cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.11413929
title: Proteome database of Pseudomonas aeruginosa ATCC 15692

description: Known to infect the lungs of cystic fibrosis patients, <i>Pseudomonas aeruginosa </i>is a Gram-negative opportunistic human pathogen. Endowed with a large genome and relatively large genetic repertoire, <i>P. aeruginosa</i> is also known for its biofilm-forming capability, which is the enabling tool that the bacterium utilizes in adhering to metal catheters in the human body. But, fundamentally, <i>P. aeruginosa</i> is an environmental bacterium that inhabits a variety of niches in soil and water. Reasons underpinning why <i>P. aeruginosa</i> cross environmental niches and adapt to human physiological conditions remain enigmatic. This work hopes to provide fundamental information about the proteome of <i>P. aeruginosa</i> ATCC 15692 that could help illuminate the protein complement of the bacterium, which indirectly informs the metabolic, signalling and regulatory capabilities of the species. Specifically, the UniProt proteome file of <i>P. aeruginosa</i> ATCC 15692 was parsed by an in-house MATLAB software yielding a database of protein name, amino acid sequence, number of residues, molecular weight and nucleotide sequence for all proteins of the species. In total, the presented proteome database of <i>P. aeruginosa</i> ATCC 15692 should find use as basic information enabling genetic studies such as modifying the genome of the bacterium to uncover the regulatory players that partake in pathogenesis of this evolutionary recent human pathogen.<br><br>
DOI: 10.6084/m9.figshare.11413881
title: Ahlgren-Belisle-Lee-2019-EM processing code

description: Processing code and files that go along with the work presented in the following paper:<br>Genomic mosaicism underlies the adaptation of marine Synechococcus ecotypes to distinct oceanic iron nichesNathan A. Ahlgren, B. Shafer Belisle, and Michael D. Lee
DOI: 10.6084/m9.figshare.11413929.v1
title: Proteome database of Pseudomonas aeruginosa ATCC 15692

description: Known to infect the lungs of cystic fibrosis patients, <i>Pseudomonas aeruginosa </i>is a Gram-negative opportunistic human pathogen. Endowed with a large genome and relatively large genetic repertoire, <i>P. aeruginosa</i> is also known for its biofilm-forming capability, which is the enabling tool that the bacterium utilizes in adhering to metal catheters in the human body. But, fundamentally, <i>P. aeruginosa</i> is an environmental bacterium that inhabits a variety of niches in soil and water. Reasons underpinning why <i>P. aeruginosa</i> cross environmental niches and adapt to human physiological conditions remain enigmatic. This work hopes to provide fundamental information about the proteome of <i>P. aeruginosa</i> ATCC 15692 that could help illuminate the protein complement of the bacterium, which indirectly informs the metabolic, signalling and regulatory capabilities of the species. Specifically, the UniProt proteome file of <i>P. aeruginosa</i> ATCC 15692 was parsed by an in-house MATLAB software yielding a database of protein name, amino acid sequence, number of residues, molecular weight and nucleotide sequence for all proteins of the species. In total, the presented proteome database of <i>P. aeruginosa</i> ATCC 15692 should find use as basic information enabling genetic studies such as modifying the genome of the bacterium to uncover the regulatory players that partake in pathogenesis of this evolutionary recent human pathogen.<br><br>
DOI: 10.6084/m9.figshare.11413881.v1
title: Ahlgren-Belisle-Lee-2019-EM processing code

description: Processing code and files that go along with the work presented in the following paper:<br>Genomic mosaicism underlies the adaptation of marine Synechococcus ecotypes to distinct oceanic iron nichesNathan A. Ahlgren, B. Shafer Belisle, and Michael D. Lee
DOI: 10.6084/m9.figshare.11413878
title: Proteome database of Staphylococcus aureus NCTC 8325

