cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8150927.v1
title: Additional file 31: of Systematic analysis of dark and camouflaged genes reveals disease-relevant genes hiding in plain sight

description: PacBio percent camouflaged genes in hg38. (TXT 31 kb)
DOI: 10.6084/m9.figshare.8150924
title: Additional file 30: of Systematic analysis of dark and camouflaged genes reveals disease-relevant genes hiding in plain sight

description: ONT dark-by-MAPQ gene annotations in hg38. (TXT 210 kb)
DOI: 10.6084/m9.figshare.8150924.v1
title: Additional file 30: of Systematic analysis of dark and camouflaged genes reveals disease-relevant genes hiding in plain sight

description: ONT dark-by-MAPQ gene annotations in hg38. (TXT 210 kb)
DOI: 10.6084/m9.figshare.8150921
title: Additional file 2: of Systematic analysis of dark and camouflaged genes reveals disease-relevant genes hiding in plain sight

description: IlluminaRL100 percent dark genes in hg38. (TXT 401 kb)
DOI: 10.6084/m9.figshare.8150921.v1
title: Additional file 2: of Systematic analysis of dark and camouflaged genes reveals disease-relevant genes hiding in plain sight

description: IlluminaRL100 percent dark genes in hg38. (TXT 401 kb)
DOI: 10.6084/m9.figshare.8150918
title: Additional file 29: of Systematic analysis of dark and camouflaged genes reveals disease-relevant genes hiding in plain sight

description: ONT percent dark-by-MAPQ genes in hg38. (TXT 17 kb)
DOI: 10.6084/m9.figshare.8150918.v1
title: Additional file 29: of Systematic analysis of dark and camouflaged genes reveals disease-relevant genes hiding in plain sight

description: ONT percent dark-by-MAPQ genes in hg38. (TXT 17 kb)
DOI: 10.6084/m9.figshare.8150915
title: Additional file 28: of Systematic analysis of dark and camouflaged genes reveals disease-relevant genes hiding in plain sight

description: ONT dark-by-depth gene annotations in hg38. (TXT 556 kb)
DOI: 10.6084/m9.figshare.8150915.v1
title: Additional file 28: of Systematic analysis of dark and camouflaged genes reveals disease-relevant genes hiding in plain sight

description: ONT dark-by-depth gene annotations in hg38. (TXT 556 kb)
DOI: 10.6084/m9.figshare.8150912
title: Additional file 27: of Systematic analysis of dark and camouflaged genes reveals disease-relevant genes hiding in plain sight

description: ONT percent dark-by-depth genes in hg38. (TXT 278 kb)
DOI: 10.6084/m9.figshare.8150912.v1
title: Additional file 27: of Systematic analysis of dark and camouflaged genes reveals disease-relevant genes hiding in plain sight

description: ONT percent dark-by-depth genes in hg38. (TXT 278 kb)
DOI: 10.6084/m9.figshare.8150909
title: Additional file 26: of Systematic analysis of dark and camouflaged genes reveals disease-relevant genes hiding in plain sight

description: ONT camouflaged gene annotations in hg38. (TXT 122 kb)
DOI: 10.6084/m9.figshare.8150909.v1
title: Additional file 26: of Systematic analysis of dark and camouflaged genes reveals disease-relevant genes hiding in plain sight

description: ONT camouflaged gene annotations in hg38. (TXT 122 kb)
DOI: 10.6084/m9.figshare.8150906
title: Additional file 25: of Systematic analysis of dark and camouflaged genes reveals disease-relevant genes hiding in plain sight

description: ONT percent camouflaged genes in hg38. (TXT 13 kb)
DOI: 10.6084/m9.figshare.8150906.v1
title: Additional file 25: of Systematic analysis of dark and camouflaged genes reveals disease-relevant genes hiding in plain sight

description: ONT percent camouflaged genes in hg38. (TXT 13 kb)
DOI: 10.6084/m9.figshare.8150903
title: Additional file 24: of Systematic analysis of dark and camouflaged genes reveals disease-relevant genes hiding in plain sight

description: IlluminaRL250 dark-by-MAPQ gene annotations in hg38. (TXT 1574 kb)
DOI: 10.6084/m9.figshare.8150903.v1
title: Additional file 24: of Systematic analysis of dark and camouflaged genes reveals disease-relevant genes hiding in plain sight

