cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3125104.v1
title: Metabolomic changes in murine serum following inhalation exposure to gasoline and diesel engine emissions

description: The adverse health effects of environmental exposure to gaseous and particulate components of vehicular emissions are a major concern among urban populations. A link has been established between respiratory exposure to vehicular emissions and the development of cardiovascular disease (CVD), but the mechanisms driving this interaction remain unknown. Chronic inhalation exposure to mixed vehicle emissions has been linked to CVD in animal models. This study evaluated the temporal effects of acute exposure to mixed vehicle emissions (MVE; mixed gasoline and diesel emissions) on potentially active metabolites in the serum of exposed mice. C57Bl/6 mice were exposed to a single 6-hour exposure to filtered air (FA) or MVE (100 or 300 μg/m<sup>3</sup>) by whole body inhalation. Immediately after and 18 hours after the end of the exposure period, animals were sacrificed for serum and tissue collection. Serum was analyzed for metabolites that were differentially present between treatment groups and time points. Changes in metabolite levels suggestive of increased oxidative stress (oxidized glutathione, cysteine disulfide, taurine), lipid peroxidation (13-HODE, 9-HODE), energy metabolism (lactate, glycerate, branched chain amino acid catabolites, butrylcarnitine, fatty acids), and inflammation (DiHOME, palmitoyl ethanolamide) were observed immediately after the end of exposure in the serum of animals exposed to MVE relative to those exposed to FA. By 18 hours post exposure, serum metabolite differences between animals exposed to MVE versus those exposed to FA were less pronounced. These findings highlight complex metabolomics alterations in the circulation following inhalation exposure to a common source of combustion emissions.
DOI: 10.6084/m9.figshare.3125086.v1
title: Ontdekking van onmogelijke anaerobe micro-organismsen

description: lecture slides for natuurwetenschappelijk genootschap wageningen on the importanc eof anaerobic microbiology and discovery of impossible microbes
DOI: 10.6084/m9.figshare.3124957
title: pairwise_ids.tsv.gz

description: Pairwise percent identities between all RecA proteins from GenomePeek. This file has [id1, id2, percent id] between the proteins as described at https://edwards.sdsu.edu/research/?p=1687
DOI: 10.6084/m9.figshare.3124939
title: Seq Batch Analysis

description: Seq Batch Analysis data set for our batch effects paper.
DOI: 10.6084/m9.figshare.3124942
title: csvFiles

description: csvFiles from our batch effects paper.
DOI: 10.6084/m9.figshare.3124957.v2
title: pairwise_ids.tsv.gz

description: Pairwise percent identities between all RecA proteins from GenomePeek. This file has [id1, id2, percent id] between the proteins as described at https://edwards.sdsu.edu/research/?p=1687
DOI: 10.6084/m9.figshare.3124939.v1
title: Seq Batch Analysis

description: Seq Batch Analysis data set for our batch effects paper.
DOI: 10.6084/m9.figshare.3124957.v1
title: pairwise_ids.tsv.gz

description: Pairwise percent identities between all RecA proteins from GenomePeek. This file has [id1, id2, percent id] between the proteins as described at https://edwards.sdsu.edu/research/?p=1687
DOI: 10.6084/m9.figshare.3124936
title: NGBatch

description: NGBatch data from our batch effects paper.
DOI: 10.6084/m9.figshare.3124942.v1
title: csvFiles

description: csvFiles from our batch effects paper.
DOI: 10.6084/m9.figshare.3124927
title: bladdercels.tgz

description: Data for Nature Genetics Batch paper.
DOI: 10.6084/m9.figshare.3124930
title: Bladder Cels

description: Bladder Cel files from Batch paper.
DOI: 10.6084/m9.figshare.3124933
title: Cheung data

description: This is the Cheung data from our batch effects paper
DOI: 10.6084/m9.figshare.3124930.v1
title: Bladder Cels

