cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7429601.v1
title: Optimizing Sedative Dose in Preterm Infants Undergoing Treatment for Respiratory Distress Syndrome

description: The intubation-surfactant-extubation (INSURE) procedure is used worldwide to treat preterm newborn infants suffering from respiratory distress syndrome, which is caused by an insufficient amount of the chemical surfactant in the lungs. With INSURE, the infant is intubated, surfactant is administered via the tube to the trachea, and at completion the infant is extubated. This improves the infant’s ability to breathe and thus decreases the risk of long-term neurological or motor disabilities. To perform the intubation safely, the newborn infant first must be sedated. Despite extensive experience with INSURE, there is no consensus on what sedative dose is best. This article describes a Bayesian sequentially adaptive design for a multi-institution clinical trial to optimize the sedative dose given to preterm infants undergoing the INSURE procedure. The design is based on three clinical outcomes, two efficacy and one adverse, using elicited numerical utilities of the eight possible elementary outcomes. A flexible Bayesian parametric trivariate dose-outcome model is assumed, with the prior derived from elicited mean outcome probabilities. Doses are chosen adaptively for successive cohorts of infants using posterior mean utilities, subject to safety and efficacy constraints. A computer simulation study of the design is presented. Supplementary materials for this article are available online.
DOI: 10.7284/133309
title: Meteorological Station data collected during research cruise NA112 using a Coastal Weatherpak-2000 instrument system onboard the platform EV Nautilus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7429598.v2
title: Early administration of Fab antivenom resulted in faster limb recovery in copperhead snake envenomation patients

description: <b>Background:</b> No previous research has studied whether early snake antivenom administration leads to better clinical outcomes than late antivenom administration in North American pit viper envenomation. <b>Methods</b>: A secondary analysis of data from a clinical trial of Fab antivenom (FabAV) versus placebo for copperhead snake envenomation was conducted. Patients treated before the median time to FabAV administration were classified as receiving early treatment and those treated after the median time were defined as the late treatment group. A Cox proportional hazards model was used to compare time to full recovery on the Patient-Specific Functional Scale (PSFS) instrument between groups. Secondary analyses compared estimated mean PSFS scores using a generalized linear model and the estimated proportion of patients with full recovery at each time point using logistic regression. To evaluate for confounding, the main analysis was repeated using data from placebo-treated subjects. <b>Results</b>: Forty-five subjects were treated with FabAV at a median of 5.47 h after envenomation. Patients in the early treatment group had a significantly shorter time to full recovery than those treated late (median time: 17 versus 28 days, <i>p</i> = .025). Model-estimated PSFS scores were numerically higher at each time point in the early group. No difference was found between patients treated early versus late with placebo. <b>Conclusions</b>: In this secondary analysis of trial data, recovery of limb function was faster when Fab antivenom was administered soon after envenomation, as opposed to late administration.
DOI: 10.6084/m9.figshare.7429598.v1
title: Early administration of Fab antivenom resulted in faster limb recovery in copperhead snake envenomation patients

description: <b>Background:</b> No previous research has studied whether early snake antivenom administration leads to better clinical outcomes than late antivenom administration in North American pit viper envenomation. <b>Methods</b>: A secondary analysis of data from a clinical trial of Fab antivenom (FabAV) versus placebo for copperhead snake envenomation was conducted. Patients treated before the median time to FabAV administration were classified as receiving early treatment and those treated after the median time were defined as the late treatment group. A Cox proportional hazards model was used to compare time to full recovery on the Patient-Specific Functional Scale (PSFS) instrument between groups. Secondary analyses compared estimated mean PSFS scores using a generalized linear model and the estimated proportion of patients with full recovery at each time point using logistic regression. To evaluate for confounding, the main analysis was repeated using data from placebo-treated subjects. <b>Results</b>: Forty-five subjects were treated with FabAV at a median of 5.47 h after envenomation. Patients in the early treatment group had a significantly shorter time to full recovery than those treated late (median time: 17 versus 28 days, <i>p</i> = .025). Model-estimated PSFS scores were numerically higher at each time point in the early group. No difference was found between patients treated early versus late with placebo. <b>Conclusions</b>: In this secondary analysis of trial data, recovery of limb function was faster when Fab antivenom was administered soon after envenomation, as opposed to late administration.
DOI: 10.7284/133304
title: Multibeam Echosounder data collected during research cruise NA112 using a Kongsberg EM302 instrument system onboard the platform EV Nautilus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7429577
title: Generalized entropy production analysis for mechanism reduction

