cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.9332012
title: Supplementary Material for: Serum Polyunsaturated Fatty Acids in Middle Childhood and Body Mass Index Change Through Adolescence

description: <b><i>Background:</i></b> Polyunsaturated fatty acids (PUFA) status in childhood may be associated with adiposity development. <b><i>Objective:</i></b> To assess associations of serum PUFA biomarkers in childhood with change in body mass index (BMI)-for-age Z scores (BMIZ) through adolescence. <b><i>Methods:</i></b> We quantified serum PUFA at ages 5 and 10 years among 418 children from Santiago, Chile. BMI was measured at 5, 10, and 16 years. We compared BMIZ change through age 16 years between quartiles of PUFA at 5 and 10 years and PUFA change 5–10 years by fitting growth curves from mixed effects models. <b><i>Results:</i></b> At age 5 years, serum docosahexaenoic acid was inversely associated with BMIZ change from ages 5 to 16 years. At age 10 years, arachidonic acid (AA) was nonlinearly positively related to BMIZ change from ages 10 to 16 years. Change in AA and the Δ5-desaturase (D5D) activity index between 5 and 10 years were each positively associated with BMIZ change from ages 10 to 16 years. Change in eicosapentaenoic acid was inversely associated with change in BMIZ. <b><i>Conclusions:</i></b> Serum long-chain n-3 PUFA in middle childhood were associated with less BMI gain through adolescence, whereas AA and D5D activity was related to greater BMI gain.
DOI: 10.6084/m9.figshare.9331895
title: Supplementary Table

description: List of candidate genes for each subject based on inheritance pattern.
DOI: 10.6084/m9.figshare.9331895.v1
title: Supplementary Table

description: List of candidate genes for each subject based on inheritance pattern.
DOI: 10.6084/m9.figshare.9331748
title: Data set for readers of International Journal of Circumpolar Health

description: Includes measurements of UV radiation, happiness, Human Development Index, genetic distance from South Africa, rule of law, government effectiveness, and economic freedom for 71 countries
DOI: 10.6084/m9.figshare.9331826
title: DEN-IM's typing database phylogenetic trees

description: We have compiled a database of 3830 complete DENV genomes obtained from the NIAID Virus Pathogen Database and Analysis Resource (ViPR) in January 2019 (1) (http://www.viprbrc.org/). A representative of DENV serotype 1 genotype III was introduced (EF457905, recovered from monkey) as no representatives were available with the search criteria used.Overly similar sequences in the collection were removed from the database by clustering the sequences in each serotype at 98% nucleotide similarity, leaving 161 representative sequences of all described DENV serotypes and genotypes, with 46 DENV-1 sequences, 63 DENV-2 , 25 DENV-3 and 27 DENV-4. <br>Phylogenetic analysis of typing collection was performed by aligning the full reference genomes with MAFFT, in auto mode and with automatic sequence orientation adjustment. A phylogenetic tree was inferred with RAxML (version 8.12.11) using the GTR-𝛤 substitution model and 500 times bootstrap. Additionally, the same analysis was performed with the envelope protein (E) only. The resulting trees are available here.
DOI: 10.6084/m9.figshare.9331724
title: Supplementary Material for: Provider Attitudes toward the Use of Hepatitis C Virus-Positive Organs in Kidney Transplantation

