cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6739232
title: TAGs lipid species

description: <b>TAGs lipid species depicts all the lipid species that were monitored for</b>. A complete list of the MRM transitions and retention time for the corresponding individual TAG species.<b></b>additional data sets
DOI: 10.6084/m9.figshare.6739232.v3
title: TAGs lipid species

description: <b>TAGs lipid species depicts all the lipid species that were monitored for</b>. A complete list of the MRM transitions and retention time for the corresponding individual TAG species.<b></b>additional data sets
DOI: 10.6084/m9.figshare.6739217.v1
title: Data and Source Code and Data Extract Files

description: Data and source code and some .sh files for data extract of manuscript entitled 'Software Change Proneness Prediction Through Combination of Bagging and Re-sampling Methods'
DOI: 10.6084/m9.figshare.6739217.v3
title: Data and Source Code and Data Extract Files

description: Data and source code and some .sh files for data extract of manuscript entitled 'Software Change Proneness Prediction Through Combination of Bagging and Re-sampling Methods'
DOI: 10.6084/m9.figshare.6739202
title: Data set for Personnel Review review process

description: Data set used in research submitted to Pertsonnel Review
DOI: 10.6084/m9.figshare.6739217.v2
title: Data and Source Code and Data Extract Files

description: Data and source code and some .sh files for data extract of manuscript entitled 'Software Change Proneness Prediction Through Combination of Bagging and Re-sampling Methods'
DOI: 10.6084/m9.figshare.6739202.v1
title: Data set for Personnel Review review process

description: Data set used in research submitted to Pertsonnel Review
DOI: 10.6084/m9.figshare.6739187
title: S-1 & S-2

description: Head and eye angular velocity during fastball hitting
DOI: 10.6084/m9.figshare.6739187.v1
title: S-1 & S-2

description: Head and eye angular velocity during fastball hitting
DOI: 10.6084/m9.figshare.6739151
title: EnabCon_analysis.csv

description: Data for evaluating the impact of ecosystem services knowledge across 15 international cases with The Natural Capital Project
DOI: 10.6084/m9.figshare.6739151.v1
title: EnabCon_analysis.csv

description: Data for evaluating the impact of ecosystem services knowledge across 15 international cases with The Natural Capital Project
DOI: 10.6084/m9.figshare.6739142
title: SC3_full_data_anonymous.csv

description: Data from surveys of county-level decision-makers in California, USA about their attitudes towards ecosystem services knowledge
DOI: 10.6084/m9.figshare.6739142.v1
title: SC3_full_data_anonymous.csv

description: Data from surveys of county-level decision-makers in California, USA about their attitudes towards ecosystem services knowledge
DOI: 10.6084/m9.figshare.6739136
title: many_variables_2.csv

description: Country variables including InVEST model runs and other variables assembled from publicly available data or other publications (see published paper for more info)
DOI: 10.6084/m9.figshare.6739091
title: Will Arnold Dissertation Appendix Data

description: This fileset contains the supplemental data for William K. Arnold's 2018 Dissertation.
DOI: 10.6084/m9.figshare.6739127
title: invest_usage_data_total.csv

description: Data for 2 years of InVEST model runs provided by the Natural Capital Project
DOI: 10.6084/m9.figshare.6739127.v1
title: invest_usage_data_total.csv

description: Data for 2 years of InVEST model runs provided by the Natural Capital Project
DOI: 10.6084/m9.figshare.6739019
title: Obras de Nietzsche en español

description: Conjunto de textos de Nietzsche en traducción al español.
DOI: 10.6084/m9.figshare.6739091.v1
title: Will Arnold Dissertation Appendix Data

description: This fileset contains the supplemental data for William K. Arnold's 2018 Dissertation.
DOI: 10.6084/m9.figshare.6739019.v1
title: Obras de Nietzsche en español

description: Conjunto de textos de Nietzsche en traducción al español.
DOI: 10.6084/m9.figshare.6739091.v3
title: Will Arnold Dissertation Appendix Data

description: This fileset contains the supplemental data for William K. Arnold's 2018 Dissertation.
DOI: 10.6084/m9.figshare.6739091.v2
title: Will Arnold Dissertation Appendix Data

description: This fileset contains the supplemental data for William K. Arnold's 2018 Dissertation.
DOI: 10.6084/m9.figshare.6738953
title: A genetically encodable bioluminescent system from fungi

