cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.21942/uva.9255311.v1
title: Phylogenetic tree doxD genes and transcripts

description: Phylogenetic tree (FastTree) based on a protein alignment of a partial thiosulfate:quinone oxidoreductases (encoded by doxD) encoded in MAGs from hypersaline soda lakes and transcribed in a metatranscriptome from the sediment of Cock Soda lake. References were obtained from the EggNog database.
DOI: 10.21942/uva.9255302.v1
title: Phylogenetic tree archaeal MAGs 16 ribosomal proteins

description: Phylogenetic tree of all archaeal MAGs analyzed in this study based on 16 ribosomal proteins. References included in the tree were obtained from Hug et al. (2016, Nature Microbiology) and Vavourakis et al. (2018, Microbiome).
DOI: 10.21942/uva.9255287
title: Phylogenetic tree CPR MAGs 16 ribosomal proteins

description: Phylogenetic tree of all MAGs assigned to the Candidate Phyla Radiation (CPR) analyzed in this study based on 16 ribosomal proteins. References included in the tree were obtained from Hug et al. (2016, Nature Microbiology) and Vavourakis et al. (2018, Microbiome).
DOI: 10.21942/uva.9255287.v1
title: Phylogenetic tree CPR MAGs 16 ribosomal proteins

description: Phylogenetic tree of all MAGs assigned to the Candidate Phyla Radiation (CPR) analyzed in this study based on 16 ribosomal proteins. References included in the tree were obtained from Hug et al. (2016, Nature Microbiology) and Vavourakis et al. (2018, Microbiome).
DOI: 10.6084/m9.figshare.9255260
title: Reactive oxygen species analysis.xlsx

description: The original data for ROS assay
DOI: 10.6084/m9.figshare.9255263
title: Fluorescence-activated cell sorting.xlsx

description: The original data for CD44+ FACS.
DOI: 10.6084/m9.figshare.9255248
title: QPCR.xlsx

description: The original data for qPCR
DOI: 10.6084/m9.figshare.9255254
title: Water-table reconstructions from European peatlands

description: Testate amoeba-derived water-table reconstructions from Europe.
DOI: 10.6084/m9.figshare.9255263.v1
title: Fluorescence-activated cell sorting.xlsx

description: The original data for CD44+ FACS.
DOI: 10.6084/m9.figshare.9255260.v1
title: Reactive oxygen species analysis.xlsx

description: The original data for ROS assay
DOI: 10.6084/m9.figshare.9255254.v1
title: Water-table reconstructions from European peatlands

description: Testate amoeba-derived water-table reconstructions from Europe.
DOI: 10.6084/m9.figshare.9255236
title: Sphere-formation assay.xlsx

description: The original data for Sphere-formation assay
DOI: 10.6084/m9.figshare.9255221
title: 16S and ITS.fna

description: microbial of continuous cropping peanut soil under humic acid treatment
DOI: 10.6084/m9.figshare.9255236.v1
title: Sphere-formation assay.xlsx

description: The original data for Sphere-formation assay
DOI: 10.6084/m9.figshare.9255221.v1
title: 16S and ITS.fna

description: microbial of continuous cropping peanut soil under humic acid treatment
DOI: 10.6084/m9.figshare.9255200
title: frequancy data.csv

description: This cross-sectional, hospital-based study conducted at Omdurman Maternity Hospital.
DOI: 10.6084/m9.figshare.9255200.v1
title: frequanvy data.csv

description: This cross-sectional, hospital-based study conducted at Omdurman Maternity Hospital.
DOI: 10.6084/m9.figshare.9255116
title: A biogeographic and evolutionary analysis of the flora of the North-eastern cerrado, Brazil

