cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.11369403.v1
title: RNA-seq transcriptome of Pseudomonas putida KT2440 subsisting on glycerol as sole carbon source

description: Glycerol is a potential carbon source for the cultivation of various bacterial species given the presence of metabolic pathways for its catabolism. But, its use lags behind the preferred carbon source, glucose. However, glycerol is increasingly being produced as a byproduct in biodiesel production, and thus, efforts have been expended in exploring the use of glycerol as carbon source in support of microbial fermentation. This work hopes to make a contribution in this direction by analysing the RNA-seq transcriptome of <i>Pseudomonas putida</i> KT2440 (ArrayExpress accession number: E-GEOD-46491) cultivated with glycerol as sole carbon source. Although <i>P. putida</i> KT2440 is commonly used in environmental remediation as opposed to biotechnology, it nevertheless might inform the metabolism of glycerol given the versatile metabolism encoded by a relatively large genome. Buttressed by a dataset comprising 0.7 million reads, the RNA-seq transcriptome of <i>P. putida</i> KT2440 showed a preponderance of non-ribosomal peptide synthesis enzymes being highly expressed together with cell surface proteins. High expression of non-ribosomal peptide synthetase is unusual given that RNA was extracted from cells in the mid-exponential phase. In total, the most highly expressed genes were: non-ribosomal peptide synthetase <i>pvdL</i>, surface adhesion protein, putative surface adhesion protein, quinoprotein ethanol dehydrogenase <i>qedH-I</i>, non-ribosomal peptide synthetase <i>pvdD</i>, aldehyde dehydrogenase <i>aldB-II</i>, diaminobutyrate-2-oxoglutarate transaminase <i>pvdH</i>, ribosome modulation factor <i>rmf</i>, non-ribosomal peptide synthetase <i>pvdJ</i>, and L-ornithine 5-monooxygenase <i>pvdA</i>. Overall, much remains to be deciphered from the RNA-seq transcriptome of <i>P. putida</i> KT2440 utilising glycerol as sole carbon source. Even though <i>P. putida</i> KT2440 is not a microbial cell factory, its gene expression pattern while utilising glycerol may still offer clues to the activation of specific branches of central carbon metabolism that have not been observed to date. <br><br>
DOI: 10.6084/m9.figshare.11369391
title: Elemental compositions of deionized water and tap water

description: Quality of water used in experiments is critical for overall experiment success. Deionized water is the de facto water source for many experiments in science ranging from chemistry to biology. However, there are few reports of elemental composition of deionized water and tap water in the literature. In this short report, the elemental composition of deionized water and tap water from a laboratory was determined by inductively coupled plasma mass spectrometry (ICP-MS). Results indicated that concentrations of various elements in both deionized water and tap water were in the parts per billion (ppb) range, except for sodium, potassium, calcium and magnesium. Overall, quality of deionized water was good and suitable for use in experiments.<br><br>
DOI: 10.6084/m9.figshare.11369364
title: How Flight Feathers Stick Together to Form a Continuous Morphing Wing Online Data

description: Data for submission of "How Flight Feathers Stick Together to Form a Continuous Morphing Wing Online Data." Authors: L.Y. Matloff, E. Chang, T.J. Feo, L. Jeffries, A. K. Stowers, C. Thomson, D. Lentink.
DOI: 10.6084/m9.figshare.11369385
title: The Effect of Age outcomes in with Severe Acute Pancreatitis.sav

description: We performed a retrospective case-control study. All patients’ information came from database of MIMIC-III. After matched for etiology of pancreatitis, body mass index and medical comorbidities between groups, 152 patients were diagnosed with severe acute pancreatitis, according to the revised Atlanta classification 2012.
DOI: 10.6084/m9.figshare.11369385.v1
title: The Effect of Age outcomes in with Severe Acute Pancreatitis.sav

description: We performed a retrospective case-control study. All patients’ information came from database of MIMIC-III. After matched for etiology of pancreatitis, body mass index and medical comorbidities between groups, 152 patients were diagnosed with severe acute pancreatitis, according to the revised Atlanta classification 2012.
DOI: 10.6084/m9.figshare.11369358
title: Phenotypes.rar

description: phenotypes of f2 chicken
DOI: 10.6084/m9.figshare.11369355
title: Turkish General Elections 2002-2018