description: A Gram-positive opportunistic human pathogen of increasing concern, <i>Staphylococcus aureus</i> is also a commensal on many parts of the human body. What remain enigmatic are the molecular switches and environmental conditions that drove a commensal into a pathogenic lifestyle. Specifically, activating pathogenesis mechanisms that harms the host may incur a counter-offensive from the body’s immune system. Thus, microorganisms capable of dual commensal and pathogenic lifestyle are of research interests, particularly from the perspective of developing therapeutic strategies that could quickly ameliorate a nascent infection which help reduce morbidity and mortality. In <i>S. aureus</i> case, increasing resistance to a variety of frontline antibiotics makes this bacterium of increasing medical concern, which motivates the search for a variety of biophysical and biochemical approaches for its eradication or keeping it under control. This work sought to provide some fundamental information of <i>S. aureus</i> NCTC 8325 to help guide experimental strategies seeking to both understand the species pathogenesis mechanisms as well as molecular events that potentiate the switch from commensal to a pathogenic lifestyle. Specifically, the UniProt proteome of <i>S. aureus</i> NCTC 8325 was parsed by an in-house MATLAB software to yield a database comprising protein name, amino acid sequence, number of residues, molecular weight and nucleotide sequence, which could collectively inform the genetic and proteomic repertoire of the organism. Knowledge of the molecular entities available would hopefully help crystallise hypothesis-driven research seeking to unveil the molecular effectors that guide pathogenesis in this otherwise commensal organism. Alternatively, a systems-based approach could also use the proteome complement as guide in designing microarray experiments to unveil differential gene expression of the species in health and disease.<br><br>
DOI: 10.6084/m9.figshare.11413875
title: Multiple membership college data

description: This dataset was used in the Bayesian multiple membership multiple classification logistic regression model on student performance with random effects in university instructors and majors.<br>
DOI: 10.6084/m9.figshare.11413869
title: tms_gene_data

description: Data for the TMS aging signature analysis paper
DOI: 10.6084/m9.figshare.11413875.v1
title: Multiple membership college data

description: These data were used in Bayesian multiple membership multiple classification logistic regression models for effects of university instructors and majors on academic performance of college students
DOI: 10.6084/m9.figshare.11413875.v2
title: Multiple membership college data

description: These data were used in Bayesian multiple membership multiple classification logistic regression models for effects of university instructors and majors on academic performance of college students
DOI: 10.6084/m9.figshare.11413875.v3
title: Multiple membership college data

description: These data were used in Bayesian multiple membership multiple classification logistic regression models for effects of university instructors and majors on academic performance of college students
DOI: 10.6084/m9.figshare.11413794
title: Process Discovery Optimization Framework

description: This zip contains the data, the batch tests, and the resultsof the experiments reported in the evaluation section of the research article titled:<br>"Optimized Discovery of Process Models From Event Logs: Framework and Evaluation"A. Augusto, M. Dumas, M. La Rosa, S.J.J. Leemans, S. K.L.M. vanden Broucke
DOI: 10.6084/m9.figshare.11413794.v1
title: Process Discovery Optimization Framework

description: This zip contains the data, the batch tests, and the resultsof the experiments reported in the evaluation section of the research article titled:<br>"Optimized Discovery of Process Models From Event Logs: Framework and Evaluation"A. Augusto, M. Dumas, M. La Rosa, S.J.J. Leemans, S. K.L.M. vanden Broucke
DOI: 10.6084/m9.figshare.11413650
title: Origin and identity of the Brokpa of Dah-Hanu, Himalayas – an NRY-HG L1a2 (M357) legacy

description: <b>Background:</b> The Brokpas are an isolated tribal population of the Dah-Hanu villages of the Leh district of India. They speak Dardic, a sub-branch of the Indo-European language family, and are putatively identified as “pure Aryan,” a hegemonic impression perpetuated by foreign tourism. <b>Aim:</b> To determine if the above is true by looking for an appreciable frequency of NRY-HG-R1a1(M17) signatures which are common to Indo-European language speakers of mainland India and elsewhere. <b>Subjects and methods:</b> We studied 75 random Brokpa males from the Dah-Hanu region, on the northern bank of the Indus river. <b>Results:</b> Interestingly, the Brokpa males possessed a high proportion of NRY-HG-L1a2(M357) (62.7%) that are found sporadically in India and her neighbourhood. A global analysis of this clade (present study, 214 of 3327 men from 63 populations; from the literature 56 of 873) suggested that they originated from southern India. <b>Conclusion:</b> The Y chromosomal studies suggest the Brokpa to be pre-Vedic settlers of the Himalayas, 9000 ybp, with an isolated evolution. The mtDNA profile shows a predominance of mtDNA HG A4 that must have arrived from outside the Indian subcontinent.
DOI: 10.6084/m9.figshare.11413650.v1
title: Origin and identity of the Brokpa of Dah-Hanu, Himalayas – an NRY-HG L1a2 (M357) legacy

