cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12316055
title: Additional file 2 of CSN: unsupervised approach for inferring biological networks based on the genome alone

description: Additional file 2. Table 13a. The new 13,157 annotations predicted for S. cerevisiae. (B) The new 392 annotations predicted for E. coli. (C) The new 693 annotations predicted for the metagenomic sample.
DOI: 10.6084/m9.figshare.12316058
title: Additional file 1 of Enabling routine β-thalassemia Prevention and Patient Management by scalable, combined Thalassemia and Hemochromatosis Mutation Analysis

description: Additional file 1.
DOI: 10.6084/m9.figshare.12316052.v1
title: Additional file 1 of CSN: unsupervised approach for inferring biological networks based on the genome alone

description: Additional file 1. Additional Methods and Results.
DOI: 10.6084/m9.figshare.12316055.v1
title: Additional file 2 of CSN: unsupervised approach for inferring biological networks based on the genome alone

description: Additional file 2. Table 13a. The new 13,157 annotations predicted for S. cerevisiae. (B) The new 392 annotations predicted for E. coli. (C) The new 693 annotations predicted for the metagenomic sample.
DOI: 10.6084/m9.figshare.12316061.v1
title: Additional file 3 of CSN: unsupervised approach for inferring biological networks based on the genome alone

description: Additional file 3. Table 13b. The new 392 annotations predicted for E. coli. (C) The new 693 annotations predicted for the metagenomic sample.
DOI: 10.6084/m9.figshare.12316058.v1
title: Additional file 1 of Enabling routine β-thalassemia Prevention and Patient Management by scalable, combined Thalassemia and Hemochromatosis Mutation Analysis

description: Additional file 1.
DOI: 10.6084/m9.figshare.12315854
title: Additional file 1 of Detecting transcriptomic structural variants in heterogeneous contexts via the Multiple Compatible Arrangements Problem

description: Additional file 1. Annotated break points predicted by D-SQUID in HCC cell line samples. Break points predicted by D-SQUID and the gene regions they react in HCC1395 and HCC1954 samples.
DOI: 10.6084/m9.figshare.12315854.v1
title: Additional file 1 of Detecting transcriptomic structural variants in heterogeneous contexts via the Multiple Compatible Arrangements Problem

description: Additional file 1. Annotated break points predicted by D-SQUID in HCC cell line samples. Break points predicted by D-SQUID and the gene regions they react in HCC1395 and HCC1954 samples.
DOI: 10.6084/m9.figshare.12315797
title: Additional file 3 of Exploring why global health needs are unmet by research efforts: the potential influences of geography, industry and publication incentives

description: Additional file 3. Correspondence Table ICD-10 – MeSH.
DOI: 10.6084/m9.figshare.12315791
title: Additional file 2 of Exploring why global health needs are unmet by research efforts: the potential influences of geography, industry and publication incentives

description: Additional file 2. Data used in figures and tables, including supplementary material.
DOI: 10.6084/m9.figshare.12315797.v1
title: Additional file 3 of Exploring why global health needs are unmet by research efforts: the potential influences of geography, industry and publication incentives

description: Additional file 3. Correspondence Table ICD-10 – MeSH.
DOI: 10.6084/m9.figshare.12315791.v1
title: Additional file 2 of Exploring why global health needs are unmet by research efforts: the potential influences of geography, industry and publication incentives

description: Additional file 2. Data used in figures and tables, including supplementary material.
DOI: 10.6084/m9.figshare.12315734
title: Birth Weight Data.sav

description: This is a retrospective data of 736 newborns showing their birth weight, mother's age during birth, hospitals they were born in, mode of delivery.
DOI: 10.6084/m9.figshare.12315758
title: Data and analysis code from Survival and selection biases in early animal evolution and a source of systematic overestimation in molecular clocks

description: Tree and XML files for BEAST2 analyses. R code for generating molecular phylogenies and Fig. 3.
DOI: 10.6084/m9.figshare.12315719
title: Sorted and mapped reads to the reference genome in bam format

description: Trimmed reads were mapped to the reference genome NC_045512.2 and sorted using Bowtie2. Bam files can be integrated to the reference genome and visualized using Geneious or Artemis<b></b>
DOI: 10.6084/m9.figshare.12315758.v1
title: Data and analysis code from Survival and selection biases in early animal evolution and a source of systematic overestimation in molecular clocks

description: Tree and XML files for BEAST2 analyses. R code for generating molecular phylogenies and Fig. 3.
DOI: 10.6084/m9.figshare.12315689
title: Table S1_Native plants collected during O. latereillei activity period in the study area..docx

