cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5829978
title: Additional file 10: Table S8. of Differential gene expression in the evolution of sex pheromone communication in New Zealand’s endemic leafroller moths of the genera Ctenopseustis and Planotortrix

description: Gene set enrichment analyses from the comparison of female antennae and pheromone glands gene expression. GSA was obtained with Piano using the statistical method “mean”. GO terms were used to define gene sets. (XLSX 3169 kb)
DOI: 10.6084/m9.figshare.5829978.v1
title: Additional file 10: Table S8. of Differential gene expression in the evolution of sex pheromone communication in New Zealand’s endemic leafroller moths of the genera Ctenopseustis and Planotortrix

description: Gene set enrichment analyses from the comparison of female antennae and pheromone glands gene expression. GSA was obtained with Piano using the statistical method “mean”. GO terms were used to define gene sets. (XLSX 3169 kb)
DOI: 10.6084/m9.figshare.12894668
title: R0191_20171006a_videos

description: Rat 0191, skilled reaching data collected in Leventhal laboratory by Alexandra Bova
DOI: 10.6084/m9.figshare.5829942
title: Additional file 2: of Phylogeographic diversity and mosaicism of the Helicobacter pylori tfs integrative and conjugative elements

description: Dataset 2. This file contains complete datasets for tfs, com and (partial) cag gene content extracted from 232 Helicobacter strains, additionally including gene/tfs ICE description, classification and nomenclature and relevant strain meta-data. (XLSX 249Â kb)
DOI: 10.6084/m9.figshare.5829942.v1
title: Additional file 2: of Phylogeographic diversity and mosaicism of the Helicobacter pylori tfs integrative and conjugative elements

description: Dataset 2. This file contains complete datasets for tfs, com and (partial) cag gene content extracted from 232 Helicobacter strains, additionally including gene/tfs ICE description, classification and nomenclature and relevant strain meta-data. (XLSX 249Â kb)
DOI: 10.6084/m9.figshare.5829939
title: Additional file 2: of Patterns of variation in cis-regulatory regions: examining evidence of purifying selection

description: Table S2. Transcription factors used in the study. (XLSX 17 kb)
DOI: 10.6084/m9.figshare.5829939.v1
title: Additional file 2: of Patterns of variation in cis-regulatory regions: examining evidence of purifying selection

description: Table S2. Transcription factors used in the study. (XLSX 17 kb)
DOI: 10.6084/m9.figshare.5829924
title: Additional file 1: of Phylogeographic diversity and mosaicism of the Helicobacter pylori tfs integrative and conjugative elements

description: Dataset 1. This file contains compiled BLASTp search results for each of 59 tfs-encoded proteins. (XLSX 3851Â kb)
DOI: 10.6084/m9.figshare.5829924.v1
title: Additional file 1: of Phylogeographic diversity and mosaicism of the Helicobacter pylori tfs integrative and conjugative elements

description: Dataset 1. This file contains compiled BLASTp search results for each of 59 tfs-encoded proteins. (XLSX 3851Â kb)
DOI: 10.6084/m9.figshare.5829882
title: Additional file 3: of SLALOM, a flexible method for the identification and statistical analysis of overlapping continuous sequence elements in sequence- and time-series data

description: Contains the R-script for addressing the three questions raised on comparison of ELM motifs in the chapter Comparison to other CSE analysis methods. (R 2 kb)
DOI: 10.6084/m9.figshare.5829882.v1
title: Additional file 3: of SLALOM, a flexible method for the identification and statistical analysis of overlapping continuous sequence elements in sequence- and time-series data

description: Contains the R-script for addressing the three questions raised on comparison of ELM motifs in the chapter Comparison to other CSE analysis methods. (R 2 kb)
DOI: 10.6084/m9.figshare.5829876
title: Additional File 1:

