cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6154331.v1
title: Toward novel inhibitors against KdsB: a highly specific and selective broad-spectrum bacterial enzyme

description: KdsB (3-deoxy-manno-octulosonate cytidylyltransferase) is a highly specific and selective bacterial enzyme that catalyzes KDO (3-Deoxy-D-mano-oct-2-ulosonic acid) activation in KDO biosynthesis pathway. Failure in KDO biosynthesis causes accumulation of lipid A in the bacterial outer membrane that leads to cell growth arrest. This study reports a combinatorial approach comprising virtual screening of natural drugs library, molecular docking, computational pharmacokinetics, molecular dynamics simulation, and binding free energy calculations for the identification of potent lead compounds against the said enzyme. Virtual screening demonstrated 1460 druglike compounds in a total of 4800, while molecular docking illustrated Ser13, Arg14, and Asp236 as the anchor amino acids for recognizing and binding the inhibitors. Functional details of the enzyme in complex with the best characterized compound-226 were explored through two hundred nanoseconds of MD simulation. The ligand after initial adjustments jumps into the active cavity, followed by the deep cavity, and ultimately backward rotating movement toward the initial docked site of the pocket. During the entire simulation period, Asp236 remained in contact with the ligand and can be considered as a major catalytic residue of the enzyme. Radial distribution function confirmed that toward the end of the simulation, strengthening of ligand-receptor occurred with ligand and enzyme active residues in close proximity. Binding free energy calculations via MM(PB/GB)SA and Waterswap reaction coordinates, demonstrated the high affinity of the compound for enzyme active site residues. These findings can provide new avenues for designing potent compounds against notorious bacterial pathogens.
DOI: 10.6084/m9.figshare.6154319
title: DGRP phenotypes

description: Phenotypes (titre or KV-induced mortality) measured in the DGRP lines. Used as input to for geneticvariation_and_GWASannotate.R to calculate genetic (co)variation and heritability. Also used as input to perform GWAS.<br>
DOI: 10.6084/m9.figshare.6154319.v1
title: DGRP phenotypes

description: Phenotypes (titre or KV-induced mortality) measured in the DGRP lines. Used as input to for geneticvariation_and_GWASannotate.R to calculate genetic (co)variation and heritability. Also used as input to perform GWAS.<br>
DOI: 10.6084/m9.figshare.6154313
title: Viral titre in RNAi knockdown crosses

description: DeltadeltaCT associated with knockdown of different genes found in GWA studies. To be analyzed with GWAS.hits.knockdown.R<br>
DOI: 10.6084/m9.figshare.6154313.v1
title: Viral titre in RNAi knockdown crosses

description: DeltadeltaCT associated with knockdown of different genes found in GWA studies. To be analyzed with GWAS.hits.knockdown.R<br>
DOI: 10.6084/m9.figshare.6154304
title: Titre GWAS permutations

description: The most significant association recorded across the genome for 1000 GWAS performed where phenotypes were randomised across genotypes.<br>
DOI: 10.6084/m9.figshare.6154304.v1
title: Titre GWAS permutations

description: The most significant association recorded across the genome for 1000 GWAS performed where phenotypes were randomised across genotypes.<br>
DOI: 10.6084/m9.figshare.6154298
title: Mortality GWAS permutations

description: The most significant association recorded across the genome for 1000 GWAS performed where phenotypes were randomised across genotypes.<br>
DOI: 10.6084/m9.figshare.6154292
title: Titre GWAS output

description: Output of GWAS for titre, including effect size and p-values for each SNP. Can be used as input for geneticvariation_and_GWASannotate.R to look at significant SNPs (based on gwas.titre.significance.permutations.p001.txt) and perform GO term analysis.
DOI: 10.6084/m9.figshare.6154292.v1
title: Titre GWAS output

description: Output of GWAS for titre, including effect size and p-values for each SNP. Can be used as input for geneticvariation_and_GWASannotate.R to look at significant SNPs (based on gwas.titre.significance.permutations.p001.txt) and perform GO term analysis.
DOI: 10.6084/m9.figshare.6154289
title: Mortality GWAS output

description: Output of GWAS for mortality, including effect size and p-values for each SNP. Can be used as input for geneticvariation_and_GWASannotate.R to look at significant SNPs (based on gwas.mort.significance.permutations.p001.txt) and perform GO term analysis.<br>
DOI: 10.6084/m9.figshare.6154289.v1
title: Mortality GWAS output

description: Output of GWAS for mortality, including effect size and p-values for each SNP. Can be used as input for geneticvariation_and_GWASannotate.R to look at significant SNPs (based on gwas.mort.significance.permutations.p001.txt) and perform GO term analysis.<br>
DOI: 10.6084/m9.figshare.6154283
title: Egg laying data

