cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.11960265.v1
title: Additional file 9 of Metabolic and evolutionary responses of Clostridium thermocellum to genetic interventions aimed at improving ethanol production

description: Additional file 9: Table S9. RNAseq expression data for each gene and strain. Units of reads per kilobase per million mapped reads (RPKM), median value for each strain (n ≥ 4). Genes are identified by Clostridium thermocellum locus number, from Genbank NC_017304.1 and NCBI GeneInfo identifier number. Strains are identified by LL number (Table 2).
DOI: 10.6084/m9.figshare.11960256.v1
title: Additional file 7 of Metabolic and evolutionary responses of Clostridium thermocellum to genetic interventions aimed at improving ethanol production

description: Additional file 7: Table S7. JGI libraries. Table describing each chemostat where samples were sent for RNAseq analysis. The ID column can be used to match RNAseq data to fermentation data. The JGI library column can be used to match individual RNAseq data.
DOI: 10.6084/m9.figshare.11960241
title: Additional file 2 of Metabolic and evolutionary responses of Clostridium thermocellum to genetic interventions aimed at improving ethanol production

description: Additional file 2: Table S2. All mutations in all strains. Genes identified by Clostridium thermocellum locus number from Genbank NC_017304.1, which is also used for chromosomal coordinates of the start region of the mutation (“StartReg” column). For each mutation, the fraction of reads that support the mutation is given.
DOI: 10.6084/m9.figshare.11960241.v1
title: Additional file 2 of Metabolic and evolutionary responses of Clostridium thermocellum to genetic interventions aimed at improving ethanol production

description: Additional file 2: Table S2. All mutations in all strains. Genes identified by Clostridium thermocellum locus number from Genbank NC_017304.1, which is also used for chromosomal coordinates of the start region of the mutation (“StartReg” column). For each mutation, the fraction of reads that support the mutation is given.
DOI: 10.6084/m9.figshare.11960208
title: Additional file 3 of Identification of universal and cell-type specific p53 DNA binding

description: Additional file 3: Table S3. List of p53 target genes used for analysis in Additional file 4: Figure S4. This list was based on [12] and removing genes with low read coverage in our dataset.
DOI: 10.6084/m9.figshare.11960208.v1
title: Additional file 3 of Identification of universal and cell-type specific p53 DNA binding

description: Additional file 3: Table S3. List of p53 target genes used for analysis in Additional file 4: Figure S4. This list was based on [12] and removing genes with low read coverage in our dataset.
DOI: 10.6084/m9.figshare.11960199
title: Additional file 1 of Identification of universal and cell-type specific p53 DNA binding

description: Additional file 1: Table S1. p53 ChIP data generated in this study and the public datasets used (in Additional file 4: Figure S1). For each cell line and condition, we also individually called peaks and report the number of peaks identified in each condition.
DOI: 10.6084/m9.figshare.11960205
title: Additional file 2 of Identification of universal and cell-type specific p53 DNA binding

description: Additional file 2: Table S2. Table of 8742 p53 ChIP peaks reported in this study. Table includes chromosome number, peak start and end coordinates, whether the peak was variably bound across 12 cell lines in this study (494 peaks marked by ‘1’ in the ‘variable peak’ column), the nearest associated gene to each peak as well as the normalized peak intensities for each cell line in this study and in published datasets (Additional file 4: Figure S1, Additional file 1: Table S1).
DOI: 10.6084/m9.figshare.11960199.v1
title: Additional file 1 of Identification of universal and cell-type specific p53 DNA binding

description: Additional file 1: Table S1. p53 ChIP data generated in this study and the public datasets used (in Additional file 4: Figure S1). For each cell line and condition, we also individually called peaks and report the number of peaks identified in each condition.
DOI: 10.6084/m9.figshare.11960205.v1
title: Additional file 2 of Identification of universal and cell-type specific p53 DNA binding

description: Additional file 2: Table S2. Table of 8742 p53 ChIP peaks reported in this study. Table includes chromosome number, peak start and end coordinates, whether the peak was variably bound across 12 cell lines in this study (494 peaks marked by ‘1’ in the ‘variable peak’ column), the nearest associated gene to each peak as well as the normalized peak intensities for each cell line in this study and in published datasets (Additional file 4: Figure S1, Additional file 1: Table S1).
DOI: 10.6084/m9.figshare.11960157
title: Additional file 7 of Molecular epidemiology and antimicrobial resistance features of Acinetobacter baumannii clinical isolates from Pakistan

