cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5686633.v1
title: calcin_data

description: Scorpions have evolved venoms with diverse variety of toxins with a plethora of biological targets, but characterizing the evolution of this molecular diversity has been limited by the lack of a comprehensive phylogenetic hypothesis of scorpion relationships. Here, we elucidate the origin of calcins and lambda potassium channel toxins (LKTx), a type of inhibitor cystine knot (ICK) toxins. In this study, we compiled the most comprehensive sampling of ICK peptide homologs across the breath of scorpion diversity. Using a de novo phylogenomic tree, and morphometric analysis of 3D molecular models of these peptides, we traced the evolutionary change in the shape of these peptides. The discovery of phylogenetic signal in 3D molecular models of calcins and LKTx, provides the first synapomorphies for the two extant scorpion parvorders, which are otherwise morphologically diverse and undefined. Our morphometric analyses further reveal that calcins and LKTx evolved different shapes with minimal overlap in morphospace, supporting their characterization as stable (non-convergent) synapomorphies.
DOI: 10.6084/m9.figshare.5686627
title: Chamber Data

description: This data is from room calorimeter and were used as a "true" data to which accelerometry data from waist and wrist were compared. <br>
DOI: 10.6084/m9.figshare.5686627.v1
title: Chamber Data

description: This data is from room calorimeter and were used as a "true" data to which accelerometry data from waist and wrist were compared. <br>
DOI: 10.6084/m9.figshare.5686591
title: Do systematic reviews in the top otolaryngology journals adequately address publication bias?

description: This is the data used for the paper "Do systematic reviews in the top otolaryngology journals adequately address publication bias?"
DOI: 10.6084/m9.figshare.5686591.v1
title: Do systematic reviews in the top otolaryngology journals adequately address publication bias?

description: This is the data used for the paper "Do systematic reviews in the top otolaryngology journals adequately address publication bias?"
DOI: 10.6084/m9.figshare.5684548
title: Internet of Things tweets (2009-2016)

description: This dataset includes all tweets posted between 2009 and 2016 with one of the following keywords: #iot, internet of things or #internetofthings.<br>This dataset released in accordance with Twitter's TOS, which allows sharing of tweet IDs and are intended for non-commercial research.<br>Note: Twitter's developer policy doesn't allow sharing more than 1,500,000 tweet IDs (https://dev.twitter.com/overview/terms/policy#updated-policy), unless the author is affiliated with an academic institution (which is my case) and tweet IDs are solely used for non-commercial purposes (https://twittercommunity.com/t/policy-update-clarification-research-use-cases/87566). Hence, by downloading these datasets you agree that you will not use it for commercial purposes.
DOI: 10.6084/m9.figshare.5684548.v1
title: Internet of Things tweets (2009-2016)

description: This dataset includes all tweets posted between 2009 and 2016 with one of the following keywords: #iot, internet of things or #internetofthings.<br>This dataset released in accordance with Twitter's TOS, which allows sharing of tweet IDs and are intended for non-commercial research.<br>Note: Twitter's developer policy doesn't allow sharing more than 1,500,000 tweet IDs (https://dev.twitter.com/overview/terms/policy#updated-policy), unless the author is affiliated with an academic institution (which is my case) and tweet IDs are solely used for non-commercial purposes (https://twittercommunity.com/t/policy-update-clarification-research-use-cases/87566). Hence, by downloading these datasets you agree that you will not use it for commercial purposes.
DOI: 10.6084/m9.figshare.5684395
title: A comprehensive profile of circulating RNAs in human serum

description: Non-coding RNA (ncRNA) molecules have fundamental roles in cells and many are also stable in body fluids as extracellular RNAs. In this study, we used RNA sequencing (RNA-seq) to investigate the profile of small non-coding RNA (sncRNA) in human serum. We analyzed 10 billion Illumina reads from 477 serum samples, included in the Norwegian population-based Janus Serum Bank (JSB). We found that the core serum RNA repertoire includes 258 micro RNAs (miRNA), 441 piwi-interacting RNAs (piRNA), 411 transfer RNAs (tRNA), 24 small nucleolar RNAs (snoRNA), 125 small nuclear RNAs (snRNA) and 123 miscellaneous RNAs (misc-RNA). We also investigated biological and technical variation in expression, and the results suggest that many RNA molecules identified in serum contain signs of biological variation. They are therefore unlikely to be random degradation by-products. In addition, the presence of specific fragments of tRNA, snoRNA, Vault RNA and Y_RNA indicates protection from degradation. Our results suggest that many circulating RNAs in serum can be potential biomarkers.
DOI: 10.6084/m9.figshare.5684395.v1
title: A comprehensive profile of circulating RNAs in human serum

