cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6652289.v1
title: The bifurcated stem loop 4 (SL4) is crucial for efficient packaging of mouse mammary tumor virus (MMTV) genomic RNA

description: Packaging the mouse mammary tumor virus (MMTV) genomic RNA (gRNA) requires the entire 5ʹ untranslated region (UTR) in conjunction with the first 120 nucleotides of the <i>gag</i> gene. This region includes several palindromic (pal) sequence(s) and stable stem loops (SLs). Among these, stem loop 4 (SL4) adopts a bifurcated structure consisting of three stems, two apical loops, and an internal loop. Pal II, located in one of the apical loops, mediates gRNA dimerization, a process intricately linked to packaging. We thus hypothesized that the bifurcated SL4 structure could constitute the major gRNA packaging determinant. To test this hypothesis, the two apical loops and the flanking sequences forming the bifurcated SL4 were individually mutated. These mutations all had deleterious effects on gRNA packaging and propagation. Next, single and compensatory mutants were designed to destabilize then recreate the bifurcated SL4 structure. A structure-function analysis using bioinformatics predictions and RNA chemical probing revealed that mutations that led to the loss of the SL4 bifurcated structure abrogated RNA packaging and propagation, while compensatory mutations that recreated the native SL4 structure restored RNA packaging and propagation to wild type levels. Altogether, our results demonstrate that SL4 constitutes the principal packaging determinant of MMTV gRNA. Our findings further suggest that SL4 acts as a structural switch that can not only differentiate between RNA for translation <i>versus</i> packaging/dimerization, but its location also allows differentiation between spliced and unspliced RNAs during gRNA encapsidation.
DOI: 10.6084/m9.figshare.6652283.v1
title: Discovery of microRNA-like RNAs during early fruiting body development in the model mushroom Coprinopsis cinerea

description: #miRCc Version 1.0 (June 2018)#This program develops algorithms for predicting microRNA-like RNAs in the model mushroom <i>Coprinopsis cinerea</i><br>Please read carefully the README.txt file before running the programs.<br>The algorithms are implemented in Perl. Please make sure that Perl (https://www.perl.org/) is properly installed on your computer.<br>All source codes are included in this fileset. You can modify some of the codes to suit the purpose of your study.<br>
DOI: 10.6084/m9.figshare.6652268
title: PCOSIHAppendixtables190618.docx

description: appendix for the manucript: <b>Testosterone levels in 3<sup>rd</sup> trimester in polycystic ovary syndrome. </b> <b>Odense Child Cohort. </b>
DOI: 10.6084/m9.figshare.6652268.v1
title: PCOSIHAppendixtables190618.docx

description: appendix for the manucript: <b>Testosterone levels in 3<sup>rd</sup> trimester in polycystic ovary syndrome. </b> <b>Odense Child Cohort. </b>
DOI: 10.6084/m9.figshare.6652091
title: Optimisation of sample pre-treatment method for the determination of triclosan in marine sediments by high-performance liquid chromatography and marine benthic quality assessment in the southern Baltic Sea

description: This study comprises optimisation of sample preparation and HPLC analytical procedure for the determination of a personal care product ingredient, triclosan (TCS), in marine sediments. The testing of several varying pre-treatment parameters confirmed that ultrasonic extraction is an effective method for the isolation of TCS from marine sediments, and that the choice of extraction solvent appeared to be of major importance. The selection of the mobile-phase composition and the absorption wavelength was made for the high-performance liquid chromatography analysis step. Based on the validated method, a preliminary assessment of the benthic ecosystem quality with regards to TCS contamination has been demonstrated in the southern Baltic Sea – a semi-enclosed sea, characterised by poor water exchange, thus particularly susceptible to anthropopression. TCS has been identified and quantified <i>in situ</i> in marine bottom sediments, sediment dwelling isopod – <i>Saduria entomon</i> L. and estimated <i>in silico</i> in pore waters based on the equilibrium partition theory in order to assess the potential exposure and uptake from the aqueous phase. TCS concentrations identified in the bottom sediments of the Gdansk Basin, as the natural habitat for studied <i>S.entomon</i> L., appear to be threatening to the benthic environment. Particularly when considering <i>S. entomon</i> L. as a major nutrition source for cod (<i>Gadus morhua</i>) undergoing the feminisation process, since the recent studies prove TCS to have a potential to induce critical alterations in the endocrine system of marine ichthyofauna.
DOI: 10.6084/m9.figshare.6652091.v1
title: Optimisation of sample pre-treatment method for the determination of triclosan in marine sediments by high-performance liquid chromatography and marine benthic quality assessment in the southern Baltic Sea