description: Simulated results of the 2002 to 2018 Turkish elections with the threshold, malapportionment, and the threshold and malapportionment combined removed. The Gallagher Index is used to assess the proportionality of each simulation and is compared to the Gallagher Index of the actual result of each election.
DOI: 10.6084/m9.figshare.11369358.v1
title: Phenotypes.rar

description: phenotypes of f2 chicken
DOI: 10.6084/m9.figshare.11369352
title: genotypes of f2 chicken data

description: genotypes of f2 chicken
DOI: 10.6084/m9.figshare.11369268
title: Data and R Code for Carter et al. 2020. Development of new food-sharing relationships in vampire bats. Current Biology.

description: These are data and R code for the paper Carter et al. 2020. Development of new food-sharing relationships in vampire bats. Current Biology.<br>"Genotypes.csv" are the microsatellite genotypes used to assign estimate genetic relatedness.<br>"Kinship.csv" are the estimates of genetic relatedness based on genotypes and known maternal kinship.<br>"new_bonds_data.RData" are the data on rates of food sharing and social grooming among bats.<br>"new_bonds_analysis23.R" is the R script for analyzing these data.
DOI: 10.6084/m9.figshare.11369202
title: Sequences information of suspected eggs from the seagrass beds of Liusha Bay, Li'an gang and Xincun Bay, China

description: The sequences (.seq) and the ABI documents (.ab1) names begin with LSB, LAG and XCB represent the suspected eggs collected in the seagrass beds of the Liusha Bay (109.9215°E, 20.4344°N) in Guangdong province, the Li'an gang (110.0528°E, 18.4105°N) and the Xincun Bay (109.9760°E, 18.4089°N) in Hainan province, respectively. The Guangdong and Hainan are the major Chinese provinces with natural seagrass distribution. The primers employed in PCR and sequencing are LCO1490/HCO2198. The species names shown in the .seq file names were determined after comparing with database of the NCBI and BOLD systems.
DOI: 10.6084/m9.figshare.11369220
title: Gene database of Saccharomyces cerevisiae S288C

description: Much of genome and modern biology research is done with reductionist approaches using model organisms. <i>Saccharomyces cerevisiae</i> S288C is one such model organism that serves as a platform for investigating eukaryotic cellular processes as well as gene regulation and genetics. Although the genome of <i>S. cerevisiae</i> S288C was sequenced early in the genomic era, its compendium of gene identifier, gene function and gene sequence remain hidden from view of biologists without access to bioinformatic tools. More importantly, the genome of <i>S. cerevisiae</i> S288C is distributed across 16 chromosomes, which makes the task of searching for particular gene and its sequence more difficult. This work sought to ameliorate the above challenge by using an in-house MATLAB software to parse the annotated genome sequence files of <i>S. cerevisiae </i>S288C obtained from Genbank. Both gene identifier and gene sequence were catalogued in an Excel database for all genes in the genome of <i>S. cerevisiae </i>S288C. Overall, the presented gene database should provide ease of access to gene information of <i>S. cerevisiae</i> S288C; thereby, serving as a useful tool in molecular cloning and genome editing studies aiming to understand fundamental cellular processes and biotechnological potential of this important eukaryotic model organism.<br><br>
DOI: 10.6084/m9.figshare.11369199
title: CTCF Motif Locations

description: CTCF Motifs were downloaded from:<br>http://compbio.mit.edu/encode-motifs/<br>The following citation should be cited when using these motifs:<br>Kheradpour P, Kellis M. Systematic discovery and characterization of regulatory motifs in ENCODE TF binding experiments. Nucleic Acids Res. 2014 Mar;42(5):2976-87.<br>For all analysis in our paper, we utilized the CTCF_known1 motif.<br>This file contains five columns:Column 1: Motif nameColumn 2: ChromsomeColumn 3: Start coordinateColumn 4: End coordinateColumn 5: Strand<br>
DOI: 10.6084/m9.figshare.11369355.v1
title: Turkish General Elections 2002-2018

description: Datasets of each Turkish election from 2002 to 2018 assessing the proportionality of each election were the threshold, malapportionment, and the threshold and malapportionment combined removed. The Gallagher Index is used to assess the proportionality of each simulation and is compared to the Gallagher Index of the actual result of each election.
DOI: 10.6084/m9.figshare.11369199.v1
title: CTCF Motif Locations