description: Bladder Cel files from Batch paper.
DOI: 10.6084/m9.figshare.3124936.v1
title: NGBatch

description: NGBatch data from our batch effects paper.
DOI: 10.6084/m9.figshare.3124933.v1
title: Cheung data

description: This is the Cheung data from our batch effects paper
DOI: 10.6084/m9.figshare.3124927.v1
title: bladdercels.tgz

description: Data for Nature Genetics Batch paper.
DOI: 10.6084/m9.figshare.3124909
title: Snowball - benchmark datasets

description: Benchmark datasets that were used to evaluate the Snowball assembler. Each dataset consist of two files, one containing first read-ends, the second containing second read-ends. Datasets 1-21 contain simulated reads of 3-9 closely related E.Coli strains. Dataset 22 contains simulated reads of 10 closely related Rhizobia strains.
DOI: 10.6084/m9.figshare.3124915
title: FGD Transcripts.zip

description: Transcripts of Focus Group Discussions focusing on obesity risk perceptions and weight loss among black obese and non-obese African men and women.
DOI: 10.6084/m9.figshare.3124906
title: GC-MS; timecourse #2; S. cerevisiae alone, A. malorum alone, co-culture; also quantification

description: This is the second experimental replicate of a GC-MS timecourse. S. cerevisiae alone, A. malorum alone, co-culture. Also includes standards for quantification. Ethanol and acetic acid quantified over time. XAD-4 and methanol extraction.
DOI: 10.6084/m9.figshare.3124903
title: GC-MS; timecourse #1; S. cerevisiae alone, A. malorum alone, co-culture; also quantification

description: This is the first experimental replicate of a GC-MS timecourse. S. cerevisiae alone, A. malorum alone, co-culture. Also includes standards for quantification. Ethanol and acetic acid quantified over time. XAD-4 and methanol extraction.<br>
DOI: 10.6084/m9.figshare.3124909.v1
title: Snowball - benchmark datasets

description: Benchmark datasets that were used to evaluate the Snowball assembler. Each dataset consist of two files, one containing first read-ends, the second containing second read-ends. Datasets 1-21 contain simulated reads of 3-9 closely related E.Coli strains. Dataset 22 contains simulated reads of 10 closely related Rhizobia strains.
DOI: 10.6084/m9.figshare.3124897
title: GC-MS Data, experimental replicate 4, co-culture and individual cultures

description: Fourth experimental replicate. GC-MS of the co-culture, S. cerevisiae alone, and A. malorum alone for initial putative identification of metabolites. Methanol extraction of XAD-4 beads. <br>
DOI: 10.6084/m9.figshare.3124903.v1
title: GC-MS; timecourse #1; S. cerevisiae alone, A. malorum alone, co-culture; also quantification

description: This is the first experimental replicate of a GC-MS timecourse. S. cerevisiae alone, A. malorum alone, co-culture. Also includes standards for quantification. Ethanol and acetic acid quantified over time. XAD-4 and methanol extraction.<br>
DOI: 10.6084/m9.figshare.3124906.v1
title: GC-MS; timecourse #2; S. cerevisiae alone, A. malorum alone, co-culture; also quantification

description: This is the second experimental replicate of a GC-MS timecourse. S. cerevisiae alone, A. malorum alone, co-culture. Also includes standards for quantification. Ethanol and acetic acid quantified over time. XAD-4 and methanol extraction.
DOI: 10.6084/m9.figshare.3124894
title: GC-MS Data, experimental replicate 3, co-culture and individual cultures

description: Third experimental replicate. GC-MS of the co-culture, S. cerevisiae alone, and A. malorum alone for initial putative identification of metabolites. Methanol extraction of XAD-4 beads.
DOI: 10.6084/m9.figshare.3124900
title: Ethanol and isobutanol standards, GC-MS

description: Ethanol and isobutanol standards for identification of metabolites in microbial groups<br>
DOI: 10.6084/m9.figshare.3124891
title: GC-MS Data, experimental replicate 2, co-culture and individual cultures