description: IlluminaRL250 dark-by-MAPQ gene annotations in hg38. (TXT 1574 kb)
DOI: 10.6084/m9.figshare.8150900
title: Additional file 23: of Systematic analysis of dark and camouflaged genes reveals disease-relevant genes hiding in plain sight

description: IlluminaRL250 percent dark-by-MAPQ genes in hg38. (TXT 188 kb)
DOI: 10.6084/m9.figshare.8150900.v1
title: Additional file 23: of Systematic analysis of dark and camouflaged genes reveals disease-relevant genes hiding in plain sight

description: IlluminaRL250 percent dark-by-MAPQ genes in hg38. (TXT 188 kb)
DOI: 10.6084/m9.figshare.8150897
title: Additional file 22: of Systematic analysis of dark and camouflaged genes reveals disease-relevant genes hiding in plain sight

description: IlluminaRL250 dark-by-depth gene annotations in hg38. (TXT 354 kb)
DOI: 10.6084/m9.figshare.8150897.v1
title: Additional file 22: of Systematic analysis of dark and camouflaged genes reveals disease-relevant genes hiding in plain sight

description: IlluminaRL250 dark-by-depth gene annotations in hg38. (TXT 354 kb)
DOI: 10.6084/m9.figshare.8150894
title: Additional file 21: of Systematic analysis of dark and camouflaged genes reveals disease-relevant genes hiding in plain sight

description: IlluminaRL250 percent dark-by-depth genes in hg38. (TXT 147 kb)
DOI: 10.6084/m9.figshare.8150894.v1
title: Additional file 21: of Systematic analysis of dark and camouflaged genes reveals disease-relevant genes hiding in plain sight

description: IlluminaRL250 percent dark-by-depth genes in hg38. (TXT 147 kb)
DOI: 10.6084/m9.figshare.8150891
title: Additional file 20: of Systematic analysis of dark and camouflaged genes reveals disease-relevant genes hiding in plain sight

description: IlluminaRL250 camouflaged gene annotations in hg38. (TXT 1279 kb)
DOI: 10.6084/m9.figshare.8150891.v1
title: Additional file 20: of Systematic analysis of dark and camouflaged genes reveals disease-relevant genes hiding in plain sight

description: IlluminaRL250 camouflaged gene annotations in hg38. (TXT 1279 kb)
DOI: 10.6084/m9.figshare.8150885
title: Additional file 19: of Systematic analysis of dark and camouflaged genes reveals disease-relevant genes hiding in plain sight

description: IlluminaRL250 percent camouflaged genes in hg38. (TXT 142 kb)
DOI: 10.6084/m9.figshare.8150885.v1
title: Additional file 19: of Systematic analysis of dark and camouflaged genes reveals disease-relevant genes hiding in plain sight

description: IlluminaRL250 percent camouflaged genes in hg38. (TXT 142 kb)
DOI: 10.6084/m9.figshare.8150882
title: Additional file 18: of Systematic analysis of dark and camouflaged genes reveals disease-relevant genes hiding in plain sight

description: IlluminaRL100 dark-by-MAPQ gene annotations in hg38. (TXT 2710 kb)
DOI: 10.6084/m9.figshare.8150882.v1
title: Additional file 18: of Systematic analysis of dark and camouflaged genes reveals disease-relevant genes hiding in plain sight

description: IlluminaRL100 dark-by-MAPQ gene annotations in hg38. (TXT 2710 kb)
DOI: 10.6084/m9.figshare.8150879
title: Additional file 17: of Systematic analysis of dark and camouflaged genes reveals disease-relevant genes hiding in plain sight

description: IlluminaRL100 percent dark-by-MAPQ genes in hg38. (TXT 253 kb)
DOI: 10.6084/m9.figshare.8150879.v1
title: Additional file 17: of Systematic analysis of dark and camouflaged genes reveals disease-relevant genes hiding in plain sight

description: IlluminaRL100 percent dark-by-MAPQ genes in hg38. (TXT 253 kb)
DOI: 10.6084/m9.figshare.8150876
title: Additional file 16: of Systematic analysis of dark and camouflaged genes reveals disease-relevant genes hiding in plain sight