description: This study comprises optimisation of sample preparation and HPLC analytical procedure for the determination of a personal care product ingredient, triclosan (TCS), in marine sediments. The testing of several varying pre-treatment parameters confirmed that ultrasonic extraction is an effective method for the isolation of TCS from marine sediments, and that the choice of extraction solvent appeared to be of major importance. The selection of the mobile-phase composition and the absorption wavelength was made for the high-performance liquid chromatography analysis step. Based on the validated method, a preliminary assessment of the benthic ecosystem quality with regards to TCS contamination has been demonstrated in the southern Baltic Sea – a semi-enclosed sea, characterised by poor water exchange, thus particularly susceptible to anthropopression. TCS has been identified and quantified <i>in situ</i> in marine bottom sediments, sediment dwelling isopod – <i>Saduria entomon</i> L. and estimated <i>in silico</i> in pore waters based on the equilibrium partition theory in order to assess the potential exposure and uptake from the aqueous phase. TCS concentrations identified in the bottom sediments of the Gdansk Basin, as the natural habitat for studied <i>S.entomon</i> L., appear to be threatening to the benthic environment. Particularly when considering <i>S. entomon</i> L. as a major nutrition source for cod (<i>Gadus morhua</i>) undergoing the feminisation process, since the recent studies prove TCS to have a potential to induce critical alterations in the endocrine system of marine ichthyofauna.
DOI: 10.6084/m9.figshare.6651860
title: Additional file 2: of Involving general practice trainees in clinical practice guideline adaptation

description: Appendix 2 Evaluation tool. The evaluation tool, based on the AGREE instrument, and tailored to assist in the evaluation of the CPG adaptation process. (XLSX 54 kb)
DOI: 10.6084/m9.figshare.6651860.v1
title: Additional file 2: of Involving general practice trainees in clinical practice guideline adaptation

description: Appendix 2 Evaluation tool. The evaluation tool, based on the AGREE instrument, and tailored to assist in the evaluation of the CPG adaptation process. (XLSX 54 kb)
DOI: 10.6084/m9.figshare.6651854
title: Additional file 1: of Involving general practice trainees in clinical practice guideline adaptation

description: Appendix 1 Example of matrix. An example of the documentation tool provided for GP-trainees to document all their steps of the CPG adaptation process. (XLSX 155 kb)
DOI: 10.6084/m9.figshare.6651854.v1
title: Additional file 1: of Involving general practice trainees in clinical practice guideline adaptation

description: Appendix 1 Example of matrix. An example of the documentation tool provided for GP-trainees to document all their steps of the CPG adaptation process. (XLSX 155 kb)
DOI: 10.6084/m9.figshare.6651845
title: Additional file 1 of A selective method for optimizing ensemble docking-based experiments on an InhA Fully-Flexible receptor model

description: Table S1 - Best FEB values obtained from e-FReDock and cross-docking experiments. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.6651845.v1
title: Additional file 1 of A selective method for optimizing ensemble docking-based experiments on an InhA Fully-Flexible receptor model

description: Table S1 - Best FEB values obtained from e-FReDock and cross-docking experiments. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.6651782
title: MOESM4 of Comparison of global geomagnetic field models and evaluation using marine datasets in the north-eastern Atlantic Ocean and western Mediterranean Sea