description: The paper introduces a generalized formulation for the computation of the relative contribution of each elementary reaction to the total entropy production, which has been proposed as a measure of the importance of elementary reactions and used for the reduction of detailed chemical reaction mechanisms. The reduction method is extended for the cases where the principle of detailed balance does not hold or apply, namely in the case of irreversible reactions or when the reverse rate constants are not computed via the thermodynamic equilibrium constants. Using a mechanism for <i>n</i>-butane consisting exclusively of reversible reactions, the new formulation is compared to the original one, and then applied for the construction of a skeletal mechanism for <i>n</i>-dodecane starting from a detailed mechanism which includes predominantly irreversible reactions. The skeletal scheme is found to accurately capture the ignition delay times over an extended range of pressure, initial temperature and equivalence ratio, the steady-state temperature as function of the residence time in a non-isothermal adiabatic perfectly stirred reactor, and the laminar flame speed of atmospheric flames at different unburned mixture temperatures and equivalence ratios.
DOI: 10.6084/m9.figshare.7429559
title: Increasing Your Research's Exposure on Figshare Using the FAIR Data Principles

description: The FAIR principles were published in 2016 in a Scientific Data article titled ‘FAIR Guiding Principles for scientific data management and stewardship’. These were developed to aid in the discovery and reuse of research data.<br>FAIR stands for Findable, Accessible, Interoperable, and Reusable. Data that meet these principles are more optimal for reuse and discoverability and in turn increase your research’s exposure.<br>Here’s how your data is more FAIR when it’s on Figshare.<br>Illustration by Jason McDermott of RedPenBlackPen.
DOI: 10.6084/m9.figshare.7429595
title: Whole genome sequencing, Amblyseius swirskii pooled population, ONT MinION -- ONT data I2 run 1 part II fast5

description: ReadMe: ONT data I2 runKim Ferguson, kim.ferguson@wur.nl or kfergy@gmail.comWageningen University and Research<br>This ReadMe file is for all files associated with this project, and is present in each data package.<br>There are five .tar file sets in total available on figshare:&gt; 20171130_1637_FAH35464_I2_run 1 part I fast5.tar&gt; 20171130_1637_FAH35464_I2_run 1 part II fast5.tar&gt; 20171201_0934_FAH35464_I2_run 1 restart 1 fast5.tar&gt; 20171201_0954_FAH35464_I2_run 1 restart 2 nobasecalling fast5.tar&gt; ONT data I2 run fastq.tar<br>Read creation dates: 30-11-2017 and 01-12-2017Albacore run date: 04-12-2017<br>Organism: Amblyseius swirskiiPopulation: Koppert biocontrol population, inbred for 10 generationsCollected: &gt;1000 individuals for DNA extraction, males, females, juveniles, placed in 96% EtOHContamination: Collected with food source, pollen from Typha latifolia, and likely was part of DNA extractionExtraction protocol: QIAGEN MagAttract HMW DNA Kit (QIAGEN) according to the manual, while the final DNA product was eluted with nuclease free waterSequenced using ONT MinION sequencing technology<br>MinION model: MinION Mk1BFlowcell: FAH35464 FLO-MIN107 R9.5Ligation kit: Ligation Sequencing Kit version 108 (SQK-LSK108) (no genomic shearing)MinKNOW: version 1.10.16Reads that were basecalled in the cloud: &gt; /20171130_1635_FAH35464_I2_run 1 mux&gt; /20171130_1635_FAH35464_I2_run 1 full&gt; /20171130_1635_FAH35464_I2_run 1 restart 1 mux&gt; /20171130_1635_FAH35464_I2_run 1 restart 1 fullReads that were basecalled using Albacore (version 2.1.3):&gt; /20171201_0952_FAH35464_I2_run 1 restart 2 nobasecalling mux&gt; /20171201_0954_FAH35464_I2_run 1 restart 2 nobasecalling fullAlbacore results:&gt; /basecalled_reads 20171201_0952_FAH35464_I2_run 1 restart 3 nobasecalling mux&gt; /basecalled_reads 20171201_0954_FAH35464_I2_run 1 restart 3 nobasecalling full<br>Data further used in Paspati et al, in prep<br>Fun facts:<br>Files have been separated into fast5 and fastq files, with additional splitting into parts I and II for "/20171130_1635_FAH35464_I2_run 1 full" due to size. Each fast5 folder has been uploaded separateley<br>fast5 folders are often separated into Fail, Pass, and Skip, this is related to the cloud basecalling by the MinKNOW program, based on initial and ongoing quality assessments.<br>fastq folders and files would be considered raw and uncorrected, and were either basecalled in th cloud or using Albacore (see below). All fastq folders have been compressed and uploaded together.<br>There are two restarts in this sequencing run, due to MinKNOW crashing, either after a few hours or overnight. After the second crash, we decided to switch to no basecalling in hope that this would solve the issues.
DOI: 10.7284/133305
title: Multibeam Echosounder data collected during research cruise NA112 using a Kongsberg EM302 instrument system onboard the platform EV Nautilus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7429577.v1
title: Generalized entropy production analysis for mechanism reduction

