cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8282540
title: O. faveolata UPRmt genes identified through WGCNA from Uncovering a mitochondrial unfolded protein response in corals and its role in adapting to a changing world

description: The Anthropocene will be characterized by increased environmental disturbances, leading to the survival of stress-tolerant organisms particularly in the oceans where novel marine diseases and elevated temperatures are re-shaping ecosystems. These environmental changes underscore the importance of identifying mechanisms which promote stress tolerance in ecologically important non-model species such as reef-building corals. Mitochondria are central regulators of cellular stress and have dedicated recovery pathways including the mitochondrial unfolded protein response, which increases the transcription of protective genes promoting protein homeostasis, free radical detoxification and innate immunity. In this investigation, we identify a mitochondrial unfolded protein response in the endangered Caribbean coral <i>Orbicella faveolata</i>, by performing <i>in vivo</i> functional replacement using a transcription factor (Of-ATF5) originating from a coral in the model organism <i>Caenorhabditis elegans</i>. In addition, we use RNA-seq network analysis and transcription factor-binding predictions to identify a transcriptional network of genes likely regulated by Of-ATF5 which is induced during the immune challenge and temperature stress. Overall, our findings uncover a conserved cellular pathway which may promote the ability of reef-building corals to survive increasing levels of environmental stress.
DOI: 10.6084/m9.figshare.8282543
title: Genes with ATF5 binding sites within their promoters from Uncovering a mitochondrial unfolded protein response in corals and its role in adapting to a changing world

description: The Anthropocene will be characterized by increased environmental disturbances, leading to the survival of stress-tolerant organisms particularly in the oceans where novel marine diseases and elevated temperatures are re-shaping ecosystems. These environmental changes underscore the importance of identifying mechanisms which promote stress tolerance in ecologically important non-model species such as reef-building corals. Mitochondria are central regulators of cellular stress and have dedicated recovery pathways including the mitochondrial unfolded protein response, which increases the transcription of protective genes promoting protein homeostasis, free radical detoxification and innate immunity. In this investigation, we identify a mitochondrial unfolded protein response in the endangered Caribbean coral <i>Orbicella faveolata</i>, by performing <i>in vivo</i> functional replacement using a transcription factor (Of-ATF5) originating from a coral in the model organism <i>Caenorhabditis elegans</i>. In addition, we use RNA-seq network analysis and transcription factor-binding predictions to identify a transcriptional network of genes likely regulated by Of-ATF5 which is induced during the immune challenge and temperature stress. Overall, our findings uncover a conserved cellular pathway which may promote the ability of reef-building corals to survive increasing levels of environmental stress.
DOI: 10.6084/m9.figshare.8282540.v1
title: O. faveolata UPRmt genes identified through WGCNA from Uncovering a mitochondrial unfolded protein response in corals and its role in adapting to a changing world

description: The Anthropocene will be characterized by increased environmental disturbances, leading to the survival of stress-tolerant organisms particularly in the oceans where novel marine diseases and elevated temperatures are re-shaping ecosystems. These environmental changes underscore the importance of identifying mechanisms which promote stress tolerance in ecologically important non-model species such as reef-building corals. Mitochondria are central regulators of cellular stress and have dedicated recovery pathways including the mitochondrial unfolded protein response, which increases the transcription of protective genes promoting protein homeostasis, free radical detoxification and innate immunity. In this investigation, we identify a mitochondrial unfolded protein response in the endangered Caribbean coral <i>Orbicella faveolata</i>, by performing <i>in vivo</i> functional replacement using a transcription factor (Of-ATF5) originating from a coral in the model organism <i>Caenorhabditis elegans</i>. In addition, we use RNA-seq network analysis and transcription factor-binding predictions to identify a transcriptional network of genes likely regulated by Of-ATF5 which is induced during the immune challenge and temperature stress. Overall, our findings uncover a conserved cellular pathway which may promote the ability of reef-building corals to survive increasing levels of environmental stress.
DOI: 10.6084/m9.figshare.8282543.v1
title: Genes with ATF5 binding sites within their promoters from Uncovering a mitochondrial unfolded protein response in corals and its role in adapting to a changing world

description: The Anthropocene will be characterized by increased environmental disturbances, leading to the survival of stress-tolerant organisms particularly in the oceans where novel marine diseases and elevated temperatures are re-shaping ecosystems. These environmental changes underscore the importance of identifying mechanisms which promote stress tolerance in ecologically important non-model species such as reef-building corals. Mitochondria are central regulators of cellular stress and have dedicated recovery pathways including the mitochondrial unfolded protein response, which increases the transcription of protective genes promoting protein homeostasis, free radical detoxification and innate immunity. In this investigation, we identify a mitochondrial unfolded protein response in the endangered Caribbean coral <i>Orbicella faveolata</i>, by performing <i>in vivo</i> functional replacement using a transcription factor (Of-ATF5) originating from a coral in the model organism <i>Caenorhabditis elegans</i>. In addition, we use RNA-seq network analysis and transcription factor-binding predictions to identify a transcriptional network of genes likely regulated by Of-ATF5 which is induced during the immune challenge and temperature stress. Overall, our findings uncover a conserved cellular pathway which may promote the ability of reef-building corals to survive increasing levels of environmental stress.
DOI: 10.6084/m9.figshare.8282537
title: Primers used for qPCR reactions from Uncovering a mitochondrial unfolded protein response in corals and its role in adapting to a changing world

description: The Anthropocene will be characterized by increased environmental disturbances, leading to the survival of stress-tolerant organisms particularly in the oceans where novel marine diseases and elevated temperatures are re-shaping ecosystems. These environmental changes underscore the importance of identifying mechanisms which promote stress tolerance in ecologically important non-model species such as reef-building corals. Mitochondria are central regulators of cellular stress and have dedicated recovery pathways including the mitochondrial unfolded protein response, which increases the transcription of protective genes promoting protein homeostasis, free radical detoxification and innate immunity. In this investigation, we identify a mitochondrial unfolded protein response in the endangered Caribbean coral <i>Orbicella faveolata</i>, by performing <i>in vivo</i> functional replacement using a transcription factor (Of-ATF5) originating from a coral in the model organism <i>Caenorhabditis elegans</i>. In addition, we use RNA-seq network analysis and transcription factor-binding predictions to identify a transcriptional network of genes likely regulated by Of-ATF5 which is induced during the immune challenge and temperature stress. Overall, our findings uncover a conserved cellular pathway which may promote the ability of reef-building corals to survive increasing levels of environmental stress.
DOI: 10.6084/m9.figshare.8282513
title: How to read the data from Universal modesty in signal-burying games

description: Why would individuals hide positive information about themselves? Evolutionary game theorists have recently developed the signal-burying game as a simple model to shed light on this puzzle. They have shown that the game has an equilibrium where some agents are better off deliberately reducing the visibility of the signal by which they broadcast their positive traits. However, this equilibrium also features individuals who fully broadcast their positive traits. Here, we show that the signal-burying framework can also explain modesty norms that everyone adheres to: the game contains an equilibrium where all agents who send a signal voluntarily reduce its conspicuousness. Surprisingly, the stability of the two kinds of equilibria rely on very different principles. The equilibrium where some agents brag is stable because of costly signalling dynamics. By contrast, the universal modesty equilibrium exists because buried signals contain probabilistic information about a sender’s type, and receivers make optimal use of this information. In the latter equilibrium, burying a signal can be understood as a handicap which makes the signal more honest, but honesty is not achieved through standard costly signalling dynamics.
DOI: 10.6084/m9.figshare.8282516
title: Simulation data from Universal modesty in signal-burying games

description: Data from the agent-based model
DOI: 10.6084/m9.figshare.8282519
title: Simulation code from Universal modesty in signal-burying games

description: Code for the agent-based model
DOI: 10.6084/m9.figshare.8282516.v1
title: Simulation data from Universal modesty in signal-burying games

description: Data from the agent-based model
DOI: 10.6084/m9.figshare.8282519.v1
title: Simulation code from Universal modesty in signal-burying games

description: Code for the agent-based model
DOI: 10.6084/m9.figshare.8282492
title: Skeleton analysis 8210 GP 1

description: Skeleton analysis 8210 GP 1 2019 paper
DOI: 10.6084/m9.figshare.8282492.v1
title: Skeleton analysis 8210 GP 1

description: Skeleton analysis 8210 GP 1 2019 paper
DOI: 10.6084/m9.figshare.8282444
title: Skeleton Analysis 8209 GP 2

description: Skeleton Analysis 8209 GP 2 2019 paper
DOI: 10.6084/m9.figshare.8282444.v1
title: Skeleton Analysis 8209 GP 2

description: Skeleton Analysis 8209 GP 2 2019 paper
DOI: 10.6084/m9.figshare.8282309
title: 2017-18 Australian fur seal counts at Seal Rocks and The Skerries, VIC, Australia

description: Data used to compare different count techniques for Australian fur seals in published article "Remotely piloted aircraft improve precision of capture-mark-resight population estimates of Australian fur seals"
DOI: 10.6084/m9.figshare.8282318
title: The Fine-scale Genetic Structure and Selection Signals of Chinese Indigenous Pigs

description: Genome-wide SNP profiling has yielded insights into the genetic structure of China indigenous pigs, but have focused on a limited number of populations. Here, we present an analysis of population structure and signals of positive selection in 41 Chinese pig populations that represent the most extensive pig phenotypic diversity in China, using genotype data of 1.1 million SNPs on customized Beadchips. This unravels the fine-scale genetic diversity, phylogentic relationships and population structure of these populations, which shows remarkably concordance between genetic clusters and geography with few exceptions. We also reveal the genetic contribution to North Chinese pigs from European modern pigs. Furthermore, we identify possible targets of selection in the Tibetan pig, including the well characterized hypoxia gene (EPAS1) and several previously unrecognized candidates. Intriguingly, the selected haplotype in the EPAS1 gene is associated with higher hemoglobin contents in Tibetan pigs, which is different from the protective role of EPAS1 in the high-altitude adaptation in Tibetan dogs and their owners. Additionally, we present evidence for the causality between EDNRB variants and the two-end-black (TEB) coat color phenotype in all Chinese pig populations except the Jinhua pig. We hypothesize that distinct targets have been independently selected for the formation of the TEB phenotype in Chinese pigs of different geographic origins. This highlights the importance of characterizing population-specific genetic determinants for heritable phenotype in diverse pig populations.
DOI: 10.6084/m9.figshare.8282309.v1
title: 2017-18 Australian fur seal counts at Seal Rocks and The Skerries, VIC, Australia

description: Data used to compare different count techniques for Australian fur seals in published article "Remotely piloted aircraft improve precision of capture-mark-resight population estimates of Australian fur seals"
DOI: 10.6084/m9.figshare.8282306
title: Graph Data Version 3

description: Gates Open Research version 3 dataset for Figure 3
DOI: 10.6084/m9.figshare.8282318.v1
title: The Fine-scale Genetic Structure and Selection Signals of Chinese Indigenous Pigs

description: Genome-wide SNP profiling has yielded insights into the genetic structure of China indigenous pigs, but have focused on a limited number of populations. Here, we present an analysis of population structure and signals of positive selection in 41 Chinese pig populations that represent the most extensive pig phenotypic diversity in China, using genotype data of 1.1 million SNPs on customized Beadchips. This unravels the fine-scale genetic diversity, phylogentic relationships and population structure of these populations, which shows remarkably concordance between genetic clusters and geography with few exceptions. We also reveal the genetic contribution to North Chinese pigs from European modern pigs. Furthermore, we identify possible targets of selection in the Tibetan pig, including the well characterized hypoxia gene (EPAS1) and several previously unrecognized candidates. Intriguingly, the selected haplotype in the EPAS1 gene is associated with higher hemoglobin contents in Tibetan pigs, which is different from the protective role of EPAS1 in the high-altitude adaptation in Tibetan dogs and their owners. Additionally, we present evidence for the causality between EDNRB variants and the two-end-black (TEB) coat color phenotype in all Chinese pig populations except the Jinhua pig. We hypothesize that distinct targets have been independently selected for the formation of the TEB phenotype in Chinese pigs of different geographic origins. This highlights the importance of characterizing population-specific genetic determinants for heritable phenotype in diverse pig populations.
DOI: 10.6084/m9.figshare.8282243
title: Development of a novel six-long non-coding RNA signature predicting survival of patients with bladder urothelial carcinoma

description: Bladder urothelial carcinoma is a malignant tumor with a high incidence in the uropoietic system. Considerable studies have shown that long non-coding RNA (lncRNA) plays an important role in the development and progression of bladder urothelial carcinoma. In this study, the lncRNA expression and clinical data of 377 bladder urothelial carcinoma patients were obtained from The Cancer Genome Atlas (TCGA) database, and differentially expressed lncRNAs in the cancer and normal groups were evaluated. Univariate COX and multivariate COX regression analyses of prognosis were performed on differentially expressed lncRNAs in the training datasets, six prognosis-related lncRNAs (LINC02195, LINC01484, LINC01468, SMC2-AS1, AC011298.1, and PTPRD-AS1) were assessed, and a 6-lncRNA signature was constructed. The predictive capability of this 6-lncRNA signature was validated in the testing datasets and entire datasets. The prognostic ability of 6-lncRNA signature was independent of other clinical elements after multivariate COX regression and stratified analyses of with other clinical elements. We performed functional enrichment analysis with the six prognosis-related lncRNAs. Results of functional enrichment revealed that these prognosis-related lncRNAs might promote the development and metastasis of bladder urothelial carcinoma. In summary, the 6-lncRNA signature that we developed could effectively predict the prognosis of bladder urothelial carcinoma patients. This 6-lncRNA signature might be a novel independent prognostic marker of bladder urothelial carcinoma. Moreover，it also provides novel insights into the mechanism of bladder urothelial carcinoma.
DOI: 10.6084/m9.figshare.8282243.v1
title: Development of a novel six-long non-coding RNA signature predicting survival of patients with bladder urothelial carcinoma

description: Bladder urothelial carcinoma is a malignant tumor with a high incidence in the uropoietic system. Considerable studies have shown that long non-coding RNA (lncRNA) plays an important role in the development and progression of bladder urothelial carcinoma. In this study, the lncRNA expression and clinical data of 377 bladder urothelial carcinoma patients were obtained from The Cancer Genome Atlas (TCGA) database, and differentially expressed lncRNAs in the cancer and normal groups were evaluated. Univariate COX and multivariate COX regression analyses of prognosis were performed on differentially expressed lncRNAs in the training datasets, six prognosis-related lncRNAs (LINC02195, LINC01484, LINC01468, SMC2-AS1, AC011298.1, and PTPRD-AS1) were assessed, and a 6-lncRNA signature was constructed. The predictive capability of this 6-lncRNA signature was validated in the testing datasets and entire datasets. The prognostic ability of 6-lncRNA signature was independent of other clinical elements after multivariate COX regression and stratified analyses of with other clinical elements. We performed functional enrichment analysis with the six prognosis-related lncRNAs. Results of functional enrichment revealed that these prognosis-related lncRNAs might promote the development and metastasis of bladder urothelial carcinoma. In summary, the 6-lncRNA signature that we developed could effectively predict the prognosis of bladder urothelial carcinoma patients. This 6-lncRNA signature might be a novel independent prognostic marker of bladder urothelial carcinoma. Moreover，it also provides novel insights into the mechanism of bladder urothelial carcinoma.
DOI: 10.6084/m9.figshare.8282201
title: NM-1.csv

description: testing dataset
DOI: 10.6084/m9.figshare.8282201.v1
title: NM-1.csv

description: testing dataset
DOI: 10.6084/m9.figshare.8282183
title: Additional file 5: of Exome sequencing in routine diagnostics: a generic test for 254 patients with primary immunodeficiencies

description: Table S5. Quality information of the WES technology, with the mean target coverage, and the % of bases with &gt;â 20Ă coverage. (XLSX 22 kb)
DOI: 10.6084/m9.figshare.8282186
title: Additional file 6: of Exome sequencing in routine diagnostics: a generic test for 254 patients with primary immunodeficiencies

description: Table S6. Information on all large &gt;â 5-Mb homozygous regions per patient, detected in the exome. Of each region, the genomic location, size, % homozygous variants, and the detected mutation are provided. (XLSX 158 kb)
DOI: 10.6084/m9.figshare.8282177
title: Additional file 3: of Exome sequencing in routine diagnostics: a generic test for 254 patients with primary immunodeficiencies

