cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6616256.v1
title: Additional file 3: of Genetic and transcriptomic analyses provide new insights on the early antiviral response to VHSV in resistant and susceptible rainbow trout

description: Description of genes significantly up- or down- regulated by incubation with attenuated VHSV in B57 or A22 cells (adj. p &lt; 0.01, FC &gt; 2,5 or &lt; 0.4). (XLSX 1214 kb)
DOI: 10.6084/m9.figshare.7664846
title: Additional file 5: of Genome-wide identification and expression analysis of expansin gene family in common wheat (Triticum aestivum L.)

description: Table S3. Coevolution sites in wheat expansin (All sites are located on the reference sequence TaEXPA1-A based on the multiple alignment results). (XLSX 10 kb)
DOI: 10.6084/m9.figshare.7664846.v1
title: Additional file 5: of Genome-wide identification and expression analysis of expansin gene family in common wheat (Triticum aestivum L.)

description: Table S3. Coevolution sites in wheat expansin (All sites are located on the reference sequence TaEXPA1-A based on the multiple alignment results). (XLSX 10 kb)
DOI: 10.6084/m9.figshare.7664849
title: Additional file 6: of Genome-wide identification and expression analysis of expansin gene family in common wheat (Triticum aestivum L.)

description: Table S4 Cis-element analysis of 2000 bp nucleotide sequences data upstream of the translation initiation codon of expansin genes. (XLSX 141 kb)
DOI: 10.6084/m9.figshare.7664849.v1
title: Additional file 6: of Genome-wide identification and expression analysis of expansin gene family in common wheat (Triticum aestivum L.)

description: Table S4 Cis-element analysis of 2000 bp nucleotide sequences data upstream of the translation initiation codon of expansin genes. (XLSX 141 kb)
DOI: 10.6084/m9.figshare.7664855
title: Additional file 7: of Genome-wide identification and expression analysis of expansin gene family in common wheat (Triticum aestivum L.)

description: Table S5. The RNA-Seq atlas data of the expansin genes. (XLSX 48 kb)
DOI: 10.6084/m9.figshare.7664855.v1
title: Additional file 7: of Genome-wide identification and expression analysis of expansin gene family in common wheat (Triticum aestivum L.)

description: Table S5. The RNA-Seq atlas data of the expansin genes. (XLSX 48 kb)
DOI: 10.6084/m9.figshare.6616277
title: Additional file 4: of Genetic and transcriptomic analyses provide new insights on the early antiviral response to VHSV in resistant and susceptible rainbow trout

description: List of rainbow trout genes significantly induced after incubation with inactivated VHSV (adj. p &lt; 0.01, FC &gt; 2,5 or &lt; 0.4), having human putative homolog(s) registered in the Interferome database (Section type I IFN) [ http://interferome.org/interferome/home.jspx ]. (XLSX 208 kb)
DOI: 10.6084/m9.figshare.6616277.v1
title: Additional file 4: of Genetic and transcriptomic analyses provide new insights on the early antiviral response to VHSV in resistant and susceptible rainbow trout

description: List of rainbow trout genes significantly induced after incubation with inactivated VHSV (adj. p &lt; 0.01, FC &gt; 2,5 or &lt; 0.4), having human putative homolog(s) registered in the Interferome database (Section type I IFN) [ http://interferome.org/interferome/home.jspx ]. (XLSX 208 kb)
DOI: 10.6084/m9.figshare.6616301
title: Additional file 5: of Genetic and transcriptomic analyses provide new insights on the early antiviral response to VHSV in resistant and susceptible rainbow trout

description: Description of genes significantly up- or down- regulated in B57 naïve cells compared to A22 naïve cells. (XLSX 878 kb)
DOI: 10.6084/m9.figshare.6616301.v1
title: Additional file 5: of Genetic and transcriptomic analyses provide new insights on the early antiviral response to VHSV in resistant and susceptible rainbow trout

description: Description of genes significantly up- or down- regulated in B57 naïve cells compared to A22 naïve cells. (XLSX 878 kb)
DOI: 10.6084/m9.figshare.19967973
title: A systematic scoping review of communication skills training in medical schools between 2000 and 2020