description: This table includes the list of the native plants collected during our study entitled " Nesting ecology and foraging biology of the mason bee <i>Osmia (Helicosmia) latreillei </i>Spinola, 1806 (Hymenoptera: Megachilidae) in western Algeria"
DOI: 10.6084/m9.figshare.12315719.v1
title: Sorted and mapped reads to the reference genome in bam format

description: Trimmed reads were mapped to the reference genome NC_045512.2 and sorted using Bowtie2. Bam files can be integrated to the reference genome and visualized using Geneious or Artemis<b></b>
DOI: 10.23641/asha.12315683
title: Taxonomic development in bilingual children (Lam & Sheng, 2020)

description: <b>Purpose: </b>Taxonomic awareness is central to vocabulary development and assessment. While taxonomic development appears largely unaffected by environmental factors, the impact of divided language input on distinct levels of the taxonomic hierarchy is unclear. The influence of scoring method on tasks that target distinct levels of the taxonomic hierarchy is unexamined.<b>Method: </b>Twenty-seven English-speaking monolingual children, 46 Mandarin–English bilingual children, and 33 Spanish–English bilingual children, ages 4–7 years, participated. We measured superordinate awareness with a category association task, coordinate awareness with a contrast association task, and vocabulary size with a picture-naming task. All bilinguals completed the tasks in both languages to generate single-language (English) scores and conceptual scores.<b>Results:</b> Single-language scoring indicated that bilingual children named fewer pictures and produced fewer superordinate-level responses in English than monolinguals. All language groups demonstrated comparable coordinate awareness. Importantly, conceptual scoring removed the bilingual disadvantage in both naming and category association tasks and revealed a bilingual advantage in coordinate awareness. Finally, the Mandarin–English and Spanish–English bilingual children performed comparably in all analyses despite differences in heritage language features and sociocultural support for bilingual development.<b>Conclusion: </b>Depending on task demand and scoring method, bilingual children exhibited slower, comparable, and faster development in taxonomic knowledge in comparison to monolingual controls. This study highlights the nuanced effect of bilingualism on different levels of the taxonomic hierarchy and the impact of scoring methods on measuring vocabulary depth. <br><b>Supplemental Material S1. </b>Stimuli used in the category association task (Table S1) and stimuli used in the contrast association task (Table S2). <br>Lam, B. P. W., & Sheng, L. (2020). Taxonomic development in young bilingual children: Task matters, and so does scoring method. <i>American Journal of Speech-Language Pathology, 29</i>(3), 1162-1177. https://doi.org/10.1044/2019_AJSLP-19-00143<br><b>Publisher Note: </b>This article is part of the Forum: Innovations in Clinical Practice for Dual Language Learners, Part 2.
DOI: 10.6084/m9.figshare.12315689.v2
title: Table S1_Native plants collected during O. latereillei activity period in the study area..docx

description: This table includes the list of the native plants collected during our study entitled " Nesting ecology and foraging biology of the mason bee <i>Osmia (Helicosmia) latreillei </i>Spinola, 1806 (Hymenoptera: Megachilidae) in western Algeria"
DOI: 10.23641/asha.12315683.v1
title: Taxonomic development in bilingual children (Lam & Sheng, 2020)

description: <b>Purpose: </b>Taxonomic awareness is central to vocabulary development and assessment. While taxonomic development appears largely unaffected by environmental factors, the impact of divided language input on distinct levels of the taxonomic hierarchy is unclear. The influence of scoring method on tasks that target distinct levels of the taxonomic hierarchy is unexamined.<b>Method: </b>Twenty-seven English-speaking monolingual children, 46 Mandarin–English bilingual children, and 33 Spanish–English bilingual children, ages 4–7 years, participated. We measured superordinate awareness with a category association task, coordinate awareness with a contrast association task, and vocabulary size with a picture-naming task. All bilinguals completed the tasks in both languages to generate single-language (English) scores and conceptual scores.<b>Results:</b> Single-language scoring indicated that bilingual children named fewer pictures and produced fewer superordinate-level responses in English than monolinguals. All language groups demonstrated comparable coordinate awareness. Importantly, conceptual scoring removed the bilingual disadvantage in both naming and category association tasks and revealed a bilingual advantage in coordinate awareness. Finally, the Mandarin–English and Spanish–English bilingual children performed comparably in all analyses despite differences in heritage language features and sociocultural support for bilingual development.<b>Conclusion: </b>Depending on task demand and scoring method, bilingual children exhibited slower, comparable, and faster development in taxonomic knowledge in comparison to monolingual controls. This study highlights the nuanced effect of bilingualism on different levels of the taxonomic hierarchy and the impact of scoring methods on measuring vocabulary depth. <br><b>Supplemental Material S1. </b>Stimuli used in the category association task (Table S1) and stimuli used in the contrast association task (Table S2). <br>Lam, B. P. W., & Sheng, L. (2020). Taxonomic development in young bilingual children: Task matters, and so does scoring method. <i>American Journal of Speech-Language Pathology, 29</i>(3), 1162-1177. https://doi.org/10.1044/2019_AJSLP-19-00143<br><b>Publisher Note: </b>This article is part of the Forum: Innovations in Clinical Practice for Dual Language Learners, Part 2.
DOI: 10.6084/m9.figshare.12315632
title: FASTA file of the reference genome NC_045512.2

