cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7849160.v2
title: Open Access Outreach Materials: Slides & Handout

description: A set of resources for open access outreach. Includes 4 slideshows and a handout:<br>- Copyright in Higher Education: Presentation on copyright in higher education. Topics include what copyright is, the purpose of copyright, using copyrighted works (permissions, exemptions, fair use), author rights, and open access.<br>- Open Access: Increase the Visibility of your Scholarship: Presentation on the fundamentals of open access. Topics include the social, political and especially economic context, defining open access, green OA, rights retention, sci-hub, and the beneficiaries of open access.<br>- Open Access: Identifying Quality Journals & Avoiding Predatory Publishers: Slideshow for presentation on open access. Topics include defining Gold OA (APCs, business models, subsidies), OA citation advantage, predatory publishers, whitelists/blacklists.<br>- Open Educational Resources: An Introduction: Slideshow for presentation on OER. Topics include textbook market, student costs, defining OER, access options, student and faculty satisfaction, student success measurements, 5 Rs.<br>- Strategies for Accessing Research After Graduation: 2 page handout with tips for how to access research post-graduation. Includes PubMed, DOAJ, Google Scholar, Unpaywall, public and academic libraries
DOI: 10.25345/c5ct9m
title: MassIVE MSV000086032 - MassIVE_C_RP_LC_MS_MS Bile Acid Identification
title: Sillner et al. : Longitudinal profiles of dietary and microbial metabolites in formula- and breastfed infants - https://doi.org/10.1101/2020.05.11.086546 Identification of bile acids in infant fecal samples via RP LC-MS by MS1 (+-0.005Da) and retention time matching by the use of authentic standards, selected and pooled samples - displayed in Figure 4A-C
DOI: 10.6084/m9.figshare.7848056
title: Epigenomic profiling of newborns with isolated orofacial clefts reveals widespread DNA methylation changes and implicates metastable epiallele regions in disease risk

description: Cleft lip with or without cleft palate (CL/P) is a common human birth defect whose etiologies remain largely unknown. Several studies have demonstrated that periconceptional supplementation of folic acid can reduce risk of CL/P in offspring. In this study, we tested the hypothesis that the preventive effect of folic acid is manifested through epigenetic modifications by determining whether DNA methylation changes are associated with CL/P. To more readily observe the potential effects of maternal folate on the offspring epigenome, we focused on births prior to mandatory dietary folate fortification in the United States (i.e. birth year 1997 or earlier). Genomic DNA methylation levels were assessed from archived newborn bloodspots in a 182-member case-control study using the Illumina® Human Beadchip 450K array. CL/P cases displayed striking epigenome-wide hypomethylation relative to controls: 63% of CpGs interrogated had lower methylation levels in case newborns, a trend which held up in racially stratified sub-groups. 28 CpG sites reached epigenome-wide significance and all were case-hypomethylated. The most significant CL/P-associated differentially methylated region encompassed the <i>VTRNA2-1</i> gene, which was also hypomethylated in cases (FWER <i>p</i> = 0.014). This region has been previously characterized as a nutritionally-responsive, metastable epiallele and CL/P-associated methylation changes, in general, were greater at or near putative metastable epiallelic regions. Gene Set Enrichment Analysis of CL/P-associated DMRs showed an over-representation of genes involved in palate development such as <i>WNT9B, MIR140</i> and <i>LHX8</i>. CL/P-associated DNA methylation changes may partly explain the mechanism by which orofacial clefts are responsive to maternal folate levels.
DOI: 10.6084/m9.figshare.7849160.v3
title: Open Access Outreach Materials: Slides & Handout

description: A set of resources for open access outreach. Includes 4 slideshows and a handout:<br>- Copyright in Higher Education: Presentation on copyright in higher education. Topics include what copyright is, the purpose of copyright, using copyrighted works (permissions, exemptions, fair use), author rights, and open access.<br>- Open Access: Increase the Visibility of your Scholarship: Presentation on the fundamentals of open access. Topics include the social, political and especially economic context, defining open access, green OA, rights retention, sci-hub, and the beneficiaries of open access.<br>- Open Access: Identifying Quality Journals & Avoiding Predatory Publishers: Slideshow for presentation on open access. Topics include defining Gold OA (APCs, business models, subsidies), OA citation advantage, predatory publishers, whitelists/blacklists.<br>- Open Educational Resources: An Introduction: Slideshow for presentation on OER. Topics include textbook market, student costs, defining OER, access options, student and faculty satisfaction, student success measurements, 5 Rs.<br>- Strategies for Accessing Research After Graduation: 2 page handout with tips for how to access research post-graduation. Includes PubMed, DOAJ, Google Scholar, Unpaywall, public and academic libraries
DOI: 10.6084/m9.figshare.7848056.v1
title: Epigenomic profiling of newborns with isolated orofacial clefts reveals widespread DNA methylation changes and implicates metastable epiallele regions in disease risk