description: Additional file 4. Comparative statistical analysis of differences in intensity values of the anomaly field (ANO) estimated up to SH degree 720 from HDGM2016 and EMM2015 and derived from EMAG2v3 and WDMAM (A) at a global scale reduced by 30° in latitude and 20° in longitude (grid spacing: 1°) and (B) for the NEAWM area (grid spacing: 0.5°).
DOI: 10.6084/m9.figshare.6651782.v1
title: MOESM4 of Comparison of global geomagnetic field models and evaluation using marine datasets in the north-eastern Atlantic Ocean and western Mediterranean Sea

description: Additional file 4. Comparative statistical analysis of differences in intensity values of the anomaly field (ANO) estimated up to SH degree 720 from HDGM2016 and EMM2015 and derived from EMAG2v3 and WDMAM (A) at a global scale reduced by 30° in latitude and 20° in longitude (grid spacing: 1°) and (B) for the NEAWM area (grid spacing: 0.5°).
DOI: 10.6084/m9.figshare.6651752
title: Additional file 1: of Red blood cell acetylcholinesterase activity among healthy dwellers of an agrarian region in Sri Lanka: a descriptive cross-sectional study

description: RBC AChE activity among healthy non-farmers of Anuradhapura, 2017. It contains the data of the entire study. (XLS 49 kb)
DOI: 10.6084/m9.figshare.6651752.v1
title: Additional file 1: of Red blood cell acetylcholinesterase activity among healthy dwellers of an agrarian region in Sri Lanka: a descriptive cross-sectional study

description: RBC AChE activity among healthy non-farmers of Anuradhapura, 2017. It contains the data of the entire study. (XLS 49 kb)
DOI: 10.6084/m9.figshare.6651749
title: MOESM2 of Comparison of global geomagnetic field models and evaluation using marine datasets in the north-eastern Atlantic Ocean and western Mediterranean Sea

description: Additional file 2. Comparative statistical analysis of differences in inclination and declination values estimated (A) at a global scale reduced by 30° in latitude and 20° in longitude (grid spacing: 1°) and (B) for the NEAWM area (grid spacing: 0.5°).
DOI: 10.6084/m9.figshare.6651749.v1
title: MOESM2 of Comparison of global geomagnetic field models and evaluation using marine datasets in the north-eastern Atlantic Ocean and western Mediterranean Sea

description: Additional file 2. Comparative statistical analysis of differences in inclination and declination values estimated (A) at a global scale reduced by 30° in latitude and 20° in longitude (grid spacing: 1°) and (B) for the NEAWM area (grid spacing: 0.5°).
DOI: 10.6084/m9.figshare.6651728
title: MOESM1 of Comparison of global geomagnetic field models and evaluation using marine datasets in the north-eastern Atlantic Ocean and western Mediterranean Sea

description: Additional file 1. Comparative statistical analysis of differences in intensity values of the internal field (INT) estimated up to SH degrees 12 and 13 from global models (A) at a global scale reduced by 30° in latitude and 20° in longitude (grid spacing: 1°) and (B) for the NEAWM area (grid spacing: 0.5°).
DOI: 10.6084/m9.figshare.6651728.v1
title: MOESM1 of Comparison of global geomagnetic field models and evaluation using marine datasets in the north-eastern Atlantic Ocean and western Mediterranean Sea

description: Additional file 1. Comparative statistical analysis of differences in intensity values of the internal field (INT) estimated up to SH degrees 12 and 13 from global models (A) at a global scale reduced by 30° in latitude and 20° in longitude (grid spacing: 1°) and (B) for the NEAWM area (grid spacing: 0.5°).
DOI: 10.6084/m9.figshare.6651725
title: Additional file 9: of Transcriptional profiling and biomarker identification reveal tissue specific effects of expanded ataxin-3 in a spinocerebellar ataxia type 3 mouse model