description: Non-coding RNA (ncRNA) molecules have fundamental roles in cells and many are also stable in body fluids as extracellular RNAs. In this study, we used RNA sequencing (RNA-seq) to investigate the profile of small non-coding RNA (sncRNA) in human serum. We analyzed 10 billion Illumina reads from 477 serum samples, included in the Norwegian population-based Janus Serum Bank (JSB). We found that the core serum RNA repertoire includes 258 micro RNAs (miRNA), 441 piwi-interacting RNAs (piRNA), 411 transfer RNAs (tRNA), 24 small nucleolar RNAs (snoRNA), 125 small nuclear RNAs (snRNA) and 123 miscellaneous RNAs (misc-RNA). We also investigated biological and technical variation in expression, and the results suggest that many RNA molecules identified in serum contain signs of biological variation. They are therefore unlikely to be random degradation by-products. In addition, the presence of specific fragments of tRNA, snoRNA, Vault RNA and Y_RNA indicates protection from degradation. Our results suggest that many circulating RNAs in serum can be potential biomarkers.
DOI: 10.6084/m9.figshare.5684383.v1
title: Detailed Secondary Structure Models of Invertebrate 7SK RNAs

description: The 7SK RNA is a small nuclear RNA that is involved in the regulation of Pol-II transcription. It is very well conserved in vertebrates, but shows extensive variations in both sequence and structure across invertebrates. A systematic homology search extended the collection of 7SK genes in both Arthropods and Lophotrochozoa making use of the large number of recently published invertebrate genomes. The extended data set made it possible to infer complete consensus structures for invertebrate 7SK RNAs. These show that not only the well-conserved 5′- and 3′- domains but all the interior Stem A domain is universally conserved. In contrast, Stem B region exhibits substantial structural variation and does not adhere to a common structural model beyond phylum level.
DOI: 10.6084/m9.figshare.5684371
title: Behavioral_data_heuristic_optimal_policy_computation.mat

description: Choice and RT data from the article "Heuristic and optimal policy computation in the human brain during sequential decision-making".<br>
DOI: 10.6084/m9.figshare.5684371.v1
title: Behavioral_data_heuristic_optimal_policy_computation.mat

description: Choice and RT data from the article "Heuristic and optimal policy computation in the human brain during sequential decision-making".<br>
DOI: 10.6084/m9.figshare.5684368
title: Using Modules in Teaching Complex Analysis

description: Educational modules can play an important part in revitalizing the teaching and learning of complex analysis. At the Westmont College workshop on the subject in June 2014, time was spent generating ideas and creating structures for module proposals. Sharing some of those ideas and giving a few example modules is the main purpose of this paper. The author has started to construct <i>Mathematica</i>-based educational modules for complex analysis, one of which is available in the online repository of supplemental materials for this article. The author has also begun work on a website called <i>The Complex Moduli Project</i> to make modules in complex analysis available worldwide, and invites others to join him in this endeavor.
DOI: 10.6084/m9.figshare.5684368.v1
title: Using Modules in Teaching Complex Analysis

description: Educational modules can play an important part in revitalizing the teaching and learning of complex analysis. At the Westmont College workshop on the subject in June 2014, time was spent generating ideas and creating structures for module proposals. Sharing some of those ideas and giving a few example modules is the main purpose of this paper. The author has started to construct <i>Mathematica</i>-based educational modules for complex analysis, one of which is available in the online repository of supplemental materials for this article. The author has also begun work on a website called <i>The Complex Moduli Project</i> to make modules in complex analysis available worldwide, and invites others to join him in this endeavor.
DOI: 10.6084/m9.figshare.5684185
title: DH Lawrence in London.kml

description: This data is used to create a map of DH Lawrence's time spent in London from 1908-1926. It includes details of his working life, writing, dealings with publishers, literary acquaintances, commentary of the cultural and political climate of the time, and personal life. All quotations from Lawrence, as on the Timeline, are taken from the Cambridge University Press Edition of the Letters and Works of D.H. Lawrence, General Editors James T. Boulton, M. H. Black, Paul Poplawski and John Worthen, ongoing since 1979.
DOI: 10.6084/m9.figshare.5684185.v1
title: DH Lawrence in London.kml