description: The paper introduces a generalized formulation for the computation of the relative contribution of each elementary reaction to the total entropy production, which has been proposed as a measure of the importance of elementary reactions and used for the reduction of detailed chemical reaction mechanisms. The reduction method is extended for the cases where the principle of detailed balance does not hold or apply, namely in the case of irreversible reactions or when the reverse rate constants are not computed via the thermodynamic equilibrium constants. Using a mechanism for <i>n</i>-butane consisting exclusively of reversible reactions, the new formulation is compared to the original one, and then applied for the construction of a skeletal mechanism for <i>n</i>-dodecane starting from a detailed mechanism which includes predominantly irreversible reactions. The skeletal scheme is found to accurately capture the ignition delay times over an extended range of pressure, initial temperature and equivalence ratio, the steady-state temperature as function of the residence time in a non-isothermal adiabatic perfectly stirred reactor, and the laminar flame speed of atmospheric flames at different unburned mixture temperatures and equivalence ratios.
DOI: 10.6084/m9.figshare.7429595.v1
title: Whole genome sequencing, Amblyseius swirskii pooled population, ONT MinION -- ONT data I2 run 1 part II fast5

description: ReadMe: ONT data I2 runKim Ferguson, kim.ferguson@wur.nl or kfergy@gmail.comWageningen University and Research<br>This ReadMe file is for all files associated with this project, and is present in each data package.<br>There are five .tar file sets in total available on figshare:&gt; 20171130_1637_FAH35464_I2_run 1 part I fast5.tar&gt; 20171130_1637_FAH35464_I2_run 1 part II fast5.tar&gt; 20171201_0934_FAH35464_I2_run 1 restart 1 fast5.tar&gt; 20171201_0954_FAH35464_I2_run 1 restart 2 nobasecalling fast5.tar&gt; ONT data I2 run fastq.tar<br>Read creation dates: 30-11-2017 and 01-12-2017Albacore run date: 04-12-2017<br>Organism: Amblyseius swirskiiPopulation: Koppert biocontrol population, inbred for 10 generationsCollected: &gt;1000 individuals for DNA extraction, males, females, juveniles, placed in 96% EtOHContamination: Collected with food source, pollen from Typha latifolia, and likely was part of DNA extractionExtraction protocol: QIAGEN MagAttract HMW DNA Kit (QIAGEN) according to the manual, while the final DNA product was eluted with nuclease free waterSequenced using ONT MinION sequencing technology<br>MinION model: MinION Mk1BFlowcell: FAH35464 FLO-MIN107 R9.5Ligation kit: Ligation Sequencing Kit version 108 (SQK-LSK108) (no genomic shearing)MinKNOW: version 1.10.16Reads that were basecalled in the cloud: &gt; /20171130_1635_FAH35464_I2_run 1 mux&gt; /20171130_1635_FAH35464_I2_run 1 full&gt; /20171130_1635_FAH35464_I2_run 1 restart 1 mux&gt; /20171130_1635_FAH35464_I2_run 1 restart 1 fullReads that were basecalled using Albacore (version 2.1.3):&gt; /20171201_0952_FAH35464_I2_run 1 restart 2 nobasecalling mux&gt; /20171201_0954_FAH35464_I2_run 1 restart 2 nobasecalling fullAlbacore results:&gt; /basecalled_reads 20171201_0952_FAH35464_I2_run 1 restart 3 nobasecalling mux&gt; /basecalled_reads 20171201_0954_FAH35464_I2_run 1 restart 3 nobasecalling full<br>Data further used in Paspati et al, in prep<br>Fun facts:<br>Files have been separated into fast5 and fastq files, with additional splitting into parts I and II for "/20171130_1635_FAH35464_I2_run 1 full" due to size. Each fast5 folder has been uploaded separateley<br>fast5 folders are often separated into Fail, Pass, and Skip, this is related to the cloud basecalling by the MinKNOW program, based on initial and ongoing quality assessments.<br>fastq folders and files would be considered raw and uncorrected, and were either basecalled in th cloud or using Albacore (see below). All fastq folders have been compressed and uploaded together.<br>There are two restarts in this sequencing run, due to MinKNOW crashing, either after a few hours or overnight. After the second crash, we decided to switch to no basecalling in hope that this would solve the issues.
DOI: 10.6084/m9.figshare.7429556
title: Whole genome sequencing, Amblyseius swirskii pooled population, ONT MinION -- ONT data I2 run 1 part I fast5