description: Number of eggs laid by each fly pair in early (1-2 days) or late (7-8 days) time points following injection with chloroform-treated Kallithea virus or Kallithea virus. Analyze with fecundity.R<br>
DOI: 10.6084/m9.figshare.6154283.v1
title: Egg laying data

description: Number of eggs laid by each fly pair in early (1-2 days) or late (7-8 days) time points following injection with chloroform-treated Kallithea virus or Kallithea virus. Analyze with fecundity.R<br>
DOI: 10.6084/m9.figshare.6154274
title: RNAseq read counts per gene

description: Per-gene counts for each Drosophila gene in uninfected and Kallithea-infected flies. Can be analysed with rnaseq_notebook.Rmd.<br>
DOI: 10.6084/m9.figshare.6154274.v1
title: RNAseq read counts per gene

description: Per-gene counts for each Drosophila gene in uninfected and Kallithea-infected flies. Can be analysed with rnaseq_notebook.Rmd.<br>
DOI: 10.6084/m9.figshare.6154271
title: Supplementary Material for: Combined Pancreatic Islet-Lung-Liver Transplantation in a Pediatric Patient with Cystic Fibrosis-Related Diabetes

description: <b><i>Background:</i></b> Cystic fibrosis-related diabetes (CFRD) is the most frequent extrapulmonary complication of cystic fibrosis (CF). <b><i>Methods:</i></b> We report the first combined pancreatic islet-lung-liver transplantation in a 14-year-old adolescent. <i>CFTR</i> was analyzed by Sanger sequencing. Further genes were analyzed by high-throughput sequencing. <b><i>Results:</i></b> The patient was diagnosed with CF at the age of 14 months. Nine years later, after diagnosis of CFRD, the patient’s BMI and lung function began to decline. Bilateral lung transplantation with simultaneous liver transplantation was performed at the age of 14.5 years. The first islet transplantation (IT) was carried out 10 days later. Six months later, C-peptide secretion after arginine stimulation showed peak values of 371 pmol/L (vs. 569 pmol/L before IT) and insulin doses had slightly increased (1.40 vs. 1.11 units/kg/day before IT). A second IT was performed at the age of 15 years, a third at 16 years. Two years after the first IT, arginine-stimulated C-peptide secretion increased to 2,956 pmol/L and insulin doses could be reduced to 0.82 units/kg/day. HbA1c decreased from 7.3% (57.4 mmol/mol) to 5.9% (41.0 mmol/mol). <b><i>Conclusion:</i></b> IT following lung and liver transplantation, with injection of islets into a transplanted organ, is feasible. It improves C-peptide secretion, decreases insulin needs, and lowers HbA1c.
DOI: 10.6084/m9.figshare.6154268
title: Drosophila Activity Monitor data

description: Number of counts per day of each individual fly. May be analyzed with dam.R<br>
DOI: 10.6084/m9.figshare.6154223
title: Supplementary Material for: Swiss (German) Version of the Actinic Keratosis Quality of Life questionnaire

description: <b><i>Background:</i></b> Actinic keratosis (AK) is a sun-induced skin lesion that may progress to invasive squamous cell carcinoma of the skin. Recently, the Actinic Keratosis Quality of Life questionnaire (AKQoL) was designed for patients with AK in Denmark as a specific quality of life instrument for AK patients. <b><i>Objective:</i></b> The objective of this study was to adapt the AKQoL for the German language region of Switzerland and to evaluate its psychometric properties (validity, reliability). <b><i>Methods:</i></b> Translation and cultural adaptation of the questionnaire were assessed by using the technique of cognitive interviewing. During the translation process, 34 patients with AK from the Department of Dermatology, University Hospital Zurich, were interviewed in 3 sessions of cognitive interviewing. The translated questionnaire was then distributed together with the Dermatology Life Quality Index (DLQI) to a second group of 113 patients for validation and reliability testing. Within this group, we measured the internal consistency by the Cronbach coefficient α and Spearman correlation coefficient between the AKQoL and the DLQI. <b><i>Results:</i></b> The problems encountered during the translation process led to changes in 5 categories as described by Epstein: stylistic changes, change in breadth, change in actual meaning, change in frequency and time frame, change in intensity. We found a Cronbach α of 0.82, an acceptable internal consistency. The Spearman correlation coefficient between total scores of AKQoL and DLQI was 0.57. <b><i>Conclusion:</i></b> We culturally adapted and validated a Swiss (German) version of the AKQoL questionnaire applicable for the population of a university center in Switzerland to measure and monitor the quality of life in patients with AK.
DOI: 10.6084/m9.figshare.6154223.v1
title: Supplementary Material for: Swiss (German) Version of the Actinic Keratosis Quality of Life questionnaire