description: IlluminaRL100 dark-by-depth gene annotations in hg38. (TXT 647 kb)
DOI: 10.6084/m9.figshare.8150876.v1
title: Additional file 16: of Systematic analysis of dark and camouflaged genes reveals disease-relevant genes hiding in plain sight

description: IlluminaRL100 dark-by-depth gene annotations in hg38. (TXT 647 kb)
DOI: 10.6084/m9.figshare.8150873
title: Additional file 15: of Systematic analysis of dark and camouflaged genes reveals disease-relevant genes hiding in plain sight

description: IlluminaRL100 percent dark-by-depth genes in hg38. (TXT 241 kb)
DOI: 10.6084/m9.figshare.8150873.v1
title: Additional file 15: of Systematic analysis of dark and camouflaged genes reveals disease-relevant genes hiding in plain sight

description: IlluminaRL100 percent dark-by-depth genes in hg38. (TXT 241 kb)
DOI: 10.6084/m9.figshare.8150870
title: Additional file 14: of Systematic analysis of dark and camouflaged genes reveals disease-relevant genes hiding in plain sight

description: IlluminaRL100 camouflaged gene annotations in hg38. (TXT 2141 kb)
DOI: 10.6084/m9.figshare.8150870.v1
title: Additional file 14: of Systematic analysis of dark and camouflaged genes reveals disease-relevant genes hiding in plain sight

description: IlluminaRL100 camouflaged gene annotations in hg38. (TXT 2141 kb)
DOI: 10.6084/m9.figshare.8150867
title: Additional file 13: of Systematic analysis of dark and camouflaged genes reveals disease-relevant genes hiding in plain sight

description: IlluminaRL100 percent camouflaged genes in hg38. (TXT 183 kb)
DOI: 10.6084/m9.figshare.8150867.v1
title: Additional file 13: of Systematic analysis of dark and camouflaged genes reveals disease-relevant genes hiding in plain sight

description: IlluminaRL100 percent camouflaged genes in hg38. (TXT 183 kb)
DOI: 10.6084/m9.figshare.8150864
title: Additional file 12: of Systematic analysis of dark and camouflaged genes reveals disease-relevant genes hiding in plain sight

description: Gene Ontology results for dark genes in IlluminaRL100 for hg38. (CSV 47 kb)
DOI: 10.6084/m9.figshare.8150864.v1
title: Additional file 12: of Systematic analysis of dark and camouflaged genes reveals disease-relevant genes hiding in plain sight

description: Gene Ontology results for dark genes in IlluminaRL100 for hg38. (CSV 47 kb)
DOI: 10.6084/m9.figshare.8150861
title: Additional file 11: of Systematic analysis of dark and camouflaged genes reveals disease-relevant genes hiding in plain sight

description: 10x Genomics dark gene annotations in hg38. (TXT 1247 kb)
DOI: 10.6084/m9.figshare.8150861.v1
title: Additional file 11: of Systematic analysis of dark and camouflaged genes reveals disease-relevant genes hiding in plain sight

description: 10x Genomics dark gene annotations in hg38. (TXT 1247 kb)
DOI: 10.6084/m9.figshare.8150858
title: Additional file 10: of Systematic analysis of dark and camouflaged genes reveals disease-relevant genes hiding in plain sight

description: 10x Genomics percent dark genes in hg38. (TXT 262 kb)
DOI: 10.6084/m9.figshare.8150858.v1
title: Additional file 10: of Systematic analysis of dark and camouflaged genes reveals disease-relevant genes hiding in plain sight

description: 10x Genomics percent dark genes in hg38. (TXT 262 kb)
DOI: 10.6084/m9.figshare.12865880.v1
title: Phasianus colchicus gene list

description: A tab delimited file of the common pheasant gene that generated by using EVM.
DOI: 10.6084/m9.figshare.8150792
title: Transcriptome sequence of Bolboschoenus planiculmis rawdata

description: we contribute a prelininary transcriptome study of <i>Bolboschoenusplaniculmis</i> using Illumina Solexa HiSeq 2000from a compounded sample of stem, leave, rhizome and tuber. In total, 59788 Unigene with an average length of 842bp and N50 of 1402 bp were obtained by de novo assembly.<br>
DOI: 10.6084/m9.figshare.8150792.v1
title: Transcriptome sequence of Bolboschoenus planiculmis rawdata

