cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5439706
title: St Petersburg traffic videos

description: The data set contains video recordings of vehicles in the area of Nevsky prospect between the Moika river and the street Bolshaya Konuyshennaya. Nevsky prospect – is a central street of Saint Petersburg with a busy traffic. The selected area includes two movement directions with three lanes of traffic. The length of the selected area is 102 meters. The resolution of each video is 330*480 pixels. The shooting frequency is 10 frames per second. The data set is 7 days in April 2017.
DOI: 10.6084/m9.figshare.5439736
title: Comparative analysis of LIN28-RNA binding sites identified at single nucleotide resolution

description: It remains a formidable challenge to characterize the diverse complexes of RNA binding proteins and their targets. While crosslink and immunoprecipitation (CLIP) methods are powerful techniques that identify RNA targets on a global scale, the resolution and consistency of these methods is a matter of debate. Here we present a comparative analysis of LIN28-pre-let-7 UV-induced crosslinking using a tandem mass spectrometry (MS/MS) and deep sequencing interrogation of <i>in vitro</i> crosslinked complexes. Interestingly, analyses by the two methods diverge in their identification of crosslinked nucleotide identity – whereas bioinformatics and sequencing analyses suggest guanine in mammalian cells, MS/MS identifies uridine. This work suggests the need for comprehensive analysis and validation of crosslinking methodologies.
DOI: 10.6084/m9.figshare.5439736.v2
title: Comparative analysis of LIN28-RNA binding sites identified at single nucleotide resolution

description: It remains a formidable challenge to characterize the diverse complexes of RNA binding proteins and their targets. While crosslink and immunoprecipitation (CLIP) methods are powerful techniques that identify RNA targets on a global scale, the resolution and consistency of these methods is a matter of debate. Here we present a comparative analysis of LIN28-pre-let-7 UV-induced crosslinking using a tandem mass spectrometry (MS/MS) and deep sequencing interrogation of <i>in vitro</i> crosslinked complexes. Interestingly, analyses by the two methods diverge in their identification of crosslinked nucleotide identity – whereas bioinformatics and sequencing analyses suggest guanine in mammalian cells, MS/MS identifies uridine. This work suggests the need for comprehensive analysis and validation of crosslinking methodologies.
DOI: 10.6084/m9.figshare.5439496
title: Exoneurella eremophila nest collections, Mildura Australia

description: Nest census data for Exoneurella eremophila. Colonies were collected from Mildura, Victoria, Australia during spring: 11-13 October 2013, summer: 21-23 January 2014 and autumn: 12-14 April 2014. These are represented as Trip 2-4 respectively in the data. The nest length (mm), number of adult females, males eggs, larvae and pupae present in the nest on collection are recorded. 'Broodyn' indicates whether the nest had brood (Y) or not (N). 'Socialyn' indicates whether the nest was social (Y) or not (N). Sex ratio was calculated as: sex.ratio = male.pupae/tot.pupae. Per capita brood production was calculated as: percap = tot.brood/female.
DOI: 10.6084/m9.figshare.5439496.v1
title: Exoneurella eremophila nest collections, Mildura Australia

description: Nest census data for Exoneurella eremophila. Colonies were collected from Mildura, Victoria, Australia during spring: 11-13 October 2013, summer: 21-23 January 2014 and autumn: 12-14 April 2014. These are represented as Trip 2-4 respectively in the data. The nest length (mm), number of adult females, males eggs, larvae and pupae present in the nest on collection are recorded. 'Broodyn' indicates whether the nest had brood (Y) or not (N). 'Socialyn' indicates whether the nest was social (Y) or not (N). Sex ratio was calculated as: sex.ratio = male.pupae/tot.pupae. Per capita brood production was calculated as: percap = tot.brood/female.
DOI: 10.6084/m9.figshare.5437975
title: Supplementary Information for the dissertation "Cerebellothalamic and thalamostriatal and pathways in a songbird, the Bengalese finch"

