cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8203304
title: The complex barnacle perfume: identification of waterborne pheromone homologues in <i>Balanus improvisus</i> and their differential expression during settlement

description: A key question in barnacle biology is the nature of cues that induce gregarious settlement. One of the characterised cues is the waterborne settlement pheromone (WSP). This study aimed to identify WSP homologues in <i>Balanus improvisus</i> and to investigate their expression during settlement. Six WSP homologues were identified, all containing an N-terminal signal peptide, a conserved core region, and a variable C-terminus comprising several -GR- and -HDDH- motifs. The <i>B. improvisus</i> WSP homologues were expressed in all settlement stages but showed different expression patterns. The homologue most similar to the <i>B. amphitrite</i> WSP was the most abundant and was constantly expressed during settlement. In contrast, several of the other WSP homologues showed the greatest expression in the juvenile stage. The presence of several WSP homologues suggests the existence of a pheromone mix, where con-specificity might be determined by a combination of sequence characteristics and the concentration of the individual components.
DOI: 10.6084/m9.figshare.8203310
title: MNIST-diff: simulation dataset of the 2D reconstruction of event sequences

description: simulation dataset of the 2D reconstruction of event sequences
DOI: 10.6084/m9.figshare.8203310.v1
title: MNIST-diff: simulation dataset of the 2D reconstruction of event sequences

description: simulation dataset of the 2D reconstruction of event sequences
DOI: 10.6084/m9.figshare.8203304.v2
title: The complex barnacle perfume: identification of waterborne pheromone homologues in <i>Balanus improvisus</i> and their differential expression during settlement

description: A key question in barnacle biology is the nature of cues that induce gregarious settlement. One of the characterised cues is the waterborne settlement pheromone (WSP). This study aimed to identify WSP homologues in <i>Balanus improvisus</i> and to investigate their expression during settlement. Six WSP homologues were identified, all containing an N-terminal signal peptide, a conserved core region, and a variable C-terminus comprising several -GR- and -HDDH- motifs. The <i>B. improvisus</i> WSP homologues were expressed in all settlement stages but showed different expression patterns. The homologue most similar to the <i>B. amphitrite</i> WSP was the most abundant and was constantly expressed during settlement. In contrast, several of the other WSP homologues showed the greatest expression in the juvenile stage. The presence of several WSP homologues suggests the existence of a pheromone mix, where con-specificity might be determined by a combination of sequence characteristics and the concentration of the individual components.
DOI: 10.6084/m9.figshare.8203304.v1
title: The complex barnacle perfume: identification of waterborne pheromone homologues in <i>Balanus improvisus</i> and their differential expression during settlement

description: A key question in barnacle biology is the nature of cues that induce gregarious settlement. One of the characterised cues is the waterborne settlement pheromone (WSP). This study aimed to identify WSP homologues in <i>Balanus improvisus</i> and to investigate their expression during settlement. Six WSP homologues were identified, all containing an N-terminal signal peptide, a conserved core region, and a variable C-terminus comprising several -GR- and -HDDH- motifs. The <i>B. improvisus</i> WSP homologues were expressed in all settlement stages but showed different expression patterns. The homologue most similar to the <i>B. amphitrite</i> WSP was the most abundant and was constantly expressed during settlement. In contrast, several of the other WSP homologues showed the greatest expression in the juvenile stage. The presence of several WSP homologues suggests the existence of a pheromone mix, where con-specificity might be determined by a combination of sequence characteristics and the concentration of the individual components.
DOI: 10.6084/m9.figshare.8203181
title: Breast cancer mutation in GATA3 zinc finger 1 induces conformational changes leading to the closer binding of ZnFn2 with a wrapping architecture

