cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5513104.v1
title: Altmetric data on journal articles with "altmetrics" in the title or abstract, October 18 2017

description: This is the full 220 item dataset from exported from Altmetric Explorer on October 18, 2017. It includes items where "altmetrics" appears in journal articles' titles or abstracts. Of the 220 items in this dataset, only 215 have online attention in the sources tracked by Altmetric.<br>The top 50 articles in this dataset (by Altmetric Attention Score) will profiled in the Open Access Week 2017 blogpost, "The top altmetrics research is impressively Open Access!" on the Altmetric blog.
DOI: 10.6084/m9.figshare.5513224.v1
title: bBSSR and BSSR-only original data

description: Original bBSSR and BSSR-only award and publication data downloaded from NIH Reporter (https://projectreporter.nih.gov/reporter.cfm). Data files used by R scripts in publication.<br>* bBSSR award data (7 csv files in total): "bBSSR [2008-2014] NIH reporter 7 August 2017"<br>* bBSSR publication data (6 csv files in total): "Publications from NIH Reporter batch [1-6]"<br>* BSSR award data (10 csv files in total): "BSSR [2008-2014, part 1/2] NIH reporter 16/17 August 2017"<br><br>* BSSR publication data (13 csv files in total): "BSSR publications batch [1-13] 17 August 2017"<br><br>* "Foward citation data for analysis": list of forward citation PMIDs retrieved from Scopus for a select subset of bBSSR publications<br>* Citation data for bBSSR and BSSR-only publications retrieved from the NIH iCite database (https://icite.od.nih.gov/analysis): "NIH iCite batch [1-40]"<br>* "List of CTSA PMIDs from Surkis et al 2016": publications and associated PMIDs that are linked to CTSA awards; data retrieved from Surkis et al 2016 (reference below)<br>ReferenceSurkis, A., Hogle, J.A., DiazGranados, D., Hunt, J.D., Mazmanian, P.E., Connors, E., Westaby, K., Whipple, E.C., Adamus, T., Mueller, M., and Aphinyanaphongs, Y. 2016. “Classifying publications from the clinical and translational science award program along the translational research spectrum: a machine learning approach.” <i>Journal of Translational Medicine</i> 14: 235. DOI: 10.1186/s12967-016-0992-8.
DOI: 10.6084/m9.figshare.5513356.v1
title: Deep phenotyping for patients by patients: a lay-friendly version of the Human Phenotype Ontology

description: The Human Phenotype Ontology (HPO) has become the de facto standard representation of clinical “deep phenotype” data for computational comparison of abnormalities and for use in genetic disease diagnostics. The HPO enables non-exact matching of sets of phenotypic features (phenotype profile) against known diseases, other patients, and model organisms. The algorithms have been implemented into many variant prioritization tools and are used by the 100,000 Genomes project, the NIH Undiagnosed Diseases Program/Network, and thousands of other clinics, labs, tools, and databases. <br>Patients themselves are an eager and untapped source of accurate information about symptoms and phenotypes - some of which may go unnoticed by the clinician. However, medical terminology is often perplexing to patients, making it difficult to use resources like the HPO. Here, we systematically added layperson synonyms with approximately 60% being translatable into layperson terminology. Analyses suggest that the lay-HPO has the features required to be useful in a diagnostic setting, in that lay terms are: a) sufficiently specific and, b) well-represented in our disease-to-phenotype database that is utilized by the aforementioned tools for differential diagnostics. A new patient-centered tool aims to help patients assist clinicians in creating robust computational phenotype profiles to improve molecular diagnostic rates and be active participants in their diagnostic odysseys.
DOI: 10.6084/m9.figshare.5513449.v4
title: Politicians by Country from the English-language Wikipedia

description: This project contains data on most English-language Wikipedia articles within the category "Category:Politicians by nationality" and subcategories, along with the code used to generate that data. Both are released under the CC-BY-SA 4.0 license.<br><b>Data</b>The data was extracted via the Wikimedia API using the associated code. It is formatted as a CSV and saved as <i>page_data.csv</i> in the "data" directory. Columns are:<br>1. "country", containing the sanitised country name, extracted from the category name;2. "page", containing the unsanitised page title.3. "last_edit", containing the edit ID of the last edit to the page.<br>Country codes are inconsistent. Where possible, they have been modified to match the country names found in http://www.prb.org/DataFinder/Topic/Rankings.aspx?ind=14 - but the PRB dataset contains nations not found in Wikipedia, and vice versa.<br>The actual recursion only went 2 levels deep into the category tree: someone listed as an Antiguan politician, say, is included - someone exclusively listed as an Antiguan politician who was assassinated is not.<br><b>Code</b>The code is written in the programming language R, and heavily commented; it can be found in the "code" directory, and is split into 3 files:<br>1. <i>utils.R, </i>which contains utilities for operating the code in the other files;2. <i>retrieve.R</i>, which contains functions for retrieving the category and page data from Wikipedia;3. <i>main.R</i>, which executes the data retrieval code and performs sanitisation before writing it to file.
DOI: 10.6084/m9.figshare.5513014
title: PTM annotations of human RRM domains