description: Second experimental replicate. GC-MS of the co-culture, S. cerevisiae alone, and A. malorum alone for initial putative identification of metabolites. Methanol extraction of XAD-4 beads Includes standards and samples used for EICs in paper.
DOI: 10.6084/m9.figshare.3124897.v1
title: GC-MS Data, experimental replicate 4, co-culture and individual cultures

description: Fourth experimental replicate. GC-MS of the co-culture, S. cerevisiae alone, and A. malorum alone for initial putative identification of metabolites. Methanol extraction of XAD-4 beads. <br>
DOI: 10.6084/m9.figshare.3124900.v1
title: Ethanol and isobutanol standards, GC-MS

description: Ethanol and isobutanol standards for identification of metabolites in microbial groups<br>
DOI: 10.6084/m9.figshare.3124918.v1
title: 9 June 2014 Field Notes

description: Field notes including image and/or video records.
DOI: 10.6084/m9.figshare.3124888
title: GC-MS Data, experimental replicate 1, co-culture and individual cultures

description: First experimental replicate. GC-MS of the co-culture, S. cerevisiae alone, and A. malorum alone for initial putative identification of metabolites. Methanol extraction of XAD-4 beads. <br>
DOI: 10.6084/m9.figshare.3124888.v1
title: GC-MS Data, experimental replicate 1, co-culture and individual cultures

description: First experimental replicate. GC-MS of the co-culture, S. cerevisiae alone, and A. malorum alone for initial putative identification of metabolites. Methanol extraction of XAD-4 beads. <br>
DOI: 10.6084/m9.figshare.3124891.v1
title: GC-MS Data, experimental replicate 2, co-culture and individual cultures

description: Second experimental replicate. GC-MS of the co-culture, S. cerevisiae alone, and A. malorum alone for initial putative identification of metabolites. Methanol extraction of XAD-4 beads Includes standards and samples used for EICs in paper.
DOI: 10.6084/m9.figshare.3124894.v2
title: GC-MS Data, experimental replicate 3, co-culture and individual cultures

description: Third experimental replicate. GC-MS of the co-culture, S. cerevisiae alone, and A. malorum alone for initial putative identification of metabolites. Methanol extraction of XAD-4 beads.
DOI: 10.6084/m9.figshare.3124894.v1
title: GC-MS of co-culture, S. cerevisiae alone, and A. malorum alone.

description: Third experimental replicate. GC-MS of the co-culture, S. cerevisiae alone, and A. malorum alone for initial putative identification of metabolites. Methanol extraction of XAD-4 beads.
DOI: 10.6084/m9.figshare.3124768
title: Data.zip

description: Data structure:<br>-Stimuli-Experiment_1-Experiment_2-Experiment_3-Experiment_4-AutismQuotient_Exp1to4<br>
DOI: 10.6084/m9.figshare.3124735
title: Raw data for Small RNA-Based Antiviral Defense in the Phytopathogenic Fungus Colletotrichum higginsianum

description: Raw data for each main and supplemental figure plus Perl and R scripts used for data processing.
DOI: 10.6084/m9.figshare.3124609
title: SPME GC-MS Raw Data 2_18, standards, co-culture#4

description: Contains the metabolite mixtures for identificaiton and quantificaiton of volatiles. Also contains another replicates of the co-culture. includes the co-culture with A. pomorum as well.
DOI: 10.6084/m9.figshare.3124606
title: SPME GC-MS Raw Data 2_17, standards, tri-culture#2

description: Dataset includes the 3 metabolite mixture used to identify and quantify metabolites. I also included raw data for the triculture using A. pomorum strains. Dataset also includes co-culture harboring A. pomorum WT or A. pomorum ADH. Also includes acetaldehyde and acetic acid supplementations to co-culture containing A. pomorum ADH<br>
DOI: 10.6084/m9.figshare.3124609.v1
title: SPME GC-MS Raw Data 2_18, standards, co-culture#4

