cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6953351
title: Identification and characterisation of microRNAs and Piwi-interacting RNAs in cockerels’ spermatozoa by Solexa sequencing

description: 1. There has been substantial research focused on the roles of microRNAs (miRNAs) and Piwi-interacting RNAs (piRNAs) derived from mammalian spermatozoa; however, comparatively little is known about the role of spermatozoa-derived miRNAs and piRNAs within breeding cockerels’ spermatozoa. 2. A small RNA library of cockerels’ spermatozoa was constructed using Illumina high-throughput sequencing technology. Unique sequences with lengths of 18–26 nucleotides were mapped to miRBase 21.0 and unique sequences with lengths of 25–37 nucleotides were mapped to a piRNA database. A total of 1311 miRNAs and 2448 potential piRNAs were identified. Based on stem-loop qRT-PCR, 8 miRNAs were validated. 3. Potential target genes of the abundant miRNAs were predicted, and further Kyoto Encyclopedia of Genes and Genomes database (KEGG) and Gene Ontology (GO) analyses were performed, which revealed that some candidate miRNAs were involved in the spermatogenesis process, spermatozoa epigenetic programming and further embryonic development. 5. GO and KEGG analyses based on mapping genes of expressed piRNAs were performed, which revealed that spermatozoal piRNAs could play important regulatory roles in embryonic development of offspring. 6. The search for endogenous spermatozoa miRNAs and piRNAs will contribute to a preliminary database for functional and molecular mechanistic studies in embryonic development and spermatozoa epigenetic programming.
DOI: 10.6084/m9.figshare.6953351.v1
title: Identification and characterisation of microRNAs and Piwi-interacting RNAs in cockerels’ spermatozoa by Solexa sequencing

description: 1. There has been substantial research focused on the roles of microRNAs (miRNAs) and Piwi-interacting RNAs (piRNAs) derived from mammalian spermatozoa; however, comparatively little is known about the role of spermatozoa-derived miRNAs and piRNAs within breeding cockerels’ spermatozoa. 2. A small RNA library of cockerels’ spermatozoa was constructed using Illumina high-throughput sequencing technology. Unique sequences with lengths of 18–26 nucleotides were mapped to miRBase 21.0 and unique sequences with lengths of 25–37 nucleotides were mapped to a piRNA database. A total of 1311 miRNAs and 2448 potential piRNAs were identified. Based on stem-loop qRT-PCR, 8 miRNAs were validated. 3. Potential target genes of the abundant miRNAs were predicted, and further Kyoto Encyclopedia of Genes and Genomes database (KEGG) and Gene Ontology (GO) analyses were performed, which revealed that some candidate miRNAs were involved in the spermatogenesis process, spermatozoa epigenetic programming and further embryonic development. 5. GO and KEGG analyses based on mapping genes of expressed piRNAs were performed, which revealed that spermatozoal piRNAs could play important regulatory roles in embryonic development of offspring. 6. The search for endogenous spermatozoa miRNAs and piRNAs will contribute to a preliminary database for functional and molecular mechanistic studies in embryonic development and spermatozoa epigenetic programming.
DOI: 10.6084/m9.figshare.6953345
title: 1.74 Ga crustal melting after rifting at the northern Indian margin: investigation of mylonitic orthogneisses in the Kathmandu area, central Nepal

description: Mylonitic orthogneisses in the Kathmandu area, central Nepal have been investigated using whole-rock and mineral chemistry, Rb-Sr isotopes, and zircon U-Pb age dating. Zircon REE patterns determined from orthogneisses are characterized by enriched HREE patterns and the prominent Eu anomalies, consistent with a magmatic origin. The U-Pb zircon age dating and Ti-in-zircon thermometry revealed crystallization took place ca. 1.74 Ga at temperatures of 705–765℃; typical of felsic magmatism in the crust. Whole-rock data from most orthogneisses in this study and from similar rocks in previous studies span the ‘syn-collisional’ and ‘post-collisional’ fields on various tectonic discrimination diagrams, while some data also plot in rift-related magmatism fields. The peraluminous compositions, very high Sr isotopic ratios (0.865–3.585) and high Th and U concentrations for all orthogneisses in this study indicate that mylonitic orthogneisses are largely of S-type crustal origins. The new data presented herein, combined with that of previous studies, outline at least two Palaeoproterozoic magmatic episodes: 1) ca. 1.92–1.90 Ga rift-related magmatism derived from mantle melting and 2) 1.84–1.74 Ga crustal melting, resulting from burial of the Indian basement during thermal subsidence after rifting. This two-stage Palaeoproterozoic magmatism in Nepal occurred along the northern passive margin of the Indian basement during and/or after the breakup of the Columbia supercontinent.
DOI: 10.6084/m9.figshare.6953345.v1
title: 1.74 Ga crustal melting after rifting at the northern Indian margin: investigation of mylonitic orthogneisses in the Kathmandu area, central Nepal