description: Includes two sets of MAFFT alignments of human RRM domains. The first set contains annotations of all PTMs that exist (April 2017 data from ProteomeScout proteomescout.wustl.edu) on RRM domains and a set that includes just phosphotyrosine and lysine ubiquitination and acetylation (based on analysis in Sloutsky and Naegle).
DOI: 10.6084/m9.figshare.5513449.v5
title: Politicians by Country from the English-language Wikipedia

description: This project contains data on most English-language Wikipedia articles within the category "Category:Politicians by nationality" and subcategories, along with the code used to generate that data. Both are released under the CC-BY-SA 4.0 license.<br><b>Data</b>The data was extracted via the Wikimedia API using the associated code. It is formatted as a CSV and saved as <i>page_data.csv</i> in the "data" directory. Columns are:<br>1. "country", containing the sanitised country name, extracted from the category name;2. "page", containing the unsanitised page title.3. "last_edit", containing the edit ID of the last edit to the page.<br>Country codes are inconsistent. Where possible, they have been modified to match the country names found in http://www.prb.org/DataFinder/Topic/Rankings.aspx?ind=14 - but the PRB dataset contains nations not found in Wikipedia, and vice versa.<br>The actual recursion only went 2 levels deep into the category tree: someone listed as an Antiguan politician, say, is included - someone exclusively listed as an Antiguan politician who was assassinated is not.<br><b>Code</b>The code is written in the programming language R, and heavily commented; it can be found in the "code" directory, and is split into 3 files:<br>1. <i>utils.R, </i>which contains utilities for operating the code in the other files;2. <i>retrieve.R</i>, which contains functions for retrieving the category and page data from Wikipedia;3. <i>main.R</i>, which executes the data retrieval code and performs sanitisation before writing it to file.
DOI: 10.6084/m9.figshare.5513014.v1
title: PTM annotations of human RRM domains

description: Includes two sets of MAFFT alignments of human RRM domains. The first set contains annotations of all PTMs that exist (April 2017 data from ProteomeScout proteomescout.wustl.edu) on RRM domains and a set that includes just phosphotyrosine and lysine ubiquitination and acetylation (based on analysis in Sloutsky and Naegle).
DOI: 10.6084/m9.figshare.5510422
title: Canine fecal samples

description: To determine the optimal method for fecal DNA preservation, we collected fecal samples from one canine donor and stored aliquots in RNAlater, 70% ethanol, 50:50 glycerol:PBS, or without buffer at 25°C, 4°C, and -80°C. Fecal DNA was extracted, quantified, and 16S rRNA gene analysis performed on days 0, 7, 14, and 56 to evaluate changes in DNA concentration, purity, and microbial diversity and composition over time
DOI: 10.6084/m9.figshare.5510440
title: Datasets - Optimal Charge-to-Spin Conversion in Graphene on Transition-Metal Dichalcogenides

description: Datasets used to generate all figures in main text and supplemental material. All data can be generated using the Mathematica notebook provided in this collection. <br>
DOI: 10.6084/m9.figshare.5510488
title: The Effects of Epidermal Fatty Acid Profiles, 1-oleoglycerol, and Triacylglycerols on the Susceptibility of Hibernating Bats to Pseudogymnoascus destructans.