description: Additional file 7: Table S5. Acquired antimicrobial resistance genes retrived from the whole genome sequences of 25 clinical isolates of Acinetobacter baumannii collected in Pakistan between 2013 and 2015.
DOI: 10.6084/m9.figshare.11960151
title: Additional file 5 of Molecular epidemiology and antimicrobial resistance features of Acinetobacter baumannii clinical isolates from Pakistan

description: Additional file 5: Table S3. Genome assembly features of 25 clinical isolates of Acinetobacter baumannii collected in Pakistan between 2013 and 2015.
DOI: 10.6084/m9.figshare.11960154
title: Additional file 6 of Molecular epidemiology and antimicrobial resistance features of Acinetobacter baumannii clinical isolates from Pakistan

description: Additional file 6: Table S4. Plasmid replicon genes in the whole genome sequences of 25 clinical isolates of Acinetobacter baumannii collected in Pakistan between 2013 and 2015.
DOI: 10.6084/m9.figshare.11960157.v1
title: Additional file 7 of Molecular epidemiology and antimicrobial resistance features of Acinetobacter baumannii clinical isolates from Pakistan

description: Additional file 7: Table S5. Acquired antimicrobial resistance genes retrived from the whole genome sequences of 25 clinical isolates of Acinetobacter baumannii collected in Pakistan between 2013 and 2015.
DOI: 10.6084/m9.figshare.11960151.v1
title: Additional file 5 of Molecular epidemiology and antimicrobial resistance features of Acinetobacter baumannii clinical isolates from Pakistan

description: Additional file 5: Table S3. Genome assembly features of 25 clinical isolates of Acinetobacter baumannii collected in Pakistan between 2013 and 2015.
DOI: 10.6084/m9.figshare.11960154.v1
title: Additional file 6 of Molecular epidemiology and antimicrobial resistance features of Acinetobacter baumannii clinical isolates from Pakistan

description: Additional file 6: Table S4. Plasmid replicon genes in the whole genome sequences of 25 clinical isolates of Acinetobacter baumannii collected in Pakistan between 2013 and 2015.
DOI: 10.6084/m9.figshare.11960139
title: Additional file 3 of Molecular epidemiology and antimicrobial resistance features of Acinetobacter baumannii clinical isolates from Pakistan

description: Additional file 3: Table S2. Antimicrobial susceptibility results for 52 clinical isolates of Acinetobacter baumannii collected in Pakistan between 2013 and 2015.
DOI: 10.6084/m9.figshare.11960139.v1
title: Additional file 3 of Molecular epidemiology and antimicrobial resistance features of Acinetobacter baumannii clinical isolates from Pakistan

description: Additional file 3: Table S2. Antimicrobial susceptibility results for 52 clinical isolates of Acinetobacter baumannii collected in Pakistan between 2013 and 2015.
DOI: 10.6084/m9.figshare.11960130
title: Additional file 2 of Molecular epidemiology and antimicrobial resistance features of Acinetobacter baumannii clinical isolates from Pakistan

description: Additional file 2: Table S1. Primers used for amplification and sequencing of the blaOXA-51-like and ampC loci in 52 clinical isolates of Acinetobacter baumannii collected in Pakistan between 2013 and 2015.
DOI: 10.6084/m9.figshare.11960130.v1
title: Additional file 2 of Molecular epidemiology and antimicrobial resistance features of Acinetobacter baumannii clinical isolates from Pakistan

description: Additional file 2: Table S1. Primers used for amplification and sequencing of the blaOXA-51-like and ampC loci in 52 clinical isolates of Acinetobacter baumannii collected in Pakistan between 2013 and 2015.
DOI: 10.6084/m9.figshare.11960049
title: Additional file 1 of Intravenous leiomyomatosis with intracardiac extension managed by one-stage surgical excision: a case presentation

description: Additional file 1: Figure S1. Axial (a) and longitudinal (b) color Doppler ultrasound images depicting dilated IVC with intra-mural thrombus (m) showing partial re-canalisation with extension into the right heart (c).
DOI: 10.6084/m9.figshare.11960055
title: Additional file 2 of Intravenous leiomyomatosis with intracardiac extension managed by one-stage surgical excision: a case presentation