description: Summary of findings from included publications (nâ =â 308). This file presents the data extracted from each of the 308 publications identified in this review. (XLSX 163 kb)
DOI: 10.6084/m9.figshare.5829876.v1
title: Additional File 1:

description: Summary of findings from included publications (nâ =â 308). This file presents the data extracted from each of the 308 publications identified in this review. (XLSX 163 kb)
DOI: 10.6084/m9.figshare.5829861
title: Additional file 2: of SLALOM, a flexible method for the identification and statistical analysis of overlapping continuous sequence elements in sequence- and time-series data

description: Contains the python code of SLALOM, the test data required to reproduce the data presented in this manuscript, as well as the User Manual for SLALOM. (ZIP 3622 kb)
DOI: 10.6084/m9.figshare.5829861.v1
title: Additional file 2: of SLALOM, a flexible method for the identification and statistical analysis of overlapping continuous sequence elements in sequence- and time-series data

description: Contains the python code of SLALOM, the test data required to reproduce the data presented in this manuscript, as well as the User Manual for SLALOM. (ZIP 3622 kb)
DOI: 10.6084/m9.figshare.5829837
title: Additional file 1: of A comparison of symptoms and quality of life before and after nasal septoplasty and radiofrequency therapy of the inferior turbinate

description: Spreadsheet that include information from the patients about symptoms given on VASs and HQOL given on SNOT-20 and SF-36. (XLS 306 kb)
DOI: 10.6084/m9.figshare.5829837.v1
title: Additional file 1: of A comparison of symptoms and quality of life before and after nasal septoplasty and radiofrequency therapy of the inferior turbinate

description: Spreadsheet that include information from the patients about symptoms given on VASs and HQOL given on SNOT-20 and SF-36. (XLS 306 kb)
DOI: 10.6084/m9.figshare.5829825
title: Additional file 1: Table S1. of Targeted next-generation sequencing analysis in couples at increased risk for autosomal recessive disorders

description: List of the 430 genes investigated in the couples. Additional file listing the 430 genes for severe AR and XL disorders investigated in the couples (XLS 142 kb)
DOI: 10.6084/m9.figshare.5829825.v1
title: Additional file 1: Table S1. of Targeted next-generation sequencing analysis in couples at increased risk for autosomal recessive disorders

description: List of the 430 genes investigated in the couples. Additional file listing the 430 genes for severe AR and XL disorders investigated in the couples (XLS 142 kb)
DOI: 10.6084/m9.figshare.5829822
title: Additional file 1: of Degree of mosaicism in trophectoderm does not predict pregnancy potential: a corrected analysis of pregnancy outcomes following transfer of mosaic embryos

description: Data for 143 NGS-tested mosaic embryos that were transferred; extracted from Table S3 in the publication by MunnĂŠ et al. [7]. (XLSX 17 kb)
DOI: 10.6084/m9.figshare.5829822.v1
title: Additional file 1: of Degree of mosaicism in trophectoderm does not predict pregnancy potential: a corrected analysis of pregnancy outcomes following transfer of mosaic embryos

description: Data for 143 NGS-tested mosaic embryos that were transferred; extracted from Table S3 in the publication by MunnĂŠ et al. [7]. (XLSX 17 kb)
DOI: 10.6084/m9.figshare.5829816
title: List of software repositories

description: Repositories of object-oriented software projects included in the structural and logical coupling data sets
DOI: 10.6084/m9.figshare.5829765
title: Figure S1.jpg

description: Fig. S1. Van Krevelen diagrams of DOM leachates (SPE-AL, SPE-PL) and the unique molecular formulas found solely in leachates from AL and PL. The color shade changes with the relative abundance weighted by peak intensity, dark color correspondent with high intensity.
DOI: 10.6084/m9.figshare.5829714
title: Supplemental Table 1: Data from Using features of a Creole language to reconstruct population history and cultural evolution: tracing the English origins of Sranan