description: <b>Background:</b> The Brokpas are an isolated tribal population of the Dah-Hanu villages of the Leh district of India. They speak Dardic, a sub-branch of the Indo-European language family, and are putatively identified as “pure Aryan,” a hegemonic impression perpetuated by foreign tourism. <b>Aim:</b> To determine if the above is true by looking for an appreciable frequency of NRY-HG-R1a1(M17) signatures which are common to Indo-European language speakers of mainland India and elsewhere. <b>Subjects and methods:</b> We studied 75 random Brokpa males from the Dah-Hanu region, on the northern bank of the Indus river. <b>Results:</b> Interestingly, the Brokpa males possessed a high proportion of NRY-HG-L1a2(M357) (62.7%) that are found sporadically in India and her neighbourhood. A global analysis of this clade (present study, 214 of 3327 men from 63 populations; from the literature 56 of 873) suggested that they originated from southern India. <b>Conclusion:</b> The Y chromosomal studies suggest the Brokpa to be pre-Vedic settlers of the Himalayas, 9000 ybp, with an isolated evolution. The mtDNA profile shows a predominance of mtDNA HG A4 that must have arrived from outside the Indian subcontinent.
DOI: 10.17608/k6.auckland.11413491
title: Chong BCAA Supplementary tables.zip

description: Supplementary tables 1 and 2 for manuscript entitled " Nutritional supplementation does not impact microbial biogeography of the gastrointestinal tract of preterm and term lambs"
DOI: 10.17608/k6.auckland.11413491.v1
title: Chong BCAA Supplementary tables.zip

description: Supplementary tables 1 and 2 for manuscript entitled " Nutritional supplementation does not impact microbial biogeography of the gastrointestinal tract of preterm and term lambs"
DOI: 10.6084/m9.figshare.11413494.v1
title: spatial-factor-analysis-IJGIS

description: Data, model code, and initial values for a Bayesian spatial factor analytic model.<br>
DOI: 10.6084/m9.figshare.11413302
title: COALA dataset from 'Transfer learning improves antibiotic resistance class prediction'

description: This includes all 3 different versions of the COALA dataset.<br>COALA100 dataset is a collection of antibiotic resistance genes from 15 databases along with metadata information from these databases which includes the respective antibiotic class.<br><br>The COALA70 dataset is the cd-hitted by 70% threshold version of the COALA100 dataset.<br><br>The COALA40 dataset is the cd-hitted by 40% threshold version of the COALA100 dataset.<br><br>All three datasets are in fasta format. The last section of the description line has the antibiotic label the gene confers resistance to. The second last section is the database name from where the gene was collected. All other sections convey information about the gene.
DOI: 10.6084/m9.figshare.11413302.v1
title: COALA datasets

description: This includes all 3 different versions of the COALA dataset.<br>COALA100 dataset is a collection of antibiotic resistance genes from 15 databases along with metadata information from these databases which includes the respective antibiotic class.<br><br>The COALA70 dataset is the cd-hitted by 70% threshold version of the COALA100 dataset.<br><br>The COALA40 dataset is the cd-hitted by 40% threshold version of the COALA100 dataset.<br>
DOI: 10.6084/m9.figshare.11413209
title: Data from: Biogeography, habitat transitions and hybridization in a radiation of South American silverside fishes revealed by mitochondrial and genomic RAD data

description: This data is from the paper:<br>Hughes, L.C., Cardoso, Y.P., Sommer, J., Cifuentes, R., Cuello, M., Somoza, G.M., González-Castro, M., Malabarba, L.R., Cussac, V., Habit, E.M., Betancur-R., R., and Ortí, G. 2020. Biogeography, habitat transitions and hybridization in a radiation of South American silverside fishes revealed by mitochondrial and genomic RAD data. (Accepted at Molecular Ecology).<br><br><br>Please see the README.txt for descriptions of each of the data files.
DOI: 10.6084/m9.figshare.11413194
title: Test

description: Not applicable
DOI: 10.6084/m9.figshare.11413128
title: RB-TnSeq data for the phage resistance landscape in Escherichia coli

