cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7108511
title: YouTube Dataset - Medical papers analising YouTube videos

description: These dataset are review from YouTube content analysis papers in Health. Data used to publish a review paper into the <b>Revista Cubana de Información en Ciencias de la Salud</b>.This dataset are a list of scientific papers that have been reviewed to analise how health care scientist classify videos they analyse.<br>The article is this one:Boté, J. (2019). Lack of standards in evaluating YouTube health videos. <i>Revista Cubana de Información en Ciencias de la Salud, 30(2)e1357, </i>http://www.acimed.sld.cu/index.php/acimed/article/view/1357/823<br><br>Este conjunto de datos es una revisión de artículos sobre el análisis de contenido en YouTube en el campo de la salud. Este dataset se ha empleado para publicar un articulo en la Revista Cubana de Información en Ciencias de la Salud. Este dataset es una lista de articulos científicos que han sido revisados para analizar como los científicos en atención médica clasifican los videos que analizan.
DOI: 10.6084/m9.figshare.7108511.v1
title: YouTube-DATA.xlsx

description: These data are review from YouTube content analysis papers in Health
DOI: 10.6084/m9.figshare.7108463
title: Custom Code

description: All the code used in the publication
DOI: 10.6084/m9.figshare.7108511.v2
title: YouTube DATA

description: These data are review from YouTube content analysis papers in Health. Data used to publish a review paper into the Revista Cubana de Información en Ciencias de la Salud.
DOI: 10.6084/m9.figshare.7108433
title: Oscarella carmela transcriptome

description: Transcriptome assembly and predicted peptides for Oscarella carmela (formerly published under the name Oscarella sp.).
DOI: 10.6084/m9.figshare.7108463.v1
title: Custom Code

description: All the code used in the publication
DOI: 10.6084/m9.figshare.7108364
title: Single Cell RNA-Seq Simulations for Ntranos, Yi, et al., 2019

description: This figshare repo contains the kallisto quantification of single cell RNA-seq simulations, which were used to benchmark differential expression methods in Ntranos, Yi et al., Nature Methods, 2019 [https://www.nature.com/articles/s41592-018-0303-9, https://github.com/pachterlab/NYMP_2018/]. Use of these simulations is welcome, given proper citation to the manuscript.<br>There are three simulations from RSEM. Each simulation has two cell groups, 105 cells from a "null" group and 105 cells from a "perturbed" group. These cells are sorted accordingly in the .rds files (first 105 vs last 105).<br>1. In the correlated changes simulation (sims_genes), genes are chosen to be perturbed and all transcripts of that gene are perturbed.<br>2. In the independent changes simulation (sims_transcripts), transcripts and independently chosen to be perturbed.<br>3. In the experimental simulation (sims_exp), effect sizes are derived from an experiment using DESeq2, and then transcripts within a gene are chosen to be perturbed with the same effect-sizes (matched by rank-order) as detected in experiment.<br>Files:- perturb.tsv list the perturbed genes / transcripts and their effect sizes.- tximport.rds and tx_tximport.rds provide the transcript counts and gene counts, accordingly.-pseudo_batch contains the directory of TCCs. matrix.tsv is the matrix of TCCs pertaining to the 210 cells. matrix.ec is a EC to transcript/TCC mapping. For more information on TCCs, consult the manuscript or ask questions at https://github.com/pachterlab/NYMP_2018.<br>Finally, we include a splatter simulation of 2 cell groups.The splat directory contains:- splat.rds which is the splatter object, containing the parameterization of the splatter simulation. Reading this file requires the splatter R library and its dependencies. 300 total cells were simulated; 105 cells from each cell group was taken and used benchmarking in our manuscript.- the transcript counts table (counts.rds) and its corresponding gene counts table (genecounts.rds). - perturb.tsv lists the perturbed transcripts.<br><br>
DOI: 10.6084/m9.figshare.7107638
title: Oscarella pearsei assemblies

description: These are published genomic/transcriptomic datasets for Oscarella pearsei (formerly Oscarella carmela).
DOI: 10.6084/m9.figshare.7107443
title: Elevated mutation and selection in wild emmer wheat in response to 28 years of global warming