description: <b>Background</b>: The forest-savanna habitat switching is thought to have been a recurrent event in evolutionary history. Notwithstanding, the centre of the Cerrado, a large biogeographic domain, may be hypothesised to be a region with historical climatic stability and thus is predicted to contain high richness of cerrado species and the presence of few species from adjacents domains. <b>Aims</b>: We tested if today’s flora of the north-eastern cerrado (NC), a peripheral province of the domain, demonstrated an observable gradient in their distribution from centre of the Cerrado towards adjacents domains. <b>Methods</b>: We compiled vegetation survey data for 178 sites in the cerrado of north-eastern Brazil. Distribution patterns of plant taxa were assessed using multivariate techniques. <b>Results</b>: We recorded 1071 species in 390 genera and 85 families. Almost 40% were monogeneric families and ca. 50% were monospecific genera. The species composition in the NC followed a gradient related to the distance from the centre of the Cerrado towards its periphery. <b>Conclusions</b>: We show that the NC flora is unique and much richer than previously thought and that it is likely to be an outcome of evolutionary processes and of today’s intermixing of species from adjacent formations.
DOI: 10.6084/m9.figshare.9255200.v2
title: frequancy data.csv

description: This cross-sectional, hospital-based study conducted at Omdurman Maternity Hospital.
DOI: 10.6084/m9.figshare.9255116.v2
title: A biogeographic and evolutionary analysis of the flora of the North-eastern cerrado, Brazil

description: <b>Background</b>: The forest-savanna habitat switching is thought to have been a recurrent event in evolutionary history. Notwithstanding, the centre of the Cerrado, a large biogeographic domain, may be hypothesised to be a region with historical climatic stability and thus is predicted to contain high richness of cerrado species and the presence of few species from adjacents domains. <b>Aims</b>: We tested if today’s flora of the north-eastern cerrado (NC), a peripheral province of the domain, demonstrated an observable gradient in their distribution from centre of the Cerrado towards adjacents domains. <b>Methods</b>: We compiled vegetation survey data for 178 sites in the cerrado of north-eastern Brazil. Distribution patterns of plant taxa were assessed using multivariate techniques. <b>Results</b>: We recorded 1071 species in 390 genera and 85 families. Almost 40% were monogeneric families and ca. 50% were monospecific genera. The species composition in the NC followed a gradient related to the distance from the centre of the Cerrado towards its periphery. <b>Conclusions</b>: We show that the NC flora is unique and much richer than previously thought and that it is likely to be an outcome of evolutionary processes and of today’s intermixing of species from adjacent formations.
DOI: 10.6084/m9.figshare.9255200.v4
title: frequancy data.csv

description: This cross-sectional, hospital-based study conducted at Omdurman Maternity Hospital.
DOI: 10.6084/m9.figshare.9255116.v1
title: A biogeographic and evolutionary analysis of the flora of the North-eastern cerrado, Brazil

description: <b>Background</b>: The forest-savanna habitat switching is thought to have been a recurrent event in evolutionary history. Notwithstanding, the centre of the Cerrado, a large biogeographic domain, may be hypothesised to be a region with historical climatic stability and thus is predicted to contain high richness of cerrado species and the presence of few species from adjacents domains. <b>Aims</b>: We tested if today’s flora of the north-eastern cerrado (NC), a peripheral province of the domain, demonstrated an observable gradient in their distribution from centre of the Cerrado towards adjacents domains. <b>Methods</b>: We compiled vegetation survey data for 178 sites in the cerrado of north-eastern Brazil. Distribution patterns of plant taxa were assessed using multivariate techniques. <b>Results</b>: We recorded 1071 species in 390 genera and 85 families. Almost 40% were monogeneric families and ca. 50% were monospecific genera. The species composition in the NC followed a gradient related to the distance from the centre of the Cerrado towards its periphery. <b>Conclusions</b>: We show that the NC flora is unique and much richer than previously thought and that it is likely to be an outcome of evolutionary processes and of today’s intermixing of species from adjacent formations.
DOI: 10.6084/m9.figshare.9255200.v3
title: frequancy data.csv

description: This cross-sectional, hospital-based study conducted at Omdurman Maternity Hospital.
DOI: 10.6084/m9.figshare.9254762
title: Additional file 2: of Expert perspectives on essential parameters to monitor during childbirth in low resource settings: a Delphi study in sub-Saharan Africa