description: Mylonitic orthogneisses in the Kathmandu area, central Nepal have been investigated using whole-rock and mineral chemistry, Rb-Sr isotopes, and zircon U-Pb age dating. Zircon REE patterns determined from orthogneisses are characterized by enriched HREE patterns and the prominent Eu anomalies, consistent with a magmatic origin. The U-Pb zircon age dating and Ti-in-zircon thermometry revealed crystallization took place ca. 1.74 Ga at temperatures of 705–765℃; typical of felsic magmatism in the crust. Whole-rock data from most orthogneisses in this study and from similar rocks in previous studies span the ‘syn-collisional’ and ‘post-collisional’ fields on various tectonic discrimination diagrams, while some data also plot in rift-related magmatism fields. The peraluminous compositions, very high Sr isotopic ratios (0.865–3.585) and high Th and U concentrations for all orthogneisses in this study indicate that mylonitic orthogneisses are largely of S-type crustal origins. The new data presented herein, combined with that of previous studies, outline at least two Palaeoproterozoic magmatic episodes: 1) ca. 1.92–1.90 Ga rift-related magmatism derived from mantle melting and 2) 1.84–1.74 Ga crustal melting, resulting from burial of the Indian basement during thermal subsidence after rifting. This two-stage Palaeoproterozoic magmatism in Nepal occurred along the northern passive margin of the Indian basement during and/or after the breakup of the Columbia supercontinent.
DOI: 10.6084/m9.figshare.6953339
title: The community succession of arthropods on a pig carcass in Lebanon: different taxonomic level approaches with faunistic notes

description: The diversity of arthropods is studied, at family and species level, on a pig carcass during a warm season in an open field in Badghan-Mount Lebanon. Ten orders of arthropods were found associated to the carcass. A total of 1168 specimens of adults Diptera and Coleoptera were collected. Among Diptera, the predator <i>Chrysomya albiceps</i> was dominant on the carcass during the active decay stage and <i>Musca</i> spp. were necrophagous. Within Coleoptera, <i>Creophilus maxillosus</i> (Linnaeus, 1758), <i>Philonthus concinnu</i>s (Gravenhorst, 1802), <i>Aleochara lata</i> Gravenhorst, 1802, and <i>Saprinus</i> sp. were the predator taxa. <i>Dermestes frischii</i> Kugelann, 1792 and <i>Necrobia rufipes</i> (De Geer, 1775) were more present during the advanced decay, together with anthicids. In addition to a list of species visiting the carcass, we carried out a multivariate analysis of principal components to explore the relationships between the pattern of presences of 16 insect families and the four decomposition stages during the first 30 days of the carcass decomposition. The groupings of insects during the four decomposition stages show significant dissimilarities, suggesting that the different stages are characterized by different insect associations, as reported in many other previous studies. <b>Résumé. La succession des communautés d’arthropodes sur une carcasse de porc au Liban : approches à divers niveaux taxonomiques et notes faunistiques</b>. La diversité des arthropodes est étudiée, au rang familial et spécifique, sur une carcasse de porc pendant la saison chaude en milieu naturel, sur le site de Badghan-Mount, au Liban. Dix ordres d’arthropodes ont été trouvés associés à la carcasse. Un total de 1168 spécimens adultes de Diptères et de Coléoptères a été collecté. Parmi les Diptères, le prédateur <i>Chrysomya albiceps</i> était dominant sur la carcasse au stade de décomposition active. Les <i>Musca</i> spp. étaient nécrophages. Parmi les Coléoptères, <i>Creophilus maxillosus</i> (Linnaeus, 1758), <i>Philonthus concinnus</i> (Gravenhorst, 1802), <i>Aleochara lata</i> Gravenhorst, 1802 et <i>Saprinus</i> sp. étaient prédateurs. <i>Dermestes frischii</i> Kugelann, 1792 et <i>Necrobia rufipes</i> (De Geer, 1775) et les Anthicidae étaient plus présents pendant la décomposition avancée. En complément à la liste des espèces visitant la carcasse, nous avons effectué une analyse multivariée en composantes principales pour explorer les relations entre le patron de présence de 16 familles d’insectes et les quatre stades de décomposition au cours des 30 premiers jours de la décomposition. Les groupements d’insectes montrent des dissimilarités significatives, ce qui suggère que les différents stades sont caractérisés par des associations différentes d’insectes, de façon analogue à ce qui a été rapporté dans plusieurs études antérieures.
DOI: 10.6084/m9.figshare.6953339.v1
title: The community succession of arthropods on a pig carcass in Lebanon: different taxonomic level approaches with faunistic notes

