cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12501701.v1
title: Combined Analysis DataFilter_Script for experiment 1 & 2

description: To determine how DEX treatment in WT and MKO mice leads to muscle atrophy, we measured muscle protein fractional synthesis rates using shot-gun LC-MS/MS analysis after <i>in vivo</i> <sup>2</sup>H<sub>2</sub>O labeling. Mice were treated with PBS or DEX for 10 days. During the final 7 days, mice were also labeled with <sup>2</sup>H<sub>2</sub>O. The sample size for wild type controls treated with PBS (WT-PBS, n=6), wild type treated with DEX (WT-DEX, n=6), MKO treated with PBS (MKO-PBS, n=5) and MKO treated with DEX (MKO-DEX, n=5). The rational for biological replicates of n=5-6 were used to ensure accurate comparison among each group. Biological replicates were chosen to asses biological variability rather than sole reliance on technical replicates. Controls included WT-PBS treated mice (n=6). Two separate dynamic proteomic experiments were completed and combined for final data analysis. This consisted of experiment 1 that included WT-PBS (n=4) and WT-DEX (n=4). Experiment 2 included the final biological replicates of WT-PBS (n=2), WT-DEX (n=2), MKO-PBS (n=5) and MKO-DEX (n=5). The data sets were combined and annotated as described by the following. We used several filtering criteria for inclusion of protein kinetic data that were included in the comparisons: more than one peptide had to be present for any protein; each peptide had to meet analytic accuracy criteria for fractional mass isotopomer abundances and for reproducibility; a protein had to be present in at least 3 animals per group; and these criteria had to be met for the protein in all 4 groups. The number of proteins meeting these criteria was 81 in WT-PBS, 88 in WT-DEX, 124 in MKO-PBS and 134 in MKO-DEX and 57 proteins met these criteria in gastrocnemius muscle in all 4 groups. To determine the difference in protein fractional synthesis rates (f), four groups were categorized as the following: WT-PBS, WT-DEX, MKO-PBS and MKO-DEX. The mean, medium, and standard deviation for each protein (n≥3 for each group) were calculated, and a 2X2 ANOVA analysis (InfernoRDN) was performed to compare the treatment, genotype, and interaction effects. Protein fractional synthesis were averaged within groups and the percent changes were compared across each group. An increase or decrease in fractional synthesis was assessed as ± 0.0 %. A binomial distribution statistical analysis was used to calculate the significance of the relative percent increase or decrease in GA protein fractional synthesis. Average protein fractional synthesis was also assessed by ANOVA followed by the Benjamini and Hochberg test for multiple comparisons (FDR=0.05, p ≤0.05) using GraphPad Prism version 8.0 for Mac, GraphPad Software, La Jolla California USA.<br>This is the combined data filter for protein kinetics data for experiment 1 and 2.
DOI: 10.6084/m9.figshare.12501614
title: SummaryTable_Script for experiment 1

description: To determine how DEX treatment in WT and MKO mice leads to muscle atrophy, we measured muscle protein fractional synthesis rates using shot-gun LC-MS/MS analysis after <i>in vivo</i> <sup>2</sup>H<sub>2</sub>O labeling . Mice were treated with PBS or DEX for 10 days. During the final 7 days, mice were also labeled with <sup>2</sup>H<sub>2</sub>O. The sample size for wild type controls treated with PBS (WT-PBS, n=6), wild type treated with DEX (WT-DEX, n=6), MKO treated with PBS (MKO-PBS, n=5) and MKO treated with DEX (MKO-DEX, n=5). The rational for biological replicates of n=5 -6 were used to ensure accurate comparison among each group. Biological replicates were chosen to asses biological variability rather than sole reliance on technical replicates. Controls included WT-PBS treated mice (n=6). Two separate dynamic proteomic experiments were completed and combined for final data analysis. This consisted of experiment 1 that included WT-PBS (n=4) and WT-DEX (n=4). Experiment 2 included the final biological replicates of WT-PBS (n=2), WT-DEX (n=2), MKO-PBS (n=5) and MKO-DEX (n=5). The data sets were combined and annotated as described by the following.<br>The summary table contains the raw data information for mass isotopomer distribution kinetic analysis for experiment 1.
DOI: 10.6084/m9.figshare.12501614.v1
title: SummaryTable_Script for experiment 1

