cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.20538063
title: <i>TRPM4</i> gene variation associated with climatic conditions in Chinese cattle

description: The transient receptor potential (TRP) superfamily has been reported to play an important role in heat tolerance pathways. Based on the Bovine Genome Variation Database and Selective Signatures, a missense mutation (NC_037345.1: c.2237A &gt; G: p. His746Arg) (rs209689836) was identified in the transient receptor potential cation channel subfamily M member 4 (<i>TRPM4</i>) gene, a member of the TRP family, corresponding to heat tolerance. Here, we explored the prevalence of this variant in 19 native Chinese cattle (comprised of 404 individuals) to determine its possible association with heat tolerance in Chinese cattle by using PCR and DNA sequencing. The distribution of alleles of NC_037345.1: c.2237A &gt; G: p. His746Arg displays significant geographical differences across native Chinese cattle breeds, consistent with the distribution of indicine and taurine cattle in China. Additionally, the association analysis indicated that the G allele was significantly associated with mean annual temperature (T), relative humidity (RH) and temperature humidity index (THI) (<i>p</i> &lt; .05), suggesting that cattle carrying allele G were distributed in regions with higher T, RH, and THI. In conclusion, our results suggested that the mutation of the <i>TRPM4</i> gene in Chinese cattle might be a candidate locus associated with heat tolerance.
DOI: 10.6084/m9.figshare.20538063.v1
title: <i>TRPM4</i> gene variation associated with climatic conditions in Chinese cattle

description: The transient receptor potential (TRP) superfamily has been reported to play an important role in heat tolerance pathways. Based on the Bovine Genome Variation Database and Selective Signatures, a missense mutation (NC_037345.1: c.2237A &gt; G: p. His746Arg) (rs209689836) was identified in the transient receptor potential cation channel subfamily M member 4 (<i>TRPM4</i>) gene, a member of the TRP family, corresponding to heat tolerance. Here, we explored the prevalence of this variant in 19 native Chinese cattle (comprised of 404 individuals) to determine its possible association with heat tolerance in Chinese cattle by using PCR and DNA sequencing. The distribution of alleles of NC_037345.1: c.2237A &gt; G: p. His746Arg displays significant geographical differences across native Chinese cattle breeds, consistent with the distribution of indicine and taurine cattle in China. Additionally, the association analysis indicated that the G allele was significantly associated with mean annual temperature (T), relative humidity (RH) and temperature humidity index (THI) (<i>p</i> &lt; .05), suggesting that cattle carrying allele G were distributed in regions with higher T, RH, and THI. In conclusion, our results suggested that the mutation of the <i>TRPM4</i> gene in Chinese cattle might be a candidate locus associated with heat tolerance.
DOI: 10.6084/m9.figshare.20476059
title: MiR-495-3p regulates myoblasts proliferation and differentiation through targeting cadherin 2

description: MircoRNAs (miRNAs) play an important role in skeletal muscle development. Previous study had found that miR-495-3p was differentially expressed in fetal and adult goat skeletal muscle, but its function in myogenic proliferation and differentiation are unclear. Herein, we found the expression of miR-495-3p in C2C12 was downregulated during proliferation stage and upregulated during differentiation stage. Functionally, overexpression of miR-495-3p in C2C12 inhibited proliferation, and promoted myogenic differentiation. Mechanistically, the luciferase reporter assay demonstrated that cadherin 2 (<i>CDH2</i>) was a potential target gene of miR-495-3p. Importantly, overexpression of miR-495-3p inhibited <i>CDH2</i> expression. Furthermore, knockdown of <i>CDH2</i> in C2C12 inhibited proliferation and promoted myogenic differentiation. Together, the results showed that miR-495-3p inhibits C2C12 proliferation and promotes myogenic differentiation through targeting <i>CDH2</i>.
DOI: 10.6084/m9.figshare.20476059.v1
title: MiR-495-3p regulates myoblasts proliferation and differentiation through targeting cadherin 2

description: MircoRNAs (miRNAs) play an important role in skeletal muscle development. Previous study had found that miR-495-3p was differentially expressed in fetal and adult goat skeletal muscle, but its function in myogenic proliferation and differentiation are unclear. Herein, we found the expression of miR-495-3p in C2C12 was downregulated during proliferation stage and upregulated during differentiation stage. Functionally, overexpression of miR-495-3p in C2C12 inhibited proliferation, and promoted myogenic differentiation. Mechanistically, the luciferase reporter assay demonstrated that cadherin 2 (<i>CDH2</i>) was a potential target gene of miR-495-3p. Importantly, overexpression of miR-495-3p inhibited <i>CDH2</i> expression. Furthermore, knockdown of <i>CDH2</i> in C2C12 inhibited proliferation and promoted myogenic differentiation. Together, the results showed that miR-495-3p inhibits C2C12 proliferation and promotes myogenic differentiation through targeting <i>CDH2</i>.
DOI: 10.6084/m9.figshare.20476059.v2
title: MiR-495-3p regulates myoblasts proliferation and differentiation through targeting cadherin 2