description: The diversity of arthropods is studied, at family and species level, on a pig carcass during a warm season in an open field in Badghan-Mount Lebanon. Ten orders of arthropods were found associated to the carcass. A total of 1168 specimens of adults Diptera and Coleoptera were collected. Among Diptera, the predator <i>Chrysomya albiceps</i> was dominant on the carcass during the active decay stage and <i>Musca</i> spp. were necrophagous. Within Coleoptera, <i>Creophilus maxillosus</i> (Linnaeus, 1758), <i>Philonthus concinnu</i>s (Gravenhorst, 1802), <i>Aleochara lata</i> Gravenhorst, 1802, and <i>Saprinus</i> sp. were the predator taxa. <i>Dermestes frischii</i> Kugelann, 1792 and <i>Necrobia rufipes</i> (De Geer, 1775) were more present during the advanced decay, together with anthicids. In addition to a list of species visiting the carcass, we carried out a multivariate analysis of principal components to explore the relationships between the pattern of presences of 16 insect families and the four decomposition stages during the first 30 days of the carcass decomposition. The groupings of insects during the four decomposition stages show significant dissimilarities, suggesting that the different stages are characterized by different insect associations, as reported in many other previous studies. <b>Résumé. La succession des communautés d’arthropodes sur une carcasse de porc au Liban : approches à divers niveaux taxonomiques et notes faunistiques</b>. La diversité des arthropodes est étudiée, au rang familial et spécifique, sur une carcasse de porc pendant la saison chaude en milieu naturel, sur le site de Badghan-Mount, au Liban. Dix ordres d’arthropodes ont été trouvés associés à la carcasse. Un total de 1168 spécimens adultes de Diptères et de Coléoptères a été collecté. Parmi les Diptères, le prédateur <i>Chrysomya albiceps</i> était dominant sur la carcasse au stade de décomposition active. Les <i>Musca</i> spp. étaient nécrophages. Parmi les Coléoptères, <i>Creophilus maxillosus</i> (Linnaeus, 1758), <i>Philonthus concinnus</i> (Gravenhorst, 1802), <i>Aleochara lata</i> Gravenhorst, 1802 et <i>Saprinus</i> sp. étaient prédateurs. <i>Dermestes frischii</i> Kugelann, 1792 et <i>Necrobia rufipes</i> (De Geer, 1775) et les Anthicidae étaient plus présents pendant la décomposition avancée. En complément à la liste des espèces visitant la carcasse, nous avons effectué une analyse multivariée en composantes principales pour explorer les relations entre le patron de présence de 16 familles d’insectes et les quatre stades de décomposition au cours des 30 premiers jours de la décomposition. Les groupements d’insectes montrent des dissimilarités significatives, ce qui suggère que les différents stades sont caractérisés par des associations différentes d’insectes, de façon analogue à ce qui a été rapporté dans plusieurs études antérieures.
DOI: 10.6084/m9.figshare.6953306
title: chick_NC-GRN_images

description: Precise control of developmental processes is encoded in the genome in the form of gene regulatory networks (GRNs). Such multi-factorial systems are difficult to decode in vertebrates owing to their complex gene hierarchies and dynamic molecular interactions. Here we present a genome-wide <i>in vivo</i> reconstruction of the GRN underlying development of the multipotent neural crest (NC) embryonic cell population. By coupling NC-specific epigenomic and transcriptional profiling at population and single-cell levels with genome/epigenome engineering <i>in vivo</i>, we identify multiple regulatory layers governing NC ontogeny, including NC-specific enhancers and super-enhancers, novel trans-factors and cis-signatures allowing to reverse engineer the NC-GRN at unprecedented resolution. Furthermore, identification and dissection of divergent upstream combinatorial regulatory codes has afforded new insights into opposing gene circuits that define canonical and neural NC fates early during NC ontogeny. Our integrated approach, allowing dissection of cell-type-specific regulatory circuits <i>in vivo</i>, has broad implications for GRN discovery and investigation.
DOI: 10.6084/m9.figshare.6953306.v1
title: chick_NC-GRN_images

