cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7312598
title: Supplementary Table 2 from Phosphorylation of Parkin at serine 65 is essential for its activation <i>in vivo</i>

description: Mutations in PINK1 and Parkin result in autosomal recessive Parkinson's disease (PD). Cell culture and <i>in vitro</i> studies have elaborated the PINK1-dependent regulation of Parkin and defined how this dyad orchestrates the elimination of damaged mitochondria via mitophagy. PINK1 phosphorylates ubiquitin at serine 65 (Ser65) and Parkin at an equivalent Ser65 residue located within its N-terminal ubiquitin-like domain, resulting in activation; however, the physiological significance of Parkin Ser65 phosphorylation <i>in vivo</i> in mammals remains unknown. To address this, we generated a <i>Parkin</i> Ser65Ala (S65A) knock-in mouse model. We observe endogenous Parkin Ser65 phosphorylation and activation in mature primary neurons following mitochondrial depolarization and reveal this is disrupted in <i>Parkin</i><sup>S65A/S65A</sup> neurons. Phenotypically, <i>Parkin</i><sup>S65A/S65A</sup> mice exhibit selective motor dysfunction in the absence of any overt neurodegeneration or alterations in nigrostriatal mitophagy. The clinical relevance of our findings is substantiated by the discovery of homozygous PARKIN (<i>PARK2</i>) p.S65N mutations in two unrelated patients with PD. Moreover, biochemical and structural analysis demonstrates that the Parkin<sup>S65N/S65N</sup> mutant is pathogenic and cannot be activated by PINK1. Our findings highlight the central role of Parkin Ser65 phosphorylation in health and disease.
DOI: 10.7284/126710
title: Gravimeter data collected during research cruise RR1713 using a Bell BGM-3 instrument system onboard the platform RV Roger Revelle

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7312592
title: Supplemental table 2 - Aguirre

description: <b>Supplemental Table 2. </b>Testosterone levels between those who were affected by the change in target testosterone levels and those who were not. <br>
DOI: 10.6084/m9.figshare.7312598.v1
title: Supplementary Table 2 from Phosphorylation of Parkin at serine 65 is essential for its activation <i>in vivo</i>

description: Mutations in PINK1 and Parkin result in autosomal recessive Parkinson's disease (PD). Cell culture and <i>in vitro</i> studies have elaborated the PINK1-dependent regulation of Parkin and defined how this dyad orchestrates the elimination of damaged mitochondria via mitophagy. PINK1 phosphorylates ubiquitin at serine 65 (Ser65) and Parkin at an equivalent Ser65 residue located within its N-terminal ubiquitin-like domain, resulting in activation; however, the physiological significance of Parkin Ser65 phosphorylation <i>in vivo</i> in mammals remains unknown. To address this, we generated a <i>Parkin</i> Ser65Ala (S65A) knock-in mouse model. We observe endogenous Parkin Ser65 phosphorylation and activation in mature primary neurons following mitochondrial depolarization and reveal this is disrupted in <i>Parkin</i><sup>S65A/S65A</sup> neurons. Phenotypically, <i>Parkin</i><sup>S65A/S65A</sup> mice exhibit selective motor dysfunction in the absence of any overt neurodegeneration or alterations in nigrostriatal mitophagy. The clinical relevance of our findings is substantiated by the discovery of homozygous PARKIN (<i>PARK2</i>) p.S65N mutations in two unrelated patients with PD. Moreover, biochemical and structural analysis demonstrates that the Parkin<sup>S65N/S65N</sup> mutant is pathogenic and cannot be activated by PINK1. Our findings highlight the central role of Parkin Ser65 phosphorylation in health and disease.
DOI: 10.6084/m9.figshare.7312586
title: Supplemental table 1 - Aguirre

description: <b>Supplemental Table 1</b>. Table of outcomes<br>
DOI: 10.6084/m9.figshare.7312592.v1
title: Supplemental table 2 - Aguirre

description: <b>Supplemental Table 2. </b>Testosterone levels between those who were affected by the change in target testosterone levels and those who were not. <br>
DOI: 10.7284/126714
title: HDSS (Hydrographic Doppler Sonar System) data collected during research cruise RR1713 using a SIO HDSS instrument system onboard the platform RV Roger Revelle