description: <b><i>Background:</i></b> Actinic keratosis (AK) is a sun-induced skin lesion that may progress to invasive squamous cell carcinoma of the skin. Recently, the Actinic Keratosis Quality of Life questionnaire (AKQoL) was designed for patients with AK in Denmark as a specific quality of life instrument for AK patients. <b><i>Objective:</i></b> The objective of this study was to adapt the AKQoL for the German language region of Switzerland and to evaluate its psychometric properties (validity, reliability). <b><i>Methods:</i></b> Translation and cultural adaptation of the questionnaire were assessed by using the technique of cognitive interviewing. During the translation process, 34 patients with AK from the Department of Dermatology, University Hospital Zurich, were interviewed in 3 sessions of cognitive interviewing. The translated questionnaire was then distributed together with the Dermatology Life Quality Index (DLQI) to a second group of 113 patients for validation and reliability testing. Within this group, we measured the internal consistency by the Cronbach coefficient α and Spearman correlation coefficient between the AKQoL and the DLQI. <b><i>Results:</i></b> The problems encountered during the translation process led to changes in 5 categories as described by Epstein: stylistic changes, change in breadth, change in actual meaning, change in frequency and time frame, change in intensity. We found a Cronbach α of 0.82, an acceptable internal consistency. The Spearman correlation coefficient between total scores of AKQoL and DLQI was 0.57. <b><i>Conclusion:</i></b> We culturally adapted and validated a Swiss (German) version of the AKQoL questionnaire applicable for the population of a university center in Switzerland to measure and monitor the quality of life in patients with AK.
DOI: 10.6084/m9.figshare.6154208
title: Exercise program using a foam-bead bag improves balance abilities and strength of lower extremities in older adults

description: Exercise program using a foam-bead bag improves balance abilities and strength of lower extremities in older adults
DOI: 10.6084/m9.figshare.6154199
title: XW Data 2016-2017

description: Demographic, clinical and neuropsychological data of 49 PD patients and 51 healthy controls.<br>The data were collected at the Xuanwu Hospital between 2016-2017. <br>
DOI: 10.6084/m9.figshare.6153245
title: MOESM1 of Evolutionary history of Mexican domesticated and wild Meleagris gallopavo

description: Additional file 1: Table S1. Haplotypes identified, polymorphic sites and absolute frequencies for each population sampled, including sequences obtained from databases.
DOI: 10.6084/m9.figshare.6153245.v1
title: MOESM1 of Evolutionary history of Mexican domesticated and wild Meleagris gallopavo

description: Additional file 1: Table S1. Haplotypes identified, polymorphic sites and absolute frequencies for each population sampled, including sequences obtained from databases.
DOI: 10.6084/m9.figshare.6153155
title: Additional file 3: of Morphology and genomic hallmarks of breast tumours developed by ATM deleterious variant carriers

description: Table S2. Comparison of genes altered at the copy number level between ATM-associated tumours and tumours from TCGA. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.6153155.v1
title: Additional file 3: of Morphology and genomic hallmarks of breast tumours developed by ATM deleterious variant carriers

description: Table S2. Comparison of genes altered at the copy number level between ATM-associated tumours and tumours from TCGA. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.6153107
title: Additional file 1: of Morphology and genomic hallmarks of breast tumours developed by ATM deleterious variant carriers

description: Table S1. Genomic regions showing copy number loss or loss/LOH in at least 70% of ATM-associated tumours. (XLSX 70 kb)
DOI: 10.6084/m9.figshare.6153107.v1
title: Additional file 1: of Morphology and genomic hallmarks of breast tumours developed by ATM deleterious variant carriers

description: Table S1. Genomic regions showing copy number loss or loss/LOH in at least 70% of ATM-associated tumours. (XLSX 70 kb)
DOI: 10.6084/m9.figshare.6153035
title: Additional file 5: of Next-generation sequencing analysis of receptor-type tyrosine kinase genes in surgically resected colon cancer: identification of gain-of-function mutations in the RET proto-oncogene

description: Table S5. List of mutations identified in CC20 after the next generation sequencing analysis pipeline. (XLSX 17Â kb)
DOI: 10.6084/m9.figshare.6153035.v1
title: Additional file 5: of Next-generation sequencing analysis of receptor-type tyrosine kinase genes in surgically resected colon cancer: identification of gain-of-function mutations in the RET proto-oncogene