description: Cleft lip with or without cleft palate (CL/P) is a common human birth defect whose etiologies remain largely unknown. Several studies have demonstrated that periconceptional supplementation of folic acid can reduce risk of CL/P in offspring. In this study, we tested the hypothesis that the preventive effect of folic acid is manifested through epigenetic modifications by determining whether DNA methylation changes are associated with CL/P. To more readily observe the potential effects of maternal folate on the offspring epigenome, we focused on births prior to mandatory dietary folate fortification in the United States (i.e. birth year 1997 or earlier). Genomic DNA methylation levels were assessed from archived newborn bloodspots in a 182-member case-control study using the Illumina® Human Beadchip 450K array. CL/P cases displayed striking epigenome-wide hypomethylation relative to controls: 63% of CpGs interrogated had lower methylation levels in case newborns, a trend which held up in racially stratified sub-groups. 28 CpG sites reached epigenome-wide significance and all were case-hypomethylated. The most significant CL/P-associated differentially methylated region encompassed the <i>VTRNA2-1</i> gene, which was also hypomethylated in cases (FWER <i>p</i> = 0.014). This region has been previously characterized as a nutritionally-responsive, metastable epiallele and CL/P-associated methylation changes, in general, were greater at or near putative metastable epiallelic regions. Gene Set Enrichment Analysis of CL/P-associated DMRs showed an over-representation of genes involved in palate development such as <i>WNT9B, MIR140</i> and <i>LHX8</i>. CL/P-associated DNA methylation changes may partly explain the mechanism by which orofacial clefts are responsive to maternal folate levels.
DOI: 10.6084/m9.figshare.7848035
title: Burden of Drug-Resistant Pulmonary Tuberculosis in Pakistani Children: A cross-sectional study (Questionnaire)

description: <b>Burden of
Drug-Resistant Pulmonary Tuberculosis in Pakistani Children: A cross-sectional
study</b>
DOI: 10.6084/m9.figshare.7849160.v4
title: Open Access Outreach Materials: Slides & Handout

description: A set of resources for open access outreach. Includes 4 slideshows and a handout:<br>- Copyright in Higher Education: Presentation on copyright in higher education. Topics include what copyright is, the purpose of copyright, using copyrighted works (permissions, exemptions, fair use), author rights, and open access.<br>- Open Access: Increase the Visibility of your Scholarship: Presentation on the fundamentals of open access. Topics include the social, political and especially economic context, defining open access, green OA, rights retention, sci-hub, and the beneficiaries of open access.<br>- Open Access: Identifying Quality Journals & Avoiding Predatory Publishers: Slideshow for presentation on open access. Topics include defining Gold OA (APCs, business models, subsidies), OA citation advantage, predatory publishers, whitelists/blacklists.<br>- Open Educational Resources: An Introduction: Slideshow for presentation on OER. Topics include textbook market, student costs, defining OER, access options, student and faculty satisfaction, student success measurements, 5 Rs.<br>- Strategies for Accessing Research After Graduation: 2 page handout with tips for how to access research post-graduation. Includes PubMed, DOAJ, Google Scholar, Unpaywall, public and academic libraries
DOI: 10.6084/m9.figshare.7849160.v5
title: Open Access Outreach Materials: Slides & Handout