description: ReadMe: ONT data I2 runKim Ferguson, kim.ferguson@wur.nl or kfergy@gmail.comWageningen University and Research<br>This ReadMe file is for all files associated with this project, and is present in each data package.<br>There are five .tar file sets in total available on figshare:&gt; 20171130_1637_FAH35464_I2_run 1 part I fast5.tar&gt; 20171130_1637_FAH35464_I2_run 1 part II fast5.tar&gt; 20171201_0934_FAH35464_I2_run 1 restart 1 fast5.tar&gt; 20171201_0954_FAH35464_I2_run 1 restart 2 nobasecalling fast5.tar&gt; ONT data I2 run fastq.tar<br>Read creation dates: 30-11-2017 and 01-12-2017Albacore run date: 04-12-2017<br>Organism: Amblyseius swirskiiPopulation: Koppert biocontrol population, inbred for 10 generationsCollected: &gt;1000 individuals for DNA extraction, males, females, juveniles, placed in 96% EtOHContamination: Collected with food source, pollen from Typha latifolia, and likely was part of DNA extractionExtraction protocol: QIAGEN MagAttract HMW DNA Kit (QIAGEN) according to the manual, while the final DNA product was eluted with nuclease free waterSequenced using ONT MinION sequencing technology<br>MinION model: MinION Mk1BFlowcell: FAH35464 FLO-MIN107 R9.5Ligation kit: Ligation Sequencing Kit version 108 (SQK-LSK108) (no genomic shearing)MinKNOW: version 1.10.16Reads that were basecalled in the cloud: &gt; /20171130_1635_FAH35464_I2_run 1 mux&gt; /20171130_1635_FAH35464_I2_run 1 full&gt; /20171130_1635_FAH35464_I2_run 1 restart 1 mux&gt; /20171130_1635_FAH35464_I2_run 1 restart 1 fullReads that were basecalled using Albacore (version 2.1.3):&gt; /20171201_0952_FAH35464_I2_run 1 restart 2 nobasecalling mux&gt; /20171201_0954_FAH35464_I2_run 1 restart 2 nobasecalling fullAlbacore results:&gt; /basecalled_reads 20171201_0952_FAH35464_I2_run 1 restart 3 nobasecalling mux&gt; /basecalled_reads 20171201_0954_FAH35464_I2_run 1 restart 3 nobasecalling full<br>Data further used in Paspati et al, in prep<br>Fun facts:<br>Files have been separated into fast5 and fastq files, with additional splitting into parts I and II for "/20171130_1635_FAH35464_I2_run 1 full" due to size. Each fast5 folder has been uploaded separateley<br>fast5 folders are often separated into Fail, Pass, and Skip, this is related to the cloud basecalling by the MinKNOW program, based on initial and ongoing quality assessments.<br>fastq folders and files would be considered raw and uncorrected, and were either basecalled in th cloud or using Albacore (see below). All fastq folders have been compressed and uploaded together.<br>There are two restarts in this sequencing run, due to MinKNOW crashing, either after a few hours or overnight. After the second crash, we decided to switch to no basecalling in hope that this would solve the issues.
DOI: 10.6084/m9.figshare.7429556.v1
title: Whole genome sequencing, Amblyseius swirskii pooled population, ONT MinION -- ONT data I2 run 1 part I fast5

