cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5427310.v1
title: Gazepoint GP3 manuscript code and data

description: All code, functions, and data required to generate the plots in the manuscript titled "Assessing the performance of the Gazepoint GP3 eye-tracker for gaze event detection using a visual search task" by Notaro et al, using main script GNotaro_Gazepointmainscript.m. The code produces plots regarding gaze event detection (i.e. short fixation events) within a visual search task. <br>(Note: run main .m script and reference Matlab data folder within matlab.zip when prompted; original raw data files in gazepointdata.zip; matlab variable eparticipant with all random indexes and values reported in manuscript located in eparticipant_struct.mat (in compressed .rar file here); if errors, check paths to files and functions!)<br>All human data anonymized and acquired under approved CPHS protocol (#21522)
DOI: 10.6084/m9.figshare.5427253
title: Integrated view of Vibrio cholerae in the Americas

description: Latin America has experienced two of the largest cholera epidemics in modern history; one in 1991 and the other in 2010. However, confusion still surrounds the relationships between globally circulating pandemic <i>Vibrio cholerae</i> clones and local bacterial populations. We used whole-genome sequencing to characterize cholera across the Americas over a 40-year time span. We found that both epidemics were the result of intercontinental introductions of seventh pandemic El Tor<i> </i><i>V. cholerae</i> and that at least nine lineages local to the Americas are associated with disease that differs epidemiologically from epidemic cholera. Our results consolidate historical accounts of pandemic cholera with data to show the significance of local lineages, presenting an integrated view of cholera that is important to the design of future disease control strategies.
DOI: 10.6084/m9.figshare.5427277.v2
title: The Evolution of Institutional Repository Technology and Scholarly Communications

description: A webinar with advice and perspectives from experts on the future directions for the institutional repository
DOI: 10.6084/m9.figshare.5427271.v2
title: Hierarchical Low Rank Approximation of Likelihoods for Large Spatial Datasets

description: Datasets in the fields of climate and environment are often very large and irregularly spaced. To model such datasets, the widely used Gaussian process models in spatial statistics face tremendous challenges due to the prohibitive computational burden. Various approximation methods have been introduced to reduce the computational cost. However, most of them rely on unrealistic assumptions for the underlying process and retaining statistical efficiency remains an issue. We develop a new approximation scheme for maximum likelihood estimation. We show how the composite likelihood method can be adapted to provide different types of hierarchical low rank approximations that are both computationally and statistically efficient. The improvement of the proposed method is explored theoretically; the performance is investigated by numerical and simulation studies; and the practicality is illustrated through applying our methods to two million measurements of soil moisture in the area of the Mississippi River basin, which facilitates a better understanding of the climate variability. Supplementary material for this article is available online.
DOI: 10.6084/m9.figshare.5427271.v1
title: Hierarchical Low Rank Approximation of Likelihoods for Large Spatial Datasets

description: Datasets in the fields of climate and environment are often very large and irregularly spaced. To model such datasets, the widely used Gaussian process models in spatial statistics face tremendous challenges due to the prohibitive computational burden. Various approximation methods have been introduced to reduce the computational cost. However, most of them rely on unrealistic assumptions for the underlying process and retaining statistical efficiency remains an issue. We develop a new approximation scheme for maximum likelihood estimation. We show how the composite likelihood method can be adapted to provide different types of hierarchical low rank approximations that are both computationally and statistically efficient. The improvement of the proposed method is explored theoretically; the performance is investigated by numerical and simulation studies; and the practicality is illustrated through applying our methods to 2 million measurements of soil moisture in the area of the Mississippi River basin, which facilitates a better understanding of the climate variability.
DOI: 10.6084/m9.figshare.5427229
title: The pro-apoptotic BAX protein influences cell growth and differentiation from the nucleus in healthy interphasic cells