description: CTCF Motifs were downloaded from:<br>http://compbio.mit.edu/encode-motifs/<br>The following citation should be cited when using these motifs:<br>Kheradpour P, Kellis M. Systematic discovery and characterization of regulatory motifs in ENCODE TF binding experiments. Nucleic Acids Res. 2014 Mar;42(5):2976-87.<br>For all analysis in our paper, we utilized the CTCF_known1 motif.<br>This file contains five columns:Column 1: Motif nameColumn 2: ChromsomeColumn 3: Start coordinateColumn 4: End coordinateColumn 5: Strand<br>
DOI: 10.6084/m9.figshare.11369352.v1
title: f2 chicken data

description: genotypes of f2 chicken
DOI: 10.6084/m9.figshare.11369187
title: Genetic repertoire of Serratia marcescens Db11

description: A natural inhabitant of soil and water, the Gram-negative rod-shaped bacterium <i>Serratia marcescens</i> is also an opportunistic pathogen known to cause a variety of infections. The bacterium is characterized by a secreted red pigment known as prodigiosin. This work sought to unveil the mysterious veil of this facultative anaerobic bacterium that is a close inhabitant of our living environment such as on the lining of bathroom tiles and toilet water line. Using an in-house MATLAB software, the annotated genome sequence of <i>Serratia marcescens</i> Db11 (Genbank accession number: NCBI Reference Sequence: NZ_HG326223.1) was parsed into its constituent gene name, gene function, and gene sequence; thereby, allowing a gene database comprising all 4710 genes of the bacterium to be constructed. Overall, the constructed gene database should serve as a useful resource for biologists seeking to understand fundamental biological and physiological mechanisms at work in this opportunistic pathogen.<br><br>
DOI: 10.6084/m9.figshare.11369355.v2
title: Turkish General Elections 2002-2018

description: Datasets of each Turkish election from 2002 to 2018 assessing the proportionality of each election were the threshold, malapportionment, and the threshold and malapportionment combined removed. The Gallagher Index is used to assess the proportionality of each simulation and is compared to the Gallagher Index of the actual result of each election.
DOI: 10.6084/m9.figshare.11369202.v1
title: Sequences information of eggs collected in the seagrass beds of Liusha Bay and Li'an Harbor-Xincun Bay

description: The sequences and the ABI documents named LS and XCNE represent the eggs collected in the seagrass beds of Liusha Bay, Guangdong province and the Li'an Harbor, Hainan province of China respectively.
DOI: 10.6084/m9.figshare.11369163
title: Database of genes in Pseudomonas aeruginosa PAO1 without recognition sequence of NdeI and BamHI

description: In restriction enzyme-based cloning method, the gene of interest should not have recognition sequence of the restriction enzymes used for the work. This work sought to provide a database of all genes in <i>Pseudomonas aeruginosa</i> PAO1 without recognition sequence of BamHI and NdeI restriction enzymes via an in-house MATLAB software. Overall, the curated database should be useful for researchers seeking to clone genes in <i>P. aeruginosa</i> PAO1 using BamHI and NdeI restriction enzymes.<br><br>
DOI: 10.6084/m9.figshare.11369202.v3
title: Sequences information of suspected eggs from the seagrass beds of Liusha Bay, Li'an gang and Xincun Bay, China

description: The sequences (.seq) and the ABI documents (.ab1) names begin with LSB, LAG and XCB represent the suspected eggs collected in the seagrass beds of the Liusha Bay (109.9215°E, 20.4344°N) in Guangdong province, the Li'an gang (110.0528°E, 18.4105°N) and the Xincun Bay (109.9760°E, 18.4089°N) in Hainan province, respectively. The Guangdong and Hainan are the major Chinese provinces with natural seagrass distribution. The primers employed in PCR and sequencing are LCO1490/HCO2198. The species names shown in the .seq file names were determined after comparing with database of the NCBI and BOLD systems.
DOI: 10.6084/m9.figshare.11369133
title: Altered autonomic functions and gut microbiome in individuals with autism spectrum disorder (ASD): implications for assisting ASD screening and diagnosis, Datasets

