cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.23902960
title: Additional file 1 of Multi-omics reveal the metabolic patterns in mouse cumulus cells during oocyte maturation

description: Additional file 1: Supplementary Table 1. Related to Fig. 1. Metabolomic profiling in cumulus cells surrounding GV/GVBD/MII oocyte.
DOI: 10.6084/m9.figshare.23902960.v1
title: Additional file 1 of Multi-omics reveal the metabolic patterns in mouse cumulus cells during oocyte maturation

description: Additional file 1: Supplementary Table 1. Related to Fig. 1. Metabolomic profiling in cumulus cells surrounding GV/GVBD/MII oocyte.
DOI: 10.6084/m9.figshare.23902963
title: Additional file 2 of Multi-omics reveal the metabolic patterns in mouse cumulus cells during oocyte maturation

description: Additional file 2: Supplementary Table 2. Related to Fig. 2. Differentially Expressed Proteins in cumulus cells surrounding GV/GVBD/MII oocyte.
DOI: 10.6084/m9.figshare.23902963.v1
title: Additional file 2 of Multi-omics reveal the metabolic patterns in mouse cumulus cells during oocyte maturation

description: Additional file 2: Supplementary Table 2. Related to Fig. 2. Differentially Expressed Proteins in cumulus cells surrounding GV/GVBD/MII oocyte.
DOI: 10.6084/m9.figshare.17087264
title: Data.xlsx

description: The dataset includes two groups of microcosm experiments, historic data of Bohai Sea and a series of numerical experiments.
DOI: 10.6084/m9.figshare.23903023
title: Additional file 1 of Whole-exome sequencing analysis identifies novel variants associated with Kawasaki disease susceptibility

description: Supplementary Material 1
DOI: 10.6084/m9.figshare.23903023.v1
title: Additional file 1 of Whole-exome sequencing analysis identifies novel variants associated with Kawasaki disease susceptibility

description: Supplementary Material 1
DOI: 10.5281/zenodo.10480939
title: Experimental materials for "The Paradox of Function Header Comments"

description: Experimental materials for the paper "The Paradox of Function Header Comments".

Includes full results of the survey conducted for this paper, and data and scripts for crawling Python projects to analyze header comments.

See README for details.
DOI: 10.5281/zenodo.10480940
title: Experimental materials for "The Paradox of Function Header Comments"

description: Experimental materials for the paper "The Paradox of Function Header Comments".

Includes full results of the survey conducted for this paper, and data and scripts for crawling Python projects to analyze header comments.

See README for details.
DOI: 10.6084/m9.figshare.17087338
title: Proton pump inhibitors may reduce the risk of high-grade dysplasia and/or esophageal adenocarcinoma in Barrett’s esophagus: a systematic review and meta-analysis

description: Barrett’s esophagus (BE) is an important risk factor for high-grade dysplasia (HGD) and/or esophageal adenocarcinoma (EAC). The effect of proton pump inhibitors (PPIs) on the chemoprevention of HGD and/or EAC arising from BE remains controversial. PubMed, EMBASE, and Cochrane Library databases were systematically searched. Risk ratios (RRs) or odds ratios (ORs) with 95% confidence intervals (CIs) were pooled by a random-effect model. Heterogeneity and its potential source were assessed. Fifteen studies with 26,291 BE patients were included. Meta-analysis of eight cohort studies showed that PPIs can significantly reduce the risk of HGD and/or EAC in BE patients (RR = 0.46; P &lt; 0.001), but meta-analysis of six case-control studies showed no significant benefit of PPIs (OR = 0.64; P = 0.334). Heterogeneity was significant among both cohort and case-control studies, which might be attributed to the information sources of PPIs. There was no significant protective effect of high-dose PPIs on HGD and/or EAC in one RCT (RR = 0.84; P = 0.21), meta-analysis of two cohort studies (RR = 0.61; P = 0.28), or meta-analysis of two case-control studies (OR = 0.32; P = 0.08). Chemoprevention of HGD and/or EAC by PPIs may be considered in BE patients. However, there might not be further preventive effect of high-dose PPIs.
DOI: 10.6084/m9.figshare.21805935
title: Table S2: Zircon U–Pb geochronology and Hf isotopic compositions of igneous rocks from Sumatra: implications for the Cenozoic magmatic evolution of the western Sunda Arc