description: To determine how DEX treatment in WT and MKO mice leads to muscle atrophy, we measured muscle protein fractional synthesis rates using shot-gun LC-MS/MS analysis after <i>in vivo</i> <sup>2</sup>H<sub>2</sub>O labeling . Mice were treated with PBS or DEX for 10 days. During the final 7 days, mice were also labeled with <sup>2</sup>H<sub>2</sub>O. The sample size for wild type controls treated with PBS (WT-PBS, n=6), wild type treated with DEX (WT-DEX, n=6), MKO treated with PBS (MKO-PBS, n=5) and MKO treated with DEX (MKO-DEX, n=5). The rational for biological replicates of n=5 -6 were used to ensure accurate comparison among each group. Biological replicates were chosen to asses biological variability rather than sole reliance on technical replicates. Controls included WT-PBS treated mice (n=6). Two separate dynamic proteomic experiments were completed and combined for final data analysis. This consisted of experiment 1 that included WT-PBS (n=4) and WT-DEX (n=4). Experiment 2 included the final biological replicates of WT-PBS (n=2), WT-DEX (n=2), MKO-PBS (n=5) and MKO-DEX (n=5). The data sets were combined and annotated as described by the following.<br>The summary table contains the raw data information for mass isotopomer distribution kinetic analysis for experiment 1.
DOI: 10.6084/m9.figshare.12501659.v1
title: DataFilter_Script for experiment 1

description: To determine how DEX treatment in WT and MKO mice leads to muscle atrophy, we measured muscle protein fractional synthesis rates using shot-gun LC-MS/MS analysis after <i>in vivo</i> <sup>2</sup>H<sub>2</sub>O labeling . Mice were treated with PBS or DEX for 10 days. During the final 7 days, mice were also labeled with <sup>2</sup>H<sub>2</sub>O. The sample size for wild type controls treated with PBS (WT-PBS, n=6), wild type treated with DEX (WT-DEX, n=6), MKO treated with PBS (MKO-PBS, n=5) and MKO treated with DEX (MKO-DEX, n=5). The rational for biological replicates of n=5 -6 were used to ensure accurate comparison among each group. Biological replicates were chosen to asses biological variability rather than sole reliance on technical replicates. Controls included WT-PBS treated mice (n=6). Two separate dynamic proteomic experiments were completed and combined for final data analysis. This consisted of experiment 1 that included WT-PBS (n=4) and WT-DEX (n=4). Experiment 2 included the final biological replicates of WT-PBS (n=2), WT-DEX (n=2), MKO-PBS (n=5) and MKO-DEX (n=5). The data sets were combined and annotated as described by the following.<br>The data filter script contains the mass isotopomer distribution processed data that includes the peptide output, protein output, parameters, and project details for experiment 1.
DOI: 10.6084/m9.figshare.12501455
title: Sub counties of Kenya based on County Intergrated Development Plans(CIDPS)

description: A geospatial layer of 295 sub-counties in Kenya created by digitizing sub-county maps available for each county from the county integrated development plans (CIDPs)
DOI: 10.6084/m9.figshare.12501419
title: Dataset_TMPRSS2.xlsx

description: The data is the genotype distributions of 41 polymorphisms of the TMPRSS2 gene in two populations: Amazonian Amerindians and Admixed population of northern Brazil.
DOI: 10.6084/m9.figshare.12501398
title: Data set children with intellectual disability University of Barcelona

description: Dataset in SPSS (.sav) including data from a Spanish sample of families with a child with intellectual disability.
DOI: 10.6084/m9.figshare.12501398.v1
title: Data set children with intellectual disability University of Barcelona

description: Dataset in SPSS (.sav) including data from a Spanish sample of families with a child with intellectual disability.
DOI: 10.6084/m9.figshare.12501398.v2
title: Data set children with Intellectual Disability University of Barcelona

description: Dataset in SPSS (.sav) including data from a Spanish sample of families with a child with intellectual disability.
DOI: 10.6084/m9.figshare.12501398.v3
title: Data set children with intellectual disability University of Barcelona

description: Dataset in SPSS (.sav) including data from a Spanish sample of families with a child with intellectual disability.
DOI: 10.6084/m9.figshare.12501128
title: Actionable mutational profiles of Vietnamese patients with NSCLC