description: Creole languages are formed in conditions where speakers from distinct languages are brought together without a shared first language, typically under the domination of speakers from one of the languages and particularly in the context of the transatlantic slave trade and European colonialism. One such Creole in Suriname, Sranan, developed around the mid-seventeenth century, primarily out of contact between varieties of English from England, spoken by the dominant group, and multiple West African languages. The vast majority of the basic words in Sranan come from the language of the dominant group, English. Here, we compare linguistic features of modern-day Sranan with those of English as spoken in 313 localities across England. By way of testing proposed hypotheses for the origin of English words in Sranan, we find that 80% of the studied features of Sranan can be explained by similarity to regional dialect features at two distinct input locations within England, a cluster of locations near the port of Bristol and another cluster near Essex in eastern England. Our new hypothesis is supported by the geographical distribution of specific regional dialect features, such as post-vocalic rhoticity and word-initial ‘h’, and by phylogenetic analysis of these features, which shows evidence favouring input from at least two English dialects in the formation of Sranan. In addition to explicating the dialect features most prominent in the <i>linguistic</i> evolution of Sranan, our historical analyses also provide supporting evidence for two distinct hypotheses about the likely <i>geographical</i> origins of the English speakers whose language was an input to Sranan. The emergence as a likely input to Sranan of the speech forms of a cluster near Bristol is consistent with historical records, indicating that most of the indentured servants going to the Americas between 1654 and 1666 were from Bristol and nearby counties, and that of the cluster near Essex is consistent with documents showing that many of the governors and important planters came from the southeast of England (including London) (Smith 1987 <i>The Genesis of the Creole Languages of Surinam</i>; Smith 2009 In <i>The handbook of pidgin and creole studies</i>, pp. 98–129).This article is part of the theme issue ‘Bridging cultural gaps: interdisciplinary studies in human cultural evolution’.
DOI: 10.6084/m9.figshare.5829714.v1
title: Supplemental Table 1: Data from Using features of a Creole language to reconstruct population history and cultural evolution: tracing the English origins of Sranan

description: Creole languages are formed in conditions where speakers from distinct languages are brought together without a shared first language, typically under the domination of speakers from one of the languages and particularly in the context of the transatlantic slave trade and European colonialism. One such Creole in Suriname, Sranan, developed around the mid-seventeenth century, primarily out of contact between varieties of English from England, spoken by the dominant group, and multiple West African languages. The vast majority of the basic words in Sranan come from the language of the dominant group, English. Here, we compare linguistic features of modern-day Sranan with those of English as spoken in 313 localities across England. By way of testing proposed hypotheses for the origin of English words in Sranan, we find that 80% of the studied features of Sranan can be explained by similarity to regional dialect features at two distinct input locations within England, a cluster of locations near the port of Bristol and another cluster near Essex in eastern England. Our new hypothesis is supported by the geographical distribution of specific regional dialect features, such as post-vocalic rhoticity and word-initial ‘h’, and by phylogenetic analysis of these features, which shows evidence favouring input from at least two English dialects in the formation of Sranan. In addition to explicating the dialect features most prominent in the <i>linguistic</i> evolution of Sranan, our historical analyses also provide supporting evidence for two distinct hypotheses about the likely <i>geographical</i> origins of the English speakers whose language was an input to Sranan. The emergence as a likely input to Sranan of the speech forms of a cluster near Bristol is consistent with historical records, indicating that most of the indentured servants going to the Americas between 1654 and 1666 were from Bristol and nearby counties, and that of the cluster near Essex is consistent with documents showing that many of the governors and important planters came from the southeast of England (including London) (Smith 1987 <i>The Genesis of the Creole Languages of Surinam</i>; Smith 2009 In <i>The handbook of pidgin and creole studies</i>, pp. 98–129).This article is part of the theme issue ‘Bridging cultural gaps: interdisciplinary studies in human cultural evolution’.
DOI: 10.6084/m9.figshare.5829711
title: Cretaceous A-type volcanic–intrusive rocks and simultaneous mafic rocks along the Gan-Hang Tectonic Belt, Southeast China: petrogenesis and implications for the transition of crust–mantle interaction

