cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.10295204.v1
title: Sperm Gatekeeping: Data tables and Analysis Script

description: The following files are included: <br> 1) “SpermGatekeeping_fixedSSTs.csv” This data file contains the major axis and minor axis diameters and lengths of SSTs from fixed zebra finch tissue samples imaged with a selective plane illumination microscope (SPIM). Descriptions of variables are included in the R code file “SpermGatekeeping-Mendonca_etal2019.R”. <br> 2) “SpermGatekeeping_LiveSSTs.csv” This data file contains the major axis and minor axis diameters and lengths of SSTs from live zebra finch tissue samples imaged with a selective plane illumination microscope (SPIM). Descriptions of variables are included in the R code file “SpermGatekeeping-Mendonca_etal2019.R”. <br> 3) “SpermGatekeeping_histology.csv” This data file contains measurements of the lumen diameter, inter-nuclear diameter and outer diameter of SSTs from histological sections. Please refer to the Supplementary Materials and Methods file for "Sperm Gatekeeping: 3D imaging reveals a constricted entrance to zebra finch sperm storage tubules" for a description of the measurements. Descriptions of variables are also included in the R code file “Zebra-finch_mid-piece_analysis.r”. <br> 4) “SpermGatekeeping-Mendonca_etal2019.R” This file provides the code for the data analysis reported in the manuscript.<br>
DOI: 10.6084/m9.figshare.10295159.v1
title: Authentication of 4-chloro-3',4'-dihydroxy-biphenyl

description: Authentication of 4-chloro-3',4'-dihydroxy-biphenyl by <sup>1</sup>HNMR and <sup>13</sup>CNMR. It was synthesized from 4-chloro-3',4'-dimethoxy-biphenyl in the presence of BBr<sub>3</sub>.
DOI: 10.6084/m9.figshare.10294937
title: Young adults make rational sexual decisions

description: The ZIP file contains all necessary codes (Matlab and R) and data for reproducing the results from the paper, "Young adults make rational sexual decisions." It also includes the instructions and stimuli we used for the monetary and sex gamble tasks from the paper.<br>The "Online_Instructions.pdf" file provides a step-by-step instruction for readers to reproduce the results.
DOI: 10.6084/m9.figshare.10294895
title: Authentication of 4-chloro-2-methoxy-biphenyl

description: Authentication of 4-chloro-2-methoxy-biphenyl by <sup>1</sup>HNMR, <sup>13</sup>CNMR, and GC-MS. The purity (&gt;99%) of the compound was determined based on relative peak area by GC-MS.<br>
DOI: 10.6084/m9.figshare.10294937.v1
title: Young adults make rational sexual decisions

description: The ZIP file contains all necessary codes (Matlab and R) and data for reproducing the results from the paper, "Young adults make rational sexual decisions." It also includes the instructions and stimuli we used for the monetary and sex gamble tasks from the paper.<br>The "Online_Instructions.pdf" file provides a step-by-step instruction for readers to reproduce the results.
DOI: 10.6084/m9.figshare.10294832
title: Skeletal Muscle Transcriptional Networks Linked to Type I Myofiber Grouping in Parkinson’s Disease • Supplementary Materials

description: Table S1: Characteristics of WGCNA modules generated from skeletal muscle biopsiesTable S2: LightCyan Module Members (n=834)Table S3: SkyBlue Module Members (n=691)Table S4: LightCyan Module HubsTable S5: Genes associated with Percent Type I fibers in groups using single-gene analysis (DESeq2, n = 1911 transcripts)Table S6: SkyBlue Module HubsTable S7: Genes associated with mean type I myofiber group size using single-gene analysis (DESeq2, n = 1153 transcripts)
DOI: 10.6084/m9.figshare.10293677
title: Suppl. Table 4

description: Summary of animal models of non-alcoholic fatty liver disease at pediatric age. HF: High-fat; HFS: High-fat, high-sucrose; HFF: High-fat, high-fructose; HFSC: High-fat, high-sucrose, high-cholesterol; HFFC: High-fat, high-fructose, high-cholesterol; CD: Choline deficient
DOI: 10.6084/m9.figshare.10293929
title: Authentication of 4-chloro-2'-methoxy-biphenyl