description: A set of resources for open access outreach. Includes 4 slideshows and a handout:<br>- Copyright in Higher Education: Presentation on copyright in higher education. Topics include what copyright is, the purpose of copyright, using copyrighted works (permissions, exemptions, fair use), author rights, and open access.<br>- Open Access: Increase the Visibility of your Scholarship: Presentation on the fundamentals of open access. Topics include the social, political and especially economic context, defining open access, green OA, rights retention, sci-hub, and the beneficiaries of open access.<br>- Open Access: Identifying Quality Journals & Avoiding Predatory Publishers: Slideshow for presentation on open access. Topics include defining Gold OA (APCs, business models, subsidies), OA citation advantage, predatory publishers, whitelists/blacklists.<br>- Open Educational Resources: An Introduction: Slideshow for presentation on OER. Topics include textbook market, student costs, defining OER, access options, student and faculty satisfaction, student success measurements, 5 Rs.<br>- Strategies for Accessing Research After Graduation: 2 page handout with tips for how to access research post-graduation. Includes PubMed, DOAJ, Google Scholar, Unpaywall, public and academic libraries
DOI: 10.6084/m9.figshare.7848023
title: A checkpoint-oriented cell cycle simulation model

description: Modeling and <i>in silico</i> simulations are of major conceptual and applicative interest in studying the cell cycle and proliferation in eukaryotic cells. In this paper, we present a cell cycle checkpoint-oriented simulator that uses agent-based simulation modeling to reproduce the dynamics of a cancer cell population in exponential growth. Our <i>in silico</i> simulations were successfully validated by experimental <i>in vitro</i> supporting data obtained with HCT116 colon cancer cells. We demonstrated that this model can simulate cell confluence and the associated elongation of the G1 phase. Using nocodazole to synchronize cancer cells at mitosis, we confirmed the model predictivity and provided evidence of an additional and unexpected effect of nocodazole on the overall cell cycle progression. We anticipate that this cell cycle simulator will be a potential source of new insights and research perspectives. This figure describes the input biological data (doubling time and cell cycle distribution) and the two main outputs of the simulator. The simulator offers several tools to analyze cell cycle progression/distribution and provides a virtual dynamic view of the cell cycle parameters. Moreover, the simulator allows testing hypotheses, such as challenging the cell cycle checkpoints.
DOI: 10.6084/m9.figshare.7847825
title: Supporting Information: Dataset_B1_Authors

description: Dataset from the integrated quantitative and qualitative data.Supporting information to the paper entitled "How to identify peer-reviewed publications: Open-identity labels in scholarly book publishing".
DOI: 10.6084/m9.figshare.7848023.v2
title: A checkpoint-oriented cell cycle simulation model

description: Modeling and <i>in silico</i> simulations are of major conceptual and applicative interest in studying the cell cycle and proliferation in eukaryotic cells. In this paper, we present a cell cycle checkpoint-oriented simulator that uses agent-based simulation modeling to reproduce the dynamics of a cancer cell population in exponential growth. Our <i>in silico</i> simulations were successfully validated by experimental <i>in vitro</i> supporting data obtained with HCT116 colon cancer cells. We demonstrated that this model can simulate cell confluence and the associated elongation of the G1 phase. Using nocodazole to synchronize cancer cells at mitosis, we confirmed the model predictivity and provided evidence of an additional and unexpected effect of nocodazole on the overall cell cycle progression. We anticipate that this cell cycle simulator will be a potential source of new insights and research perspectives. This figure describes the input biological data (doubling time and cell cycle distribution) and the two main outputs of the simulator. The simulator offers several tools to analyze cell cycle progression/distribution and provides a virtual dynamic view of the cell cycle parameters. Moreover, the simulator allows testing hypotheses, such as challenging the cell cycle checkpoints.
DOI: 10.6084/m9.figshare.7848023.v1
title: A CHECKPOINT-ORIENTED CELL CYCLE SIMULATION MODEL

description: Modeling and <i>in silico</i> simulations are of major conceptual and applicative interest for studying the cell cycle and proliferation in eukaryotic cells. In this paper, we present a cell cycle checkpoint-oriented simulator that uses agent-based simulation modeling to reproduce the dynamics of a cancer cell population in exponential growth. Our <i>in silico</i> simulations were successfully validated by experimental <i>in vitro</i> supporting data obtained with HCT116 colon cancer cells. We demonstrated that this model can simulate cell confluence and the associated elongation of the G1 phase. Using nocodazole to synchronize cancer cells at mitosis, we confirmed the model predictivity, and provided evidence of an additional and unexpected effect of nocodazole on the overall cell cycle progression. We anticipate that this cell cycle simulator will be a potential source of new insights and research perspectives.
DOI: 10.6084/m9.figshare.7847825.v1
title: Supporting Information: Dataset_B1_Authors

description: Dataset from the integrated quantitative and qualitative data.Supporting information to the paper entitled "How to identify peer-reviewed publications: Open-identity labels in scholarly book publishing".
DOI: 10.6084/m9.figshare.7846688
title: GNPS Molecular Network for Actinobacteria associated with kelps.