description: File S1: File S1. Alignment of fungal luciferases (protein sequences).<br>File S2: BAM and BAI files with alignments of Pichia pastoris genome sequencing reads.<br>File "Neonothopanus_nambi_transcriptome.fa": assembled transcriptome of glowing Neonothopanus nambi mycelium.<br>File "Mycena_citricolor_transcriptome.fa": assembled transcriptome of glowing Mycena citricolor mycelium.<br><br>For more sequencing data from our study, including genomes of Neonothopanus nambi and Mycena citricolor, follow the link:https://www.ncbi.nlm.nih.gov/bioproject/PRJNA476325<br>
DOI: 10.6084/m9.figshare.6738917
title: Supplemental Table 6

description: Values of Jaccard dissimilarity based on incidence datasets measured within and between communities. Identical = 0; completely dissimilar = 1. Abbreviations: MT, morphotypes; EE, evolutionary independent entities obtained with GMYC; OTU, operational taxonomic units obtained with single individuals; eOTU, operational taxonomic units obtained with environmental samples; SV, sequence variants. L, littoral; SL, sublittoral; O, offshore. Dissimilarity values were estimated using both the focal phyla (SV; eOTU) and whole meiofauna dataset (SV2; eOTU2).
DOI: 10.6084/m9.figshare.6738917.v1
title: Supplemental Table 6

description: Values of Jaccard dissimilarity based on incidence datasets measured within and between communities. Identical = 0; completely dissimilar = 1. Abbreviations: MT, morphotypes; EE, evolutionary independent entities obtained with GMYC; OTU, operational taxonomic units obtained with single individuals; eOTU, operational taxonomic units obtained with environmental samples; SV, sequence variants. L, littoral; SL, sublittoral; O, offshore. Dissimilarity values were estimated using both the focal phyla (SV; eOTU) and whole meiofauna dataset (SV2; eOTU2).
DOI: 10.6084/m9.figshare.6738890
title: Supplemental Table 5

description: Values of richness estimation (underlined) obtained using Chao and Jackknife algorithms on morphotypes (MT) and sequence variants (SV). The richness is estimated for each phylum and for the total sampled area. Actual richness identified with each method is shown for a direct comparison. Species were estimated using both the focal phyla (SV) and whole meiofauna dataset (SV2). “*” indicates phyla which richness estimated using metabarcoding is lower than number of actual morphotypes identified with morphological taxonomy.<br>
DOI: 10.6084/m9.figshare.6738890.v1
title: Supplemental Table 5

description: Values of richness estimation (underlined) obtained using Chao and Jackknife (abbreviated as Jack) algorithms on morphotypes and SVs. The richness is estimated for each phylum and for the total sampled area. Actual richness identified with each method is shown for a direct comparison. Species were estimated using both the focal phyla (SV) and whole meiofauna dataset (SV2). “*” indicates phyla which richness estimated using metabarcoding is lower than number of actual morphotypes identified with morphological taxonomy.<br>
DOI: 10.6084/m9.figshare.6738890.v3
title: Supplemental Table 5

description: Values of richness estimation (underlined) obtained using Chao and Jackknife algorithms on morphotypes (MT) and sequence variants (SV). The richness is estimated for each phylum and for the total sampled area. Actual richness identified with each method is shown for a direct comparison. Species were estimated using both the focal phyla (SV) and whole meiofauna dataset (SV2). “*” indicates phyla which richness estimated using metabarcoding is lower than number of actual morphotypes identified with morphological taxonomy.<br>
DOI: 10.6084/m9.figshare.6738872
title: Tuberculous Uveitis Presenting with a Bullous Exudative Retinal Detachment: A Case Report and Systematic Literature Review

description: <i>Purpose</i>: To describe tuberculous uveitis (TU) presenting as a bullous retinal detachment (RD) and to perform a comprehensive literature review on TU with similar features. <i>Methods</i>: Observational case report and systematic literature review. <i>Results</i>: An 84-year-old woman presented with bilateral granulomatous uveitis and bullous RD in the left eye. The interferon gamma release assay was strongly positive, but all other tests were unremarkable. The patient was diagnosed with TU and started on anti-tubercular therapy (ATT) and systemic steroids with excellent treatment response. Twenty-six articles (32 cases) reported TU with exudative RD. Choroidal tuberculoma was the most common clinical manifestation, followed by optic disc edema and retinal exudate. Systemic steroids with ATT improved vision in more patients (78.6%) than ATT alone (50.0%) or oral steroids followed by ATT (50.0%). <i>Conclusion</i>: Atypical presentations of TU make diagnosis and treatment difficult. A high level of suspicion for TU is needed to minimize ocular morbidity.
DOI: 10.6084/m9.figshare.6738872.v1
title: Tuberculous Uveitis Presenting with a Bullous Exudative Retinal Detachment: A Case Report and Systematic Literature Review