description: Contains the metabolite mixtures for identificaiton and quantificaiton of volatiles. Also contains another replicates of the co-culture. includes the co-culture with A. pomorum as well.
DOI: 10.6084/m9.figshare.3124735.v1
title: Raw data for Small RNA-Based Antiviral Defense in the Phytopathogenic Fungus Colletotrichum higginsianum

description: Raw data for each main and supplemental figure plus Perl and R scripts used for data processing.
DOI: 10.6084/m9.figshare.3124579
title: SPME GC-MS Raw Data 2_16 , co-culture quantification exp#3, tri-culture#1

description: Another experiment to identify and quantify metabolites in the co-culture. Also included the tri-culture (Yeast, LAB, AAB) to compare with the co-culture.<br>
DOI: 10.6084/m9.figshare.3124606.v1
title: SPME GC-MS Raw Data 2_17, standards, tri-culture#2

description: Dataset includes the 3 metabolite mixture used to identify and quantify metabolites. I also included raw data for the triculture using A. pomorum strains. Dataset also includes co-culture harboring A. pomorum WT or A. pomorum ADH. Also includes acetaldehyde and acetic acid supplementations to co-culture containing A. pomorum ADH<br>
DOI: 10.6084/m9.figshare.3124573
title: SPME GC-MS Raw Data 1_30, co-culture quantification exp#2

description: Raw data for metabolite quantification in the co-culture. Also contains unused data regarding SCAP WT co-culture, SCAP ADH co-culture, and SCAP ADH co-culture with acetic acid and acetaldehyde supplementations<br>
DOI: 10.6084/m9.figshare.3124573.v1
title: SPME GC-MS Raw Data 1_30, co-culture quantification exp#2

description: Raw data for metabolite quantification in the co-culture. Also contains unused data regarding SCAP WT co-culture, SCAP ADH co-culture, and SCAP ADH co-culture with acetic acid and acetaldehyde supplementations<br>
DOI: 10.6084/m9.figshare.3124540
title: SPME GC-MS Raw Data 1_20, split series, co-culture quantification exp#1

description: Raw chemistry files associated with metabolite identification and quantification
DOI: 10.6084/m9.figshare.3124348
title: Data from « Plant size and leaf area influence phenological and reproductive responses to warming in semiarid Mediterranean species »

description: Data from "Valencia, E., Méndez, M., Saavedra, N. & Maestre, F. T. Plant size and leaf area influence phenological and reproductive responses to warming in semiarid Mediterranean species. Perspectives in Plant Ecology, Evolution and Systematics.doi:10.1016/j.ppees.2016.05.003"<br>There are two spreadsheets with data. The spreadsheet "Data" contains the raw data at the different years. The spreadsheet "Metadata" contains the associated metadata, where a description of all the variables and units can be found. All the methodological details can be found in the article.<br>Flowering phenology and flower and fruit production in all the plants of each microcosm were scored every two-three days throughout the spring flowering period (from March to early July) of 2012 and 2013. All inflorescences or infructescences were counted in all plant of each microcosm in each census.<br>
DOI: 10.6084/m9.figshare.3124540.v1
title: SPME GC-MS Raw Data 1_20, split series, co-culture quantification exp#1

description: Raw chemistry files associated with metabolite identification and quantification
DOI: 10.6084/m9.figshare.3124348.v1
title: Data from « Plant size and leaf area influence phenological and reproductive responses to warming in semiarid Mediterranean species »