description: Table S3. Variants of unknown significance (class 3) and variants in TRAF3 identified in 17 patients suffering from primary immunodeficiencies. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.8282180
title: Additional file 4: of Exome sequencing in routine diagnostics: a generic test for 254 patients with primary immunodeficiencies

description: Table S4. (A) The number of patients with isolated or combined infections, and (B) the number of patients with isolated or combined immunophenotypes, and the percentage for which we have reported a genetic diagnosis. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.8282183.v1
title: Additional file 5: of Exome sequencing in routine diagnostics: a generic test for 254 patients with primary immunodeficiencies

description: Table S5. Quality information of the WES technology, with the mean target coverage, and the % of bases with &gt;â 20Ă coverage. (XLSX 22 kb)
DOI: 10.6084/m9.figshare.8282186.v1
title: Additional file 6: of Exome sequencing in routine diagnostics: a generic test for 254 patients with primary immunodeficiencies

description: Table S6. Information on all large &gt;â 5-Mb homozygous regions per patient, detected in the exome. Of each region, the genomic location, size, % homozygous variants, and the detected mutation are provided. (XLSX 158 kb)
DOI: 10.6084/m9.figshare.8282174
title: Additional file 2: of Exome sequencing in routine diagnostics: a generic test for 254 patients with primary immunodeficiencies

description: Table S2. Shows all causative mutations identified in 72 patients from 68 families suffering from primary immunodeficiencies. (XLSX 17 kb)
DOI: 10.6084/m9.figshare.8282177.v1
title: Additional file 3: of Exome sequencing in routine diagnostics: a generic test for 254 patients with primary immunodeficiencies

description: Table S3. Variants of unknown significance (class 3) and variants in TRAF3 identified in 17 patients suffering from primary immunodeficiencies. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.8282180.v1
title: Additional file 4: of Exome sequencing in routine diagnostics: a generic test for 254 patients with primary immunodeficiencies

description: Table S4. (A) The number of patients with isolated or combined infections, and (B) the number of patients with isolated or combined immunophenotypes, and the percentage for which we have reported a genetic diagnosis. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.8282171
title: Additional file 1: of Exome sequencing in routine diagnostics: a generic test for 254 patients with primary immunodeficiencies

description: Table S1. Overview of all clinical characteristics of the patients included in our diagnostic PID cohort, including all immunophenotype characteristics. (XLSX 63 kb)
DOI: 10.6084/m9.figshare.8282174.v1
title: Additional file 2: of Exome sequencing in routine diagnostics: a generic test for 254 patients with primary immunodeficiencies

description: Table S2. Shows all causative mutations identified in 72 patients from 68 families suffering from primary immunodeficiencies. (XLSX 17 kb)
DOI: 10.6084/m9.figshare.8282171.v1
title: Additional file 1: of Exome sequencing in routine diagnostics: a generic test for 254 patients with primary immunodeficiencies

description: Table S1. Overview of all clinical characteristics of the patients included in our diagnostic PID cohort, including all immunophenotype characteristics. (XLSX 63 kb)
DOI: 10.6084/m9.figshare.8282123
title: LS3_1_2.fq.gz

description: A part of transcriptome sequencing raw data of safflower flowers which were cultivated under different light intensities.
DOI: 10.6084/m9.figshare.8282117
title: HS3_3_2.fq.gz

description: A part of transcriptome sequencing raw data of safflower flowers which were cultivated under different light intensities.
DOI: 10.6084/m9.figshare.8282120
title: LS3_1_1.fq.gz

description: A part of transcriptome sequencing raw data of safflower flowers which were cultivated under different light intensities.
DOI: 10.6084/m9.figshare.8282123.v1
title: LS3_1_2.fq.gz

description: A part of transcriptome sequencing raw data of safflower flowers which were cultivated under different light intensities.
DOI: 10.6084/m9.figshare.8282120.v1
title: LS3_1_1.fq.gz

description: A part of transcriptome sequencing raw data of safflower flowers which were cultivated under different light intensities.