cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7680287
title: Exonuclease domain mutants of yeast <i>DIS3</i> display genome instability

description: The exosome functions to regulate the cellular transcriptome through RNA biogenesis, surveillance, and decay. Mutations in Dis3, a catalytic subunit of the RNA exosome with separable endonuclease and exonuclease activities, are linked to multiple myeloma. Here we report that a cancer-associated <i>DIS3</i> allele, <i>dis3<sup>E729K</sup></i>, provides evidence for <i>DIS3</i> functioning in mitotic fidelity in yeast. This <i>dis3<sup>E729K</sup></i> allele does not induce defects in 7S→5.8S rRNA processing, although it elicits a requirement for P-body function. While it does not significantly influence cell cycle progression alone, the allele reduces the efficiency of cell cycle arrest in strains with defects in kinetochore assembly. Finally, point mutations in the exonuclease domains of yeast Dis3 elicit genome instability phenotypes; however, these <i>DIS3</i> mutations do not increase DNA damage or RNA processing defects that lead to the accumulation of polyadenylated RNA in the nucleus. These data suggest that specific <i>DIS3</i> activities support mitotic fidelity in yeast.
DOI: 10.7284/129415
title: Multibeam Echosounder data collected during research cruise AT39-06 using a Kongsberg EM122 instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/129421
title: Radiometer data collected during research cruise AT39-06 using a Eppley RAD instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7680233
title: Supplementary Material for: Fetoscopic Release of Amniotic Bands Causing Limb Constriction: Case Series and Review of the Literature

description: The aim of this study was to review the perioperative complication rates and neonatal outcomes after fetoscopic release of amniotic bands that caused bilateral limb constrictions. We present 5 cases of limb constriction by amniotic bands occurring spontaneously or following fetoscopic surgery and also include a review of 21 previously published cases. The cases were analyzed for indication, surgical technique, and postoperative follow-up. In our population and the literature, the majority of the children acquired a functional limb (75%), with few perioperative complications (15%). Fetal morbidity was mainly linked to the consequences of preterm premature rupture of the membranes (38.4%) and preterm birth (34.7 GW). The mortality rate was low (7.7%). This review only describes amniotic bands causing limb constriction, and illustrates that fetoscopic surgery for their release is technically feasible with an acceptable perioperative complication rate. However, the 75% success rate is very likely to be an overestimation of the true success rate. In view of these observations we cannot recommend treatment for cases where the fetus has been extensively affected by the bands. We believe, however, that we could consider this technique for a fraction of amniotic band syndrome cases isolated to the limb constrictions. This kind of surgery should be proposed as a potential treatment for amniotic band syndrome.
DOI: 10.6084/m9.figshare.7680254
title: ITEM 3 -- Domains assigned to each project

description: tab and comma-separated dataset:<br>"project URL" "list of domains" (Comma-separated)
DOI: 10.7284/129425
title: Water Temperature data collected during research cruise AT39-06 using a Sea-Bird SBE-48 instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7680287.v2
title: Exonuclease domain mutants of yeast <i>DIS3</i> display genome instability

description: The exosome functions to regulate the cellular transcriptome through RNA biogenesis, surveillance, and decay. Mutations in Dis3, a catalytic subunit of the RNA exosome with separable endonuclease and exonuclease activities, are linked to multiple myeloma. Here we report that a cancer-associated <i>DIS3</i> allele, <i>dis3<sup>E729K</sup></i>, provides evidence for <i>DIS3</i> functioning in mitotic fidelity in yeast. This <i>dis3<sup>E729K</sup></i> allele does not induce defects in 7S→5.8S rRNA processing, although it elicits a requirement for P-body function. While it does not significantly influence cell cycle progression alone, the allele reduces the efficiency of cell cycle arrest in strains with defects in kinetochore assembly. Finally, point mutations in the exonuclease domains of yeast Dis3 elicit genome instability phenotypes; however, these <i>DIS3</i> mutations do not increase DNA damage or RNA processing defects that lead to the accumulation of polyadenylated RNA in the nucleus. These data suggest that specific <i>DIS3</i> activities support mitotic fidelity in yeast.
DOI: 10.6084/m9.figshare.7680287.v3
title: Exonuclease domain mutants of yeast <i>DIS3</i> display genome instability