description: Data summarized in a PLoS ONE article in press.<br>
DOI: 10.6084/m9.figshare.5510251
title: Supplementary Material for: Effectiveness of a Home-Based Active Video Game Programme in Young Cystic Fibrosis Patients

description: <b><i>Background:</i></b> Exercise-based rehabilitation is already a part of cystic fibrosis (CF) treatment; however, patient adherence is low. <b><i>Objectives:</i></b> To assess the effectiveness of a home exercise programme using active video games (AVGs) as a training modality for children and adolescents with CF. <b><i>Methods:</i></b> Thirty-nine children with CF were randomised to a control group (CG, <i>n</i> = 20, age 11 ± 6 years; FEV<sub>1</sub> 86.2 ± 20.5% of predicted) or a training group (AVGG, <i>n</i> = 19, age 13 ± 3 years; FEV<sub>1</sub> 82.7 ± 21.7% of predicted). The home training protocol consisted of 30- to 60-min sessions, 5 days/week, for 6 weeks using a Nintendo Wii™ platform. Exercise capacity was measured by the 6-min walk test (6MWT) and modified shuttle walk test (MSWT); muscular strength was estimated using the horizontal jump test (HJT), medicine ball throw (MBT), and hand grip strength (right [RHG]; left [LHG]); and quality of life was rated using the Cystic Fibrosis Questionnaire-Revised (CFQ-R). All the children were measured at baseline, after rehabilitation, and at 12 months. <b><i>Results:</i></b> For the group × time interaction ANOVAs, the AVGG showed significant between-group differences in exercise capacity: 6MWT farthest walking distance, 38.4 m (<i>p</i> &lt; 0.01); MSWT farthest walking distance, 78.4 m (<i>p</i> &lt; 0.05); and muscular strength: HJT 9.8 cm, MBT 30.8 cm, RHG 7 kg, and LHG 6.5 kg (<i>p</i> &lt; 0.01), before versus after intervention. The CFQ-R reported significantly higher scores on respiratory symptoms after the intervention and favoured the AVGG, and there was an improvement in other domains after 12 months. Adherence to the home exercise programme was 95% during the 6- week intervention period. <b><i>Conclusion:</i></b> A home-based programme using AVGs can effectively improve exercise capacity, muscular strength and quality of life in the short-term in children and adolescents with CF. The effects of training on muscle performance and quality of life were sustained over 12 months.
DOI: 10.6084/m9.figshare.5510488.v1
title: The Effects of Epidermal Fatty Acid Profiles, 1-oleoglycerol, and Triacylglycerols on the Susceptibility of Hibernating Bats to Pseudogymnoascus destructans.

description: Data summarized in a PLoS ONE article in press.<br>
DOI: 10.6084/m9.figshare.5510200
title: Supplementary Material for: Subfoveal Choroidal and Macular Thickness Changes after Phacoemulsification Using Enhanced Depth Imaging Optical Coherence Tomography

description: <b><i>Purpose:</i></b> To assess changes in the thickness of the subfoveal retina and choroid after phacoemulsification using enhanced depth imaging optical coherence tomography (EDI-OCT). <b><i>Methods:</i></b> A prospective study was conducted on 100 patients. The subfoveal choroidal thickness (SFCT) was measured at 7 points and the retinal thickness was measured at 5 points (before surgery, and 1 day, 1 week, 1 month, and 3 months after surgery). <b><i>Results:</i></b> The foveal choroidal thickness showed a thickening trend (but <i>p</i> &gt; 0.05). Compared to the change from baseline to day 1, the changes from baseline were significantly different at nasal 3 mm and 6 mm at all other time points (all <i>p</i> &lt; 0.05). Choroidal thickness changes at temporal 6 mm correlated negatively with intraocular pressure (IOP) at 1 week and 1 month; changes at nasal 3 mm correlated negatively with IOP at 1 week and 1 month (all <i>p</i> &lt; 0.05); changes at nasal 3 mm, temporal 3 mm, and temporal 6 mm correlated with average ultrasonic energy. Choroidal thickness changes correlated with ultrasound (US) time at day 1. <b><i>Conclusions:</i></b> Uncomplicated phacoemulsification led to changes in choroidal thickness. IOP and choroidal thickness changes were negatively correlated. The foveal retinal thickness was correlated with age. SFCT was correlated with sex, axial length, IOP, and US time.
DOI: 10.6084/m9.figshare.5510245
title: Supplementary Material for: Prevalence Estimates of Rare Congenital Anomalies by Integrating Two Population-Based Registries in Tuscany, Italy

