cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.11379744
title: Supplementary Material for: Effect of Transcranial Alternating Current Stimulation for the Treatment of Chronic Insomnia: A Randomized, Double-Blind, Parallel-Group, Placebo-Controlled Clinical Trial

description: <b><i>Background:</i></b> Not all adults with chronic insomnia respond to the recommended therapeutic options of cognitive behavioral therapy and approved hypnotic drugs. Transcranial alternating current stimulation (tACS) may offer a novel potential treatment modality for insomnia. <b><i>Objectives:</i></b> This study aimed to examine the efficacy and safety of tACS for treating adult patients with chronic insomnia. <b><i>Methods:</i></b> Sixty-two participants with chronic primary insomnia received 20 daily 40-min, 77.5-Hz, 15-mA sessions of active or sham tACS targeting the forehead and both mastoid areas in the laboratory on weekdays for 4 consecutive weeks, followed by a 4-week follow-up period. The primary outcome was response rate measured by the Pittsburgh Sleep Quality Index (PSQI) at week 8. Secondary outcomes were remission rate, insomnia severity, sleep onset latency (SOL), total sleep time (TST), sleep efficiency, sleep quality, daily disturbances, and adverse events at the end of the 4-week intervention and at the 4-week follow-up. <b><i>Results:</i></b> Of 62 randomized patients, 60 completed the trial. During the 4-week intervention, 1 subject per group withdrew due to loss of interest and time restriction, respectively. Based on PSQI, at 4-week follow-up, the active group had a higher response rate compared to the sham group (53.4% [16/30] vs. 16.7% [5/30], <i>p</i> = 0.009), but remission rates were not different between groups. At the end of the 4-week intervention, the active group had higher response and remission rates than the sham group (<i>p</i> &lt; 0.001 and <i>p</i> = 0.026, respectively). During the trial, compared with the sham group, the active group showed a statistically significant decrease in PSQI total score, a shortened SOL, an increased TST, improved sleep efficiency, and improved sleep quality (<i>p</i> &lt; 0.05 or <i>p</i> &lt; 0.001). Post hoc analysis revealed that, in comparison with the sham group, the active group had improved symptoms, except for daily disturbances, at the end of the 4-week intervention, and significant improvements in all symptoms at the 4-week follow-up. No adverse events or serious adverse responses occurred during the study. <b><i>Conclusion:</i></b> The findings show that the tACS applied in the present study has potential as an effective and safe intervention for chronic insomnia within 8 weeks.
DOI: 10.6084/m9.figshare.11379753
title: Extended Data Table S2

description: Extended Data Table S2 for the mSWEEP manuscript.
DOI: 10.6084/m9.figshare.11379762.v1
title: Extended Data Table S4

description: Extended Data Table S4 for the mSWEEP manuscript.
DOI: 10.6084/m9.figshare.11379705.v1
title: Extended Data Table S1

description: Extended Data Table S1 for the mSWEEP manuscript.
DOI: 10.6084/m9.figshare.11379744.v1
title: Supplementary Material for: Effect of Transcranial Alternating Current Stimulation for the Treatment of Chronic Insomnia: A Randomized, Double-Blind, Parallel-Group, Placebo-Controlled Clinical Trial

description: <b><i>Background:</i></b> Not all adults with chronic insomnia respond to the recommended therapeutic options of cognitive behavioral therapy and approved hypnotic drugs. Transcranial alternating current stimulation (tACS) may offer a novel potential treatment modality for insomnia. <b><i>Objectives:</i></b> This study aimed to examine the efficacy and safety of tACS for treating adult patients with chronic insomnia. <b><i>Methods:</i></b> Sixty-two participants with chronic primary insomnia received 20 daily 40-min, 77.5-Hz, 15-mA sessions of active or sham tACS targeting the forehead and both mastoid areas in the laboratory on weekdays for 4 consecutive weeks, followed by a 4-week follow-up period. The primary outcome was response rate measured by the Pittsburgh Sleep Quality Index (PSQI) at week 8. Secondary outcomes were remission rate, insomnia severity, sleep onset latency (SOL), total sleep time (TST), sleep efficiency, sleep quality, daily disturbances, and adverse events at the end of the 4-week intervention and at the 4-week follow-up. <b><i>Results:</i></b> Of 62 randomized patients, 60 completed the trial. During the 4-week intervention, 1 subject per group withdrew due to loss of interest and time restriction, respectively. Based on PSQI, at 4-week follow-up, the active group had a higher response rate compared to the sham group (53.4% [16/30] vs. 16.7% [5/30], <i>p</i> = 0.009), but remission rates were not different between groups. At the end of the 4-week intervention, the active group had higher response and remission rates than the sham group (<i>p</i> &lt; 0.001 and <i>p</i> = 0.026, respectively). During the trial, compared with the sham group, the active group showed a statistically significant decrease in PSQI total score, a shortened SOL, an increased TST, improved sleep efficiency, and improved sleep quality (<i>p</i> &lt; 0.05 or <i>p</i> &lt; 0.001). Post hoc analysis revealed that, in comparison with the sham group, the active group had improved symptoms, except for daily disturbances, at the end of the 4-week intervention, and significant improvements in all symptoms at the 4-week follow-up. No adverse events or serious adverse responses occurred during the study. <b><i>Conclusion:</i></b> The findings show that the tACS applied in the present study has potential as an effective and safe intervention for chronic insomnia within 8 weeks.
DOI: 10.6084/m9.figshare.11379402
title: Supplementary Material for: Hourly Fluid Balance in Patients Receiving Continuous Renal Replacement Therapy