description: It has become more and more evident that the BCL-2 family proteins mediate a wide range of non-apoptotic functions. The pro-apoptotic BAX protein has been reported in interphasic nuclei. Whether the nuclear form of BAX could be involved in non-apoptotic function is still unknown. Our study showed for the first time that BAX was associated with chromatin in vitro. Next, we used gain and loss of function approaches to decipher the potential role of nuclear BAX in non-apoptotic cells. In vitro, nuclear BAX promoted cell proliferation in lung epithelial cells and primary human lung fibroblasts by modulating CDKN1A expression. Interestingly, BAX occupancy of <i>CDKN1A</i> promoter was specifically enriched close to the transcription-starting site. Nuclear BAX also modulated the basal myofibroblastic differentiation and migration of primary human lung fibroblasts. Finally, BAX nuclear localization was associated in vivo with the remodelling of lung parenchyma during development, tumorigenesis as well as fibrosis compared to control adult human lungs. Hence, our study established for the first time, a strong link between the nuclear localization of the pro-apoptotic BAX protein and key basic cellular functions in the non-apoptotic setting.
DOI: 10.6084/m9.figshare.5427229.v1
title: The pro-apoptotic BAX protein influences cell growth and differentiation from the nucleus in healthy interphasic cells

description: It has become more and more evident that the BCL-2 family proteins mediate a wide range of non-apoptotic functions. The pro-apoptotic BAX protein has been reported in interphasic nuclei. Whether the nuclear form of BAX could be involved in non-apoptotic function is still unknown. Our study showed for the first time that BAX was associated with chromatin in vitro. Next, we used gain and loss of function approaches to decipher the potential role of nuclear BAX in non-apoptotic cells. In vitro, nuclear BAX promoted cell proliferation in lung epithelial cells and primary human lung fibroblasts by modulating CDKN1A expression. Interestingly, BAX occupancy of <i>CDKN1A</i> promoter was specifically enriched close to the transcription-starting site. Nuclear BAX also modulated the basal myofibroblastic differentiation and migration of primary human lung fibroblasts. Finally, BAX nuclear localization was associated in vivo with the remodelling of lung parenchyma during development, tumorigenesis as well as fibrosis compared to control adult human lungs. Hence, our study established for the first time, a strong link between the nuclear localization of the pro-apoptotic BAX protein and key basic cellular functions in the non-apoptotic setting.
DOI: 10.6084/m9.figshare.5427181.v1
title: Analysis of the small non-protein-coding RNA profile of mouse spermatozoa reveals specific enrichment of piRNAs within mature spermatozoa

description: Post-testicular sperm maturation and storage within the epididymis is a key determinant of gamete quality and fertilization competence. Here we demonstrate that mouse spermatozoa possess a complex small non-protein-coding RNA (sRNA) profile, the composition of which is markedly influenced by their epididymal transit. Thus, although microRNAs (miRNAs) are highly represented in the spermatozoa of the proximal epididymis, this sRNA class is largely diminished in mature spermatozoa of the distal epididymis. Coincident with this, a substantial enrichment in Piwi-interacting RNA (piRNA) abundance in cauda spermatozoa was detected. Further, features of cauda piRNAs, including; predominantly 29–31 nts in length; preference for uracil at their 5' terminus; no adenine enrichment at piRNA nt 10, and; predominantly mapping to intergenic regions of the mouse genome, indicate that these piRNAs are generated by the PIWIL1-directed primary piRNA production pathway. Accordingly, PIWIL1 was detected via immunoblotting and mass spectrometry in epididymal spermatozoa. These data provide insight into the complexity and dynamic nature of the sRNA profile of spermatozoa and raise the intriguing prospect that piRNAs are generated <i>in situ</i> in maturing spermatozoa. Such information is of particular interest in view of the potential role for paternal sRNAs in influencing conception, embryo development and intergenerational inheritance.
DOI: 10.6084/m9.figshare.5427139
title: Unintentional non-traffic injury and fatal events: Threats to children in and around vehicles