description: <b><i>Background:</i></b> Direct-acting antivirals have changed the landscape of hepatitis C virus (HCV) care. While transplantation with HCV-positive donor organs is increasing, little is known about providers’ attitudes toward this topic. The aim of this study is to determine providers’ attitudes toward HCV-positive kidney transplantation. <b><i>Methods:</i></b> Willing transplant and nontransplant nephrologists, transplant surgeons, and mid-level providers completed an online survey from April through May 2018. The survey asked about HCV knowledge and willingness to transplant HCV-positive antibody, nucleic acid testing-positive kidneys into HCV-negative recipients. Descriptive analyses including mean and median for continuous variables and frequencies for categorical variables were calculated. <b><i>Results:</i></b> Seven-hundred surveys were emailed and 99 providers (62 transplant nephrologists, 28 nontransplant nephrologists, 7 transplant surgeons, and 2 advanced practice providers) completed the survey (participation rate 14.1%). All providers knew that HCV was curable, with 60% believing that it had no effect on transplant success and 32% thinking it reduced transplant success. Providers were significantly more likely to offer a HCV-positive organ to HCV-positive recipients compared to HCV-negative recipients in all queried circumstances (<i>p</i> &lt; 0.005 in all cases), especially with increasing impact on patient’s quality of life. While only 39% of providers would offer a HCV-positive organ for transplant to a patient without HCV if it reduced the waitlist time by 1 year, 92% would offer a HCV-positive organ if it reduced the waitlist time by 4 years. However, only 47% thought that the use of HCV-positive kidneys should be for routine care, while 38% believed it should be reserved for research purposes only. There were no significant differences between transplant and nontransplant nephrologists in attitudes toward HCV-positive kidney transplantation. Providers believed that donor organs from those who were obese, &gt;50 years old, or had died from a cardiac arrest were significantly more likely to reduce the likelihood of a successful transplant 1-year posttransplant when compared with a HCV-positive organ (<i>p</i> &lt; 0.005 in all cases). Eighty-six percent of providers had concerns about HCV curability posttransplant. <b><i>Conclusion:</i></b> Although 92% of providers were willing to offer a HCV-positive kidney for transplant as patient waitlist time increases, less than half supported offering HCV-positive transplantation for routine care rather than for research. The results underscore the need for further education and data about the efficacy and safety of HCV-positive kidney transplantation.
DOI: 10.6084/m9.figshare.9331826.v1
title: DEN-IM's typing database phylogenetic trees

description: We have compiled a database of 3830 complete DENV genomes obtained from the NIAID Virus Pathogen Database and Analysis Resource (ViPR) in January 2019 (1) (http://www.viprbrc.org/). A representative of DENV serotype 1 genotype III was introduced (EF457905, recovered from monkey) as no representatives were available with the search criteria used.Overly similar sequences in the collection were removed from the database by clustering the sequences in each serotype at 98% nucleotide similarity, leaving 161 representative sequences of all described DENV serotypes and genotypes, with 46 DENV-1 sequences, 63 DENV-2 , 25 DENV-3 and 27 DENV-4. <br>Phylogenetic analysis of typing collection was performed by aligning the full reference genomes with MAFFT, in auto mode and with automatic sequence orientation adjustment. A phylogenetic tree was inferred with RAxML (version 8.12.11) using the GTR-𝛤 substitution model and 500 times bootstrap. Additionally, the same analysis was performed with the envelope protein (E) only. The resulting trees are available here.
DOI: 10.6084/m9.figshare.9331643
title: Supplementary Excel File.xlsx

description: List of candidate genetic variants for all 9 subjects
DOI: 10.6084/m9.figshare.9331724.v1
title: Supplementary Material for: Provider Attitudes toward the Use of Hepatitis C Virus-Positive Organs in Kidney Transplantation

description: <b><i>Background:</i></b> Direct-acting antivirals have changed the landscape of hepatitis C virus (HCV) care. While transplantation with HCV-positive donor organs is increasing, little is known about providers’ attitudes toward this topic. The aim of this study is to determine providers’ attitudes toward HCV-positive kidney transplantation. <b><i>Methods:</i></b> Willing transplant and nontransplant nephrologists, transplant surgeons, and mid-level providers completed an online survey from April through May 2018. The survey asked about HCV knowledge and willingness to transplant HCV-positive antibody, nucleic acid testing-positive kidneys into HCV-negative recipients. Descriptive analyses including mean and median for continuous variables and frequencies for categorical variables were calculated. <b><i>Results:</i></b> Seven-hundred surveys were emailed and 99 providers (62 transplant nephrologists, 28 nontransplant nephrologists, 7 transplant surgeons, and 2 advanced practice providers) completed the survey (participation rate 14.1%). All providers knew that HCV was curable, with 60% believing that it had no effect on transplant success and 32% thinking it reduced transplant success. Providers were significantly more likely to offer a HCV-positive organ to HCV-positive recipients compared to HCV-negative recipients in all queried circumstances (<i>p</i> &lt; 0.005 in all cases), especially with increasing impact on patient’s quality of life. While only 39% of providers would offer a HCV-positive organ for transplant to a patient without HCV if it reduced the waitlist time by 1 year, 92% would offer a HCV-positive organ if it reduced the waitlist time by 4 years. However, only 47% thought that the use of HCV-positive kidneys should be for routine care, while 38% believed it should be reserved for research purposes only. There were no significant differences between transplant and nontransplant nephrologists in attitudes toward HCV-positive kidney transplantation. Providers believed that donor organs from those who were obese, &gt;50 years old, or had died from a cardiac arrest were significantly more likely to reduce the likelihood of a successful transplant 1-year posttransplant when compared with a HCV-positive organ (<i>p</i> &lt; 0.005 in all cases). Eighty-six percent of providers had concerns about HCV curability posttransplant. <b><i>Conclusion:</i></b> Although 92% of providers were willing to offer a HCV-positive kidney for transplant as patient waitlist time increases, less than half supported offering HCV-positive transplantation for routine care rather than for research. The results underscore the need for further education and data about the efficacy and safety of HCV-positive kidney transplantation.
DOI: 10.6084/m9.figshare.9327833
title: Risk and outcome of hepatocellular carcinoma in liver cirrhosis in Southern Sweden: a population-based study