description: Reference genome from Wuhan coronavirus in FASTA fomat. GenBank accession number: NC_045512.2. Severe acute respiratory syndrome coronavirus 2 isolate Wuhan-Hu-1, complete genome
DOI: 10.6084/m9.figshare.12315689.v1
title: Table S1.docx

description: This table includes the list of the native plants collected during our study entitled " Nesting ecology and foraging biology of the mason bee <i>Osmia (Helicosmia) latreillei </i>Spinola, 1806 (Hymenoptera: Megachilidae) in western Algeria"
DOI: 10.6084/m9.figshare.12315659
title: Alignment of 4 complete coronavirus genomes

description: Multiple sequence alignment of 4 genome sequences: 1. The reference genome, 2 and 3 the Peru genome downloaded from GenBank and GISAID, and 4 the Peru genome reassembled using the information from the SRA database (SRR11508492)<br>
DOI: 10.6084/m9.figshare.12315659.v1
title: Alignment of 4 complete coronavirus genomes

description: Multiple sequence alignment of 4 genome sequences: 1. The reference genome, 2 and 3 the Peru genome downloaded from GenBank and GISAID, and 4 the Peru genome reassembled using the information from the SRA database (SRR11508492)<br>
DOI: 10.6084/m9.figshare.12315473
title: High expression of cholecystokinin A receptor appears to promote the growth of Lueyang black-boned chicken by increasing feed efficiency

description: Body weight, feed intake, pedigree, genotype and CCKAR expression data of Lueyang black-boned chickens from 4 generations of breeding population<br>
DOI: 10.6084/m9.figshare.12315443
title: OncoSig Input Data

description: This is the input data needed to run the analyses described in the OncoSig data package. <br>See github here for full description of analyses: https://github.com/califano-lab/OncoSig<br>
DOI: 10.6084/m9.figshare.12315473.v1
title: growth and CCKAR expression data of Lueyang chicken

description: body weight, feed intake, feed conversion ratio data of 129 Lueyang black-boned chickens. Delta Ct data of CCKAR exprssion in five organs of 30 samples
DOI: 10.6084/m9.figshare.12315389
title: Supplementary data-1.docx

description: depression
DOI: 10.6084/m9.figshare.12315380
title: Supplementary material.docx

description: Supplementary material
DOI: 10.6084/m9.figshare.12315389.v1
title: Supplementary data-1.docx

description: depression
DOI: 10.6084/m9.figshare.12315380.v2
title: Supplementary material.docx

description: Supplementary material
DOI: 10.6084/m9.figshare.12315380.v1
title: Supplementary material1.docx

description: Supplementary material
DOI: 10.6084/m9.figshare.12315473.v2
title: growth and CCKAR expression data of Lueyang chicken

description: body weight, feed intake, feed conversion ratio data of 129 Lueyang black-boned chickens. Delta Ct data of CCKAR exprssion in five organs of 30 samples
DOI: 10.6084/m9.figshare.12315290
title: Soil_qPCR Data for Peerj.xlsx

description: This q-PCR raw data is used as the supplymentary information for the manuscript titled "Antibiotic Resistance Gene Prevalence in Soils due to Animal Manure Deposition and Long-term Pasture Management" and will be published on the journal of Peerj.<b></b>
DOI: 10.6084/m9.figshare.12315473.v3
title: High expression of cholecystokinin A receptor appears to promote the growth of Lueyang black-boned chicken by increasing feed efficiency

description: Body weight, feed intake, pedigree, genotype and CCKAR expression data of Lueyang black-boned chickens from 4 generations of breeding population<br>
DOI: 10.6084/m9.figshare.12315290.v1
title: Soil_qPCR Data for Peerj.xlsx

