cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17632/sv2byw2v5f.1
title: Data for: Transcript-wide association study identifies genes associated with aerobic and anaerobic intervention and prospective free-living active energy expenditure

description: Physical activity is associated with decreased risk for many chronic and acute conditions and is increasingly used as a therapeutic intervention for diabetes, cardiovascular disease among others. In this study, we aimed to identify common changes in expression of genes due to aerobic and anaerobic physical activity and investigated the efficacy of the identified exercise intervention signature in predicting prospective “real life” activity and sedentary behavior. We performed a multi-cohort analysis of twenty publicly available datasets (N=638) and identified a 23-gene set that discriminated between pre- and post- exercise in four independent interventional cohorts (N=245) validation sets with an average area under the curve (AUC) of 0.75. Our results suggest that our PA signature can be used be used as a means to assess physical activity intervention aggregated over a period of time, irrespective of the exercise modality and intensity of exercise. The data deposited here represent the 638 samples that were used for Discovery of the signature and the 245 samples that were used for validation. All of these datasets are publicly available Gene Expression Omnibus. The dataset included here provides the original Gene Expression Omnibus accession number (GSE), together with high level details on the protocol, the total number of samples available, the exercise protocol, the sample type. We also include information on the number of samples that were used in our analysis to identify the 23 gene signature of physical activity together with the phase (Discovery vs Validation) information.
DOI: 10.17632/tbrxk378kh.1
title: Genome-wide CRISPR-Cas9 screens expose genetic vulnerabilities and mechanisms of TMZ sensitivity in glioblastoma stem cells. MacLeod and Bozek et al 2019.

description: Representative western blot analysis of total protein lysate from G510NS-Cas9, G523NS-Cas9 and HF7450-Cas9 cells expressing the indicated gRNAs. Uncropped images used in the creation of Figure S3E.
DOI: 10.17632/jk2p9k43f8.1
title: Promotor FASTA sequences

description: Promoter sequences of the primers used in the RT-qPCR analysis for public consultation
DOI: 10.17632/mcb726kcbx.1
title: Species Distribution Modelling of Corals and Sponges in the Eastern Arctic for Use in the Identification of Significant Benthic Areas

description: Species distribution modelling using a random forest (RF) machine learning approach was used to predict the probability of occurrence and biomass of sponges, sea pens, and large and small gorgonian corals in the Hudson Strait portion of Fisheries and Oceans, Canada's (DFO) Hudson Bay Complex Biogeographic Zone (sponges only), and in the eastern extent (Davis Strait and Southern Baffin Bay) of the Eastern Arctic Biogeographic Zone. A suite of 54 environmental predictor variables from different data sources were used. Models utilized catch records from the DFO multispecies trawl surveys and DFO/industry northern shrimp surveys collected between 2006 and 2014. For each taxonomic group in each region, both presence-absence random forest models using data collected across gear types (Alfredo, Campelen, and Cosmos trawls), and biomass random forest models using data collected within gear types were run. Most presence-absence models had good predictive capacity with cross-validated Area Under the Receiver Operating Characteristic Curve (AUC) values ranging from 0.643 to 0.894. The lower AUC was produced from the Hudson Strait sponge model, which also had poor sensitivity and specificity relative to the models performed in the Eastern Arctic Biogeographic Zone. The random forest biomass models performed inconsistently within taxa by gear type, with the models for sponges using data from Alfredo and Campelen trawl surveys perfoming best (R2 = 0.327 and 0.480 respectively). Generalized additive models (GAMs) were developed to predict the biomass distribution of each taxonomic group and serve as a comparison to the RF models. Aside from providing continuous prediction maps of significant benthic taxa for these regions, our results will be useful in ecosystem management decision-making processes. In particular, good SDM models could be used to refine the outer boundaries of significant concentrations of these organisms identified by kernel density analyses and identify new suitable habitat not sampled by the trawl surveys in areas of extrapolation.
DOI: 10.17632/pg8fpsxytb.1
title: Distribution Modelling of Sea Pens, Sponges, Stalked Tunicates and Soft Corals from Research Vessel Survey Data in the Gulf of St. Lawrence for Use in the Identification of Significant Benthic Areas

