cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5183368
title: Details on photosynthesis-related gene models in Arabidopsis thaliana from Enhancing (crop) plant photosynthesis by introducing novel genetic diversity

description: Gene locus ID, symbol(s), functional description, chromosomal position and coding sequence length are given for full length cDNA supported gene models. The presented data was extracted from the TAIR data base (Oct 24th 2016) querying the GO terms “photosynthesis” and “photosystem”.
DOI: 10.6084/m9.figshare.5183368.v1
title: Details on photosynthesis-related gene models in Arabidopsis thaliana from Enhancing (crop) plant photosynthesis by introducing novel genetic diversity

description: Gene locus ID, symbol(s), functional description, chromosomal position and coding sequence length are given for full length cDNA supported gene models. The presented data was extracted from the TAIR data base (Oct 24th 2016) querying the GO terms “photosynthesis” and “photosystem”.
DOI: 10.6084/m9.figshare.5183212
title: PLOS2017adolescents_dataset.tsv

description: This data set uses data publicly available data from the Panel Survey of Income Dynamics (http://psidonline.isr.umich.edu/) to study the effect of early-life exposure to low family income and adolescent subjective well-being
DOI: 10.6084/m9.figshare.5183203
title: Monitoring Joint Convergence of MCMC Samplers

description: We present a diagnostic for monitoring convergence of a Markov chain Monte Carlo (MCMC) sampler to its target distribution. In contrast to popular existing methods, we monitor convergence to the joint target distribution directly rather than a select scalar projection. The method uses a simple nonparametric posterior approximation based on a state-space partition obtained by clustering the pooled draws from multiple chains, and convergence is determined when the estimated posterior probabilities of partition elements under each chain are sufficiently similar. This framework applies to a wide variety of problems, and generalizes directly to non-Euclidean state spaces. Our method also provides approximate high-posterior-density regions, and a characterization of differences between nonconverged chains, all with little additional computational burden. We demonstrate this approach on applications to sampling posterior distributions over Rp, graphs, and partitions. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.5183197
title: <i>α-Adducin</i> gene promoter DNA methylation and the risk of essential hypertension

description: This study was conducted to test the association between promoter DNA methylation of <i>α-Adducin</i> (ADD1) gene and the risk of essential hypertension (EH). A total of 150 EH patients and 100 aged- and gender-matched controls were investigated. DNA methylation levels of five cytosine-phosphate-guanine (CpG) dinucleotides on ADD1 promoter were measured employing bisulfite pyrosequencing technology. Our results showed that females have a higher ADD1 DNA methylation than males and a significantly lower CpG1 methylation level is associated with increased risk of EH among them. As for males, a significant association between lower CpG2-5 methylation levels and increased risk of EH was shown. In addition, CpG2-5 methylation was found to be a highly significant predictor for EH among males. In females, CpG1 methylation was considered a predictor of hypertension. No significant correlations were found with biochemical measures, apart from the concentration of aspartate aminotransferase which was inversely correlated with ADD1 CpG2-5 methylation levels among female controls (<i>r</i> = −0.703). These findings highlight that ADD1 methylation may have a contributing role in the pathogenesis of EH with varying implications for both genders.
DOI: 10.6084/m9.figshare.5183203.v2
title: Monitoring Joint Convergence of MCMC Samplers

description: We present a diagnostic for monitoring convergence of a Markov chain Monte Carlo (MCMC) sampler to its target distribution. In contrast to popular existing methods, we monitor convergence to the joint target distribution directly rather than a select scalar projection. The method uses a simple nonparametric posterior approximation based on a state-space partition obtained by clustering the pooled draws from multiple chains, and convergence is determined when the estimated posterior probabilities of partition elements under each chain are sufficiently similar. This framework applies to a wide variety of problems, and generalizes directly to non-Euclidean state spaces. Our method also provides approximate high-posterior-density regions, and a characterization of differences between nonconverged chains, all with little additional computational burden. We demonstrate this approach on applications to sampling posterior distributions over Rp, graphs, and partitions. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.5183197.v1
title: <i>α-Adducin</i> gene promoter DNA methylation and the risk of essential hypertension