description: Additional file 2: Figure S2. CECT Axial (a ) and sagittal (b) images revealing a dilated IVC with heterogeneously enhancing mass extending into the right ventricle (arrows).
DOI: 10.6084/m9.figshare.11960055.v1
title: Additional file 2 of Intravenous leiomyomatosis with intracardiac extension managed by one-stage surgical excision: a case presentation

description: Additional file 2: Figure S2. CECT Axial (a ) and sagittal (b) images revealing a dilated IVC with heterogeneously enhancing mass extending into the right ventricle (arrows).
DOI: 10.6084/m9.figshare.11960049.v1
title: Additional file 1 of Intravenous leiomyomatosis with intracardiac extension managed by one-stage surgical excision: a case presentation

description: Additional file 1: Figure S1. Axial (a) and longitudinal (b) color Doppler ultrasound images depicting dilated IVC with intra-mural thrombus (m) showing partial re-canalisation with extension into the right heart (c).
DOI: 10.6084/m9.figshare.11959917
title: Additional file 2 of MOMO - multi-objective metabolic mixed integer optimization: application to yeast strain engineering

description: Additional file 2 Table S1: Flux distribution at each Pareto point. Table S2: All deletion candidates enumerated by Momo.
DOI: 10.6084/m9.figshare.11959917.v1
title: Additional file 2 of MOMO - multi-objective metabolic mixed integer optimization: application to yeast strain engineering

description: Additional file 2 Table S1: Flux distribution at each Pareto point. Table S2: All deletion candidates enumerated by Momo.
DOI: 10.6084/m9.figshare.11959737
title: Competitive ability of weedy rice: toward breeding weed-suppressive rice cultivars

description: Rice (<i>Oryza sativa</i> L.) is a vital crop for achieving global food security. Unfortunately, weeds are the major yield-constraining factor in rice production systems worldwide. Development of rice with higher competitive ability than weeds will help achieve sustainable weed management, as robust rice cultivars will have a competitive advantage over weeds. As wild relatives are often explored by plant breeders in crop improvement programs, greenhouse studies were conducted to evaluate weed-suppressive potential of 54 weedy rice accessions (weedy relatives of cultivated rice) against barnyardgrass (<i>Echinochloa crus-galli</i>) and Amazon sprangletop (<i>Leptochloa panicoides</i>). Three allelopathic rice cultivars (PI312777, PI338046, and Rondo), and two commercial rice cultivars (CL163 and REX) were included as a positive and negative control, respectively. Among all the test accessions of weedy rice, B2 suppressed the growth of <i>E. crus-galli</i> by 52%, whereas accession B81 suppressed <i>L. panicoides</i> growth by 61%. Accession B81 caused greater than 50% growth inhibition of both <i>E. crus-galli</i> and <i>L. panicoides</i>. Thus, B2 and B81 were identified as the most weed-suppressive weedy rice accessions. Weed-suppressive potential in weedy rice was associated morphologically with hull type and awn length. Weed-suppressive weedy rice accessions identified from this study can be used as a source of raw genetic material in rice improvement programs. Future research should focus on identifying the underlying mechanism for a high weed-suppressive potential of specific weedy rice accessions.
DOI: 10.6084/m9.figshare.11959737.v1
title: Competitive ability of weedy rice: toward breeding weed-suppressive rice cultivars

description: Rice (<i>Oryza sativa</i> L.) is a vital crop for achieving global food security. Unfortunately, weeds are the major yield-constraining factor in rice production systems worldwide. Development of rice with higher competitive ability than weeds will help achieve sustainable weed management, as robust rice cultivars will have a competitive advantage over weeds. As wild relatives are often explored by plant breeders in crop improvement programs, greenhouse studies were conducted to evaluate weed-suppressive potential of 54 weedy rice accessions (weedy relatives of cultivated rice) against barnyardgrass (<i>Echinochloa crus-galli</i>) and Amazon sprangletop (<i>Leptochloa panicoides</i>). Three allelopathic rice cultivars (PI312777, PI338046, and Rondo), and two commercial rice cultivars (CL163 and REX) were included as a positive and negative control, respectively. Among all the test accessions of weedy rice, B2 suppressed the growth of <i>E. crus-galli</i> by 52%, whereas accession B81 suppressed <i>L. panicoides</i> growth by 61%. Accession B81 caused greater than 50% growth inhibition of both <i>E. crus-galli</i> and <i>L. panicoides</i>. Thus, B2 and B81 were identified as the most weed-suppressive weedy rice accessions. Weed-suppressive potential in weedy rice was associated morphologically with hull type and awn length. Weed-suppressive weedy rice accessions identified from this study can be used as a source of raw genetic material in rice improvement programs. Future research should focus on identifying the underlying mechanism for a high weed-suppressive potential of specific weedy rice accessions.
DOI: 10.6084/m9.figshare.11959347
title: Additional file 2: Table S1-S2.docx

description: Supplemental Tables. <b>Table S1. </b>Correlation analysis between five lipids for CAP and clinical indicators -Pearson’s correlation coefficient. <b>Table S2.</b> Correlation analysis between five lipids for CAP and clinical indicators-<i>p</i> value
DOI: 10.6084/m9.figshare.11959347.v1
title: Additional file 2: Table S1-S2.docx

description: Supplemental Tables. <b>Table S1. </b>Correlation analysis between five lipids for CAP and clinical indicators -Pearson’s correlation coefficient. <b>Table S2.</b> Correlation analysis between five lipids for CAP and clinical indicators-<i>p</i> value
DOI: 10.6084/m9.figshare.11959299
title: A New Bifuzzy Optimization Method for Remanufacturing Scheduling Using Extended Discrete Particle Swarm Optimization Algorithm

description: This is the experimental data of the manuscript entitled “A New Bifuzzy Optimization Method for Remanufacturing Scheduling Using Extended Discrete Particle Swarm Optimization Algorithm”. All data are generated through computer simulation and saved in the file with csv format. There are 32 instances for these experiments. The datasets show the number of end-of-life products, the number of non-identical parallel processing lines and the number of processing cells in each processing line. The bifuzzy processing time and bifuzzy processing cost of each product remanufactured at each processing cell of each line and the bifuzzy processing reliability of each product remanufactured at each processing line also show in the datasets. Each bifuzzy variables in the data is composed of five groups of triangular fuzzy numbers with possibilities. The values in each group represent the smallest possible value of triangular fuzzy number, the most promising value of triangular fuzzy number, the largest possible value of triangular fuzzy number, and the possibility of this bifuzzy vairbale to take the triangular fuzzy number in this group by this bifuzzy variable.
DOI: 10.6084/m9.figshare.11959299.v1
title: A New Bifuzzy Optimization Method for Remanufacturing Scheduling Using Extended Discrete Particle Swarm Optimization Algorithm

description: This is the experimental data of the manuscript entitled “A New Bifuzzy Optimization Method for Remanufacturing Scheduling Using Extended Discrete Particle Swarm Optimization Algorithm”. All data are generated through computer simulation and saved in the file with csv format. There are 32 instances for these experiments. The datasets show the number of end-of-life products, the number of non-identical parallel processing lines and the number of processing cells in each processing line. The bifuzzy processing time and bifuzzy processing cost of each product remanufactured at each processing cell of each line and the bifuzzy processing reliability of each product remanufactured at each processing line also show in the datasets. Each bifuzzy variables in the data is composed of five groups of triangular fuzzy numbers with possibilities. The values in each group represent the smallest possible value of triangular fuzzy number, the most promising value of triangular fuzzy number, the largest possible value of triangular fuzzy number, and the possibility of this bifuzzy vairbale to take the triangular fuzzy number in this group by this bifuzzy variable.
DOI: 10.6084/m9.figshare.11959284
title: Cones structure and Seed traits of Four Species of Large-Seeded pines: Adaptation to Animal-mediated Dispersal

description: originaldata on traits of cone, seed, seed scale and cone structure
DOI: 10.6084/m9.figshare.11959284.v1
title: Cones structure and Seed traits of Four Species of Large-Seeded pines: Adaptation to Animal-mediated Dispersal

description: originaldata on traits of cone, seed, seed scale and cone structure
DOI: 10.6084/m9.figshare.11959287.v1
title: Instances, results and codes of "Efficient formulations for the Traveling Car Renter Problemand its Quota variant", by Lacroix, Rios-Solis, Wolfler-Calvo