description: Abundant evidence points to the Cretaceous crust–mantle interaction and plate subduction in the Gan-Hang Tectonic Belt (GHTB), southeastern China, but the evolutionary process remains poorly constrained. Here we conduct a comprehensive study on Daqiaowu granitic porphyry and diabase dikes in the eastern GHTB, in conjunction with previous studies on simultaneous felsic and mafic rocks along the GHTB, to demonstrate their petrogenesis and geodynamic evolutionary process. The Daqiaowu granitic porphyry (125 Ma), as well as the coeval granitic rocks, exhibits high zircon saturation temperatures, alkalis, 10<sup>4</sup>*Ga/Al ratios, and Zr + Nb + Ce + Y contents, concluding a distinctive belt of the Early Cretaceous (~137–125 Ma) A-type volcanic–intrusive rocks in the GHTB. Their ε<sub>Nd</sub>(t) and zircon ε<sub>Hf</sub>(t) values gradually increased through time from approximately −9.0 to −1.0 and −10.0 to +4.0, respectively, implying increasing contribution of mantle-derived components to their formation, and hence progressively intensified crust–mantle interaction in an intra-arc rift environment (a geodynamic transition stage from continental arc to back-arc) during the Early Cretaceous. This plausibility is further supported by the Early Cretaceous Daqiaowu diabase dikes and coeval mafic rocks which exhibit arc-like magmatic signatures and were derived from mantle wedge. In contrast, the Late Cretaceous mafic rocks show ocean island basalt-like geochemical characteristics, reflecting a depleted asthenosphere mantle source. This discrepancy of mantle sources concludes that the geodynamic setting in the GHTB may have basically transferred to back-arc regime in the Late Cretaceous. Thus, the Cretaceous geodynamic evolutionary process in the GHTB can be defined as the Early Cretaceous gradually intensified crust–mantle interaction in a geodynamic transition stage (from continental arc to back-arc extension) and the Late Cretaceous back-arc extensional setting.
DOI: 10.6084/m9.figshare.5829687
title: Single-cell RNA-seq data from Smart-seq2 sequencing of FACS sorted cells (v2)

description: Gene-count tables for FACS sorted cells sequenced with Smart-Seq2 from 20 organs of 7 mice. Cells are grouped by tissue of origin.<br><br>Includes data for 53,760 cells, 44,879 of which passed a QC cutoff of at least 500 genes and 50,000 reads.<br>Cell annotations using the Cell Ontology [1] controlled vocabulary are in a separate csv.<br>This differs from v1 by renaming "Brain_Neurons" --&gt; "Brain_Non-microglia" to be consistent with the manuscript.<br><br>Update 2018-09-20: Updated annotations to latest manuscript version<br>Update 2018-02-16: Separated Diaphragm cells from Muscle cells, and Aorta cells from Heart cells.<br>Update 2018-02-20: Aorta and Heart erroneously contained Diaphragm and Muscle data, and have now been corrected.<br>Update 2018-03-09: Renamed tissues for nomenclature standards: "Colon" --&gt; "Large_Intestine" "Muscle" --&gt; "Limb_Muscle" "Mammary" --&gt; "Mammary_Gland" "Brain_Microglia" --&gt; "Brain_Myeloid" "Brain_Non-microglia" --&gt; "Brain_Non-Myeloid"Update 2018-03-22: Renamed subtissues:<br>- tissue: Heart, subtissue: ? --&gt; tissue: Heart, subtissue: Unknown- tissue: Skin, subtissue: NA --&gt; tissue: Skin, subtissue: Telogen<br>Update 2018-03-23: Removed row numbers in first column of metadata_FACS.csv<br>Update 2018-03-27: Added tissue tSNEs and cluster ids<br><br>[1] http://purl.obolibrary.org/obo/cl.owl<br>
DOI: 10.6084/m9.figshare.5829687.v2
title: Single-cell RNA-seq data from Smart-seq2 sequencing of FACS sorted cells (v2)