description: Communication skills training (CST) remains poorly represented and prioritised in medical schools despite its importance. A systematic scoping review (SSR) of CST is proposed to better appreciate current variability in their structure, content, and assessment. This is to guide their future design in medical school curricula. The Systematic Evidence-Based Approach (SEBA) was used to guide concurrent SSRs of teaching and assessment in CST. After independent database searches, concurrent thematic and content analysis of included articles were conducted separately. Resultant themes/categories were combined via the jigsaw perspective to provide a more holistic view of the data. These were then compared to tabulated summaries of the included articles to create funnelled domains. 52,300 papers were identified, 150 full-text articles included, and four funnelled domains were identified: Indications, Design, Assessment, and Barriers and Enablers of CST. CSTs confer numerous benefits to physicians and patients. It saw increased confidence, improved diagnostic capabilities and better clinical management, as well as greater patient satisfaction and treatment compliance. Skills may be divided into core, prerequisite competencies, and advanced skills pertinent to more challenging and nuanced scenarios – such as population or setting-specific situations. CST teaching and assessment modalities were found to align with Miller’s Pyramid, with didactic teaching gradually infused with experiential approaches to enhance their understanding and integration. A plethora of CST frameworks, teaching and assessment methods were identified and are presented together. While variable in approach, content and assessment, CST in medical schools often employ stage-based curricula to instil competency-based topics of increasing complexity throughout medical school education. This process builds on the application of prior knowledge and skills, influencing practice and, potentially, the students’ professional identity formation. In addition, the institution plays a critical role in overseeing training, ensuring longitudinal guidance and holistic assessments of the students’ progress.
DOI: 10.6084/m9.figshare.19967973.v1
title: A systematic scoping review of communication skills training in medical schools between 2000 and 2020

description: Communication skills training (CST) remains poorly represented and prioritised in medical schools despite its importance. A systematic scoping review (SSR) of CST is proposed to better appreciate current variability in their structure, content, and assessment. This is to guide their future design in medical school curricula. The Systematic Evidence-Based Approach (SEBA) was used to guide concurrent SSRs of teaching and assessment in CST. After independent database searches, concurrent thematic and content analysis of included articles were conducted separately. Resultant themes/categories were combined via the jigsaw perspective to provide a more holistic view of the data. These were then compared to tabulated summaries of the included articles to create funnelled domains. 52,300 papers were identified, 150 full-text articles included, and four funnelled domains were identified: Indications, Design, Assessment, and Barriers and Enablers of CST. CSTs confer numerous benefits to physicians and patients. It saw increased confidence, improved diagnostic capabilities and better clinical management, as well as greater patient satisfaction and treatment compliance. Skills may be divided into core, prerequisite competencies, and advanced skills pertinent to more challenging and nuanced scenarios – such as population or setting-specific situations. CST teaching and assessment modalities were found to align with Miller’s Pyramid, with didactic teaching gradually infused with experiential approaches to enhance their understanding and integration. A plethora of CST frameworks, teaching and assessment methods were identified and are presented together. While variable in approach, content and assessment, CST in medical schools often employ stage-based curricula to instil competency-based topics of increasing complexity throughout medical school education. This process builds on the application of prior knowledge and skills, influencing practice and, potentially, the students’ professional identity formation. In addition, the institution plays a critical role in overseeing training, ensuring longitudinal guidance and holistic assessments of the students’ progress.
DOI: 10.6084/m9.figshare.6616319
title: Additional file 6: of Genetic and transcriptomic analyses provide new insights on the early antiviral response to VHSV in resistant and susceptible rainbow trout

description: Mapping of DEG and innate immune-related genes on the rainbow trout reference genome. (XLSX 17 kb)
DOI: 10.6084/m9.figshare.6616319.v1
title: Additional file 6: of Genetic and transcriptomic analyses provide new insights on the early antiviral response to VHSV in resistant and susceptible rainbow trout

description: Mapping of DEG and innate immune-related genes on the rainbow trout reference genome. (XLSX 17 kb)
DOI: 10.6084/m9.figshare.5567746
title: Garnet amphibolites from the Ganzi–Litang fault zone, eastern Tibetan Plateau: mineralogy, geochemistry, and implications for evolution of the eastern Palaeo-Tethys Realm