description: This q-PCR raw data is used as the supplymentary information for the manuscript titled "Antibiotic Resistance Gene Prevalence in Soils due to Animal Manure Deposition and Long-term Pasture Management" and will be published on the journal of Peerj.<b></b>
DOI: 10.6084/m9.figshare.12315473.v5
title: High expression of cholecystokinin A receptor appears to promote the growth of Lueyang black-boned chicken by increasing feed efficiency

description: Body weight, feed intake, pedigree, genotype and CCKAR expression data of Lueyang black-boned chickens from 4 generations of breeding population<br>
DOI: 10.6084/m9.figshare.12315227
title: House

description: Picture of house.
DOI: 10.6084/m9.figshare.12315230
title: Aspergillus fumigatus transcription factors involved in the caspofungin paradoxical effect, supplementary files

description: <i>Aspergillus fumigatus </i>is the leading cause of pulmonary fungal diseases. Azoles have been used for many years as the main antifungal agents to treat and prevent invasive aspergillosis. However, in the last ten years there are several reports of azole resistance in <i>A. fumigatus</i> and new strategies are needed to combat invasive aspergillosis. Caspofungin is effective against other human fungal pathogens, but it is only fungistatic against <i>A. fumigatus</i>. Resistance to caspofungin in <i>A. fumigatus</i> have been linked to mutations in the <i>fksA</i> gene that encodes the target enzyme of the drug, β-1,3-glucan synthase. However, tolerance to high caspofungin concentrations, a phenomenon known as caspofungin paradoxical effect (CPE), is also important for subsequent adaptation and drug resistance evolution. Here, we have identified and characterized the transcription factors involved in the response to CPE by screening an <i>A. fumigatus</i> library of 484 null transcription factors (TFs) in CPE drug concentrations. We have identified eleven TFs that had reduced CPE encoding proteins involved in the basal modulation of the RNA polymerase II initiation sites, calcium metabolism and cell wall remodelling. One of theseTFs FhdA was important for mitochondrial respiratory function and iron metabolism. The Δ<i>fhdA</i> mutant had decreased growth when exposed to Congo Red or at high temperature. RNAseq analysis and further experimental validation indicate that the Δ<i>fhdA</i> mutant showed diminished respiratory capacity, probably affecting several pathways related to the caspofungin tolerance and resistance. Our results provide the foundation to understand signaling pathways that are important for caspofungin tolerance and resistance.
DOI: 10.6084/m9.figshare.12315473.v4
title: High expression of cholecystokinin A receptor appears to promote the growth of Lueyang black-boned chicken by increasing feed efficiency

description: Body weight, feed intake, pedigree, genotype and CCKAR expression data of Lueyang black-boned chickens from 4 generations of breeding population<br>
DOI: 10.6084/m9.figshare.12315227.v1
title: House

description: Picture of house.
DOI: 10.6084/m9.figshare.12315212
title: Phosphoproteomics of Aspergillus fumigatus exposed to the antifungal drug caspofungin, Supplementary files

description: <em>Aspergillus fumigatus</em> is an opportunistic and allergenic pathogenic fungus, responsible for fungal infections in humans. <em>A. fumigatus </em>infections are usually treated with polyenes, azoles, or echinocandins. Echinocandins, such as caspofungin, can inhibit the biosynthesis of the β-1,3-glucan polysaccharide, affecting the cell wall integrity and leading to fungal death. In some <em>A. fumigatus </em>strains, caspofungin treatment at high concentrations induces an increase of fungal growth, a phenomenon called Caspofungin Paradoxical Effect (CPE). Here, we analyze the proteome and phosphoproteome of <em>A. fumigatus</em> wild-type and the mitogen-activated protein kinases <em>mpkA</em> and <em>sakA </em>null mutant strains during CPE (2 µg/ml caspofungin for 1 hour). The wild-type proteome shows 75 proteins and 814 phosphopeptides (corresponding to 520 proteins) altered in abundance in response to caspofungin treatment. The <em>ΔmpkA </em>(<em>ΔmpkA </em>caspofungin/wild-type caspofungin) and <em>ΔsakA</em> (<em>ΔsakA </em>caspofungin/wild-type caspofungin) display 626 proteins and 1236 phosphopeptides (corresponding to 703 proteins) and 101 proteins and 1217 phosphopeptides (corresponding to 645 proteins), respectively, altered in abundance. Functional characterization of the phosphopeptides from the wild-type exposed to caspofungin show enrichment for transcription factors, protein kinases, and cytoskeleton proteins. Proteomic analysis for the Δ<em>mpkA</em> and Δ<em>sakA</em> mutants indicates that the control of proteins involved in metabolism, such as in secondary metabolites production, was highly represented in both mutants. Functional categorization of phosphopeptides from both mutants is very similar, and show a high number of proteins with decreased phosphorylation of proteins involved in transcriptional control, DNA/RNA binding, cell cycle control, and DNA processing. This study reveals novel transcription factors involved in caspofungin tolerance.
DOI: 10.6084/m9.figshare.12315230.v1
title: Untitled Item