description: Table S5. List of mutations identified in CC20 after the next generation sequencing analysis pipeline. (XLSX 17Â kb)
DOI: 10.6084/m9.figshare.6153020
title: Additional file 4: of Next-generation sequencing analysis of receptor-type tyrosine kinase genes in surgically resected colon cancer: identification of gain-of-function mutations in the RET proto-oncogene

description: Table S4. Sequencing metrics of the identified RET mutations. (XLSX 10Â kb)
DOI: 10.6084/m9.figshare.6153020.v1
title: Additional file 4: of Next-generation sequencing analysis of receptor-type tyrosine kinase genes in surgically resected colon cancer: identification of gain-of-function mutations in the RET proto-oncogene

description: Table S4. Sequencing metrics of the identified RET mutations. (XLSX 10Â kb)
DOI: 10.6084/m9.figshare.6153014
title: Additional file 3: of Mapping a male-fertility restoration locus for the A4 cytoplasmic-genic male-sterility system in pearl millet using a genotyping-by-sequencing-based linkage map

description: Table S2. List of all F2 individuals, their haplotypes based on the two functional markers developed for the the identified QTL, and their phenotypes. (XLSX 17Â kb)
DOI: 10.6084/m9.figshare.6153014.v1
title: Additional file 3: of Mapping a male-fertility restoration locus for the A4 cytoplasmic-genic male-sterility system in pearl millet using a genotyping-by-sequencing-based linkage map

description: Table S2. List of all F2 individuals, their haplotypes based on the two functional markers developed for the the identified QTL, and their phenotypes. (XLSX 17Â kb)
DOI: 10.6084/m9.figshare.6152999
title: Additional file 3: of Next-generation sequencing analysis of receptor-type tyrosine kinase genes in surgically resected colon cancer: identification of gain-of-function mutations in the RET proto-oncogene

description: Table S3. List of mutated RTKs in each patient included in the study. (XLSX 11Â kb)
DOI: 10.6084/m9.figshare.6152999.v1
title: Additional file 3: of Next-generation sequencing analysis of receptor-type tyrosine kinase genes in surgically resected colon cancer: identification of gain-of-function mutations in the RET proto-oncogene

description: Table S3. List of mutated RTKs in each patient included in the study. (XLSX 11Â kb)
DOI: 10.6084/m9.figshare.6152996
title: Additional file 2: of Mapping a male-fertility restoration locus for the A4 cytoplasmic-genic male-sterility system in pearl millet using a genotyping-by-sequencing-based linkage map

description: SNP marker information including the location in the reference genome. (TSV 1238Â kb)
DOI: 10.6084/m9.figshare.6152996.v1
title: Additional file 2: of Mapping a male-fertility restoration locus for the A4 cytoplasmic-genic male-sterility system in pearl millet using a genotyping-by-sequencing-based linkage map

description: SNP marker information including the location in the reference genome. (TSV 1238Â kb)
DOI: 10.6084/m9.figshare.6152981
title: Additional file 2: of Next-generation sequencing analysis of receptor-type tyrosine kinase genes in surgically resected colon cancer: identification of gain-of-function mutations in the RET proto-oncogene

description: Table S2. Summary of the variants identified in RTKs. (XLSX 16Â kb)
DOI: 10.6084/m9.figshare.6152981.v1
title: Additional file 2: of Next-generation sequencing analysis of receptor-type tyrosine kinase genes in surgically resected colon cancer: identification of gain-of-function mutations in the RET proto-oncogene

description: Table S2. Summary of the variants identified in RTKs. (XLSX 16Â kb)
DOI: 10.6084/m9.figshare.6152978
title: Additional file 1: of Mapping a male-fertility restoration locus for the A4 cytoplasmic-genic male-sterility system in pearl millet using a genotyping-by-sequencing-based linkage map

description: Table S1. Distances between SNP marker in the genetic linkage map. (XLSX 24Â kb)
DOI: 10.6084/m9.figshare.6152978.v1
title: Additional file 1: of Mapping a male-fertility restoration locus for the A4 cytoplasmic-genic male-sterility system in pearl millet using a genotyping-by-sequencing-based linkage map

description: Table S1. Distances between SNP marker in the genetic linkage map. (XLSX 24Â kb)
DOI: 10.6084/m9.figshare.6152966
title: Additional file 1: of Next-generation sequencing analysis of receptor-type tyrosine kinase genes in surgically resected colon cancer: identification of gain-of-function mutations in the RET proto-oncogene