description: Instances, results and codes of the paper: "Efficient formulations for the Traveling Car Renter Problemand its Quota variant", Lacroix, Rios-Solis, Wolfler-Calvo<br>Abstract of the paper: In this paper we study the recently introduced Traveling Car Renter Problem. This latter is a generalization of the well-known TSP where a solution is a set of paths of different colors as well as an orientation of each path in such a way that the union forms a directed Hamiltonian circuit. Considering costs associated with all edges and all ordered pairs of nodes for each color, the cost of a solution is the sum of the costs of its colored oriented paths, the cost of these latter being the sum of the edge costs plus the costs from their origin to their destination. We also consider the Quota version of this problem where a weight is associated with every node and the circuit formed by a solution covers a subset of nodes whose sum of weights meets a fixed value. We propose integer linear programming formulations for these problems. We also propose some valid inequalities for strengthening the models. The computational results show the efficiency of our formulations as we solve to optimality almost all the instances of the literature and outperform by an order of magnitude all the already published approaches.
DOI: 10.6084/m9.figshare.11959221
title: Film Industry Network Data

description: These network data tables describe nodes and edges in three film industries (Australia, Germany, Sweden). Data was obtained from different sources. Australian data was derived from the annual awards of the Australian Film Institute. German film industry data was supplied by Elizabeth Prommer at the University of Rostock. Swedish film industry data was supplied by the Swedish Film Institute. Date ranges and attributes were aligned as closely as possible: Australia (2006-15), Sweden (2006-16), Germany (2006-16).<br><br>
DOI: 10.6084/m9.figshare.11959062
title: Filtered Input Data

description: The filtered input data needed for all analyses for the paper "matrix factorization and transfer learning uncover regulatory biology across multiple single-cell ATAC-seq data sets".
DOI: 10.6084/m9.figshare.11959062.v1
title: Filtered Input Data

description: The filtered input data needed for all analyses for the paper "matrix factorization and transfer learning uncover regulatory biology across multiple single-cell ATAC-seq data sets".
DOI: 10.6084/m9.figshare.11958975
title: Cerulean Warbler Geolocator Analysis

description: These files are light-level data (.lux files) and R code to analyze the geolocator data.
DOI: 10.15131/shef.data.11958954
title: Data for MicroCT-based MicroFE of human vertebrae

description: This file contains the results collected in the study: "Effect of size and location of simulated lytic lesions on the structural properties of human vertebral bodies, a micro-finite element study" by "M.C. Costa, L.B. Bresani Campello, M. Ryan, J. Rochester, M. Viceconti, E. Dall’Ara" published in Bone Reports:<br>https://doi.org/10.1016/j.bonr.2020.100257.<br>In order to access the original raw files the reader can contact the the corresponding author (Dr Enrico Dall'Ara, e.dallara@sheffield.ac.uk). The files are stored in the University of Sheffield file-store at the link:https://web-unidrive.sheffield.ac.uk/shared/bone_biomechanics1/Projects/15_METVERT/DD_SimulatedMetastases/
DOI: 10.15131/shef.data.11958954.v1
title: Data for MicroCT-based MicroFE of human vertebrae

description: This file contains the results collected in the study: "Effect of size and location of simulated lytic lesions on the structural properties of human vertebral bodies, a micro-finite element study" by "M.C. Costa, L.B. Bresani Campello, M. Ryan, J. Rochester, M. Viceconti, E. Dall’Ara" published in Bone Reports:<br>https://doi.org/10.1016/j.bonr.2020.100257.<br>In order to access the original raw files the reader can contact the the corresponding author (Dr Enrico Dall'Ara, e.dallara@sheffield.ac.uk). The files are stored in the University of Sheffield file-store at the link:https://web-unidrive.sheffield.ac.uk/shared/bone_biomechanics1/Projects/15_METVERT/DD_SimulatedMetastases/
DOI: 10.6084/m9.figshare.11958831
title: Flowsquare Apatosaurus dorsals for CFD

description: Bitmap image that contains the boundary conditions and text file that contains simulation parameters for the Flowsquare analysis of pressure fields around the <i>Apatosaurus </i>dorsals.
DOI: 10.6084/m9.figshare.11958831.v1
title: Flowsquare Apatosaurus dorsals for CFD

description: Bitmap image that contains the boundary conditions and text file that contains simulation parameters for the Flowsquare analysis of pressure fields around the <i>Apatosaurus </i>dorsals.