cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5501605
title: Cerebral perfusion and hemodyamics in Alzheimer mouse models

description: ArcAb mouse model of AD and wild-type littermates at 6-months and 24-months of age.<br>1) ASL-MRI for perfusion imaging<br>2) MSOT imaging for brain oxygenation <br><br>Ten Wild-type C57/B6 mice at 12 weeks for oxygen-challenged MSOT measurement under normoxia and hyperoxia conditions.<br>3) MSOT imaging for brain oxygenation<br>4) Calcuated Oxygen saturation (SO2) color map in mouse brain under different oxygen supply.<br><br>
DOI: 10.6084/m9.figshare.5501593
title: Supplementary data and R code for Soulsbury et al. Stabilising selection on immune response in male black grouse Lyrurus tetrix. Oecologia.

description: This is the dataset (FigShare data.xlsx) and the R code (R code.R) that replicates the analyses presented in: Soulsbury et al. Stabilising selection on immune response in male black grouse Lyrurus tetrix. Oecologia. <br>
DOI: 10.6084/m9.figshare.5501614.v1
title: Sequencing CV2025 transaminase

description: Sequencing of CV2025 transaminase was performed using these primers:-CV2025.opt.Mid_Rev-JH3AOX1<br>-5AOX1JH<br>
DOI: 10.6084/m9.figshare.5501587
title: Glucocorticoids modulate gastrointestinal microbiome in a wild bird

description: Physiological and biometric database
DOI: 10.6084/m9.figshare.5501587.v1
title: Glucocorticoids modulate gastrointestinal microbiome in a wild bird

description: Physiological and biometric database
DOI: 10.6084/m9.figshare.5501605.v1
title: Cerebral perfusion and hemodyamics in Alzheimer mouse models

description: ArcAb mouse model of AD and wild-type littermates at 6-months and 24-months of age.<br>1) ASL-MRI for perfusion imaging<br>2) MSOT imaging for brain oxygenation <br><br>Ten Wild-type C57/B6 mice at 12 weeks for oxygen-challenged MSOT measurement under normoxia and hyperoxia conditions.<br>3) MSOT imaging for brain oxygenation<br>4) Calcuated Oxygen saturation (SO2) color map in mouse brain under different oxygen supply.<br><br>
DOI: 10.6084/m9.figshare.5501542
title: Supplementary Material for: ALS-Related Mutant FUS Protein Is Mislocalized to Cytoplasm and Is Recruited into Stress Granules of Fibroblasts from Asymptomatic FUS P525L Mutation Carriers

description: <i>Background:</i> Amyotrophic lateral sclerosis (ALS) shows a strong genetic basis, with <i>SOD1</i>, <i>FUS</i>, <i>TARDBP</i>, and <i>C9ORF72 </i>being the genes most frequently involved<i>. </i>This has allowed identification of asymptomatic mutation carriers, which may be of help in understanding the molecular changes preceding disease onset. <i>Objectives:</i> We studied the cellular expression of FUS protein and the effect of heat-shock- and dithiothreitol-induced stress in fibroblasts from <i>FUS</i> P525L mutation carriers, healthy controls, and patients with sporadic ALS. <i>Methods:</i> Western blots and immunocytochemistry were performed to study the subcellular localization of FUS protein. Control and stressed cells were double stained with FUS and the stress marker TIA-R. <i>Results:</i> Fibroblasts from healthy controls and sporadic ALS cases showed a prominent nuclear FUS expression. In the 2 <i>FUS</i> P525L mutation carriers, instead, most cells showed a protein localization in both nucleus and cytoplasm, or exclusively in the cytoplasm. Stress prompted the formation of cytoplasmic granules in all subjects and in sporadic ALS FUS mislocalization to the cytoplasm. Cytoplasmic FUS was recruited into stress granules, which showed a time-dependent decrease in all subjects. However, in the <i>FUS</i> P525L fibroblasts, the granules persisted longer, and they were more numerous than those detected in the cells from controls and sporadic ALS patients. <i>Conclusions:</i> We show that in fibroblasts of <i>FUS</i> P525L mutation carriers, FUS mislocalized to the cytoplasm where it redistributed into stress granules with likely a dose effect, i.e. a higher number of cells with granules, which persist longer, than in controls and ALS cases. These data represent an early molecular change occurring before ALS onset, suggesting a transient preaggregative state.
DOI: 10.6084/m9.figshare.5501539
title: DVS event-stream image super resolution dataset