description: Gene-count tables for FACS sorted cells sequenced with Smart-Seq2 from 20 organs of 7 mice. Cells are grouped by tissue of origin.<br><br>Includes data for 53,760 cells, 44,879 of which passed a QC cutoff of at least 500 genes and 50,000 reads.<br>Cell annotations using the Cell Ontology [1] controlled vocabulary are in a separate csv.<br>This differs from v1 by renaming "Brain_Neurons" --&gt; "Brain_Non-microglia" to be consistent with the manuscript.<br><br>Update 2018-02-16: Separated Diaphragm cells from Muscle cells, and Aorta cells from Heart cells.<br>[1] http://purl.obolibrary.org/obo/cl.owl<br>
DOI: 10.6084/m9.figshare.5829687.v3
title: Single-cell RNA-seq data from Smart-seq2 sequencing of FACS sorted cells (v2)

description: Gene-count tables for FACS sorted cells sequenced with Smart-Seq2 from 20 organs of 7 mice. Cells are grouped by tissue of origin.<br><br>Includes data for 53,760 cells, 44,879 of which passed a QC cutoff of at least 500 genes and 50,000 reads.<br>Cell annotations using the Cell Ontology [1] controlled vocabulary are in a separate csv.<br>This differs from v1 by renaming "Brain_Neurons" --&gt; "Brain_Non-microglia" to be consistent with the manuscript.<br><br>Update 2018-02-16: Separated Diaphragm cells from Muscle cells, and Aorta cells from Heart cells.<br>Update 2018-02-20: Aorta and Heart erroneously contained Diaphragm and Muscle data, and have now been corrected.<br>[1] http://purl.obolibrary.org/obo/cl.owl<br>
DOI: 10.6084/m9.figshare.5829687.v4
title: Single-cell RNA-seq data from Smart-seq2 sequencing of FACS sorted cells (v2)

description: Gene-count tables for FACS sorted cells sequenced with Smart-Seq2 from 20 organs of 7 mice. Cells are grouped by tissue of origin.<br><br>Includes data for 53,760 cells, 44,879 of which passed a QC cutoff of at least 500 genes and 50,000 reads.<br>Cell annotations using the Cell Ontology [1] controlled vocabulary are in a separate csv.<br>This differs from v1 by renaming "Brain_Neurons" --&gt; "Brain_Non-microglia" to be consistent with the manuscript.<br><br>Update 2018-02-16: Separated Diaphragm cells from Muscle cells, and Aorta cells from Heart cells.<br>Update 2018-02-20: Aorta and Heart erroneously contained Diaphragm and Muscle data, and have now been corrected.<br>Update 2018-03-09: Renamed tissues for nomenclature standards: "Colon" --&gt; "Large_Intestine" "Muscle" --&gt; "Limb_Muscle" "Mammary" --&gt; "Mammary_Gland" "Brain_Microglia" --&gt; "Brain_Myeloid" "Brain_Non-microglia" --&gt; "Brain_Non-Myeloid"<br>[1] http://purl.obolibrary.org/obo/cl.owl<br>
DOI: 10.6084/m9.figshare.5829687.v5
title: Single-cell RNA-seq data from Smart-seq2 sequencing of FACS sorted cells (v2)

