folder with all of the scripts used in the analyses in this study. It contains a readme file to describe the use of these scripts. (ZIP 23 kb)
DOI: 10.6084/m9.figshare.8080148
title: Additional file 1: of Effect of triploidy on liver gene expression in coho salmon (Oncorhynchus kisutch) under different metabolic states

description: Supporting Tables. This is a document file with supporting/supplementary tables. (ZIP 13 kb)
DOI: 10.6084/m9.figshare.8080145.v1
title: Additional file 10: of Effect of triploidy on liver gene expression in coho salmon (Oncorhynchus kisutch) under different metabolic states

description: Python Scripts. This is a compressed folder with all of the scripts used in the analyses in this study. It contains a readme file to describe the use of these scripts. (ZIP 23 kb)
DOI: 10.6084/m9.figshare.8080148.v1
title: Additional file 1: of Effect of triploidy on liver gene expression in coho salmon (Oncorhynchus kisutch) under different metabolic states

description: Supporting Tables. This is a document file with supporting/supplementary tables. (ZIP 13 kb)
DOI: 10.6084/m9.figshare.8080130
title: Additional file 2: of Genetic factors affecting Fusarium head blight resistance improvement from introgression of exotic Sumai 3 alleles (including Fhb1, Fhb2, and Fhb5) in hard red spring wheat

description: List of annotated genes in the intervals of FHB resistance loci. (XLSX 429 kb)
DOI: 10.6084/m9.figshare.8080130.v1
title: Additional file 2: of Genetic factors affecting Fusarium head blight resistance improvement from introgression of exotic Sumai 3 alleles (including Fhb1, Fhb2, and Fhb5) in hard red spring wheat

description: List of annotated genes in the intervals of FHB resistance loci. (XLSX 429 kb)
DOI: 10.6084/m9.figshare.8080106
title: Additional file 1: of Two novel amino acid substitutions in highly conserved regions of prion protein (PrP) and a high frequency of a scrapie protective variant in native Ethiopian goats

description: Prion protein gene polymorphism in native Ethiopian goats. Excel file that include all information related to each single goat in the three Ethiopian regions. For each goat, information regarding sex, age in months and the related prion polymorphisms are reported. (XLS 60 kb)
DOI: 10.6084/m9.figshare.8080106.v1
title: Additional file 1: of Two novel amino acid substitutions in highly conserved regions of prion protein (PrP) and a high frequency of a scrapie protective variant in native Ethiopian goats

description: Prion protein gene polymorphism in native Ethiopian goats. Excel file that include all information related to each single goat in the three Ethiopian regions. For each goat, information regarding sex, age in months and the related prion polymorphisms are reported. (XLS 60 kb)
DOI: 10.6084/m9.figshare.8079959
title: Effects of a herbicide on paddy predatory insects depend on their microhabitat use and an insecticide application (dataset)

description: 1. Hashimoto_et_al.2019_Community2017.csv<br>Abundance data of the paddy mesocosm experiment described in the manuscript. <br>Contain time-series abundance of each observed species in each tank.<br><br>2. Hashimoto_et_al.2019_SagaCensus2018March.csv<br>Abundance data of the natural field observation described in the manuscript.<br>Contain abundance of each observed Odonata species in each sampling site.<br><br>3. Hashimoto_et_al.2019_waterConc.csv<br>Data of water concentration of the insecticide (fipronil) and the herbicide (pentoxaxone).<br>Contain time-series concentration of each chemical in each tank.<br><br>4. Hashimoto_et_al.2019_sedimentConc.csv<br>Data of sediment concentration of the insecticide (fipronil) and the herbicide (pentoxaxone).<br>Contain time-series concentration of each chemical in each tank.
DOI: 10.6084/m9.figshare.8079968
title: Supplemental Materials and Tables

description: Supplemental Materials and Tables
DOI: 10.6084/m9.figshare.8079944
title: Code and summary results for: Discovering cross-reactivity in urine drug screening immunoassays through large-scale analysis of electronic health records

description: Zip file contains parameter and metadata files, data from spiking experiments, sql and R scripts, and results in the form of figures and csv files.
DOI: 10.6084/m9.figshare.8079959.v1
title: Effects of a herbicide on paddy predatory insects depend on their microhabitat use and an insecticide application (dataset)

description: 1. Hashimoto_et_al.2019_Community2017.csv<br>Abundance data of the paddy mesocosm experiment described in the manuscript. <br>Contain time-series abundance of each observed species in each tank.<br><br>2. Hashimoto_et_al.2019_SagaCensus2018March.csv<br>Abundance data of the natural field observation described in the manuscript.<br>Contain abundance of each observed Odonata species in each sampling site.<br><br>3. Hashimoto_et_al.2019_waterConc.csv<br>Data of water concentration of the insecticide (fipronil) and the herbicide (pentoxaxone).<br>Contain time-series concentration of each chemical in each tank.<br><br>4. Hashimoto_et_al.2019_sedimentConc.csv<br>Data of sediment concentration of the insecticide (fipronil) and the herbicide (pentoxaxone).<br>Contain time-series concentration of each chemical in each tank.
DOI: 10.6084/m9.figshare.8079968.v1
title: Supplemental Materials and Tables

description: Supplemental Materials and Tables
DOI: 10.6084/m9.figshare.8079893
title: Gold Open Access 2013-2018 (GOA4)