description: This study was conducted to test the association between promoter DNA methylation of <i>α-Adducin</i> (ADD1) gene and the risk of essential hypertension (EH). A total of 150 EH patients and 100 aged- and gender-matched controls were investigated. DNA methylation levels of five cytosine-phosphate-guanine (CpG) dinucleotides on ADD1 promoter were measured employing bisulfite pyrosequencing technology. Our results showed that females have a higher ADD1 DNA methylation than males and a significantly lower CpG1 methylation level is associated with increased risk of EH among them. As for males, a significant association between lower CpG2-5 methylation levels and increased risk of EH was shown. In addition, CpG2-5 methylation was found to be a highly significant predictor for EH among males. In females, CpG1 methylation was considered a predictor of hypertension. No significant correlations were found with biochemical measures, apart from the concentration of aspartate aminotransferase which was inversely correlated with ADD1 CpG2-5 methylation levels among female controls (<i>r</i> = −0.703). These findings highlight that ADD1 methylation may have a contributing role in the pathogenesis of EH with varying implications for both genders.
DOI: 10.6084/m9.figshare.5183203.v1
title: Monitoring Joint Convergence of MCMC Samplers

description: We present a diagnostic for monitoring convergence of a Markov chain Monte Carlo (MCMC) sampler to its target distribution. In contrast to popular existing methods, we monitor convergence to the joint target distribution directly rather than a select scalar projection. The method uses a simple nonparametric posterior approximation based on a state-space partition obtained by clustering the pooled draws from multiple chains, and convergence is determined when the estimated posterior probabilities of partition elements under each chain are sufficiently similar. This framework applies to a wide variety of problems, and generalizes directly to non-Euclidean state spaces. Our method also provides approximate high-posterior-density regions, and a characterization of differences between nonconverged chains, all with little additional computational burden. We demonstrate this approach on applications to sampling posterior distributions over Rp, graphs, and partitions. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.5183140
title: Coordinates of sampling points in the prospective area: Study of Particles from the Kafang Copper Deposit in Gejiu City, Yunnan

description: EDS spectra of particles and coordinates of sampling points in the mining area, limestone area, and prospecting area
DOI: 10.6084/m9.figshare.5183140.v1
title: Coordinates of sampling points in the prospective area: Study of Particles from the Kafang Copper Deposit in Gejiu City, Yunnan

description: EDS spectra of particles and coordinates of sampling points in the mining area, limestone area, and prospecting area
DOI: 10.6084/m9.figshare.5183110
title: Coordinates of sampling points in the mining area: Study of Particles from the Kafang Copper Deposit in Gejiu City, Yunnan

description: EDS spectra of particles and coordinates of sampling points in the mining area, limestone area, and prospecting area
DOI: 10.6084/m9.figshare.5183110.v1
title: Coordinates of sampling points in the mining area: Study of Particles from the Kafang Copper Deposit in Gejiu City, Yunnan

description: EDS spectra of particles and coordinates of sampling points in the mining area, limestone area, and prospecting area
DOI: 10.6084/m9.figshare.5183092
title: 3 gold junctions, varying crystal plane

description: xyz files of 3 different initial gold structures. They differ mainly in the direction of the junction compared to the crystal planes (100), (110), (111)
DOI: 10.6084/m9.figshare.5183092.v1
title: 3 gold junctions, varying crystal plane

description: xyz files of 3 different initial gold structures. They differ mainly in the direction of the junction compared to the crystal planes (100), (110), (111)
DOI: 10.6084/m9.figshare.5182915
title: An update of the equation for predicting the dissolution rate of glass fibers from their chemical compositions

description: An update of the equation for predicting the dissolution rate of glass fibers from their chemical compositions
DOI: 10.6084/m9.figshare.5182909
title: Barriers to timely diagnosis and treatment for children with hearing impairment in a southern Indian city: a qualitative study of parents and clinic staff