description: The dataset for the project and the manuscript.
DOI: 10.6084/m9.figshare.11369163.v1
title: Database of genes in Pseudomonas aeruginosa PAO1 without recognition sequence of NdeI and BamHI

description: In restriction enzyme-based cloning method, the gene of interest should not have recognition sequence of the restriction enzymes used for the work. This work sought to provide a database of all genes in <i>Pseudomonas aeruginosa</i> PAO1 without recognition sequence of BamHI and NdeI restriction enzymes via an in-house MATLAB software. Overall, the curated database should be useful for researchers seeking to clone genes in <i>P. aeruginosa</i> PAO1 using BamHI and NdeI restriction enzymes.<br><br>
DOI: 10.6084/m9.figshare.11369355.v3
title: Turkish General Elections 2002-2018

description: Datasets of each Turkish election from 2002 to 2018 assessing the proportionality of each election were the threshold, malapportionment, and the threshold and malapportionment combined removed. The Gallagher Index is used to assess the proportionality of each simulation and is compared to the Gallagher Index of the actual result of each election.
DOI: 10.6084/m9.figshare.11369130
title: Manuscript Dataset

description: The dataset for the project and the manuscript.
DOI: 10.6084/m9.figshare.11369202.v2
title: Sequences information of suspected eggs from the seagrass beds of Liusha Bay, Li'an gang and Xincun Bay, China

description: The sequences (.seq) and the ABI documents (.ab1) names begin with LSB, LAG and XCB represent the suspected eggs collected in the seagrass beds of the Liusha Bay (109.9215°E, 20.4344°N) in Guangdong province, the Li'an gang (110.0528°E, 18.4105°N) and the Xincun Bay (109.9760°E, 18.4089°N) in Hainan province, respectively. The Guangdong and Hainan are the major Chinese provinces with natural seagrass distribution. The primers employed in PCR and sequencing are LCO1490/HCO2198. The species names shown in the .seq file names were determined after comparing with database of the NCBI and BOLD systems.
DOI: 10.6084/m9.figshare.11369118
title: Dataset for: Sex Differences in Head-fixed Voluntary Running Behavior in C57BL/6J mice

description: Sex differences in running behaviors between female and male mice occur naturally in the wild. Recent experiments using head-fixed mice on a voluntary running wheel have exploited analogous locomotor activity to gain insight into the neural underpinnings of a number of behaviors ranging from spatial navigation to decision making. It is however largely unknown if sex differences exist between females and males in a head-fixed experimental paradigm. To address this, we characterized locomotor activity in head-fixed female and male C57BL/6J mice on a voluntary running wheel. First, we found that over the initial 7-day period, on average, animals increased both the velocity and the time spent running. Furthermore, we found that female mice habituated to running forward over the initial 2 days of encountering the wheel, while male mice took to up to 4 days to habituate to running forward. Taken together, we characterized features of a sexually divergent behavior in head-fixed running that should be considered in experiments employing female and male mice.
DOI: 10.6084/m9.figshare.11369118.v1
title: Dataset for: Sex Differences in Head-fixed Voluntary Running Behavior in C57BL/6J mice

description: Sex differences in running behaviors between female and male mice occur naturally in the wild. Recent experiments using head-fixed mice on a voluntary running wheel have exploited analogous locomotor activity to gain insight into the neural underpinnings of a number of behaviors ranging from spatial navigation to decision making. It is however largely unknown if sex differences exist between females and males in a head-fixed experimental paradigm. To address this, we characterized locomotor activity in head-fixed female and male C57BL/6J mice on a voluntary running wheel. First, we found that over the initial 7-day period, on average, animals increased both the velocity and the time spent running. Furthermore, we found that female mice habituated to running forward over the initial 2 days of encountering the wheel, while male mice took to up to 4 days to habituate to running forward. Taken together, we characterized features of a sexually divergent behavior in head-fixed running that should be considered in experiments employing female and male mice.
DOI: 10.6084/m9.figshare.11369130.v1
title: Manuscript Dataset

description: The dataset for the project and the manuscript.
DOI: 10.6084/m9.figshare.11369355.v4
title: Turkish General Elections 2002-2018