description: <b>Objective</b>: There have been substantial reductions in motor vehicle crash–related child fatalities due to advances in legislation, public safety campaigns, and engineering. Less is known about non-traffic injuries and fatalities to children in and around motor vehicles. The objective of this study was to describe the frequency of various non-traffic incidents, injuries, and fatalities to children using a unique surveillance system and database. <b>Methods</b>: Instances of non-traffic injuries and fatalities in the United States to children 0–14 years were tracked from January 1990 to December 2014 using a compilation of sources including media reports, individual accounts from families of affected children, medical examiner reports, police reports, child death review teams, coroner reports, medical professionals, legal professionals, and other various modes of publication. <b>Results</b>: Over the 25-year period, there were at least 11,759 events resulting in 3,396 deaths. The median age of the affected child was 3.7 years. The incident types included 3,115 children unattended in hot vehicles resulting in 729 deaths, 2,251 backovers resulting in 1,232 deaths, 1,439 frontovers resulting in 692 deaths, 777 vehicles knocked into motion resulting in 227 deaths, 415 underage drivers resulting in 203 deaths, 172 power window incidents resulting in 61 deaths, 134 falls resulting in 54 deaths, 79 fires resulting in 41 deaths, and 3,377 other incidents resulting in 157 deaths. <b>Conclusions</b>: Non-traffic injuries and fatalities present an important threat to the safety and lives of very young children. Future efforts should consider complementary surveillance mechanisms to systematically and comprehensively capture all non-traffic incidents. Continued education, engineering modifications, advocacy, and legislation can help continue to prevent these incidents and must be incorporated in overall child vehicle safety initiatives.
DOI: 10.6084/m9.figshare.5427139.v1
title: Unintentional nontraffic injury and fatal events: threats to children in and around vehicles

description: <b>Objective</b> There have been substantial reductions in motor vehicle crash-related child fatalities due to advances in legislation, public safety campaigns, and engineering. Less is known about nontraffic injuries and fatalities to children in and around motor vehicles. The objective of this study was to describe the frequency of various nontraffic incidents, injuries, and fatalities to children using a unique surveillance system and database. <b>Methods</b> Instances of nontraffic injuries and fatalities in the United States to children 0–14 years were tracked from January 1990 – December 2014 using a compilation of sources including media reports, individual accounts from families of affected children, medical examiner reports, police reports, child death review teams, coroner reports, medical professionals, legal professionals, and other various modes of publication. <b>Results</b> Over the 25-year period, there were at least 11,759 events resulting in 3,396 deaths. The median age of the affected child was 3.7 years. The incident types included 3,115 children unattended in hot vehicles 729 deaths, 2,251 backovers 1,232 deaths, 1,439 frontovers 692 deaths, 777 vehicles knocked into motion 227 deaths, 415 underage drivers 203 deaths, 172 power window incidents 61 deaths, 134 falls 54 deaths and 79 fires 41 deaths, and 3,377 other incidents 157 deaths. <b>Conclusions</b> Nontraffic injuries and fatalities present an important threat to the safety and lives of very young children. Future efforts should consider complimentary surveillance mechanisms to systematically and comprehensively capture of all nontraffic incidents. Continued education, engineering modifications, advocacy, and legislation can help continue to prevent these incidents and must be incorporated in overall child vehicle safety initiatives.
DOI: 10.6084/m9.figshare.5427001
title: Metadata associated with seasonal influenza A(H3N2) viruses sampled in the 2014/15 season in Scotland.

description: Dataset associated with 150 influenza A(H3N2) positive clinical specimens with linked epidemiological data, from the 2014/15 season in Scotland. Sample metadata consists of GISAID isolate ID, strain name, sample ID, date of sampling, week of influenza season sampled, Health Board (AA=Ayrshire and Arran, BR=Borders, DG=Dumfries and Galloway, FF=Fife, FV=Forth Valley, GGC=Greater Glasgow and Clyde, GR=Grampian, HG=Highlands, LN=Lanarkshire, LO=Lothian, TA=Tayside), patient age, severe acute respiratory illness (SARI) status, whether the virus was identified as an inter-subgroup reassortant, whether the sample was identified as reassortant using the GiRaF software, and the inferred genetic lineage of each gene segment.
DOI: 10.6084/m9.figshare.5427139.v2
title: Unintentional non-traffic injury and fatal events: Threats to children in and around vehicles

