cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7423157.v1
title: Genome-epigenome interactions associated with Myalgic Encephalomyelitis/Chronic Fatigue Syndrome

description: Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) is a complex disease of unknown etiology. Multiple studies point to disruptions in immune functioning in ME/CFS patients as well as specific genetic polymorphisms and alterations of the DNA methylome in lymphocytes. However, potential interactions between DNA methylation and genetic background in relation to ME/CFS have not been examined. In this study we explored this association by characterizing the epigenetic (~480 thousand CpG loci) and genetic (~4.3 million SNPs) variation between cohorts of ME/CFS patients and healthy controls. We found significant associations of DNA methylation states in T-lymphocytes at several CpG loci and regions with ME/CFS phenotype. These methylation anomalies are in close proximity to genes involved with immune function and cellular metabolism. Finally, we found significant correlations of genotypes with methylation modifications associated with ME/CFS. The findings from this study highlight the role of epigenetic and genetic interactions in complex diseases, and suggest several genetic and epigenetic elements potentially involved in the mechanisms of disease in ME/CFS.
DOI: 10.6084/m9.figshare.7423163.v1
title: Destabilization of the MiniChromosome Maintenance (MCM) complex modulates the cellular response to DNA double strand breaks.

description: DNA replication during S phase involves thousands of replication forks that must be coordinated to ensure that every DNA section is replicated only once. The minichromosome maintenance proteins, MCM2 to MCM7, form a heteromeric DNA helicase required for both the initiation and elongation of DNA replication. Although only two DNA helicase activities are necessary to establish a bidirectional replication fork from each replication origin, a large excess of MCM complexes is amassed and distributed along the chromatin. The function of the additional MCM complexes is not well understood, as most are displaced from the DNA during the S-phase, apparently without playing an active role in DNA replication. DNA damage response (DDR) kinases activated by stalled forks prevent the replication machinery from being activated, indicating a tight relationship between DDR and DNA replication. To investigate the role of MCM proteins in the cellular response to DNA damage, we used shRNA targeting MCM2 or MCM3 to determine the impact of a reduction in MCM complex. The alteration of MCM proteins induced a change in the activation of key factors of the DDR in response to Etoposide treatment. Etoposide-induced DNA damage affected the phosphorylation of γ-H2AX, CHK1 and CHK2 without affecting cell viability. Using assays measuring homologous recombination (HR) and non-homologous end-joining (NHEJ), we identified a decrease in both HR and NHEJ associated with a decrease in MCM complex.
DOI: 10.7284/113001
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise NH1312 using a Hawaii UHDAS instrument system onboard the platform RV New Horizon

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7423028
title: The bumblebee Bombus terrestris carries a primary inoculum of Tomato brown rugose fruit virus contributing to disease spread in tomatoes

description: <b>Fig 3. </b><b>ToBRFV contaminates bumblebee hive components.</b> <b>a.</b> Internal bumblebee hive components. <b>b.</b> ToBRFV detection in individual bumblebees from beehives A, B, C, N by RT-PCR analysis using F-5476 and R-6287 primers. <b>c.</b> ToBRFV detection in comb and cotton from beehives A-C by RT-PCR using F-1 and R-1572 primers. <b>d.</b> ToBRFV detection by RT-PCR in comb and cotton from a naive beehive using F-1 and R-1572 primers. <b>e,f.</b> Detection of ToBRFV coat protein in beehive components by Western blot analysis. N, naïve beehive; M, molecular size marker; W, water control; *, amplicon subjected to Sanger sequencing; D1, a bumblebee from contaminated beehive D; v, viral extraction; CP, coat protein.
DOI: 10.7284/113000
title: CTD (Conductivity, Temperature, Depth) data collected during research cruise NH1312 using a Sea-Bird SBE-911+ instrument system onboard the platform RV New Horizon

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/113004
title: GNSS (Global Navigation Satellite System) data collected during research cruise NH1312 using a Furuno GP-150 instrument system onboard the platform RV New Horizon

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/113006
title: GNSS (Global Navigation Satellite System) data collected during research cruise NH1312 using a Garmin GPS-17HVS instrument system onboard the platform RV New Horizon