description: <b><i>Background/Aims:</i></b> Population-based registries play a key role in the epidemiological surveillance of congenital anomalies (CAs). This study is aimed at improving the epidemiological surveillance and providing prevalence estimates of rare CAs using the Registry of Rare Diseases as an added data source to the Registry of Congenital Anomalies. <b><i>Methods:</i></b> Cases of diagnosed rare CAs (2006-2013) were extracted from the Tuscany Registry of Rare Diseases and the Tuscany Registry of Congenital Anomalies in order to set up an integrated dataset. Prevalence (per 100,000 births; 95% confidence interval) was calculated for each rare CA. <b><i>Results:</i></b> Overall, 56 rare CAs were analyzed including 656 cases, of whom 121 (18.4%) were retrieved from the Registry of Rare Diseases that provided a major contribution for rare CAs for which a prenatal diagnosis is difficult, or for CAs more easily diagnosed in the postneonatal period. After data integration, an increased prevalence estimate was observed in particular for atresia of bile ducts (6.24; 3.57-10.14), tuberous sclerosis (2.34; 0.86-5.10), Kabuki syndrome (1.95; 0.63-4.55), and some monogenic CAs. <b><i>Conclusions:</i></b> This study represents an example of integration of registries operating in the field of rare diseases. Providing the accurate prevalence of rare CAs is a key point to improving surveillance, supporting public health policies, and planning healthcare.
DOI: 10.6084/m9.figshare.5510251.v1
title: Supplementary Material for: Effectiveness of a Home-Based Active Video Game Programme in Young Cystic Fibrosis Patients

description: <b><i>Background:</i></b> Exercise-based rehabilitation is already a part of cystic fibrosis (CF) treatment; however, patient adherence is low. <b><i>Objectives:</i></b> To assess the effectiveness of a home exercise programme using active video games (AVGs) as a training modality for children and adolescents with CF. <b><i>Methods:</i></b> Thirty-nine children with CF were randomised to a control group (CG, <i>n</i> = 20, age 11 ± 6 years; FEV<sub>1</sub> 86.2 ± 20.5% of predicted) or a training group (AVGG, <i>n</i> = 19, age 13 ± 3 years; FEV<sub>1</sub> 82.7 ± 21.7% of predicted). The home training protocol consisted of 30- to 60-min sessions, 5 days/week, for 6 weeks using a Nintendo Wii™ platform. Exercise capacity was measured by the 6-min walk test (6MWT) and modified shuttle walk test (MSWT); muscular strength was estimated using the horizontal jump test (HJT), medicine ball throw (MBT), and hand grip strength (right [RHG]; left [LHG]); and quality of life was rated using the Cystic Fibrosis Questionnaire-Revised (CFQ-R). All the children were measured at baseline, after rehabilitation, and at 12 months. <b><i>Results:</i></b> For the group × time interaction ANOVAs, the AVGG showed significant between-group differences in exercise capacity: 6MWT farthest walking distance, 38.4 m (<i>p</i> &lt; 0.01); MSWT farthest walking distance, 78.4 m (<i>p</i> &lt; 0.05); and muscular strength: HJT 9.8 cm, MBT 30.8 cm, RHG 7 kg, and LHG 6.5 kg (<i>p</i> &lt; 0.01), before versus after intervention. The CFQ-R reported significantly higher scores on respiratory symptoms after the intervention and favoured the AVGG, and there was an improvement in other domains after 12 months. Adherence to the home exercise programme was 95% during the 6- week intervention period. <b><i>Conclusion:</i></b> A home-based programme using AVGs can effectively improve exercise capacity, muscular strength and quality of life in the short-term in children and adolescents with CF. The effects of training on muscle performance and quality of life were sustained over 12 months.
DOI: 10.6084/m9.figshare.5510176
title: Daily stream flow - negative values

description: This zipped file contains 64 x raster stacks containing all negative values of daily stream flow (m3 s-1) for Germany on a 1km gridded stream network for the whole time series (1950-2013). One raster stack represents one year. Each individual layer in the stack contains the daily values for all grid cells on the network. The stack contains every day in the year i.e. 365, or 366 if it is a leap year.
DOI: 10.6084/m9.figshare.5510104
title: Stochastic Spanning

description: This study develops and implements methods for determining whether introducing new securities or relaxing investment constraints improves the investment opportunity set for all risk averse investors. We develop a test procedure for “stochastic spanning” for two nested portfolio sets based on subsampling and linear programming. The test is statistically consistent and asymptotically exact for a class of weakly dependent processes. A Monte Carlo simulation experiment shows good statistical size and power properties in finite samples of realistic dimensions. In an application to standard datasets of historical stock market returns, we accept market portfolio efficiency but reject two-fund separation, which suggests an important role for higher-order moment risk in portfolio theory and asset pricing. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.5510245.v1
title: Supplementary Material for: Prevalence Estimates of Rare Congenital Anomalies by Integrating Two Population-Based Registries in Tuscany, Italy