description: Supplementary Information for the dissertation "Cerebellothalamic and thalamostriatal pathways in a songbird", as referenced in the text. Non-exclusionary copyright belongs to David Nicholson and Emory University. Also referenced by the pre-print of a paper on Biorxiv, https://www.biorxiv.org/content/early/2017/10/02/197590<br>
DOI: 10.6084/m9.figshare.5439382
title: Plling et al. 2017 UKB parents attained age GWAS

description: Analysis of genotypes associated with parents attained age (lifespan) in the UK Biobank. If used please reference:<br><br><b>Pilling et al. 2016. Human longevity: 25 genetic loci associated in 389,166 UK biobank participants. Aging US<br></b>http://www.aging-us.com/article/101334/text<br><br>Results are from BOLT-LMM analysis of European participants, adjusted for age, sex, assessment centre and array type.<br><br>7 phenotypes:<br>* Mothers age at death<br>* Fathers age at death<br><br>* Mothers attained age (including alive parents)<br>* Fathers attained age (including alive parents)<br><br>* Combined parents age at death<br>* Combined parents attained age (including alive parents)<br><br>* [Binary] both parents reached top 10% of survival (&gt;=90 mothers, &gt;=87 fathers) vs. both parents died before age 80<br><br>&gt;&gt; For each analysis there is an accompanying GIV dataset. The UK Biobank sample was randomly split in half, and the analysis repeated. This is for use in Genetic Instrumental Variable (GIV) Regression analysis.<br><br>Fields are as follows<br> SNP: dnSNP name of genetic marker, if available<br> CHR: chromosome<br> BP: base-pair position on CHR (hg19 / b37)<br> ALLELE1: effect allele<br> ALLELE0: non-effect allele<br> A1FREQ: frequency of ALLELE1<br> BETA: effect size from BOLT-LMM approximation to infinitesimal mixed model<br> SE: standard error of effect size<br> P_BOLT_LMM: non-infinitesimal mixed model association test p-value
DOI: 10.6084/m9.figshare.5437459
title: Mixed Posters

description: Posters for NNDC 2017 meeting on mixed states in bipolar disorder and suicide risk.
DOI: 10.6084/m9.figshare.5437975.v1
title: Supplementary Information for "Thalamostriatal and cerebellothalamic pathways in a songbird"

description: Supplementary Information for the paper "Thalamostriatal and cerebellothalamic pathways in a songbird", as referenced in the text.<br>
DOI: 10.6084/m9.figshare.5437459.v1
title: Mixed Posters

description: Posters for NNDC 2017 meeting on mixed states in bipolar disorder and suicide risk.
DOI: 10.6084/m9.figshare.5437975.v2
title: Supplementary Information for "Thalamostriatal and cerebellothalamic pathways in a songbird, the Bengalese finch"

description: Supplementary Information for the paper "Thalamostriatal and cerebellothalamic pathways in a songbird", as referenced in the text.<br>
DOI: 10.6084/m9.figshare.5437420
title: mtCOI reference data for species ID of Bemisia tabaci

description: mtCOI reference data set for Bemisia tabaci whitefly updated from GenBank on 22 May 2017.
DOI: 10.6084/m9.figshare.5437975.v4
title: Supplementary Information for the dissertation "Cerebellothalamic and thalamostriatal and pathways in a songbird, the Bengalese finch"

description: Supplementary Information for the dissertation "Cerebellothalamic and thalamostriatal pathways in a songbird", as referenced in the text. Non-exclusionary copyright belongs to David Nicholson and Emory University. Also referenced by the pre-print of a paper on Biorxiv, https://www.biorxiv.org/content/early/2017/10/02/197590<br>
DOI: 10.6084/m9.figshare.5437399