description: Blood metabolites. (XLSX 38 kb)
DOI: 10.6084/m9.figshare.6651725.v1
title: Additional file 9: of Transcriptional profiling and biomarker identification reveal tissue specific effects of expanded ataxin-3 in a spinocerebellar ataxia type 3 mouse model

description: Blood metabolites. (XLSX 38 kb)
DOI: 10.6084/m9.figshare.6651722
title: Additional file 5: of Gene length corrected trimmed mean of M-values (GeTMM) processing of RNA-seq data performs similarly in intersample analyses while improving intrasample comparisons

description: Correlation coefficients for each method compared to RT-qPCR. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.6651722.v1
title: Additional file 5: of Gene length corrected trimmed mean of M-values (GeTMM) processing of RNA-seq data performs similarly in intersample analyses while improving intrasample comparisons

description: Correlation coefficients for each method compared to RT-qPCR. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.6651686
title: Additional file 3: of Gene length corrected trimmed mean of M-values (GeTMM) processing of RNA-seq data performs similarly in intersample analyses while improving intrasample comparisons

description: Details on the RT-qPCR assays. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.6651686.v1
title: Additional file 3: of Gene length corrected trimmed mean of M-values (GeTMM) processing of RNA-seq data performs similarly in intersample analyses while improving intrasample comparisons

description: Details on the RT-qPCR assays. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.6651659
title: Additional file 5: of Transcriptional profiling and biomarker identification reveal tissue specific effects of expanded ataxin-3 in a spinocerebellar ataxia type 3 mouse model

description: Canonical pathways ingenuity. (XLSX 257 kb)
DOI: 10.6084/m9.figshare.6651659.v1
title: Additional file 5: of Transcriptional profiling and biomarker identification reveal tissue specific effects of expanded ataxin-3 in a spinocerebellar ataxia type 3 mouse model

description: Canonical pathways ingenuity. (XLSX 257 kb)
DOI: 10.6084/m9.figshare.6651629
title: Additional file 10: of Gene length corrected trimmed mean of M-values (GeTMM) processing of RNA-seq data performs similarly in intersample analyses while improving intrasample comparisons

description: Signal-to-Noise Ratios. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.6651629.v1
title: Additional file 10: of Gene length corrected trimmed mean of M-values (GeTMM) processing of RNA-seq data performs similarly in intersample analyses while improving intrasample comparisons

description: Signal-to-Noise Ratios. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.6651581
title: Additional file 11: of Transcriptional profiling and biomarker identification reveal tissue specific effects of expanded ataxin-3 in a spinocerebellar ataxia type 3 mouse model

description: Blood lipids. (XLSX 82 kb)
DOI: 10.6084/m9.figshare.6651581.v1
title: Additional file 11: of Transcriptional profiling and biomarker identification reveal tissue specific effects of expanded ataxin-3 in a spinocerebellar ataxia type 3 mouse model

description: Blood lipids. (XLSX 82 kb)
DOI: 10.6084/m9.figshare.6651539
title: Additional file 5: of Computational analysis of mRNA expression profiling in the inner ear reveals candidate transcription factors associated with proliferation, differentiation, and deafness

description: Transcription factors affecting transcription. Motifs enriched in genes differentially expressed between ages, tissues, and the interaction of age and tissue, and the expression of the TFs associated with the enriched motifs. (XLSX 324 kb)
DOI: 10.6084/m9.figshare.6651539.v1
title: Additional file 5: of Computational analysis of mRNA expression profiling in the inner ear reveals candidate transcription factors associated with proliferation, differentiation, and deafness

description: Transcription factors affecting transcription. Motifs enriched in genes differentially expressed between ages, tissues, and the interaction of age and tissue, and the expression of the TFs associated with the enriched motifs. (XLSX 324 kb)
DOI: 10.6084/m9.figshare.6651521
title: Additional file 4: of Computational analysis of mRNA expression profiling in the inner ear reveals candidate transcription factors associated with proliferation, differentiation, and deafness