description: The videos are the results of the super-resolution of DVS recordigns. The file name ended with "_SR" is the super-resolution results.
DOI: 10.6084/m9.figshare.5501542.v1
title: Supplementary Material for: ALS-Related Mutant FUS Protein Is Mislocalized to Cytoplasm and Is Recruited into Stress Granules of Fibroblasts from Asymptomatic FUS P525L Mutation Carriers

description: <i>Background:</i> Amyotrophic lateral sclerosis (ALS) shows a strong genetic basis, with <i>SOD1</i>, <i>FUS</i>, <i>TARDBP</i>, and <i>C9ORF72 </i>being the genes most frequently involved<i>. </i>This has allowed identification of asymptomatic mutation carriers, which may be of help in understanding the molecular changes preceding disease onset. <i>Objectives:</i> We studied the cellular expression of FUS protein and the effect of heat-shock- and dithiothreitol-induced stress in fibroblasts from <i>FUS</i> P525L mutation carriers, healthy controls, and patients with sporadic ALS. <i>Methods:</i> Western blots and immunocytochemistry were performed to study the subcellular localization of FUS protein. Control and stressed cells were double stained with FUS and the stress marker TIA-R. <i>Results:</i> Fibroblasts from healthy controls and sporadic ALS cases showed a prominent nuclear FUS expression. In the 2 <i>FUS</i> P525L mutation carriers, instead, most cells showed a protein localization in both nucleus and cytoplasm, or exclusively in the cytoplasm. Stress prompted the formation of cytoplasmic granules in all subjects and in sporadic ALS FUS mislocalization to the cytoplasm. Cytoplasmic FUS was recruited into stress granules, which showed a time-dependent decrease in all subjects. However, in the <i>FUS</i> P525L fibroblasts, the granules persisted longer, and they were more numerous than those detected in the cells from controls and sporadic ALS patients. <i>Conclusions:</i> We show that in fibroblasts of <i>FUS</i> P525L mutation carriers, FUS mislocalized to the cytoplasm where it redistributed into stress granules with likely a dose effect, i.e. a higher number of cells with granules, which persist longer, than in controls and ALS cases. These data represent an early molecular change occurring before ALS onset, suggesting a transient preaggregative state.
DOI: 10.6084/m9.figshare.5501533
title: Minidiscus-Minutocellus-V9_data.xlsx

description: <b>Tara Oceans </b><b>V9-</b><b>18S rDNA metabarcodes</b><b> </b>-<b> </b>We used the global metabarcoding data set generated from the biological samples collected from 146 sampling locations during the <i>Tara</i> Oceans expedition. We extracted ribotypes that were assigned to <i>Minidiscus </i>and <i>Minutocellus </i>from the three depths - surface (SRF), deep chlorophyll maximum (DCM) and mesopelagic (MESO)- within the different size class filters (ranging from 0.8 - 2,000 µm, with the smallest fraction being 0.8 to 5 µm). The taxonomic assignations was done using PR2 reference database which has six reference sequences from <i>Minidiscus</i> <i>trioculatus</i>, 2 from <i>Minidiscus</i> sp., and one is environmental sequence. Relative abundance was calculated with respect to total diatom reads and to total phytosynthetic reads, which comprised reads assigned to major phytoplanktonic groups, namely Bacillariophyta, Chlorophyceae, Cryptophyta, Dictyochophyceae, Dinophyceae, Haptophyta, Mamiellophyceae, Pelagophyceae and Raphidophyceae. Exponentiated Shannon-Weiner H’ diversity index was used as the estimates of diversity at each station. All the analyses were conducted using open source R version 3.3.1.<br>
DOI: 10.6084/m9.figshare.5501533.v1
title: Minidiscus-Minutocellus-V9_data.xlsx

description: <b>Tara Oceans </b><b>V9-</b><b>18S rDNA metabarcodes</b><b> </b>-<b> </b>We used the global metabarcoding data set generated from the biological samples collected from 146 sampling locations during the <i>Tara</i> Oceans expedition. We extracted ribotypes that were assigned to <i>Minidiscus </i>and <i>Minutocellus </i>from the three depths - surface (SRF), deep chlorophyll maximum (DCM) and mesopelagic (MESO)- within the different size class filters (ranging from 0.8 - 2,000 µm, with the smallest fraction being 0.8 to 5 µm). The taxonomic assignations was done using PR2 reference database which has six reference sequences from <i>Minidiscus</i> <i>trioculatus</i>, 2 from <i>Minidiscus</i> sp., and one is environmental sequence. Relative abundance was calculated with respect to total diatom reads and to total phytosynthetic reads, which comprised reads assigned to major phytoplanktonic groups, namely Bacillariophyta, Chlorophyceae, Cryptophyta, Dictyochophyceae, Dinophyceae, Haptophyta, Mamiellophyceae, Pelagophyceae and Raphidophyceae. Exponentiated Shannon-Weiner H’ diversity index was used as the estimates of diversity at each station. All the analyses were conducted using open source R version 3.3.1.<br>
DOI: 10.6084/m9.figshare.5501494
title: Supplementary Table S2 from What drives the evolution of condition-dependent recombination in diploids? Some insights from simulation modelling