description: The main purpose of this study is to determine the didactic strategies to increase the reading comprehension to 7-year-old students at Academia Naval Altamar. The information for this research were gathered through an investigation of several didactic strategies choosing the ones for those students. The didactic strategies were selected to help students to increase the reading comprehension skill, so they can interact in a better way using the language without any problem.
DOI: 10.6084/m9.figshare.5437975.v3
title: Supplementary Information for "Thalamostriatal and cerebellothalamic pathways in a songbird, the Bengalese finch"

description: Supplementary Information for the paper "Thalamostriatal and cerebellothalamic pathways in a songbird", as referenced in the text.<br>
DOI: 10.6084/m9.figshare.5437330
title: Herpes zoster incidence and cost in patients receiving autologous hematopoietic stem-cell transplant

description: <b>Objective:</b> Among patients receiving autologous hematopoietic stem cell transplant (Auto-HSCT), this study estimated the incidence of herpes zoster (HZ), compared healthcare costs among patients with and without HZ, and evaluated antiviral prophylaxis (AP) use. <b>Research design and methods:</b> A retrospective study was conducted using data from a large health plan to identify patients ≥18 years with ≥1 claim for an Auto-HSCT procedure during 2006–2011 (<i>n</i> = 2,530). Patients were followed from date of Auto-HSCT until risk-end date, defined as development of HZ, end of enrollment, death, or December 31, 2011. HZ incidence was calculated as cases observed after Auto-HSCT, divided by accrued time-at-risk in person-years (PY). AP use and duration were defined by prescription fills. One-year medical and pharmacy costs were calculated as combined health plan and patient paid amounts. <b>Main outcome measures:</b> HZ incidence and healthcare costs were calculated using administrative claims data. <b>Results:</b> Overall HZ incidence was 62.2/1,000 PY (95% CI = 54.3–70.9). Most (72.3%) patients were prescribed AP. During the first 90-days post-Auto-HSCT, patients without AP had increased incidence (151.6/1,000 PY, 95% CI = 88.3–242.6) compared to those prescribed AP pre- (30.9/1,000 PY, 95% CI = 11.3–67.2) or post-Auto-HSCT (33.0/1,000 PY, 95% CI = 13.3–67.9). Total adjusted mean 1-year all-cause healthcare costs were $74,875 for patients who developed HZ and $70,279 for patients who did not (difference = $4,596 (cost ratio = 1.07, 95% CI = 0.86–1.32, <i>p</i> = .566)). <b>Conclusions:</b> HZ incidence was high, despite AP use. Mean annual healthcare costs were higher for patients with HZ, but the difference was not statistically significant. An effective vaccine against HZ could be useful in decreasing both incidence of and cost for HZ in this population.
DOI: 10.6084/m9.figshare.5437330.v2
title: Herpes zoster incidence and cost in patients receiving autologous hematopoietic stem-cell transplant

description: <b>Objective:</b> Among patients receiving autologous hematopoietic stem cell transplant (Auto-HSCT), this study estimated the incidence of herpes zoster (HZ), compared healthcare costs among patients with and without HZ, and evaluated antiviral prophylaxis (AP) use. <b>Research design and methods:</b> A retrospective study was conducted using data from a large health plan to identify patients ≥18 years with ≥1 claim for an Auto-HSCT procedure during 2006–2011 (<i>n</i> = 2,530). Patients were followed from date of Auto-HSCT until risk-end date, defined as development of HZ, end of enrollment, death, or December 31, 2011. HZ incidence was calculated as cases observed after Auto-HSCT, divided by accrued time-at-risk in person-years (PY). AP use and duration were defined by prescription fills. One-year medical and pharmacy costs were calculated as combined health plan and patient paid amounts. <b>Main outcome measures:</b> HZ incidence and healthcare costs were calculated using administrative claims data. <b>Results:</b> Overall HZ incidence was 62.2/1,000 PY (95% CI = 54.3–70.9). Most (72.3%) patients were prescribed AP. During the first 90-days post-Auto-HSCT, patients without AP had increased incidence (151.6/1,000 PY, 95% CI = 88.3–242.6) compared to those prescribed AP pre- (30.9/1,000 PY, 95% CI = 11.3–67.2) or post-Auto-HSCT (33.0/1,000 PY, 95% CI = 13.3–67.9). Total adjusted mean 1-year all-cause healthcare costs were $74,875 for patients who developed HZ and $70,279 for patients who did not (difference = $4,596 (cost ratio = 1.07, 95% CI = 0.86–1.32, <i>p</i> = .566)). <b>Conclusions:</b> HZ incidence was high, despite AP use. Mean annual healthcare costs were higher for patients with HZ, but the difference was not statistically significant. An effective vaccine against HZ could be useful in decreasing both incidence of and cost for HZ in this population.
DOI: 10.6084/m9.figshare.5437276
title: Supplementary Material for: Next-Generation Sequencing in Gynaecological Tumours: The Prognostic and Predictive Value of the Most Common Mutations Found in Ovarian, Endometrial, and Cervical Tumours: Literature Review and the University Medical Centre Utrecht Next-Generation Sequencing Data