description: <b>Background and aims:</b> Liver cirrhosis is a risk factor for hepatocellular carcinoma (HCC). While the HCC risk is thought to be highest in hepatitis B and hepatitis C, the risk in other cirrhosis etiologies is not fully established. Therefore, we aimed to study the risk and outcome of HCC in alcoholic cirrhosis compared to cirrhosis of other etiologies, in Sweden. <b>Material and methods:</b> We used population-based medical registries to identify patients diagnosed with cirrhosis in the Scania region in southern Sweden between 2001 and 2010. Medical records were reviewed to identify all HCC cases and to register clinical parameters. All patients were followed until death, emigration or December 2017. <b>Results:</b> The cohort comprised 1317 patients with cirrhosis. A total of 200 patient developed HCC, including 75 with prevalent HCC. The annual incidence of HCC after six months was 1.5% in alcoholic cirrhosis and 4.7% in hepatitis C cirrhosis. In alcoholic cirrhosis, 40 patients were diagnosed with HCC during follow-up, of which 15 patients fulfilled the Milan criteria and 10 received treatment, curative or palliative. The overall median survival after HCC diagnosis was 7.7 months, with 4.5, 11 and 9.3 months, in cirrhosis due to alcohol, hepatitis C or remaining causes, respectively. <b>Conclusion:</b> We find an annual incidence of HCC in alcoholic cirrhosis of 1.5% indicating need for surveillance in these patients. Survival after HCC diagnosis was worst in alcoholic cirrhosis due to more advanced stage at diagnosis with few patients eligible for treatment.
DOI: 10.6084/m9.figshare.9327911
title: How does medical education affect empathy and compassion in medical students? A meta-ethnography: BEME Guide No. 57

description: <b>Background:</b> Empathy and compassion are important in healthcare delivery, and are necessary qualities in medical students. <b>Aims:</b> To explore medical students', patients' and educators' perceptions of what affects empathy and the expression of compassion; and to address gaps in knowledge, attitudes and skills on how education affects empathy and the expression of compassion in medical students. <b>Methods:</b> The seven steps by Noblit and Hare were used for this meta-ethnography. Databases were searched for studies in English, published from 2007 to 2017 with outcomes of empathy and compassion. Key themes and concepts were identified, and accounts from the studies were used to build interpretations. <b>Findings:</b> Thirty-three qualitative studies were included and four main themes were derived: seeing the patient as a person; appreciating the elements of empathy and compassion; navigating in the training environment; and being guided by ideals. Interactions between the patient, the medical student and training environment which affect the development of empathy and compassion are illustrated in a conceptual model. <b>Conclusions:</b> This meta-ethnography extends our understanding of how medical education affects the expression of empathy and compassion in medical students. The results provide important considerations for medical educators and faculty developers in further developing and improving medical curricula.
DOI: 10.6084/m9.figshare.9327911.v1
title: How does medical education affect empathy and compassion in medical students? A meta-ethnography: BEME Guide No. 57