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7312370
title: Supplemental tables one to three - Aguirre

description: <b>Supplemental Table 1</b>. Table of outcomes<br><b>Supplemental Table 2. </b>Testosterone levels between those who were affected by the change in target testosterone levels and those who were not. <br><br><b>Supplemental Table 3</b>. Adverse Events After 18 Months of Testosterone Therapy<br>
DOI: 10.6084/m9.figshare.7312370.v1
title: Supplemental tables one to three - Aguirre

description: <b>Supplemental Table 1</b>. Table of outcomes<br><b>Supplemental Table 2. </b>Testosterone levels between those who were affected by the change in target testosterone levels and those who were not. <br><br><b>Supplemental Table 3</b>. Adverse Events After 18 Months of Testosterone Therapy<br>
DOI: 10.6084/m9.figshare.7312586.v1
title: Supplemental table 1 - Aguirre

description: <b>Supplemental Table 1</b>. Table of outcomes<br>
DOI: 10.7284/126713
title: INS (Inertial Navigation System) data collected during research cruise RR1713 using a iXSea Phins instrument system onboard the platform RV Roger Revelle

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7312337
title: Mesh feed spacer under forward and reverse flow with fluorescent beads to track flow paths.

description: Conventional mesh feed spacers in the spiral wound elements contribute to membrane fouling. The attached video shows the flow profile using 1.9 μm diameter fluorescent green styrene beads purchased from Bangs Laboratories (Fishers, IN) confirming the flow profiles predicted by CFD modeling by different researcher
DOI: 10.6084/m9.figshare.7312337.v1
title: Mesh feed spacer under forward and reverse flow with fluorescent beads to track flow paths.

description: Conventional mesh feed spacers in the spiral wound elements contribute to membrane fouling. The attached video shows the flow profile using 1.9 μm diameter fluorescent green styrene beads purchased from Bangs Laboratories (Fishers, IN) confirming the flow profiles predicted by CFD modeling by different researcher
DOI: 10.7284/126718
title: INS (Inertial Navigation System) data collected during research cruise RR1713 using a Kongsberg Seapath 320+ instrument system onboard the platform RV Roger Revelle

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/126705
title: Meteorological Station data collected during research cruise RR1713 using a SIO MET-System instrument system onboard the platform RV Roger Revelle

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/126708
title: Multibeam Echosounder data collected during research cruise RR1713 using a Kongsberg EM122 instrument system onboard the platform RV Roger Revelle

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7312283
title: IIPC Presentation.pptx

description: <sub>Presentation to web-archiving conference 2018 in Wellington. Title "Utilizing the Internet Archive while retiring legacy websites and establishing a digital preservation system".</sub><br><sub><br></sub><sub><br></sub>
DOI: 10.7284/128408
title: Multibeam Echosounder data collected during research cruise RR1713 using a Kongsberg EM122 instrument system onboard the platform RV Roger Revelle

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/126712
title: Winch data collected during research cruise RR1713 using a Markey DUTW-9-11 instrument system onboard the platform RV Roger Revelle

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/126716
title: Winch data collected during research cruise RR1713 using a Markey DUSH-5 instrument system onboard the platform RV Roger Revelle

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7312283.v3
title: IIPC Presentation.pptx

description: <sub>Presentation to web-archiving conference 2018 in Wellington. Title "Utilizing the Internet Archive while retiring legacy websites and establishing a digital preservation system".</sub><br><sub><br></sub><sub><br></sub>
DOI: 10.7284/128241
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise RR1714 using a Hawaii UHDAS instrument system onboard the platform RV Roger Revelle