description: GNPS-based molecular network of LC-HRMS/MS data for crude extracts obtained from kelp-associated actinobacteria isolates.
DOI: 10.6084/m9.figshare.7846688.v1
title: GNPS Molecular Network for Actinobacteria associated with kelps.

description: GNPS-based molecular network of LC-HRMS/MS data for crude extracts obtained from kelp-associated actinobacteria isolates.
DOI: 10.6084/m9.figshare.7845290
title: Identification of Hfq-binding RNAs in <i>Caulobacter crescentus</i>

description: Small RNAs are important for post-transcriptional regulation of gene expression, affecting stability and activity of their target mRNAs. The bacterial Sm-like protein Hfq is required to promote pairing between both RNAs when their sequence complementarity is limited. To provide a first global view on the post-transcriptional landscape of the α-proteobacterium <i>Caulobacter crescentus</i>, we have identified the Hfq-binding RNAs employing High-throughput sequencing of RNA isolated by cross-linking immunoprecipitation (HITS-CLIP). A total of 261 RNAs, including 3 unannotated RNAs, were successfully identified and classified according to putative function. Moreover, possible interactions between the identified sRNAs with mRNA targets were postulated through computational target predictions.
DOI: 10.6084/m9.figshare.7845236
title: Spatial data and R code for the paper: "Anthropocene refugia: integrating history and predictive modelling to assess the space available for biodiversity in a human-dominated world"

description: This folder contains the spatial data and R code used to produce the maps in Box 1 and Supplementary Information of the paper entitled "Anthropocene refugia: concept and applications in conservation" by S. Monsarrat, S. Jarvie and J-C. Svenning.
DOI: 10.6084/m9.figshare.7845290.v2
title: Identification of Hfq-binding RNAs in <i>Caulobacter crescentus</i>

description: Small RNAs are important for post-transcriptional regulation of gene expression, affecting stability and activity of their target mRNAs. The bacterial Sm-like protein Hfq is required to promote pairing between both RNAs when their sequence complementarity is limited. To provide a first global view on the post-transcriptional landscape of the α-proteobacterium <i>Caulobacter crescentus</i>, we have identified the Hfq-binding RNAs employing High-throughput sequencing of RNA isolated by cross-linking immunoprecipitation (HITS-CLIP). A total of 261 RNAs, including 3 unannotated RNAs, were successfully identified and classified according to putative function. Moreover, possible interactions between the identified sRNAs with mRNA targets were postulated through computational target predictions.
DOI: 10.6084/m9.figshare.7845221
title: Unfaking Andalucia.xlsx

description: Dataset con los tuits retuiteados por el bot unfaking_es durante la campaña electoral de las elecciones autonómicas andaluzas de 2018.<br>
DOI: 10.6084/m9.figshare.7845236.v1
title: Spatial data and R code for the paper: "Anthropocene refugia: integrating history and predictive modelling to assess the space available for biodiversity in a human-dominated world"

description: This folder contains the spatial data and R code used to produce the maps in Box 1 and Supplementary Information of the paper entitled "Anthropocene refugia: concept and applications in conservation" by S. Monsarrat, S. Jarvie and J-C. Svenning.
DOI: 10.6084/m9.figshare.7845221.v1
title: Unfaking Andalucia.xlsx

description: Dataset con los tuits retuiteados por el bot unfaking_es durante la campaña electoral de las elecciones autonómicas andaluzas de 2018.<br>
DOI: 10.6084/m9.figshare.7845290.v1
title: Identification of Hfq-binding RNAs in <i>Caulobacter crescentus</i>

description: Small RNAs are important for post-transcriptional regulation of gene expression, affecting stability and activity of their target mRNAs. The bacterial Sm-like protein Hfq is required to promote pairing between both RNAs when their sequence complementarity is limited. To provide a first global view on the post-transcriptional landscape of the α-proteobacterium <i>Caulobacter crescentus</i>, we have identified the Hfq-binding RNAs employing High-throughput sequencing of RNA isolated by cross-linking immunoprecipitation (HITS-CLIP). A total of 261 RNAs, including 3 unannotated RNAs, were successfully identified and classified according to putative function. Moreover, possible interactions between the identified sRNAs with mRNA targets were postulated through computational target predictions.
DOI: 10.6084/m9.figshare.7845188
title: Larsen et al 2019 Supplementary Figures and tables