description: <b><i>Background/Aims:</i></b> Population-based registries play a key role in the epidemiological surveillance of congenital anomalies (CAs). This study is aimed at improving the epidemiological surveillance and providing prevalence estimates of rare CAs using the Registry of Rare Diseases as an added data source to the Registry of Congenital Anomalies. <b><i>Methods:</i></b> Cases of diagnosed rare CAs (2006-2013) were extracted from the Tuscany Registry of Rare Diseases and the Tuscany Registry of Congenital Anomalies in order to set up an integrated dataset. Prevalence (per 100,000 births; 95% confidence interval) was calculated for each rare CA. <b><i>Results:</i></b> Overall, 56 rare CAs were analyzed including 656 cases, of whom 121 (18.4%) were retrieved from the Registry of Rare Diseases that provided a major contribution for rare CAs for which a prenatal diagnosis is difficult, or for CAs more easily diagnosed in the postneonatal period. After data integration, an increased prevalence estimate was observed in particular for atresia of bile ducts (6.24; 3.57-10.14), tuberous sclerosis (2.34; 0.86-5.10), Kabuki syndrome (1.95; 0.63-4.55), and some monogenic CAs. <b><i>Conclusions:</i></b> This study represents an example of integration of registries operating in the field of rare diseases. Providing the accurate prevalence of rare CAs is a key point to improving surveillance, supporting public health policies, and planning healthcare.
DOI: 10.6084/m9.figshare.5510101
title: Estimation of Models With Multiple-Valued Explanatory Variables

description: We study estimation and inference when there are multiple values (“matches”) for the explanatory variables and only one of the matches is the correct one. This problem arises often when two datasets are linked together on the basis of information that does not uniquely identify regressor values. We offer a set of two intuitive conditions that ensure consistent inference using the average of the possible matches in a linear framework. The first condition is the exogeneity of the false match with respect to the regression error. The second condition is a notion of exchangeability between the true and false matches. Conditioning on the observed data, the probability that each match is correct is completely unrestricted. We perform a Monte Carlo study to investigate the estimator’s finite-sample performance relative to others proposed in the literature. Finally, we provide an empirical example revisiting a main area of application: the measurement of intergenerational elasticities in income. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.5510176.v1
title: Daily stream flow - negative values

description: This zipped file contains 64 x raster stacks containing all negative values of daily stream flow (m3 s-1) for Germany on a 1km gridded stream network for the whole time series (1950-2013). One raster stack represents one year. Each individual layer in the stack contains the daily values for all grid cells on the network. The stack contains every day in the year i.e. 365, or 366 if it is a leap year.
DOI: 10.6084/m9.figshare.5510200.v1
title: Supplementary Material for: Subfoveal Choroidal and Macular Thickness Changes after Phacoemulsification Using Enhanced Depth Imaging Optical Coherence Tomography

description: <b><i>Purpose:</i></b> To assess changes in the thickness of the subfoveal retina and choroid after phacoemulsification using enhanced depth imaging optical coherence tomography (EDI-OCT). <b><i>Methods:</i></b> A prospective study was conducted on 100 patients. The subfoveal choroidal thickness (SFCT) was measured at 7 points and the retinal thickness was measured at 5 points (before surgery, and 1 day, 1 week, 1 month, and 3 months after surgery). <b><i>Results:</i></b> The foveal choroidal thickness showed a thickening trend (but <i>p</i> &gt; 0.05). Compared to the change from baseline to day 1, the changes from baseline were significantly different at nasal 3 mm and 6 mm at all other time points (all <i>p</i> &lt; 0.05). Choroidal thickness changes at temporal 6 mm correlated negatively with intraocular pressure (IOP) at 1 week and 1 month; changes at nasal 3 mm correlated negatively with IOP at 1 week and 1 month (all <i>p</i> &lt; 0.05); changes at nasal 3 mm, temporal 3 mm, and temporal 6 mm correlated with average ultrasonic energy. Choroidal thickness changes correlated with ultrasound (US) time at day 1. <b><i>Conclusions:</i></b> Uncomplicated phacoemulsification led to changes in choroidal thickness. IOP and choroidal thickness changes were negatively correlated. The foveal retinal thickness was correlated with age. SFCT was correlated with sex, axial length, IOP, and US time.