cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7688093
title: Genomic_Epidemiology_of_Syphilis_&_Evolution_of_Macrolide_Resistance__v7.Rcode

description: R Code and source data for Beale et al (2019) "Genomic epidemiology of syphilis reveals independent emergence of macrolide resistance across multiple circulating lineages
DOI: 10.7284/123705
title: Meteorological Station data collected during research cruise AT37-05 using a Vaisala WXT520 instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/123703
title: Multibeam Echosounder data collected during research cruise AT37-05 using a Kongsberg EM122 instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/123710
title: Radiometer data collected during research cruise AT37-05 using a Eppley RAD instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/123709
title: Water Temperature data collected during research cruise AT37-05 using a Sea-Bird SBE-48 instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/123708
title: TSG (Thermosalinograph) data collected during research cruise AT37-05 using a Sea-Bird SBE-45 instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/123796
title: Multiplexed data collected during research cruise AT37-06 using a WHOI Calliope instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/123792
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise AT37-06 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.7687985
title: Supplementary Material for: miR-192 Is Overexpressed and Promotes Cell Proliferation in Prostate Cancer

description: <b><i>Objective:</i></b> Prostate cancer (PCa) is one of the most prevalent types of cancer among men worldwide. The incidence of PCa is increasing in China. Therefore, there is an urgent need to identify novel diagnostic and prognostic markers for PCa to improve the treatment of the disease. <b><i>Methods:</i></b> The Cancer Genome Atlas (TCGA) and GEO database were used to analyze the expression of miR-192, and the relationship between miR-192 and the clinical features of patients with PCa. Cell cycle and cell proliferation assay were used to detect the functional roles of miR-192 in PCa. Bioinformatic analysis for miR-192–5p was performed using gene ontology and KEGG analysis. <b><i>Results:</i></b> By analyzing the dataset of TCGA, we found that miR-192 was overexpressed in PCa samples compared to normal tissues and was upregulated in high-grade PCa compared to low-grade PCa. We also observed that higher miR-192 expression was associated with a shorter biochemical recurrence-free survival time. Our results also demonstrated that miR-192 promoted PCa cell proliferation and cell cycle progression. <b><i>Conclusion:</i></b> These results suggest that miR-192 may be considered for use as a potential diagnostic and therapeutic target of PCa.
DOI: 10.6084/m9.figshare.7687985.v1
title: Supplementary Material for: miR-192 Is Overexpressed and Promotes Cell Proliferation in Prostate Cancer

description: <b><i>Objective:</i></b> Prostate cancer (PCa) is one of the most prevalent types of cancer among men worldwide. The incidence of PCa is increasing in China. Therefore, there is an urgent need to identify novel diagnostic and prognostic markers for PCa to improve the treatment of the disease. <b><i>Methods:</i></b> The Cancer Genome Atlas (TCGA) and GEO database were used to analyze the expression of miR-192, and the relationship between miR-192 and the clinical features of patients with PCa. Cell cycle and cell proliferation assay were used to detect the functional roles of miR-192 in PCa. Bioinformatic analysis for miR-192–5p was performed using gene ontology and KEGG analysis. <b><i>Results:</i></b> By analyzing the dataset of TCGA, we found that miR-192 was overexpressed in PCa samples compared to normal tissues and was upregulated in high-grade PCa compared to low-grade PCa. We also observed that higher miR-192 expression was associated with a shorter biochemical recurrence-free survival time. Our results also demonstrated that miR-192 promoted PCa cell proliferation and cell cycle progression. <b><i>Conclusion:</i></b> These results suggest that miR-192 may be considered for use as a potential diagnostic and therapeutic target of PCa.
DOI: 10.7284/123793
title: CTD (Conductivity, Temperature, Depth) data collected during research cruise AT37-06 using a Sea-Bird SBE-911+ instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/123791
title: Expendable Probe data collected during research cruise AT37-06 using a Sippican MK12 instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7687889
title: Supplementary Material for: A Multicenter Lung Ultrasound Study on Transient Tachypnea of the Neonate