description: This data is used to create a map of DH Lawrence's time spent in London from 1908-1926. It includes details of his working life, writing, dealings with publishers, literary acquaintances, commentary of the cultural and political climate of the time, and personal life. All quotations from Lawrence, as on the Timeline, are taken from the Cambridge University Press Edition of the Letters and Works of D.H. Lawrence, General Editors James T. Boulton, M. H. Black, Paul Poplawski and John Worthen, ongoing since 1979.
DOI: 10.6084/m9.figshare.5684182
title: Manual to measure and model leaf area index and its spatial variability on local and landscape scale

description: Updated protocol for measuring canopies of vegetation in the field.
DOI: 10.6084/m9.figshare.5684146
title: Supersonic shear imaging for the diagnosis of liver fibrosis and portal hypertension in liver diseases: a meta-analysis

description: <b>Background and aims</b>: The meta-analysis aimed to summarize the technical success rate of supersonic shear imaging (SSI) and to evaluate the diagnostic performance of liver and spleen stiffness measurement (LSM and SSM) with SSI for the detection of liver fibrosis, portal hypertension, and gastroesophageal varices in liver diseases. <b>Methods</b>: PubMed, EMBASE, and Cochrane Library databases were searched. Technical success rate of SSI was pooled. Area under curve (AUC), sensitivity, and specificity with corresponding 95% confidence interval (CI) were calculated. <b>Results</b>: Included studies regarding the diagnostic performance of SSI for liver fibrosis, portal hypertension, and esophageal varices numbered 28, 4, and 4 respectively. The pooled technical success rates of LSM and SSM were 95.3% and 75.5%, respectively. The AUC, sensitivity, and specificity of LSM/SSM for different stages of liver fibrosis were 0.85–0.94, 0.7–0.89, and 0.82–0.92, respectively. The AUC, sensitivity, and specificity of LSM were 0.84 (95%CI = 0.8–0.86), 0.79 (95%CI = 0.7–0.85), and 0.82 (95%CI = 0.72–0.88) for clinically significant portal hypertension, 0.85 (95%CI = 0.82–0.88), 0.8 (95%CI = 0.68–0.88), and 0.8 (95%CI = 0.6–0.92) for any varices, and 0.86 (95%CI = 0.83–0.89), 0.86 (95%CI = 0.76–0.92), and 0.61 (95%CI = 0.35–0.83) for high-risk varices, respectively. <b>Conclusions</b>: LSM with SSI had a high diagnostic accuracy for liver fibrosis, but a moderate diagnostic accuracy for portal hypertension and esophageal varices.
DOI: 10.6084/m9.figshare.5684146.v1
title: Supersonic shear imaging for the diagnosis of liver fibrosis and portal hypertension in liver diseases: a meta-analysis

description: <b>Background and aims</b>: The meta-analysis aimed to summarize the technical success rate of supersonic shear imaging (SSI) and to evaluate the diagnostic performance of liver and spleen stiffness measurement (LSM and SSM) with SSI for the detection of liver fibrosis, portal hypertension, and gastroesophageal varices in liver diseases. <b>Methods</b>: PubMed, EMBASE, and Cochrane Library databases were searched. Technical success rate of SSI was pooled. Area under curve (AUC), sensitivity, and specificity with corresponding 95% confidence interval (CI) were calculated. <b>Results</b>: Included studies regarding the diagnostic performance of SSI for liver fibrosis, portal hypertension, and esophageal varices numbered 28, 4, and 4 respectively. The pooled technical success rates of LSM and SSM were 95.3% and 75.5%, respectively. The AUC, sensitivity, and specificity of LSM/SSM for different stages of liver fibrosis were 0.85–0.94, 0.7–0.89, and 0.82–0.92, respectively. The AUC, sensitivity, and specificity of LSM were 0.84 (95%CI = 0.8–0.86), 0.79 (95%CI = 0.7–0.85), and 0.82 (95%CI = 0.72–0.88) for clinically significant portal hypertension, 0.85 (95%CI = 0.82–0.88), 0.8 (95%CI = 0.68–0.88), and 0.8 (95%CI = 0.6–0.92) for any varices, and 0.86 (95%CI = 0.83–0.89), 0.86 (95%CI = 0.76–0.92), and 0.61 (95%CI = 0.35–0.83) for high-risk varices, respectively. <b>Conclusions</b>: LSM with SSI had a high diagnostic accuracy for liver fibrosis, but a moderate diagnostic accuracy for portal hypertension and esophageal varices.
DOI: 10.6084/m9.figshare.5684119
title: Split Miner With Guarantees

description: This zip contains all the data and tools used for the evaluation of the automated process discovery tool Split Miner. It's related paper is titled: "Fast, Accurate and Simple Automated Process Discovery".
DOI: 10.6084/m9.figshare.5683975
title: NTR_GLP1_ISI_model.txt