description: The exosome functions to regulate the cellular transcriptome through RNA biogenesis, surveillance, and decay. Mutations in Dis3, a catalytic subunit of the RNA exosome with separable endonuclease and exonuclease activities, are linked to multiple myeloma. Here we report that a cancer-associated <i>DIS3</i> allele, <i>dis3<sup>E729K</sup></i>, provides evidence for <i>DIS3</i> functioning in mitotic fidelity in yeast. This <i>dis3<sup>E729K</sup></i> allele does not induce defects in 7S→5.8S rRNA processing, although it elicits a requirement for P-body function. While it does not significantly influence cell cycle progression alone, the allele reduces the efficiency of cell cycle arrest in strains with defects in kinetochore assembly. Finally, point mutations in the exonuclease domains of yeast Dis3 elicit genome instability phenotypes; however, these <i>DIS3</i> mutations do not increase DNA damage or RNA processing defects that lead to the accumulation of polyadenylated RNA in the nucleus. These data suggest that specific <i>DIS3</i> activities support mitotic fidelity in yeast.
DOI: 10.6084/m9.figshare.7680221
title: The desaturase1 gene affects reproduction before, during and after copulation in <i>Drosophila melanogaster</i>

description: Desaturase1 (desat1) is one of the few genes known to be involved in the two complementary aspects of sensory communication — signal emission and signal reception — in <i>Drosophila melanogaster</i>. In particular, desat1 is necessary for the biosynthesis of major cuticular pheromones in both males and females. It is also involved in the male ability to discriminate sex pheromones. Each of these two sensory communication aspects depends on distinct desat1 putative regulatory regions. Here, we used (i) mutant alleles resulting from the insertion/excision of a transposable genomic element inserted in a desat1 regulatory region, and (ii) transgenics made with desat1 regulatory regions used to target desat1 RNAi. These genetic variants were used to study several reproduction-related phenotypes. In particular, we compared the fecundity of various mutant and transgenic desat1 females with regard to the developmental fate of their progeny. We also compared the mating performance in pairs of flies with altered desat1 expression in various desat1-expressing tissues together with their inability to disengage at the end of copulation. Moreover, we investigated the developmental origin of altered sex pheromone discrimination in male flies. We attempted to map some of the tissues involved in these reproduction-related phenotypes. Given that desat1 is expressed in many brain neurons and in non-neuronal tissues required for varied aspects of reproduction, our data suggest that the regulation of this gene has evolved to allow the optimal reproduction and a successful adaptation to varied environments in this cosmopolitan species.
DOI: 10.6084/m9.figshare.7680254.v1
title: Domains assigned to each project

description: tab and comma-separated dataset:<br>"project URL" "list of domains" (Comma-separated)
DOI: 10.6084/m9.figshare.7680221.v1
title: The desaturase1 gene affects reproduction before, during and after copulation in <i>Drosophila melanogaster</i>

description: Desaturase1 (desat1) is one of the few genes known to be involved in the two complementary aspects of sensory communication — signal emission and signal reception — in <i>Drosophila melanogaster</i>. In particular, desat1 is necessary for the biosynthesis of major cuticular pheromones in both males and females. It is also involved in the male ability to discriminate sex pheromones. Each of these two sensory communication aspects depends on distinct desat1 putative regulatory regions. Here, we used (i) mutant alleles resulting from the insertion/excision of a transposable genomic element inserted in a desat1 regulatory region, and (ii) transgenics made with desat1 regulatory regions used to target desat1 RNAi. These genetic variants were used to study several reproduction-related phenotypes. In particular, we compared the fecundity of various mutant and transgenic desat1 females with regard to the developmental fate of their progeny. We also compared the mating performance in pairs of flies with altered desat1 expression in various desat1-expressing tissues together with their inability to disengage at the end of copulation. Moreover, we investigated the developmental origin of altered sex pheromone discrimination in male flies. We attempted to map some of the tissues involved in these reproduction-related phenotypes. Given that desat1 is expressed in many brain neurons and in non-neuronal tissues required for varied aspects of reproduction, our data suggest that the regulation of this gene has evolved to allow the optimal reproduction and a successful adaptation to varied environments in this cosmopolitan species.
DOI: 10.7284/129424
title: TSG (Thermosalinograph) data collected during research cruise AT39-06 using a Sea-Bird SBE-45 instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/130665
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise AT40-01 using a Hawaii UHDAS instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7680128
title: Supplementary Material for: Gender- and Age-Specific Associations between Visceral Obesity and Renal Function Impairment