description: Zircon U–Pb ages used in this study.
DOI: 10.6084/m9.figshare.17087338.v1
title: Proton pump inhibitors may reduce the risk of high-grade dysplasia and/or esophageal adenocarcinoma in Barrett’s esophagus: a systematic review and meta-analysis

description: Barrett’s esophagus (BE) is an important risk factor for high-grade dysplasia (HGD) and/or esophageal adenocarcinoma (EAC). The effect of proton pump inhibitors (PPIs) on the chemoprevention of HGD and/or EAC arising from BE remains controversial. PubMed, EMBASE, and Cochrane Library databases were systematically searched. Risk ratios (RRs) or odds ratios (ORs) with 95% confidence intervals (CIs) were pooled by a random-effect model. Heterogeneity and its potential source were assessed. Fifteen studies with 26,291 BE patients were included. Meta-analysis of eight cohort studies showed that PPIs can significantly reduce the risk of HGD and/or EAC in BE patients (RR = 0.46; P &lt; 0.001), but meta-analysis of six case-control studies showed no significant benefit of PPIs (OR = 0.64; P = 0.334). Heterogeneity was significant among both cohort and case-control studies, which might be attributed to the information sources of PPIs. There was no significant protective effect of high-dose PPIs on HGD and/or EAC in one RCT (RR = 0.84; P = 0.21), meta-analysis of two cohort studies (RR = 0.61; P = 0.28), or meta-analysis of two case-control studies (OR = 0.32; P = 0.08). Chemoprevention of HGD and/or EAC by PPIs may be considered in BE patients. However, there might not be further preventive effect of high-dose PPIs.
DOI: 10.6084/m9.figshare.21805935.v1
title: Table S2: Zircon U–Pb geochronology and Hf isotopic compositions of igneous rocks from Sumatra: implications for the Cenozoic magmatic evolution of the western Sunda Arc

description: Zircon U–Pb ages used in this study.
DOI: 10.6084/m9.figshare.21805941
title: Table S3: Zircon U–Pb geochronology and Hf isotopic compositions of igneous rocks from Sumatra: implications for the Cenozoic magmatic evolution of the western Sunda Arc

description: Zircon Hf isotopes used in this study.
DOI: 10.6084/m9.figshare.21805941.v1
title: Table S3: Zircon U–Pb geochronology and Hf isotopic compositions of igneous rocks from Sumatra: implications for the Cenozoic magmatic evolution of the western Sunda Arc

description: Zircon Hf isotopes used in this study.
DOI: 10.6084/m9.figshare.21805947
title: Table S1: Zircon U–Pb geochronology and Hf isotopic compositions of igneous rocks from Sumatra: implications for the Cenozoic magmatic evolution of the western Sunda Arc

description: Age results from previous studies.
DOI: 10.6084/m9.figshare.21805947.v1
title: Table S1: Zircon U–Pb geochronology and Hf isotopic compositions of igneous rocks from Sumatra: implications for the Cenozoic magmatic evolution of the western Sunda Arc

description: Age results from previous studies.
DOI: 10.5281/zenodo.6341953
title: MerchiSolla/GPR_Geothermal: v1

description: raw data
DOI: 10.5281/zenodo.6341972
title: MerchiSolla/GPR_Geothermal: raw data

description: 200 MHz and 500 MHz data
DOI: 10.5281/zenodo.6341952
title: MerchiSolla/GPR_Geothermal: raw data

description: 200 MHz and 500 MHz data
DOI: 10.5281/zenodo.7845887
title: GerPS-onto

description: GerPS-onto models the process of a German public service.It was created by extending the BBO with some domain specific concepts.In addition, some concepts are also mapped to the e-Government Core Vocabularies.The ontology was automatically populated with an exemplary German public service by parsing XML-based (XProzess, XDatenfelder files used for describing administrative BPMN-processes and form fields involved in executing the specific service.More details available on: Github