description: Authentication of 4-chloro-2'-methoxy-biphenyl by GC-MS. The purity (&gt;99%) of the compound was determined based on relative peak area by GC-MS.<br>
DOI: 10.6084/m9.figshare.10293929.v1
title: Authentication of 4-chloro-2'-methoxy-biphenyl

description: Authentication of 4-chloro-2'-methoxy-biphenyl by GC-MS. The purity (&gt;99%) of the compound was determined based on relative peak area by GC-MS.<br>
DOI: 10.6084/m9.figshare.10293671
title: Suppl. Table 2

description: Target and reference gene primer information for quantitative PCR assays in liver, jejunum, ileum and colon tissue of 83-d-old Iberian pigs fed 1 of the 4 liquid diets: 1) control (CON-N; n = 8, 4 M/4 F), 2) high-fructose high-fat (HFF-N; n = 6, 3M/3F), 3) CON + 6.2 × 10<sup>4</sup> cfu ∙ mL<sup>-1</sup> probiotics (CON-P; n = 8, 5M/3F), and 4) HFF-N + 6.2 × 10<sup>4</sup> cfu ∙ mL<sup>-1</sup> probiotics (HFF-P; n = 6, 3M/3F). Animals were fed 45 mL · kg BW<sup>-1</sup> at 6-h intervals during 10 consecutive weeks.
DOI: 10.6084/m9.figshare.10293674
title: Suppl. Table 1

description: Summary of histological features in livers collected from 83 d-old Iberian pigs fed 1 of the 4 liquid diets: 1) control (CON-N; n = 8), 2) high-fructose high-fat (HFF-N; n = 6), 3) CON + 6.2 × 10<sup>4</sup> cfu ∙ mL<sup>-1</sup> probiotics (CON-P; n = 8), and 4) HFF-N + 6.2 × 10<sup>4</sup> cfu ∙ mL<sup>-1</sup> probiotics (HFF-P; n = 6). The probiotic mixture contained <i>Pediococcus acidilactici</i>, <i>Pediococcus</i> <i>pentosaceus</i>, <i>Lactobacillus plantarum</i> and <i>Bacillus subtilis</i> (MultiBio 3PS; BiOWiSH Technologies, Cincinnati, OH). Animals were fed 45 mL · kg BW<sup>-1</sup> at 6-h intervals during 10 consecutive weeks.
DOI: 10.6084/m9.figshare.10293677.v1
title: Suppl. Table 2.docx

description: Daily nutrient (g ∙ kg body weight (BW)<sup>-1 </sup>· d<sup>-1</sup>) and metabolizable energy (ME; kcal · kg BW<sup>-1 </sup>· d<sup>-1</sup>) of control and high-fructose high-fat diets fed to 13-d old pigs during 10 consecutive weeks. Values are calculated, and expressed <i>as fed</i>.
DOI: 10.6084/m9.figshare.10293671.v1
title: Suppl. Table 3.docx

description: Target and reference gene primer information for quantitative PCR assays in the liver.
DOI: 10.6084/m9.figshare.10293677.v2
title: Suppl. Table 3

description: Summary of animal models of non-alcoholic fatty liver disease at pediatric age. HF: High-fat; HFS: High-fat, high-sucrose; HFF: High-fat, high-fructose; HFSC: High-fat, high-sucrose, high-cholesterol; HFFC: High-fat, high-fructose, high-cholesterol; CD: Choline deficient
DOI: 10.6084/m9.figshare.10293674.v1
title: Suppl Table 1.docx

description: Ingredient composition (%) of control and high-fructose high-fat diets fed to 13-d-old pigs during 10 consecutive weeks.
DOI: 10.6084/m9.figshare.10293677.v3
title: Suppl. Table 5

description: Summary of animal models of non-alcoholic fatty liver disease at pediatric age. HF: High-fat; HFS: High-fat, high-sucrose; HFF: High-fat, high-fructose; HFSC: High-fat, high-sucrose, high-cholesterol; HFFC: High-fat, high-fructose, high-cholesterol; CD: Choline deficient
DOI: 10.6084/m9.figshare.10293671.v2
title: Suppl. Table 2