description: Population-specific profiling of mutations in cancer genes is of critical importance for the understanding of cancer biology in general as well as the establishment of optimal diagnostics and treatment guidelines for that particular population. Although genetic analysis of tumor tissue is often used to detect mutations in cancer genes, the invasiveness and limited accessibility hinders its application in large-scale population studies. In this study, we used ultra-deep massive parallel sequencing to compare actionable mutation profiles of two different cohorts of Vietnamese patients with non-small cell lung cancer (NSCLC). The first cohort, called cfDNA (cell free DNA) cohort, included plasma samples collected from a total of 265 treatment naive patients with advanced stage NSCLC (stage III-IV). The second cohort, called ttDNA (tumour tissue DNA) cohort, comprised of tissue samples from 285 NSCLC patients with matched tumour stages and treatment status of the cfDNA cohort. We found that ultra-deep sequencing of plasma cfDNA represents an alternative approach for population-wide genetic profiling of cancer genes where recruitment of patients is limited to the accessibility of tumour tissue site.
DOI: 10.6084/m9.figshare.12499463
title: Nicotiana corolla mouth micrographs

description: Tiled fluorescence micrographs of <i>Nicotiana</i> corolla mouth tissue stained with aniline blue to measure cell width, cell number, and tissue circumference. Includes data from <i>Nicotiana sylvestris</i>, <i>N. tomentosiformis</i>, <i>N. tabacum</i> 095-55, <i>N. tabacum</i> 'Chulumani,' and synthetic <i>N. tabacum</i> lines QM20, QM24, and QM25. Numbers after species name indicate the plant the flower was taken from. The synthetic <i>N. tabacum </i>lines are first generation polyploids; therefore, only one plant per line was available. The letters after the synthetic lines indicate different flowers.<br>
DOI: 10.6084/m9.figshare.12501128.v2
title: Actionable mutational profiles of Vietnamese patients with NSCLC

description: Population-specific profiling of mutations in cancer genes is of critical importance for the understanding of cancer biology in general as well as the establishment of optimal diagnostics and treatment guidelines for that particular population. Although genetic analysis of tumor tissue is often used to detect mutations in cancer genes, the invasiveness and limited accessibility hinders its application in large-scale population studies. In this study, we used ultra-deep massive parallel sequencing to compare actionable mutation profiles of two different cohorts of Vietnamese patients with non-small cell lung cancer (NSCLC). The first cohort, called cfDNA (cell free DNA) cohort, included plasma samples collected from a total of 265 treatment naive patients with advanced stage NSCLC (stage III-IV). The second cohort, called ttDNA (tumour tissue DNA) cohort, comprised of tissue samples from 285 NSCLC patients with matched tumour stages and treatment status of the cfDNA cohort. We found that ultra-deep sequencing of plasma cfDNA represents an alternative approach for population-wide genetic profiling of cancer genes where recruitment of patients is limited to the accessibility of tumour tissue site.
DOI: 10.6084/m9.figshare.12499463.v1
title: Nicotiana corolla mouth micrographs

description: Tiled fluorescence micrographs of <i>Nicotiana</i> corolla mouth tissue stained with aniline blue to measure cell width, cell number, and tissue circumference. Includes data from <i>Nicotiana sylvestris</i>, <i>N. tomentosiformis</i>, <i>N. tabacum</i> 095-55, <i>N. tabacum</i> 'Chulumani,' and synthetic <i>N. tabacum</i> lines QM20, QM24, and QM25. Numbers after species name indicate the plant the flower was taken from. The synthetic <i>N. tabacum </i>lines are first generation polyploids; therefore, only one plant per line was available. The letters after the synthetic lines indicate different flowers.<br>
DOI: 10.6084/m9.figshare.12498989
title: Raw data of the study from Fine-scale genital morphology affects male ejaculation success: an experimental test

description: A file including the raw data
DOI: 10.6084/m9.figshare.12498989.v1
title: Raw data of the study from Fine-scale genital morphology affects male ejaculation success: an experimental test

description: A file including the raw data
DOI: 10.6084/m9.figshare.12498965
title: Data for figure 4 from Comparative micromechanics of bushcricket ears with and without a specialized auditory fovea region in the crista acustica

description: Mecopoda elongata: Amplitude and phase data for each measured position along the CA and stimulus frequency
DOI: 10.6084/m9.figshare.12498959
title: Data for figure 5 from Comparative micromechanics of bushcricket ears with and without a specialized auditory fovea region in the crista acustica

description: Area under curve values for each animal and stimulus frequency
DOI: 10.6084/m9.figshare.12498965.v1
title: Data for figure 4 from Comparative micromechanics of bushcricket ears with and without a specialized auditory fovea region in the crista acustica

description: Mecopoda elongata: Amplitude and phase data for each measured position along the CA and stimulus frequency
DOI: 10.6084/m9.figshare.12498944
title: Data for figure 3 from Comparative micromechanics of bushcricket ears with and without a specialized auditory fovea region in the crista acustica

