cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.2069692.v3
title: Biomarker Benchmark - Gene expression data from Gene Expression Omnibus - GSE4271

description: <br>"Novel prognostic subclasses of high-grade astrocytoma are identified and discovered to resemble stages in neurogenesis. One tumor class displaying neuronal lineage markers shows longer survival, while two tumor classes enriched for neural stem cell markers display equally short survival. Poor prognosis subclasses exhibit either markers of proliferation or of angiogenesis and mesenchyme. Analysis of gene expression data is described in Phillips et al., Cancer Cell, 2006.<br>Keywords: Disease state comparison"<br> <br>http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4271<br>We have included gene-expression data, the outcome (class) being predicted, and any clinical covariates. When gene-expression data were processed in multiple batches, we have provided batch information. Each data set is organized into a file set, where each contains all pertinent files for an individual dataset. The gene expression files have been normalized using both the SCAN and UPC methods using the SCAN.UPC package in Bioconductor (https://www.bioconductor.org/packages/release/bioc/html/SCAN.UPC.html). We summarized the data at the gene level using the BrainArray resource (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/20.0.0/ensg.asp). We used Ensembl identifiers. The class, clinical, and batch data were hand curated to ensure consistency ("tidy data" formatting). In addition, the data files have been formatted to be imported easily into the ML-Flex machine learning package (http://mlflex.sourceforge.net/).
DOI: 10.6084/m9.figshare.2069692.v5
title: Biomarker Benchmark - GSE4271

description: <b><br>[NOTICE: This data set has been deprecated. Please see our new version of the data (and additional data sets) here: https://osf.io/mhk93 ]</b><br><br>"Novel prognostic subclasses of high-grade astrocytoma are identified and discovered to resemble stages in neurogenesis. One tumor class displaying neuronal lineage markers shows longer survival, while two tumor classes enriched for neural stem cell markers display equally short survival. Poor prognosis subclasses exhibit either markers of proliferation or of angiogenesis and mesenchyme. Analysis of gene expression data is described in Phillips et al., Cancer Cell, 2006.<br>Keywords: Disease state comparison"<br> <br>http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4271<br>We have included gene-expression data, the outcome (class) being predicted, and any clinical covariates. When gene-expression data were processed in multiple batches, we have provided batch information. Each data set is organized into a file set, where each contains all pertinent files for an individual dataset. The gene expression files have been normalized using both the SCAN and UPC methods using the SCAN.UPC package in Bioconductor (https://www.bioconductor.org/packages/release/bioc/html/SCAN.UPC.html). We summarized the data at the gene level using the BrainArray resource (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/20.0.0/ensg.asp). We used Ensembl identifiers. The class, clinical, and batch data were hand curated to ensure consistency ("tidy data" formatting). In addition, the data files have been formatted to be imported easily into the ML-Flex machine learning package (http://mlflex.sourceforge.net/).
DOI: 10.6084/m9.figshare.2069696.v5
title: Biomarker Benchmark - Gene expression data from Gene Expression Omnibus - GSE15296

description: <br>"In the present work, we have used whole genome expression profiling of peripheral blood samples from 51 patients with biopsy-proven acute kidney transplant rejection and 24 patients with excellent function and biopsy-proven normal transplant histology. The results demonstrate that there are 1738 probesets on the Affymetrix HG-U133 Plus 2.0 GeneChip representing 1472 unique genes which are differentially expressed in the peripheral blood during an acute kidney transplant rejection. By ranking these results we have identified minimal sets of 50 to 150 probesets with predictive classification accuracies for AR of greater than 90% established with several different prediction tools including DLDA and PAM. We have demonstrated that a subset of peripheral blood gene expression signatures can also diagnose four different subtypes of AR (Banff Borderline, IA, IB and IIA) and the top 100 ranked classifiers have greater than 89% predictive accuracy. Finally, we have demonstrated that there are gene signatures for early and late AR defined as less than or greater than one year post-transplant with greater than 86% predictive accuracies. We also confirmed that there are 439 time-independent gene classifiers for AR. Based on these results, we conclude that peripheral blood gene expression profiling can be used to diagnose AR at any time in the first 5 years post-transplant in the setting of acute kidney transplant dysfunction not caused by BK nephropathy, other infections, drug-induced nephrotoxicity or ureteral obstruction.<br><br>Keywords: kidney transplantation, peripheral blood, DNA microarrays, acute kidney rejection, biomarkers"<br><br>http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE15296<br>We have included gene-expression data, the outcome (class) being predicted, and any clinical covariates. When gene-expression data were processed in multiple batches, we have provided batch information. Each data set is organized into a file set, where each contains all pertinent files for an individual dataset. The gene expression files have been normalized using both the SCAN and UPC methods using the SCAN.UPC package in Bioconductor (https://www.bioconductor.org/packages/release/bioc/html/SCAN.UPC.html). We summarized the data at the gene level using the BrainArray resource (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/20.0.0/ensg.asp). We used Ensembl identifiers. The class, clinical, and batch data were hand curated to ensure consistency ("tidy data" formatting). In addition, the data files have been formatted to be imported easily into the ML-Flex machine learning package (http://mlflex.sourceforge.net/).
DOI: 10.6084/m9.figshare.2069674
title: Adaptive trait evolution in random environment