description: <b><i>Objective:</i></b> Although obesity is associated with an increased risk of chronic kidney disease, this trend becomes nonsignificant following adjustment for cardiovascular risk factors. The present study aims to investigate whether visceral obesity is independently associated with renal function impairment. <b><i>Method:</i></b> The medical records of 14,529 male and 10,561 female Chinese adults undergoing health check-ups during 2013–2015 were retrospectively collected. The baseline characteristics, including the degree of visceral fat and the percentage of body fat, were compared. The association between study groups and renal function impairment was investigated using regression models adjusted for confounding factors. <b><i>Results:</i></b> All variables differed significantly among non-obese, peripheral, and central type obese subjects, both younger and older, and of both genders, except for hsCRP in older male subjects (<i>p</i> = 0.053) and eGFR in older female subjects (<i>p</i> = 0.098). Unadjusted univariate analysis showed that central obesity contributed significantly to renal function impairment in all age groups and in both genders. After adjusting for possible confounding factors, only central obesity was found to be an independent factor of renal function impairment in all groups, except for men under 45 years of age. <b><i>Conclusion:</i></b> Visceral obesity is independently associated with renal function impairment in all ages and both genders, except for males younger than 45 years.
DOI: 10.6084/m9.figshare.7680083
title: Beyond counts and averages: relating geodiversity to dimensions of biodiversity

description: <b>Introduction</b>. Code to accompany Read et al. manuscript on levels and dimensions of biodiversity, entitled "Beyond counts and averages: relating geodiversity to dimensions of biodiversity." Currently in press at <i>Global Ecology and Biogeography. <br></i><i><br></i><b>Model fitting</b>. This code will allow the user to reproduce the models fit in the manuscript. For the model fitting steps, we are providing all the data used to fit the models in the manuscript, except for the true locations of the FIA plots due to confidentiality. FIA location data were provided through U.S Forest Service agreement No. 17-MU-11261919-021.<br>List of files:<i>model_fitting.r</i> : R script that reproduces all model fitting, model validation, and extraction of summary statistics from model objects<i>bbs_biodiversity.csv</i> : Biodiversity data for bird locations<br><i>bbs_geodiversity.csv</i> : Geodiversity data for bird locations<br><i>fia_biodiversity.csv</i> : Biodiversity data for tree locations<br><i>fia_geodiversity.csv</i> : Geodiversity data for tree locations<br><i>tnc_adjacencymatrix.csv</i> : Adjacency matrix (binary) of Nature Conservancy ecoregions in contiguous USA<br><i>ecoregion_folds.csv</i> : List of ecoregions that are sequentially held out in model cross-validation procedure<br><i>prior_table.csv</i> : Parameters for prior distributions used in model fitting<br> <br><b>Modification history:</b>Originally created February 2019<br>Modified May 2019 to include changes in analysis from manuscript revisions<br>
DOI: 10.6084/m9.figshare.7680128.v1
title: Supplementary Material for: Gender- and Age-Specific Associations between Visceral Obesity and Renal Function Impairment