description: <i>Purpose</i>: To describe tuberculous uveitis (TU) presenting as a bullous retinal detachment (RD) and to perform a comprehensive literature review on TU with similar features. <i>Methods</i>: Observational case report and systematic literature review. <i>Results</i>: An 84-year-old woman presented with bilateral granulomatous uveitis and bullous RD in the left eye. The interferon gamma release assay was strongly positive, but all other tests were unremarkable. The patient was diagnosed with TU and started on anti-tubercular therapy (ATT) and systemic steroids with excellent treatment response. Twenty-six articles (32 cases) reported TU with exudative RD. Choroidal tuberculoma was the most common clinical manifestation, followed by optic disc edema and retinal exudate. Systemic steroids with ATT improved vision in more patients (78.6%) than ATT alone (50.0%) or oral steroids followed by ATT (50.0%). <i>Conclusion</i>: Atypical presentations of TU make diagnosis and treatment difficult. A high level of suspicion for TU is needed to minimize ocular morbidity.
DOI: 10.6084/m9.figshare.6738800
title: Table including sampled sites and environmental parameters

description: List of sampled locations and environmental parameters investigated. Coordinates are indicated in decimal system. Abbreviations: Lat, Latitude; Long, Longitude; MGS, mean grain size.
DOI: 10.6084/m9.figshare.6738725
title: Dynamically Updated Spatially Varying Parameterizations of Hierarchical Bayesian Models for Spatial Data

description: Fitting hierarchical Bayesian models to spatially correlated datasets using Markov chain Monte Carlo (MCMC) techniques is computationally expensive. Complicated covariance structures of the underlying spatial processes, together with high-dimensional parameter space, mean that the number of calculations required grows cubically with the number of spatial locations at each MCMC iteration. This necessitates the need for efficient model parameterizations that hasten the convergence and improve the mixing of the associated algorithms. We consider partially centred parameterizations (PCPs) which lie on a continuum between what are known as the centered (CP) and noncentered parameterizations (NCP). By introducing a weight matrix we remove the conditional posterior correlation between the fixed and the random effects, and hence construct a PCP which achieves immediate convergence for a three-stage model, based on multiple Gaussian processes with known covariance parameters. When the covariance parameters are unknown we dynamically update the parameterization within the sampler. The PCP outperforms both the CP and the NCP and leads to a fully automated algorithm which has been demonstrated in two simulation examples. The effectiveness of the spatially varying PCP is illustrated with a practical dataset of nitrogen dioxide concentration levels. Supplemental materials consisting of appendices, datasets, and computer code to reproduce the results are available online.
DOI: 10.6084/m9.figshare.6738800.v1
title: TableS1

description: List of sampled locations and environmental parameters investigated. Coordinates are indicated in decimal system. Abbreviations: Lat, Latitude; Long, Longitude; MGS, mean grain size.
DOI: 10.6084/m9.figshare.6738725.v2
title: Dynamically Updated Spatially Varying Parameterizations of Hierarchical Bayesian Models for Spatial Data

description: Fitting hierarchical Bayesian models to spatially correlated datasets using Markov chain Monte Carlo (MCMC) techniques is computationally expensive. Complicated covariance structures of the underlying spatial processes, together with high-dimensional parameter space, mean that the number of calculations required grows cubically with the number of spatial locations at each MCMC iteration. This necessitates the need for efficient model parameterizations that hasten the convergence and improve the mixing of the associated algorithms. We consider partially centred parameterizations (PCPs) which lie on a continuum between what are known as the centered (CP) and noncentered parameterizations (NCP). By introducing a weight matrix we remove the conditional posterior correlation between the fixed and the random effects, and hence construct a PCP which achieves immediate convergence for a three-stage model, based on multiple Gaussian processes with known covariance parameters. When the covariance parameters are unknown we dynamically update the parameterization within the sampler. The PCP outperforms both the CP and the NCP and leads to a fully automated algorithm which has been demonstrated in two simulation examples. The effectiveness of the spatially varying PCP is illustrated with a practical dataset of nitrogen dioxide concentration levels. Supplemental materials consisting of appendices, datasets, and computer code to reproduce the results are available online.
DOI: 10.6084/m9.figshare.6738725.v1
title: Dynamically Updated Spatially Varying Parameterizations of Hierarchical Bayesian Models for Spatial Data