description: Current phylogenetic comparative methods generally employ the Ornstein–Uhlenbeck(OU) process for modeling trait evolution. Being able of tracking the optimum of a trait within a group of related species, the OU process provides information about the stabilizing selection where the population mean adopts a particular trait value. The optima of a trait may follow certain stochastic dynamics along the evolutionary history. In this paper, we extend the current framework by adopting a rate of evolution which behave according to pertinent stochastic dynamics. The novel model is applied to analyze about 225 datasets collected from the existing literature. Results validate that the new framework provides a better fit for the majority of these datasets.
DOI: 10.6084/m9.figshare.2069692.v4
title: Biomarker Benchmark - Gene expression data from Gene Expression Omnibus - GSE4271

description: <br>"Novel prognostic subclasses of high-grade astrocytoma are identified and discovered to resemble stages in neurogenesis. One tumor class displaying neuronal lineage markers shows longer survival, while two tumor classes enriched for neural stem cell markers display equally short survival. Poor prognosis subclasses exhibit either markers of proliferation or of angiogenesis and mesenchyme. Analysis of gene expression data is described in Phillips et al., Cancer Cell, 2006.<br>Keywords: Disease state comparison"<br> <br>http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4271<br>We have included gene-expression data, the outcome (class) being predicted, and any clinical covariates. When gene-expression data were processed in multiple batches, we have provided batch information. Each data set is organized into a file set, where each contains all pertinent files for an individual dataset. The gene expression files have been normalized using both the SCAN and UPC methods using the SCAN.UPC package in Bioconductor (https://www.bioconductor.org/packages/release/bioc/html/SCAN.UPC.html). We summarized the data at the gene level using the BrainArray resource (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/20.0.0/ensg.asp). We used Ensembl identifiers. The class, clinical, and batch data were hand curated to ensure consistency ("tidy data" formatting). In addition, the data files have been formatted to be imported easily into the ML-Flex machine learning package (http://mlflex.sourceforge.net/).
DOI: 10.17028/rd.lboro.2069672
title: Constant Temperature Induced Stress in Evacuated Enclosures for Flat Plate Solar Thermal Collectors - dataset

description: Finite element model predictions and experimental digital image correlation stress data for a prototype flat plate solar thermal collector fabricated at Loughborough University.
DOI: 10.6084/m9.figshare.2069674.v1
title: Adaptive trait evolution in random environment

description: Current phylogenetic comparative methods generally employ the Ornstein–Uhlenbeck(OU) process for modeling trait evolution. Being able of tracking the optimum of a trait within a group of related species, the OU process provides information about the stabilizing selection where the population mean adopts a particular trait value. The optima of a trait may follow certain stochastic dynamics along the evolutionary history. In this paper, we extend the current framework by adopting a rate of evolution which behave according to pertinent stochastic dynamics. The novel model is applied to analyze about 225 datasets collected from the existing literature. Results validate that the new framework provides a better fit for the majority of these datasets.
DOI: 10.6084/m9.figshare.2069646
title: Reporting Bias Inflates the Reputation of Medical Treatments: Datasets and analysis syntax

description: Dataset and analysis syntax associated with " Reporting Bias Inflates the Reputation of Medical Treatments: A Comparison of Outcomes in Clinical Trials and Online Product Reviews" Social Science and Medicine, 2017
DOI: 10.6084/m9.figshare.2069622
title: Additional files for paper "Plasma metabolome signature in patients with early-stage Parkinson disease".