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/113007
title: GNSS (Global Navigation Satellite System) data collected during research cruise NH1312 using a Ashtech ADU2 instrument system onboard the platform RV New Horizon

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/113008
title: GNSS (Global Navigation Satellite System) data collected during research cruise NH1312 using a Furuno GP-90D instrument system onboard the platform RV New Horizon

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/113005
title: Gyrocompass data collected during research cruise NH1312 using a Sperry MK-37 instrument system onboard the platform RV New Horizon

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/113002
title: Meteorological Station data collected during research cruise NH1312 using a SIO MET-System instrument system onboard the platform RV New Horizon

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/113009
title: Meteorological Station data collected during research cruise NH1312 using a SIO MET-System instrument system onboard the platform RV New Horizon

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/112999
title: Singlebeam Echosounder data collected during research cruise NH1312 using a Knudsen 320B/R instrument system onboard the platform RV New Horizon

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/113003
title: Winch data collected during research cruise NH1312 using a Markey DUSH-5 instrument system onboard the platform RV New Horizon

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/113010
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise NH1313 using a Hawaii UHDAS instrument system onboard the platform RV New Horizon

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/113013
title: GNSS (Global Navigation Satellite System) data collected during research cruise NH1313 using a Furuno GP-150 instrument system onboard the platform RV New Horizon

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.25375/uct.7422890
title: Quantitative Indicators for Tearfund’s environmental and economic sustainability framework

description: Quantitative Indicators - developed for Tearfund’s environmental and economic sustainability framework.
DOI: 10.7284/113015
title: GNSS (Global Navigation Satellite System) data collected during research cruise NH1313 using a Garmin GPS-17HVS instrument system onboard the platform RV New Horizon

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.25375/uct.7422890.v1
title: Quantitative Indicators for Tearfund’s environmental and economic sustainability framework

description: Quantitative Indicators - developed for Tearfund’s environmental and economic sustainability framework.
DOI: 10.6084/m9.figshare.7422902
title: Supplementary Material for: The Chick Caudolateral Epiblast Acts as a Permissive Niche for Generating Neuromesodermal Progenitor Behaviours

description: Neuromesodermal progenitors (NMps) are a population of bipotent progenitors that maintain competence to generate both spinal cord and paraxial mesoderm throughout the elongation of the posterior body axis. Recent studies have generated populations of NMp-like cells in culture, which have been shown to differentiate to both neural and mesodermal cell fates when transplanted into either mouse or chick embryos. Here, we aim to compare the potential of mouse embryonic stem (ES) cell-derived progenitor populations to generate NMp behaviour against both undifferentiated and differentiated populations. We define NMp behaviour as the ability of cells to: (i) contribute to a significant proportion of the anterior-posterior body axis, (ii) enter into both posterior neural and somitic compartments, and (iii) retain a proportion of the progenitor population within the posterior growth zone. We compare previously identified ES cell-derived NMp-like populations to undifferentiated mouse ES cells and find that they all display similar potentials to generate NMp behaviour in vivo. To assess whether this competence is lost upon further differentiation, we generated anterior and posterior embryonic cell types through the generation of 3D gastruloids and show that NMp competence is lost within the anterior (Brachyury-negative) portion of the gastruloid. Together this suggests that in vitro-derived NMp-like cells maintain an ability to contribute to multiple germ layers that is also present within pluripotent ES cells, rather than acquiring a neuromesodermal competent state through differentiation.
DOI: 10.7284/113016
title: GNSS (Global Navigation Satellite System) data collected during research cruise NH1313 using a Ashtech ADU2 instrument system onboard the platform RV New Horizon