description: <b><i>Introduction:</i></b> Little is known about early (first 48 h) hourly and cumulative fluid balance (FB) during continuous renal replacement therapy (CRRT). <b><i>Objectives:</i></b> To study the characteristics and outcome associations of early hourly and cumulative FB. <b><i>Methods:</i></b> We studied FB in CRRT patients (2016–2018). <b><i>Results:</i></b> Among 350 patients, mean hourly FB became negative after 20 CRRT hours, but within 6 CRRT hours in patients with baseline fluid overload. A negative early FB was never achieved in patients receiving vasopressor therapy (<i>p</i> &lt; 0.001). Mortality was 31%. The percentage of hourly negative FB was independently associated with decreased ICU mortality. A time-weighted hourly FB between 18.5 and –33 mL/h was also significantly and independently associated with decreased mortality. <b><i>Conclusions:</i></b> In CRRT patients, an early FB conservative approach is possible, modulated by patient characteristics, and associated with a low mortality. Moreover, avoidance of an early positive FB is associated with decreased mortality.
DOI: 10.6084/m9.figshare.11379120
title: Data for "Suggesting Comment Completions for Python Using Neural Language Models"

description: Data used for training and evaluating the ML models presented in the "Suggesting Comment Completions for Python Using Neural Language Models" paper (SANER 2020).
DOI: 10.6084/m9.figshare.11379126
title: Interviews Scrn + BIT Students (acknowledgements)

description: Reference of the acknowledgements. We thank the people we were involved in this research.
DOI: 10.6084/m9.figshare.11379120.v1
title: Data for "Suggesting Comment Completions for Python Using Neural Language Models"

description: Data used for training and evaluating the ML models presented in the "Suggesting Comment Completions for Python Using Neural Language Models" paper (SANER 2020).
DOI: 10.6084/m9.figshare.11379084
title: Help sheet usability test

description: This sheet was allowed to be used during the usability test of the interactive prototype dashboard
DOI: 10.6084/m9.figshare.11379126.v1
title: Interviews Scrn + BIT Students (acknowledgements)

description: Reference of the acknowledgements. We thank the people we were involved in this research.
DOI: 10.6084/m9.figshare.11379039
title: Format notes usability test

description: This format was used to take notes during the usability test
DOI: 10.6084/m9.figshare.11379084.v1
title: Help sheet usability test

description: This sheet was allowed to be used during the usability test of the interactive prototype dashboard
DOI: 10.6084/m9.figshare.11379021
title: Paper Prototype Evaluation PO Pivotal Tracker

description: An interview held with a PO to evaluate the paper prototype.
DOI: 10.6084/m9.figshare.11379051
title: The usability test and results

description: This is the usability test of the research, with the results in a spreadsheet.
DOI: 10.6084/m9.figshare.11379021.v1
title: Paper Prototype Evaluation PO Pivotal Tracker

description: An interview held with a PO to evaluate the paper prototype.
DOI: 10.6084/m9.figshare.11379039.v1
title: Format notes usability test

description: This format was used to take notes during the usability test
DOI: 10.6084/m9.figshare.11379051.v1
title: The usability test and results

description: This is the usability test of the research, with the results in a spreadsheet.
DOI: 10.6084/m9.figshare.11378955
title: Pre-design interview PO Pivotal Tracker

description: Interview held with a PO which uses Pivotal Tracker, to verify the framework and form a basis on the design of the paper prototype.
DOI: 10.6084/m9.figshare.11378955.v1
title: Pre-design interview PO Pivotal Tracker