description: <b>Background:</b> Empathy and compassion are important in healthcare delivery, and are necessary qualities in medical students. <b>Aims:</b> To explore medical students', patients' and educators' perceptions of what affects empathy and the expression of compassion; and to address gaps in knowledge, attitudes and skills on how education affects empathy and the expression of compassion in medical students. <b>Methods:</b> The seven steps by Noblit and Hare were used for this meta-ethnography. Databases were searched for studies in English, published from 2007 to 2017 with outcomes of empathy and compassion. Key themes and concepts were identified, and accounts from the studies were used to build interpretations. <b>Findings:</b> Thirty-three qualitative studies were included and four main themes were derived: seeing the patient as a person; appreciating the elements of empathy and compassion; navigating in the training environment; and being guided by ideals. Interactions between the patient, the medical student and training environment which affect the development of empathy and compassion are illustrated in a conceptual model. <b>Conclusions:</b> This meta-ethnography extends our understanding of how medical education affects the expression of empathy and compassion in medical students. The results provide important considerations for medical educators and faculty developers in further developing and improving medical curricula.
DOI: 10.6084/m9.figshare.9327833.v1
title: Risk and outcome of hepatocellular carcinoma in liver cirrhosis in Southern Sweden: a population-based study

description: <b>Background and aims:</b> Liver cirrhosis is a risk factor for hepatocellular carcinoma (HCC). While the HCC risk is thought to be highest in hepatitis B and hepatitis C, the risk in other cirrhosis etiologies is not fully established. Therefore, we aimed to study the risk and outcome of HCC in alcoholic cirrhosis compared to cirrhosis of other etiologies, in Sweden. <b>Material and methods:</b> We used population-based medical registries to identify patients diagnosed with cirrhosis in the Scania region in southern Sweden between 2001 and 2010. Medical records were reviewed to identify all HCC cases and to register clinical parameters. All patients were followed until death, emigration or December 2017. <b>Results:</b> The cohort comprised 1317 patients with cirrhosis. A total of 200 patient developed HCC, including 75 with prevalent HCC. The annual incidence of HCC after six months was 1.5% in alcoholic cirrhosis and 4.7% in hepatitis C cirrhosis. In alcoholic cirrhosis, 40 patients were diagnosed with HCC during follow-up, of which 15 patients fulfilled the Milan criteria and 10 received treatment, curative or palliative. The overall median survival after HCC diagnosis was 7.7 months, with 4.5, 11 and 9.3 months, in cirrhosis due to alcohol, hepatitis C or remaining causes, respectively. <b>Conclusion:</b> We find an annual incidence of HCC in alcoholic cirrhosis of 1.5% indicating need for surveillance in these patients. Survival after HCC diagnosis was worst in alcoholic cirrhosis due to more advanced stage at diagnosis with few patients eligible for treatment.
DOI: 10.6084/m9.figshare.9318851
title: DEN-IM: Dengue virus genotyping from amplicon and shotgun metagenomics - HTML reports

description: To evaluate the DEN-IM’s workflow performance, we analysed two datasets, one containing shotgun metagenomics sequencing data of patient samples, and a second with targeted metagenomics sequencing data obtained from PRJNA394021 ( 106 paired-end samples) and PRJNA321963 (78 single-end samples). The shotgun metagenomic dataset comprised of 22 shotgun metagenomics paired-end short-read Illumina sequencing samples datasets from clinical positive dengue cases (identified as such by a positive qRT-PCR/RT-PCR test and seroconversion test), one positive control (purified from a DENV culture), one negative control (blank), and an in vitro spiked sample containing the 4 DENV serotypes.The third dataset contains publicly available sequences, both from shotgun and targeted metagenomics, containing 45 CHIKV, 66 ZKV, and 21 YFV samplesThe analyses were executed with the default resources and parameters, with the option to include NCBI references and the closest typing reference in the final tree set to true on the shotgun metagenomics dataset. The resulting HTML reports for all analysis are available as compressed files. To open the report in your default browser uncompress the folders and open the pipeline_report.html file inside.
DOI: 10.6084/m9.figshare.9318851.v1
title: DEN-IM's reports on shotgun and targeted metagenomics datasets