description: Patients.pdf - Clinical characteristics of patients. Mass list.zip - Mass lists.Mass spectra.zip - Mass spectra in mzXL format. Mass spectra.tif - Mass spectra (screenshots) of the metabolites listed in the Table 2.<br><br>
DOI: 10.6084/m9.figshare.2069616
title: Drosophila_melanogaster_wings_NutritionalGeometry

description: This is a stub for now.. More details to be added<br>Provenance of samples:<br>6 "genotypes" of Drosophila melanogaster were used.5 are DGRP (Drosophila Genetic Resource Panel) strains specifically chosen based on preliminary data on how they varied for sexual size dimorphism (SSD) and sexual shape dimorphism. The final was from an outbred population colllected at Country Mill Orchard, in Charlotte Michigan, USA in the fall of 2014. This final population was maintained at large population sizes with relatively relaxed selection, but some lab domestication is inevitable.<br>In the fall of 2015, several distinct diets (varying yeast and molasses primarily) were created to vary protein, sugars and total calories. Eggs from each of the strains above (25 eggs/vial) were placed into vials containing 3 mL of each food type. Once adult flies emerged (we will add survival data for each food type), adults were allowed to scleratize and then stored in 70% ethanol until dissection. <br>A single wing was dissected from individuals. between 5-10 males and females (when survival was high enough for each vial) were dissected (or as many as available).<br>Imaging:These images were all captured on a Zeiss (??) microscope at 50X magnification (5X objective). All images were captured as 16bit tifs (so you may need to convert to 8 bit for specific applications).
DOI: 10.6084/m9.figshare.2069646.v1
title: Lay Communication About Medicine’s Effectiveness is Biased by Under-Reporting of Negative Outcomes

description: Dataset and analysis syntax associated with "Lay Communication About Medicine’s Effectiveness is Biased by Under-Reporting of Negative Outcomes"
DOI: 10.6084/m9.figshare.2069646.v3
title: Reporting Bias Inflates the Reputation of Medical Treatments: Datasets and analysis syntax

description: Dataset and analysis syntax associated with " Reporting Bias Inflates the Reputation of Medical Treatments: A Comparison of Outcomes in Clinical Trials and Online Product Reviews" Social Science and Medicine, 2017
DOI: 10.6084/m9.figshare.2069622.v1
title: Mass spectra for paper "Diagnosing Parkinson's disease using mass spectrometric metabolome signature of blood plasma".

description: Zip archive of mass spectra in mzXL format. Details see in paper.
DOI: 10.6084/m9.figshare.2069646.v2
title: Why people overestimate the effectiveness of medical treatments: Cross-sectional survey of Amazon reviews suggests widespread over-reporting of positive outcomes

description: Dataset and analysis syntax associated with "Why people overestimate the effectiveness of medical treatments: Cross-sectional survey of Amazon reviews suggests widespread over-reporting of positive outcomes"
DOI: 10.6084/m9.figshare.2069586
title: Evolutionary conservation of the circadian gene timeout in Metazoa

description: <i>Timeless </i>(<i>Tim</i>) is considered to function as an essential circadian clock gene in <i>Drosophila</i>. Putative homologues of the <i>Drosophila timeless </i>gene have been identified in both mice and humans. While <i>Drosophila </i>contains two paralogs, <i>timeless </i>and <i>timeout</i>, acting in clock/light entrainment and chromosome integrity/photoreception, respectively, mammals contain only one <i>Tim </i>homolog. In this paper, we study the phylogeny of the <i>timeless</i>/<i>timeout </i>family in 48 species [including 1 protozoan (<i>Guillardia theta</i>), 1 nematode (<i>Caenorhabditis elegans</i>), 8 arthropods and 38 chordates], for which whole genome data are available by using MEGA (Molecular Evolutionary Genetics Analysis). Phylogenetic Analysis by Maximum Likelihood (PAML) was used to analyze the selective pressure acting on metazoan <i>timeless</i>/<i>timeout </i>genes. Our phylogeny clearly separates insect <i>timeless </i>and <i>timeout </i>lineages and shows that non-insect animal <i>Tim </i>genes are homologs of insect <i>timeout</i>. In this study, we explored the relatively rapidly evolving <i>timeless </i>lineage that was apparently lost from most deuterostomes, including chordates, and from <i>Caenorhabditis elegans</i>. In contrast, we found that the <i>timeout </i>protein, often confusingly called “<i>timeless</i>” in the vertebrate literature, is present throughout the available animal genomes. Selection results showed that <i>timeout </i>is under weaker negative selection than <i>timeless</i>. Finally, our phylogeny of <i>timeless</i>/<i>timeout </i>showed an evolutionary conservation of the circadian clock gene <i>timeout </i>in Metazoa. This conservation is in line with its multifunctionality, being essential for embryonic development and maintenance of chromosome integrity, among others.
DOI: 10.6084/m9.figshare.2069586.v1
title: Evolutionary conservation of the circadian gene timeout in Metazoa