description: Interview held with a PO which uses Pivotal Tracker, to verify the framework and form a basis on the design of the paper prototype.
DOI: 10.6084/m9.figshare.11378847
title: figshare.tar.gz

description: MAGs associated with the pre-print entitled: "Near-complete Lokiarchaeota genomes from complex environmental samples using long and short read metagenomic analyses"<br>This entry includes Lokiarchaeota MAGs obtained from hybrid assemblies using both short- and long-read metagenomics (Illumina and Nanopore data). <br>Note that the data included here might change before the final publication.
DOI: 10.6084/m9.figshare.11378802
title: Supplementary Material for: Kommunikation entlang der Behandlungsmeilensteine bei Patienten mit fortgeschrittenem Lungenkrebs

description: Patienten mit fortgeschrittenem Lungenkrebs und ihre Betreuungspersonen sind mit einer komplexen Situation konfrontiert, da ihre krankheitsbezogene Belastung physische, psychosoziale und spirituelle Bedürfnisse umfasst. Im Verlauf ihrer Krankheit, die mit einer begrenzten Prognose verbunden ist, sind sie verschiedenen multidisziplinären Gesundheitssystemumfeldern und -anbietern ausgesetzt, was eine kontinuierliche und koordinierte Versorgung erschwert. Darüber hinaus stellt die Entscheidung zwischen aktiver Krebstherapie und End-of-Life-Care einen ständigen Balanceakt dar. Mehrere Studien haben gezeigt, dass eine frühzeitige Palliativversorgung und entsprechendes Advance Care Planning die Lebensqualität und die Zufriedenheit mit der Versorgung verbessern. Für diese Strategie müssen die Kommunikationsfähigkeiten der Gesundheitsdienstleister und die interprofessionelle Zusammenarbeit gestärkt werden. Ein longitudinal strukturierter Kommunikationsansatz entlang der wichtigen Meilensteine der Erkrankung kann die Patienten unterstützen, da er die Bewältigung erleichtert, das prognostische Bewusstsein fördert und eine frühzeitige palliative Versorgung sowie Advance Care Planning ermöglicht. Gute interprofessionelle Zusammenarbeit und Kommunikation führen zu einer besseren Koordination und Kontinuität der Versorgung.
DOI: 10.6084/m9.figshare.11378802.v1
title: Supplementary Material for: Kommunikation entlang der Behandlungsmeilensteine bei Patienten mit fortgeschrittenem Lungenkrebs

description: Patienten mit fortgeschrittenem Lungenkrebs und ihre Betreuungspersonen sind mit einer komplexen Situation konfrontiert, da ihre krankheitsbezogene Belastung physische, psychosoziale und spirituelle Bedürfnisse umfasst. Im Verlauf ihrer Krankheit, die mit einer begrenzten Prognose verbunden ist, sind sie verschiedenen multidisziplinären Gesundheitssystemumfeldern und -anbietern ausgesetzt, was eine kontinuierliche und koordinierte Versorgung erschwert. Darüber hinaus stellt die Entscheidung zwischen aktiver Krebstherapie und End-of-Life-Care einen ständigen Balanceakt dar. Mehrere Studien haben gezeigt, dass eine frühzeitige Palliativversorgung und entsprechendes Advance Care Planning die Lebensqualität und die Zufriedenheit mit der Versorgung verbessern. Für diese Strategie müssen die Kommunikationsfähigkeiten der Gesundheitsdienstleister und die interprofessionelle Zusammenarbeit gestärkt werden. Ein longitudinal strukturierter Kommunikationsansatz entlang der wichtigen Meilensteine der Erkrankung kann die Patienten unterstützen, da er die Bewältigung erleichtert, das prognostische Bewusstsein fördert und eine frühzeitige palliative Versorgung sowie Advance Care Planning ermöglicht. Gute interprofessionelle Zusammenarbeit und Kommunikation führen zu einer besseren Koordination und Kontinuität der Versorgung.
DOI: 10.6084/m9.figshare.11378796
title: Supplementary Material for: Duktales Adenokarzinom des Pankreas: biologische Merkmale, Stand der Dinge und Ausblick auf multimodale Behandlungsansätze der Zukunft