description: <i>Objective:</i> To investigate whether next-generation sequencing (NGS) in ovarian and endometrial tumours can discover mutations with a relevant prognostic or predictive value. <i>Methods:</i> After a literature search, selected studies were critically appraised using the Quality in Prognostic Studies tool. Data on mutation incidence and correlations with prognostic and predictive items were extracted from relevant studies and compared to our own cohort consisting of 28 patients analysed using NGS. <i>Results:</i> Eight out of 739 articles were found eligible, including different tumour types. Prevalence of mutations in the <i>KRAS</i> gene ranged between 5.34 and 58.8% in ovarian cancer. Two studies showed a significant correlation between <i>KRAS</i> mutations and an improved disease free- and overall survival. Clinical data were available for 17 of our patients, mostly cases of endometrial carcinomas. <i>KRAS</i>, <i>PIK3CA</i>, <i>CTNNB1</i>, and <i>TP53</i>were the most frequently mutated genes in endometrial carcinomas, and <i>PTEN</i> and <i>CTNNB1</i> correlated with a higher FIGO stage. <i>Conclusion:</i> In the ovary <i>KRAS</i> mutation is associated with type I ovarian tumours (low-grade serous, mucinous, endometrioid, and clear-cell) and may seem to have a more favourable prognosis. The prognostic value of <i>TP53</i> is still controversial. In endometrial tumours, <i>PTEN</i> shows a positive correlation with better prognosis. <i>PIK3CA</i> may have a correlation with poorer prognosis. <i>CTNNB1</i> mutations in endometrial carcinomas could predict a worse prognosis.
DOI: 10.6084/m9.figshare.5437330.v1
title: Herpes zoster incidence and cost in patients receiving autologous hematopoietic stem-cell transplant

description: Objective: Among patients receiving autologous hematopoietic stem cell transplant (Auto-HSCT), we estimated the incidence of herpes zoster (HZ), compared health care costs among patients with and without HZ, and evaluated antiviral prophylaxis (AP) use. Research Design and Methods: We conducted a retrospective study using data from a large health plan to identify patients ≥18 years with ≥1 claim for an Auto-HSCT procedure during 2006-2011 (N = 2,530). Patients were followed from date of Auto-HSCT until risk-end date, defined as development of HZ, end of enrollment, death, or 12/31/2011. HZ incidence was calculated as cases observed after Auto-HSCT divided by accrued time-at-risk in person-years (PY). AP use and duration were defined by prescription fills. One-year medical and pharmacy costs were calculated as combined health plan and patient paid amounts. Main outcome measures: HZ incidence and health care costs were calculated using administrative claims data. Results: Overall HZ incidence was 62.2/1000 PY (95% CI 54.3-70.9). Most (72.3%) patients were prescribed AP. During the first 90-days post-Auto-HSCT, patients without AP had increased incidence (151.6/1000 PY, 95% CI 88.3-242.6) compared to those prescribed AP pre- (30.9/1000 PY, 95% CI 11.3-67.2) or post-Auto-HSCT (33.0/1000 PY, 95% CI 13.3-67.9). Total adjusted mean one-year all-cause healthcare costs were $74,875 for patients who developed HZ and $70,279 for patients who did not (difference $4,596 (cost ratio: 1.07, 95% CI: 0.86-1.32, p = 0.566)). Conclusions: HZ incidence was high despite AP use. Mean annual health care costs were higher for patients with HZ but the difference was not statistically significant. An effective vaccine against HZ could be useful in decreasing both incidence of and cost for HZ in this population.
DOI: 10.6084/m9.figshare.5437276.v1
title: Supplementary Material for: Next-Generation Sequencing in Gynaecological Tumours: The Prognostic and Predictive Value of the Most Common Mutations Found in Ovarian, Endometrial, and Cervical Tumours: Literature Review and the University Medical Centre Utrecht Next-Generation Sequencing Data