description: <i>Objective</i>: In low income countries, deaf children are identified late due to the absence of a universal screening. Hearing impairment is a common yet neglected disability in India that leads to loss of speech and language. This qualitative study explored barriers to accessing appropriate hearing services in one city in southern India. <i>Design</i>: To identify the barriers in timely management of deafness, 25 semi-structured interviews were conducted. Data were examined using Applied Thematic Analysis. <i>Study sample</i>: Seventeen mothers of deaf children, primarily from low socioeconomic backgrounds, and eight staff members at a charitable hearing centre in Hyderabad. <i>Results:</i> Barriers to accessing hearing services included failure to recognise deafness, the dominant role of elders in household decisions, belief that deafness would resolve, reassurance from a child’s overall good health, lack of funds and transportation barriers to reach the centre particularly from rural areas. Parents frequently learned about services through word of mouth. <i>Conclusions</i>: The challenges to accessing appropriate services for deafness operate prior to presentation and include educational, cultural, navigational and financial barriers especially for those of lower socioeconomic status and residents of rural areas. The findings highlighted the need to raise awareness and implement wider screening programmes for early interventions.
DOI: 10.6084/m9.figshare.5182909.v1
title: Barriers to timely diagnosis and treatment for children with hearing impairment in a southern Indian city: a qualitative study of parents and clinic staff

description: <i>Objective</i>: In low income countries, deaf children are identified late due to the absence of a universal screening. Hearing impairment is a common yet neglected disability in India that leads to loss of speech and language. This qualitative study explored barriers to accessing appropriate hearing services in one city in southern India. <i>Design</i>: To identify the barriers in timely management of deafness, 25 semi-structured interviews were conducted. Data were examined using Applied Thematic Analysis. <i>Study sample</i>: Seventeen mothers of deaf children, primarily from low socioeconomic backgrounds, and eight staff members at a charitable hearing centre in Hyderabad. <i>Results:</i> Barriers to accessing hearing services included failure to recognise deafness, the dominant role of elders in household decisions, belief that deafness would resolve, reassurance from a child’s overall good health, lack of funds and transportation barriers to reach the centre particularly from rural areas. Parents frequently learned about services through word of mouth. <i>Conclusions</i>: The challenges to accessing appropriate services for deafness operate prior to presentation and include educational, cultural, navigational and financial barriers especially for those of lower socioeconomic status and residents of rural areas. The findings highlighted the need to raise awareness and implement wider screening programmes for early interventions.
DOI: 10.6084/m9.figshare.5182915.v1
title: An update of the equation for predicting the dissolution rate of glass fibers from their chemical compositions

description: An update of the equation for predicting the dissolution rate of glass fibers from their chemical compositions
DOI: 10.6084/m9.figshare.5182897
title: GimmeMotifs example data

description: Example data set for the GimmeMotifs package. See http://gimmemotifs.readthedocs.io<br>
DOI: 10.6084/m9.figshare.5182861
title: Assembly and annotation for haddock with script

description: Approximately 160x coverage of Illumina paired end reads and 20x coverage of PacBio reads were assembled with the Celera Assembler resulting in a contig assembly . All Illumina reads were mapped to the contig assembly with BWA, and the scaffold module from SGA was used to scaffold the contigs. To reduce gaps and to improve the accuracy of the consensus sequence, all Illumina reads were mapped to the scaffold assembly, and Pilon was run to improve the contigs using high-coverage short-read information. <br>An iterative automatic annotation with MAKER using an Illumina based transcriptome of haddock, and proteins from UniProt/SwissProt, annotated 96,576 gene models. InterProScan was run on the predicted proteins of these, and gene names were allocated based on match with proteins in UniProt/SwissProt. We created a filtered set where all genes had an Annotation Edit Distance (AED) of less than 0.5 (where 0.0 indicates perfect accordance between the gene model and evidence (mRNA and/or protein alignments), and 1.0 no accordance). This resulted in 27,437 gene models.
DOI: 10.6084/m9.figshare.5182897.v1
title: GimmeMotifs example data

description: Example data set for the GimmeMotifs package. See http://gimmemotifs.readthedocs.io<br>
DOI: 10.17028/rd.lboro.5182837
title: Supplementary files for "Continuous synthesis of PVP stabilized biocompatible gold nanoparticles with a controlled size using a 3D glass capillary microfluidic device"