description: Round 2 Questionnaire. (XLSX 23 kb)
DOI: 10.6084/m9.figshare.9254762.v1
title: Additional file 2: of Expert perspectives on essential parameters to monitor during childbirth in low resource settings: a Delphi study in sub-Saharan Africa

description: Round 2 Questionnaire. (XLSX 23 kb)
DOI: 10.6084/m9.figshare.9254744
title: Additional file 1: of Expert perspectives on essential parameters to monitor during childbirth in low resource settings: a Delphi study in sub-Saharan Africa

description: Round 1 Questionnaire. (XLSX 32 kb)
DOI: 10.6084/m9.figshare.9254744.v1
title: Additional file 1: of Expert perspectives on essential parameters to monitor during childbirth in low resource settings: a Delphi study in sub-Saharan Africa

description: Round 1 Questionnaire. (XLSX 32 kb)
DOI: 10.6084/m9.figshare.9254675
title: Additional file 7: of Genetic diversity and population structure of the Sapsaree, a native Korean dog breed

description: File S7. Genotype information of Sapsaree. (BED 524 kb)
DOI: 10.6084/m9.figshare.9254678
title: Additional file 8: of Genetic diversity and population structure of the Sapsaree, a native Korean dog breed

description: File S8. Genotype information of Sapsaree. (BIM 697 kb)
DOI: 10.6084/m9.figshare.9254681
title: Additional file 9: of Genetic diversity and population structure of the Sapsaree, a native Korean dog breed

description: File S9. Genotype information of Sapsaree. (FAM 2 kb)
DOI: 10.6084/m9.figshare.9254675.v1
title: Additional file 7: of Genetic diversity and population structure of the Sapsaree, a native Korean dog breed

description: File S7. Genotype information of Sapsaree. (BED 524 kb)
DOI: 10.6084/m9.figshare.9254678.v1
title: Additional file 8: of Genetic diversity and population structure of the Sapsaree, a native Korean dog breed

description: File S8. Genotype information of Sapsaree. (BIM 697 kb)
DOI: 10.6084/m9.figshare.9254681.v1
title: Additional file 9: of Genetic diversity and population structure of the Sapsaree, a native Korean dog breed

description: File S9. Genotype information of Sapsaree. (FAM 2 kb)
DOI: 10.6084/m9.figshare.9254552
title: Additional file 2: of Risk of bias judgments for random sequence generation in Cochrane systematic reviews wereÂ frequently not in line with Cochrane Handbook

description: One of the final VBA modules used for extraction of RoB tables from separate spreadsheets. The module includes search code for strings indicating the beginning and the end of RoB tables, as well as code for extraction of original domains and customized domains. All modules were written in VBA originally with .bas extension. Raw code is presented; notice single quotation marks for the exclusion of parts of code while testing. (TXT 1 kb)
DOI: 10.6084/m9.figshare.9254552.v1
title: Additional file 2: of Risk of bias judgments for random sequence generation in Cochrane systematic reviews wereÂ frequently not in line with Cochrane Handbook

description: One of the final VBA modules used for extraction of RoB tables from separate spreadsheets. The module includes search code for strings indicating the beginning and the end of RoB tables, as well as code for extraction of original domains and customized domains. All modules were written in VBA originally with .bas extension. Raw code is presented; notice single quotation marks for the exclusion of parts of code while testing. (TXT 1 kb)
DOI: 10.6084/m9.figshare.9254540
title: Additional file 1: of Risk of bias judgments for random sequence generation in Cochrane systematic reviews wereÂ frequently not in line with Cochrane Handbook

description: The short module used for data scraping from the webpage. The module uses a formatted spreadsheet containing web addresses of Cochrane reviews. (TXT 38 kb)
DOI: 10.6084/m9.figshare.9254540.v1
title: Additional file 1: of Risk of bias judgments for random sequence generation in Cochrane systematic reviews wereÂ frequently not in line with Cochrane Handbook