description: <i>Objective:</i> To investigate whether next-generation sequencing (NGS) in ovarian and endometrial tumours can discover mutations with a relevant prognostic or predictive value. <i>Methods:</i> After a literature search, selected studies were critically appraised using the Quality in Prognostic Studies tool. Data on mutation incidence and correlations with prognostic and predictive items were extracted from relevant studies and compared to our own cohort consisting of 28 patients analysed using NGS. <i>Results:</i> Eight out of 739 articles were found eligible, including different tumour types. Prevalence of mutations in the <i>KRAS</i> gene ranged between 5.34 and 58.8% in ovarian cancer. Two studies showed a significant correlation between <i>KRAS</i> mutations and an improved disease free- and overall survival. Clinical data were available for 17 of our patients, mostly cases of endometrial carcinomas. <i>KRAS</i>, <i>PIK3CA</i>, <i>CTNNB1</i>, and <i>TP53</i>were the most frequently mutated genes in endometrial carcinomas, and <i>PTEN</i> and <i>CTNNB1</i> correlated with a higher FIGO stage. <i>Conclusion:</i> In the ovary <i>KRAS</i> mutation is associated with type I ovarian tumours (low-grade serous, mucinous, endometrioid, and clear-cell) and may seem to have a more favourable prognosis. The prognostic value of <i>TP53</i> is still controversial. In endometrial tumours, <i>PTEN</i> shows a positive correlation with better prognosis. <i>PIK3CA</i> may have a correlation with poorer prognosis. <i>CTNNB1</i> mutations in endometrial carcinomas could predict a worse prognosis.
DOI: 10.6084/m9.figshare.5437126
title: Code to perform simulations_Ecological Limits to Species Diversification

description: Spatially explicit model of speciation and local extinction
DOI: 10.6084/m9.figshare.5437126.v2
title: Code to perform simulations_Ecological Limits to Species Diversification

description: Spatially explicit model of speciation and local extinction
DOI: 10.6084/m9.figshare.5437126.v1
title: Code to perform simulations_Ecological Limits to Species Diversification

description: Spatially explicit model of speciation and local extinction
DOI: 10.6084/m9.figshare.5437048
title: GaitParameters.rar

description: Gait parameters data extracted from experimental study: 'Gait parameters are differently affected by concurrent smartphone-based activities with scaled levels of cognitive effort'.Please refer to the readme.txt file for the additional information<br><br>
DOI: 10.6084/m9.figshare.5437045
title: Table S3. Assignment of proteins to Homology Groups from Novel and divergent genes in the evolution of placental mammals

description: List of all 20363 Homology Groups giving the number of proteins in each Homology Group in each species, and which HG belong to the Novel Ancestral Placental and Novel Core Placental categories. Excel file.
DOI: 10.6084/m9.figshare.5437048.v1
title: GaitParameters.rar