description: <i>Timeless </i>(<i>Tim</i>) is considered to function as an essential circadian clock gene in <i>Drosophila</i>. Putative homologues of the <i>Drosophila timeless </i>gene have been identified in both mice and humans. While <i>Drosophila </i>contains two paralogs, <i>timeless </i>and <i>timeout</i>, acting in clock/light entrainment and chromosome integrity/photoreception, respectively, mammals contain only one <i>Tim </i>homolog. In this paper, we study the phylogeny of the <i>timeless</i>/<i>timeout </i>family in 48 species [including 1 protozoan (<i>Guillardia theta</i>), 1 nematode (<i>Caenorhabditis elegans</i>), 8 arthropods and 38 chordates], for which whole genome data are available by using MEGA (Molecular Evolutionary Genetics Analysis). Phylogenetic Analysis by Maximum Likelihood (PAML) was used to analyze the selective pressure acting on metazoan <i>timeless</i>/<i>timeout </i>genes. Our phylogeny clearly separates insect <i>timeless </i>and <i>timeout </i>lineages and shows that non-insect animal <i>Tim </i>genes are homologs of insect <i>timeout</i>. In this study, we explored the relatively rapidly evolving <i>timeless </i>lineage that was apparently lost from most deuterostomes, including chordates, and from <i>Caenorhabditis elegans</i>. In contrast, we found that the <i>timeout </i>protein, often confusingly called “<i>timeless</i>” in the vertebrate literature, is present throughout the available animal genomes. Selection results showed that <i>timeout </i>is under weaker negative selection than <i>timeless</i>. Finally, our phylogeny of <i>timeless</i>/<i>timeout </i>showed an evolutionary conservation of the circadian clock gene <i>timeout </i>in Metazoa. This conservation is in line with its multifunctionality, being essential for embryonic development and maintenance of chromosome integrity, among others.
DOI: 10.6084/m9.figshare.2069622.v2
title: Mass spectra for paper "Diagnosing Parkinson's disease using mass spectrometric metabolome signature of blood plasma".

description: Patients.pdf - Clinical characteristics of patients. Mass list.zip - mass lists.Mass spectra.zip - archive of mass spectra in mzXL format. Details see in paper.
DOI: 10.6084/m9.figshare.2069622.v3
title: Additional files for paper "Diagnosing Parkinson's disease using mass spectrometric metabolome signature of blood plasma".

description: Patients.pdf - Clinical characteristics of patients. Mass list.zip - Mass lists.Mass spectra.zip - Mass spectra in mzXL format. <br>
DOI: 10.6084/m9.figshare.2069616.v3
title: Drosophila_melanogaster_wings_NutritionalGeometry