description: To evaluate the DEN-IM’s workflow performance, we analysed two datasets, one containing shotgun metagenomics sequencing data of patient samples, and a second with targeted metagenomics sequencing data obtained from PRJNA394021. The shotgun metagenomic dataset comprised of 22 shotgun metagenomics paired-end short-read Illumina sequencing samples datasets from clinical positive dengue cases (identified as such by a positive qRT-PCR/RT-PCR test and seroconversion test), one positive control (purified from a DENV culture), one negative control (blank), and an in vitro spiked sample containing the 4 DENV serotypes.<br>The analyses were executed with the default resources and parameters, with the option to include the closest typing reference in the final tree set to true on the shotgun metagenomics dataset. The resulting HTML reports for both analysis are available as compressed files.
DOI: 10.6084/m9.figshare.9317432
title: Data Volleyball Study

description: Data colums 1-14 contain demographic information related to participants (e.g., gender, age, handedness, volleyball league played etc.). Then, their scores on the MRF 3 are reported prior to receiving the PPR (PreWorried, PreTense, PreNotConfident) and after receiving the PPR (PostWorried, PostTense, PostNotConfident). Thereupon, accuracy scores for the serves prior to PPR are provided (PreShot1-10). The lower the score, the less the distance to the target. These scores are followed by the numbers of errors made prior to PPR use (PreOuts, PreNetzs, Pre_Errors). Accuracy scores for the serves after the routine are provided (PostShot1-10) and agin errors after PPR use (PostOuts, PostNets, Post_Errors). After this, the average accuracy prior to PPR (PreShotsDis) and after PPR (PostShotsDis) as well as SDs for both are provided (PreShotsSD, PostShotsSD). Last summarized anxiety scores for the MRF 3 (anxiety_pre, anxiety_post) and number of errors per player (Errors) are presented.
DOI: 10.6084/m9.figshare.9318851.v2
title: DEN-IM: Dengue virus genotyping from shotgun and targeted metagenomics - HTML reports

description: To evaluate the DEN-IM’s workflow performance, we analysed two datasets, one containing shotgun metagenomics sequencing data of patient samples, and a second with targeted metagenomics sequencing data obtained from PRJNA394021. The shotgun metagenomic dataset comprised of 22 shotgun metagenomics paired-end short-read Illumina sequencing samples datasets from clinical positive dengue cases (identified as such by a positive qRT-PCR/RT-PCR test and seroconversion test), one positive control (purified from a DENV culture), one negative control (blank), and an in vitro spiked sample containing the 4 DENV serotypes.The third dataset contains publicly available sequences, both from shotgun and targeted metagenomics, containing 4 CHIKV, 16 ZKV, and 21 YFV samples<br>The analyses were executed with the default resources and parameters, with the option to include NCBI references and the closest typing reference in the final tree set to true on the shotgun metagenomics dataset. The resulting HTML reports for all analysis are available as compressed files.
DOI: 10.6084/m9.figshare.9318851.v4
title: DEN-IM: Dengue virus genotyping from amplicon and shotgun metagenomics - HTML reports

description: To evaluate the DEN-IM’s workflow performance, we analysed two datasets, one containing shotgun metagenomics sequencing data of patient samples, and a second with targeted metagenomics sequencing data obtained from PRJNA394021 ( 106 paired-end samples) and PRJNA321963 (78 single-end samples). The shotgun metagenomic dataset comprised of 22 shotgun metagenomics paired-end short-read Illumina sequencing samples datasets from clinical positive dengue cases (identified as such by a positive qRT-PCR/RT-PCR test and seroconversion test), one positive control (purified from a DENV culture), one negative control (blank), and an in vitro spiked sample containing the 4 DENV serotypes.The third dataset contains publicly available sequences, both from shotgun and targeted metagenomics, containing 45 CHIKV, 66 ZKV, and 21 YFV samplesThe analyses were executed with the default resources and parameters, with the option to include NCBI references and the closest typing reference in the final tree set to true on the shotgun metagenomics dataset. The resulting HTML reports for all analysis are available as compressed files. To open the report in your default browser uncompress the folders and open the pipeline_report.html file inside.