description: GATA3 is a transcription factor, known to regulate the transcriptional network and several pathways using two zinc fingers. Its mutation is associated with a higher risk of breast cancer. The molecular mechanisms of these mutations are poorly understood. It recognizes -GATA- sites on the DNA, using its two zinc fingers ZnFn1 and ZnFn2. Mutations in ZnFn2 have been studied in the past and well known but recently ZnFn1 mutations are also being reported very frequently in breast cancer patients and there is very less knowledge available regarding the binding modes and mechanism. Here, we have investigated the structural and functional impact of GATA3 mutation M294K on the DNA-binding property. The structure was obtained and mutation was induced before subjecting it to the molecular docking followed by MD simulation. Our findings indicate that the somatic mutation M294K, reported in the GATA3 gene destabilizes the unbound structure but, when it forms the DNA-complex, its overall structural stability is restored by the wrapping architecture of ZnFn2 around the DNA in the palindromic region, leading to the enhanced kinetic stability. The mutation not only affects the ZnFn1 region alone but also influences the whole complex by inducing the conformational changes in the linker region between the two zinc fingers, bringing the two zinc fingers to closer proximity representing the flexibility in binding sites. Our findings provide a better understanding of ZnFn1 mutations and the possibility of a different strategy to target these genes for their clinical relevance. Communicated by Ramaswamy H. Sarma
DOI: 10.17028/rd.lboro.8203175
title: 2-port Device for Segregated Cell Seeding - MASK DESIGN

description: This is a master mask design for a 2-port device in which two populations of cells can be cultured separately yet connected via an array of 5 um width channels.Two mask are needed: one for channels and the other for the reservoirs.
DOI: 10.6084/m9.figshare.8203172
title: Evaluation of EHR system

description: Electronic health recording system is essential to facilitate clinical and administrative processes. It also allows clinical information gathering and access at the point of patient care. The advantage of implementing the system is more intensified in facilities where there is a high volume of patients, complex work flow, frequent emergency situations and involving multiple personnel. Here, we introduce that the usefulness and satisfaction with the EHR system varies by department and by specific task within a department.The study was conducted after ethical clearance was obtained from the Institutional Ethical Review Committee of Addis Ababa University School of Commerce. During the data collection period, the participants were well informed about the purpose of the study. Informed verbal consent was obtained from each participant. Involvement was fully decided by the participants. The response was confidential. The study used a formative evaluation method to address the objective. <br>
DOI: 10.6084/m9.figshare.8203181.v1
title: Breast cancer mutation in GATA3 zinc finger 1 induces conformational changes leading to the closer binding of ZnFn2 with a wrapping architecture

description: GATA3 is a transcription factor, known to regulate the transcriptional network and several pathways using two zinc fingers. Its mutation is associated with a higher risk of breast cancer. The molecular mechanisms of these mutations are poorly understood. It recognizes -GATA- sites on the DNA, using its two zinc fingers ZnFn1 and ZnFn2. Mutations in ZnFn2 have been studied in the past and well known but recently ZnFn1 mutations are also being reported very frequently in breast cancer patients and there is very less knowledge available regarding the binding modes and mechanism. Here, we have investigated the structural and functional impact of GATA3 mutation M294K on the DNA-binding property. The structure was obtained and mutation was induced before subjecting it to the molecular docking followed by MD simulation. Our findings indicate that the somatic mutation M294K, reported in the GATA3 gene destabilizes the unbound structure but, when it forms the DNA-complex, its overall structural stability is restored by the wrapping architecture of ZnFn2 around the DNA in the palindromic region, leading to the enhanced kinetic stability. The mutation not only affects the ZnFn1 region alone but also influences the whole complex by inducing the conformational changes in the linker region between the two zinc fingers, bringing the two zinc fingers to closer proximity representing the flexibility in binding sites. Our findings provide a better understanding of ZnFn1 mutations and the possibility of a different strategy to target these genes for their clinical relevance. Communicated by Ramaswamy H. Sarma
DOI: 10.17028/rd.lboro.8203175.v1
title: 2-port Device for Segregated Cell Seeding - MASK DESIGN

description: This is a master mask design for a 2-port device in which two populations of cells can be cultured separately yet connected via an array of 5 um width channels.Two mask are needed: one for channels and the other for the reservoirs.
DOI: 10.6084/m9.figshare.8203172.v1
title: Evaluation of EHR system