description: we contribute a prelininary transcriptome study of <i>Bolboschoenusplaniculmis</i> using Illumina Solexa HiSeq 2000from a compounded sample of stem, leave, rhizome and tuber. In total, 59788 Unigene with an average length of 842bp and N50 of 1402 bp were obtained by de novo assembly.<br>
DOI: 10.6084/m9.figshare.8150711
title: 2019 Untreated JDM RNA-Seq: otoferlin RT-qPCR

description: This is a dataset related to an RNA-Seq experiment examining 1) the transcriptome alterations in untreated and inactive juvenile dermatomyositis, and 2) a separate cohort of inactive JDM patients that later developed psoriasis.<br>This file contains the raw quantification cycle (Cq) data for otoferlin confirmatory RT-qPCRs.<br>
DOI: 10.6084/m9.figshare.8150711.v1
title: 2019 Untreated JDM RNA-Seq: otoferlin RT-qPCR

description: This is a dataset related to an RNA-Seq experiment examining 1) the transcriptome alterations in untreated and inactive juvenile dermatomyositis, and 2) a separate cohort of inactive JDM patients that later developed psoriasis.<br>This file contains the raw quantification cycle (Cq) data for otoferlin confirmatory RT-qPCRs.<br>
DOI: 10.6084/m9.figshare.8150708
title: 2019 Untreated JDM RNA-Seq: gene counts

description: This is a dataset related to an RNA-Seq experiment examining 1) the transcriptome alterations in untreated and inactive juvenile dermatomyositis, and 2) a separate cohort of inactive JDM patients that later developed psoriasis.<br>This file contains the gene counts from the RNA-Seq analysis using GRCh38 human genome, STAR aligner, and featureCounts counting.<br>
DOI: 10.6084/m9.figshare.8150690
title: Lacertidae phylogenomic alignments and morphological matrix

description: Lacertidae phylotranscriptomic alignments: misgen_10<br>Lacertidae morphological matrix for phylogenetic analysis: lacertidae_morph_matrix_20_02_reduced.nex<br>Complete concatenated matrix: lacertidae_v7 files, containing:- A zipped file with the entire, concatenated alignment in Fasta format- a text file with partition information. 12S, 16S, cytb, nd4, cmos are the genes traditionally used in lacertid phylogenetics; L1-L346 are the anchored derived from anchored phylogenomics; the remaining loci are derived from RNAseq and included also in the misgen_10 phylotranscriptomic alignment.<br><br>
DOI: 10.6084/m9.figshare.8150663
title: Data 2-25-19.sav

description: The attached data was collected to determine if there are QEEG differences in BAP+ and neurotypicals on QEEG indicators. IRB approved.
DOI: 10.6084/m9.figshare.8150663.v1
title: Data 2-25-19.sav

description: The attached data was collected to determine if there are QEEG differences in BAP+ and neurotypicals on QEEG indicators. IRB approved.
DOI: 10.6084/m9.figshare.8150645
title: Alterations in the relative abundance of <i>Faecalibacterium prausnitzii</i> correlate with changes in fecal calprotectin in patients with ileal Crohn’s disease: a longitudinal study