description: Models of probability of occurrence and predicted biomass distribution have been created using random forest (RF) machine learning techniques for different invertebrate taxa in the Gulf of St. Lawrence. Response data were derived from by-catch data collected from DFO research vessel trawl surveys following a stratified random design based on depth and geographic region. Predictors were drawn from 78 environmental data layers. Occurrence models performed very well for sea pens and stalked tunicates and better than those for soft corals and sponges, with cross-validated AUC (area under the receiver operating characteristic curve) values ranging from 0.71 to 0.91. For the models based on biomass, soft corals and sea pens had the highest R2 values (0.42 and 0.37, respectively) in the southern Gulf of St. Lawrence and stalked tunicates and sea pens in the north (0.41 and 0.27, respectively). Sponges had R2 values less than 0.1 in both areas indicating poor model performance. Biomass models from RF were compared with Generalized Additive Models (GAM). In most of the cases RF and GAM models provided similar results and were both good options, although the fewer assumptions required for RF makes this method more convenient. These results could be used to identify the potential distribution of some vulnerable marine ecosystems indicator taxa and help to refine the borders of the significant benthic area polygons defining significant concentrations of these taxa as identified through the kernel density analyses. In particular these models can be used to extrapolate to areas not covered by the research vessel surveys.
DOI: 10.17632/vhyfvrc2sj.1
title: CEBPB VEGF - Neurite Count & Length Raw Data
DOI: 10.17632/3mwkv3jwr5.1
title: Effect of CEBP or CHOP-10 deletion on neurosphere cell counts
DOI: 10.17632/s6bpbbshjn.1
title: Effect of CEBPB or CHOP-10 deletion on neurosphere diameter
DOI: 10.17632/zwvv3xx3rc.1
title: Species Distribution Modelling of Corals and Sponges from Research Vessel Survey Data in the Newfoundland and Labrador Region for Use in the Identification of Significant Benthic Areas

description: We used a species distribution modelling approach called random forest (RF) to predict the probability of occurrence and biomass of sponges, sea pens, and large and small gorgonian corals across the entire spatial extent of Fisheries and Oceans, Canada's (DFO) Newfoundland and Labrador Region. A suite of 66 environmental variables from different data sources were used. Models utilized catch records from the DFO multispecies trawl survey, DFO/industry northern shrimp surveys, and Spanish trawl surveys. Most models had excellent predictive capacity with cross-validated Area Under the Receiver Operating Characteristic Curve (AUC) values ranging from 0.786 to 0.926. Areas of suitable habitat were identified for each taxon and were contrasted against their known distribution. Generalized additive models (GAMs) were developed to predict the biomass distribution of each taxonomic group and serve as a comparison to the RF models. The RF and GAM models provided similar results, although GAMs provided superior predictions of biomass along the slopes of Newfoundland and Labrador for some taxonomic groups. Aside from providing continuous prediction maps of significant benthic taxa for the entire Newfoundland and Labrador Region that will be useful in ecosystem management decision-making processes, these results could be used to refine the outer boundaries of significant concentrations of these organisms identified by kernel density analyses and identify new suitable habitat not sampled by the trawl surveys.
DOI: 10.17632/9h564xrc5p.1
title: Flight data

description: The data include 66 radar tracks of aircraft pairs with short-term conflict alerts.
DOI: 10.17632/br4hyykj9k.1
title: Data for: 3320058

description: (Abstract) The purpose of this study is to analyze manufacturing firms’ choice of production as a strategic decision to increase their product innovation and internationalization using firm-survey data collected from Korea. The independent and moderating variables are derived from the transaction cost perspective, industry-based perspective and institution-based perspective. By bringing together the three (3) perspectives, this research attempts to investigate the extent to which outsourcing strategy decisions of the firms and the environmental context in which the firms operate determine the level of innovation and internationalization performance. With a sample of 164 manufacturing firms form Korea, the data was tested using logistic and linear (OLS) regression analysis to analyze the effects of outsourcing, competitive pressure and property right protection on product innovation and internationalization. The findings show that outsourcing helps firms to reduce the resources required to manufacture existing products and enable a firm capacity to utilize those saved resources on core competencies needed to create innovation. Furthermore, the study observes a negative moderating effect of competitive pressure on the relationship between outsourcing and innovation, indicating that in a highly competitive environment, firms should seriously consider internal production to prevent potential knowledge spillovers to other competitors. Finally, this study finds that the strength of the property right has a significant moderating effect towards firm’s export capacity. Through the results of this research, implications for managers and policy makers on how to increase product innovation and internationalization can be derived.
DOI: 10.17632/fmphzvrzh6.1
title: Unconformities, neptunian dykes and mass-transport deposits as an evidence for Early Cretaceous syn-sedimentary tectonics: new insights from the Central Apennines