description: This is a stub for now.. More details to be added<br>Provenance of samples:<br>6 "genotypes" of Drosophila melanogaster were used.5 are DGRP (Drosophila Genetic Resource Panel) strains specifically chosen based on preliminary data on how they varied for sexual size dimorphism (SSD) and sexual shape dimorphism. The final was from an outbred population colllected at Country Mill Orchard, in Charlotte Michigan, USA in the fall of 2014. This final population was maintained at large population sizes with relatively relaxed selection, but some lab domestication is inevitable.<br>In the fall of 2015, several distinct diets (varying yeast and molasses primarily) were created to vary protein, sugars and total calories. Eggs from each of the strains above (25 eggs/vial) were placed into vials containing 3 mL of each food type. Once adult flies emerged (we will add survival data for each food type), adults were allowed to scleratize and then stored in 70% ethanol until dissection. <br>A single wing was dissected from individuals. between 5-10 males and females (when survival was high enough for each vial) were dissected (or as many as available).<br>Imaging:These images were all captured on a Zeiss (??) microscope at 50X magnification (5X objective). All images were captured as 16bit tifs (so you may need to convert to 8 bit for specific applications).
DOI: 10.6084/m9.figshare.2069622.v4
title: Additional files for paper "Diagnosing Parkinson's disease using mass spectrometric metabolome signature of blood plasma".

description: Patients.pdf - Clinical characteristics of patients. Mass list.zip - Mass lists.Mass spectra.zip - Mass spectra in mzXL format. <br>
DOI: 10.6084/m9.figshare.2069616.v5
title: Drosophila_melanogaster_wings_NutritionalGeometry

description: This is a stub for now.. More details to be added<br>Provenance of samples:<br>6 "genotypes" of Drosophila melanogaster were used.5 are DGRP (Drosophila Genetic Resource Panel) strains specifically chosen based on preliminary data on how they varied for sexual size dimorphism (SSD) and sexual shape dimorphism. The final was from an outbred population colllected at Country Mill Orchard, in Charlotte Michigan, USA in the fall of 2014. This final population was maintained at large population sizes with relatively relaxed selection, but some lab domestication is inevitable.<br>In the fall of 2015, several distinct diets (varying yeast and molasses primarily) were created to vary protein, sugars and total calories. Eggs from each of the strains above (25 eggs/vial) were placed into vials containing 3 mL of each food type. Once adult flies emerged (we will add survival data for each food type), adults were allowed to scleratize and then stored in 70% ethanol until dissection. <br>A single wing was dissected from individuals. between 5-10 males and females (when survival was high enough for each vial) were dissected (or as many as available).<br>Imaging:These images were all captured on a Zeiss (??) microscope at 50X magnification (5X objective). All images were captured as 16bit tifs (so you may need to convert to 8 bit for specific applications).
DOI: 10.6084/m9.figshare.2069573
title: endo_et-al_table1.xls

description: Table 1 from Endo et al. PeerJ 2016 https://doi.org/10.7717/peerj.1562/table-1<br>
DOI: 10.6084/m9.figshare.2069573.v1
title: endo_et-al_table1.xls

description: Table 1 from Endo et al. PeerJ 2016 https://doi.org/10.7717/peerj.1562/table-1<br>
DOI: 10.6084/m9.figshare.2069616.v4
title: Drosophila_melanogaster_wings_NutritionalGeometry

description: This is a stub for now.. More details to be added<br>Provenance of samples:<br>6 "genotypes" of Drosophila melanogaster were used.5 are DGRP (Drosophila Genetic Resource Panel) strains specifically chosen based on preliminary data on how they varied for sexual size dimorphism (SSD) and sexual shape dimorphism. The final was from an outbred population colllected at Country Mill Orchard, in Charlotte Michigan, USA in the fall of 2014. This final population was maintained at large population sizes with relatively relaxed selection, but some lab domestication is inevitable.<br>In the fall of 2015, several distinct diets (varying yeast and molasses primarily) were created to vary protein, sugars and total calories. Eggs from each of the strains above (25 eggs/vial) were placed into vials containing 3 mL of each food type. Once adult flies emerged (we will add survival data for each food type), adults were allowed to scleratize and then stored in 70% ethanol until dissection. <br>A single wing was dissected from individuals. between 5-10 males and females (when survival was high enough for each vial) were dissected (or as many as available).<br>Imaging:These images were all captured on a Zeiss (??) microscope at 50X magnification (5X objective). All images were captured as 16bit tifs (so you may need to convert to 8 bit for specific applications).
DOI: 10.6084/m9.figshare.2069622.v5
title: Additional files for paper "Diagnosing Parkinson's disease using direct infusion mass spectrometry of blood plasma metabolites".

description: Patients.pdf - Clinical characteristics of patients. Mass list.zip - Mass lists.Mass spectra.zip - Mass spectra in mzXL format. <br>