description: <b>Objective</b>: There have been substantial reductions in motor vehicle crash–related child fatalities due to advances in legislation, public safety campaigns, and engineering. Less is known about non-traffic injuries and fatalities to children in and around motor vehicles. The objective of this study was to describe the frequency of various non-traffic incidents, injuries, and fatalities to children using a unique surveillance system and database. <b>Methods</b>: Instances of non-traffic injuries and fatalities in the United States to children 0–14 years were tracked from January 1990 to December 2014 using a compilation of sources including media reports, individual accounts from families of affected children, medical examiner reports, police reports, child death review teams, coroner reports, medical professionals, legal professionals, and other various modes of publication. <b>Results</b>: Over the 25-year period, there were at least 11,759 events resulting in 3,396 deaths. The median age of the affected child was 3.7 years. The incident types included 3,115 children unattended in hot vehicles resulting in 729 deaths, 2,251 backovers resulting in 1,232 deaths, 1,439 frontovers resulting in 692 deaths, 777 vehicles knocked into motion resulting in 227 deaths, 415 underage drivers resulting in 203 deaths, 172 power window incidents resulting in 61 deaths, 134 falls resulting in 54 deaths, 79 fires resulting in 41 deaths, and 3,377 other incidents resulting in 157 deaths. <b>Conclusions</b>: Non-traffic injuries and fatalities present an important threat to the safety and lives of very young children. Future efforts should consider complementary surveillance mechanisms to systematically and comprehensively capture all non-traffic incidents. Continued education, engineering modifications, advocacy, and legislation can help continue to prevent these incidents and must be incorporated in overall child vehicle safety initiatives.
DOI: 10.6084/m9.figshare.5427001.v1
title: Metadata associated with seasonal influenza A(H3N2) viruses sampled in the 2014/15 season in Scotland.

description: Dataset associated with 150 influenza A(H3N2) positive clinical specimens with linked epidemiological data, from the 2014/15 season in Scotland. Sample metadata consists of GISAID isolate ID, strain name, sample ID, date of sampling, week of influenza season sampled, Health Board (AA=Ayrshire and Arran, BR=Borders, DG=Dumfries and Galloway, FF=Fife, FV=Forth Valley, GGC=Greater Glasgow and Clyde, GR=Grampian, HG=Highlands, LN=Lanarkshire, LO=Lothian, TA=Tayside), patient age, severe acute respiratory illness (SARI) status, whether the virus was identified as an inter-subgroup reassortant, whether the sample was identified as reassortant using the GiRaF software, and the inferred genetic lineage of each gene segment.
DOI: 10.6084/m9.figshare.5427139.v4
title: Unintentional non-traffic injury and fatal events: Threats to children in and around vehicles

description: <b>Objective</b>: There have been substantial reductions in motor vehicle crash–related child fatalities due to advances in legislation, public safety campaigns, and engineering. Less is known about non-traffic injuries and fatalities to children in and around motor vehicles. The objective of this study was to describe the frequency of various non-traffic incidents, injuries, and fatalities to children using a unique surveillance system and database. <b>Methods</b>: Instances of non-traffic injuries and fatalities in the United States to children 0–14 years were tracked from January 1990 to December 2014 using a compilation of sources including media reports, individual accounts from families of affected children, medical examiner reports, police reports, child death review teams, coroner reports, medical professionals, legal professionals, and other various modes of publication. <b>Results</b>: Over the 25-year period, there were at least 11,759 events resulting in 3,396 deaths. The median age of the affected child was 3.7 years. The incident types included 3,115 children unattended in hot vehicles resulting in 729 deaths, 2,251 backovers resulting in 1,232 deaths, 1,439 frontovers resulting in 692 deaths, 777 vehicles knocked into motion resulting in 227 deaths, 415 underage drivers resulting in 203 deaths, 172 power window incidents resulting in 61 deaths, 134 falls resulting in 54 deaths, 79 fires resulting in 41 deaths, and 3,377 other incidents resulting in 157 deaths. <b>Conclusions</b>: Non-traffic injuries and fatalities present an important threat to the safety and lives of very young children. Future efforts should consider complementary surveillance mechanisms to systematically and comprehensively capture all non-traffic incidents. Continued education, engineering modifications, advocacy, and legislation can help continue to prevent these incidents and must be incorporated in overall child vehicle safety initiatives.
DOI: 10.6084/m9.figshare.5427139.v3
title: Unintentional non-traffic injury and fatal events: Threats to children in and around vehicles