description: <b>Objectives:</b> Crohn’s disease is characterized by a gut dysbiosis with decreased abundance of butyrate producers such as <i>Faecalibacterium prausnitzii</i>. Although <i>F. prausnitzii</i> secretes anti-inflammatory molecules, few studies have addressed the importance of <i>F. prausnitzii</i> in a longitudinal setting. We aimed to examine the relationship between temporal profiles of <i>F. prausnitzii</i>, the <i>C. leptum</i> group, overall butyrate production, and inflammatory activity. <b>Material and methods:</b> Fecal samples (<i>n</i> = 59) were collected every third month from nine patients with ileal Crohn’s disease. The abundance of <i>F. prausnitzii</i> and <i>C. leptum</i> was quantified relative to the total amount of bacteria using quantitative-PCR. To assess butyrate production of gut microbiota, gene copy numbers of the butyryl-CoA:acetate-CoA transferase (BCoAT) gene were quantified by qPCR. The inflammatory activity was defined by fecal (f)-calprotectin. <b>Results:</b> No correlation between the relative abundance of <i>F. prausnitzii</i>, the <i>C. leptum</i> group, or copy numbers of the BCoAT gene, and f-calprotectin was observed in the total sample set. By analyzing alterations between consecutive samples, a negative correlation between changes in the relative abundance of <i>F. prausnitzii</i> and f-calprotectin was observed (<i>R</i> = −0.39; <i>p</i> = .009). Changes in <i>C. leptum</i> (<i>R</i> = −0.18, <i>p</i> = .23) and number of copies of the BCoAT gene (<i>R</i> = −0.12; <i>p</i> = .42) did not correlate with f-calprotectin. <b>Conclusions:</b> There was an inverse correlation between temporal changes in the relative abundance of <i>F. prausnitzii</i>, but not overall butyrate producing capacity, and changes in inflammatory activity in ileal Crohn’s disease. These findings indicate that <i>F. prausnitzii</i> may play a role in gut homeostasis, even though causality is still to be demonstrated.
DOI: 10.6084/m9.figshare.8150645.v1
title: Alterations in the relative abundance of <i>Faecalibacterium prausnitzii</i> correlate with changes in fecal calprotectin in patients with ileal Crohn’s disease: a longitudinal study

description: <b>Objectives:</b> Crohn’s disease is characterized by a gut dysbiosis with decreased abundance of butyrate producers such as <i>Faecalibacterium prausnitzii</i>. Although <i>F. prausnitzii</i> secretes anti-inflammatory molecules, few studies have addressed the importance of <i>F. prausnitzii</i> in a longitudinal setting. We aimed to examine the relationship between temporal profiles of <i>F. prausnitzii</i>, the <i>C. leptum</i> group, overall butyrate production, and inflammatory activity. <b>Material and methods:</b> Fecal samples (<i>n</i> = 59) were collected every third month from nine patients with ileal Crohn’s disease. The abundance of <i>F. prausnitzii</i> and <i>C. leptum</i> was quantified relative to the total amount of bacteria using quantitative-PCR. To assess butyrate production of gut microbiota, gene copy numbers of the butyryl-CoA:acetate-CoA transferase (BCoAT) gene were quantified by qPCR. The inflammatory activity was defined by fecal (f)-calprotectin. <b>Results:</b> No correlation between the relative abundance of <i>F. prausnitzii</i>, the <i>C. leptum</i> group, or copy numbers of the BCoAT gene, and f-calprotectin was observed in the total sample set. By analyzing alterations between consecutive samples, a negative correlation between changes in the relative abundance of <i>F. prausnitzii</i> and f-calprotectin was observed (<i>R</i> = −0.39; <i>p</i> = .009). Changes in <i>C. leptum</i> (<i>R</i> = −0.18, <i>p</i> = .23) and number of copies of the BCoAT gene (<i>R</i> = −0.12; <i>p</i> = .42) did not correlate with f-calprotectin. <b>Conclusions:</b> There was an inverse correlation between temporal changes in the relative abundance of <i>F. prausnitzii</i>, but not overall butyrate producing capacity, and changes in inflammatory activity in ileal Crohn’s disease. These findings indicate that <i>F. prausnitzii</i> may play a role in gut homeostasis, even though causality is still to be demonstrated.
DOI: 10.17632/24kkg2hctg.4
title: EDXRF Raw data of Sonora obsidian

description: 566 geochemical raw data, corresponding to 133 specimens of geological and archaeological obsidian artifacts mostly, including flaked and ground stone, were determined by an X-Ray Fluorescence XL3t series NITON Analyzer from Thermo Fisher Scientific with support of the software Thermo Scientific™ Niton Data Transfer (NDT™). The analysis had an experimental stage to generate a final analytical protocol, based in a repetition of at least 3 analyzes per obsidian sample, procuring 120 counts per second, under the SOIL or TestAllGeo condition programs of Niton. Table 1. Geochemical selected data of geological and archaeological obsidian specimens analyzed from Sonora, Mexico. See description and localization of the sites and regions in [1]. Concentrations are in mg/kg. Confidence limit (± CL1-α = 95) are displayed with a 95% probability (2-Tail Alpha X mean). The empty cells (NA) correspond to elements that were not analyzed or below to the detection limit of the instrument. The table only includes calculations of the confidence limit for samples with three or more repetitions. Figure 1. Analytical process concept map of the geological and archaeological specimens of obsidian from Sonora, Mexico. Figure 2. Graphical representation of the concentration and types of geological and archaeological specimens of obsidian from Sonora, Mexico, analyzed by the dispersive-energy XRF technique (Table 1).
DOI: 10.6084/m9.figshare.8150624
title: VTKEL dataset