description: <b><i>Objective:</i></b> Although obesity is associated with an increased risk of chronic kidney disease, this trend becomes nonsignificant following adjustment for cardiovascular risk factors. The present study aims to investigate whether visceral obesity is independently associated with renal function impairment. <b><i>Method:</i></b> The medical records of 14,529 male and 10,561 female Chinese adults undergoing health check-ups during 2013–2015 were retrospectively collected. The baseline characteristics, including the degree of visceral fat and the percentage of body fat, were compared. The association between study groups and renal function impairment was investigated using regression models adjusted for confounding factors. <b><i>Results:</i></b> All variables differed significantly among non-obese, peripheral, and central type obese subjects, both younger and older, and of both genders, except for hsCRP in older male subjects (<i>p</i> = 0.053) and eGFR in older female subjects (<i>p</i> = 0.098). Unadjusted univariate analysis showed that central obesity contributed significantly to renal function impairment in all age groups and in both genders. After adjusting for possible confounding factors, only central obesity was found to be an independent factor of renal function impairment in all groups, except for men under 45 years of age. <b><i>Conclusion:</i></b> Visceral obesity is independently associated with renal function impairment in all ages and both genders, except for males younger than 45 years.
DOI: 10.6084/m9.figshare.7680026
title: Supplementary Material for: Dynamic Thiol/Disulphide Homeostasis in Children with Nephrotic Syndrome

description: <b><i>Background:</i></b> There is a growing body of evidence showing that there is an association between oxidative damage and kidney injury in patients with nephrotic syndrome (NS). Dynamic thiol/disulphide homeostasis (DTDH) is an important antioxidant system. The aim of this study was to determine if DTDH could be used as a biomarker of antioxidant status in pediatric NS patients using a novel automated method. <b><i>Methods:</i></b> The study included 39 patients with NS and 40 healthy controls. The DTDH level was measured using a calorimetric and automated method developed by Erel and Neselioglu. In the NS group, DTDH was measured during first-attack episode, relapse, and remission. <b><i>Results:</i></b> The native thiol, total thiol, and disulphide levels were significantly lower, the native thiol/total thiol ratio was significantly lower, and the disulphide/native thiol and disulphide/total thiol ratios were significantly higher in the NS patients during relapse and first-attack episode than during remission and in the controls. In addition, the native thiol and total thiol levels, and the native thiol/total thiol ratio were significantly lower, and the disulphide/native thiol and disulphide/total thiol ratios were significantly higher in the NS group during remission than those in the control group. <b><i>Conclusions:</i></b> The present findings show that DTDH shifted toward disulphide formation in the NS patients, even during remission. A clearer understanding of the mechanism of this disruption to homeostasis in NS patients might lead to the development of novel therapeutic strategies.
DOI: 10.6084/m9.figshare.7680107
title: Genome of Symsagittifera roscoffensis

description: Two denovo draft assemblies of the genome of Symsagittifera roscoffensis. 1) A Soadenovo2 and a Celera assembly of fragment reads only were joined by minimus (Sros_scf_deg500_minimus_ALL.fasta2* files). 2) A Soapdenovo2 assembly using Mate pair reads (graph* files).<br>May contain environmental and endosymbiontic contaminants.<br>Links to NCBI SRA Bioproject PRJNA517079 for raw reads
DOI: 10.7284/130672
title: Fluorometer data collected during research cruise AT40-01 using a WET Labs WETStar instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7680083.v1
title: Beyond counts and averages: relating geodiversity to dimensions of biodiversity

description: Code to accompany Read et al. manuscript on levels and dimensions of biodiversity, entitled "Beyond counts and averages: relating geodiversity to dimensions of biodiversity." Currently (06 Feb 2019) under consideration for publication in <i>Ecology Letters.</i><i></i><br> Consists of two parts:(1) <b>Data processing pipeline</b>. This code will allow the user to follow the entire data processing pipeline described in the manuscript. However, to maintain small file sizes, we are only providing a small subset of the data encompassing the US state of New Hampshire. In addition, we are only providing a subset of the environmental covariate layers. All data used are publicly available.<br> (2) <b>Model fitting</b>. This code will allow the user to reproduce the models fit in the manuscript. For the model fitting steps, we are providing all the data used to fit the models in the manuscript, except for the true locations of the FIA plots due to confidentiality. FIA location data were provided through U.S Forest Service agreement No. 17-MU-11261919-021. <br>
DOI: 10.7284/130664
title: GNSS (Global Navigation Satellite System) data collected during research cruise AT40-01 using a C&C C-Nav 3050 instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7679987
title: Challenges in osteoporosis awareness and management: results from a survey of US postmenopausal women