description: Supplementary files for Continuous synthesis of PVP stabilized biocompatible gold nanoparticles with a controlled size using a 3D glass capillary microfluidic device.<br>Abstract:A reliable glass capillary microfluidic method was developed for a continuous production of well-controlled gold nanoparticles (AuNPs) capped with polyvinylpyrrolidone (PVP) of different molecular weights (PVP K15, PVP K30 and PVP K90). A two-phase co-flow glass capillary microfluidic device with an injection orifice diameter ranging between 100 and 240 µm was used to synthesise 100–240 µm was used to synthesise AuNPs via the chemical reduction between tetrachloroaurate trihydrate (HAuCl<sub>4</sub>·3H<sub>2</sub>O) and ascorbic acid. AuNPs with an average diameter between 48 and 135 nm were synthesised, as determined by DLS measurements. Decreasing the injection orifice diameter, increasing the flow rate of ascorbic acid stream and its pH resulted in smaller AuNPs. The polydispersity index (PDI) was found to be independent on the injection orifice diameter or the molecular weight of PVP, but increased with the increase of flow rate and the pH of ascorbic acid stream. The stability study over 6-week period confirmed that PVP K30 with an average M<sub>w</sub> of 40000 g/mol was the best capping agent to synthesize and stabilise smaller AuNPs. The reactor fouling due to deposition of AuNPs on reactor walls and orifices was mitigated by hydrophobization of reactor/capillary walls with octadecyltrimethoxisilane and the use of ascorbic acid solution of higher pH.<br>
DOI: 10.6084/m9.figshare.5182810
title: Understanding the factors influencing linkage to HIV care after testing HIV positive in rural Mbeya, Tanzania

description: In Mbeya region of Tanzania, the rate of linkage into HIV care was estimated at 28% in 2014. This study explored the facilitators, barriers to linkage to HIV care at individual/patient, health care provider, health system, and contextual levels to inform the design of interventions to improve linkage to HIV care. A descriptive qualitative study was conducted between August 2014 and July 2015, nested in a cohort study following 1,012 individuals newly diagnosed HIV positive for 6 months. We conducted 8 focus group discussions and 10 in-depth interviews with recently diagnosed HIV-positive individuals from the cohort, and 20 individual interviews with healthcare providers. Transcripts were transcribed verbatim in Swahili, translated into English and analyzed through thematic content analysis supported by Atlas.ti qualitative analysis software.
DOI: 10.17028/rd.lboro.5182837.v1
title: Supplementary files for "Continuous synthesis of PVP stabilized biocompatible gold nanoparticles with a controlled size using a 3D glass capillary microfluidic device"

description: Supplementary files for Continuous synthesis of PVP stabilized biocompatible gold nanoparticles with a controlled size using a 3D glass capillary microfluidic device.<br>Abstract:A reliable glass capillary microfluidic method was developed for a continuous production of well-controlled gold nanoparticles (AuNPs) capped with polyvinylpyrrolidone (PVP) of different molecular weights (PVP K15, PVP K30 and PVP K90). A two-phase co-flow glass capillary microfluidic device with an injection orifice diameter ranging between 100 and 240 µm was used to synthesise 100–240 µm was used to synthesise AuNPs via the chemical reduction between tetrachloroaurate trihydrate (HAuCl<sub>4</sub>·3H<sub>2</sub>O) and ascorbic acid. AuNPs with an average diameter between 48 and 135 nm were synthesised, as determined by DLS measurements. Decreasing the injection orifice diameter, increasing the flow rate of ascorbic acid stream and its pH resulted in smaller AuNPs. The polydispersity index (PDI) was found to be independent on the injection orifice diameter or the molecular weight of PVP, but increased with the increase of flow rate and the pH of ascorbic acid stream. The stability study over 6-week period confirmed that PVP K30 with an average M<sub>w</sub> of 40000 g/mol was the best capping agent to synthesize and stabilise smaller AuNPs. The reactor fouling due to deposition of AuNPs on reactor walls and orifices was mitigated by hydrophobization of reactor/capillary walls with octadecyltrimethoxisilane and the use of ascorbic acid solution of higher pH.<br>
DOI: 10.6084/m9.figshare.5182810.v1
title: Understanding the factors influencing linkage to HIV care after testing HIV positive in rural Mbeya, Tanzania