description: The short module used for data scraping from the webpage. The module uses a formatted spreadsheet containing web addresses of Cochrane reviews. (TXT 38 kb)
DOI: 10.6084/m9.figshare.12869648
title: Base de données pour tableaux.xlsx

description: <i>Background and Objectives: </i>Interest in the use of aminoglycosides is becoming more prevalent in clinical practice with the emergence of Gram-negative infections resistant to contemporary antibiotics. For patients undergoing chronic hemodialysis, aminoglycosides are usually administered at a low dose at the end of their hemodialysis session, but this approach remains controversial. Intradialytic infusion (IDI) of high dose of tobramycin could yield better exposure when administered early in the hemodialysis session. This study sought to characterize the pharmacokinetic profile of tobramycin IDI dosed in infected patients receiving chronic intermittent hemodialysis and to determine whether it is possible to achieve favorable pharmacokinetic targets using this approach.<i></i><br> <i>Design, setting, participants, and measurements: </i>In this prospective pharmacokinetic study, a single dose (5 mg/kg) of tobramycin was administered IDI to eleven non-critically ill patients undergoing chronic intermittent hemodialysis. Blood samples were collected at selected time to determine tobramycin serum concentrations. Pharmacokinetic analysis, modelling and Monte Carlo simulations (MCS) were performed using Phoenix<sup>TM</sup> NLME. The efficacy exposure target for non-severe Gram-negative infections and CMI≤1 were maximum concentration (C<sub>max</sub>≥10 mg/L) and area under the curve (AUC<sub>24h</sub>&gt;30 mg*h/L). For toxicity, the goal was to identify plasma trough concentrations &lt;2 mg/L. <i></i><br> <i>Results: </i>Tobramycin disposition was best described by a zero-order input one-compartment model with two clearances. Tobramycin mean (SD) C<sub>max</sub>, trough levels and AUC<sub>24h</sub> were 13.1(1.3) mg/L, 1.32(0.47) mg/L and 61(23) mg*h/L, respectively. MCS run with 1000 virtual patients showed that a 5 mg/kg dose of tobramycin IDI outperformed the usual post-dialysis dosing (80% meeting all targets vs &lt; 1%, respectively).<i></i><br> <i>Conclusions: </i>A single high-dose of tobramycin can achieve favorable pharmacokinetic endpoints when administered using IHI in hemodialysis patients. This dosing regimen may represent an effective and safer alternative to the usual dosing in the treatment of non-severe Gram-negative infection.<br>
DOI: 10.6084/m9.figshare.12869648.v1
title: Base de données pour tableaux.xlsx

description: <i>Background and Objectives: </i>Interest in the use of aminoglycosides is becoming more prevalent in clinical practice with the emergence of Gram-negative infections resistant to contemporary antibiotics. For patients undergoing chronic hemodialysis, aminoglycosides are usually administered at a low dose at the end of their hemodialysis session, but this approach remains controversial. Intradialytic infusion (IDI) of high dose of tobramycin could yield better exposure when administered early in the hemodialysis session. This study sought to characterize the pharmacokinetic profile of tobramycin IDI dosed in infected patients receiving chronic intermittent hemodialysis and to determine whether it is possible to achieve favorable pharmacokinetic targets using this approach.<i></i><br> <i>Design, setting, participants, and measurements: </i>In this prospective pharmacokinetic study, a single dose (5 mg/kg) of tobramycin was administered IDI to eleven non-critically ill patients undergoing chronic intermittent hemodialysis. Blood samples were collected at selected time to determine tobramycin serum concentrations. Pharmacokinetic analysis, modelling and Monte Carlo simulations (MCS) were performed using Phoenix<sup>TM</sup> NLME. The efficacy exposure target for non-severe Gram-negative infections and CMI≤1 were maximum concentration (C<sub>max</sub>≥10 mg/L) and area under the curve (AUC<sub>24h</sub>&gt;30 mg*h/L). For toxicity, the goal was to identify plasma trough concentrations &lt;2 mg/L. <i></i><br> <i>Results: </i>Tobramycin disposition was best described by a zero-order input one-compartment model with two clearances. Tobramycin mean (SD) C<sub>max</sub>, trough levels and AUC<sub>24h</sub> were 13.1(1.3) mg/L, 1.32(0.47) mg/L and 61(23) mg*h/L, respectively. MCS run with 1000 virtual patients showed that a 5 mg/kg dose of tobramycin IDI outperformed the usual post-dialysis dosing (80% meeting all targets vs &lt; 1%, respectively).<i></i><br> <i>Conclusions: </i>A single high-dose of tobramycin can achieve favorable pharmacokinetic endpoints when administered using IHI in hemodialysis patients. This dosing regimen may represent an effective and safer alternative to the usual dosing in the treatment of non-severe Gram-negative infection.<br>
DOI: 10.6084/m9.figshare.9254489
title: Additional file 2: of Experiences of capacity strengthening in sanitation and hygiene research in Africa and Asia: the SHARE Research Consortium