description: <b>Background:</b> Osteoporotic fractures are a serious public health burden, leading to excess morbidity, mortality, and high costs for post-fracture care. <b>Objectives:</b> To evaluate the perception of osteoporotic fracture risk and to identify potential barriers associated with osteoporosis diagnosis and treatment in US postmenopausal women. <b>Methods:</b> An online survey was conducted by The Harris Poll in 2017 that included 1,012 postmenopausal women 50 years and older. The survey comprised eight screening questions and 35 mandatory questions pertaining to lifestyle, general health, bone fracture awareness, osteoporosis, and demographics, with additional follow-up questions where applicable. An oversample of 102 women with osteoporosis and a fragility fracture (from a fall from a standing height or lower) yielded a total of 280 subjects with osteoporosis and a fracture. <b>Results:</b> A total of 1,012 postmenopausal women were included in the survey; 501 self-reported a diagnosis of osteoporosis and 511 had no known osteoporosis diagnosis. Ninety-six percent of women with a first fracture but no osteoporosis diagnosis did not recall being told by their physicians that their fracture might be related to osteoporosis. Forty-four percent of respondents reported that they had not undergone screening for osteoporosis. Among those considered at risk for osteoporosis, 42% had not undergone screening. Only 45% of women surveyed agreed that a fracture is “a potential sign of more fractures/breaks to come”. Twenty-four percent believed there is no way to build new bone at their age; 18% answered that they could not do much to reduce the risk of fracture at their age. <b>Conclusions:</b> This survey reveals a lack of awareness of the diagnosis of osteoporosis and osteoporotic fracture risk among postmenopausal women. Future studies evaluating the perceptions of osteoporosis and its management are warranted.
DOI: 10.6084/m9.figshare.7679987.v1
title: Challenges in osteoporosis awareness and management: results from a survey of US postmenopausal women

description: <b>Background:</b> Osteoporotic fractures are a serious public health burden, leading to excess morbidity, mortality, and high costs for post-fracture care. <b>Objectives:</b> To evaluate the perception of osteoporotic fracture risk and to identify potential barriers associated with osteoporosis diagnosis and treatment in US postmenopausal women. <b>Methods:</b> An online survey was conducted by The Harris Poll in 2017 that included 1,012 postmenopausal women 50 years and older. The survey comprised eight screening questions and 35 mandatory questions pertaining to lifestyle, general health, bone fracture awareness, osteoporosis, and demographics, with additional follow-up questions where applicable. An oversample of 102 women with osteoporosis and a fragility fracture (from a fall from a standing height or lower) yielded a total of 280 subjects with osteoporosis and a fracture. <b>Results:</b> A total of 1,012 postmenopausal women were included in the survey; 501 self-reported a diagnosis of osteoporosis and 511 had no known osteoporosis diagnosis. Ninety-six percent of women with a first fracture but no osteoporosis diagnosis did not recall being told by their physicians that their fracture might be related to osteoporosis. Forty-four percent of respondents reported that they had not undergone screening for osteoporosis. Among those considered at risk for osteoporosis, 42% had not undergone screening. Only 45% of women surveyed agreed that a fracture is “a potential sign of more fractures/breaks to come”. Twenty-four percent believed there is no way to build new bone at their age; 18% answered that they could not do much to reduce the risk of fracture at their age. <b>Conclusions:</b> This survey reveals a lack of awareness of the diagnosis of osteoporosis and osteoporotic fracture risk among postmenopausal women. Future studies evaluating the perceptions of osteoporosis and its management are warranted.
DOI: 10.7284/130667
title: Gravimeter data collected during research cruise AT40-01 using a Bell BGM-3 instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/130666
title: Meteorological Station data collected during research cruise AT40-01 using a Vaisala WXT520 instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition