cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5662231
title: Dataset for: Protection of macrophages from intracellular pathogens by miR-182-5p mimic: a gene expression meta-analysis approach

description: The goals of this study were to i) define which host genes are of particular importance during the interactions between macrophages and intracellular pathogens, and ii) use this knowledge to gain fresh, experimental understanding of how macrophage activities may be manipulated during host defence. We designed an in silico method for meta-analysis of microarray gene expression data, and used this to combine data from 16 different studies of cells in the monocyte-macrophage lineage infected with 7 different pathogens. 3,498 genes were identified, which we call the Macrophage Intracellular Pathogen Response (macIPR) gene-set. As expected, the macIPR gene-set showed a strong bias towards genes previously associated with the immune response. Predicted target sites for miR-182-5p were strongly over-represented among macIPR genes, indicating an unexpected role for miR-182-regulatable genes during intracellular pathogenesis. We therefore transfected primary human alveolar macrophage-like monocyte derived macrophages from multiple different donors with synthetic miR-182-5p, and found that miR-182 overexpression i) increases proinflammatory gene induction during infection with <i>Francisella tularensis</i> LVS, ii) primes macrophages for increased autophagy, and iii) enhances macrophage control of both Gram negative <i>F. tularensis</i> LVS and Gram positive <i>Bacillus anthracis</i> ANR-1 spores. These data therefore suggest a new application for miR-182 in promoting resistance to intracellular pathogens
DOI: 10.6084/m9.figshare.5662231.v1
title: Dataset for: Protection of macrophages from intracellular pathogens by miR-182-5p mimic: a gene expression meta-analysis approach

description: The goals of this study were to i) define which host genes are of particular importance during the interactions between macrophages and intracellular pathogens, and ii) use this knowledge to gain fresh, experimental understanding of how macrophage activities may be manipulated during host defence. We designed an in silico method for meta-analysis of microarray gene expression data, and used this to combine data from 16 different studies of cells in the monocyte-macrophage lineage infected with 7 different pathogens. 3,498 genes were identified, which we call the Macrophage Intracellular Pathogen Response (macIPR) gene-set. As expected, the macIPR gene-set showed a strong bias towards genes previously associated with the immune response. Predicted target sites for miR-182-5p were strongly over-represented among macIPR genes, indicating an unexpected role for miR-182-regulatable genes during intracellular pathogenesis. We therefore transfected primary human alveolar macrophage-like monocyte derived macrophages from multiple different donors with synthetic miR-182-5p, and found that miR-182 overexpression i) increases proinflammatory gene induction during infection with <i>Francisella tularensis</i> LVS, ii) primes macrophages for increased autophagy, and iii) enhances macrophage control of both Gram negative <i>F. tularensis</i> LVS and Gram positive <i>Bacillus anthracis</i> ANR-1 spores. These data therefore suggest a new application for miR-182 in promoting resistance to intracellular pathogens
DOI: 10.6084/m9.figshare.5662219
title: DBS_RHI_dataset.xls

description: Results of a Rubber Hand Illusion experiment in people with Parkinson's disease (treated with deep brain stimulation to the sub-thalamic nucleus) and healthy controls.
DOI: 10.6084/m9.figshare.5662219.v1
title: DBS_RHI_dataset.xls

description: Results of a Rubber Hand Illusion experiment in people with Parkinson's disease (treated with deep brain stimulation to the sub-thalamic nucleus) and healthy controls.
DOI: 10.6084/m9.figshare.5662213
title: Identification of Berenil Target Sites in Plasmid pBR322

description: Berenil, a minor groove DNA binding molecule, has been extensively used in veterinary medicine. Modeling studies have suggested that berenil binds to A/T rich regions on the DNA and the product of this interaction causes the formation of crosslinks between opposite DNA strands. These crosslinks could potentially inhibit fundamental biological processes including transcription and DNA replication. We had previously used the pBR322 genome as a model system to investigate the role of A/T sequences on berenil activity. We reported that the insertion of poly(dA)poly(dT) sequences into the pBR322 genome causes replication inhibition of the recombinant plasmids when cultures were exposed to berenil. However, we noticed that even in the absence of these sequences the parental plasmid replication was also inhibited, albeit less than the recombinants. This observation led us to the present study were we attempted to identify the location of natural berenil target sites in the pBR322 genome. Through a combination of deletion analysis, recombinant DNA and a replication assay we uncovered a 378 bp DNA fragment that has all the hallmarks of a berenil target site. A recombinant plasmid lacking this region is more refractive to the drug than the parental plasmid, and another variant containing and extra copy of this region increases the susceptibility of the plasmid towards berenil. The 378 bp region is about 60% A/T rich and contains about 21 potential berenil binding sites.
DOI: 10.6084/m9.figshare.5662213.v2
title: Identification of Berenil Target Sites in Plasmid pBR322

description: Berenil, a minor groove DNA binding molecule, has been extensively used in veterinary medicine. Modeling studies have suggested that berenil binds to A/T rich regions on the DNA and the product of this interaction causes the formation of crosslinks between opposite DNA strands. These crosslinks could potentially inhibit fundamental biological processes including transcription and DNA replication. We had previously used the pBR322 genome as a model system to investigate the role of A/T sequences on berenil activity. We reported that the insertion of poly(dA)poly(dT) sequences into the pBR322 genome causes replication inhibition of the recombinant plasmids when cultures were exposed to berenil. However, we noticed that even in the absence of these sequences the parental plasmid replication was also inhibited, albeit less than the recombinants. This observation led us to the present study were we attempted to identify the location of natural berenil target sites in the pBR322 genome. Through a combination of deletion analysis, recombinant DNA and a replication assay we uncovered a 378 bp DNA fragment that has all the hallmarks of a berenil target site. A recombinant plasmid lacking this region is more refractive to the drug than the parental plasmid, and another variant containing and extra copy of this region increases the susceptibility of the plasmid towards berenil. The 378 bp region is about 60% A/T rich and contains about 21 potential berenil binding sites.
DOI: 10.6084/m9.figshare.5662153
title: Additional file 5: of Transcriptional changes in mesenteric and subcutaneous adipose tissue from Holstein cows in response to plane of dietary energy

description: Integration of significant KEGG pathways, biological processes (BP), molecular functions (MF), cellular component (CC) and structures inside proteins (INTERPRO) related to differentially expressed genes (P value &lt;0.05; FDR
DOI: 10.6084/m9.figshare.5662153.v1
title: Additional file 5: of Transcriptional changes in mesenteric and subcutaneous adipose tissue from Holstein cows in response to plane of dietary energy

description: Integration of significant KEGG pathways, biological processes (BP), molecular functions (MF), cellular component (CC) and structures inside proteins (INTERPRO) related to differentially expressed genes (P value &lt;0.05; FDR
DOI: 10.6084/m9.figshare.5662150
title: Additional file 4: of Transcriptional changes in mesenteric and subcutaneous adipose tissue from Holstein cows in response to plane of dietary energy

description: Integration of significant KEGG pathways, biological processes (BP), molecular functions (MF), cellular component (CC) and structures inside proteins (INTERPRO) related to differentially expressed genes (P value &lt;0.05; FDR
DOI: 10.6084/m9.figshare.5662150.v1
title: Additional file 4: of Transcriptional changes in mesenteric and subcutaneous adipose tissue from Holstein cows in response to plane of dietary energy

description: Integration of significant KEGG pathways, biological processes (BP), molecular functions (MF), cellular component (CC) and structures inside proteins (INTERPRO) related to differentially expressed genes (P value &lt;0.05; FDR
DOI: 10.6084/m9.figshare.5662138
title: Additional file 3: of Transcriptional changes in mesenteric and subcutaneous adipose tissue from Holstein cows in response to plane of dietary energy

description: Entrez gene ID, gene symbol, fold change, false discovery rate (FDR) and P values of the oligonucleotides considered in the microarray analysis for the comparisons of MAT vs. SAT and HIGH vs. CON.. (XLSX 121 kb)
DOI: 10.6084/m9.figshare.5662138.v1
title: Additional file 3: of Transcriptional changes in mesenteric and subcutaneous adipose tissue from Holstein cows in response to plane of dietary energy

description: Entrez gene ID, gene symbol, fold change, false discovery rate (FDR) and P values of the oligonucleotides considered in the microarray analysis for the comparisons of MAT vs. SAT and HIGH vs. CON.. (XLSX 121 kb)
DOI: 10.6084/m9.figshare.5662126
title: Additional file 2: Figure S1. of Transcriptional changes in mesenteric and subcutaneous adipose tissue from Holstein cows in response to plane of dietary energy

description: Significant KEGG pathways, biological processes (BP), molecular functions (MF), cellular component (CC) and structures inside proteins (INTERPRO) of differentially expressed genes (P value &lt;0.05; FDR
DOI: 10.6084/m9.figshare.5662126.v1
title: Additional file 2: Figure S1. of Transcriptional changes in mesenteric and subcutaneous adipose tissue from Holstein cows in response to plane of dietary energy

description: Significant KEGG pathways, biological processes (BP), molecular functions (MF), cellular component (CC) and structures inside proteins (INTERPRO) of differentially expressed genes (P value &lt;0.05; FDR
DOI: 10.6084/m9.figshare.5662123
title: Additional file 1: of Variations in the practice of molecular radiotherapy and implementation of dosimetry: results from a European survey

description: IDTF electronic version of survey results submission and EANM Internal Dosimetry Task Force Survey. (ZIP 801 kb)
DOI: 10.6084/m9.figshare.5662123.v1
title: Additional file 1: of Variations in the practice of molecular radiotherapy and implementation of dosimetry: results from a European survey

description: IDTF electronic version of survey results submission and EANM Internal Dosimetry Task Force Survey. (ZIP 801 kb)
DOI: 10.4225/03/5a24c43b2e43a
title: Visual Search and Crowding Abilities in Autism Spectrum Disorder Dataset

description: This dataset relates to a research study entitled: 'Superior Visual Search and Crowding Abilities Are Not Characteristic of All Individuals on the Autism Spectrum.'
DOI: 10.6084/m9.figshare.5662081
title: R code used in Mazor & Doropoulos et al. (2018, Nature Ecology and Evolution)

description: This script categorizes a database of article (48,234) downloaded from the Web of Science using the package bibliometrix into systems (Terrestrial, Marine, Freshwater), and into driver of biodiversity loss (Climate Change, Habitat Change, Invasive Species, Overexploitation and Pollution).
DOI: 10.6084/m9.figshare.5662081.v1
title: R code used in Mazor & Doropoulos et al. (2018, Nature Ecology and Evolution)

description: This script categorizes a database of article (48,234) downloaded from the Web of Science using the package bibliometrix into systems (Terrestrial, Marine, Freshwater), and into driver of biodiversity loss (Climate Change, Habitat Change, Invasive Species, Overexploitation and Pollution).
DOI: 10.4225/03/5a24b0d9180e4
title: Distractor Inhibition in Autism Spectrum Disorder Dataset

description: This dataset relates to a research study entitled: 'Distractor Inhibition in Autism Spectrum Disorder: Evidence of a Selective Impairment for Individuals with Co-occurring Motor Difficulties.'
DOI: 10.6084/m9.figshare.5662072
title: Database of Articles used in Mazor & Doropoulos et al. (2018, Nature Ecology and Evolution)

description: This is a database of journals downloaded from the Web of Science from 2006-2016. These include 21 ecology and conservation journals. R package bibliometrix was used to classify papers into systems (Terrestrial, Marine, Freshwater), and into driver of biodiversity loss (Climate Change, Habitat Change, Invasive Species, Overexploitation and Pollution). <br>
DOI: 10.6084/m9.figshare.5662072.v1
title: Database of Articles used in Mazor & Doropoulos et al. (2018, Nature Ecology and Evolution)

description: This is a database of journals downloaded from the Web of Science from 2006-2016. These include 21 ecology and conservation journals. R package bibliometrix was used to classify papers into systems (Terrestrial, Marine, Freshwater), and into driver of biodiversity loss (Climate Change, Habitat Change, Invasive Species, Overexploitation and Pollution). <br>
DOI: 10.6084/m9.figshare.5662033
title: Jasmonate defences do not affect the larvae of the omnivorous thrips Frankliniella occidentalis via indirect effects on prey quality

description: All data from the manuscript of Livia M. S. Ataide <i>et al.</i>, entitled "Jasmonate defences do not affect the larvae of the omnivorous thrips Frankliniella occidentalis via indirect effects on prey quality" to be submitted to Journal of Animal Ecology in 2017
DOI: 10.6084/m9.figshare.5662033.v1
title: Jasmonate defences do not affect the larvae of the omnivorous thrips Frankliniella occidentalis via indirect effects on prey quality

description: All data from the manuscript of Livia M. S. Ataide <i>et al.</i>, entitled "Jasmonate defences do not affect the larvae of the omnivorous thrips Frankliniella occidentalis via indirect effects on prey quality" to be submitted to Journal of Animal Ecology in 2017
DOI: 10.4225/03/5a95fa8310958
title: Social media nutrition systematic review

description: These data were collected from a systematic literature review examining social media and nutrition outcomes in young adults.
DOI: 10.6084/m9.figshare.5661988
title: Genome-wide microsatellite panel for Brycon orbignyanus