description: A genome-wide association study of GLP-1 stimulated insulin secretion in individuals from the Netherland twin register (NTR). For information on the study cohort, phenotype, genotyping, quality control and association analysis see/cite Gudmundsdottir et al., Plos One, 2017.<br>The file NTR_GLP1_ISI_model.txt contains summary statistics for the GWAS for GLP-1 stimulated insulin secretion in the NTR cohort (n = 126), adjusted for age, gender, glucose tolerance status, insulin sensitivity index, and familiarity.<br>marker: marker IDchr: chromosome numberposition: genome position (Genome Build 37)effect_alleleother_allelepval: P-value from association analysisEAF: effect allele frequencyR2T: imputation quality measurebeta: beta estimateSE: standard error of beta estimate
DOI: 10.6084/m9.figshare.5683975.v1
title: NTR_GLP1_ISI_model.txt

description: A genome-wide association study of GLP-1 stimulated insulin secretion in individuals from the Netherland twin register (NTR). For information on the study cohort, phenotype, genotyping, quality control and association analysis see/cite Gudmundsdottir et al., Plos One, 2017.<br>The file NTR_GLP1_ISI_model.txt contains summary statistics for the GWAS for GLP-1 stimulated insulin secretion in the NTR cohort (n = 126), adjusted for age, gender, glucose tolerance status, insulin sensitivity index, and familiarity.<br>marker: marker IDchr: chromosome numberposition: genome position (Genome Build 37)effect_alleleother_allelepval: P-value from association analysisEAF: effect allele frequencyR2T: imputation quality measurebeta: beta estimateSE: standard error of beta estimate
DOI: 10.6084/m9.figshare.5683963
title: altmetric_top_100_authors_2017.csv

description: Extracted authors and institutions (mapped where possible to GRiD IDs) for articles in Altmetric's Top 100 for 2017.<br><br>
DOI: 10.6084/m9.figshare.5683963.v1
title: altmetric_top_100_authors_2017.csv

description: Extracted authors and institutions (mapped where possible to GRiD IDs) for articles in Altmetric's Top 100 for 2017.<br><br>
DOI: 10.6084/m9.figshare.5683957.v2
title: Top 100 2017

description: This is a CSV file containing the data behind the Altmetric Top 100 for 2017 along with extracted authors and institutions (mapped where possible to GRiD IDs) data.<br><br>
DOI: 10.6084/m9.figshare.5683957.v1
title: Top 100 2017

description: This is a CSV file containing the data behind the Altmetric Top 100 for 2017.<br>A second dataset pulls out the authors and institutions:<br>https://figshare.com/articles/altmetric_top_100_authors_2017_csv/5683963
DOI: 10.6084/m9.figshare.5683945
title: Supplementary Material for: The Protective Effects of Κ-Opioid Receptor Stimulation in Hypoxic Pulmonary Hypertension Involve Inhibition of Autophagy Through the AMPK-MTOR Pathway

description: <b><i>Background/Aims:</i></b> In a previous study, we showed that κ-opioid receptor stimulation with the selective agonist U50,488H ameliorated hypoxic pulmonary hypertension (HPH). However, the roles that pulmonary arterial smooth muscle cell (PASMC) proliferation, apoptosis, and autophagy play in κ-opioid receptor-mediated protection against HPH are still unknown. The goal of the present study was to investigate the role of autophagy in U50,488H-induced HPH protection and the underlying mechanisms. <b><i>Methods:</i></b> Rats were exposed to 10% oxygen for three weeks to induce HPH. After hypoxia, the mean pulmonary arterial pressure (mPAP) and the right ventricular pressure (RVP) were measured. Cell viability was monitored using the Cell Counting Kit-8 (CCK-8) assay. Cell apoptosis was detected by flow cytometry and Western blot. Autophagy was assessed by means of the mRFP-GFP-LC3 adenovirus transfection assay and by Western blot. <b><i>Results:</i></b> Inhibition of autophagy by the administration of chloroquine prevented the development of HPH in the rat model, as evidenced by significantly reduced mPAP and RVP, as well as decreased autophagy. U50,488H mimicked the effects of chloroquine, and the effects of U50,488H were blocked by nor-BNI, a selective κ-opioid receptor antagonist. <i>In vitro</i> experiments showed that the inhibition of autophagy by chloroquine was associated with decreased proliferation and increased apoptosis of PASMCs. Under hypoxia, U50,488H also significantly inhibited autophagy, reduced proliferation and increased apoptosis of PASMCs. These effects of U50,488H were blocked by nor-BNI. Moreover, exposure to hypoxic conditions significantly increased AMPK phosphorylation and reduced mTOR phosphorylation, and these effects were abrogated by U50,488H. The effects of U50,488H on PASMC autophagy were inhibited by AICAR, a selective AMPK agonist, or by rapamycin, a selective mTOR inhibitor. <b><i>Conclusion:</i></b> Our data provide evidence for the first time that κ-opioid receptor stimulation protects against HPH by inhibiting PASMCs autophagy via the AMPK-mTOR pathway.
DOI: 10.6084/m9.figshare.5683921
title: Viscoelastic properties of Xanthan gum (0.3% to 0.6%) at different gas injection rate (0.5LPM to 2LPM)