description: Precise control of developmental processes is encoded in the genome in the form of gene regulatory networks (GRNs). Such multi-factorial systems are difficult to decode in vertebrates owing to their complex gene hierarchies and dynamic molecular interactions. Here we present a genome-wide <i>in vivo</i> reconstruction of the GRN underlying development of the multipotent neural crest (NC) embryonic cell population. By coupling NC-specific epigenomic and transcriptional profiling at population and single-cell levels with genome/epigenome engineering <i>in vivo</i>, we identify multiple regulatory layers governing NC ontogeny, including NC-specific enhancers and super-enhancers, novel trans-factors and cis-signatures allowing to reverse engineer the NC-GRN at unprecedented resolution. Furthermore, identification and dissection of divergent upstream combinatorial regulatory codes has afforded new insights into opposing gene circuits that define canonical and neural NC fates early during NC ontogeny. Our integrated approach, allowing dissection of cell-type-specific regulatory circuits <i>in vivo</i>, has broad implications for GRN discovery and investigation.
DOI: 10.6084/m9.figshare.6953294
title: chick_NC-GRN_RData

description: Precise control of developmental processes is encoded in the genome in the form of gene regulatory networks (GRNs). Such multi-factorial systems are difficult to decode in vertebrates owing to their complex gene hierarchies and dynamic molecular interactions. Here we present a genome-wide <i>in vivo</i> reconstruction of the GRN underlying development of the multipotent neural crest (NC) embryonic cell population. By coupling NC-specific epigenomic and transcriptional profiling at population and single-cell levels with genome/epigenome engineering <i>in vivo</i>, we identify multiple regulatory layers governing NC ontogeny, including NC-specific enhancers and super-enhancers, novel trans-factors and cis-signatures allowing to reverse engineer the NC-GRN at unprecedented resolution. Furthermore, identification and dissection of divergent upstream combinatorial regulatory codes has afforded new insights into opposing gene circuits that define canonical and neural NC fates early during NC ontogeny. Our integrated approach, allowing dissection of cell-type-specific regulatory circuits <i>in vivo</i>, has broad implications for GRN discovery and investigation.<br>
DOI: 10.6084/m9.figshare.6953291
title: Data for: Estimating the effects of variation in viremia on mosquito susceptibility, infectiousness, and R0 of Zika in Aedes aegypti

description: Data for paper "Estimating the effects of variation in viremia on mosquito susceptibility, infectiousness, and <i>R<sub>0 </sub></i>of Zika in <i>Aedes aegypti". Published in PLoS NTD. </i>
DOI: 10.6084/m9.figshare.6953291.v1
title: Data for: Estimating the effects of variation in viremia on mosquito susceptibility, infectiousness, and R0 of Zika in Aedes aegypti

description: Data for paper "Estimating the effects of variation in viremia on mosquito susceptibility, infectiousness, and <i>R<sub>0 </sub></i>of Zika in <i>Aedes aegypti". Published in PLoS NTD. </i>
DOI: 10.6084/m9.figshare.6953294.v1
title: chick_NC-GRN_RData

description: Precise control of developmental processes is encoded in the genome in the form of gene regulatory networks (GRNs). Current understanding of vertebrate embryonic GRNs is fragmentary due to complex cell-type and developmental composition. Here we present a genome-wide <i>in vivo</i> study of the GRN underlying neural crest (NC), an emblematic stem cell-like population with unique migratory ability and multipotency. Analysis of NC chromatin and transcriptional dynamics<i> </i>revealed the full complement of NC enhancers and transcription factor inputs including ‘super-enhancer’-like clusters, which we tested using <i>in vivo</i> reporters and epigenome engineering. Integration of <i>cis</i>-regulatory and single-cell data enabled construction and functional validation of the NC-GRN at unprecedented resolution. Our integrated approach allowing dissection of cell-type-specific gene regulatory circuits <i>in vivo </i>has broad implications for GRN discovery and investigation.<br>
DOI: 10.6084/m9.figshare.6953240
title: Supplemental Tables- A pre-pregnancy biomarker risk score improves prediction of future gestational diabetes