description: Deafness genes prediction. Probabilities assigned to genes by the deafness genes prediction algorithm. (XLSX 4789 kb)
DOI: 10.6084/m9.figshare.6651521.v1
title: Additional file 4: of Computational analysis of mRNA expression profiling in the inner ear reveals candidate transcription factors associated with proliferation, differentiation, and deafness

description: Deafness genes prediction. Probabilities assigned to genes by the deafness genes prediction algorithm. (XLSX 4789 kb)
DOI: 10.6084/m9.figshare.6651503
title: Additional file 3: of Computational analysis of mRNA expression profiling in the inner ear reveals candidate transcription factors associated with proliferation, differentiation, and deafness

description: Deafness genes. Genes associated with deafness compiled from www.hereditaryhearingloss.org (updated 3/13/17), and the differential expression results for the mouse orthologs of the deafness genes. (XLSX 37 kb)
DOI: 10.6084/m9.figshare.6651503.v1
title: Additional file 3: of Computational analysis of mRNA expression profiling in the inner ear reveals candidate transcription factors associated with proliferation, differentiation, and deafness

description: Deafness genes. Genes associated with deafness compiled from www.hereditaryhearingloss.org (updated 3/13/17), and the differential expression results for the mouse orthologs of the deafness genes. (XLSX 37 kb)
DOI: 10.6084/m9.figshare.6651476
title: Additional file 2: of Computational analysis of mRNA expression profiling in the inner ear reveals candidate transcription factors associated with proliferation, differentiation, and deafness

description: Enrichment Analysis. Enrichments in genes differentially expressed between ages, tissues, and the interaction of age and tissue. (XLSX 234 kb)
DOI: 10.6084/m9.figshare.6651476.v1
title: Additional file 2: of Computational analysis of mRNA expression profiling in the inner ear reveals candidate transcription factors associated with proliferation, differentiation, and deafness

description: Enrichment Analysis. Enrichments in genes differentially expressed between ages, tissues, and the interaction of age and tissue. (XLSX 234 kb)
DOI: 10.6084/m9.figshare.6651467
title: Additional file 9: of TM8 represses developmental timing in Nicotiana benthamiana and has functionally diversified in angiosperms

description: Primer list. (XLSX 43 kb)
DOI: 10.6084/m9.figshare.6651467.v1
title: Additional file 9: of TM8 represses developmental timing in Nicotiana benthamiana and has functionally diversified in angiosperms

description: Primer list. (XLSX 43 kb)
DOI: 10.6084/m9.figshare.6651377
title: Additional file 6: of Pan-cancer adaptive immune resistance as defined by the Tumor Inflammation Signature (TIS): results from The Cancer Genome Atlas (TCGA)

description: Table S1. For each cancer type, GO terms with negative associations with TIS, defined as a GSA score below â â 1. (CSV 48Â kb)
DOI: 10.6084/m9.figshare.6651377.v1
title: Additional file 6: of Pan-cancer adaptive immune resistance as defined by the Tumor Inflammation Signature (TIS): results from The Cancer Genome Atlas (TCGA)

description: Table S1. For each cancer type, GO terms with negative associations with TIS, defined as a GSA score below â â 1. (CSV 48Â kb)
DOI: 10.6084/m9.figshare.6651338
title: Additional file 2: of TM8 represses developmental timing in Nicotiana benthamiana and has functionally diversified in angiosperms

description: TM8 alignment and complete phylogeny with accession numbers. (NEWICK 19 kb)
DOI: 10.6084/m9.figshare.6651338.v1
title: Additional file 2: of TM8 represses developmental timing in Nicotiana benthamiana and has functionally diversified in angiosperms

description: TM8 alignment and complete phylogeny with accession numbers. (NEWICK 19 kb)
DOI: 10.6084/m9.figshare.6651332
title: Additional file 8: of Quantitative evolutionary proteomics of seminal fluid from primates with different mating systems