description: VTKEL subset dataset for framework evaluations.
DOI: 10.17632/3tkzv5vg6n.1
title: Intravenous injection of Muse cells as a potential therapeutic approach for epidermolysis bullosa

description: Epidermolysis bullosa (EB) is a congenital and refractory blistering skin disease. Few definitive treatments have been established. In the manuscript, we show the potential of Multilineage-differentiating stress-enduring (Muse) cells for the novel treatment against EB using model mice. Muse cells, collectable as pluripotent marker SSEA-3(+), are able to develop into three germ layers and can differentiate into skin components including keratinocytes, fibroblasts and melanocytes. In this study, systemically administered human Muse cells preferentially engrafted into injured skin in type XVII collagen (Col17)-knockout EB model mice without an immunosuppressant. Of note, the spontaneous differentiation of engrafted Muse cells into keratinocytes, hair follicle cells, vascular endothelial cells and sebaceous gland cells, as well as the expression of human type VII collagen (COL7) and COL17, were observed. We also investigated CL2020, a newly-developed cell-based product for Muse cell preparation, for the treatment of EB. CL2020-treated adult Col17-knockout mice exhibited human COL7 and COL17 expression in re-epithelialized skin, and showed more moderate clinical manifestations than vehicle-treated mice showed.
DOI: 10.6084/m9.figshare.8150624.v2
title: VTKEL dataset

description: VTKEL subset dataset for framework evaluations.
DOI: 10.6084/m9.figshare.8150624.v1
title: Gold standard VTKEL dataset for 300 documents

description: VTKEL subset dataset for framework evaluations.
DOI: 10.17632/nzk5hx94py.1
title: devereux_saito_yu_jie

description: All data used in International Capital Flows, Portfolio Composition, and the Stability of External Imbalances ⋆ Michael B. Devereux Makoto Saito, Changhua Yu
DOI: 10.6084/m9.figshare.8150618
title: Table 1

description: At P30 urinary osmolality is lower in the cKO mice compared with the control, with no changes in urinary output. At P50 in the cKO the urinary concentrating defect becomes evident, with a strong polyuria, polydipsia and reduced urinary osmolality.
DOI: 10.6084/m9.figshare.8150618.v1
title: Table 1

description: At P30 urinary osmolality is lower in the cKO mice compared with the control, with no changes in urinary output. At P50 in the cKO the urinary concentrating defect becomes evident, with a strong polyuria, polydipsia and reduced urinary osmolality.
DOI: 10.6084/m9.figshare.8150600
title: Fig-S3. Dicer dependent cystogenesis is not associated with mTOR/S6 activation

description: Fig-S3 shows the immunoblotting of samples from renal cortex of P30 (panel a) and P50 (panel b) mice. The relative abundance of mTOR and its phosphorilated form S2448 together with S6 and its phosphorilated form S235-236, is report. Dicer cKO mice present lower abundance of mTOR at P30 compared to control mice. Data are expressed as mean ± sem; n power is 5 vs 5. * is for p value &lt; 0.05.
DOI: 10.6084/m9.figshare.8150600.v1
title: Fig-S3. Dicer dependent cystogenesis is not associated with mTOR/S6 activation

description: Fig-S3 shows the immunoblotting of samples from renal cortex of P30 (panel a) and P50 (panel b) mice. The relative abundance of mTOR and its phosphorilated form S2448 together with S6 and its phosphorilated form S235-236, is report. Dicer cKO mice present lower abundance of mTOR at P30 compared to control mice. Data are expressed as mean ± sem; n power is 5 vs 5. * is for p value &lt; 0.05.