description: Provided are: (i) the field pictures of outcrops without line drawings; (ii) the comprehensive view of the full thin sections, samples AC198A, AC938, AC1026, AC1032, AC1032a; (iii) 2D block diagram, not to scale, reconstructing the tectono-sedimentary evolution of the study area.
DOI: 10.17632/mwsns7fgb4.1
title: Species Distribution Modelling of Corals and Sponges in the Maritimes Region for Use in the Identification of Significant Benthic Areas

description: Effective fisheries and habitat management processes require knowledge of the distribution of areas of high ecological or biological significance. On the Scotian Shelf and Slope, a number of benthic ecologically or biologically significant areas consisting of habitat-forming species such as sponges and deep-water corals have been identified. However, knowledge of their spatial distribution is largely based on targeted surveys that are limited in their spatial extent. We used a species distribution modelling approach called random forest (RF) to predict the probability of occurrence and biomass of sponges, sea pens, and large and small gorgonian corals across the entire spatial extent of Fisheries and Oceans Canada’s (DFO) Maritimes Region. We also modelled the rare sponge Vazella pourtalesi, which forms the largest known aggregation of its kind on the Scotian Shelf. We utilized a number of data sources including DFO multispecies trawl catch data and in situ benthic imagery observations. Most models had excellent predictive capacity with cross-validated Area Under the Receiver Operating Characteristic Curve (AUC) values ranging from 0.760 to 0.977. Areas of suitable habitat were identified for each taxon and were contrasted against their known distribution and when applicable, the location of closure areas designated for their protection. Generalized additive models (GAMs) were developed to predict the biomass distribution of each taxonomic group and serve as a comparison to the RF models. The RF and GAM models provided comparable results, although GAMs provided superior predictions of biomass along the continental slope for some taxonomic groups. In the absence of data observations, the results of this study could be used to identify the potential distribution of sensitive benthic taxa for use in fisheries and habitat management applications. These results could also be used to refine significant concentrations of these taxa as identified through the kernel density analyses.
DOI: 10.17632/7fg9ytrgfm.1
title: Dislocation density of plasma-exposed tungsten and corresponding force-depth relationships obtained by nano-indentation

description: Dislocation density of plasma-exposed tungsten and corresponding force-depth relationships obtained by nano-indentation
DOI: 10.17632/jw3zwf8rdp.2
title: Sepehr_RumTel01

description: The expansion of social networks has accelerated the transmission of information and news at every communities. Over the past few years, the number of users, audiences and social networking publishers, are increased dramatically too. Among the massive amounts of information and news reported on these networks, we are faced with issues that have not been verified which is called “rumors”. Identifying rumors on social networks is carried out in the form of rumor detection approaches; the massive amount of these news and information force to use the machine learning techniques. The most important problem with auto-detection approaches is the lack of a database of rumors. For that matter, in this article, a collection of rumors published on the social network “telegrams” have been collected. These data are gathered from five Persian-language channels that have specially reviewed this issue. The collected data set contains 3283 messages with 2829 attachments, having a volume of over 1.6 gigabytes. This dataset can also be used for different purposes of natural language processing.
DOI: 10.17632/kb4x29z3wj.1
title: Data for: A reef coral in the condensed Maiolica facies on the Mt. Nerone pelagic carbonate platform (Marche Apennines): the enigma of ancient pelagic deposits

description: In this datasetare provided: - digital 3D model in .PLY format of the coral Ogilvinella elegans from the Upper Jurassic of Monte Nerone pelagic carbonate platform; - comprehensive view of the full four thin sections obtained from the coral; - information about the 3D photogrammetric model.
DOI: 10.17632/prdtw5jgcd.1
title: Parallel multimodal circuits control an innate foraging behavior