description: Das duktale Adenokarzinom des Pankreas (PDAC) ist eine verheerende Erkrankung mit schlechter Prognose und steigender Inzidenz. Diagnostizierung in späten Stadien und eine besonders aggressive Tumorbiologie sind die wichtigsten Herausforderungen und Faktoren für die therapeutische Erfolglosigkeit. In der vorliegenden Arbeit geben wir einen Überblick über den gegenwärtigen Stand der Dinge und aktuelle Fortschritte der PDAC-Therapie und beschreiben die biologischen und immunologischen Hauptmerkmal dieser Krebsentität. Darauf aufbauend stellen wir neuartige Therapieansätze vor, die unterschiedliche Modalitäten miteinander kombinieren, um die therapeutische Wirksamkeit und das klinische Outcome zu verbessern, mit besonderem Schwerpunkt auf Protokollen mit Beteiligung einer Radio(chemo)therapie.
DOI: 10.6084/m9.figshare.11378796.v1
title: Supplementary Material for: Duktales Adenokarzinom des Pankreas: biologische Merkmale, Stand der Dinge und Ausblick auf multimodale Behandlungsansätze der Zukunft

description: Das duktale Adenokarzinom des Pankreas (PDAC) ist eine verheerende Erkrankung mit schlechter Prognose und steigender Inzidenz. Diagnostizierung in späten Stadien und eine besonders aggressive Tumorbiologie sind die wichtigsten Herausforderungen und Faktoren für die therapeutische Erfolglosigkeit. In der vorliegenden Arbeit geben wir einen Überblick über den gegenwärtigen Stand der Dinge und aktuelle Fortschritte der PDAC-Therapie und beschreiben die biologischen und immunologischen Hauptmerkmal dieser Krebsentität. Darauf aufbauend stellen wir neuartige Therapieansätze vor, die unterschiedliche Modalitäten miteinander kombinieren, um die therapeutische Wirksamkeit und das klinische Outcome zu verbessern, mit besonderem Schwerpunkt auf Protokollen mit Beteiligung einer Radio(chemo)therapie.
DOI: 10.6084/m9.figshare.11378772
title: Consensus bayesian trees of RhcI T3SS cluster gene families

description: A custom set of 155 genomes was gathered covering 28 different Bradyrhizobium species, as well as selected genomes from the genera Nitrobacter and Rhodopseudomonas as outgroups. Genomes listed in Table S1 were downloaded from NCBI RefSeq or GenBank databases and used as input for the bioinformatic pipeline Pantagruel to build a phylogenomic database. In short, coding sequences (CDS) and the corresponding protein sequences were extracted from the RefSeq or GenBank annotation and then clustered into homologous gene families using MMSeqs2. Homologues were aligned with ClustalOmega and reverse-translated into CDS alignment with PAL2NAL. <br>Bayesian samples of gene trees were inferred from CDS alignments with MrBayes (v 3.2.6) using a Metropolis-coupled Monte-Carlo Markov chain (MCMCMC) approach, with two independent sets of four chains (one cold, three heated) running for 2,000,000 generations and sampled every 500; presented trees are majority-rule consensus trees, discarding the first 25% of the chain as burn-in.<br>Consensus gene trees are presented for gene families with homologs (based on the best BlastP search hit) to the reference CDS sequences in RhcI cluster from <i>Bradyrhizobium japonicum</i> reference strain USDA110, as indicated by the bll/blr locus tag and the corresponding NCBI RefSeq protein identifier.<br><br>
DOI: 10.6084/m9.figshare.11378772.v1
title: Consensus bayesian trees of RhcI T3SS cluster gene families

description: A custom set of 155 genomes was gathered covering 28 different Bradyrhizobium species, as well as selected genomes from the genera Nitrobacter and Rhodopseudomonas as outgroups. Genomes listed in Table S1 were downloaded from NCBI RefSeq or GenBank databases and used as input for the bioinformatic pipeline Pantagruel to build a phylogenomic database. In short, coding sequences (CDS) and the corresponding protein sequences were extracted from the RefSeq or GenBank annotation and then clustered into homologous gene families using MMSeqs2. Homologues were aligned with ClustalOmega and reverse-translated into CDS alignment with PAL2NAL. <br>Bayesian samples of gene trees were inferred from CDS alignments with MrBayes (v 3.2.6) using a Metropolis-coupled Monte-Carlo Markov chain (MCMCMC) approach, with two independent sets of four chains (one cold, three heated) running for 2,000,000 generations and sampled every 500; presented trees are majority-rule consensus trees, discarding the first 25% of the chain as burn-in.<br>Consensus gene trees are presented for gene families with homologs (based on the best BlastP search hit) to the reference CDS sequences in RhcI cluster from <i>Bradyrhizobium japonicum</i> reference strain USDA110, as indicated by the bll/blr locus tag and the corresponding NCBI RefSeq protein identifier.<br><br>
DOI: 10.6084/m9.figshare.11378727
title: Fbxo9 functions downstream of Sox10 to determine neuron-glial fate choice in the dorsal root ganglia through Neurog2 destabilization