description: Supplemental tables to accompany "A pre-pregnancy biomarker risk score improves prediction of future gestational diabetes" <br>Contents:Supplemental Table 1. Mutually adjusted associations of biomarkers assessed at the preconception examination with GDM among women with fasting samplesSupplemental Table 2. Associations of the preconception biomarker score with gestational diabetes among women with fasting samplesSupplemental Table 3. AUC for predictive value for gestational diabetes risk among women with fasting samples<br><br>
DOI: 10.6084/m9.figshare.6953276
title: DRX013192.bw

description: DRX013192.bw
DOI: 10.6084/m9.figshare.6953231
title: Latency for facultative expression of male-typical courtship behaviour by female bluehead wrasses depends on social rank: The ‘priming/gating’ hypothesis.

description: While socially-controlled sex transformation in fishes is well established, the underlying mechanisms are not well understood. Particularly enigmatic is behavioural transformation, in which fish can rapidly switch from exhibiting female to male-typical courtship behaviours following removal of ‘supermales’. Bluehead wrasses are a model system for investigating environmental control of sex determination, particularly the social control of sex transformation. Here we show that the onset of this behavioural transformation was delayed in females that occupied low-ranking positions in the female dominance hierarchy. We also establish that expression of male-typical courtship behaviours in competent ‘initial-phase’ (IP) females is facultative and gated by the presence of terminal-phase (TP) males. Dominant females displayed reliable TP male-typical courtship behaviours within approximately two days after the removal of a TP male; immediately following reintroduction of the TP male, however, females reverted back to female-typical behaviours. These results demonstrate a remarkable plasticity of sexual behaviour and support a ‘priming/gating’ hypothesis for the control of behavioural transformation in bluehead wrasses. <br>
DOI: 10.6084/m9.figshare.6953219
title: OrthoMCL output groups file of orthologs in the 88 isolates

description: orthoMCL groups.txt output file used to quantify the rare and common gene families in the E. tracheiphila pangenome
DOI: 10.6084/m9.figshare.6953231.v2
title: Latency for facultative expression of male-typical courtship behaviour by female bluehead wrasses depends on social rank: The ‘priming/gating’ hypothesis.

description: While socially-controlled sex transformation in fishes is well established, the underlying mechanisms are not well understood. Particularly enigmatic is behavioural transformation, in which fish can rapidly switch from exhibiting female to male-typical courtship behaviours following removal of ‘supermales’. Bluehead wrasses are a model system for investigating environmental control of sex determination, particularly the social control of sex transformation. Here we show that the onset of this behavioural transformation was delayed in females that occupied low-ranking positions in the female dominance hierarchy. We also establish that expression of male-typical courtship behaviours in competent ‘initial-phase’ (IP) females is facultative and gated by the presence of terminal-phase (TP) males. Dominant females displayed reliable TP male-typical courtship behaviours within approximately two days after the removal of a TP male; immediately following reintroduction of the TP male, however, females reverted back to female-typical behaviours. These results demonstrate a remarkable plasticity of sexual behaviour and support a ‘priming/gating’ hypothesis for the control of behavioural transformation in bluehead wrasses. <br>
DOI: 10.6084/m9.figshare.6953231.v1
title: 2018 JEB Wrasse Priming Gating Data

description: While socially-controlled sex transformation in fishes is well established, the underlying mechanisms are not well understood. Particularly enigmatic is behavioural transformation, in which fish can rapidly switch from exhibiting female to male-typical courtship behaviours following removal of ‘supermales’. Bluehead wrasses are a model system for investigating environmental control of sex determination, particularly the social control of sex transformation. Here we show that the onset of this behavioural transformation was delayed in females that occupied low-ranking positions in the female dominance hierarchy. We also establish that expression of male-typical courtship behaviours in competent ‘initial-phase’ (IP) females is facultative and gated by the presence of terminal-phase (TP) males. Dominant females displayed reliable TP male-typical courtship behaviours within approximately two days after the removal of a TP male; immediately following reintroduction of the TP male, however, females reverted back to female-typical behaviours. These results demonstrate a remarkable plasticity of sexual behaviour and support a ‘priming/gating’ hypothesis for the control of behavioural transformation in bluehead wrasses. <br>