cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17637/rh.12707840.v1
title: UKGEOS pore network models from Glasgow and Sellafield samples

description: <pre>This folder contains files for analysis of 3D micro CT images for the article "Pore Scale Assessment of Subsurface Carbon Storage Potential: Implications for the UK Geoenergy Observatories Project" by Payton, Fellgett, Clark, Chiarella and Hier-Majumder. To create the figures presented in the article run the python script analysis.py Description of data: - overall_GG_SF_poro_perm.csv = porosity and permeability data collected in this study, obtained from measurements on the micro CT images using PerGeos. - Each folder with the prefix 'GG' (Glasgow) contains 2 files: - all_pores.csv = measurements made characterising the pore geometry within the sample using PerGeos on the micro CT images. 'all' indicates both connected and disconnected porosity. - all_throats.csv = measurements made characterising the throat geometry within the sample using PerGeos on the micro CT images. 'all' indicates both connected and disconnected porosity. - Each folder with the prefix 'SF' (Sellafield) contains 4 files: - all_pores.csv (see above) - all_grains.csv (see above) - effective_pores.csv = measurements made characterising the pore geometry within the sample using PerGeos on the micro CT images. 'effective' indicates only connected porosity. - effective_throats.csv = measurements made characterising the throat geometry within the sample using PerGeos on the micro CT images. 'effective' indicates only connected porosity. - The folder 'literature_data' contains the supporting data used to plot the figures in this article which are fully referenced in the article itself. We uses these data as a comparison to our own. - 'Poro_Perm' contains the supporting porosity and permeability measurements used where each CSV file in this folder is named after the original author, referenced in the article. - 'Paul' contains the supporting data from our research group in CSV file format where the file name reflects the reference in our article. Funding London NERC DTP Studentship (NE/L002485/1) British Geological Survey University Funding Initiative (BUFI) CASE studentship </pre>
DOI: 10.6084/m9.figshare.12707444
title: SAXJ1808_Bary.fits

description: File containing the observation of SAX J1808.4-3658 performed at INAF's 3.6 m Telescopio Nazionale Galileo equipped with the fast optical photometer SiFAP2.
DOI: 10.6084/m9.figshare.12707444.v1
title: SAXJ1808_Bary.fits

description: File containing the observation of SAX J1808.4-3658 performed at INAF's 3.6 m Telescopio Nazionale Galileo equipped with the fast optical photometer SiFAP2.
DOI: 10.6084/m9.figshare.12707084
title: Supplementary Material for: Global Response of <b><i>Phaeobacter inhibens</i></b> DSM 17395 to Deletion of Its 262-kb Chromid Encoding Antibiotic Synthesis

description: The marine alphaproteobacterium <i>Phaeobacter inhibens</i> DSM 17395, a member of the <i>Roseobacter</i> group, was recently shown to markedly enhance growth upon deletion of its 262-kb chromid encoding biosynthesis of tropodithietic acid (TDA). To scrutinize the metabolic/regulatory adaptations that underlie enhanced growth of the Δ262 mutant, its transcriptome and proteome compared to the wild type were investigated in process-controlled bioreactors with Casamino Acids as growth substrate. Genome resequencing revealed only few additional genetic changes (a heterogenic insertion, prophage activation, and several point mutations) between wild type and Δ262 mutant, albeit with no conceivable effect on the studied growth physiology. The abundances of the vast majority of transcripts and proteins involved in the catabolic network for complete substrate oxidation to CO<sub>2</sub> were found to be unchanged, suggesting that the enhanced amino acid utilization of the Δ262 mutant did not require elevated synthesis of most enzymes of the catabolic network. Similarly, constituents of genetic information processing and cellular processes remained mostly unchanged. In contrast, 426 genes displayed differential expression, of which 410 were localized on the 3.2-Mb chromosome, 5 on the 65-kb chromid, and 11 on the 78-kb chromid. Notably, the branched-chain amino transferase IlvE acting on rapidly utilized Val, Ile, and Leu was upregulated. Moreover, the transportome was reconfigured, as evidenced from increased abundances of transcripts and proteins of several uptake systems for amino acids and inorganic nutrients (e.g., phosphate). Some components of the respiratory chain were also upregulated, which correlates with the higher respiration rates of the Δ262 mutant. Furthermore, chromosomally encoded transcripts and proteins that are peripherally related to TDA biosynthesis (e.g., the serine acyl transferase CysE) were strongly downregulated in the Δ262 mutant. Taken together, these observations reflect adaptations to enhanced growth as well as the functional interconnectivity of the replicons of <i>P. inhibens</i> DSM 17395.
DOI: 10.6084/m9.figshare.12706598
title: frugiv_data.csv