description: Target and reference gene primer information for quantitative PCR assays in the liver.
DOI: 10.6084/m9.figshare.10293674.v2
title: Suppl. Table 1.docx

description: Summary of histological features in pig livers collected on d 70 of the study.
DOI: 10.6084/m9.figshare.10293671.v3
title: Suppl. Table 2

description: Target and reference gene primer information for quantitative PCR assays in liver, jejunum, ileum and colon tissue of 83-d-old Iberian pigs fed 1 of the 4 liquid diets: 1) control (CON-N; n = 8, 4 M/4 F), 2) high-fructose high-fat (HFF-N; n = 6, 3M/3F), 3) CON + 6.2 × 10<sup>4</sup> cfu ∙ mL<sup>-1</sup> probiotics (CON-P; n = 8, 5M/3F), and 4) HFF-N + 6.2 × 10<sup>4</sup> cfu ∙ mL<sup>-1</sup> probiotics (HFF-P; n = 6, 3M/3F). Animals were fed 45 mL · kg BW<sup>-1</sup> at 6-h intervals during 10 consecutive weeks.
DOI: 10.6084/m9.figshare.10293677.v4
title: Suppl. Table 4

description: Summary of animal models of non-alcoholic fatty liver disease at pediatric age. HF: High-fat; HFS: High-fat, high-sucrose; HFF: High-fat, high-fructose; HFSC: High-fat, high-sucrose, high-cholesterol; HFFC: High-fat, high-fructose, high-cholesterol; CD: Choline deficient
DOI: 10.6084/m9.figshare.10293674.v3
title: Suppl. Table 1

description: Summary of histological features in livers collected from 83 d-old Iberian pigs fed 1 of the 4 liquid diets: 1) control (CON-N; n = 8), 2) high-fructose high-fat (HFF-N; n = 6), 3) CON + 6.2 × 10<sup>4</sup> cfu ∙ mL<sup>-1</sup> probiotics (CON-P; n = 8), and 4) HFF-N + 6.2 × 10<sup>4</sup> cfu ∙ mL<sup>-1</sup> probiotics (HFF-P; n = 6). The probiotic mixture contained <i>Pediococcus acidilactici</i>, <i>Pediococcus</i> <i>pentosaceus</i>, <i>Lactobacillus plantarum</i> and <i>Bacillus subtilis</i> (MultiBio 3PS; BiOWiSH Technologies, Cincinnati, OH). Animals were fed 45 mL · kg BW<sup>-1</sup> at 6-h intervals during 10 consecutive weeks.
DOI: 10.6084/m9.figshare.10293641
title: Manuscript 476421- LB 27 LB 28 RAW data

description: 476421
DOI: 10.6084/m9.figshare.10293641.v1
title: Manuscript 476421- LB 27 LB 28 RAW data

description: 476421
DOI: 10.6084/m9.figshare.10293434
title: Authentication of 4-chloro-2-hydroxy-biphenyl

description: Authentication of 4-chloro-2-hydroxy-biphenyl by <sup>1</sup>HNMR, <sup>13</sup>CNMR, and GCMS. It was synthesized from 4-chloro-2-methoxy-biphenyl in the presence of BBr<sub>3</sub>. The purity (&gt;99%) of the compound was determined based on relative peak area by GC-MS.
DOI: 10.6084/m9.figshare.10293458
title: Supplementary data Horgby et al. ERL

description: This data is supplementary to the article by Horgby et al. in Environmental Research Letters.
DOI: 10.6084/m9.figshare.10293425
title: Supplementary data 2. Picoplankton OTUs with assignation and read abundance at the different stations (Excel file)

description: Picoplankton OTUs with assignation and read abundance at the different stations (Excel file)
DOI: 10.6084/m9.figshare.10293425.v1
title: Supplementary data 2. Picoplankton OTUs with assignation and read abundance at the different stations (Excel file)

description: Picoplankton OTUs with assignation and read abundance at the different stations (Excel file)
DOI: 10.6084/m9.figshare.10293254
title: Chapter5_supplementary_tables

description: Supplementary tables for chapter 5, "Closed <i>Bordetella pertussis </i>genomes uncover changes in Filamentous Haemagglutinin gene"
DOI: 10.6084/m9.figshare.10293194
title: Raw QMC dataset for water at 13.4 au from Pt(111) with pre-adsorbed CO.