description: Supplementary Table S2 - A broad genomic panel with potentially amplifiable microsatellite loci for <i>Brycon orbignyanus</i> is publicly made available. Loci marked with an asterisk (*) have been empirically validated as polymorphic (Arias et al., 2016; Conservation Genetics Resources, Volume 8, issue 1, p 43-81). These results are part of the article "A broad genomic panel of microsatellite loci from Brycon orbignyanus (Characiformes: Bryconidae), an endangered migratory Neotropical fish". Scientific Reports, 8: 8511, 2918
DOI: 10.6084/m9.figshare.5661919
title: apple_leaf

description: Contains genetic data and binary images associated with the manuscript "Morphometrics reveals complex and heritable apple leaf shapes" ####Folder: genetic_dataContains the genetic data (ped and map files) used in this study.File 1: ApeKI_PstI-EcoT22I_Malv1.0p_bwa_maf0.01_min2alleles_noIndels_dp5_miss70_imputed_plink_leaf_miss0_maf05_hetero90.pedDescription: Genotype table in PLINK .ped format. Genotypes were obtained using GBS (ApeKI and PstI-EcoT221I). The PED file is a white-space (space or tab) delimited file. the first six columns are:Family ID / Individual ID / Paternal ID / Maternal ID / Sex (1=male; 2=female; other=unknown) / PhenotypeGenotypes (biallelic) are column 7 onwards. apple_ids (unique per cultivar) are used for Family ID and Individual ID, these can be linked with the binary images using leaf_binary_image_info.txt File 2: ApeKI_PstI-EcoT22I_Malv1.0p_bwa_maf0.01_min2alleles_noIndels_dp5_miss70_imputed_plink_leaf_miss0_maf05_hetero90.mapDescription:Each line of the .map file describes a single marker and contains 4 columns:chromosome (1-18, X, Y or 0 if unplaced) / rs# or snp identifier / Genetic distance (morgans) / Base-pair position (bp units)chromosome 18 indicates contigs that are unanchored to the reference genome ###Folder: apple_leaf_binary_imagesDescription:Contains all binary images of apple leaves used in this study. Files are named after the nursery ID, which is the value before “-“ and can be linked with the apple IDs used in this study through the leaf_binary_image_info.txt info file. ###Folder: leaf_genetic_image_infoDescription:Info file (leaf_binary_image_info.txt) which links the name of the images (image_name) with the nursery_id (unique per tree in the orchard) and apple_id (unique per cultivar) for the study. The image_name/nursery_id is used in the leaf images, but the apple IDs are used in the genotype files.
DOI: 10.6084/m9.figshare.5661916
title: Intergenerational transmission of Japanese in Argentina

description: Paper presented at ITML3 http://latllab.canterbury.ac.nz/intergenerational-transmission-japanese-argentina/<br><br>Intergenerational transmission of Japanese in Argentina<br><br>Migration movements are the driving force behind language contact situations, which in turn may produce a change in linguistic behavior, oftentimes towards language shift. In point, the intergenerational transmission of language offers itself as a critical aspect in the ethnolinguistic vitality of immigrant languages. As Haque (2010) suggests, language transmission and language practices are often subjected to issues related to national, family and local language(s) policies. <br>This communication presents a number of aspects affecting the intergenerational transmission of Japanese as an immigrant language in Argentina, namely the role of family language planning, language ideologies in the host country and educational language policies. Following Onaha (2012), a distinction is made between Pre-war and Post-war period in the history of the community, WW2 being a crucial event as from permanent settling in South America became the norm and, with it, a relative loosening of the immigrant language transmission practices. Through sociolinguistic and ethnographic research, an outline of the results of in-depth interviews, and archive resources consulting is offered.<br>
DOI: 10.6084/m9.figshare.5661808
title: Language choices of siblings in Italian/English families

description: Paper presented at ITML3 http://latllab.canterbury.ac.nz/language-choices-siblings-italianenglish-families/<br><br><br>Within the framework of language socialization and Family Language Policy studies, this qualitative study explores the language choices of bilingual siblings and their parents in Italian/English families residing in Sydney. The main source of data is video recordings of naturally occurring parent-children and child-to-child interactions during every day routines (i.e., family mealtimes and sibling playtime) in the home environment. The analysis of recurrent interactional practices is performed according to a conversational analytical approach. The focus of this presentation is on the language choices negotiated during the mealtime conversations of a ‘one-person-one-language’ family. More specifically, the analysis of sequences of bilingual exchanges involving the children and the minority language parent provides insights into the relationship between the parental strategies aiming to heritage language maintenance and the responsiveness of the children. The early findings show the dynamic ways in which family language policy is interactionally constructed and instantiated as well as the challenges of intergenerational language transmission in bilingual families with more than one child. <br><br>
DOI: 10.6084/m9.figshare.5661802
title: Brycon_orbignyanus_Assembly_1_A1_k55.fsa