description: Gold Open Access 2013-2018: articles in issues (GOA4) is the dataset behind the GOA4 PDF and paperback: one row for each of 12,415 in the Directory of Open Access Journals as of the start of 2019, showing article counts and other added information. [PubCat data restored with modifications]<br>
DOI: 10.6084/m9.figshare.8079911
title: CCDB_6347.jpg

description: Single computed slice through a tomographic reconstruction of a lamellar structure observed in HeLa cells transfected with mutant connexin 50, imaged using intermediate voltage electron microscopy, and labeled using the tetracysteine-ReHAsH system and fluorescence photoooxidation.
DOI: 10.6084/m9.figshare.8079911.v1
title: CCDB_6347.jpg

description: Single computed slice through a tomographic reconstruction of a lamellar structure observed in HeLa cells transfected with mutant connexin 50, imaged using intermediate voltage electron microscopy, and labeled using the tetracysteine-ReHAsH system and fluorescence photoooxidation.
DOI: 10.6084/m9.figshare.8079743
title: Ocular and Systemic findings in Patients with Novel A/H1N1 infection

description: clinical and ocular findings in patients with novel A/H1N1 infection: an observational study
DOI: 10.6084/m9.figshare.8079893.v1
title: Gold Open Access 2013-2018 (GOA4)

description: Gold Open Access 2013-2018: articles in issues (GOA4) is the dataset behind the GOA4 PDF and paperback: one row for each of 12,415 in the Directory of Open Access Journals as of the start of 2019, showing article counts and other added information.<br>
DOI: 10.6084/m9.figshare.8079713
title: Figure data

description: This file is for the publication:<br>Pilosof S, He Q, Tiedje KE, Ruybal-Pesántez S, Day KP, Pascual M. Competition for hosts modulates vast antigenic diversity to generate persistent strain structure in <i>Plasmodium falciparum</i>.PLOS Biology (accepted)<br>A set of zip files containing the data used to produce all the figures. Files are names after the figure they belong to. If data were used to produce specific panels this is specified (e.g., Fig_S2B.zip has data for reproducing figure S2 panel B).<br>Code to produce figures should be consulted in: https://github.com/pascualgroup/Pf_temporal_networks/wiki
DOI: 10.6084/m9.figshare.8079635
title: CCDB_6334.jpg

description: Single image through a serial section electron microscopic reconstruction of the cell body of a cortical pyramidal neuron from a biopsy sample obtained from the cortex of a patient with Alzheimer's disease.
DOI: 10.6084/m9.figshare.8079713.v1
title: Figure data

description: This file is for the publication:<br>Pilosof S, He Q, Tiedje KE, Ruybal-Pesántez S, Day KP, Pascual M. Competition for hosts modulates vast antigenic diversity to generate persistent strain structure in <i>Plasmodium falciparum</i>.PLOS Biology (accepted)<br>A set of zip files containing the data used to produce all the figures. Files are names after the figure they belong to. If data were used to produce specific panels this is specified (e.g., Fig_S2B.zip has data for reproducing figure S2 panel B).<br>Code to produce figures should be consulted in: https://github.com/pascualgroup/Pf_temporal_networks/wiki
DOI: 10.6084/m9.figshare.8079743.v1
title: H1N1_figshare.xlsx

description: clinical and ocular findings in patients with novel A/H1N1 infection: an observational study
DOI: 10.6084/m9.figshare.8079623
title: CCDB_6333.jpg

description: Single image through a serial section electron microscopic reconstruction of the cell body of a cortical pyramidal neuron from a biopsy sample obtained from the cortex of a patient with Alzheimer's disease.
DOI: 10.6084/m9.figshare.8079635.v1
title: CCDB_6334.jpg

description: Single image through a serial section electron microscopic reconstruction of the cell body of a cortical pyramidal neuron from a biopsy sample obtained from the cortex of a patient with Alzheimer's disease.
DOI: 10.6084/m9.figshare.8079623.v1
title: CCDB_6333.jpg

description: Single image through a serial section electron microscopic reconstruction of the cell body of a cortical pyramidal neuron from a biopsy sample obtained from the cortex of a patient with Alzheimer's disease.
DOI: 10.6084/m9.figshare.8079644.v1
title: Optimizing Sample Size Allocation and Power in a Bayesian Two-Stage Drop-The-Losers Design

description: When a researcher desires to test several treatment arms against a control arm, a two-stage adaptive design can be more efficient than a single-stage design where patients are equally allocated to all treatment arms and the control. We see this type of approach in clinical trials as a seamless Phase II – Phase III design. These designs require more statistical support and are less straightforward to plan and analyze than a standard single-stage design. To diminish the barriers associated with a Bayesian two-stage drop-the-losers design, we built a user-friendly point-and-click graphical user interface with <i>R Shiny</i> to aid researchers in planning such designs by allowing them to easily obtain trial operating characteristics, estimate statistical power and sample size, and optimize patient allocation in each stage to maximize power. We assume that endpoints are distributed normally with unknown but common variance between treatments. We recommend this software as an easy way to engage statisticians and researchers in two-stage designs as well as to actively investigate the power of two-stage designs relative to more traditional approaches. The software is freely available at https://github.com/stefangraw/Allocation-Power-Optimizer.