description: MircoRNAs (miRNAs) play an important role in skeletal muscle development. Previous study had found that miR-495-3p was differentially expressed in fetal and adult goat skeletal muscle, but its function in myogenic proliferation and differentiation are unclear. Herein, we found the expression of miR-495-3p in C2C12 was downregulated during proliferation stage and upregulated during differentiation stage. Functionally, overexpression of miR-495-3p in C2C12 inhibited proliferation, and promoted myogenic differentiation. Mechanistically, the luciferase reporter assay demonstrated that cadherin 2 (<i>CDH2</i>) was a potential target gene of miR-495-3p. Importantly, overexpression of miR-495-3p inhibited <i>CDH2</i> expression. Furthermore, knockdown of <i>CDH2</i> in C2C12 inhibited proliferation and promoted myogenic differentiation. Together, the results showed that miR-495-3p inhibits C2C12 proliferation and promotes myogenic differentiation through targeting <i>CDH2</i>.
DOI: 10.6084/m9.figshare.21202862
title: Cross-population genetic analysis revealed genetic variation and selection in the <i>Ovar-DRB1</i> gene of Indian sheep breeds

description: In sheep, MHC variability is studied widely to explore disease association. The aim of the current study was to explore the genetic diversity of <i>Ovar</i>-DRB diversity across sheep breeds of India. Here, <i>Ovar-</i>DRB1 locus was studied across 20 sheep breeds. DRB1 was amplified (301 bp) and sequenced using a PCR-sequence-based typing approach. Results revealed a high degree of heterozygosity across breeds (mean: 73.99%). Overall mean distance for DRB1 was highest in Sangamneri (0.18) and lowest in Madgyal sheep (0.10). There was a higher rate of transition, across breeds. Further, 39 alleles were isolated in different breeds, out of which 10 were new. To allow easy access and use of the immune-polymorphic database, an online database management system was launched (http://www.mhcdbms.in/). Nucleotide content across breeds for the DRB1 region revealed the richness of GC content (59.26%). Wu-Kabat index revealed vast genetic variation across peptide binding sites (PBS) of DRB1. Residues 6, 66, 69, 52, and 81, were polymorphic showing utility for antigen presentation. All breeds were under positive selection for DRB1 locus (dN &gt; dS). Study revealed the importance of DRB locus diversity for beta chain specifically at PBS across sheep breeds of the Indian subcontinent and presented evidence of positive selection for DRB owing to its evolutionary significance.
DOI: 10.6084/m9.figshare.20601419
title: A long non-coding RNA lnc210 promotes adipogenic differentiation of buffalo intramuscular adipocytes

description: Intramuscular fat (IMF) content is one of the most significant factors influencing beef quality in terms of tenderness, flavor, and juiciness. Thus, internal factors affecting IMF deposition have received considerable attention for decades. In this study, we demonstrated a long non-coding RNA, lnc210, promoted adipogenic differentiation of buffalo intramuscular adipocytes. lnc210 was rich in adipose tissue and showed increased expression with the adipogenic differentiation of buffalo intramuscular adipocytes. lnc210 was mainly expressed in the nucleus of adipocytes. Full-length lnc210 was obtained by rapid amplification of cDNA ends technology. lnc210 overexpression promoted lipid accumulation by upregulating the mRNA expression of peroxisome proliferator-activated receptor gamma (PPARG) and CCAAT enhancer binding protein alpha (C/EBPα) in buffalo intramuscular adipocytes. These results provide a basis for an in-depth analysis of the role of lnc210 in accelerating IMF deposition in buffaloes.
DOI: 10.6084/m9.figshare.21202862.v1
title: Cross-population genetic analysis revealed genetic variation and selection in the <i>Ovar-DRB1</i> gene of Indian sheep breeds