description: These are three supplemental output data sets for the paper published in PNAS.<br>
DOI: 10.6084/m9.figshare.7107443.v1
title: Elevated mutation and selection in wild emmer wheat in response to 28 years of global warming

description: These are three supplemental output data sets for the paper published in PNAS.<br>
DOI: 10.6084/m9.figshare.7106495
title: A comparative analysis of <i>Lophodermium fissuratum</i>, sp. nov., found in haploxylon pine needles in the Pacific Northwest, and other <i>Lophodermium</i> endophytes

description: <i>Lophodermium</i> is a large fungal genus consisting of over 100 named species, with ca. 38 of these commonly found as endophytes of pine needles. In this study, we use both morphological and sequencing data to describe a new <i>Lophodermium</i> species associated with haploxylon pines from the Pacific Northwest. This new species resembled the morphology of <i>L. nitens</i>, another commonly occurring species from the same geographic regions and host species. They both present dark subcuticular ascocarps without lips. However, the upper walls of their ascocarps are different, as the new species forms an inward V-shaped folding, not present in <i>L. nitens</i>. Phylogenies using nuc rDNA internal transcribed spacer barcodes (ITS1-5.8S-ITS2 = ITS), partial D1–D2 domains of nuc rDNA 28S, and partial sequences of the nuc actin gene confirmed that this species represents a unique lineage not closely related to <i>L. nitens</i>. We discuss the current state of the phylogeny in light of all currently available sequences from pine-associated <i>Lophodermium</i> species.
DOI: 10.6084/m9.figshare.7106495.v1
title: A comparative analysis of <i>Lophodermium fissuratum</i>, sp. nov., found in haploxylon pine needles in the Pacific Northwest, and other <i>Lophodermium</i> endophytes

description: <i>Lophodermium</i> is a large fungal genus consisting of over 100 named species, with ca. 38 of these commonly found as endophytes of pine needles. In this study, we use both morphological and sequencing data to describe a new <i>Lophodermium</i> species associated with haploxylon pines from the Pacific Northwest. This new species resembled the morphology of <i>L. nitens</i>, another commonly occurring species from the same geographic regions and host species. They both present dark subcuticular ascocarps without lips. However, the upper walls of their ascocarps are different, as the new species forms an inward V-shaped folding, not present in <i>L. nitens</i>. Phylogenies using nuc rDNA internal transcribed spacer barcodes (ITS1-5.8S-ITS2 = ITS), partial D1–D2 domains of nuc rDNA 28S, and partial sequences of the nuc actin gene confirmed that this species represents a unique lineage not closely related to <i>L. nitens</i>. We discuss the current state of the phylogeny in light of all currently available sequences from pine-associated <i>Lophodermium</i> species.
DOI: 10.6084/m9.figshare.7106453
title: SNP Position Table

description: SNP position table
DOI: 10.6084/m9.figshare.7106453.v1
title: SNP Position Table

description: SNP position table
DOI: 10.6084/m9.figshare.7106444
title: AAT1 Phenotype Dataset

description: The complete phenotype dataset for the F2 acyltransferase mutant population. Compatible with TASSEL 5.0 format.
DOI: 10.6084/m9.figshare.7106444.v1
title: AAT1 Phenotype Dataset

description: The complete phenotype dataset for the F2 acyltransferase mutant population. Compatible with TASSEL 5.0 format.
DOI: 10.6084/m9.figshare.7106411
title: Approximate Bayesian analysis of doubly censored samples from mixture of two Weibull distributions

description: The purpose of the paper is to estimate the parameters of the two-component mixture of Weibull distribution under doubly censored samples using Bayesian approach. The choice of Weibull distribution is made due to its (i) capability to model failure time data from engineering, medical and biological sciences (ii) added advantages over the well-known lifetime distributions such as exponential, Raleigh, lognormal and gamma distribution in terms of flexibility, increasing and decreasing hazard rate and closed-form distribution function and hazard rate. The proposed two-component mixture of Weibull distribution is even more flexible than its conventional form. However, the estimation of the parameters from the proposed mixture is more complex. Further, we have assumed couple of loss functions under non informative prior for the Bayesian analysis of the parameters from the mixture model. As the resultant Bayes estimators and associated posterior risks cannot be derived in the closed form, we have used the importance sampling and Lindley’s approximation to obtain the approximate estimates for the parameters of the mixture model. The comparison between the performances of approximation techniques has been made on the basis of simulation study and real-life data analysis. The importance sampling is found to be better than Lindley’s approximation as it gives better estimation for shape and mixing parameters of the mixture model and computations under this technique are much easier/shorter than those under Lindley’s approximation.
DOI: 10.6084/m9.figshare.7106411.v1
title: Approximate Bayesian analysis of doubly censored samples from mixture of two Weibull distributions