description: This is a set of fleshy-fruited tree - frugivorous bird interaction records, with independant estimations of species relative abundances.Data was collected by Daniel Martinez in New Zealand in 2012 in 9 different sites.The dataset columns are the following:Location: site namesfreq : frugivorous interaction frequenciesrow abun : plant abundancescol. abun : bird abundances <br>exotic.plant = logical: TRUE suggests the plant species is exotic in NZ.exotic.bird: same for birdsint.origin: for interaction origin. 2 previous columns pasted togetherfrugiv_exot_bird: sum of interaction ferquencies involving an exotic bird divided by the sum of all interaction frequencies of that siteorigin: a more-explicit factor describing species origin<br> <br>
DOI: 10.6084/m9.figshare.12706523
title: Metadata record for: Global gridded dataset of crop-specific green and blue water requirements, the WATNEEDS model

description: This dataset contains key characteristics about the data described in the Data Descriptor Global gridded dataset of crop-specific green and blue water requirements, the WATNEEDS model. <br> Contents: <br> 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format
DOI: 10.6084/m9.figshare.12706523.v1
title: Metadata record for: Global gridded dataset of crop-specific green and blue water requirements, the WATNEEDS model

description: This dataset contains key characteristics about the data described in the Data Descriptor Global gridded dataset of crop-specific green and blue water requirements, the WATNEEDS model. <br> Contents: <br> 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format
DOI: 10.6084/m9.figshare.12706247
title: Leontodon longirostris genome draft 418Mb

description: <b>1-Leontodon-genome-draft-418Mb.fasta</b>: sequences in FASTA format of the 410,019 scaffolds and contigs that were considered the 418 Mb genome draft for <i>Leontodon longirostris</i>. <br> <b>2-Maker853GeneModels-in1007LongestFragments.gff</b>: the 853 MAKER-based gene models deduced from the 1007 longest (&gt;10 kb) fragments of the 418 Mb genome draft. <br> <b>3-FunctionalAnnot-MakerGeneModels-in1007LongestFragments.tsv</b>: Functional annotation of the predicted 853 proteins deduced from MAKER-based gene models. <br> <b>4-Reconstructed-472ChimaericModels.fasta</b>: sequences in FASTA format of the 472 GeneAssembler-based gene models reconstructed using the short (&lt;10 kb) genome fragments from the 418 Mb genome draft. <br> <b>5-ShortGenomeFragments-in472ChimaericModels.tsv</b>: list of contigs and scaffolds from the 418 Mb genome draft that were used to reconstruct each chimaeric, GeneAssembler-based gene model. <br> <b>6-GeneAssemblerChimaericModels-in472ChimaericModels.gff</b>: annotation of the 472 GeneAssember-based, chimaeric gene models by genome location. <br> <b>7-FunctionalAnnotation472ChimaericModels.xlsx</b>: comprehensive functional annotation of the 472 GeneAssember-based, chimaeric gene models, including the predicted protein length, the number of exons identified in that gene model, a fragmentation index (0-1 range, where 0 means that all exons in the model come from one single sequence contig, and 1 means that each exon comes from a different contig) and the human-readable description of the predicted protein sequence taken from the GFF file.<br>
DOI: 10.6084/m9.figshare.12706223
title: Diet Kuwait.csv