description: In sheep, MHC variability is studied widely to explore disease association. The aim of the current study was to explore the genetic diversity of <i>Ovar</i>-DRB diversity across sheep breeds of India. Here, <i>Ovar-</i>DRB1 locus was studied across 20 sheep breeds. DRB1 was amplified (301 bp) and sequenced using a PCR-sequence-based typing approach. Results revealed a high degree of heterozygosity across breeds (mean: 73.99%). Overall mean distance for DRB1 was highest in Sangamneri (0.18) and lowest in Madgyal sheep (0.10). There was a higher rate of transition, across breeds. Further, 39 alleles were isolated in different breeds, out of which 10 were new. To allow easy access and use of the immune-polymorphic database, an online database management system was launched (http://www.mhcdbms.in/). Nucleotide content across breeds for the DRB1 region revealed the richness of GC content (59.26%). Wu-Kabat index revealed vast genetic variation across peptide binding sites (PBS) of DRB1. Residues 6, 66, 69, 52, and 81, were polymorphic showing utility for antigen presentation. All breeds were under positive selection for DRB1 locus (dN &gt; dS). Study revealed the importance of DRB locus diversity for beta chain specifically at PBS across sheep breeds of the Indian subcontinent and presented evidence of positive selection for DRB owing to its evolutionary significance.
DOI: 10.6084/m9.figshare.20601419.v1
title: A long non-coding RNA lnc210 promotes adipogenic differentiation of buffalo intramuscular adipocytes

description: Intramuscular fat (IMF) content is one of the most significant factors influencing beef quality in terms of tenderness, flavor, and juiciness. Thus, internal factors affecting IMF deposition have received considerable attention for decades. In this study, we demonstrated a long non-coding RNA, lnc210, promoted adipogenic differentiation of buffalo intramuscular adipocytes. lnc210 was rich in adipose tissue and showed increased expression with the adipogenic differentiation of buffalo intramuscular adipocytes. lnc210 was mainly expressed in the nucleus of adipocytes. Full-length lnc210 was obtained by rapid amplification of cDNA ends technology. lnc210 overexpression promoted lipid accumulation by upregulating the mRNA expression of peroxisome proliferator-activated receptor gamma (PPARG) and CCAAT enhancer binding protein alpha (C/EBPα) in buffalo intramuscular adipocytes. These results provide a basis for an in-depth analysis of the role of lnc210 in accelerating IMF deposition in buffaloes.
DOI: 10.6084/m9.figshare.21191018.v1
title: Single nucleotide polymorphisms cumulating to genetic variation for fertility in crossbred (<i>Bos taurus</i> × <i>Bos indicus</i>) bull spermatozoa

description: Spermatozoa from high-fertile (HF) and low-fertile (LF) breeding bulls were subjected to high-throughput next-generation sequencing to identify important Single nucleotide polymorphisms (SNPs) and novel variants associated with fertility. A total of 77,038 genome-wide SNPs were identified, among which, 10,788 were novel variants. A total of 42,290 and 34,748 variants were recorded with 6115 and 4673 novel variants in in HF and LF bulls, respectively. Higher number of SNPs were identified in HF compared to LF bulls. GO analysis of filtered genes with significant variations in HF bulls indicated their involvement in oxidative phosphorylation and metabolic pathways. GO analysis of filtered genes with significant variation in LF bulls revealed their involvement in Ca<sup>2++</sup> ion binding, structural constituent of ribosome, and biological processes like translation and ribosomal small subunit assembly. The study identified SNPs in candidate genes including <i>TPT1</i>, <i>BOLA-DRA</i>, <i>CD74</i>, <i>RPS17</i>, <i>RPS28</i>, <i>RPS29</i>, <i>RPL14</i>, <i>RPL13</i>, and <i>RPS27A</i>, which are linked to sperm functionality, survival, oxidative stress, and bull fertility. The identified SNPs could be used in selection of bulls for high fertility and the variation in these genes could be established as an explanation for the fertility differences in bulls upon validation in large number of bulls.
DOI: 10.6084/m9.figshare.21191018
title: Single nucleotide polymorphisms cumulating to genetic variation for fertility in crossbred (<i>Bos taurus</i> × <i>Bos indicus</i>) bull spermatozoa