description: In Mbeya region of Tanzania, the rate of linkage into HIV care was estimated at 28% in 2014. This study explored the facilitators, barriers to linkage to HIV care at individual/patient, health care provider, health system, and contextual levels to inform the design of interventions to improve linkage to HIV care. A descriptive qualitative study was conducted between August 2014 and July 2015, nested in a cohort study following 1,012 individuals newly diagnosed HIV positive for 6 months. We conducted 8 focus group discussions and 10 in-depth interviews with recently diagnosed HIV-positive individuals from the cohort, and 20 individual interviews with healthcare providers. Transcripts were transcribed verbatim in Swahili, translated into English and analyzed through thematic content analysis supported by Atlas.ti qualitative analysis software.
DOI: 10.6084/m9.figshare.5182861.v1
title: Assembly and annotation for haddock

description: Approximately 160x coverage of Illumina paired end reads and 20x coverage of PacBio reads were assembled with the Celera Assembler resulting in a contig assembly . All Illumina reads were mapped to the contig assembly with BWA, and the scaffold module from SGA was used to scaffold the contigs. To reduce gaps and to improve the accuracy of the consensus sequence, all Illumina reads were mapped to the scaffold assembly, and Pilon was run to improve the contigs using high-coverage short-read information. <br>An iterative automatic annotation with MAKER using an Illumina based transcriptome of haddock, and proteins from UniProt/SwissProt, annotated 96,576 gene models. InterProScan was run on the predicted proteins of these, and gene names were allocated based on match with proteins in UniProt/SwissProt. We created a filtered set where all genes had an Annotation Edit Distance (AED) of less than 0.5 (where 0.0 indicates perfect accordance between the gene model and evidence (mRNA and/or protein alignments), and 1.0 no accordance). This resulted in 27,437 gene models.
DOI: 10.6084/m9.figshare.5182702
title: 6 donors brains Freesurfer

description: 6 Donors brain processed using recon-all (Freesurfer)<br>
DOI: 10.6084/m9.figshare.5182711
title: Supplementary Material for: Global Application of the Assessment of Communication Skills of Paediatric Endocrinology Fellows in the Management of Differences in Sex Development Using the ESPE E-Learning.Org Portal

description: <b><i>Background:</i></b> Information sharing in chronic conditions such as disorders of/differences in sex development (DSD) is essential for a comprehensive understanding by parents and patients. We report on a qualitative analysis of communication skills of fellows undergoing training in paediatric endocrinology. Guidelines are created for the assessment of communication between health professionals and individuals with DSD and their parents. <b><i>Methods:</i></b> Paediatric endocrinology fellows worldwide were invited to study two interactive online cases (www.espe-elearning.org) and to describe a best practice communication with (i) the parents of a newborn with congenital adrenal hyperplasia and (ii) a young woman with 46,XY gonadal dysgenesis. The replies were analysed regarding completeness, quality, and evidence of empathy. Guidelines for structured assessment of responses were developed by 22 senior paediatric endocrinologists worldwide who assessed 10 selected replies. Consensus of assessors was established and the evaluation guidelines were created. <b><i>Results:</i></b> The replies of the fellows showed considerable variation in completeness, quality of wording, and evidence of empathy. Many relevant aspects of competent clinical communication were not mentioned; 15% (case 1) and 17% (case 2) of the replies were considered poor/insufficient. There was also marked variation between 17 senior experts in the application of the guidelines to assess communication skills. The guidelines were then adjusted to a 3-level assessment with empathy as a separate key item to better reflect the qualitative differences in the replies and for simplicity of use by evaluators. <b><i>Conclusions:</i></b> E-learning can play an important role in assessing communication skills. A practical tool is provided to assess how information is shared with patients with DSD and their families and should be refined by all stakeholders, notably interdisciplinary health professionals and patient representatives.