description: <i> </i>Supplementary Data S3: <i>Brycon orbignyanus</i> (Characiformes: Bryconidae) draft partial genome assembly (~10X) in fasta format (.fsa). Assembled from Illumina HiSeq 2000 short reads (retrievable from NCBI-SRA <b> SRX3350440</b>)<b>,</b> using SOAPdenovo 2 (k-mer=55) with the intention to screen for microsatellite loci. This assembly A1 was the base for the alignments performed with SOAPaligner retrivable from NCBI-SRA <b>SRX3427716</b>). <br>The final size of the genomic assembly A1 is 1,113,754,917 bp (including unknown base calls and gaps, N) and 1,039,212,289 bp (not counting Ns – Δ=74,542,628). A total of 1,273,306 contigs or scaffolds were obtained, the shortest being 100 bp and the longest 172,138 bp (average=874). Only 55 scaffolds were longer than 100 kbp; 1.97% longer than 10 kbp; 11% longer than 1 kbps and 18.09% of 500 bp or more. The A1 assembly had the CG content of 41.18% and N50=8,463.<br>These results are part of the article "A broad genomic panel of microsatellite loci from <i>Brycon orbignyanus</i> (Characiformes: Bryconidae), an endangered migratory Neotropical fish".<b> </b><b>Scientific Reports, 8: 8511, 2918</b>
DOI: 10.6084/m9.figshare.5661799
title: Leersia perrieri leaf transcriptome

description: De novo transcriptome assembly of Leersia perrieri based on leaf RNAseq data (SRA SRR1171869). Trinity v2.4.0 was used for assembly using default parameters, with Trimmomatic for trimming of reads before assembly.<br>
DOI: 10.6084/m9.figshare.5661799.v1
title: Leersia perrieri leaf transcriptome

description: De novo transcriptome assembly of Leersia perrieri based on leaf RNAseq data (SRA SRR1171869). Trinity v2.4.0 was used for assembly using default parameters, with Trimmomatic for trimming of reads before assembly.<br>
DOI: 10.6084/m9.figshare.5661796
title: Oryza punctata leaf transcriptome

description: De novo transcriptome assembly of Oryza punctata based on leaf RNAseq data (SRA SRR1171005). Trinity v2.4.0 was used for assembly using default parameters, with Trimmomatic for trimming of reads before assembly.<br>
DOI: 10.6084/m9.figshare.5661796.v1
title: Oryza punctata leaf transcriptome

description: De novo transcriptome assembly of Oryza punctata based on leaf RNAseq data (SRA SRR1171005). Trinity v2.4.0 was used for assembly using default parameters, with Trimmomatic for trimming of reads before assembly.<br>
DOI: 10.6084/m9.figshare.5661793
title: Oryza minuta leaf transcriptome

description: De novo transcriptome assembly of Oryza minuta based on leaf RNAseq data (SRA SRR1179197). Trinity v2.4.0 was used for assembly using default parameters, with Trimmomatic for trimming of reads before assembly.<br>
DOI: 10.6084/m9.figshare.5661793.v1
title: Oryza minuta leaf transcriptome

description: De novo transcriptome assembly of Oryza minuta based on leaf RNAseq data (SRA SRR1179197). Trinity v2.4.0 was used for assembly using default parameters, with Trimmomatic for trimming of reads before assembly.<br>
DOI: 10.6084/m9.figshare.5661790
title: Oryza meyeriana leaf transcriptome

description: De novo transcriptome assembly of Oryza meyeriana based on leaf RNAseq data (SRA SRR1178918). Trinity v2.4.0 was used for assembly using default parameters, with Trimmomatic for trimming of reads before assembly.<br>
DOI: 10.6084/m9.figshare.5661790.v1
title: Oryza meyeriana leaf transcriptome

description: De novo transcriptome assembly of Oryza meyeriana based on leaf RNAseq data (SRA SRR1178918). Trinity v2.4.0 was used for assembly using default parameters, with Trimmomatic for trimming of reads before assembly.<br>
DOI: 10.6084/m9.figshare.5661787
title: Oryza officinalis leaf transcriptome

description: De novo transcriptome assembly of Oryza officinalis based on leaf RNAseq data (SRA SRR1179193). Trinity v2.4.0 was used for assembly using default parameters, with Trimmomatic for trimming of reads before assembly.<br>