description: <b>Dataset S1. </b>RNA-seq dataset normalized to the controlDataset S2. List of up- and down-regulated genes by Sox10 overexpression <br>
DOI: 10.6084/m9.figshare.11378745
title: Comparing laboratory-based and population-based antimicrobial resistance surveillance in urinary tract infections in Indonesia

description: The project assessed the difference in point prevalence of antimicrobial resistance (AMR) when using routine laboratory-based surveillance and active population-based surveillance (survey). The data are restricted to the prevalence of AMR in isolates of<i> Escherichia coli</i> and <i>Klebsiella pneumoniae</i> cultured from urine samples from all patients presenting with signs and/or symptoms of a urinary tract infection in either the outpatient or the inpatient setting. <br><br>Laboratory-based surveillance used Vitek methodology to assess resistance, while the population-based surveillance used the conventional culture methods using MacConkey agar plates incubated for 18 hours. Resistance was defined by applying CLSI breakpoints (2012).. The data from both sources covered exactly the same period (1 April 2014 - 31 May 2015) in which there were no reports of outbreaks in the hospital setting.<br>Data structureThe file is in a .csv format outputted through STATA version 16.0. The dataset is organised in the long format with the combination of the variables ID(), micro-organism(), and antibiotic() identifying a unique record.<br>
DOI: 10.6084/m9.figshare.11378661
title: Supplementary Material for: Cyclooxygenase-2 Gene Polymorphisms –765G&gt;C and –1195A&gt;G and Mycosis Fungoides Risk

description: <b><i>Background:</i></b> Cyclooxygenase-2 (COX-2) is an inducible modulator of inflammation that acts through increasing prostaglandin levels and has been described as a major mediator linking inflammation to cancer. Previous studies supported that COX-2<i></i>–765G&gt;C and –1195A&gt;G polymorphisms were associated with increased risk of several solid tissue cancers as well as some hematological malignancies. <b><i>Objective:</i></b> The aim of the study was to elucidate the association between functional COX-2 genotypes (–765G&gt;C and –1195A&gt;G) polymorphisms and the risk of developing mycosis fungoides (MF). <b><i>Methods:</i></b> This was a hospital-based, case-control study of 70 MF patients and 100 MF-free controls. We genotyped COX-2 –1195A&gt;G, –765G&gt;C, and –8473T&gt;C polymorphisms by using the PCR-restriction fragment length polymorphism method. <b><i>Results:</i></b> The AA genotype in the COX-2 –1195A&gt;G gene polymorphism and the GC genotype in the COX-2 −765G&gt;C gene were significantly more frequent among MF patients compared to controls (<i>p</i>&lt; 0.001 and <i>p</i> = 0.002, respectively). <b><i>Conclusion:</i></b> The ­results indicate a possible role of COX-2 genes in the pathogenesis of MF. These novel findings may allow for notable future advances, as it will enable the identification of the ­individuals most susceptible to MF.
DOI: 10.6084/m9.figshare.11378661.v1
title: Supplementary Material for: Cyclooxygenase-2 Gene Polymorphisms –765G&gt;C and –1195A&gt;G and Mycosis Fungoides Risk

description: <b><i>Background:</i></b> Cyclooxygenase-2 (COX-2) is an inducible modulator of inflammation that acts through increasing prostaglandin levels and has been described as a major mediator linking inflammation to cancer. Previous studies supported that COX-2<i></i>–765G&gt;C and –1195A&gt;G polymorphisms were associated with increased risk of several solid tissue cancers as well as some hematological malignancies. <b><i>Objective:</i></b> The aim of the study was to elucidate the association between functional COX-2 genotypes (–765G&gt;C and –1195A&gt;G) polymorphisms and the risk of developing mycosis fungoides (MF). <b><i>Methods:</i></b> This was a hospital-based, case-control study of 70 MF patients and 100 MF-free controls. We genotyped COX-2 –1195A&gt;G, –765G&gt;C, and –8473T&gt;C polymorphisms by using the PCR-restriction fragment length polymorphism method. <b><i>Results:</i></b> The AA genotype in the COX-2 –1195A&gt;G gene polymorphism and the GC genotype in the COX-2 −765G&gt;C gene were significantly more frequent among MF patients compared to controls (<i>p</i>&lt; 0.001 and <i>p</i> = 0.002, respectively). <b><i>Conclusion:</i></b> The ­results indicate a possible role of COX-2 genes in the pathogenesis of MF. These novel findings may allow for notable future advances, as it will enable the identification of the ­individuals most susceptible to MF.