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7422905.v1
title: The First Virtual Altmetricon

description: Download the presentations from The First Virtual Altmetricon exploring the latest uses of altmetrics data including:<br>Keynote: <b>James Wilsdon - </b>Professor of Research Policy in the Faculty of Social Sciences at the<b>University of Sheffield: </b>Has the tide turned towards responsible metrics – and will altmetrics help us to sink or swim? <b>Jean Liu -</b>Head of Product at Altmetric: The road ahead: What will Altmetric build in 2019? <b>Dr Thomas Fink - </b>Director and a Trustee of the London Institute of Mathematical Sciences:<b> </b>How Altmetric helps the London Institute for Mathematical Sciences understand its own research output and adjust course to increase its global visibility <b>Dr Arfon Powell - </b>Wcat Fellow in the School of Medicine at Cardiff University: Altmetric versus bibliometric perspective regarding publication impact and force<b></b> <b>Lily Troia - </b>Engagement Manager at Altmetric: Strategic Organizational Approaches to Altmetric data: methods and pathways for impact evaluation and beyond <b>Stacy Konkiel - </b>Director of Research Relations at Altmetric and Dimensions: Towards ‘humane’ metrics for the arts and humanities: are altmetrics the answer?<b> </b><b>Josh Clark - </b>Marketing Executive at Altmetric:<b></b>The Altmetric Ambassador program: How joining our international community of engaged users can benefit you and your institution!<b></b><br><br>
DOI: 10.7284/113017
title: GNSS (Global Navigation Satellite System) data collected during research cruise NH1313 using a Furuno GP-90D instrument system onboard the platform RV New Horizon

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/113014
title: Gyrocompass data collected during research cruise NH1313 using a Sperry MK-37 instrument system onboard the platform RV New Horizon

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7422824
title: Supplementary Material for: Pericardium in Reconstructive Urologic Surgeries: A Systematic Review and Meta-Analysis

description: <b><i>Introduction:</i></b> The use of pericardium has been expanded into different surgical modalities; however, there are scarce data regarding the feasibility of the pericardium in reconstructive urologic surgeries. We systematically reviewed the literature on the effectiveness of the pericardial tissue for reconstructive urologic surgeries. <b><i>Materials and Methods:</i></b> PubMed and Scopus were searched online for evidence on the use of the pericardium in urologic surgeries. Through the methodology recommended by the Preferred Reporting Items for Systematic Reviews and Meta-analysis guidelines, 38 of 4,071 studies were identified. <b><i>Results:</i></b> A total of 715 patients and 139 animals underwent reconstructive urologic surgeries using the pericardium. Bladder, urethral, and renal reconstructions were successful in 100% of the human cases. The rates of dissatisfaction, glans hypoesthesia, and penile shortening were comparable between the pericardial graft surgeries and the other operations during penile straightening, but there was a trend among the patients with pericardial grafts toward having a more penile curvature at follow-up (risk ratio [RR] 2.03, 95% CI 0.90–4.61, <i>p</i> = 0.09; <i>I</i><sup>2</sup> = 0%). Among the animal studies, there were 4 reports of penile reconstruction, 7 studies of bladder reconstruction, and 1 study of urethroplasty. Bladder reconstruction and urethroplasty were successful in 83 and 20% of the animals, respectively. The pooled result of the stimulated intracorporeal pressure 5 V significantly favored pericardial grafts during penile reconstruction (RR 2.61, 95% CI 1.26–3.97, <i>p</i> = 0.0002; <i>I</i><sup>2</sup> = 0%). <b><i>Conclusions:</i></b> Our systematic review demonstrates the feasibility of the pericardium, regardless of its type, in urologic surgeries. It, however, seems that urethral substitution needs further investigation. Given the lower cost, easier handling, and less immunogenicity of the pericardium, further studies are required to examine its pros and cons.
DOI: 10.6084/m9.figshare.7422824.v1
title: Supplementary Material for: Pericardium in Reconstructive Urologic Surgeries: A Systematic Review and Meta-Analysis