description: Electronic health recording system is essential to facilitate clinical and administrative processes. It also allows clinical information gathering and access at the point of patient care. The advantage of implementing the system is more intensified in facilities where there is a high volume of patients, complex work flow, frequent emergency situations and involving multiple personnel. Here, we introduce that the usefulness and satisfaction with the EHR system varies by department and by specific task within a department.The study was conducted after ethical clearance was obtained from the Institutional Ethical Review Committee of Addis Ababa University School of Commerce. During the data collection period, the participants were well informed about the purpose of the study. Informed verbal consent was obtained from each participant. Involvement was fully decided by the participants. The response was confidential. The study used a formative evaluation method to address the objective. <br>
DOI: 10.6084/m9.figshare.8202980
title: Additional file 9: of The association of germline variants with chronic lymphocytic leukemia outcome suggests the implication of novel genes and pathways in clinical evolution

description: Table S1. GWAS results of the additive Cox regression model for TTT. Polymorphisms with a BH-adjusted P-value
DOI: 10.6084/m9.figshare.8202980.v1
title: Additional file 9: of The association of germline variants with chronic lymphocytic leukemia outcome suggests the implication of novel genes and pathways in clinical evolution

description: Table S1. GWAS results of the additive Cox regression model for TTT. Polymorphisms with a BH-adjusted P-value
DOI: 10.6084/m9.figshare.8202953
title: Additional file 1: of Airborne fungal spores and invasive aspergillosis in hematologic units in a tertiary hospital during construction: a prospective cohort study

description: Table S1. Baseline characteristics of admitted patients during periods 1 and 2. Figure S1. Cases of Aspergillus spp. isolation from clinical specimens from January 2016 to December 2018. (ZIP 671 kb)
DOI: 10.6084/m9.figshare.8202953.v1
title: Additional file 1: of Airborne fungal spores and invasive aspergillosis in hematologic units in a tertiary hospital during construction: a prospective cohort study

description: Table S1. Baseline characteristics of admitted patients during periods 1 and 2. Figure S1. Cases of Aspergillus spp. isolation from clinical specimens from January 2016 to December 2018. (ZIP 671 kb)
DOI: 10.6084/m9.figshare.8202884
title: Additional file 1: of Geographical patterns of the incidence and mortality of colorectal cancer in mainland Portugal municipalities (2007â 2011)

description: SIR and SMR of colorectal cancer in mainland Portugal, by sex. (ZIP 1260 kb)
DOI: 10.6084/m9.figshare.8202884.v1
title: Additional file 1: of Geographical patterns of the incidence and mortality of colorectal cancer in mainland Portugal municipalities (2007â 2011)

description: SIR and SMR of colorectal cancer in mainland Portugal, by sex. (ZIP 1260 kb)
DOI: 10.6084/m9.figshare.8202821
title: MOESM6 of Comparative Subsequence Sets Analysis (CoSSA) is a robust approach to identify haplotype specific SNPs; mapping and pedigree analysis of a potato wart disease resistance gene Sen3

description: Additional file 6. Summary of the sequencing data used and of the CoSSA k-mers subsets. For all the samples sequenced, the number of reads and the sequencing depth is given. The number of unique k-mers (Nu) and the number of total k-mers (Nt) is given for all the sequenced samples and several subsets obtained after basic set operations for different depth cut-offs.
DOI: 10.6084/m9.figshare.8202821.v1
title: MOESM6 of Comparative Subsequence Sets Analysis (CoSSA) is a robust approach to identify haplotype specific SNPs; mapping and pedigree analysis of a potato wart disease resistance gene Sen3

description: Additional file 6. Summary of the sequencing data used and of the CoSSA k-mers subsets. For all the samples sequenced, the number of reads and the sequencing depth is given. The number of unique k-mers (Nu) and the number of total k-mers (Nt) is given for all the sequenced samples and several subsets obtained after basic set operations for different depth cut-offs.
DOI: 10.6084/m9.figshare.8202806
title: MOESM4 of Comparative Subsequence Sets Analysis (CoSSA) is a robust approach to identify haplotype specific SNPs; mapping and pedigree analysis of a potato wart disease resistance gene Sen3

description: Additional file 4. KASP primers used in the study. For each KASP marker used in the study is given: the marker name (chromosome_position), the experiment in which it was used, the population in which it was used, the two forward primer sequences and the common primer sequence.
DOI: 10.6084/m9.figshare.8202806.v1
title: MOESM4 of Comparative Subsequence Sets Analysis (CoSSA) is a robust approach to identify haplotype specific SNPs; mapping and pedigree analysis of a potato wart disease resistance gene Sen3

description: Additional file 4. KASP primers used in the study. For each KASP marker used in the study is given: the marker name (chromosome_position), the experiment in which it was used, the population in which it was used, the two forward primer sequences and the common primer sequence.
DOI: 10.6084/m9.figshare.8202788
title: MOESM1 of Comparative Subsequence Sets Analysis (CoSSA) is a robust approach to identify haplotype specific SNPs; mapping and pedigree analysis of a potato wart disease resistance gene Sen3

description: Additional file 1. Phenotypic and genotypic data of the K*L population. The Excel sheet comprises: the genotypic data for all the tested markers, the number of tubers tested per genotype, the average score of the Glynne-Lemmerzahl assays performed in 2016 and 2017 for the pathotypes 2, 6 and 18, the individuals included in the subset (n = 83) used for the validation of the CoSSA results and the individuals selected for the R-bulk and the S-bulk.
DOI: 10.6084/m9.figshare.8202788.v1
title: MOESM1 of Comparative Subsequence Sets Analysis (CoSSA) is a robust approach to identify haplotype specific SNPs; mapping and pedigree analysis of a potato wart disease resistance gene Sen3

description: Additional file 1. Phenotypic and genotypic data of the K*L population. The Excel sheet comprises: the genotypic data for all the tested markers, the number of tubers tested per genotype, the average score of the Glynne-Lemmerzahl assays performed in 2016 and 2017 for the pathotypes 2, 6 and 18, the individuals included in the subset (n = 83) used for the validation of the CoSSA results and the individuals selected for the R-bulk and the S-bulk.
DOI: 10.6084/m9.figshare.8202764
title: Additional file 1: of Continuous monitoring of intrinsic PEEP based on expired CO2 kinetics: an experimental validation study

description: Figure S1. Experimental setup in a single-limb circuit configuration. Figure S2. Setup for a double-limb circuit configuration. (ZIP 161 kb)
DOI: 10.6084/m9.figshare.8202764.v1
title: Additional file 1: of Continuous monitoring of intrinsic PEEP based on expired CO2 kinetics: an experimental validation study

description: Figure S1. Experimental setup in a single-limb circuit configuration. Figure S2. Setup for a double-limb circuit configuration. (ZIP 161 kb)
DOI: 10.6084/m9.figshare.8202734
title: Additional file 1: of Fatty corner lesions in T1-weighted magnetic resonance imaging as an alternative to sacroiliitis for diagnosis of axial spondyloarthritis

description: Using fatty corner lesions for diagnosis of axial spondyloarthritis data file. (SAV 55 kb)
DOI: 10.6084/m9.figshare.8202734.v1
title: Additional file 1: of Fatty corner lesions in T1-weighted magnetic resonance imaging as an alternative to sacroiliitis for diagnosis of axial spondyloarthritis

description: Using fatty corner lesions for diagnosis of axial spondyloarthritis data file. (SAV 55 kb)
DOI: 10.6084/m9.figshare.8202689
title: Additional file 2 of Identifying lncRNA-mediated regulatory modules via ChIA-PET network analysis

description: In this excel file we provide the results from clustering analysis of the biggest connected component of each chromosome, in order to assist future experimental studies. For each component, we report the results from those values of α and θ yielding the best partition according to the MI ratio criteria. We report the clustering parameters, the resulting MI ratio, the number of obtained modules per component, the number of lncRNAs, protein-coding gene, as well as the overall number of nodes for each component. Note when the genomic coordinates of a gene and a lncRNA overlap, both the gene and the lncRNA name are reported for the same node. Sheet 2 of this file contains the results of GO/KEGG enrichment analysis for the modules of each chromosome’s biggest component. (XLSX 25 kb)
DOI: 10.6084/m9.figshare.8202686
title: Additional file 2: of The role of patient organizations in the rare disease ecosystem in India: an interview based study