description: Complete foraging data in Lopez-Cruz et. al Neuron 2019.
DOI: 10.17632/2tn6gjbt5j.1
title: imageRBC

description: This repository contains data extracted from experiments with images obtained via optical microscope coupled via USB on a computer. The images are proportional to the frames of the Neubauer camera, these images were separated in the High, Normal and Low directories, proportional to the concentration of the quantitative red cells in each image. In the repository are files compressed with the images by the algorithms of binarization in its components. Just like the codes in Matlab.
DOI: 10.17632/698xxsvfzw.2
title: SmallScaleSMR

description: The data consists the following items: 1. The pinch analysis stream information and grand composite curve data points. 2. Exergy balance results across different sections of the small-scale SMR process at different reforming temperatures.
DOI: 10.17632/9cbkcpm7tg.1
title: Single-molecule imaging of mRNA localization and regulation during the integrated stress response

description: Images used in figures
DOI: 10.17632/t5xb48z959.1
title: MHC Ligandomes of Reovirus-Treated Tumors

description: Using a mass spectrometry (MS)-based MHC-I ligandome discovery platform, we determined differential tumor MHC-I ligand expression following treatment with oncolytic reovirus in a murine ovarian cancer model. We then tested the immunogenicity and antitumor immune effects of CD8 T cells specific to these reovirus-induced ligands.
DOI: 10.17632/wr4xddybvg.1
title: Analysis of the S. pombe meiotic proteome reveals a switch from anabolic to catabolic processes and extensive post-transcriptional regulation

description: Meiotic progression in S. pombe is regulated by stage-specific gene expression and translation, changes in RNA stability, expression of anti-sense transcripts and targetted proteolysis of regulatory proteins. We have used SILAC labelling to examine the relative levels of proteins in diploid S. pombe cells during meiosis. Among the 3268 proteins quantified at all time points, the level of 880 proteins changed at least two-fold; the majority of proteins showed a stepwise increase or decrease during the meiotic divisions, while some changed transiently. Overall, we observed a reduction in proteins involved in anabolism and an increase in proteins involved in catabolism. We also saw an increase in the level of proteins of the ESCRT-III complex and revealed a role for ESCRT-III components in chromosome segregation and spore formation. Correlation with studies of meiotic gene expression and ribosome occupancy reveals that many of the changes in steady state protein levels are post-transcriptional.
DOI: 10.17632/zkxbj44zmd.1
title: DNA Data base entropy

description: The Shannon entropy of mtDNA of each species is converted into fractal entropy
DOI: 10.17632/6dzmrjngcg.2
title: AFM images and processing routine

description: The aim of this study was to investigate the correlation between inorganic scale formation and booth surface free energy and surface roughness. This data includes both atomic force microscopy images from stainless steel and carbon-coated stainless steel samples and the ImageJ routine developed to measure the roughness exponent of those images. In this area of research, the surface average roughness is the parameter of choice to describe the surface roughness. However, it is not intrinsic to the surface, as it depends on the measuring method. Therefore, the roughness exponent, a parameter independent of the measuring method and able to describe the roughness across a range of different length scales, is advantageous.
DOI: 10.17632/sx9xxkkfxj.1
title: Implant stability measurement between resonance frequency analysis device and a novel damping capacity analysis device

description: Peak insertion torque (PIT); peak removal torque (PRT); implant stability quotient (ISQ) value; and implant stability test (IST) value
DOI: 10.17632/wgmfxds99c.1
title: hESC-derived thalamic organoids form reciprocal projections when fused with cortical organoids, Xiang et al.