description: List of researchers networks created during theÂ SHARE programme. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.9254489.v1
title: Additional file 2: of Experiences of capacity strengthening in sanitation and hygiene research in Africa and Asia: the SHARE Research Consortium

description: List of researchers networks created during theÂ SHARE programme. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.9254471
title: Additional file 1: of Experiences of capacity strengthening in sanitation and hygiene research in Africa and Asia: the SHARE Research Consortium

description: List of peer-reviewed manuscripts published during the SHARE programme. (XLSX 70 kb)
DOI: 10.6084/m9.figshare.9254471.v1
title: Additional file 1: of Experiences of capacity strengthening in sanitation and hygiene research in Africa and Asia: the SHARE Research Consortium

description: List of peer-reviewed manuscripts published during the SHARE programme. (XLSX 70 kb)
DOI: 10.6084/m9.figshare.9254372
title: Additional file 2: of Population genomics of an exceptional hybridogenetic system of Pelophylax water frogs

description: Table S1. Origin and details on the individuals used in this study. (XLSX 26 kb)
DOI: 10.6084/m9.figshare.9254372.v1
title: Additional file 2: of Population genomics of an exceptional hybridogenetic system of Pelophylax water frogs

description: Table S1. Origin and details on the individuals used in this study. (XLSX 26 kb)
DOI: 10.6084/m9.figshare.9254225
title: Additional file 4: of Palmitoylation is required for TNF-R1 signaling

description: Table S1. Proteins identified by mass spectrometry after enrichment of palmitoylated proteins by acylRAC after 0–60 min TNF incubation. The sample processing and data analysis is described in table. (XLSX 346 kb)
DOI: 10.6084/m9.figshare.9254225.v1
title: Additional file 4: of Palmitoylation is required for TNF-R1 signaling

description: Table S1. Proteins identified by mass spectrometry after enrichment of palmitoylated proteins by acylRAC after 0–60 min TNF incubation. The sample processing and data analysis is described in table. (XLSX 346 kb)
DOI: 10.6084/m9.figshare.9254192
title: Additional file 5: of Metabolic flux analysis for metabolome data validation of naturally xylose-fermenting yeasts