description: This submission contains the raw rheometer files from time sweep and creep test measurements for 4 different concentration of Xanthan gum (concentration = 0.3wt %, 0.4wt %, 0.5wt % &0.6wt %). The Xanthan gum samples were measured at four different gas flow rates (0.5 LPM, 1.0 LPM, 1.5 LPM & 2.0 LPM). The dynamic time sweep measurements were generated from the Xanthan gum sample first without gas at 0.15% strain across 1500 seconds. Then the sample was conditioned and the gas was injected for 20 minutes before the measurement at similar conditions. Similarly, the dynamic creep test measurements were generated from the xanthan gum sample first without gas at 3 pa stress across 1500 seconds. <br> The measurements were carried out on a DHR-3 rheometer (TA-Instruments), equipped with custom made cup.<br>Detailed experimental protocol is recorded in the .tri (TRIOS) file attached with each data set. This file can be read using the TRIOS software made available on TA-Instruments website (http://www.tainstruments.com/support/software-downloads-support/downloads/). Rheometer geometry dimensions and other details are also obtainable from these files.<br><br>
DOI: 10.6084/m9.figshare.5683921.v1
title: Viscoelastic properties of Xanthan gum (0.3% to 0.6%) at different gas injection rate (0.5LPM to 2LPM)

description: This submission contains the raw rheometer files from time sweep and creep test measurements for 4 different concentration of Xanthan gum (concentration = 0.3wt %, 0.4wt %, 0.5wt % &0.6wt %). The Xanthan gum samples were measured at four different gas flow rates (0.5 LPM, 1.0 LPM, 1.5 LPM & 2.0 LPM). The dynamic time sweep measurements were generated from the Xanthan gum sample first without gas at 0.15% strain across 1500 seconds. Then the sample was conditioned and the gas was injected for 20 minutes before the measurement at similar conditions. Similarly, the dynamic creep test measurements were generated from the xanthan gum sample first without gas at 3 pa stress across 1500 seconds. <br> The measurements were carried out on a DHR-3 rheometer (TA-Instruments), equipped with custom made cup.
DOI: 10.6084/m9.figshare.5683831
title: Supplementary 4 from Genetics redraws pelagic biogeography of <i>Calanus</i>

description: Comparison species identification between InDels and 16S in Saltenfjord - Skjerstadfjord; plus prosome length measurements
DOI: 10.6084/m9.figshare.5683831.v1
title: Supplementary 4 from Genetics redraws pelagic biogeography of <i>Calanus</i>

description: Comparison species identification between InDels and 16S in Saltenfjord - Skjerstadfjord; plus prosome length measurements
DOI: 10.6084/m9.figshare.5683822
title: Supplementary 3 from Genetics redraws pelagic biogeography of <i>Calanus</i>

description: Comparison species identification between InDels and 16S throughout entire species distributional ranges
DOI: 10.6084/m9.figshare.5683822.v1
title: Supplementary 3 from Genetics redraws pelagic biogeography of <i>Calanus</i>

description: Comparison species identification between InDels and 16S throughout entire species distributional ranges
DOI: 10.6084/m9.figshare.5683789
title: Metabolite BridgeDb ID Mapping Database (20171203)

description: BridgeDb ID mapping database for metabolites, using HMDB 4.0 (3 December 2017), ChEBI 158, and Wikidata (3 December 2017) as data sources. No significant changes but just updated data.<br>If you use this data in your research, please cite this data set, and the BridgeDb, ChEBI, and HMDB articles.
DOI: 10.6084/m9.figshare.5683789.v1
title: Metabolite BridgeDb ID Mapping Database (20171203)

description: BridgeDb ID mapping database for metabolites, using HMDB 4.0 (3 December 2017), ChEBI 158, and Wikidata (3 December 2017) as data sources. No significant changes but just updated data.<br>If you use this data in your research, please cite this data set, and the BridgeDb, ChEBI, and HMDB articles.