description: see CO+water on Pt(111) as in QUA-2019-0517
DOI: 10.6084/m9.figshare.10293227
title: manuscript 476421- LB27 LB 28 search engine result files (2)

description: 476421
DOI: 10.6084/m9.figshare.10293227.v1
title: manuscript 476421- LB27 LB 28 search engine result files (2)

description: 476421
DOI: 10.6084/m9.figshare.10293149
title: Raw QMC TS concerted mechanism for water dissociation and CO attack on Pt(111)

description: CO+water on Pt(111) as in QUA-2019-0517
DOI: 10.6084/m9.figshare.10293194.v1
title: Raw QMC dataset for water at 13.4 au from Pt(111) with pre-adsorbed CO.

description: see CO+water on Pt(111) as in QUA-2019-0517
DOI: 10.6084/m9.figshare.10293044
title: Chapter2_supplementary_tables

description: Supplementary tables for chapter 2, as published in Microbial Genomics in "Resolving the complex <i>Bordetella pertussis </i>genome using barcoded nanopore sequencing".
DOI: 10.6084/m9.figshare.10293041
title: PVC-7 data-subset as a Mesmerize project

description: Please see the attached README for details.OverviewThis dataset contains a portion of the the pvc-7 dataset available on CRCNS.org in the form of a Mesmerize project (mesmerizelab.org). Please see the original dataset for information regarding the experiment. http://dx.doi.org/10.6080/K0C8276GWe are not affiliated with the authors of the original dataset who did the experiment. The purpose of this sub-dataset is to illustrate an application of Mesmerize.Opening the datasetThe dataset is compresed in tar archive with gzip compression. Decompression can take a while, you may get better performance if you read from a different filesystem than the one that you write to. I recommend using a fast filesystem to store the decompressed data since the image data is large.<strong><br></strong><strong>pigz</strong> should be faster for decompression compared to standard tar. For Ubuntu & Debian based distros you can install pigz through apt. For other distros please check your repositories.<br><code>sudo apt install pigz</code><br>On Mac OSX you can install pigz through brew. See this: https://brewinstall.org/Install-pigz-on-Mac-with-Brew/<br>Decompressing:<code><br></code><code>pigz -dc pvc7_subdataset_mesmerize.tar.gz | tar -xf</code><br>If you cannot install pigz you can decompress with tar. This may take a long time.<code><br></code><code>tar xvzf pvc7_subdataset_mesmerize.tar.gz</code><br>This will probably decompress into a directory called "share". Navigate to <code>share/data/temp/kushal</code> and you should see the project directory "pvc7_subdataset_mesmerize".Once decompressed, you can explore the dataset using Mesmerize. Simply open the Project Directory through the Mesmerize Welcome Window (the window that you are presented with when you launch Mesmerize). You will see the available analysis flowcharts and plots similar to this: http://www.mesmerizelab.org/Overview.html#welcome-windowDouble click on a flowchart or plot to open it. See the "Flowchart" and "Plots" sections below for details.You can explore individual project samples by using the Project Browser and double-clicking on the samples of interest. Note that the image sequence is large (~50GB) so make sure you have enough RAM available if you want to view it.
DOI: 10.6084/m9.figshare.10293149.v1
title: Raw QMC TS concerted mechanism for water dissociation and CO attack on Pt(111)

description: CO+water on Pt(111) as in QUA-2019-0517
DOI: 10.6084/m9.figshare.10293254.v1
title: Chapter5_supplementary_tables.xlsx

description: Supplementary tables for chapter 5, "Closed <i>Bordetella pertussis </i>genomes uncover changes in Filamentous Haemagglutinin gene"
DOI: 10.6084/m9.figshare.10293044.v2
title: Chapter2_supplementary_tables.xlsx

description: Supplementary tables for chapter 2, as published in Microbial Genomics in "Resolving the complex <i>Bordetella pertussis </i>genome using barcoded nanopore sequencing".
DOI: 10.6084/m9.figshare.10293254.v3
title: Chapter5_supplementary_tables

description: Supplementary tables for chapter 5, "Closed <i>Bordetella pertussis </i>genomes uncover changes in Filamentous Haemagglutinin gene"
DOI: 10.6084/m9.figshare.10293044.v1
title: Chapter2_supplementary_tables.xlsx