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7312271
title: Messy Directory Teaching Example

description: Files for an exercise on file, data, and code documentation and organization. <br>Files can be used to help students identify problems that make it difficult to share or reuse analyses. There are many problems with the folder structure, file naming, data organization, and code organization in this exampledirectory. <br>This was originally created for the NEON Data Science Institute 2016 (https://www.neonscience.org/neon-data-institute-2016) by Naupaka Zimmerman (https://github.com/naupaka).The data and files are for the most part derived from various NEON remote sensing (AOP) products from the D17 California sites.<br>Students can be shown the introductory slides (http://neonscience.github.io/slide-shows/intro-reprod-science.html) and then asked to identify problems in the directory.<br>This fileset is designed as a teaching example. No data in this fileset should be used for research. Please visit data.neonscience.org for research data. <br>
DOI: 10.6084/m9.figshare.7312271.v1
title: Messy Directory Teaching Example

description: Files for an exercise on file, data, and code documentation and organization. <br>Files can be used to help students identify problems that make it difficult to share or reuse analyses. There are many problems with the folder structure, file naming, data organization, and code organization in this exampledirectory. <br>This was originally created for the NEON Data Science Institute 2016 (https://www.neonscience.org/neon-data-institute-2016) by Naupaka Zimmerman (https://github.com/naupaka).The data and files are for the most part derived from various NEON remote sensing (AOP) products from the D17 California sites.<br>Students can be shown the introductory slides (http://neonscience.github.io/slide-shows/intro-reprod-science.html) and then asked to identify problems in the directory.<br>This fileset is designed as a teaching example. No data in this fileset should be used for research. Please visit data.neonscience.org for research data. <br>
DOI: 10.6084/m9.figshare.7312283.v4
title: IIPC Presentation.pptx

description: <sub>Presentation to web-archiving conference 2018 in Wellington. Title "Utilizing the Internet Archive while retiring legacy websites and establishing a digital preservation system".</sub><br><sub><br></sub><sub><br></sub>
DOI: 10.6084/m9.figshare.7312265
title: Simple Structure Detection Through Bayesian Exploratory Multidimensional IRT Models

description: In modern validity theory, a major concern is the construct validity of a test, which is commonly assessed through confirmatory or exploratory factor analysis. In the framework of Bayesian exploratory Multidimensional Item Response Theory (MIRT) models, we discuss two methods aimed at investigating the underlying structure of a test, in order to verify if the latent model adheres to a chosen simple factorial structure. This purpose is achieved without imposing hard constraints on the discrimination parameter matrix to address the rotational indeterminacy. The first approach prescribes a 2-step procedure. The parameter estimates are obtained through an unconstrained MCMC sampler. The simple structure is, then, inspected with a post-processing step based on the Consensus Simple Target Rotation technique. In the second approach, both rotational invariance and simple structure retrieval are addressed within the MCMC sampling scheme, by introducing a sparsity-inducing prior on the discrimination parameters. Through simulation as well as real-world studies, we demonstrate that the proposed methods are able to correctly infer the underlying sparse structure and to retrieve interpretable solutions.
DOI: 10.7284/128250
title: CTD (Conductivity, Temperature, Depth) data collected during research cruise RR1714 using a Sea-Bird SBE-911+ instrument system onboard the platform RV Roger Revelle

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7312265.v2
title: Simple Structure Detection Through Bayesian Exploratory Multidimensional IRT Models

description: In modern validity theory, a major concern is the construct validity of a test, which is commonly assessed through confirmatory or exploratory factor analysis. In the framework of Bayesian exploratory Multidimensional Item Response Theory (MIRT) models, we discuss two methods aimed at investigating the underlying structure of a test, in order to verify if the latent model adheres to a chosen simple factorial structure. This purpose is achieved without imposing hard constraints on the discrimination parameter matrix to address the rotational indeterminacy. The first approach prescribes a 2-step procedure. The parameter estimates are obtained through an unconstrained MCMC sampler. The simple structure is, then, inspected with a post-processing step based on the Consensus Simple Target Rotation technique. In the second approach, both rotational invariance and simple structure retrieval are addressed within the MCMC sampling scheme, by introducing a sparsity-inducing prior on the discrimination parameters. Through simulation as well as real-world studies, we demonstrate that the proposed methods are able to correctly infer the underlying sparse structure and to retrieve interpretable solutions.
DOI: 10.7284/128254
title: Expendable Probe data collected during research cruise RR1714 using a Turo Quoll instrument system onboard the platform RV Roger Revelle