description: Data from "Valencia, E., Méndez, M., Saavedra, N. & Maestre, F. T. Plant size and leaf area influence phenological and reproductive responses to warming in semiarid Mediterranean species. Perspectives in Plant Ecology, Evolution and Systematics.doi:10.1016/j.ppees.2016.05.003"<br>There are two spreadsheets with data. The spreadsheet "Data" contains the raw data at the different years. The spreadsheet "Metadata" contains the associated metadata, where a description of all the variables and units can be found. All the methodological details can be found in the article.<br>Flowering phenology and flower and fruit production in all the plants of each microcosm were scored every two-three days throughout the spring flowering period (from March to early July) of 2012 and 2013. All inflorescences or infructescences were counted in all plant of each microcosm in each census.<br>
DOI: 10.6084/m9.figshare.3124138
title: PloS One Raw data

description: raw data for figures used in PLoS One Manuscript
DOI: 10.6084/m9.figshare.3124324
title: Minimization and estimation of the variance of prediction errors for cross-validation designs

description: We consider the mean prediction error of a classification or regression procedure as well as its cross-validation estimates, and investigate the variance of this estimate as a function of an arbitrary cross-validation design. We decompose this variance into a scalar product of coefficients and certain covariance expressions, such that the coefficients depend solely on the resampling design, and the covariances depend solely on the data’s probability distribution. We rewrite this scalar product in such a form that the initially large number of summands can gradually be decreased down to three under the validity of a quadratic approximation to the core covariances. We show an analytical example in which this quadratic approximation holds true exactly. Moreover, in this example, we show that the leave-<i>p</i>-out estimator of the error depends on <i>p</i> only by means of a constant and can, therefore, be written in a much simpler form. Furthermore, there is an unbiased estimator of the variance of <i>K</i>-fold cross-validation, in contrast to a claim in the literature. As a consequence, we can show that balanced incomplete block designs have smaller variance than <i>K</i>-fold cross-validation. In a real data example from the UCI machine learning repository, this property can be confirmed. We finally show how to find balanced incomplete block designs in practice.
DOI: 10.6084/m9.figshare.3124324.v1
title: Minimization and estimation of the variance of prediction errors for cross-validation designs

description: We consider the mean prediction error of a classification or regression procedure as well as its cross-validation estimates, and investigate the variance of this estimate as a function of an arbitrary cross-validation design. We decompose this variance into a scalar product of coefficients and certain covariance expressions, such that the coefficients depend solely on the resampling design, and the covariances depend solely on the data’s probability distribution. We rewrite this scalar product in such a form that the initially large number of summands can gradually be decreased down to three under the validity of a quadratic approximation to the core covariances. We show an analytical example in which this quadratic approximation holds true exactly. Moreover, in this example, we show that the leave-<i>p</i>-out estimator of the error depends on <i>p</i> only by means of a constant and can, therefore, be written in a much simpler form. Furthermore, there is an unbiased estimator of the variance of <i>K</i>-fold cross-validation, in contrast to a claim in the literature. As a consequence, we can show that balanced incomplete block designs have smaller variance than <i>K</i>-fold cross-validation. In a real data example from the UCI machine learning repository, this property can be confirmed. We finally show how to find balanced incomplete block designs in practice.
DOI: 10.6084/m9.figshare.3124042
title: Electrophysiological Correlates of Morphological Neuroplasticity in Human Callosal Dysgenesis

description: T1-weighted sagittal views and DTI FA maps of the patients.<br>Interhemispheric coherence between homologous leads.<br>Interhemispheric coherence between heterologous leads.<br>Long-distance intrahemispheric coherence.<br>The minimal data set underlying the findings in the manuscript submitted to PLOS ONE, 2016.<br><br><br><br><br>
DOI: 10.6084/m9.figshare.3124132
title: An evaluation of the guidelines of the Society of Obstetricians and Gynaecologists of Canada

description: Clinical practice guidelines hope to offer unbiased, evidence-based guidance for clinicians. This paper examines levels of evidence contained within the guidelines of the Society of Obstetricians and Gynaecologists of Canada and compares classification of the recommendation (CoR) A/B/C/D/E/L (derived from evidence and consensus) versus quality of evidence assessment (QoEA) I-III. 1250 recommendations were analysed and 43% of recommendations were graded as “good” evidence, the highest grade of CoR, while just 24.6% of recommendations were based on the highest level of QoEA (level I). The paper discusses possible reasons for this discrepancy. The authors hope that this analysis promotes greater transparency in evidence-based medicine ultimately leading to using the best quality of evidence available yet taking into account any areas of scientific uncertainty. This will enhance respectful care of patients, while taking into account their autonomy and furthering the cause of patient centre care.
DOI: 10.6084/m9.figshare.3124132.v1
title: An evaluation of the guidelines of the Society of Obstetricians and Gynaecologists of Canada

description: Clinical practice guidelines hope to offer unbiased, evidence-based guidance for clinicians. This paper examines levels of evidence contained within the guidelines of the Society of Obstetricians and Gynaecologists of Canada and compares classification of the recommendation (CoR) A/B/C/D/E/L (derived from evidence and consensus) versus quality of evidence assessment (QoEA) I-III. 1250 recommendations were analysed and 43% of recommendations were graded as “good” evidence, the highest grade of CoR, while just 24.6% of recommendations were based on the highest level of QoEA (level I). The paper discusses possible reasons for this discrepancy. The authors hope that this analysis promotes greater transparency in evidence-based medicine ultimately leading to using the best quality of evidence available yet taking into account any areas of scientific uncertainty. This will enhance respectful care of patients, while taking into account their autonomy and furthering the cause of patient centre care.
DOI: 10.6084/m9.figshare.3124042.v1
title: Electrophysiological Correlates of Morphological Neuroplasticity in Human Callosal Dysgenesis

description: T1-weighted sagittal views and DTI FA maps of the patients.<br>Interhemispheric coherence between homologous leads.<br>Interhemispheric coherence between heterologous leads.<br>Long-distance intrahemispheric coherence.<br>The minimal data set underlying the findings in the manuscript submitted to PLOS ONE, 2016.<br><br><br><br><br>
DOI: 10.6084/m9.figshare.3123985
title: COFINS: UMA ANÁLISE TRIBUTÁRIA DA TERCEIRIZAÇÃO

description: Through a remote view of labor law is sought to enrich the debate about “"ACTIVITIES SHARING" demonstrating the lack of productivity of the strident speech, the inability to hear and following attempts to demonstrate the difficulty in defining what is core business . Advancing at work seeks to demonstrate how the state encouraged first by fiscal means and then with encouragement the opening of micro and small businesses a flattening of the means of production, which in other words is nothing more than an "ACTIVITIES SHARING"of the core business . Finally seek once again demonstrating unproductive shallow criticism and the need for research in sectors which indeed can suffer from a careless regulation of "ACTIVITIES SHARING".
DOI: 10.6084/m9.figshare.3124006
title: EHB Phylogeny Genomic Accession Numbers

description: Accession numbers for all genomes used to build phylogenies for our manuscript.
DOI: 10.6084/m9.figshare.3124015
title: EH_incidence_2009_2012.sav

description: incidence of endometrial hyperplasia
DOI: 10.6084/m9.figshare.3123982
title: Ulysses S. Grant Manumits William Jones

description: This issue of Middle Level Learning includes two articles written by Mary Katherine Morgan and me about Grant and slavery
DOI: 10.6084/m9.figshare.3124006.v1
title: EHB Phylogeny Genomic Accession Numbers

description: Accession numbers for all genomes used to build phylogenies for our manuscript.
DOI: 10.6084/m9.figshare.3124030.v1
title: Original data.xlsx

description: Elevational Variation in Soil Amino Acid and Inorganic Nitrogen Concentrations in Taibai Mountain, China
DOI: 10.6084/m9.figshare.3123982.v1
title: Ulysses S. Grant Manumits William Jones

description: This issue of Middle Level Learning includes two articles written by Mary Katherine Morgan and me about Grant and slavery