description: The purpose of the paper is to estimate the parameters of the two-component mixture of Weibull distribution under doubly censored samples using Bayesian approach. The choice of Weibull distribution is made due to its (i) capability to model failure time data from engineering, medical and biological sciences (ii) added advantages over the well-known lifetime distributions such as exponential, Raleigh, lognormal and gamma distribution in terms of flexibility, increasing and decreasing hazard rate and closed-form distribution function and hazard rate. The proposed two-component mixture of Weibull distribution is even more flexible than its conventional form. However, the estimation of the parameters from the proposed mixture is more complex. Further, we have assumed couple of loss functions under non informative prior for the Bayesian analysis of the parameters from the mixture model. As the resultant Bayes estimators and associated posterior risks cannot be derived in the closed form, we have used the importance sampling and Lindley’s approximation to obtain the approximate estimates for the parameters of the mixture model. The comparison between the performances of approximation techniques has been made on the basis of simulation study and real-life data analysis. The importance sampling is found to be better than Lindley’s approximation as it gives better estimation for shape and mixing parameters of the mixture model and computations under this technique are much easier/shorter than those under Lindley’s approximation.
DOI: 10.6084/m9.figshare.7106396
title: A likelihood based approach for joint modeling of longitudinal trajectories and informative censoring process

description: We propose a joint modeling likelihood-based approach for studies with repeated measures and informative right censoring. Joint modeling of longitudinal and survival data are common approaches but could result in biased estimates if proportionality of hazards is violated. To overcome this issue, and given that the exact time of dropout is typically unknown, we modeled the censoring time as the number of follow-up visits and extended it to be dependent on selected covariates. Longitudinal trajectories for each subject were modeled to provide insight into disease progression and incorporated with the number follow-up visits in one likelihood function.
DOI: 10.6084/m9.figshare.7106396.v1
title: A likelihood based approach for joint modeling of longitudinal trajectories and informative censoring process

description: We propose a joint modeling likelihood-based approach for studies with repeated measures and informative right censoring. Joint modeling of longitudinal and survival data are common approaches but could result in biased estimates if proportionality of hazards is violated. To overcome this issue, and given that the exact time of dropout is typically unknown, we modeled the censoring time as the number of follow-up visits and extended it to be dependent on selected covariates. Longitudinal trajectories for each subject were modeled to provide insight into disease progression and incorporated with the number follow-up visits in one likelihood function.
DOI: 10.6084/m9.figshare.7106357
title: A study of type, pattern, and clinical profile of retained musculoskeletal foreign bodies of extremities in a tertiary care hospital of North India.

description: Background: The presence of foreign body in musculoskeletal tissue is a major concern for the patient and treating doctor with regard to its varied presentations and appropriate management. Both metallic and nonmetallic foreign bodies have been studied extensively with special emphasis on its detection by various imaging modalities and unusual presentations of retained foreign ones. An early detection and retrieval is the mainstay of management, leading to an uneventful recovery. It also prevents subsequent complications of neglected, missed, or retained foreign bodies. The increased indulgence in recreational and industrial activities in recent times has increased prevalence and scope of penetrating injuries with various objects. Detailed data regarding patterns and presentations of various foreign body retention of musculoskeletal tissue, both acute and chronic, thus are helpful to format an anticipatory or preventive workup. Furthermore, the knowledge of the types of common foreign bodies in a region helps in drafting investigative and ameliorative public health strategies.Materials and Methods: The current study is a retrospective account of pattern and presentation of non firearm foreign bodies managed in a tertiary care teaching hospital within a defined period. Besides it, patient characteristics and relevant details of trauma and associated findings were listed with at least 4-month follow-up.Results: Male sex, upper extremity, and left side of body were commonly involved. There was predilection for acral parts such as hand and feet. Agricultural and industrial setup was the common scenario associated with the injuries, and vegetative foreign bodies were mostly found followed by metallic ones among others.Conclusion: The study highlights various aspects of acute or chronic foreign body retention in clinical settings and is helpful to know type, pattern and presentation in a geographical region.
DOI: 10.6084/m9.figshare.7106243
title: China city-level socioeconomic inventory, 2010

description: As the centre of human activity and being under the threat of climate change, cities are considered to be major components in the implementation of climate change mitigation and CO<sub>2</sub> emission reduction strategies. Inventories of cities’ emissions serve as the foundation for the analysis of emissions characteristics and policymaking. China is the world’s top energy consumer and CO<sub>2</sub> emitter, and it is facing great potential harm from climate change. Consequently, China is taking increasing responsibility in the fight against global climate change. Many energy/emissions control policies have been implemented in China, most of which are designed at the national level. However, cities are at different stages of industrialization and have distinct development pathways; they need specific control policies designed based on their current emissions characteristics. This study is the first to construct emissions inventories for 182 Chinese cities. The inventories are constructed using 17 fossil fuels and 47 socioeconomic sectors. These city-level emissions inventories have a scope and format consistent with China’s national/provincial inventories. Some socioeconomic data of the cities, such as GDP, population, industrial structures, are included in the datasets as well. The dataset provides transparent, accurate, complete, comparable, and verifiable data support for further city-level emissions studies and low-carbon/sustainable development policy design. The dataset also offers insights for other countries by providing an emissions accounting method with limited data.
DOI: 10.6084/m9.figshare.7106219
title: China city-level emissions inventory, 2010

description: As the centre of human activity and being under the threat of climate change, cities are considered to be major components in the implementation of climate change mitigation and CO<sub>2</sub> emission reduction strategies. Inventories of cities’ emissions serve as the foundation for the analysis of emissions characteristics and policymaking. China is the world’s top energy consumer and CO<sub>2</sub> emitter, and it is facing great potential harm from climate change. Consequently, China is taking increasing responsibility in the fight against global climate change. Many energy/emissions control policies have been implemented in China, most of which are designed at the national level. However, cities are at different stages of industrialization and have distinct development pathways; they need specific control policies designed based on their current emissions characteristics. This study is the first to construct emissions inventories for 182 Chinese cities. The inventories are constructed using 17 fossil fuels and 47 socioeconomic sectors. These city-level emissions inventories have a scope and format consistent with China’s national/provincial inventories. Some socioeconomic data of the cities, such as GDP, population, industrial structures, are included in the datasets as well. The dataset provides transparent, accurate, complete, comparable, and verifiable data support for further city-level emissions studies and low-carbon/sustainable development policy design. The dataset also offers insights for other countries by providing an emissions accounting method with limited data.
DOI: 10.6084/m9.figshare.7106075
title: PLEWA04_ORF.pep.fa.gz

description: P. waltl ORF prediction (translated)Ver. PLEWA04<br>
DOI: 10.6084/m9.figshare.7106033
title: Trinity_Pwal_v2.fasta.gz

description: Trinity assembly of P. waltl. (Ver. 2)<br>
DOI: 10.6084/m9.figshare.7106069
title: PLEWA04_ORF.cds.fa.gz

description: P. waltl ORF prediction (CDS)Ver. PLEWA04_ORF<br>
DOI: 10.6084/m9.figshare.7106009
title: Comparative chloroplast genomics of series <i>Sakawanum</i> in genus <i>Asarum</i> (Aristolochiaceae) to develop single nucleotide polymorphisms (SNPs) and simple sequence repeat (SSR) markers

description: Series <i>Sakawanum</i> (genus <i>Asarum</i>, Aristolochiaceae) comprises four taxa of forest understory herbaceous plants, which exhibits a geographical cline of calyx lobe length across taxonomic units. To understand the formation process of this series, it is necessary to investigate the evolutionary history based on maternally inherited seed-mediated plastid markers. Using pyrosequencing technique, nearly complete chloroplast genomes of two species (<i>A. minamitanianum</i> and <i>A. costatum</i>) were obtained. Furthermore, nine polymorphic chloroplast single nucleotide polymorphisms (SNPs) and 11 simple sequence repeat (SSR) markers were developed. Most of these markers showed interspecific variations and all markers showed transferability to other <i>Asarum</i> species, while most of markers showed little intra-population variations. These chloroplast genomes and markers can be applied in future studies investigating the contributions of the maternal lineage in shaping the population genetic structure of series <i>Sakawanum</i> and the evolutionary processes underlying their morphological diversification including the characteristic calyx lobe length variation. Moreover, this study showed the applicability of comparative chloroplast genome analysis to develop the chloroplast markers for species group for which it is difficult to obtain polymorphism data using the universal primers.
DOI: 10.6084/m9.figshare.7106009.v1
title: Comparative chloroplast genomics of series <i>Sakawanum</i> in genus <i>Asarum</i> (Aristolochiaceae) to develop single nucleotide polymorphisms (SNPs) and simple sequence repeat (SSR) markers

description: Series <i>Sakawanum</i> (genus <i>Asarum</i>, Aristolochiaceae) comprises four taxa of forest understory herbaceous plants, which exhibits a geographical cline of calyx lobe length across taxonomic units. To understand the formation process of this series, it is necessary to investigate the evolutionary history based on maternally inherited seed-mediated plastid markers. Using pyrosequencing technique, nearly complete chloroplast genomes of two species (<i>A. minamitanianum</i> and <i>A. costatum</i>) were obtained. Furthermore, nine polymorphic chloroplast single nucleotide polymorphisms (SNPs) and 11 simple sequence repeat (SSR) markers were developed. Most of these markers showed interspecific variations and all markers showed transferability to other <i>Asarum</i> species, while most of markers showed little intra-population variations. These chloroplast genomes and markers can be applied in future studies investigating the contributions of the maternal lineage in shaping the population genetic structure of series <i>Sakawanum</i> and the evolutionary processes underlying their morphological diversification including the characteristic calyx lobe length variation. Moreover, this study showed the applicability of comparative chloroplast genome analysis to develop the chloroplast markers for species group for which it is difficult to obtain polymorphism data using the universal primers.
DOI: 10.6084/m9.figshare.7105937
title: Inductively coupled plasma mass spectrometry (ICP-MS) on Rhodospirillum rubrum, Pyrococcus furiosus and Haliangium ochraceum encapsulated ferritis (EncFtn)

description: ICP-MS was conducted on purified fractions of Rhodospirillum rubrum, Pyrococcus furiosus, and Haliangium ochraceum encapsulated ferritin variants (EncFtn_Strep) in order to quantify 56-57Fe and 65-66Zn content.Samples were diluted 10-fold into a solution of 2.5 % HNO3 containing 20 ug/L Pt and 20 ug/L Ag as internal standards. Matrix-matched elemental standards, were prepared by serial dilution by individual metal stocks (VWR) with identical solution composition, including the internal standard. All standards and samples were analysed by ICP-MS using a Thermo x-series instrument (Thermo Fisher scientific) operating in collision cell mode.
DOI: 10.6084/m9.figshare.7105928
title: Looking back: understanding visits to museums in the UK since the nineteenth century

description: Looking back: understanding visits to museums in the UK since the nineteenth century
DOI: 10.6084/m9.figshare.7105928.v1
title: Looking back: understanding visits to museums in the UK since the nineteenth century

description: Looking back: understanding visits to museums in the UK since the nineteenth century
DOI: 10.6084/m9.figshare.7105937.v1
title: Inductively coupled plasma mass spectrometry (ICP-MS) on Rhodospirillum rubrum, Pyrococcus furiosus and Haliangium ochraceum encapsulated ferritis (EncFtn)

description: ICP-MS was conducted on purified fractions of Rhodospirillum rubrum, Pyrococcus furiosus, and Haliangium ochraceum encapsulated ferritin variants (EncFtn_Strep) in order to quantify 56-57Fe and 65-66Zn content.Samples were diluted 10-fold into a solution of 2.5 % HNO3 containing 20 ug/L Pt and 20 ug/L Ag as internal standards. Matrix-matched elemental standards, were prepared by serial dilution by individual metal stocks (VWR) with identical solution composition, including the internal standard. All standards and samples were analysed by ICP-MS using a Thermo x-series instrument (Thermo Fisher scientific) operating in collision cell mode.