description: Supplementary tables for chapter 2, as published in Microbial Genomics in "Resolving the complex <i>Bordetella pertussis </i>genome using barcoded nanopore sequencing".
DOI: 10.6084/m9.figshare.10293254.v2
title: Chapter5_supplementary_tables

description: Supplementary tables for chapter 5, "Closed <i>Bordetella pertussis </i>genomes uncover changes in Filamentous Haemagglutinin gene"
DOI: 10.6084/m9.figshare.10292765
title: manuscript 476421- LB27 y LB28 search engine results files.zip

description: 476421
DOI: 10.6084/m9.figshare.10292765.v1
title: manuscript 476421- LB27 y LB28 search engine results files.zip

description: 476421
DOI: 10.6084/m9.figshare.10292573
title: Entropy Based Analysis of Vertebrate Sperm Protamines Sequences: Evidence of Dityrosine and Cysteine-Tyrosine Cross-Linking in Sperm Protamines

description: Datasets, figures, and scripts used for the analysis of alignments of vertebrate sperm protamine sequences.
DOI: 10.6084/m9.figshare.10292573.v1
title: Entropy Based Analysis of Vertebrate Sperm Protamines Sequences: Evidence of Dityrosine and Cysteine-Tyrosine Cross-Linking in Sperm Protamines

description: Datasets, figures, and scripts used for the analysis of alignments of vertebrate sperm protamine sequences.
DOI: 10.6084/m9.figshare.10291970
title: Predictors of fatal outcomes in pedestrian accidents in Tabriz Metropolis of Iran: Application of PLS-DA method

description: <b>Objectives:</b> Road traffic deaths in walking pedestrians are a global public health problem. Considering that in Iran pedestrians have a high proportion of deaths caused by traffic accidents, the objective of the present study was to investigate mortality rate and related factors of fatal injury in pedestrian crashes in Tabriz Metropolis of Iran as the largest and most populous city of the northwest of Iran. <b>Methods:</b> The design of this study is case-control based on police and Forensic Medicine Organization data. All registered fatal pedestrian crashes in Tabriz Metropolis from 2014 to 2015 (146 cases) were included in the study as the case group. Also, 292 pedestrians (the ratio of cases to controls was 1:2) with non-fatal crashes were considered as the control group. Due to high dimensional data and multicollinearity issue, Partial least squares discriminant analysis (PLS-DA) was used for data analysis. Importance of the variables was determined by the VIP (Variable Importance in the Projection) index. Performance of the model was assessed by using training and test set validation method. The area under the ROC curve (AUC) and classification error rates were calculated for the test set. R software version 3.5.1 (mixOmcs packages) was used for data analysis. <b>Results:</b> According to the results of PLS-DA, the most important variables related to fatal outcome in pedestrian crashes with VIP &gt; 1 were: pedestrian age (positive effect), type of vehicle (light machinery with a negative effect), kind of vehicle plate (private plate with a negative effect), season of accident occurrence (winter season with a positive effect), type of driver’s licenses (Class A with a positive effect), pedestrian gender (male with a positive effect) and Fault of Pedestrian (At-fault with a positive effect). The overall accuracy for the fitted model and AUC were 0.77 and 0.79, respectively. <b>Conclusions:</b> The results show that predictors of a fatal outcome in pedestrian accidents in Tabriz can be attributed to the pedestrian characteristics (which notably account for differences in vulnerability in case of an accident), the car and driver features, and weather (which may all notably influence the amount of energy involved in the collision, through the car mass, speed, and conditions delaying the braking response or reducing the braking effectiveness). Regarding the statistical method, the PLS-DA is a powerful method which can be used to analyze high dimension data with multicollinearity issue.
DOI: 10.6084/m9.figshare.10291970.v1
title: Predictors of fatal outcomes in pedestrian accidents in Tabriz Metropolis of Iran: Application of PLS-DA method