Change Log
DOI: 10.6084/m9.figshare.7125908
title: Additional file 10: of The key genes and pathways related to male sterility of eggplant revealed by comparative transcriptome analysis

description: Table S4. The genes in module â lightcyanâ . (XLSX 173 kb)
DOI: 10.6084/m9.figshare.7125908.v1
title: Additional file 10: of The key genes and pathways related to male sterility of eggplant revealed by comparative transcriptome analysis

description: Table S4. The genes in module â lightcyanâ . (XLSX 173 kb)
DOI: 10.6084/m9.figshare.7125917
title: Additional file 11: of The key genes and pathways related to male sterility of eggplant revealed by comparative transcriptome analysis

description: Table S5. The genes in module â midnightblueâ . (XLSX 323 kb)
DOI: 10.6084/m9.figshare.7125917.v1
title: Additional file 11: of The key genes and pathways related to male sterility of eggplant revealed by comparative transcriptome analysis

description: Table S5. The genes in module â midnightblueâ . (XLSX 323 kb)
DOI: 10.6084/m9.figshare.8174522
title: A simple, real-time assay of horseradish peroxidase using biolayer interferometry

description: Horseradish peroxidase (HRP) isoenzyme C1a is one of the most widely used enzymes for various analytical methods in bioscience research and medical fields. In these fields, real-time monitoring of HRP activity is highly desirable because the utility of HRP as a reporter enzyme would be expanded. In this study, we developed a simple assay system enabling real-time monitoring of HRP activity by using biolayer interferometry (BLI). The HRP activity was quantitatively detected on a BLI sensor chip by tracing a binding response of tyramide, a substrate of HRP, onto an immobilized protein. This system could be applied to analyses related to oxidase activity, as well as to the functional analysis of recombinant HRP. Scheme of HRP assay with BLItz.
DOI: 10.6084/m9.figshare.8174522.v1
title: A simple, real-time assay of horseradish peroxidase using biolayer interferometry

description: Horseradish peroxidase (HRP) isoenzyme C1a is one of the most widely used enzymes for various analytical methods in bioscience research and medical fields. In these fields, real-time monitoring of HRP activity is highly desirable because the utility of HRP as a reporter enzyme would be expanded. In this study, we developed a simple assay system enabling real-time monitoring of HRP activity by using biolayer interferometry (BLI). The HRP activity was quantitatively detected on a BLI sensor chip by tracing a binding response of tyramide, a substrate of HRP, onto an immobilized protein. This system could be applied to analyses related to oxidase activity, as well as to the functional analysis of recombinant HRP. Scheme of HRP assay with BLItz.
DOI: 10.6084/m9.figshare.7125977
title: Additional file 16: of The key genes and pathways related to male sterility of eggplant revealed by comparative transcriptome analysis

description: Table S6. Primers used for qRT-PCR assays. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.7125977.v1
title: Additional file 16: of The key genes and pathways related to male sterility of eggplant revealed by comparative transcriptome analysis

description: Table S6. Primers used for qRT-PCR assays. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.7125980
title: Additional file 1: of The key genes and pathways related to male sterility of eggplant revealed by comparative transcriptome analysis

description: Table S1. The differentially expressed genes between the MS line and its maintainer line. (XLSX 4983 kb)
DOI: 10.6084/m9.figshare.7125980.v1
title: Additional file 1: of The key genes and pathways related to male sterility of eggplant revealed by comparative transcriptome analysis

description: Table S1. The differentially expressed genes between the MS line and its maintainer line. (XLSX 4983 kb)
DOI: 10.6084/m9.figshare.7125992
title: Additional file 2: of The key genes and pathways related to male sterility of eggplant revealed by comparative transcriptome analysis

description: Table S2. The expression patterns of 1,716 shared DEGs. (XLSX 461 kb)
DOI: 10.6084/m9.figshare.7125992.v1
title: Additional file 2: of The key genes and pathways related to male sterility of eggplant revealed by comparative transcriptome analysis

description: Table S2. The expression patterns of 1,716 shared DEGs. (XLSX 461 kb)
DOI: 10.6084/m9.figshare.8174603
title: Deciphering the rules of mRNA structure differentiation in <i>Saccharomyces cerevisiae in vivo</i> and <i>in vitro</i> with deep neural networks

description: The structure of mRNA <i>in vivo</i> is unwound to some extent in response to multiple factors involved in the translation process, resulting in significant differences from the structure of the same mRNA <i>in vitro</i>. In this study, we have proposed a novel application of deep neural networks, named DeepDRU, to predict the degree of mRNA structure unwinding <i>in vivo</i> by fitting five quantifiable features that may affect mRNA folding: ribosome density (RD), minimum folding free energy (MFE), GC content, translation initiation ribosome density (INI) and mRNA structure position (POS). mRNA structures with adjustment of the simulated structural features were designed and then fed into the trained DeepDRU model. We found unique effect regions of these five features on mRNA structure <i>in vivo</i>. Strikingly, INI is the most critical factor affecting the structure of mRNA <i>in vivo</i>, and structural sequence features, including MFE and GC content, have relatively smaller effects. DeepDRU provides a new paradigm for predicting the unwinding capability of mRNA structure <i>in vivo</i>. This improved knowledge about the mechanisms of factors influencing the structural capability of mRNA to unwind will facilitate the design and functional analysis of mRNA structure <i>in vivo</i>.
DOI: 10.6084/m9.figshare.8174603.v1
title: Deciphering the rules of mRNA structure differentiation in <i>Saccharomyces cerevisiae in vivo</i> and <i>in vitro</i> with deep neural networks