description: Fitting hierarchical Bayesian models to spatially correlated data sets using Markov chain Monte Carlo (MCMC) techniques is computationally expensive. Complicated covariance structures of the underlying spatial processes, together with high dimensional parameter space, mean that the number of calculations required grows cubically with the number of spatial locations at each MCMC iteration. This necessitates the need for efficient model parameterisations that hasten the convergence and improve the mixing of the associated algorithms. We consider partially centred parameterisations (PCPs) which lie on a continuum between what are known as the centred (CP) and noncentered parameterisations (NCP). By introducing a weight matrix we remove the conditional posterior correlation between the fixed and the random effects, and hence construct a PCP which achieves immediate convergence for a three stage model, based on multiple Gaussian processes with known covariance parameters. When the covariance parameters are unknown we dynamically update the parameterisation within the sampler. The PCP outperforms both the CP and the NCP and leads to a fully automated algorithm which has been demonstrated in two simulation examples. The effectiveness of the spatially varying PCP is illustrated with a practical data set of nitrogen dioxide concentration levels. Supplemental materials consisting of appendices, data sets and computer code to reproduce the results are available online.
DOI: 10.6084/m9.figshare.6738800.v2
title: Supplemental Table 1

description: List of sampled locations and environmental parameters investigated. Coordinates are indicated in decimal system. Abbreviations: Lat, Latitude; Long, Longitude; MGS, mean grain size.
DOI: 10.6084/m9.figshare.6738800.v4
title: Supplemental Table 1

description: List of sampled locations and environmental parameters investigated. Coordinates are indicated in decimal system. Abbreviations: Lat, Latitude; Long, Longitude; MGS, mean grain size.
DOI: 10.6084/m9.figshare.6738224
title: The key informant strategy to determine the prevalence and causes of functional low vision among children in South India

description: <b><i>Purpose</i></b>: To report the prevalence and causes of functional low vision (FLV) in school-age children in Coimbatore District, Tamil Nadu, India and to report our experience using the key informant (KI) method in this setting. <b><i>Methods</i></b>: Children suspected of having low vision were identified by KIs or Aravind Eye Hospital personnel in Coimbatore District. All identified children underwent a cycloplegic refraction and full eye exam. A primary cause of decreased vision was determined for each child. The prevalence of FLV was calculated for children 6–14 years old. Spectacles and low vision devices were provided free of charge. <b><i>Results</i></b>: 345 children aged 6–14 years were referred and 231 had FLV. The positive-predictive value of KI referrals was 64.5%. The prevalence of FLV was 0.071% (7.1 per 10,000; 95% CI 0.062–0.080%) and ranged from 0.026% to 0.141% across the district’s blocks. Older children (age 11–14 years; OR 1.41; 95% CI 1.09–1.82) and males (OR 1.52; 95% CI 1.16–1.98) had greater odds of being diagnosed with FLV. The most common causes of FLV were retinal disorders (30.0%) and amblyopia (25.5%). Low vision devices were provided to 169 children who had a mean near and distance visual acuity improvement of 0.31 and 0.63 logMAR, respectively (<i>p</i> <b><i>Conclusions</i></b>: This study reports a moderate prevalence of FLV and demonstrates the ability of KIs to identify school-age children with FLV in South India. The provision of basic low vision services can improve visual outcomes in this population.
DOI: 10.6084/m9.figshare.6738224.v1
title: The key informant strategy to determine the prevalence and causes of functional low vision among children in South India