description: Spermatozoa from high-fertile (HF) and low-fertile (LF) breeding bulls were subjected to high-throughput next-generation sequencing to identify important Single nucleotide polymorphisms (SNPs) and novel variants associated with fertility. A total of 77,038 genome-wide SNPs were identified, among which, 10,788 were novel variants. A total of 42,290 and 34,748 variants were recorded with 6115 and 4673 novel variants in in HF and LF bulls, respectively. Higher number of SNPs were identified in HF compared to LF bulls. GO analysis of filtered genes with significant variations in HF bulls indicated their involvement in oxidative phosphorylation and metabolic pathways. GO analysis of filtered genes with significant variation in LF bulls revealed their involvement in Ca<sup>2++</sup> ion binding, structural constituent of ribosome, and biological processes like translation and ribosomal small subunit assembly. The study identified SNPs in candidate genes including <i>TPT1</i>, <i>BOLA-DRA</i>, <i>CD74</i>, <i>RPS17</i>, <i>RPS28</i>, <i>RPS29</i>, <i>RPL14</i>, <i>RPL13</i>, and <i>RPS27A</i>, which are linked to sperm functionality, survival, oxidative stress, and bull fertility. The identified SNPs could be used in selection of bulls for high fertility and the variation in these genes could be established as an explanation for the fertility differences in bulls upon validation in large number of bulls.
DOI: 10.5281/zenodo.10849706
title: Dataset for Gas-centered Mutation Testing of Ethereum Smart Contracts

description: This dataset contains additional material for the paper entitled "Gas-centered Mutation Testing of Ethereum Smart Contracts", published by Journal of Software: Evolution and Process. This material includes:



Mutation tool, with the implementation of our gas-centered mutation operators.

Mutation operators - Example, with the code excerpts used to illustrate the gas perturbation caused by the mutation operators.

Smart contract - Accelerator_0b58e2.dir, with the mutants generated in a smart contract and their execution results.

Smart contracts_features.xlsx, with the complete list of smart contracts and their characteristics.
DOI: 10.5281/zenodo.10849707
title: Dataset for Gas-centered Mutation Testing of Ethereum Smart Contracts

description: This dataset contains additional material for the paper entitled "Gas-centered Mutation Testing of Ethereum Smart Contracts", published by Journal of Software: Evolution and Process. This material includes:



Mutation tool, with the implementation of our gas-centered mutation operators.

Mutation operators - Example, with the code excerpts used to illustrate the gas perturbation caused by the mutation operators.

Smart contract - Accelerator_0b58e2.dir, with the mutants generated in a smart contract and their execution results.

Smart contracts_features.xlsx, with the complete list of smart contracts and their characteristics.
DOI: 10.5281/zenodo.10849030
title: 11 April 2019 MRMS Data Subset for Harkema et al. (2024)

description: Subset of Multi-Radar Multi-Sensor (MRMS) data: 3D Reflectivity, Composite Reflectivity, and Isothermal Reflectivity. More specifically, the subset data is between 00 and 16 UTC 11 April 2019. Note: Some time(s) and file(s) maybe be missing between the subset period.
DOI: 10.6084/m9.figshare.14931601.v3
title: Pneumococcal surface adhesion A protein (PsaA) interacts with human Annexin A2 on airway epithelial cells

description: <i>Streptococcus pneumoniae</i> (pneumococcus) is a normal colonizer of the human nasopharynx capable of causing serious invasive disease. Since colonization of the nasopharynx is a prerequisite for progression to invasive diseases, the development of future protein-based vaccines requires an understanding of the intimate interaction of bacterial adhesins with host receptors. In this study, we identified that pneumococcal surface adhesin A (PsaA), a highly conserved pneumococcal protein known to play an important role in colonization of pneumococcus, can interact with Annexin A2 (ANXA2) on Detroit 562 nasopharyngeal epithelial cells. Lentiviral expression of ANXA2 in HEK 293 T/17 cells, which normally express minimal ANXA2, significantly increased pneumococcal adhesion. Blocking of ANXA2 with recombinant PsaA negatively impacted pneumococcal adherence to ANXA2-transduced HEK cells. These results suggest that ANXA2 is an important host cellular receptor for pneumococcal colonization.
DOI: 10.6084/m9.figshare.14931601.v2
title: Pneumococcal surface adhesion A protein (PsaA) interacts with human Annexin A2 on airway epithelial cells

description: <i>Streptococcus pneumoniae</i> (pneumococcus) is a normal colonizer of the human nasopharynx capable of causing serious invasive disease. Since colonization of the nasopharynx is a prerequisite for progression to invasive diseases, the development of future protein-based vaccines requires an understanding of the intimate interaction of bacterial adhesins with host receptors. In this study, we identified that pneumococcal surface adhesin A (PsaA), a highly conserved pneumococcal protein known to play an important role in colonization of pneumococcus, can interact with Annexin A2 (ANXA2) on Detroit 562 nasopharyngeal epithelial cells. Lentiviral expression of ANXA2 in HEK 293 T/17 cells, which normally express minimal ANXA2, significantly increased pneumococcal adhesion. Blocking of ANXA2 with recombinant PsaA negatively impacted pneumococcal adherence to ANXA2-transduced HEK cells. These results suggest that ANXA2 is an important host cellular receptor for pneumococcal colonization.
DOI: 10.6084/m9.figshare.25452274
title: Supplementary Table 2. Endocannabinoid system-associated genes of interest assessed in bulk RNA-seq analysis following canonical and inflammatory lipolysis in dairy cows' adipocytes.