description: The structure of mRNA <i>in vivo</i> is unwound to some extent in response to multiple factors involved in the translation process, resulting in significant differences from the structure of the same mRNA <i>in vitro</i>. In this study, we have proposed a novel application of deep neural networks, named DeepDRU, to predict the degree of mRNA structure unwinding <i>in vivo</i> by fitting five quantifiable features that may affect mRNA folding: ribosome density (RD), minimum folding free energy (MFE), GC content, translation initiation ribosome density (INI) and mRNA structure position (POS). mRNA structures with adjustment of the simulated structural features were designed and then fed into the trained DeepDRU model. We found unique effect regions of these five features on mRNA structure <i>in vivo</i>. Strikingly, INI is the most critical factor affecting the structure of mRNA <i>in vivo</i>, and structural sequence features, including MFE and GC content, have relatively smaller effects. DeepDRU provides a new paradigm for predicting the unwinding capability of mRNA structure <i>in vivo</i>. This improved knowledge about the mechanisms of factors influencing the structural capability of mRNA to unwind will facilitate the design and functional analysis of mRNA structure <i>in vivo</i>.
DOI: 10.6084/m9.figshare.7126076
title: Additional file 9: of The key genes and pathways related to male sterility of eggplant revealed by comparative transcriptome analysis

description: Table S3. KEGG enrichment analysis for DEGs at three stages and 1,716 shared DEGs. (XLSX 114 kb)
DOI: 10.6084/m9.figshare.14596849.v1
title: Data from Individual telomere dynamics and their links to life history in a viviparous lizard

description: Emerging patterns suggest telomere dynamics and life history are fundamentally linked in endotherms through life-history traits that mediate the processes underlying telomere attrition. Unlike endotherms, ectotherms maintain the ability to lengthen somatic telomeres throughout life and the link between life-history strategies and ectotherm telomere dynamics is unknown. In a well-characterized model system (<i>Niveoscincus ocellatus</i>), we used long-term longitudinal data to study telomere dynamics across climatically divergent populations. We found longer telomeres in individuals from the cool highlands than those from the warm lowlands at birth and as adults. The key determinant of adult telomere length across populations was telomere length at birth, with population-specific effects of age and growth on adult telomere length. The reproductive effort had no proximate effect on telomere length in either population. Maternal factors influenced telomere length at birth in the warm lowlands but not the cool highlands. Our results demonstrate that life-history traits can have pervasive and context-dependent effects on telomere dynamics in ectotherms both within and between populations. We argue that these telomere dynamics may reflect the populations' different life histories, with the slow-growing cool highland population investing more into telomere lengthening compared to the earlier-maturing warm lowland population.
DOI: 10.6084/m9.figshare.14596849
title: Data from Individual telomere dynamics and their links to life history in a viviparous lizard

description: Emerging patterns suggest telomere dynamics and life history are fundamentally linked in endotherms through life-history traits that mediate the processes underlying telomere attrition. Unlike endotherms, ectotherms maintain the ability to lengthen somatic telomeres throughout life and the link between life-history strategies and ectotherm telomere dynamics is unknown. In a well-characterized model system (<i>Niveoscincus ocellatus</i>), we used long-term longitudinal data to study telomere dynamics across climatically divergent populations. We found longer telomeres in individuals from the cool highlands than those from the warm lowlands at birth and as adults. The key determinant of adult telomere length across populations was telomere length at birth, with population-specific effects of age and growth on adult telomere length. The reproductive effort had no proximate effect on telomere length in either population. Maternal factors influenced telomere length at birth in the warm lowlands but not the cool highlands. Our results demonstrate that life-history traits can have pervasive and context-dependent effects on telomere dynamics in ectotherms both within and between populations. We argue that these telomere dynamics may reflect the populations' different life histories, with the slow-growing cool highland population investing more into telomere lengthening compared to the earlier-maturing warm lowland population.
DOI: 10.6084/m9.figshare.12199409
title: Transposable element sequence library for Neurospora species