description: Simulated results of the 2002 to 2018 Turkish elections with the threshold, malapportionment, and the threshold and malapportionment combined removed. The Gallagher Index is used to assess the proportionality of each simulation and is compared to the Gallagher Index of the actual result of each election.
DOI: 10.6084/m9.figshare.11369103
title: Polygenic Risk Scores (PRSs) for cardiometabolic diseases used to identify associated plasma protein changes

description: Polygenic risk scores (PRS) for:<br><br>- Atrial Fibrillation- Chronic Kidney Disease (CKD)<br>- Type 2 Diabetes (T2D)<br>- Stroke (any type)<br><br>These scores were used to test associations between polygenic risk of these diseases and levels of 3,442 plasma proteins in 3,175 healthy individuals from the INTERVAL blood donor cohort.<br><br>Each PRS file contains a set of 1.96 - 2.21 million SNPs, their genomic location (hg19/GRCh37 coordinates), and weights (effect sizes from GWAS).<br><br>
DOI: 10.6084/m9.figshare.11369034
title: Figure 14.xlsx

description: Figure 14
DOI: 10.6084/m9.figshare.11369067.v1
title: Aggregation on trees does not elevate inbreeding risk in the Shedao pit vipers Gloydius shedaoensis

description: With the fragmentation of critical resources (e.g. habitat or foraging site), a number of threatened species choose to aggregate with many individuals living together. This may increase their survival, nevertheless, this would also dramatically increases the likelihood of mating among relatives and aggravate inbreeding risk. Uncovering the relationship between aggregation and inbreeding risk becomes increasingly urgent, and it would contribute a lot to the conservation in endangered species. Using one endangered species pit viper (<i>Gloydius shedaoensis</i>) from “snake island in China, we examined whether aggregation on trees increase the inbreeding risk. The genotypes of 45 individual snakes were collected using 17 microsatellite DNA loci.
DOI: 10.6084/m9.figshare.11369025
title: Stromal-associated cytokines bias the interplay between gene expression and DNA methylation in human breast cancers

description: In human tumours, the crosstalk between cancer cells and their microenvironment is involved in tumour progression, metastasis and resistance to anti-cancer therapies. Among the factors involved in this exchange of information pro-inflammatory cytokines seem to play a crucial role. We observed that a group of pro-inflammatory cytokines, interleukin 6 (IL6), interleukin 1-beta (IL1b), and tumour necrosis factor-alpha (TNFa), preferentially activated genes exhibiting a high basal methylation level at their transcription start sites, in the human breast cancer cell line MCF7. In human breast tumours, these responding genes were also hypermethylated, and some of them (N = 104) were differentially methylated across human breast tumour samples (The Cancer Genome Atlas cohort). While their expression was positively correlated with the stromal content of the tumours and the expression of stromal-associated pro-inflammatory cytokines, the expression of this subset of genes was negatively correlated with their methylation level at their 5ʹ end. Nevertheless, while the methylation level of this subset of genes was not correlated with the stromal cell content of the tumours, this negative correlation was partially lost in tumours with high stromal cell content. Consistently, we observed that the methylation level in this subset of genes influenced the correlation between gene expression and stromal cell content. Thus, these data indicated that the stromal component of breast tumours should be taken into account for DNA methylation and gene expression studies and suggest an additional pathway, via DNA methylation, in the cross-talk between cancer cells and their microenvironment in human breast cancers.
DOI: 10.6084/m9.figshare.11369040.v2
title: Genetic adaptations of an island pit-viper to aunique sedentarylife with extreme seasonal food availability

description: Figure S1 contains estimates of divergence time. File S1 contains codon sequences with evidences of positive selection in FASTA format. File S2 contains protein sequences containing convergent/parallel substitutionsin FASTA format. File S3 contains protein sequences containing multiple amino acid substitutions specific to Shedao pit-viper in FASTA format. File S4 contains codon sequence alignmentsof all single-copy genes used in this study in FASTA format.Table S1 contains genomic data, assembly version, and data sources used in this study. Table S2 contains calibration points used in divergence date estimation. Table S3 contains list of genes that bear signals of positive selection in the Shedao pit-viper. Table S4 contains list of genes that possess sites of convergent substitutions. Table S5 contains list of genes that possess sites of parallel substitutions.