description: <b><i>Introduction:</i></b> The use of pericardium has been expanded into different surgical modalities; however, there are scarce data regarding the feasibility of the pericardium in reconstructive urologic surgeries. We systematically reviewed the literature on the effectiveness of the pericardial tissue for reconstructive urologic surgeries. <b><i>Materials and Methods:</i></b> PubMed and Scopus were searched online for evidence on the use of the pericardium in urologic surgeries. Through the methodology recommended by the Preferred Reporting Items for Systematic Reviews and Meta-analysis guidelines, 38 of 4,071 studies were identified. <b><i>Results:</i></b> A total of 715 patients and 139 animals underwent reconstructive urologic surgeries using the pericardium. Bladder, urethral, and renal reconstructions were successful in 100% of the human cases. The rates of dissatisfaction, glans hypoesthesia, and penile shortening were comparable between the pericardial graft surgeries and the other operations during penile straightening, but there was a trend among the patients with pericardial grafts toward having a more penile curvature at follow-up (risk ratio [RR] 2.03, 95% CI 0.90–4.61, <i>p</i> = 0.09; <i>I</i><sup>2</sup> = 0%). Among the animal studies, there were 4 reports of penile reconstruction, 7 studies of bladder reconstruction, and 1 study of urethroplasty. Bladder reconstruction and urethroplasty were successful in 83 and 20% of the animals, respectively. The pooled result of the stimulated intracorporeal pressure 5 V significantly favored pericardial grafts during penile reconstruction (RR 2.61, 95% CI 1.26–3.97, <i>p</i> = 0.0002; <i>I</i><sup>2</sup> = 0%). <b><i>Conclusions:</i></b> Our systematic review demonstrates the feasibility of the pericardium, regardless of its type, in urologic surgeries. It, however, seems that urethral substitution needs further investigation. Given the lower cost, easier handling, and less immunogenicity of the pericardium, further studies are required to examine its pros and cons.
DOI: 10.6084/m9.figshare.7422821
title: Supplementary Material for: Serum Neuroendocrine Markers Predict Therapy Outcome of Patients with Metastatic Castration-Resistant Prostate Cancer: A Meta-Analysis

description: <b><i>Purpose:</i></b> To evaluate whether serum neuroendocrine markers could effectively predict treatment outcomes in patients with metastatic castration-resistant prostate cancer (mCRPC). <b><i>Methods:</i></b> The PubMed, Cochrane Library and Embase databases were sought to identify eligible studies concerning serum neuroendocrine markers and the prognosis of post-treatment mCRPC from inception to April 2018. The association between serum neuroendocrine markers, that is, chromogranin A (CgA) and neurone-specific enolase (NSE), levels and the prognosis of post-treatment mCRPC were summarized using a random-effects model and hazard ratio (HR) with 95% CI Sensitivity analyses were conducted to assess potential bias. <b><i>Results:</i></b> A total of 234 participants are included in this meta-analysis (mean age = 71.3 years) from 6 studies. The pooled results show that higher markers’ levels at baseline in patients were associated with unfavorable overall survival (OS; univariate analysis: HR 3.775, 95% CI 1.469–9.698, <i>p</i> = 0.006; multivariate analysis: HR 3.838, 95% CI 1.774–8.304, <i>p</i> = 0.001), and a similar situation was observed in progression-free survival (PFS; univariate analysis: HR 2.785, 95% CI 1.315–5.898, <i>p</i> = 0.007; multivariate analysis: HR 1.266, 95% CI 1.017–1.577, <i>p</i> = 0.035). Estimates of the total effects were generally consistent in the sensitivity analysis. Publication bias was observed when performing the univariate analysis of PFS, and we have the explanation accordingly. <b><i>Conclusions:</i></b> The results of this pooled analysis confirm serum neuroendocrine markers could be the effective predictor of treatment outcome in patients with mCRPC. In addition, a combination of CgA and NSE is more valuable to predict worse OS. Further randomized case-control trials are required to validate this relationship.
DOI: 10.7284/113011
title: Meteorological Station data collected during research cruise NH1313 using a SIO MET-System instrument system onboard the platform RV New Horizon