description: a Correlation (R2) between calculated and measured fluxes - S. stipitis. Acetyl-CoA (ACCOA), dihydroxy-acetone-phosphate (DHAP), erythrose-4-phosphate (E4P), fructose-6-phosphate (F6P), glucose-6-phosphate (G6P), malate (MAL), phosphoenolpyruvate (PEP), pyruvate (PEP), ribose-5-phosphate (R5P), ribulose-5-phosphate (RU5P), and sedoheptulose-7-phosphate (S7P) were the metabolites measured. (X-axis) show the calculated fluxes using the constrained values of products formation. (Y-axis) show measured fluxes with respectively metabolites concentrations. Graphics in square presents a correlation higher than 0.9. Flux rates are in mmol/gCDW.h− 1. b Correlation (R2) between calculated and measured fluxes - S. arborariae. Acetyl-CoA (ACCOA), dihydroxy-acetone-phosphate (DHAP), erythrose-4-phosphate (E4P), fructose-6-phosphate (F6P), glucose-6-phosphate (G6P), malate (MAL), phosphoenolpyruvate (PEP), pyruvate (PYR), ribose-5-phosphate (R5P), ribulose-5-phosphate (RU5P), and sedoheptulose-7-phosphate (S7P) were the metabolites measured. (X-axis) show the calculated fluxes using the constrained values of products formation. (Y-axis) show measured fluxes with respectively metabolites concentrations. Graphics in square presents a correlation higher than 0.9. Flux rates are in mmol/gCDW.h− 1. c Correlation (R2) between calculated and measured fluxes - S. passalidarum. Acetyl-CoA (ACCOA), dihydroxy-acetone-phosphate (DHAP), erythrose-4-phosphate (E4P), fructose-6-phosphate (F6P), glucose-6-phosphate (G6P), malate (MAL), phosphoenolpyruvate (PEP), pyruvate (PYR), ribose-5-phosphate (R5P), ribulose-5-phosphate (RU5P), and sedoheptulose-7-phosphate (S7P) were the metabolites measured. (X-axis) show the calculated fluxes using the constrained values of products formation. (Y-axis) show measured fluxes with respectively metabolites concentrations. Graphics in square presents a correlation higher than 0.9. Flux rates are in mmol/gCDW.h− 1. (ZIP 183 kb)
DOI: 10.6084/m9.figshare.9254192.v1
title: Additional file 5: of Metabolic flux analysis for metabolome data validation of naturally xylose-fermenting yeasts

description: a Correlation (R2) between calculated and measured fluxes - S. stipitis. Acetyl-CoA (ACCOA), dihydroxy-acetone-phosphate (DHAP), erythrose-4-phosphate (E4P), fructose-6-phosphate (F6P), glucose-6-phosphate (G6P), malate (MAL), phosphoenolpyruvate (PEP), pyruvate (PEP), ribose-5-phosphate (R5P), ribulose-5-phosphate (RU5P), and sedoheptulose-7-phosphate (S7P) were the metabolites measured. (X-axis) show the calculated fluxes using the constrained values of products formation. (Y-axis) show measured fluxes with respectively metabolites concentrations. Graphics in square presents a correlation higher than 0.9. Flux rates are in mmol/gCDW.h− 1. b Correlation (R2) between calculated and measured fluxes - S. arborariae. Acetyl-CoA (ACCOA), dihydroxy-acetone-phosphate (DHAP), erythrose-4-phosphate (E4P), fructose-6-phosphate (F6P), glucose-6-phosphate (G6P), malate (MAL), phosphoenolpyruvate (PEP), pyruvate (PYR), ribose-5-phosphate (R5P), ribulose-5-phosphate (RU5P), and sedoheptulose-7-phosphate (S7P) were the metabolites measured. (X-axis) show the calculated fluxes using the constrained values of products formation. (Y-axis) show measured fluxes with respectively metabolites concentrations. Graphics in square presents a correlation higher than 0.9. Flux rates are in mmol/gCDW.h− 1. c Correlation (R2) between calculated and measured fluxes - S. passalidarum. Acetyl-CoA (ACCOA), dihydroxy-acetone-phosphate (DHAP), erythrose-4-phosphate (E4P), fructose-6-phosphate (F6P), glucose-6-phosphate (G6P), malate (MAL), phosphoenolpyruvate (PEP), pyruvate (PYR), ribose-5-phosphate (R5P), ribulose-5-phosphate (RU5P), and sedoheptulose-7-phosphate (S7P) were the metabolites measured. (X-axis) show the calculated fluxes using the constrained values of products formation. (Y-axis) show measured fluxes with respectively metabolites concentrations. Graphics in square presents a correlation higher than 0.9. Flux rates are in mmol/gCDW.h− 1. (ZIP 183 kb)