description: Human brain organoid techniques have rapidly advanced to facilitate investigating human brain development and diseases. Recent reports in generation and fusion of regionally defined brain organoids provide further opportunities to investigate the specific brain domains and their interactions. Focus of brain organoids has been to generate telencephalon due to its direct relevance in a variety of forebrain disorders. Despite its importance as a relay hub between cortex and peripheral tissues, the investigation of three-dimensional (3D) organoid model for the human thalamus has not yet been explored. Here, we describe a method to differentiate human embryonic stem cells (hESCs) to the thalamic organoids (hThOs) that specifically recapitulate the development of thalamus. Single-cell RNA sequencing (scRNA-seq) revealed a formation of distinct thalamic lineage cells, a lineage divergence from telencephalic lineage. Importantly, we developed a 3D system to create the reciprocal projections between thalamus and cortex by fusing the two distinct region-specific organoids representing the developing thalamus or cortex. Our study provides a platform for understanding human thalamic development and modeling circuit organizations and related disorders in the brain.
DOI: 10.17632/xj73dc2gsb.1
title: Supplemental data for Cretaceous Research Paper: “Regional upper Albian-lower Cenomanian sequence boundaries, Texas Comanche shelf: Is timing related to oceanic tectonics?”

description: This Chronostratigraphic Database is a compilation of more than 3400 fossil taxa and marker beds calibrated to a numerical mega-annum scale. These events are integrated from more than 300 published worldwide sections that span from the Jurassic/Cretaceous boundary to the Cretaceous/Paleogene boundary. This list is specificaly extracted for Albian-lower Cenomanian stratigraphic sections in Texas. The numerical ages of the ranges have been interpolated by graphic correlation of these sections. Thus the ages and stratigraphic order of taxa, event beds and of key sequence contacts in defined reference sections can be tested and objectively analyzed. The ranges of First Appearance and Last Appearance Datums (FAD/LAD) are presented in mega-annums calibrated to the 2016 Cretaceous Time Scale (Ogg et al. 2016). Stages are defined by Global Stratotype and Section Points or to reference sections where GSSPs are not yet designated. The ages of the taxa and marker beds are preliminary because ranges of some taxa are constrained by very few sections so that their ages may extend as new sections are added to the database
DOI: 10.17632/2hfw99xz44.1
title: Distinguishing hashtags of the active and passive communities detected on the subject of vaccinations in Italy

description: The dataset reports the distinguishing hashtags of the active and passive communities detected on the subject of vaccinations in Italy in August 2018 on Twitter. Each worksheet refers to a different scenario (i.e., a different set of considered communities) and shows, for each hashtag in each community, the term frequency, and the term frequency ratio.
DOI: 10.17632/sxsydxhwbs.1
title: Data for Ti-Nb-Ta

description: Experimental data and TDB file for Ti-Nb-Ta system
DOI: 10.17632/x7r44fgzxc.1
title: Retapamulin-assisted ribosome profiling reveals the alternative bacterial proteome
DOI: 10.17632/z67h8mwcvj.1
title: Force-depth relationships of ion-irradiated SS304

description: Force-depth relationship of SS304 with/without irradiation effect
DOI: 10.17632/zs9bn74j4c.1
title: Self-Mention Markers-UK vs. TR Dissertations

description: Raw and normalized frequencies of self-mention markers in the dissertations of literature (UK vs. TR)
DOI: 10.5281/zenodo.2547427
title: Dataset _ Seasonal variation of biogas upgrading coupled with digestate treatment in an outdoors pilot scale algal-bacterial photobioreactor

description: This is the dataset used for the publication of the journal article title<em> “</em><strong>Seasonal variation of biogas upgrading coupled with digestate treatment in an outdoors pilot scale algal-bacterial photobioreactor</strong><strong>”. </strong>In this dataset there is all the information collected in the experimentation process.
description: {"references": ["Alc\u00e1ntara et al (2015), Andriani et al (2014), APHA (2005), Bahr et al (2014), Bi and He (2013)", "Cai et al (2013), European Biogas Association (2016), Farroq et al (2018), Lebrero et al (2016)", "Meier et al (2015), Mendoza et al (2013), Metcalf (2003), Mu\u00f1oz et al (2015), Norvill et al (2017)", "Park et al (2011), Posadas et al (2017a), Posadas et al (2014), Posadas et al (2015)", "Posadas et al (2016), Posadas et al (2017b), Ryckebosch et al (2011), Sander (2015)", "Serejo et al (2015), Toledo-Cervantes et al (2016), Toledo-cervantes et al (2017a)", "Toledo-Cervantes et al (2017b), Torzillo el al (2003)"]}