description: Table S1. Clinical-pathological characteristics of the 37 colon cancer patients included in the study. (XLSX 12Â kb)
DOI: 10.6084/m9.figshare.6152966.v1
title: Additional file 1: of Next-generation sequencing analysis of receptor-type tyrosine kinase genes in surgically resected colon cancer: identification of gain-of-function mutations in the RET proto-oncogene

description: Table S1. Clinical-pathological characteristics of the 37 colon cancer patients included in the study. (XLSX 12Â kb)
DOI: 10.6084/m9.figshare.6152960
title: MOESM3 of Deletion of HP1Îł in cardiac myocytes affects H4K20me3 levels but does not impact cardiac growth

description: Additional file 3. qPCR primer and antibody list.
DOI: 10.6084/m9.figshare.6152960.v1
title: MOESM3 of Deletion of HP1Îł in cardiac myocytes affects H4K20me3 levels but does not impact cardiac growth

description: Additional file 3. qPCR primer and antibody list.
DOI: 10.6084/m9.figshare.6152942
title: MOESM2 of Deletion of HP1Îł in cardiac myocytes affects H4K20me3 levels but does not impact cardiac growth

description: Additional file 2. DiffGene list after TAC.
DOI: 10.6084/m9.figshare.6152942.v1
title: MOESM2 of Deletion of HP1Îł in cardiac myocytes affects H4K20me3 levels but does not impact cardiac growth

description: Additional file 2. DiffGene list after TAC.
DOI: 10.6084/m9.figshare.6152906
title: MOESM4 of Plasma proteomic analysis reveals altered protein abundances in cardiovascular disease

description: Additional file 4. Ingenuity Pathway Analysis of the verified proteins. Lists of the canonical pathways and biological functions that resulted from the Ingenuity Pathway Analysis of the 39 verified proteins.
DOI: 10.6084/m9.figshare.6152906.v1
title: MOESM4 of Plasma proteomic analysis reveals altered protein abundances in cardiovascular disease

description: Additional file 4. Ingenuity Pathway Analysis of the verified proteins. Lists of the canonical pathways and biological functions that resulted from the Ingenuity Pathway Analysis of the 39 verified proteins.
DOI: 10.6084/m9.figshare.6152897
title: Additional file 3: of Identification and characterization of functional modules reflecting transcriptome transition during human neuron maturation

description: Table S2. Gene ontology and pathway enrichment of the discriminating functional modules. (XLSX 296 kb)
DOI: 10.6084/m9.figshare.6152897.v1
title: Additional file 3: of Identification and characterization of functional modules reflecting transcriptome transition during human neuron maturation

description: Table S2. Gene ontology and pathway enrichment of the discriminating functional modules. (XLSX 296 kb)
DOI: 10.6084/m9.figshare.6152891
title: MOESM3 of Plasma proteomic analysis reveals altered protein abundances in cardiovascular disease

description: Additional file 3. Test set analysis results. List of peptides and proteins along with the detailed protein identification and relative quantification data per sample in the test set. The detailed list of the differentially expressed proteins following the same expression trend (â Ľâ twofold change) in both discovery and test sets is also provided.
DOI: 10.6084/m9.figshare.6152891.v1
title: MOESM3 of Plasma proteomic analysis reveals altered protein abundances in cardiovascular disease

description: Additional file 3. Test set analysis results. List of peptides and proteins along with the detailed protein identification and relative quantification data per sample in the test set. The detailed list of the differentially expressed proteins following the same expression trend (â Ľâ twofold change) in both discovery and test sets is also provided.
DOI: 10.6084/m9.figshare.6152882
title: Additional file 2: of Identification and characterization of functional modules reflecting transcriptome transition during human neuron maturation

description: Table S1. Characteristics of the identified functional modules. (XLSX 252 kb)
DOI: 10.6084/m9.figshare.6152882.v1
title: Additional file 2: of Identification and characterization of functional modules reflecting transcriptome transition during human neuron maturation

description: Table S1. Characteristics of the identified functional modules. (XLSX 252 kb)
DOI: 10.6084/m9.figshare.6152873
title: MOESM2 of Plasma proteomic analysis reveals altered protein abundances in cardiovascular disease

description: Additional file 2. Pathway annotation results. Pathway (Cytoscape) analysis of the proteins identified in the discovery set. Pathways predicted based on proteins identified by at least two peptides are also shown.
DOI: 10.6084/m9.figshare.6152873.v1
title: MOESM2 of Plasma proteomic analysis reveals altered protein abundances in cardiovascular disease

description: Additional file 2. Pathway annotation results. Pathway (Cytoscape) analysis of the proteins identified in the discovery set. Pathways predicted based on proteins identified by at least two peptides are also shown.