description: <b>Objectives:</b> Road traffic deaths in walking pedestrians are a global public health problem. Considering that in Iran pedestrians have a high proportion of deaths caused by traffic accidents, the objective of the present study was to investigate mortality rate and related factors of fatal injury in pedestrian crashes in Tabriz Metropolis of Iran as the largest and most populous city of the northwest of Iran. <b>Methods:</b> The design of this study is case-control based on police and Forensic Medicine Organization data. All registered fatal pedestrian crashes in Tabriz Metropolis from 2014 to 2015 (146 cases) were included in the study as the case group. Also, 292 pedestrians (the ratio of cases to controls was 1:2) with non-fatal crashes were considered as the control group. Due to high dimensional data and multicollinearity issue, Partial least squares discriminant analysis (PLS-DA) was used for data analysis. Importance of the variables was determined by the VIP (Variable Importance in the Projection) index. Performance of the model was assessed by using training and test set validation method. The area under the ROC curve (AUC) and classification error rates were calculated for the test set. R software version 3.5.1 (mixOmcs packages) was used for data analysis. <b>Results:</b> According to the results of PLS-DA, the most important variables related to fatal outcome in pedestrian crashes with VIP &gt; 1 were: pedestrian age (positive effect), type of vehicle (light machinery with a negative effect), kind of vehicle plate (private plate with a negative effect), season of accident occurrence (winter season with a positive effect), type of driver’s licenses (Class A with a positive effect), pedestrian gender (male with a positive effect) and Fault of Pedestrian (At-fault with a positive effect). The overall accuracy for the fitted model and AUC were 0.77 and 0.79, respectively. <b>Conclusions:</b> The results show that predictors of a fatal outcome in pedestrian accidents in Tabriz can be attributed to the pedestrian characteristics (which notably account for differences in vulnerability in case of an accident), the car and driver features, and weather (which may all notably influence the amount of energy involved in the collision, through the car mass, speed, and conditions delaying the braking response or reducing the braking effectiveness). Regarding the statistical method, the PLS-DA is a powerful method which can be used to analyze high dimension data with multicollinearity issue.
DOI: 10.6084/m9.figshare.10291634
title: Darunavir/cobicistat/emtricitabine/tenofovir alafenamide in treatment-naïve patients with HIV-1: subgroup analyses of the phase 3 AMBER study

description: <b>Background</b>: The once-daily, single-tablet regimen darunavir/cobicistat/emtricitabine/tenofovir alafenamide (D/C/F/TAF) 800/150/200/10 mg is approved for the treatment of HIV-1 infection. The 48-week efficacy and safety of D/C/F/TAF versus darunavir/cobicistat + emtricitabine/tenofovir disoproxil fumarate (control) in treatment-naïve adults were demonstrated in the phase 3 AMBER study. <b>Objective</b>: To describe AMBER outcomes across patient subgroups based on demographic and clinical characteristics at baseline. <b>Methods</b>: AMBER patients had viral load (VL) ≥1000 copies/mL, CD4<sup>+</sup> cell count &gt;50 cells/µL, and genotypic susceptibility to darunavir, emtricitabine, and tenofovir. Primary endpoint was the proportion of patients with virologic response (VL &lt;50 copies/mL; FDA snapshot). Safety was assessed by adverse events, estimated glomerular filtration rate (cystatin C; eGFR<sub>cystC</sub>), and bone mineral density. Outcomes were assessed by age (≤/&gt;50 years), gender, race (black/non-black), baseline VL (≤/&gt;100,000 copies/mL), baseline CD4<sup>+</sup> cell count ( <b>Results</b>: For the 725 AMBER patients (D/C/F/TAF: 362; control: 363), virologic response rates at week 48 were similar with D/C/F/TAF (91%) and control (88%), and this was consistent across all subgroups. Adverse event rates were similar in both arms, although numerically higher among patients &gt;50 years and women, relative to their comparator groups, regardless of treatment arm (notably, sample sizes were small for patients &gt;50 years and women). Improvements in eGFR<sub>cystC</sub> and stable bone mineral density were observed with D/C/F/TAF overall, and results were generally consistent across subgroups. <b>Conclusions</b>: For treatment-naïve patients in AMBER, initiating therapy with the D/C/F/TAF single-tablet regimen was an effective and well-tolerated option, regardless of demographic or clinical characteristics. <b>Trial registration:</b>ClinicalTrials.gov identifier: NCT02431247.