description: The Ganzi<i>–</i>Litang fault zone, an outstanding tectonic element in the eastern Tibetan Plateau has been intensively debated as an in-situ suture zone marking relict of a subducted Palaeo-Tethyan oceanic crust or a failed intracontinental rift. This paper reports the garnet amphibolites discovered along the Ganzi–Litang fault zone, eastern Tibetan Plateau. These garnet amphibolites are characterized by the garnet–hornblende–rutile–sphene–plagioclase–quartz assemblage. Conventional geothermobarometry figures out the metamorphic temperature and pressure conditions at 582–626°C and 1.61–1.82 GPa, respectively. Geochemical analysis (no Nb–Ta deletions and left-inclined to flat patterns of rare-earth elements) indicates that the garnet amphibolites could represent metamorphic product of the mid-ocean-ridge (MORB)-type mafic rocks that were contaminated by a mantle plume. The protolith of the garnet amphibolites was dated at 236 Ma using in-situ U–Pb zircon method, and the retrograde metamorphism was dated at 218 Ma using in-situ U–Pb sphene method. A comprehensive analysis combined with the development of the Palaeo-Tethys Ocean and the Yidun arc through geologic time indicates a Triassic to Early Jurassic age (236–195 Ma) for the metamorphism of the garnet amphibolites. The low geothermal gradient of 9.8ºC/km and the N-MORB nature of the garnet amphibolites suggest a subduction-zone environment for the high-pressure metamorphism. Therefore, the Ganzi<i>–</i>Litang fault zone is a Palaeo-Tethyan suture separating the Yidun arc and the Songpan–Ganzi terrane, representing the relics of a branch of the Palaeo-Tethys Ocean that was contaminated by a mantle plume.
DOI: 10.6084/m9.figshare.5567746.v1
title: Garnet amphibolites from the Ganzi–Litang fault zone, eastern Tibetan Plateau: mineralogy, geochemistry, and implications for evolution of the eastern Palaeo-Tethys Realm

description: The Ganzi<i>–</i>Litang fault zone, an outstanding tectonic element in the eastern Tibetan Plateau has been intensively debated as an in-situ suture zone marking relict of a subducted Palaeo-Tethyan oceanic crust or a failed intracontinental rift. This paper reports the garnet amphibolites discovered along the Ganzi–Litang fault zone, eastern Tibetan Plateau. These garnet amphibolites are characterized by the garnet–hornblende–rutile–sphene–plagioclase–quartz assemblage. Conventional geothermobarometry figures out the metamorphic temperature and pressure conditions at 582–626°C and 1.61–1.82 GPa, respectively. Geochemical analysis (no Nb–Ta deletions and left-inclined to flat patterns of rare-earth elements) indicates that the garnet amphibolites could represent metamorphic product of the mid-ocean-ridge (MORB)-type mafic rocks that were contaminated by a mantle plume. The protolith of the garnet amphibolites was dated at 236 Ma using in-situ U–Pb zircon method, and the retrograde metamorphism was dated at 218 Ma using in-situ U–Pb sphene method. A comprehensive analysis combined with the development of the Palaeo-Tethys Ocean and the Yidun arc through geologic time indicates a Triassic to Early Jurassic age (236–195 Ma) for the metamorphism of the garnet amphibolites. The low geothermal gradient of 9.8ºC/km and the N-MORB nature of the garnet amphibolites suggest a subduction-zone environment for the high-pressure metamorphism. Therefore, the Ganzi<i>–</i>Litang fault zone is a Palaeo-Tethyan suture separating the Yidun arc and the Songpan–Ganzi terrane, representing the relics of a branch of the Palaeo-Tethys Ocean that was contaminated by a mantle plume.
DOI: 10.6084/m9.figshare.6616334
title: Additional file 7: of Genetic and transcriptomic analyses provide new insights on the early antiviral response to VHSV in resistant and susceptible rainbow trout

description: Mapping of candidates genes and microsatellite/SNP markers on the two versions of the rainbow trout genome. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.6616334.v1
title: Additional file 7: of Genetic and transcriptomic analyses provide new insights on the early antiviral response to VHSV in resistant and susceptible rainbow trout

description: Mapping of candidates genes and microsatellite/SNP markers on the two versions of the rainbow trout genome. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.7664936
title: MOESM2 of Heterologous phosphoketolase expression redirects flux towards acetate, perturbs sugar phosphate pools and increases respiratory demand in Saccharomyces cerevisiae

description: Additional file 2. Differential gene expression analysis data.
DOI: 10.6084/m9.figshare.7664936.v1
title: MOESM2 of Heterologous phosphoketolase expression redirects flux towards acetate, perturbs sugar phosphate pools and increases respiratory demand in Saccharomyces cerevisiae