description: <b><i>Purpose</i></b>: To report the prevalence and causes of functional low vision (FLV) in school-age children in Coimbatore District, Tamil Nadu, India and to report our experience using the key informant (KI) method in this setting. <b><i>Methods</i></b>: Children suspected of having low vision were identified by KIs or Aravind Eye Hospital personnel in Coimbatore District. All identified children underwent a cycloplegic refraction and full eye exam. A primary cause of decreased vision was determined for each child. The prevalence of FLV was calculated for children 6–14 years old. Spectacles and low vision devices were provided free of charge. <b><i>Results</i></b>: 345 children aged 6–14 years were referred and 231 had FLV. The positive-predictive value of KI referrals was 64.5%. The prevalence of FLV was 0.071% (7.1 per 10,000; 95% CI 0.062–0.080%) and ranged from 0.026% to 0.141% across the district’s blocks. Older children (age 11–14 years; OR 1.41; 95% CI 1.09–1.82) and males (OR 1.52; 95% CI 1.16–1.98) had greater odds of being diagnosed with FLV. The most common causes of FLV were retinal disorders (30.0%) and amblyopia (25.5%). Low vision devices were provided to 169 children who had a mean near and distance visual acuity improvement of 0.31 and 0.63 logMAR, respectively (<i>p</i> <b><i>Conclusions</i></b>: This study reports a moderate prevalence of FLV and demonstrates the ability of KIs to identify school-age children with FLV in South India. The provision of basic low vision services can improve visual outcomes in this population.
DOI: 10.6084/m9.figshare.6737282
title: Survival and prognostic indicators of Budd–Chiari syndrome: a systematic review of 79 studies

description: This paper aimed to systematically review the survival of Budd–Chiari syndrome and to identify the most robust prognostic predictors. Overall, 79 studies were included. According to the treatment modalities, the median 1-, 5- and 10-year survival rate was 93, 83 and 73% after interventional radiological treatment; 81, 75 and 72.5% after surgery other than liver transplantation; 82.5, 70.2 and 66.5% after liver transplantation and 68.1, 44.4% and unavailable after medical therapy alone. According to the publication years, the median 1-, 5- and 10-year survival rate was 68.6, 44.4% and unavailable before 1990; 75.1, 69.5 and 57% during the year 1991–1995; 77, 69.6 and 65.6% during the year 1996–2000; 86.5, 74 and 63.5% during the year 2001–2005 and 90, 82.5 and 72% after 2006. Bilirubin, creatinine and ascites were more frequently identified as significant prognostic factors in univariate analyses. But their statistical significance was less frequently achieved in multivariate analyses.
DOI: 10.6084/m9.figshare.6737273
title: Cladribine in combination with entinostat synergistically elicits anti-proliferative/anti-survival effects on multiple myeloma cells

description: Cladribine (2CdA), a synthetic purine analog interfering with DNA synthesis, is a medication used to treat hairy cell leukemia (HCL) and B-cell chronic lymphocytic leukemia. Entinostat, a selective class I histone deacetylase (HDAC) inhibitor, shows antitumor activity in various human cancers, including hematological malignancies. The therapeutic potential of cladribine and entinostat against multiple myeloma (MM) remains unclear. Here we investigate the combinatorial effects of cladribine and entinostat within the range of their clinical achievable concentrations on MM cells. While either agent alone inhibited MM cell proliferation in a dose-dependent manner, their combinations synergistically induced anti-proliferative/anti-survival effects on all MM cell lines (RPMI8226, U266, and MM1.R) tested. Further studies showed that the combinations of cladribine and entinostat as compared to either agent alone more potently induced mitotic catastrophe in the MM cells, and resulted in a marked increase of the cells at G1 phase associated with decrease of Cyclin D1 and E2F-1 expression and upregulation of p21<sup>waf−1</sup>. Apoptotic ELISA and western blot analyses revealed that the combinations of cladribine and entinostat exerted a much more profound activity to induce apoptosis and DNA damage response, evidenced by enhanced phosphorylation of histone H2A.X and the DNA repair enzymes Chk1 and Chk2. Collectively, our data demonstrate that the combinations of cladribine and entinostat exhibit potent activity to induce anti-proliferative/anti-survival effects on MM cells via induction of cell cycle G1 arrest, apoptosis, and DNA damage response. Regimens consisting of cladribine and/or entinostat may offer a new treatment option for patients with MM. <b>Abbreviations:</b> MM, multiple myeloma; HCL, hairy cell leukemia; HDAC, histone deacetylase; Ab, antibody; mAb, monoclonal Ab; FBS, fetal bovine serum; CI, combination index; PAGE, polyacrylamide gel electrophoresis; ELISA, enzyme-linked immunosorbent assay; PARP, poly(ADP-ribose) polymerase; MTS, 3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium,inner salt