description: Gene-count tables for FACS sorted cells sequenced with Smart-Seq2 from 20 organs of 7 mice. Cells are grouped by tissue of origin.<br><br>Includes data for 53,760 cells, 44,879 of which passed a QC cutoff of at least 500 genes and 50,000 reads.<br>Cell annotations using the Cell Ontology [1] controlled vocabulary are in a separate csv.<br>This differs from v1 by renaming "Brain_Neurons" --&gt; "Brain_Non-microglia" to be consistent with the manuscript.<br><br>Update 2018-02-16: Separated Diaphragm cells from Muscle cells, and Aorta cells from Heart cells.<br>Update 2018-02-20: Aorta and Heart erroneously contained Diaphragm and Muscle data, and have now been corrected.<br>Update 2018-03-09: Renamed tissues for nomenclature standards: "Colon" --&gt; "Large_Intestine" "Muscle" --&gt; "Limb_Muscle" "Mammary" --&gt; "Mammary_Gland" "Brain_Microglia" --&gt; "Brain_Myeloid" "Brain_Non-microglia" --&gt; "Brain_Non-Myeloid"Update 2018-03-22: Renamed subtissues:<br>- tissue: Heart, subtissue: ? --&gt; tissue: Heart, subtissue: Unknown- tissue: Skin, subtissue: NA --&gt; tissue: Skin, subtissue: Telogen<br>[1] http://purl.obolibrary.org/obo/cl.owl<br>
DOI: 10.6084/m9.figshare.5829687.v6
title: Single-cell RNA-seq data from Smart-seq2 sequencing of FACS sorted cells (v2)

description: Gene-count tables for FACS sorted cells sequenced with Smart-Seq2 from 20 organs of 7 mice. Cells are grouped by tissue of origin.<br><br>Includes data for 53,760 cells, 44,879 of which passed a QC cutoff of at least 500 genes and 50,000 reads.<br>Cell annotations using the Cell Ontology [1] controlled vocabulary are in a separate csv.<br>This differs from v1 by renaming "Brain_Neurons" --&gt; "Brain_Non-microglia" to be consistent with the manuscript.<br><br>Update 2018-02-16: Separated Diaphragm cells from Muscle cells, and Aorta cells from Heart cells.<br>Update 2018-02-20: Aorta and Heart erroneously contained Diaphragm and Muscle data, and have now been corrected.<br>Update 2018-03-09: Renamed tissues for nomenclature standards: "Colon" --&gt; "Large_Intestine" "Muscle" --&gt; "Limb_Muscle" "Mammary" --&gt; "Mammary_Gland" "Brain_Microglia" --&gt; "Brain_Myeloid" "Brain_Non-microglia" --&gt; "Brain_Non-Myeloid"Update 2018-03-22: Renamed subtissues:<br>- tissue: Heart, subtissue: ? --&gt; tissue: Heart, subtissue: Unknown- tissue: Skin, subtissue: NA --&gt; tissue: Skin, subtissue: Telogen<br>Update 2018-03-23: Removed row numbers in first column of metadata_FACS.csv<br><br>[1] http://purl.obolibrary.org/obo/cl.owl<br>
DOI: 10.6084/m9.figshare.5829633
title: Quantifying an Adherence Path-Specific Effect of Antiretroviral Therapy in the Nigeria PEPFAR Program

description: Since the early 2000s, evidence has accumulated for a significant differential effect of first-line antiretroviral therapy (ART) regimens on human immunodeficiency virus (HIV) viral load suppression. This finding was replicated in our data from the Harvard President’s Emergency Plan for AIDS Relief (PEPFAR) program in Nigeria. Investigators were interested in finding the source of these differences, that is, understanding the mechanisms through which one regimen outperforms another, particularly via adherence. This question can be naturally formulated via mediation analysis with adherence playing the role of a mediator. Existing mediation analysis results, however, have relied on an assumption of no exposure-induced confounding of the intermediate variable, and generally require an assumption of no unmeasured confounding for nonparametric identification. Both assumptions are violated by the presence of drug toxicity. In this article, we relax these assumptions and show that certain path-specific effects remain identified under weaker conditions. We focus on the path-specific effect solely mediated by adherence and not by toxicity and propose an estimator for this effect. We illustrate with simulations and present results from a study applying the methodology to the Harvard PEPFAR data. Supplementary materials for this article are available online.