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7422818
title: ESM from Autism sensory dysfunction in an evolutionarily conserved system

description: There is increasing evidence for a strong genetic basis for autism, with many genetic models being developed in an attempt to replicate autistic symptoms in animals. However, current animal behaviour paradigms rarely match the social and cognitive behaviours exhibited by autistic individuals. Here, we instead assay another functional domain—sensory processing—known to be affected in autism to test a novel genetic autism model in <i>Drosophila melanogaster</i>. We show similar visual response alterations and a similar development trajectory in <i>Nhe3</i> mutant flies (total <i>N</i> = 72) and in autistic human participants (total <i>N</i> = 154). We report a dissociation between first- and second-order electrophysiological visual responses to steady-state stimulation in adult mutant fruit flies that is strikingly similar to the response pattern in human adults with ASD as well as that of a large sample of neurotypical individuals with high numbers of autistic traits. We explain this as a genetically driven, selective signalling alteration in transient visual dynamics. In contrast to adults, autistic children show a decrease in the first-order response that is matched by the fruit fly model, suggesting that a compensatory change in processing occurs during development. Our results provide the first animal model of autism comprising a differential developmental phenotype in visual processing.
DOI: 10.6084/m9.figshare.7422818.v1
title: ESM from Autism sensory dysfunction in an evolutionarily conserved system

description: There is increasing evidence for a strong genetic basis for autism, with many genetic models being developed in an attempt to replicate autistic symptoms in animals. However, current animal behaviour paradigms rarely match the social and cognitive behaviours exhibited by autistic individuals. Here, we instead assay another functional domain—sensory processing—known to be affected in autism to test a novel genetic autism model in <i>Drosophila melanogaster</i>. We show similar visual response alterations and a similar development trajectory in <i>Nhe3</i> mutant flies (total <i>N</i> = 72) and in autistic human participants (total <i>N</i> = 154). We report a dissociation between first- and second-order electrophysiological visual responses to steady-state stimulation in adult mutant fruit flies that is strikingly similar to the response pattern in human adults with ASD as well as that of a large sample of neurotypical individuals with high numbers of autistic traits. We explain this as a genetically driven, selective signalling alteration in transient visual dynamics. In contrast to adults, autistic children show a decrease in the first-order response that is matched by the fruit fly model, suggesting that a compensatory change in processing occurs during development. Our results provide the first animal model of autism comprising a differential developmental phenotype in visual processing.
DOI: 10.6084/m9.figshare.7422821.v1
title: Supplementary Material for: Serum Neuroendocrine Markers Predict Therapy Outcome of Patients with Metastatic Castration-Resistant Prostate Cancer: A Meta-Analysis

description: <b><i>Purpose:</i></b> To evaluate whether serum neuroendocrine markers could effectively predict treatment outcomes in patients with metastatic castration-resistant prostate cancer (mCRPC). <b><i>Methods:</i></b> The PubMed, Cochrane Library and Embase databases were sought to identify eligible studies concerning serum neuroendocrine markers and the prognosis of post-treatment mCRPC from inception to April 2018. The association between serum neuroendocrine markers, that is, chromogranin A (CgA) and neurone-specific enolase (NSE), levels and the prognosis of post-treatment mCRPC were summarized using a random-effects model and hazard ratio (HR) with 95% CI Sensitivity analyses were conducted to assess potential bias. <b><i>Results:</i></b> A total of 234 participants are included in this meta-analysis (mean age = 71.3 years) from 6 studies. The pooled results show that higher markers’ levels at baseline in patients were associated with unfavorable overall survival (OS; univariate analysis: HR 3.775, 95% CI 1.469–9.698, <i>p</i> = 0.006; multivariate analysis: HR 3.838, 95% CI 1.774–8.304, <i>p</i> = 0.001), and a similar situation was observed in progression-free survival (PFS; univariate analysis: HR 2.785, 95% CI 1.315–5.898, <i>p</i> = 0.007; multivariate analysis: HR 1.266, 95% CI 1.017–1.577, <i>p</i> = 0.035). Estimates of the total effects were generally consistent in the sensitivity analysis. Publication bias was observed when performing the univariate analysis of PFS, and we have the explanation accordingly. <b><i>Conclusions:</i></b> The results of this pooled analysis confirm serum neuroendocrine markers could be the effective predictor of treatment outcome in patients with mCRPC. In addition, a combination of CgA and NSE is more valuable to predict worse OS. Further randomized case-control trials are required to validate this relationship.
DOI: 10.7284/113018
title: Meteorological Station data collected during research cruise NH1313 using a SIO MET-System instrument system onboard the platform RV New Horizon

description: Original (unprocessed) data collected during a Field_expedition