description: Numerical characteristics of selection regimes with non-trivial optimum and their outcomes
DOI: 10.6084/m9.figshare.5501494.v1
title: Supplementary Table S2 from What drives the evolution of condition-dependent recombination in diploids? Some insights from simulation modelling

description: Numerical characteristics of selection regimes with non-trivial optimum and their outcomes
DOI: 10.6084/m9.figshare.5501461
title: Supplementary Table S5 from What drives the evolution of condition-dependent recombination in diploids? Some insights from simulation modelling

description: Numerical characteristics of selection regimes with zero optimum and their outcomes
DOI: 10.6084/m9.figshare.5501461.v1
title: Supplementary Table S5 from What drives the evolution of condition-dependent recombination in diploids? Some insights from simulation modelling

description: Numerical characteristics of selection regimes with zero optimum and their outcomes
DOI: 10.6084/m9.figshare.5501413
title: Simulation code from Host–parasite fluctuating selection in the absence of specificity

description: Fluctuating selection driven by coevolution between hosts and parasites is important for the generation of host and parasite diversity across space and time. Theory has focused primarily on infection genetics, with highly specific ‘matching-allele’ frameworks more likely to generate fluctuating selection dynamics (FSD) than ‘gene-for-gene’ (generalist–specialist) frameworks. However, the environment, ecological feedbacks and life-history characteristics may all play a role in determining when FSD occurs. Here, we develop eco-evolutionary models with explicit ecological dynamics to explore the ecological, epidemiological and host life-history drivers of FSD. Our key result is to demonstrate for the first time that specificity between hosts and parasites is not required to generate FSD. Furthermore, highly specific host–parasite interactions produce unstable, less robust stochastic fluctuations in contrast to interactions that lack specificity altogether or those that vary from generalist to specialist, which produce predictable limit cycles. Given the ubiquity of ecological feedbacks and the variation in the nature of specificity in host–parasite interactions, our work emphasizes the underestimated potential for host–parasite coevolution to generate fluctuating selection.
DOI: 10.6084/m9.figshare.5501413.v1
title: Simulation code from Host–parasite fluctuating selection in the absence of specificity

description: Fluctuating selection driven by coevolution between hosts and parasites is important for the generation of host and parasite diversity across space and time. Theory has focused primarily on infection genetics, with highly specific ‘matching-allele’ frameworks more likely to generate fluctuating selection dynamics (FSD) than ‘gene-for-gene’ (generalist–specialist) frameworks. However, the environment, ecological feedbacks and life-history characteristics may all play a role in determining when FSD occurs. Here, we develop eco-evolutionary models with explicit ecological dynamics to explore the ecological, epidemiological and host life-history drivers of FSD. Our key result is to demonstrate for the first time that specificity between hosts and parasites is not required to generate FSD. Furthermore, highly specific host–parasite interactions produce unstable, less robust stochastic fluctuations in contrast to interactions that lack specificity altogether or those that vary from generalist to specialist, which produce predictable limit cycles. Given the ubiquity of ecological feedbacks and the variation in the nature of specificity in host–parasite interactions, our work emphasizes the underestimated potential for host–parasite coevolution to generate fluctuating selection.
DOI: 10.6084/m9.figshare.5501377
title: Database Experimental Study from Mitochondria-targeted molecules determine the redness of the zebra finch bill

description: Experimental study excel file
DOI: 10.6084/m9.figshare.5501377.v1
title: Database Experimental Study from Mitochondria-targeted molecules determine the redness of the zebra finch bill

description: Experimental study excel file
DOI: 10.6084/m9.figshare.5501344
title: Database Pilot Study from Mitochondria-targeted molecules determine the redness of the zebra finch bill

description: Pilot study excel file
DOI: 10.6084/m9.figshare.5501350
title: AMINO-ACID-SEQ from Mitochondrial determinants of mammalian longevity