description: Genes of interest were divided into functional group within the endocannabinoid system and subdivided by role for the analysis of sequencing data. Gene identifiers (Ensembl ID), chromosome number (Chr.), location (gene start, end), strand (positive strand, +; negative strand, -), gene length (in base pairs), and description of genes of interest are included. <i>Abbreviations:</i><i> </i><i>eCB, </i><i>endocannabinoid; </i><i>NAE, N</i><i>-acylethanolamine; </i><i>2-AG</i><i>, 2-arachidonoyl glycerol; </i><i>FFA</i><i>, free fatty acid; </i><i>PL</i><i>, phospholipid. </i>
DOI: 10.5281/zenodo.10714017
title: Associated data from: An end-to-end workflow to study newly synthesized mRNA following rapid protein depletion in Saccharomyces cerevisiae

description: This dataset includes two custom BED files described in "An end-to-end workflow to study newly synthesized mRNA following rapid protein depletion in Saccharomyces cerevisiae" (Ridenour and Donczew, submitted), which were used to define counting windows for processing SLAM-seq data in SLAM-DUNK (version 0.4.3) [1]. The BED files contain all annotated open reading frames (ORFs) in the Saccharomyces cerevisiae genome or the Schizosaccharomyces pombe genome and were created using BEDOPS (version 2.4.3) [2]. All ORFs were then extended 250 bp beyond their stop position to capture 3′ untranslated regions (UTRs) using SAMtools (version 1.14) [3] and BEDTools (version 2.30.0) [4]. The reference genome annotations for S. cerevisiae strain S288C (version R64-3-1, RefSeq Assembly GCF_000146045.2) and S. pombe strain 972h- (version ASM294v2, RefSeq Assembly GCF_000002945.1) were retrieved from the NCBI Datasets repository. The S. cerevisiae chromosome names were modified to reflect standard nomenclature (https://www.yeastgenome.org/).
DOI: 10.5281/zenodo.10714018
title: Associated data from: An end-to-end workflow to study newly synthesized mRNA following rapid protein depletion in Saccharomyces cerevisiae

description: This dataset includes two custom BED files described in "An end-to-end workflow to study newly synthesized mRNA following rapid protein depletion in Saccharomyces cerevisiae" (Ridenour and Donczew, submitted), which were used to define counting windows for processing SLAM-seq data in SLAM-DUNK (version 0.4.3) [1]. The BED files contain all annotated open reading frames (ORFs) in the Saccharomyces cerevisiae genome or the Schizosaccharomyces pombe genome and were created using BEDOPS (version 2.4.3) [2]. All ORFs were then extended 250 bp beyond their stop position to capture 3′ untranslated regions (UTRs) using SAMtools (version 1.14) [3] and BEDTools (version 2.30.0) [4]. The reference genome annotations for S. cerevisiae strain S288C (version R64-3-1, RefSeq Assembly GCF_000146045.2) and S. pombe strain 972h- (version ASM294v2, RefSeq Assembly GCF_000002945.1) were retrieved from the NCBI Datasets repository. The S. cerevisiae chromosome names were modified to reflect standard nomenclature (https://www.yeastgenome.org/).
DOI: 10.6084/m9.figshare.16837410
title: How the Trick is Done – Conditions of Success in Entrepreneurial Digital Journalism

description: Entrepreneurial journalism is often ascribed the potential to partly close the supply gap in digital journalism caused by the effects of digitization. Decreasing fixed costs on the production stage, in particular, have enabled smaller entities, entrepreneurs and start-ups to produce high quality journalistic content. While there is a broad stream of literature on entrepreneurial success in general, empirical research says little about the reasons for digital journalistic entrepreneurs’ success (or lack thereof). This study aims at empirically investigating success conditions associated with entrepreneurship in the digital news business. Seven broader “super”-conditional prerequisites are considered: Experience, skills, personality, product, business model, company organization, and broader environment. The data, collected through 49 interviews with digital journalistic entrepreneurs in Germany, is analysed with Qualitative Comparative Analysis (QCA), a set theoretical method to determine necessity/sufficiency of preformulated conditions for a respective outcome (i.e., entrepreneurial (non-)success). The results indicate high importance of, first, the experience of the founder, and, second, the functioning organization of the company, while, interestingly, third, only absence of support from the broader environment and/or government contributed to the success.