description: Supplementary figures and tables for Larsen et al 2019
DOI: 10.6084/m9.figshare.7845182
title: Wu - Tables - V2Final.docx

description: Table 1. Posterior mean estimates of genotyping error rates per sample evaluated on four commercial bovine SNP chips;Table 2. Posterior means (PMU) and standard deviations (PSD) of chromosome-wise genotyping error rate (%) estimated in the GeneSeek SNP genotyping quality assurance type II data.
DOI: 10.6084/m9.figshare.7845167
title: The global-scale distributions of soil protists and their contributions to belowground systems.

description: Associated files for analyses
DOI: 10.6084/m9.figshare.7845170
title: Wu - Supplementary tables - V2Final.docx

description: Table S1 Descriptive information of Neogen GeneSeek quality assurance type 1 samples;Table S2 Descriptive information of Neogen GeneSeek quality assurance type II samples;Table S3 Posterior mean estimate of genotyping discordance rates using Neogen GeneSeek quality assurance (QA) type 1 and type 2 data, respectively;Table S4 Posterior mean estimates of genotyping discordance rates (GDR,%) of common SNPs by chromosomes Neogen GeneSeek quality assurance (QA) type I and II data;Table S5 List of SNPs with greater than 1% genotype error rates, as evaluated in the QA type II genotype data provided by Neogen GeneSeek.
DOI: 10.6084/m9.figshare.7845182.v1
title: Wu - Tables - V2Final.docx

description: Table 1. Posterior mean estimates of genotyping error rates per sample evaluated on four commercial bovine SNP chips;Table 2. Posterior means (PMU) and standard deviations (PSD) of chromosome-wise genotyping error rate (%) estimated in the GeneSeek SNP genotyping quality assurance type II data.
DOI: 10.6084/m9.figshare.7845170.v1
title: Wu - Supplementary tables - V2Final.docx

description: Table S1 Descriptive information of Neogen GeneSeek quality assurance type 1 samples;Table S2 Descriptive information of Neogen GeneSeek quality assurance type II samples;Table S3 Posterior mean estimate of genotyping discordance rates using Neogen GeneSeek quality assurance (QA) type 1 and type 2 data, respectively;Table S4 Posterior mean estimates of genotyping discordance rates (GDR,%) of common SNPs by chromosomes Neogen GeneSeek quality assurance (QA) type I and II data;Table S5 List of SNPs with greater than 1% genotype error rates, as evaluated in the QA type II genotype data provided by Neogen GeneSeek.
DOI: 10.6084/m9.figshare.7845101
title: Supplementary figures

description: Figure S1 - Histograms of posterior mean estimates of genotyping error rates per animal genotyped on each of four bovine SNP arrays: (A) GGP LD V3, (B) GGP LD V4, (C) GGP HD 80K, and (D) GGP HD 150K;<br> Figure S2 - Frequencies of six types of genotyping errors evaluated in QA type II data.
DOI: 10.17028/rd.lboro.7845062
title: Supplementary information files for article: 'Life-cycle assessment of microwave-assisted pectin extraction at pilot scale'

description: Supplementary information files for article: 'Life-cycle assessment of microwave-assisted pectin extraction at pilot scale'.<br>Abstract: The first Life-Cycle Assessment (LCA) of an acid-free, microwave-assisted process for pectin production at pilot scale is reported. The properties of the resulting pectin were measured and compared against the criteria for commercial pectin, while the energy consumption of the microwave process was measured to compare its life cycle impacts with that of the current commercial process. Overall, the pectin met all the criteria for food-grade commercial pectin. The microwave unit was estimated to have &lt;25% of the environmental impact of traditional acid-assisted thermal process in all categories measured and provided an improved yield of 5% (wet weight basis) compared to 3% by thermal heating under normalized conditions. The readouts were comparable with each other over three runs indicating a robust and reproducible process, crucial for scale-up purposes. With the product meeting the relevant criteria and the process being robust and more environmentally friendly, this work demonstrates the practical and commercial potential of microwave technology to succeed conventional acid-based extraction of pectin production.