description: <b>Objective</b>: There have been substantial reductions in motor vehicle crash–related child fatalities due to advances in legislation, public safety campaigns, and engineering. Less is known about non-traffic injuries and fatalities to children in and around motor vehicles. The objective of this study was to describe the frequency of various non-traffic incidents, injuries, and fatalities to children using a unique surveillance system and database. <b>Methods</b>: Instances of non-traffic injuries and fatalities in the United States to children 0–14 years were tracked from January 1990 to December 2014 using a compilation of sources including media reports, individual accounts from families of affected children, medical examiner reports, police reports, child death review teams, coroner reports, medical professionals, legal professionals, and other various modes of publication. <b>Results</b>: Over the 25-year period, there were at least 11,759 events resulting in 3,396 deaths. The median age of the affected child was 3.7 years. The incident types included 3,115 children unattended in hot vehicles resulting in 729 deaths, 2,251 backovers resulting in 1,232 deaths, 1,439 frontovers resulting in 692 deaths, 777 vehicles knocked into motion resulting in 227 deaths, 415 underage drivers resulting in 203 deaths, 172 power window incidents resulting in 61 deaths, 134 falls resulting in 54 deaths, 79 fires resulting in 41 deaths, and 3,377 other incidents resulting in 157 deaths. <b>Conclusions</b>: Non-traffic injuries and fatalities present an important threat to the safety and lives of very young children. Future efforts should consider complementary surveillance mechanisms to systematically and comprehensively capture all non-traffic incidents. Continued education, engineering modifications, advocacy, and legislation can help continue to prevent these incidents and must be incorporated in overall child vehicle safety initiatives.
DOI: 10.6084/m9.figshare.5426737
title: Kettering General Hospital NHS Foundation Trust

description: Response to our Freedom of Information Act request received from this NHS Trust.
DOI: 10.6084/m9.figshare.5426737.v1
title: Kettering General Hospital NHS Foundation Trust

description: Response to our Freedom of Information Act request received from this NHS Trust.
DOI: 10.4225/22/59c3b22d40756
title: Supplementary tables and CONSORT diagram for the HIP trial

description: Tables 1 through 6CONSORT flow diagram
DOI: 10.6084/m9.figshare.5426728
title: Kent and Medway NHS and Social Care Partnership Trust

description: Response to our Freedom of Information Act request received from this NHS Trust.
DOI: 10.6084/m9.figshare.5426734
title: Kent Community Health NHS Foundation Trust

description: Response to our Freedom of Information Act request received from this NHS Trust.<br>
DOI: 10.6084/m9.figshare.5426719
title: Isle Of Wight NHS Trust

description: Response to our Freedom of Information Act request received from this NHS Trust.
DOI: 10.6084/m9.figshare.5426722
title: James Paget University Hospitals NHS Foundation Trust

description: Response to our Freedom of Information Act request received from this NHS Trust.
DOI: 10.6084/m9.figshare.5426725
title: PathTrace Demo (BLAST output)

description: This is the BLAST output file, produced by running BLAST for the PathTrace Demo (Query) FASTA file against PathTrace Demo (Target) sequences.<br>This BLAST output was used for the PathTrace Case Study (https://github.com/CGU-CERTH/PathTrace)
DOI: 10.6084/m9.figshare.5426728.v1
title: Kent and Medway NHS and Social Care Partnership Trust

description: Response to our Freedom of Information Act request received from this NHS Trust.
DOI: 10.6084/m9.figshare.5426722.v1
title: James Paget University Hospitals NHS Foundation Trust

description: Response to our Freedom of Information Act request received from this NHS Trust.
DOI: 10.6084/m9.figshare.5426734.v1
title: Kent Community Health NHS Foundation Trust

description: Response to our Freedom of Information Act request received from this NHS Trust.<br>
DOI: 10.6084/m9.figshare.5426713
title: Humber NHS Foundation Trust

description: Response to our Freedom of Information Act request received from this NHS Trust.
DOI: 10.6084/m9.figshare.5426716
title: Imperial College Healthcare NHS Trust

description: Response to our Freedom of Information Act request received from this NHS Trust.
DOI: 10.6084/m9.figshare.5426719.v1
title: Isle Of Wight NHS Trust

description: Response to our Freedom of Information Act request received from this NHS Trust.
DOI: 10.6084/m9.figshare.5426725.v1
title: PathTrace Demo (BLAST output)

description: This is the BLAST output file, produced by running BLAST for the PathTrace Demo (Query) FASTA file against PathTrace Demo (Target) sequences.<br>This BLAST output was used for the PathTrace Case Study (https://github.com/CGU-CERTH/PathTrace)