description: Current ageing theories are far from satisfactory because of the many determinants involved in ageing. The well-known rate-of-living theory assumes that the product (lifetime energy expenditure (LEE)) of maximum lifespan (MLS) and mass-specific basal metabolic rate (msBMR) is approximately constant. Although this theory provides a significant inverse correlation between msBMR and MLS as a whole for mammals, it remains problematic for two reasons. First, several interspecies studies within respective orders (typically within rodents) have shown no inverse relationships between msBMR and MLS. Second, LEE values widely vary in mammals and birds. Here, to solve these two problems, we introduced a new quantity designated as mitochondrial (mt) lifetime energy output, mtLEO = MLS × mtMR in place of LEE, by using the mt metabolic rate (mtMR) per mitochondrion. Thereby, we found that mtLEO values were distributed more narrowly than LEE ones, and strongly correlated with the four amino-acid variables (AAVs) of Ser, Thr and Cys contents and hydrophobicity of mtDNA-encoded membrane proteins (these variables were related to the stability of these proteins). Consequently, only these 2 mt items, mtMR and the AAVs, solved the above-mentioned problems in the rate-of-living theory, and thus extensively improved the correlation with MLS compared with that given by LEE.
DOI: 10.6084/m9.figshare.5501344.v1
title: Database Pilot Study from Mitochondria-targeted molecules determine the redness of the zebra finch bill

description: Pilot study excel file
DOI: 10.6084/m9.figshare.5501329
title: Supplemental Table S1.zip

description: List of 3,289,847 intervarietal SNPs with fraction (ISBP or low-copy sequence), chromosomal origin, corresponding IWGSC contig, and context sequence.<br>Rimbert et al. (2017) High throughput SNP discovery and genotyping in hexaploid wheat. PLoS One.
DOI: 10.6084/m9.figshare.5501332
title: DWI MRI, T2 MRI, MMP hemodynamics MSOT in tMCAO mouse model

description: Data set for measurement in tMCAO mouse model and sham-operated model after occlusion and 48 h after reperfusion.1) in vivo DWI MRI,2) in vivo T2 MRI,3) in vivo MMP measurement by using MSOT4) in vivo oxygenation measurement by using MSOT4) Postmortem TTC staining5) Postmortem NIRF staining for MMP<br>Data set for phantom experiment MMPsense probe measurement using MSOT
DOI: 10.6084/m9.figshare.5501350.v1
title: AMINO-ACID-SEQ from Mitochondrial determinants of mammalian longevity

description: Current ageing theories are far from satisfactory because of the many determinants involved in ageing. The well-known rate-of-living theory assumes that the product (lifetime energy expenditure (LEE)) of maximum lifespan (MLS) and mass-specific basal metabolic rate (msBMR) is approximately constant. Although this theory provides a significant inverse correlation between msBMR and MLS as a whole for mammals, it remains problematic for two reasons. First, several interspecies studies within respective orders (typically within rodents) have shown no inverse relationships between msBMR and MLS. Second, LEE values widely vary in mammals and birds. Here, to solve these two problems, we introduced a new quantity designated as mitochondrial (mt) lifetime energy output, mtLEO = MLS × mtMR in place of LEE, by using the mt metabolic rate (mtMR) per mitochondrion. Thereby, we found that mtLEO values were distributed more narrowly than LEE ones, and strongly correlated with the four amino-acid variables (AAVs) of Ser, Thr and Cys contents and hydrophobicity of mtDNA-encoded membrane proteins (these variables were related to the stability of these proteins). Consequently, only these 2 mt items, mtMR and the AAVs, solved the above-mentioned problems in the rate-of-living theory, and thus extensively improved the correlation with MLS compared with that given by LEE.
DOI: 10.6084/m9.figshare.5501314
title: “中国省级科技普及资源开发影响空间差异能耗碳足迹”实证模型计算的数据集

description: “中国省级科技普及资源开发影响空间差异能耗碳足迹”实证模型计算的数据集<br>
DOI: 10.6084/m9.figshare.5501326
title: Resettlement Management Transcripts.zip

description: This dataset contains transcripts from the group discussions of the study conducted in Bududa District, Mt Elgon region of Uganda
DOI: 10.6084/m9.figshare.5501329.v1
title: Supplemental Table S1.zip

description: List of 3,289,847 intervarietal SNPs with fraction (ISBP or low-copy sequence), chromosomal origin, corresponding IWGSC contig, and context sequence.<br>Rimbert et al. (2017) High throughput SNP discovery and genotyping in hexaploid wheat. PLoS One.
DOI: 10.6084/m9.figshare.5501314.v1
title: “中国省级科技普及资源开发影响空间差异能耗碳足迹”实证模型计算的数据集