description: Neurospora transposable element library modified from Gioti et al (2012) which can be found here: http://fungalgenomes.org/ public/neurospora/data/repeatlib/Gioti_neurospora_repeats.renamed.lib<br>Our current version of the library has been curated to remove LTR and nonLTR sequences from the Gioti_neurospora_repeats.renamed.lib that were identified with LTRharvest that however did not have retroelement domains. For those sequences that were identified with RepeatModeler, host genes were also removed.<br>Additionally, our library includes sequences from NCBI, Selker et al (2003) and Wang et al (2015).<br><br><br>References:<br>Gioti A, Mushegian AA, Strandberg R, et al. Unidirectional evolutionary transitions in fungal mating systems and the role of transposable elements. Molecular Biology and Evolution. 2012;29(10):3215-3226.<br>Selker EU, Tountas NA, Cross SH, et al. The methylated component of the Neurospora crassa genome. Nature. 2003;422(6934):893-897.<br>Wang Y, Smith KM, Taylor JW, et al. Endogenous small RNA mediates meiotic silencing of a novel DNA transposon. G3: Genes|Genomes|Genetics. 2015;5(10):1949-1960.<br>
DOI: 10.6084/m9.figshare.12199409.v1
title: Transposable element sequence library for Neurospora species

description: Neurospora transposable element library modified from Gioti et al (2012) which can be found here: http://fungalgenomes.org/ public/neurospora/data/repeatlib/Gioti_neurospora_repeats.renamed.lib<br>Our current version of the library has been curated to remove LTR and nonLTR sequences from the Gioti_neurospora_repeats.renamed.lib that were identified with LTRharvest that however did not have retroelement domains. For those sequences that were identified with RepeatModeler, host genes were also removed.<br>Additionally, our library includes sequences from NCBI, Selker et al (2003) and Wang et al (2015).<br><br><br>References:<br>Gioti A, Mushegian AA, Strandberg R, et al. Unidirectional evolutionary transitions in fungal mating systems and the role of transposable elements. Molecular Biology and Evolution. 2012;29(10):3215-3226.<br>Selker EU, Tountas NA, Cross SH, et al. The methylated component of the Neurospora crassa genome. Nature. 2003;422(6934):893-897.<br>Wang Y, Smith KM, Taylor JW, et al. Endogenous small RNA mediates meiotic silencing of a novel DNA transposon. G3: Genes|Genomes|Genetics. 2015;5(10):1949-1960.<br>
DOI: 10.6084/m9.figshare.7352207
title: RepeatMasker output tables of repetitive sequences for Neurospora species

description: RepeatMasker output tables (.out and .tbl) of repetitive sequences from high-quality genome assemblies of Neurospora strains, based on PacBio RSII long-read sequencing data, and from reference strains (2508, 2509, 2489). Strains are listed using the strain number from the Fungal Genetics Stock Center (www.fgsc.net) or from the D Jacobson's personal collection (W1426, W1434).<br><br>Strain list:<br><br>FGSC # | Species<br>-------+----------------------<br><br>2508 | Neurospora tetrasperma L6<br>2509 | Neurospora tetrasperma L6<br>10752 | Neurospora tetrasperma L9<br>9045 | Neurospora tetrasperma L7<br>9046 | Neurospora tetrasperma L7<br>2503 | Neurospora tetrasperma L8<br>2504 | Neurospora tetrasperma L8<br>8817 | Neurospora hispaniola<br>W1426 | Neurospora sitophila<br>W1434 | Neurospora sitophila<br>5940 | Neurospora sitophila<br>5941 | Neurospora sitophila<br>2489 | Neurospora crassa<br>8761 | Neurospora intermedia<br>8767 | Neurospora intermedia<br>8807 | Neurospora intermedia<br>10397 | Neurospora metzenbergii<br>8579 | Neurospora discreta<br><br>Reference: <br>Jacobson, D. J., et al. New findings of Neurospora in Europe and comparisons of diversity in temperate climates on continental scales. Mycologia 98, 550–559 (2006). <br><br>For further information on the strains and the genome assemblies, please see:<br>Nguyen et al., (2021) "Transposons and genome dynamics in the fungal genus Neurospora: insights from nearly gapless genome assemblies ", in preparation.<br>