description: Gait parameters data extracted from experimental study: 'Gait parameters are differently affected by concurrent smartphone-based activities with scaled levels of cognitive effort'.Please refer to the readme.txt file for the additional information<br><br>
DOI: 10.6084/m9.figshare.5437042
title: Table S1. Protein sequence accession numbers from Novel and divergent genes in the evolution of placental mammals

description: List of NCBI and Ensembl protein IDs used to generate the combined data set, numerical identifiers for the Homology Group each protein was placed into, and indication of whether genes/HG were assigned to Novel Ancestral Placental and Novel Core Placental HG. Excel file.
DOI: 10.6084/m9.figshare.5437045.v1
title: Table S3. Assignment of proteins to Homology Groups from Novel and divergent genes in the evolution of placental mammals

description: List of all 20363 Homology Groups giving the number of proteins in each Homology Group in each species, and which HG belong to the Novel Ancestral Placental and Novel Core Placental categories. Excel file.
DOI: 10.6084/m9.figshare.5437036
title: Table S4. Proteins used for phylogenetic analysis from Novel and divergent genes in the evolution of placental mammals

description: IDs of the selected proteins from each Novel Core Placental Homology Group used for phylogenetic analysis, including amino acid sequences after alignment and trimming. Excel file.
DOI: 10.6084/m9.figshare.5437042.v1
title: Table S1. Protein sequence accession numbers from Novel and divergent genes in the evolution of placental mammals

description: List of NCBI and Ensembl protein IDs used to generate the combined data set, numerical identifiers for the Homology Group each protein was placed into, and indication of whether genes/HG were assigned to Novel Ancestral Placental and Novel Core Placental HG. Excel file.
DOI: 10.6084/m9.figshare.5437036.v1
title: Table S4. Proteins used for phylogenetic analysis from Novel and divergent genes in the evolution of placental mammals

description: IDs of the selected proteins from each Novel Core Placental Homology Group used for phylogenetic analysis, including amino acid sequences after alignment and trimming. Excel file.
DOI: 10.6084/m9.figshare.5437024
title: Table S2. Numbers of proteins analysed per species from Novel and divergent genes in the evolution of placental mammals

description: The number of protein IDs in the original NCBI and Ensembl protein data used. Excel file.
DOI: 10.6084/m9.figshare.5437024.v1
title: Table S2. Numbers of proteins analysed per species from Novel and divergent genes in the evolution of placental mammals

description: The number of protein IDs in the original NCBI and Ensembl protein data used. Excel file.
DOI: 10.6084/m9.figshare.5437018
title: Table S5. Expression data for human genes from Novel and divergent genes in the evolution of placental mammals

description: Raw and normalised FPKM gene expression values for all human genes in Novel Ancestral Placental and Novel Core Placental Homology Groups. Excel file.
DOI: 10.6084/m9.figshare.5436940
title: SCRIPTS

description: This repository contains the bash scripts and intermediate data files used during bioinformatics analysis.<br><br><b>merger.sh</b> = bash script for merging contigs from nucleotide and protein annotations<br><br><b>ws11blastn.sh</b> = bash script (196 cores) for annotating nucleotide sequences by blastn wordsize 11.<br><br><b>blastx.sh</b> = bash script for annotating nucleotide sequences by DIAMOND blast<br><br><b>trinity.sh</b> = bash script for assembling high quality NGS reads into contigs by the Trinity algorithm<br><br><b>abundance_analysis.tar </b>= archive of text files containing the commands used for abundance analysis. Briefly, taxon-binned contigs are collected and build into a reference for subsequent HISAT2 aligment of forward NGS reads.<br><br><b>counts.csv</b> = summary table of counts generated by the abundance analysis<br><br><b>lengths.csv</b> = summary table of reference lengths generated by the abundance analysis<br><br><b>pcr.csv</b> = summary table of RT-PCR confirmation <br><br><b>heatmap2.Rmd</b> = R script used for processing and visualizing the results of the abundance analysis.<br><br><br>