description: <b>Background</b>Despite the public health importance of documenting the burden of physical inactivity and weight gain, there is a paucity of such data in Kuwait during the lockdown for Covid-19 pandemic. Therefore, this survey was designed to estimate: the burden of poor eating habits particularly binge eating habits, fluctuations in weight and its predictors among the Kuwaiti public.<b>Methods</b>This cross-sectional survey was conducted from 2<sup>nd</sup> to 12<sup>th</sup> April 2020 among the general public in Kuwait. All data were collected through social media platform (WhatsApp groups), through convenience and snowball sampling methods. comprised of three sections: a) demographic characteristics of respondents, b) eating habits particularly binge eating, consumption of snacks and beverages c) subjective feelings of anxiety and d) weight before and during the pandemic. The data set is in CSV format.
DOI: 10.6084/m9.figshare.12705173
title: Supplementary Material for: Hepatic Arterial Infusion Chemotherapy versus Sorafenib in Patients with Advanced Hepatocellular Carcinoma

description: <b><i>Background:</i></b> Prior to the approval of sorafenib, hepatic arterial infusion chemotherapy (HAIC) was offered to patients with advanced hepatocellular carcinoma (HCC) in East Asia, particularly Japan. According to the Japanese guidelines, HAIC is recommended as one of the treatment options in patients without extrahepatic metastasis (EHM). <b><i>Methods:</i></b> The present cohort study compared the use of HAIC and sorafenib on outcomes of patients with advanced HCC. Consecutive patients with advanced HCC who received HAIC or sorafenib as a first-line systemic therapy were enrolled from 10 Japanese institutions. The primary outcomes were overall survival (OS) in patients with macrovascular invasion (MVI), but without EHM, and OS in patients without both MVI and EHM. <b><i>Results:</i></b> Between 2009 and 2016, 2,006 patients were enrolled (541 HAIC patients, 1,465 sorafenib patients). After propensity score matching, the OS of patients with MVI but without EHM was significantly longer in the HAIC group compared with the sorafenib group (10.1 vs. 9.1 months for the HAIC and sorafenib groups, respectively; <i>n</i> = 170 for each group; hazard ratio [HR] 0.668; 95% confidence interval [95% CI] 0.475–0.935; <i>p</i> = 0.018). There was no significant difference in OS between patients without both MVI and EHM (12.2 vs. 15.4 months for the HAIC and sorafenib groups, respectively; <i>n</i> = 76 in each cohort after propensity score matching; HR 1.227; 95% CI 0.699–2.155; <i>p</i> = 0.475). <b><i>Conclusion:</i></b> HAIC is a potential front-line treatment choice in a subpopulation of patients with advanced HCC with MVI but without EHM.
DOI: 10.6084/m9.figshare.12705770
title: Supplementary Material for: Polyostotic Fibrous Dysplasia Mimicking Bone Involvement in Hodgkin Lymphoma: A Pediatric Case and Literature Review

description: Bone involvement in Hodgkin lymphoma (HL) is rare. The differential diagnosis between HL bone localization and other malignant or benign skeletal diseases is challenging. We report the case of a girl affected by classic HL, initially staged IVA because of supradiaphragmatic lymph nodes and skeletal involvement. After 6 ABVD (adriamycin, bleomycin, vinblastine, dacarbazine) cycles, positron emission tomography (PET) showed a complete metabolic response of the nodal localizations and a persistent, high metabolic activity of bone lesions. Salvage treatment followed by autologous stem cell transplant was carried out. After the transplant, the bone lesions maintained a high metabolic activity at PET. A targeted bone biopsy led to the diagnosis of a fibrous dysplasia excluding the presence of HL. To our knowledge, the concomitant presence of HL and fibrous dysplasia has not been previously reported. An in-depth evaluation of disease response to frontline treatment with a biopsy of the PET-hypercaptant bone lesions could have avoided overtreatment in this patient.
DOI: 10.6084/m9.figshare.12705173.v1
title: Supplementary Material for: Hepatic Arterial Infusion Chemotherapy versus Sorafenib in Patients with Advanced Hepatocellular Carcinoma