description: Additional file 2. Differential gene expression analysis data.
DOI: 10.6084/m9.figshare.12569336
title: Additional file 1 of Chi-miR-30b-5p inhibits dermal papilla cells proliferation by targeting CaMKIIδ gene in cashmere goat

description: Additional file 1. List of sRNA quantity and type after length screening (18-35 nt) and mapped to goat genome.
DOI: 10.6084/m9.figshare.12569336.v1
title: Additional file 1 of Chi-miR-30b-5p inhibits dermal papilla cells proliferation by targeting CaMKIIδ gene in cashmere goat

description: Additional file 1. List of sRNA quantity and type after length screening (18-35 nt) and mapped to goat genome.
DOI: 10.6084/m9.figshare.12383537
title: Optimal Distributed Subsampling for Maximum Quasi-Likelihood Estimators With Massive Data

description: Nonuniform subsampling methods are effective to reduce computational burden and maintain estimation efficiency for massive data. Existing methods mostly focus on subsampling with replacement due to its high computational efficiency. If the data volume is so large that nonuniform subsampling probabilities cannot be calculated all at once, then subsampling with replacement is infeasible to implement. This article solves this problem using Poisson subsampling. We first derive optimal Poisson subsampling probabilities in the context of quasi-likelihood estimation under the A- and L-optimality criteria. For a practically implementable algorithm with approximated optimal subsampling probabilities, we establish the consistency and asymptotic normality of the resultant estimators. To deal with the situation that the full data are stored in different blocks or at multiple locations, we develop a distributed subsampling framework, in which statistics are computed simultaneously on smaller partitions of the full data. Asymptotic properties of the resultant aggregated estimator are investigated. We illustrate and evaluate the proposed strategies through numerical experiments on simulated and real datasets. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.12383537.v2
title: Optimal Distributed Subsampling for Maximum Quasi-Likelihood Estimators With Massive Data

description: Nonuniform subsampling methods are effective to reduce computational burden and maintain estimation efficiency for massive data. Existing methods mostly focus on subsampling with replacement due to its high computational efficiency. If the data volume is so large that nonuniform subsampling probabilities cannot be calculated all at once, then subsampling with replacement is infeasible to implement. This article solves this problem using Poisson subsampling. We first derive optimal Poisson subsampling probabilities in the context of quasi-likelihood estimation under the A- and L-optimality criteria. For a practically implementable algorithm with approximated optimal subsampling probabilities, we establish the consistency and asymptotic normality of the resultant estimators. To deal with the situation that the full data are stored in different blocks or at multiple locations, we develop a distributed subsampling framework, in which statistics are computed simultaneously on smaller partitions of the full data. Asymptotic properties of the resultant aggregated estimator are investigated. We illustrate and evaluate the proposed strategies through numerical experiments on simulated and real datasets. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.7664960
title: MOESM2 of Baduanjin exerts anti-diabetic and anti-depression effects by regulating the expression of mRNA, lncRNA, and circRNA

description: Additional file 2. Differentially expressed mRNAs.
DOI: 10.6084/m9.figshare.7664960.v1
title: MOESM2 of Baduanjin exerts anti-diabetic and anti-depression effects by regulating the expression of mRNA, lncRNA, and circRNA

description: Additional file 2. Differentially expressed mRNAs.
DOI: 10.6084/m9.figshare.7664969
title: MOESM3 of Baduanjin exerts anti-diabetic and anti-depression effects by regulating the expression of mRNA, lncRNA, and circRNA

description: Additional file 3. Â Differentially expressed circRNAs.
DOI: 10.6084/m9.figshare.7664969.v1
title: MOESM3 of Baduanjin exerts anti-diabetic and anti-depression effects by regulating the expression of mRNA, lncRNA, and circRNA

description: Additional file 3. Â Differentially expressed circRNAs.
DOI: 10.6084/m9.figshare.7664972
title: MOESM4 of Baduanjin exerts anti-diabetic and anti-depression effects by regulating the expression of mRNA, lncRNA, and circRNA

description: Additional file 4. Differentially expressed lncRNAs.
DOI: 10.6084/m9.figshare.7664972.v1
title: MOESM4 of Baduanjin exerts anti-diabetic and anti-depression effects by regulating the expression of mRNA, lncRNA, and circRNA