description: ReadMe: ONT data I2 runKim Ferguson, kim.ferguson@wur.nl or kfergy@gmail.comWageningen University and Research<br>This ReadMe file is for all files associated with this project, and is present in each data package.<br>There are five .tar file sets in total available on figshare:&gt; 20171130_1637_FAH35464_I2_run 1 part I fast5.tar&gt; 20171130_1637_FAH35464_I2_run 1 part II fast5.tar&gt; 20171201_0934_FAH35464_I2_run 1 restart 1 fast5.tar&gt; 20171201_0954_FAH35464_I2_run 1 restart 2 nobasecalling fast5.tar&gt; ONT data I2 run fastq.tar<br>Read creation dates: 30-11-2017 and 01-12-2017Albacore run date: 04-12-2017<br>Organism: Amblyseius swirskiiPopulation: Koppert biocontrol population, inbred for 10 generationsCollected: &gt;1000 individuals for DNA extraction, males, females, juveniles, placed in 96% EtOHContamination: Collected with food source, pollen from Typha latifolia, and likely was part of DNA extractionExtraction protocol: QIAGEN MagAttract HMW DNA Kit (QIAGEN) according to the manual, while the final DNA product was eluted with nuclease free waterSequenced using ONT MinION sequencing technology<br>MinION model: MinION Mk1BFlowcell: FAH35464 FLO-MIN107 R9.5Ligation kit: Ligation Sequencing Kit version 108 (SQK-LSK108) (no genomic shearing)MinKNOW: version 1.10.16Reads that were basecalled in the cloud: &gt; /20171130_1635_FAH35464_I2_run 1 mux&gt; /20171130_1635_FAH35464_I2_run 1 full&gt; /20171130_1635_FAH35464_I2_run 1 restart 1 mux&gt; /20171130_1635_FAH35464_I2_run 1 restart 1 fullReads that were basecalled using Albacore (version 2.1.3):&gt; /20171201_0952_FAH35464_I2_run 1 restart 2 nobasecalling mux&gt; /20171201_0954_FAH35464_I2_run 1 restart 2 nobasecalling fullAlbacore results:&gt; /basecalled_reads 20171201_0952_FAH35464_I2_run 1 restart 3 nobasecalling mux&gt; /basecalled_reads 20171201_0954_FAH35464_I2_run 1 restart 3 nobasecalling full<br>Data further used in Paspati et al, in prep<br>Fun facts:<br>Files have been separated into fast5 and fastq files, with additional splitting into parts I and II for "/20171130_1635_FAH35464_I2_run 1 full" due to size. Each fast5 folder has been uploaded separateley<br>fast5 folders are often separated into Fail, Pass, and Skip, this is related to the cloud basecalling by the MinKNOW program, based on initial and ongoing quality assessments.<br>fastq folders and files would be considered raw and uncorrected, and were either basecalled in th cloud or using Albacore (see below). All fastq folders have been compressed and uploaded together.<br>There are two restarts in this sequencing run, due to MinKNOW crashing, either after a few hours or overnight. After the second crash, we decided to switch to no basecalling in hope that this would solve the issues.
DOI: 10.7284/133306
title: Singlebeam Echosounder data collected during research cruise NA112 using a Knudsen 3260 instrument system onboard the platform EV Nautilus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7429559.v1
title: Increasing Your Research's Exposure on Figshare Using the FAIR Data Principles

description: In 2016, Force11 - a community of scholars, librarians, archivists, publishers and research funders that help facilitate change toward improved knowledge creation and sharing in research - developed the FAIR data principles to aid in the discovery and reuse of research data.<br>FAIR stands for Findable, Accessible, Interoperable, and Reusable. Data that meet these principles are more optimal for reuse and discoverability and in turn increase your research’s exposure.<br>Here’s how your data is more FAIR when it’s on Figshare.<br>Illustration by Jason McDermott of RedPenBlackPen.
DOI: 10.6084/m9.figshare.7429520
title: Additional file 3: of Assessment of HIV prevalence among MSM in Tokyo using self-collected dried blood spots delivered through the postal service

description: Table S2A. The intra-assay valiability. Table S2B. The inter-assay valiability. Table S2C. Sensitivity analysis with diluted samples. Table S2D. Association of C.O.I using eluted DBS and serum sample. (ZIP 31 kb)
DOI: 10.7284/133302
title: SSV (Sound Speed Velocimeter) data collected during research cruise NA112 using a AML SVXchange instrument system onboard the platform EV Nautilus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7429520.v1
title: Additional file 3: of Assessment of HIV prevalence among MSM in Tokyo using self-collected dried blood spots delivered through the postal service

description: Table S2A. The intra-assay valiability. Table S2B. The inter-assay valiability. Table S2C. Sensitivity analysis with diluted samples. Table S2D. Association of C.O.I using eluted DBS and serum sample. (ZIP 31 kb)
DOI: 10.7284/133315
title: Expendable Probe data collected during research cruise NA114 using a Sippican MK21 instrument system onboard the platform EV Nautilus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/133311
title: INS (Inertial Navigation System) data collected during research cruise NA114 using a Kongsberg Seatex MRU-5 instrument system onboard the platform EV Nautilus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7429490
title: Additional file 2: of Differentiation of haploid and diploid fertilities in Gracilaria chilensis affect ploidy ratio

description: All.mat. (MAT 64 kb)
DOI: 10.7284/133316
title: INS (Inertial Navigation System) data collected during research cruise NA114 using a Kongsberg Seapath 330+ instrument system onboard the platform EV Nautilus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7429490.v1
title: Additional file 2: of Differentiation of haploid and diploid fertilities in Gracilaria chilensis affect ploidy ratio

description: All.mat. (MAT 64 kb)