description: <b><i>Background:</i></b> Prior to the approval of sorafenib, hepatic arterial infusion chemotherapy (HAIC) was offered to patients with advanced hepatocellular carcinoma (HCC) in East Asia, particularly Japan. According to the Japanese guidelines, HAIC is recommended as one of the treatment options in patients without extrahepatic metastasis (EHM). <b><i>Methods:</i></b> The present cohort study compared the use of HAIC and sorafenib on outcomes of patients with advanced HCC. Consecutive patients with advanced HCC who received HAIC or sorafenib as a first-line systemic therapy were enrolled from 10 Japanese institutions. The primary outcomes were overall survival (OS) in patients with macrovascular invasion (MVI), but without EHM, and OS in patients without both MVI and EHM. <b><i>Results:</i></b> Between 2009 and 2016, 2,006 patients were enrolled (541 HAIC patients, 1,465 sorafenib patients). After propensity score matching, the OS of patients with MVI but without EHM was significantly longer in the HAIC group compared with the sorafenib group (10.1 vs. 9.1 months for the HAIC and sorafenib groups, respectively; <i>n</i> = 170 for each group; hazard ratio [HR] 0.668; 95% confidence interval [95% CI] 0.475–0.935; <i>p</i> = 0.018). There was no significant difference in OS between patients without both MVI and EHM (12.2 vs. 15.4 months for the HAIC and sorafenib groups, respectively; <i>n</i> = 76 in each cohort after propensity score matching; HR 1.227; 95% CI 0.699–2.155; <i>p</i> = 0.475). <b><i>Conclusion:</i></b> HAIC is a potential front-line treatment choice in a subpopulation of patients with advanced HCC with MVI but without EHM.
DOI: 10.6084/m9.figshare.12705770.v1
title: Supplementary Material for: Polyostotic Fibrous Dysplasia Mimicking Bone Involvement in Hodgkin Lymphoma: A Pediatric Case and Literature Review

description: Bone involvement in Hodgkin lymphoma (HL) is rare. The differential diagnosis between HL bone localization and other malignant or benign skeletal diseases is challenging. We report the case of a girl affected by classic HL, initially staged IVA because of supradiaphragmatic lymph nodes and skeletal involvement. After 6 ABVD (adriamycin, bleomycin, vinblastine, dacarbazine) cycles, positron emission tomography (PET) showed a complete metabolic response of the nodal localizations and a persistent, high metabolic activity of bone lesions. Salvage treatment followed by autologous stem cell transplant was carried out. After the transplant, the bone lesions maintained a high metabolic activity at PET. A targeted bone biopsy led to the diagnosis of a fibrous dysplasia excluding the presence of HL. To our knowledge, the concomitant presence of HL and fibrous dysplasia has not been previously reported. An in-depth evaluation of disease response to frontline treatment with a biopsy of the PET-hypercaptant bone lesions could have avoided overtreatment in this patient.
DOI: 10.6084/m9.figshare.12706247.v1
title: Leontodon longirostris genome draft 418Mb

description: <b>1-Leontodon-genome-draft-418Mb.fasta</b>: sequences in FASTA format of the 410,019 scaffolds and contigs that were considered the 418 Mb genome draft for <i>Leontodon longirostris</i>. <br> <b>2-Maker853GeneModels-in1007LongestFragments.gff</b>: the 853 MAKER-based gene models deduced from the 1007 longest (&gt;10 kb) fragments of the 418 Mb genome draft. <br> <b>3-FunctionalAnnot-MakerGeneModels-in1007LongestFragments.tsv</b>: Functional annotation of the predicted 853 proteins deduced from MAKER-based gene models. <br> <b>4-Reconstructed-472ChimaericModels.fasta</b>: sequences in FASTA format of the 472 GeneAssembler-based gene models reconstructed using the short (&lt;10 kb) genome fragments from the 418 Mb genome draft. <br> <b>5-ShortGenomeFragments-in472ChimaericModels.tsv</b>: list of contigs and scaffolds from the 418 Mb genome draft that were used to reconstruct each chimaeric, GeneAssembler-based gene model. <br> <b>6-GeneAssemblerChimaericModels-in472ChimaericModels.gff</b>: annotation of the 472 GeneAssember-based, chimaeric gene models.
DOI: 10.6084/m9.figshare.12705059
title: uneven-hiseq-simulated-reads

description: uneven-hiseq-simulated-reads, see: https://hackmd.io/@astrobiomike/simulating-illumina-reads
DOI: 10.6084/m9.figshare.12705059.v1
title: uneven-hiseq-simulated-reads

description: uneven-hiseq-simulated-reads, see: https://hackmd.io/@astrobiomike/simulating-illumina-reads
DOI: 10.6084/m9.figshare.12706247.v2
title: Leontodon longirostris genome draft 418Mb

description: <b>1-Leontodon-genome-draft-418Mb.fasta</b>: sequences in FASTA format of the 410,019 scaffolds and contigs that were considered the 418 Mb genome draft for <i>Leontodon longirostris</i>. <br> <b>2-Maker853GeneModels-in1007LongestFragments.gff</b>: the 853 MAKER-based gene models deduced from the 1007 longest (&gt;10 kb) fragments of the 418 Mb genome draft. <br> <b>3-FunctionalAnnot-MakerGeneModels-in1007LongestFragments.tsv</b>: Functional annotation of the predicted 853 proteins deduced from MAKER-based gene models. <br> <b>4-Reconstructed-472ChimaericModels.fasta</b>: sequences in FASTA format of the 472 GeneAssembler-based gene models reconstructed using the short (&lt;10 kb) genome fragments from the 418 Mb genome draft. <br> <b>5-ShortGenomeFragments-in472ChimaericModels.tsv</b>: list of contigs and scaffolds from the 418 Mb genome draft that were used to reconstruct each chimaeric, GeneAssembler-based gene model. <br> <b>6-GeneAssemblerChimaericModels-in472ChimaericModels.gff</b>: annotation of the 472 GeneAssember-based, chimaeric gene models.
DOI: 10.6084/m9.figshare.12705023
title: uneven-perfect-simulated-reads

description: uneven-perfect-simulated-reads, see: https://hackmd.io/@astrobiomike/simulating-illumina-reads
DOI: 10.6084/m9.figshare.12705026
title: even-hiseq-simulated-reads

description: even-hiseq-simulated-reads, see: https://hackmd.io/@astrobiomike/simulating-illumina-reads
DOI: 10.6084/m9.figshare.12705044
title: A high resolution DEM of Tongziba River around the MD Fault

description: A high resolution DEM of Tongziba River around the MD Fault
DOI: 10.6084/m9.figshare.12705020
title: even-perfect-simulated-reads

description: even-perfect-simulated-reads, see: https://hackmd.io/@astrobiomike/simulating-illumina-reads
DOI: 10.6084/m9.figshare.12705023.v1
title: uneven-perfect-simulated-reads

description: uneven-perfect-simulated-reads, see: https://hackmd.io/@astrobiomike/simulating-illumina-reads
DOI: 10.6084/m9.figshare.12705002
title: Bankit

description: SqnBiosample tableSRA table
DOI: 10.6084/m9.figshare.12705020.v1
title: even-perfect-simulated-reads

description: even-perfect-simulated-reads, see: https://hackmd.io/@astrobiomike/simulating-illumina-reads
DOI: 10.6084/m9.figshare.12704999
title: ENCFF001NUM.sort.rmdup.unique.bam.bw

description: bigwig
DOI: 10.6084/m9.figshare.12704999.v1
title: ENCFF001NUM.sort.rmdup.unique.bam.bw

description: bigwig
DOI: 10.6084/m9.figshare.12705002.v1
title: Bankit

description: SqnBiosample tableSRA table
DOI: 10.6084/m9.figshare.12704939.v1
title: Data Set S1. Zhongba Paleomagnetic raw data.rar

description: It includes the 592 accepted paleomagnetic raw results which were obtained by thermally demagnetizing the samples in Zhongba section of Xining baisn.
DOI: 10.6084/m9.figshare.12703986
title: Additional file 2 of Polyvalent therapeutic vaccine for type 2 diabetes mellitus: Immunoinformatics approach to study co-stimulation of cytokines and GLUT1 receptors

description: Additional file 2.
DOI: 10.6084/m9.figshare.12703983
title: Additional file 1 of Polyvalent therapeutic vaccine for type 2 diabetes mellitus: Immunoinformatics approach to study co-stimulation of cytokines and GLUT1 receptors

description: Additional file 1.
DOI: 10.6084/m9.figshare.12703983.v1
title: Additional file 1 of Polyvalent therapeutic vaccine for type 2 diabetes mellitus: Immunoinformatics approach to study co-stimulation of cytokines and GLUT1 receptors

description: Additional file 1.
DOI: 10.6084/m9.figshare.12703986.v1
title: Additional file 2 of Polyvalent therapeutic vaccine for type 2 diabetes mellitus: Immunoinformatics approach to study co-stimulation of cytokines and GLUT1 receptors

description: Additional file 2.
DOI: 10.6084/m9.figshare.12703968
title: Additional file 1 of A case report of thrombotic complete obstruction of the ascending aorta as a complication of Venoarterial extracorporeal membrane oxygenation support: steps to prevent thrombosis

description: Additional file 1: Table S1. Results of blood examination over time.
DOI: 10.6084/m9.figshare.12703968.v1
title: Additional file 1 of A case report of thrombotic complete obstruction of the ascending aorta as a complication of Venoarterial extracorporeal membrane oxygenation support: steps to prevent thrombosis

description: Additional file 1: Table S1. Results of blood examination over time.
DOI: 10.6084/m9.figshare.12703946
title: Additional file 1 of A prospective feasibility study of one-year administration of adjuvant S-1 therapy for resected biliary tract cancer in a multi-institutional trial (Tokyo Study Group for Biliary Cancer: TOSBIC01)

description: Additional file 1: Table S1. Univariate analysis for early discontinuation (within 2 courses)
DOI: 10.6084/m9.figshare.12703944
title: Additional file 1 of The impact of scrubber discharge on the water quality in estuaries and ports

description: Additional file 1: Table S1. An Excel file that contains the compiled database on scrubber use and washwater quality. A total of 127 samples, based on own sampling, received datasets and literature.
DOI: 10.6084/m9.figshare.12703944.v1
title: Additional file 1 of The impact of scrubber discharge on the water quality in estuaries and ports

description: Additional file 1: Table S1. An Excel file that contains the compiled database on scrubber use and washwater quality. A total of 127 samples, based on own sampling, received datasets and literature.
DOI: 10.6084/m9.figshare.12703946.v1
title: Additional file 1 of A prospective feasibility study of one-year administration of adjuvant S-1 therapy for resected biliary tract cancer in a multi-institutional trial (Tokyo Study Group for Biliary Cancer: TOSBIC01)

description: Additional file 1: Table S1. Univariate analysis for early discontinuation (within 2 courses)
DOI: 10.6084/m9.figshare.12703898
title: Additional file 1 of Males of a sexually cannibalistic spider chemically assess relative female quality

description: Additional file 1. Raw data of mating tests. Table including the raw data of the experiment.
DOI: 10.6084/m9.figshare.12703898.v1
title: Additional file 1 of Males of a sexually cannibalistic spider chemically assess relative female quality

description: Additional file 1. Raw data of mating tests. Table including the raw data of the experiment.
DOI: 10.6084/m9.figshare.12703889
title: Additional file 1 of Peer support for disadvantaged parents: a narrative review of strategies used in home visiting health interventions in high-income countries

description: Additional file 1.
DOI: 10.6084/m9.figshare.12703889.v1
title: Additional file 1 of Peer support for disadvantaged parents: a narrative review of strategies used in home visiting health interventions in high-income countries

description: Additional file 1.