description: <i>Aspergillus fumigatus </i>is the leading cause of pulmonary fungal diseases. Azoles have been used for many years as the main antifungal agents to treat and prevent invasive aspergillosis. However, in the last ten years there are several reports of azole resistance in <i>A. fumigatus</i> and new strategies are needed to combat invasive aspergillosis. Caspofungin is effective against other human fungal pathogens, but it is only fungistatic against <i>A. fumigatus</i>. Resistance to caspofungin in <i>A. fumigatus</i> have been linked to mutations in the <i>fksA</i> gene that encodes the target enzyme of the drug, β-1,3-glucan synthase. However, tolerance to high caspofungin concentrations, a phenomenon known as caspofungin paradoxical effect (CPE), is also important for subsequent adaptation and drug resistance evolution. Here, we have identified and characterized the transcription factors involved in the response to CPE by screening an <i>A. fumigatus</i> library of 484 null transcription factors (TFs) in CPE drug concentrations. We have identified eleven TFs that had reduced CPE encoding proteins involved in the basal modulation of the RNA polymerase II initiation sites, calcium metabolism and cell wall remodelling. One of theseTFs FhdA was important for mitochondrial respiratory function and iron metabolism. The Δ<i>fhdA</i> mutant had decreased growth when exposed to Congo Red or at high temperature. RNAseq analysis and further experimental validation indicate that the Δ<i>fhdA</i> mutant showed diminished respiratory capacity, probably affecting several pathways related to the caspofungin tolerance and resistance. Our results provide the foundation to understand signaling pathways that are important for caspofungin tolerance and resistance.
DOI: 10.6084/m9.figshare.12315212.v2
title: Phosphoproteomics of Aspergillus fumigatus exposed to the antifungal drug caspofungin, Supplementary files

description: <em>Aspergillus fumigatus</em> is an opportunistic and allergenic pathogenic fungus, responsible for fungal infections in humans. <em>A. fumigatus </em>infections are usually treated with polyenes, azoles, or echinocandins. Echinocandins, such as caspofungin, can inhibit the biosynthesis of the β-1,3-glucan polysaccharide, affecting the cell wall integrity and leading to fungal death. In some <em>A. fumigatus </em>strains, caspofungin treatment at high concentrations induces an increase of fungal growth, a phenomenon called Caspofungin Paradoxical Effect (CPE). Here, we analyze the proteome and phosphoproteome of <em>A. fumigatus</em> wild-type and the mitogen-activated protein kinases <em>mpkA</em> and <em>sakA </em>null mutant strains during CPE (2 µg/ml caspofungin for 1 hour). The wild-type proteome shows 75 proteins and 814 phosphopeptides (corresponding to 520 proteins) altered in abundance in response to caspofungin treatment. The <em>ΔmpkA </em>(<em>ΔmpkA </em>caspofungin/wild-type caspofungin) and <em>ΔsakA</em> (<em>ΔsakA </em>caspofungin/wild-type caspofungin) display 626 proteins and 1236 phosphopeptides (corresponding to 703 proteins) and 101 proteins and 1217 phosphopeptides (corresponding to 645 proteins), respectively, altered in abundance. Functional characterization of the phosphopeptides from the wild-type exposed to caspofungin show enrichment for transcription factors, protein kinases, and cytoskeleton proteins. Proteomic analysis for the Δ<em>mpkA</em> and Δ<em>sakA</em> mutants indicates that the control of proteins involved in metabolism, such as in secondary metabolites production, was highly represented in both mutants. Functional categorization of phosphopeptides from both mutants is very similar, and show a high number of proteins with decreased phosphorylation of proteins involved in transcriptional control, DNA/RNA binding, cell cycle control, and DNA processing. This study reveals novel transcription factors involved in caspofungin tolerance.
DOI: 10.6084/m9.figshare.12315125
title: Supplementary Table S4

description: Enrichment for functional protein kinases association networks.
DOI: 10.6084/m9.figshare.12315125.v1
title: Supplementary Table S4

description: Enrichment for functional protein kinases association networks.