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7312265.v1
title: Simple Structure Detection Through Bayesian Exploratory Multidimensional IRT Models

description: In modern validity theory, a major concern is the construct validity of a test, which is commonly assessed through confirmatory or exploratory factor analysis. In the framework of Bayesian exploratory Multidimensional Item Response Theory (MIRT) models, we discuss two methods aimed at investigating the underlying structure of a test, in order to verify if the latent model adheres to a chosen simple factorial structure. This purpose is achieved without imposing hard constraints on the discrimination parameter matrix to address the rotational indeterminacy. The first approach prescribes a 2-step procedure. The parameter estimates are obtained through an unconstrained MCMC sampler. The simple structure is, then, inspected with a post-processing step based on the Consensus Simple Target Rotation technique. In the second approach, both rotational invariance and simple structure retrieval are addressed within the MCMC sampling scheme, by introducing a sparsity-inducing prior on the discrimination parameters. Through simulation as well as real-world studies, we demonstrate that the proposed methods are able to correctly infer the underlying sparse structure and to retrieve interpretable solutions.
DOI: 10.7284/128242
title: GNSS (Global Navigation Satellite System) data collected during research cruise RR1714 using a Furuno GP-150 instrument system onboard the platform RV Roger Revelle

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/128244
title: GNSS (Global Navigation Satellite System) data collected during research cruise RR1714 using a Ashtech ADU2 instrument system onboard the platform RV Roger Revelle

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7312247
title: Dataset for: The role of infectious disease in the evolution of females: evidence from anther-smut disease on a gynodioecious alpine carnation.

description: In flowering plants, the evolution of females is widely hypothesized to be the first step in the evolutionary pathway to separate male and female sexes, or dioecy. Natural enemies have the potential to drive this evolution if they preferentially attack hermaphrodites over females. We studied sex-based differences in exposure to anther-smut (<i>Microbotryum</i>), a sterilizing pollinator-transmitted disease, in <i>Dianthus pavonius</i>, a gynodioecious perennial herb. We found that within a heavily diseased population, females consistently had lower levels of <i>Microbotryum</i> spore deposition relative to hermaphrodites and that this is difference was driven by rapid floral closing in females following successful pollination. We further show that this protective closing behavior is frequency-dependent; females close faster when they are rare. These results indicate that anther-smut disease is an important source of selection for females, especially since we found in a common garden experiment no evidence that females have any inherent fecundity advantages over hermaphrodites. Finally, we show that among populations, those where anther-smut is present have a significantly higher frequency of females than those where the disease is absent. Taken together our results indicate that anther-smut disease is likely an important biotic factor driving the evolution and maintenance of females in this gynodioecious species.
DOI: 10.6084/m9.figshare.7312241
title: Data for Registration practices of clinic trials in rhinosinusitis

description: Data for Registration practices of clinic trials in rhinosinusitis study
DOI: 10.6084/m9.figshare.7312247.v1
title: Dataset for: The role of infectious disease in the evolution of females: evidence from anther-smut disease on a gynodioecious alpine carnation.

description: In flowering plants, the evolution of females is widely hypothesized to be the first step in the evolutionary pathway to separate male and female sexes, or dioecy. Natural enemies have the potential to drive this evolution if they preferentially attack hermaphrodites over females. We studied sex-based differences in exposure to anther-smut (<i>Microbotryum</i>), a sterilizing pollinator-transmitted disease, in <i>Dianthus pavonius</i>, a gynodioecious perennial herb. We found that within a heavily diseased population, females consistently had lower levels of <i>Microbotryum</i> spore deposition relative to hermaphrodites and that this is difference was driven by rapid floral closing in females following successful pollination. We further show that this protective closing behavior is frequency-dependent; females close faster when they are rare. These results indicate that anther-smut disease is an important source of selection for females, especially since we found in a common garden experiment no evidence that females have any inherent fecundity advantages over hermaphrodites. Finally, we show that among populations, those where anther-smut is present have a significantly higher frequency of females than those where the disease is absent. Taken together our results indicate that anther-smut disease is likely an important biotic factor driving the evolution and maintenance of females in this gynodioecious species.
DOI: 10.6084/m9.figshare.7312241.v1
title: Data for Registration practices of clinic trials in rhinosinusitis

description: Data for Registration practices of clinic trials in rhinosinusitis study
DOI: 10.7284/128252
title: GNSS (Global Navigation Satellite System) data collected during research cruise RR1714 using a Trimble SPS351 instrument system onboard the platform RV Roger Revelle