description: Table S33-S34. The overall output from tests of positive selection using the paml program. ST33 Test of positive selection in 1161 SFPs. ST34 Branch-site test of positive selection in 1161 SFPs. (XLS 253 kb)
DOI: 10.6084/m9.figshare.6651332.v1
title: Additional file 8: of Quantitative evolutionary proteomics of seminal fluid from primates with different mating systems

description: Table S33-S34. The overall output from tests of positive selection using the paml program. ST33 Test of positive selection in 1161 SFPs. ST34 Branch-site test of positive selection in 1161 SFPs. (XLS 253 kb)
DOI: 10.6084/m9.figshare.6651323
title: Additional file 1: of TM8 represses developmental timing in Nicotiana benthamiana and has functionally diversified in angiosperms

description: List of blasted genomes. (XLSX 42 kb)
DOI: 10.6084/m9.figshare.6651323.v1
title: Additional file 1: of TM8 represses developmental timing in Nicotiana benthamiana and has functionally diversified in angiosperms

description: List of blasted genomes. (XLSX 42 kb)
DOI: 10.6084/m9.figshare.6651308
title: Additional file 7: of Quantitative evolutionary proteomics of seminal fluid from primates with different mating systems

description: Tables S21-S32. The seminal fluid peptides identified from each chimpanzee, baboon, drill, cynomolgus macaque, marmoset, and vervet individuals that underwent MS/MS using the MSDaPl program. ST21 A parsimonious list of SFPs inferred from MSDaPl for chimpanzee 1A. ST22 A parsimonious list of SFPs inferred from MSDaPl for chimpanzee 1B. ST23 A parsimonious list of SFPs inferred from MSDaPl for baboon 1. ST24 A parsimonious list of SFPs inferred from MSDaPl for baboon 2. ST25 A parsimonious list of SFPs inferred from MSDaPl for drill 1. ST26 A parsimonious list of SFPs inferred from MSDaPl for drill 2. ST27 A parsimonious list of SFPs inferred from MSDaPl for cynomolgus macaque 1. ST28 A parsimonious list of SFPs inferred from MSDaPl for cynomolgus macaque 2. ST29 A parsimonious list of SFPs inferred from MSDaPl for marmoset 1. ST30 A parsimonious list of SFPs inferred from MSDaPl for marmoset 2. ST31 A parsimonious list of SFPs inferred from MSDaPl for vervet 1. ST32 A parsimonious list of SFPs inferred from MSDaPl for vervet 2. (XLS 551 kb)
DOI: 10.6084/m9.figshare.6651308.v1
title: Additional file 7: of Quantitative evolutionary proteomics of seminal fluid from primates with different mating systems

description: Tables S21-S32. The seminal fluid peptides identified from each chimpanzee, baboon, drill, cynomolgus macaque, marmoset, and vervet individuals that underwent MS/MS using the MSDaPl program. ST21 A parsimonious list of SFPs inferred from MSDaPl for chimpanzee 1A. ST22 A parsimonious list of SFPs inferred from MSDaPl for chimpanzee 1B. ST23 A parsimonious list of SFPs inferred from MSDaPl for baboon 1. ST24 A parsimonious list of SFPs inferred from MSDaPl for baboon 2. ST25 A parsimonious list of SFPs inferred from MSDaPl for drill 1. ST26 A parsimonious list of SFPs inferred from MSDaPl for drill 2. ST27 A parsimonious list of SFPs inferred from MSDaPl for cynomolgus macaque 1. ST28 A parsimonious list of SFPs inferred from MSDaPl for cynomolgus macaque 2. ST29 A parsimonious list of SFPs inferred from MSDaPl for marmoset 1. ST30 A parsimonious list of SFPs inferred from MSDaPl for marmoset 2. ST31 A parsimonious list of SFPs inferred from MSDaPl for vervet 1. ST32 A parsimonious list of SFPs inferred from MSDaPl for vervet 2. (XLS 551 kb)