description: a) Details of each PG. Name, legal status, international partners, regional chapters, whether first PG in India, patient registry, number of patients associated with the PG and website. b) RD management. Name of PG; PGsâ views on alternative treatment options; globally available modes of management or treatment not yet available in India; whether prenatal diagnosis is possible; counselling provided to patients by the PGs; research by the PGs, directly or in collaboration; and whether RD is covered by the Rights of Persons with Disabilities Act, 2016. c) Challenges faced by the PGs. Challenges faced by patients in the diagnosis, treatment and management of the disease or condition. d) Support received by PGs from various sources. Support was received from the following sources, largely within the country: central government; local authorities or state government; public (crowd funding); industry; healthcare providers; philanthropic organizations; company CSR funds; local organizations or NGOs. e) Recommendations made by the PGs to various stake holders. f) Interviewee story. Each interviewee had a reason to join or start a PG. These stories are captured here in brief. (XLSX 38 kb)
DOI: 10.6084/m9.figshare.8202689.v1
title: Additional file 2 of Identifying lncRNA-mediated regulatory modules via ChIA-PET network analysis

description: In this excel file we provide the results from clustering analysis of the biggest connected component of each chromosome, in order to assist future experimental studies. For each component, we report the results from those values of α and θ yielding the best partition according to the MI ratio criteria. We report the clustering parameters, the resulting MI ratio, the number of obtained modules per component, the number of lncRNAs, protein-coding gene, as well as the overall number of nodes for each component. Note when the genomic coordinates of a gene and a lncRNA overlap, both the gene and the lncRNA name are reported for the same node. Sheet 2 of this file contains the results of GO/KEGG enrichment analysis for the modules of each chromosome’s biggest component. (XLSX 25 kb)
DOI: 10.6084/m9.figshare.8202686.v1
title: Additional file 2: of The role of patient organizations in the rare disease ecosystem in India: an interview based study

description: a) Details of each PG. Name, legal status, international partners, regional chapters, whether first PG in India, patient registry, number of patients associated with the PG and website. b) RD management. Name of PG; PGsâ views on alternative treatment options; globally available modes of management or treatment not yet available in India; whether prenatal diagnosis is possible; counselling provided to patients by the PGs; research by the PGs, directly or in collaboration; and whether RD is covered by the Rights of Persons with Disabilities Act, 2016. c) Challenges faced by the PGs. Challenges faced by patients in the diagnosis, treatment and management of the disease or condition. d) Support received by PGs from various sources. Support was received from the following sources, largely within the country: central government; local authorities or state government; public (crowd funding); industry; healthcare providers; philanthropic organizations; company CSR funds; local organizations or NGOs. e) Recommendations made by the PGs to various stake holders. f) Interviewee story. Each interviewee had a reason to join or start a PG. These stories are captured here in brief. (XLSX 38 kb)
DOI: 10.6084/m9.figshare.8202584
title: Additional file 4: of Cognitive assessment of idiopathic intracranial hypertension patients

description: Spread sheet of psychometric tests. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.8202584.v1
title: Additional file 4: of Cognitive assessment of idiopathic intracranial hypertension patients

description: Spread sheet of psychometric tests. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.8202545
title: Additional file 6: of Time varying causal network reconstruction of a mouse cell cycle

description: Complete list of interactions identified in reconstruction of the three networks incorporating transcription factors using data from the {1â 14.5} hour, {1â 24.5} hour and {1â 28.5} hour intervals. (XLSX 25 kb)
DOI: 10.6084/m9.figshare.8202545.v1
title: Additional file 6: of Time varying causal network reconstruction of a mouse cell cycle

description: Complete list of interactions identified in reconstruction of the three networks incorporating transcription factors using data from the {1â 14.5} hour, {1â 24.5} hour and {1â 28.5} hour intervals. (XLSX 25 kb)
DOI: 10.6084/m9.figshare.8202533
title: Additional file 4: of Time varying causal network reconstruction of a mouse cell cycle

description: Complete list of interactions identified in reconstruction of G1 phase followed by S phase in the {1â 24.5} hour interval. (XLSX 21 kb)
DOI: 10.6084/m9.figshare.8202536
title: Additional file 5: of Time varying causal network reconstruction of a mouse cell cycle

description: Complete list of interactions identified in reconstruction of the G1 and S phases followed by G2/M phases in the {1â 28.5} hour interval. (XLSX 21 kb)
DOI: 10.6084/m9.figshare.8202524
title: Additional file 3: of Time varying causal network reconstruction of a mouse cell cycle

description: Complete list of interactions identified in reconstruction of G1 phase in the {1â 14.5} hour interval. (XLSX 23 kb)