description: Transposon mutagenesis data (RB-TnSeq) for two strains of Escherichia coli exposed to diverse bacteriophage<br>
DOI: 10.6084/m9.figshare.11413194.v1
title: Neutral Model (QRule) Landscapes

description: This dataset contains 37,620 binary rasters generated from the software QRule (https://www.umces.edu/qrule). Each raster (landscape) is a 512x512 raster. Each landscape was generated using one of 19 proportion values (P), where P ranges [5,95] in increments of 5. Each landscape was generated using one of 20 H values, where H ranges [0,95] in increments of 5. There are 380 unique P-H combinations, and we generated 99 repetitions of each for a total of 37,620 landscapes.
DOI: 10.6084/m9.figshare.11413194.v2
title: Neutral Model (QRule) Landscapes and Downscaling Code

description: The QRule_NeutralModels.zip dataset contains 37,620 binary rasters generated from the software QRule (https://www.umces.edu/qrule). Each raster (landscape) is a 512x512 raster. Each landscape was generated using one of 19 proportion values (P), where P ranges [5,95] in increments of 5. Each landscape was generated using one of 20 H values, where H ranges [0,95] in increments of 5. There are 380 unique P-H combinations, and we generated 99 repetitions of each for a total of 37,620 landscapes.<br>computeDownscaledMetrics.m is Matlab code for fitting scaling functions, downscaling those functions to predict values at 30 m resolution, and comparing predicted values to true values computed directly from the neutral model landscapes. The NeutralModels.xlsx contains a set of sample data for running the Matlab code.
DOI: 10.6084/m9.figshare.11413038.v1
title: Particle motions over plane-bed and bedform topography

description: Dataset and code related to the manuscript titled "Probability distributions of particle hop distance and travel time over equilibrium mobile bedforms" (Ashley et al., in revision)
DOI: 10.6084/m9.figshare.11413038.v3
title: Particle motions over plane-bed and bedform topography

description: Dataset and code related to the manuscript titled "Probability distributions of particle hop distance and travel time over equilibrium mobile bedforms" (Ashley et al., in revision)
DOI: 10.6084/m9.figshare.11413008
title: Marine sediments illuminate Chlamydiae diversity and evolution - additional data

description: Full alignments (.align), trimmed alignments (.align.trim), and phylogenetic trees in nexus format (.tree) for all phylogenetic inferences presented in the study. This includes concatenated protein alignments (.align.trim.concat) and trees (.tree). All 16S rRNA gene OTUs generated from amplicon sequencing of the 30 marine sediment samples are also included, alongside their taxonomic classification (.fasta). Genbank assembly accessions for Chlamydiae MAGs are also provided (.xlsx).
DOI: 10.6084/m9.figshare.11413038.v2
title: Particle motions over plane-bed and bedform topography

description: Dataset and code related to the manuscript titled "Probability distributions of particle hop distance and travel time over equilibrium mobile bedforms" (Ashley et al., in revision)
DOI: 10.6084/m9.figshare.11410917
title: Simulated auv data

description: This repo provides a simulated dataset of an auv trajectory<br>
DOI: 10.6084/m9.figshare.11410917.v1
title: Simulated auv data

description: This repo provides a simulated dataset of an auv trajectory<br>
DOI: 10.6084/m9.figshare.11410212
title: MSB Gene Expression Variability

description: This is data collected for a Molecular Systems Biology publication.
DOI: 10.6084/m9.figshare.11410122
title: The relationship between anthropogenic light and noise in U.S. National Parks

description: Noise and light pollution in 270*270 m pixels in each National Park across the continental United States. Also included are important landscape factors that may influence noise and light levels in parks.
DOI: 10.6084/m9.figshare.11410023
title: A morphologically unique species of Ptinidae (Coleoptera) and the first found in mid-Cretaceous Kachin amber (Myanmar)