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7312235
title: Post-licensure experience with rotavirus vaccination in Latin America and the Caribbean: a systematic review and meta-analysis

description: <b>Introduction</b>: Latin American countries were among the first to adopt rotavirus vaccines into national immunization programs; we reviewed one decade of their experience with rotavirus vaccination. <b>Areas covered</b>: We systematically reviewed manuscripts published January 1990–January 2018 to assess rotavirus vaccine effectiveness (VE) via meta-analysis; describe trends in rotavirus and acute gastroenteritis (AGE)-associated hospitalizations and mortality before and after vaccine introduction; and estimate annual hospitalizations and deaths averted by rotavirus vaccination in Latin American and Caribbean children &lt;5 years. Rotavirus vaccines demonstrated VE against rotavirus hospitalization of 76% (95% CI: 58–87) in low-mortality countries and 67% (95% CI: 54–76) in high-mortality countries for children &lt;1 year of age. Reductions of 64.0% (interquartile range (IQR): 49.9–69.2) were observed in rotavirus hospitalizations, 32.8% (IQR 29.0–40.3) in AGE hospitalizations, and 53.5% (IQR: 40.4–57.1) in AGE-related mortalities in children &lt;5 years. In 2015, an estimated 125,000 rotavirus-associated hospitalizations and 800 rotavirus-related deaths were prevented in countries that implemented rotavirus vaccines. <b>Expert Commentary</b>: Rotavirus vaccines remain an effective tool against diarrheal disease. The continued success of rotavirus vaccines provides evidence for adoption in Latin American and Caribbean countries that have not yet introduced it, and improvement within those with low coverage.
DOI: 10.6084/m9.figshare.7312235.v1
title: Post-licensure experience with rotavirus vaccination in Latin America and the Caribbean: a systematic review and meta-analysis

description: <b>Introduction</b>: Latin American countries were among the first to adopt rotavirus vaccines into national immunization programs; we reviewed one decade of their experience with rotavirus vaccination. <b>Areas covered</b>: We systematically reviewed manuscripts published January 1990–January 2018 to assess rotavirus vaccine effectiveness (VE) via meta-analysis; describe trends in rotavirus and acute gastroenteritis (AGE)-associated hospitalizations and mortality before and after vaccine introduction; and estimate annual hospitalizations and deaths averted by rotavirus vaccination in Latin American and Caribbean children &lt;5 years. Rotavirus vaccines demonstrated VE against rotavirus hospitalization of 76% (95% CI: 58–87) in low-mortality countries and 67% (95% CI: 54–76) in high-mortality countries for children &lt;1 year of age. Reductions of 64.0% (interquartile range (IQR): 49.9–69.2) were observed in rotavirus hospitalizations, 32.8% (IQR 29.0–40.3) in AGE hospitalizations, and 53.5% (IQR: 40.4–57.1) in AGE-related mortalities in children &lt;5 years. In 2015, an estimated 125,000 rotavirus-associated hospitalizations and 800 rotavirus-related deaths were prevented in countries that implemented rotavirus vaccines. <b>Expert Commentary</b>: Rotavirus vaccines remain an effective tool against diarrheal disease. The continued success of rotavirus vaccines provides evidence for adoption in Latin American and Caribbean countries that have not yet introduced it, and improvement within those with low coverage.
DOI: 10.7284/128245
title: Gravimeter data collected during research cruise RR1714 using a Bell BGM-3 instrument system onboard the platform RV Roger Revelle

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/128249
title: HDSS (Hydrographic Doppler Sonar System) data collected during research cruise RR1714 using a SIO HDSS instrument system onboard the platform RV Roger Revelle

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/128248
title: INS (Inertial Navigation System) data collected during research cruise RR1714 using a iXSea Phins instrument system onboard the platform RV Roger Revelle

description: Original (unprocessed) data collected during a Field_expedition