description: Additional file 4. Differentially expressed lncRNAs.
DOI: 10.6084/m9.figshare.12383570
title: Spike-and-Slab Group Lassos for Grouped Regression and Sparse Generalized Additive Models

description: <b><i>Abstract–</i>We introduce the spike-and-slab group lasso (SSGL) for Bayesian estimation and variable selection in linear regression with grouped variables. We further extend the SSGL to sparse generalized additive models (GAMs), thereby introducing the first nonparametric variant of the spike-and-slab lasso methodology. Our model simultaneously performs group selection and estimation, while our fully Bayes treatment of the mixture proportion allows for model complexity control and automatic self-adaptivity to different levels of sparsity. We develop theory to uniquely characterize the global posterior mode under the SSGL and introduce a highly efficient block coordinate ascent algorithm for maximum a posteriori estimation. We further employ de-biasing methods to provide uncertainty quantification of our estimates. Thus, implementation of our model avoids the computational intensiveness of Markov chain Monte Carlo in high dimensions. We derive posterior concentration rates for both grouped linear regression and sparse GAMs when the number of covariates grows at nearly exponential rate with sample size. Finally, we illustrate our methodology through extensive simulations and data analysis. Supplementary materials for this article are available online.</b>
DOI: 10.6084/m9.figshare.12383570.v2
title: Spike-and-Slab Group Lassos for Grouped Regression and Sparse Generalized Additive Models

description: <b><i>Abstract–</i>We introduce the spike-and-slab group lasso (SSGL) for Bayesian estimation and variable selection in linear regression with grouped variables. We further extend the SSGL to sparse generalized additive models (GAMs), thereby introducing the first nonparametric variant of the spike-and-slab lasso methodology. Our model simultaneously performs group selection and estimation, while our fully Bayes treatment of the mixture proportion allows for model complexity control and automatic self-adaptivity to different levels of sparsity. We develop theory to uniquely characterize the global posterior mode under the SSGL and introduce a highly efficient block coordinate ascent algorithm for maximum a posteriori estimation. We further employ de-biasing methods to provide uncertainty quantification of our estimates. Thus, implementation of our model avoids the computational intensiveness of Markov chain Monte Carlo in high dimensions. We derive posterior concentration rates for both grouped linear regression and sparse GAMs when the number of covariates grows at nearly exponential rate with sample size. Finally, we illustrate our methodology through extensive simulations and data analysis. Supplementary materials for this article are available online.</b>
DOI: 10.6084/m9.figshare.11859297
title: Additional file 2 of Circular RNA CRIM1 functions as a ceRNA to promote nasopharyngeal carcinoma metastasis and docetaxel chemoresistance through upregulating FOXQ1

description: Additional file 2. List of circRNA isoforms derived from the CRIM1 gene based on circBase database.
DOI: 10.6084/m9.figshare.11859297.v1
title: Additional file 2 of Circular RNA CRIM1 functions as a ceRNA to promote nasopharyngeal carcinoma metastasis and docetaxel chemoresistance through upregulating FOXQ1

description: Additional file 2. List of circRNA isoforms derived from the CRIM1 gene based on circBase database.
DOI: 10.6084/m9.figshare.12569348
title: Additional file 3 of Chi-miR-30b-5p inhibits dermal papilla cells proliferation by targeting CaMKIIδ gene in cashmere goat

description: Additional file 3. The information of mapped annotated miRNA.
DOI: 10.6084/m9.figshare.12569348.v1
title: Additional file 3 of Chi-miR-30b-5p inhibits dermal papilla cells proliferation by targeting CaMKIIδ gene in cashmere goat

description: Additional file 3. The information of mapped annotated miRNA.
DOI: 10.5281/zenodo.10673385
title: Lexicostatistics Calculation on Manggarai and Bima Languages: A Comparative Historical Linguistics Study
DOI: 10.5281/zenodo.10673386
title: Lexicostatistics Calculation on Manggarai and Bima Languages: A Comparative Historical Linguistics Study
DOI: 10.5281/zenodo.10673962
title: Lexicostatistics Calculation on Manggarai and Bima Languages: A Comparative Historical Linguistics Study
DOI: 10.5281/zenodo.10677049
title: Lexicostatistics Calculation on Manggarai and Bima Languages: A Comparative Historical Linguistics Study
DOI: 10.5281/zenodo.10677379
title: Lexicostatistics Calculation on Manggarai and Bima Languages: A Comparative Historical Linguistics Study