description: Ancylecha fenestrata: Amplitude and phase data for each measured position along the CA and stimulus frequency
DOI: 10.6084/m9.figshare.12498959.v1
title: Data for figure 5 from Comparative micromechanics of bushcricket ears with and without a specialized auditory fovea region in the crista acustica

description: Area under curve values for each animal and stimulus frequency
DOI: 10.6084/m9.figshare.12498719
title: ASV Taxonomy Assignment

description: Full taxonomy for all ASV representative sequences as classified by the SILVA v138 database
DOI: 10.6084/m9.figshare.12498719.v1
title: ASV Taxonomy Assignment

description: Full taxonomy for all ASV representative sequences as classified by the SILVA v138 database
DOI: 10.6084/m9.figshare.12498533
title: Actual Sequence Variant (ASV) count table

description: Actual Sequence Variant (ASV) count table for all samples
DOI: 10.6084/m9.figshare.12498533.v1
title: Actual Sequence Variant (ASV) count table

description: Actual Sequence Variant (ASV) count table for all samples
DOI: 10.6084/m9.figshare.12498479
title: FGB_Sponge_Metadata.txt

description: Sample Metadata
DOI: 10.6084/m9.figshare.12498446
title: Designing a sustainable humanitarian relief logistics model in pre- and postdisaster management

description: In this study, a three-level relief chain problem is proposed in pre- and postdisaster phases in order to support sustainability in the context of humanitarian relief operations. We develop a comprehensive relief logistics network considering the strategic and tactical planning issues of facility location, procurement, and resource allocation, and including multi-objective mixed-integer stochastic programing model which minimizes total costs of the humanitarian relief supply chain (the costs of the preparedness and response phases), maximizes the social welfare (through maximizing the minimum satisfaction rates among the disaster areas), and minimizes the environmental impacts (ecological impacts of the packaging of relief goods, and CO<sub>2</sub> emissions in transportation routes of the proposed network in pre- and postdisaster phases), simultaneously. The proposed multi-objective sustainable humanitarian relief logistics problem (SHRLP) is solved using the Compromise Programing (CP) technique and Lexicographic Optimization Method (LOM). Two numerical examples with different scales are provided based on surveying data of possible Tehran earthquakes. The results of solving numerical examples via CP and LOM methods are presented and compared. The efficient Pareto optimal solutions are also provided to examine different preferences of the objectives. LOM produces better solutions than the CP technique in terms of the satisfaction rates and fair distribution of relief items. Also, the results indicate that the novel model is able to survey and model both the sustainability approach and the uncertainty of a disaster relief condition in support of more efficient and effective plans for sustainable facility locations, and procurement and delivery of reliefs.
DOI: 10.6084/m9.figshare.12498479.v1
title: FGB_Sponge_Metadata.txt

description: Sample Metadata
DOI: 10.6084/m9.figshare.12498446.v1
title: Designing a sustainable humanitarian relief logistics model in pre- and postdisaster management

description: In this study, a three-level relief chain problem is proposed in pre- and postdisaster phases in order to support sustainability in the context of humanitarian relief operations. We develop a comprehensive relief logistics network considering the strategic and tactical planning issues of facility location, procurement, and resource allocation, and including multi-objective mixed-integer stochastic programing model which minimizes total costs of the humanitarian relief supply chain (the costs of the preparedness and response phases), maximizes the social welfare (through maximizing the minimum satisfaction rates among the disaster areas), and minimizes the environmental impacts (ecological impacts of the packaging of relief goods, and CO<sub>2</sub> emissions in transportation routes of the proposed network in pre- and postdisaster phases), simultaneously. The proposed multi-objective sustainable humanitarian relief logistics problem (SHRLP) is solved using the Compromise Programing (CP) technique and Lexicographic Optimization Method (LOM). Two numerical examples with different scales are provided based on surveying data of possible Tehran earthquakes. The results of solving numerical examples via CP and LOM methods are presented and compared. The efficient Pareto optimal solutions are also provided to examine different preferences of the objectives. LOM produces better solutions than the CP technique in terms of the satisfaction rates and fair distribution of relief items. Also, the results indicate that the novel model is able to survey and model both the sustainability approach and the uncertainty of a disaster relief condition in support of more efficient and effective plans for sustainable facility locations, and procurement and delivery of reliefs.
DOI: 10.6084/m9.figshare.12498434
title: File S1.csv from Comparison of solitary and collective foraging strategies of <i>Caenorhabditis elegans</i> in patchy food distributions