description: “中国省级科技普及资源开发影响空间差异能耗碳足迹”实证模型计算的数据集<br>
DOI: 10.6084/m9.figshare.5501266
title: A case study of low-level jets in Yerevan simulated by the WRF model

description: The data for the manuscript entitled as "A case study of low-level jets in Yerevan simulated by the WRF model", revision submitted to Journal of Geophysical Research - Atmospheres (Paper #2017JD027629).
DOI: 10.6084/m9.figshare.5501284
title: A seasonal climatology of UV reflectivity for southern South America

description: A seasonal climatology for the Lambertian equivalent reflectivity (LER) in ultraviolet (UV) for southern South America is introduced. The study region was limited by 10° and 60°S and by 100° and 30°W; the data set spanned the period 1978–2015. Features of the seasonal means and of the quarterly (Q) and the interannual (IA) variabilities for each season were ascribed to atmospheric and oceanic processes of local, regional, or global origin which lead to the formation or maintenance of clouds. Shifts in the Q and IA time series were detected, most notably in the early 1990s. Linear trends were also estimated. The largest positive and negative trends in the Q time series were found along the Peruvian Andes (PA) (3.20 reflectivity units [RU] decade<sup>−1</sup>) and east of the Chapada Diamantina (CD) and the Serra do Espinhaço (SE) in Brazil (−1.40 RU decade<sup>−1</sup>), respectively. The largest positive and negative trends in the IA time series were found in PA (6 RU decade<sup>−1</sup>, summer) and east of CD and SE (−2.50 RU decade<sup>−1</sup>, spring), respectively. The linkages between UV LER and regional or global circulation indices were also studied. The largest relationships were found with the Dipole Mode Index on a Q basis and with the Southern Oscillation Index on an IA basis in winter.
DOI: 10.6084/m9.figshare.5501284.v1
title: A seasonal climatology of UV reflectivity for southern South America

description: A seasonal climatology for the Lambertian equivalent reflectivity (LER) in ultraviolet (UV) for southern South America is introduced. The study region was limited by 10° and 60°S and by 100° and 30°W; the data set spanned the period 1978–2015. Features of the seasonal means and of the quarterly (Q) and the interannual (IA) variabilities for each season were ascribed to atmospheric and oceanic processes of local, regional, or global origin which lead to the formation or maintenance of clouds. Shifts in the Q and IA time series were detected, most notably in the early 1990s. Linear trends were also estimated. The largest positive and negative trends in the Q time series were found along the Peruvian Andes (PA) (3.20 reflectivity units [RU] decade<sup>−1</sup>) and east of the Chapada Diamantina (CD) and the Serra do Espinhaço (SE) in Brazil (−1.40 RU decade<sup>−1</sup>), respectively. The largest positive and negative trends in the IA time series were found in PA (6 RU decade<sup>−1</sup>, summer) and east of CD and SE (−2.50 RU decade<sup>−1</sup>, spring), respectively. The linkages between UV LER and regional or global circulation indices were also studied. The largest relationships were found with the Dipole Mode Index on a Q basis and with the Southern Oscillation Index on an IA basis in winter.
DOI: 10.6084/m9.figshare.5501248
title: Arthropods dataset from different genetically modified maize events and associated controls

description: The food-web graph index data contains the number of nodes (species) and the number of edges (trophic relations between species) for each maize entry. Values in degree represents the number of trophic links toward the species in food web (number of other species feeding with this species). Values out degree represents the number of trophic links from the species (number of other species eaten by the species). K indexes or keystone index are quantitative rank of species by their topological importance. As the K index increase the species importance are higher in the functioning of the food-web.<br>Sample 1_Pitfall Traps_2007-2008 contains arthropods data collected with pitfall traps in different maize development stages. (eight leaves stage (V8), twelve leaves stage (V12), vegetative stage, tasseling (VT) and reproductive stage, milk (R3)). <br><br>Sample 2_Yellow Traps_2007-2008 contains arthropods data collected with yellow traps in different maize development stages. (eight leaves stage (V8), twelve leaves stage (V12), vegetative stage, tasseling (VT) and reproductive stage, milk (R3)). <br><br>Sample 3_Plant Assessment_2007-2008 contains arthropods data assessed from plants in different maize development stages. (eight leaves stage (V8), twelve leaves stage (V12), vegetative stage, tasseling (VT) and reproductive stage, milk (R3)). <br><br>Sample 4_Weed coverage_2007-2008 contains weed assessment in different maize development stages. (eight leaves stage (V8), twelve leaves stage (V12), vegetative stage, tasseling (VT) and reproductive stage, milk (R3)). <br>