description: Some groups of fossil beetles are difficult to study because the characters needed for identification or classification are hidden and difficult to study. Ptinidae is one of these groups. We describe herein <i>Cretasernus spinosus</i> gen. et sp. nov. (Coleoptera: Ptinidae) based on one fossil specimen, the only known specimen of this family from Kachin amber (mid-Cretaceous of Myanmar). The holotype was imaged using an X-ray micro-CT system to obtain high-quality 3D images to complement the structures visualized using optical microscopes. The new species shows two autapomorphic characters never described in any extant or extinct species in this family: a groove near the base of the 11th antennomere, which makes it appear as a much smaller additional antennomere, and transverse metacoxae touching at the middle. Phylogenetic analysis of the new species clearly supports this new genus as part of Anobiidae <i>sensu stricto</i> (i.e. excluding the spider beetles) despite antennae that are certainly more similar to those seen in the many of the spider beetles (except for the modified 11th antennomere). Some of the extant species in this family are wood-borers and the involvement of beetles in resin production during the Cretaceous is a hypothesis that is suggested often. However, some ideas against the involvement of Ptinidae in resin production within the mid-Cretaceous forests of Myanmar are discussed. http://zoobank.org/urn:lsid:zoobank.org:pub:02CE8BF8-FC0C-4E39-8B75-FA70F2CBE2BB
DOI: 10.6084/m9.figshare.11410023.v1
title: A morphologically unique species of Ptinidae (Coleoptera) and the first found in mid-Cretaceous Kachin amber (Myanmar)

description: Some groups of fossil beetles are difficult to study because the characters needed for identification or classification are hidden and difficult to study. Ptinidae is one of these groups. We describe herein <i>Cretasernus spinosus</i> gen. et sp. nov. (Coleoptera: Ptinidae) based on one fossil specimen, the only known specimen of this family from Kachin amber (mid-Cretaceous of Myanmar). The holotype was imaged using an X-ray micro-CT system to obtain high-quality 3D images to complement the structures visualized using optical microscopes. The new species shows two autapomorphic characters never described in any extant or extinct species in this family: a groove near the base of the 11th antennomere, which makes it appear as a much smaller additional antennomere, and transverse metacoxae touching at the middle. Phylogenetic analysis of the new species clearly supports this new genus as part of Anobiidae <i>sensu stricto</i> (i.e. excluding the spider beetles) despite antennae that are certainly more similar to those seen in the many of the spider beetles (except for the modified 11th antennomere). Some of the extant species in this family are wood-borers and the involvement of beetles in resin production during the Cretaceous is a hypothesis that is suggested often. However, some ideas against the involvement of Ptinidae in resin production within the mid-Cretaceous forests of Myanmar are discussed. http://zoobank.org/urn:lsid:zoobank.org:pub:02CE8BF8-FC0C-4E39-8B75-FA70F2CBE2BB
DOI: 10.6084/m9.figshare.11410122.v1
title: The relationship between anthropogenic light and noise in U.S. National Parks

description: Noise and light pollution in 270*270 m pixels in each National Park across the continental United States. Also included are important landscape factors that may influence noise and light levels in parks.
DOI: 10.6084/m9.figshare.11409813
title: Sorghum Data Edited

description: University foodservice sensory evaluation in college students.
DOI: 10.6084/m9.figshare.11409807
title: Detecting a downward shift in a proportion using a geometric CUSUM chart

description: In monitoring an ordered stream of discrete items from a repetitive process, the geometric CUSUM chart may be used to detect sudden shifts from an acceptable level for a process-proportion (<i>p</i>) such as fraction nonconforming. Much of the investigative effort for this CUSUM scheme has been concentrated on the detection of upward shifts, and a recent paper has provided guidance to quality engineers in choosing the parameters (<i>k</i>, <i>h</i>) of such a scheme. In this article, the corresponding task of aiding the choice of parameters for detecting a downward shift is addressed. It is shown, using extensive numerical investigations, that the use of a value for the parameter <i>k</i> based on the Sequential Probability Ratio is not optimal when one is using steady-state evaluation of the detection performance of the CUSUM scheme. Tables are presented listing recommended values of parameters for detection of five sizes of downward shift, for each of 27 in-control levels for <i>p</i> in the range 0.20 to 0.001. Interpolation and extrapolation to find parameter values for other in-control levels of <i>p</i> are also considered, and a range of examples presented. There is an equivalence between a geometric CUSUM scheme and a Bernoulli CUSUM scheme, so that the results of this investigation may also be used in choosing parameter values for a Bernoulli CUSUM chart.
DOI: 10.6084/m9.figshare.11409708
title: Central data set

description: Central data set for: Damsbo-Svendsen, Søren. (Forthcoming). 'How weather experiences strengthen climate change awareness in Europe'.<br>