description: Collective foraging has been shown to benefit organisms in environments where food is patchily distributed, but whether this is true in the case where organisms do not rely on long-range communications to coordinate their collective behaviour has been understudied. To address this question, we use the tractable laboratory model organism <i>Caenorhabditis elegans</i>, where a social strain (<i>npr-1</i> mutant) and a solitary strain (N2) are available for direct comparison of foraging strategies. We first developed an on-lattice minimal model for comparing collective and solitary foraging strategies, finding that social agents benefit from feeding faster and more efficiently simply due to group formation. Our laboratory foraging experiments with <i>npr-1</i> and N2 worm populations, however, show an advantage for solitary N2 in all food distribution environments that we tested. We incorporated additional strain-specific behavioural parameters of <i>npr-1</i> and N2 worms into our model and computationally identified N2's higher feeding rate to be the key factor underlying its advantage, without which it is possible to recapitulate the advantage of collective foraging in patchy environments. Our work highlights the theoretical advantage of collective foraging due to group formation alone without long-range interactions and the valuable role of modelling to guide experiments.This article is part of the theme issue ‘Multi-scale analysis and modelling of collective migration in biological systems'.
DOI: 10.6084/m9.figshare.12498434.v1
title: File S1.csv from Comparison of solitary and collective foraging strategies of <i>Caenorhabditis elegans</i> in patchy food distributions

description: Collective foraging has been shown to benefit organisms in environments where food is patchily distributed, but whether this is true in the case where organisms do not rely on long-range communications to coordinate their collective behaviour has been understudied. To address this question, we use the tractable laboratory model organism <i>Caenorhabditis elegans</i>, where a social strain (<i>npr-1</i> mutant) and a solitary strain (N2) are available for direct comparison of foraging strategies. We first developed an on-lattice minimal model for comparing collective and solitary foraging strategies, finding that social agents benefit from feeding faster and more efficiently simply due to group formation. Our laboratory foraging experiments with <i>npr-1</i> and N2 worm populations, however, show an advantage for solitary N2 in all food distribution environments that we tested. We incorporated additional strain-specific behavioural parameters of <i>npr-1</i> and N2 worms into our model and computationally identified N2's higher feeding rate to be the key factor underlying its advantage, without which it is possible to recapitulate the advantage of collective foraging in patchy environments. Our work highlights the theoretical advantage of collective foraging due to group formation alone without long-range interactions and the valuable role of modelling to guide experiments.This article is part of the theme issue ‘Multi-scale analysis and modelling of collective migration in biological systems'.
DOI: 10.6084/m9.figshare.12498296
title: Data of hypertensive patients who have actively attended the Integrated Health Service Post for the Elderly (IHSP-Elderly)

description: this is data of hypertensive patients who have actively attended the Integrated Health Service Post for the Elderly (IHSP-Elderly) in malang Indonesia
DOI: 10.6084/m9.figshare.12498062
title: JVASP-12070 to JVASP-12868

description: JARVIS-DFT input/output files
DOI: 10.6084/m9.figshare.12498065
title: JVASP-12869 to JVASP-14087

description: JARVIS-DFT input/output files
DOI: 10.6084/m9.figshare.12498056
title: JVASP-8888 to JVASP-9674

description: JARVIS-DFT input/output files
DOI: 10.6084/m9.figshare.12498059
title: JVASP-11301 to JVASP-12069

description: JARVIS-DFT input/output files
DOI: 10.6084/m9.figshare.12497993
title: GS_sample

description: phenotype for GS&GP
DOI: 10.6084/m9.figshare.12497993.v1
title: GS_sample

description: phenotype for GS&GP
DOI: 10.6084/m9.figshare.12497942
title: GSQC_bed.bim

description: BIM文件
DOI: 10.6084/m9.figshare.12497963
title: GSQC_bed

description: Geno dataset for GP&GS
DOI: 10.6084/m9.figshare.12497900
title: Complete plastome sequence of Aspidopterys obcordata (Malpighiaceae), a traditional Dai medicinal plant from Xishuangbanna, Yunnan, China

description: Complete plastome sequence of Aspidopterys obcordata (Malpighiaceae), a traditional Dai medicinal plant from Xishuangbanna, Yunnan, China
DOI: 10.6084/m9.figshare.12497942.v1
title: GSQC_bed.bim

description: BIM文件
DOI: 10.6084/m9.figshare.12497963.v1
title: GSQC_bed

description: Geno dataset for GP&GS