description: <b><i>Background and Aim:</i></b> Discordant results that demand clarification have been published on diagnostic lung ultrasound (LUS) signs of transient tachypnea of the neonate (TTN) in previous cross-sectional, single-center studies. This work was conducted to correlate clinical and imaging data in a longitudinal and multicenter fashion. <b><i>Methods:</i></b> Neonates with a gestational age of 34–40 weeks and presenting with TTN underwent a first LUS scan at 60–180 min of life. LUS scans were repeated every 6–12 h if signs of respiratory distress persisted. Images were qualitatively described and a LUS aeration score was calculated. Clinical data were collected during respiratory distress.<b><i> Results:</i></b> We enrolled 65 TTN patients. Thirty-one (47.6%) had a sharp echogenicity increase in the lower lung fields (the “double lung point” or DLP sign). On admission, there was no significant difference between patients with and without DLP in Silverman scores (4 ± 1.5 vs. 4 ± 2.1; <i>p</i> = 0.9) or LUS scores (7.6 ± 2.6 vs. 5.6 ± 3.8<i>; p</i> = 0.12); PaO<sub>2</sub>/FiO<sub>2</sub> (249 ± 93 vs. 252 ± 125; <i>p</i> = 0.91). All initial LUS scans (performed at the onset of distress) and 99.5% of all scans showed a regular pleural line with no consolidation, with only 1 neonate showing consolidation in the follow-up scans. The Silverman and LUS scores were significantly correlated (rho = 0.27; <i>p</i> = 0.02). <b><i>Conclusion:</i></b> A regular pleural line with no consolidation is a consistent finding in TTN. The presence of a DLP is not essential for the LUS diagnosis of TTN. A semi-quantitative LUS score correlates well with the clinical course and could be useful in monitoring changes in lung aeration during TTN.
DOI: 10.6084/m9.figshare.7687889.v1
title: Supplementary Material for: A Multicenter Lung Ultrasound Study on Transient Tachypnea of the Neonate

description: <b><i>Background and Aim:</i></b> Discordant results that demand clarification have been published on diagnostic lung ultrasound (LUS) signs of transient tachypnea of the neonate (TTN) in previous cross-sectional, single-center studies. This work was conducted to correlate clinical and imaging data in a longitudinal and multicenter fashion. <b><i>Methods:</i></b> Neonates with a gestational age of 34–40 weeks and presenting with TTN underwent a first LUS scan at 60–180 min of life. LUS scans were repeated every 6–12 h if signs of respiratory distress persisted. Images were qualitatively described and a LUS aeration score was calculated. Clinical data were collected during respiratory distress.<b><i> Results:</i></b> We enrolled 65 TTN patients. Thirty-one (47.6%) had a sharp echogenicity increase in the lower lung fields (the “double lung point” or DLP sign). On admission, there was no significant difference between patients with and without DLP in Silverman scores (4 ± 1.5 vs. 4 ± 2.1; <i>p</i> = 0.9) or LUS scores (7.6 ± 2.6 vs. 5.6 ± 3.8<i>; p</i> = 0.12); PaO<sub>2</sub>/FiO<sub>2</sub> (249 ± 93 vs. 252 ± 125; <i>p</i> = 0.91). All initial LUS scans (performed at the onset of distress) and 99.5% of all scans showed a regular pleural line with no consolidation, with only 1 neonate showing consolidation in the follow-up scans. The Silverman and LUS scores were significantly correlated (rho = 0.27; <i>p</i> = 0.02). <b><i>Conclusion:</i></b> A regular pleural line with no consolidation is a consistent finding in TTN. The presence of a DLP is not essential for the LUS diagnosis of TTN. A semi-quantitative LUS score correlates well with the clinical course and could be useful in monitoring changes in lung aeration during TTN.
DOI: 10.7284/123799
title: Fluorometer data collected during research cruise AT37-06 using a WET Labs WETStar instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/123790
title: GNSS (Global Navigation Satellite System) data collected during research cruise AT37-06 using a C&C C-Nav 2050G instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/123797
title: Gravimeter data collected during research cruise AT37-06 using a Bell BGM-3 instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7687823
title: LSR_data abstraction form_20190129.xlsx

description: This is a pilot-tested standardized data extraction form with detailed instructions.
DOI: 10.6084/m9.figshare.7687826
title: Supplementary Material for: Clinical Characteristics and Outcomes of Kidney Transplantation under Urgency Priority Condition

description: <b><i>Background:</i></b> In several countries, patients with end-stage renal disease who are ineligible for dialysis are considered urgency priority (UP) for kidney transplantation (KT) through distinct allocation rules. There are scarce published data on clinical features and outcomes after KT of these patients. <b><i>Methods:</i></b> We retrospectively reviewed and compared demographic and clinical pretransplant characteristics and outcomes after KT of all patients transplanted under UP allocation in a single Brazilian transplant center from January 10 to March 16 (<i>n</i> = 74) and 1: 1 patients transplanted under standard allocation in the same period (<i>n</i> = 74). A propensity score (PS) matching analysis was performed to evaluate risk factors for death-censored graft loss. <b><i>Results:</i></b> UP KT group presented higher percentage of women (58.1 vs. 33.8%, <i>p</i> = 0.005), higher class I (22.2 ± 32.9 vs. 13.1 ± 25.3%, <i>p</i> = 0.027) and class II panel reactive antibodies (11.5 ± 24 vs. 5.2 ± 19.1%, <i>p</i> = 0.002), higher HLA mismatches (4.9 ± 0.9 vs. 3.7 ± 1.2, <i>p</i> &lt; 0.001), higher percentage of retransplants (27 vs. 4.1%, <i>p</i> &lt; 0.001), and spent longer time on dialysis off the waiting list (WL; 54.5 ± 52.5 vs. 31.2 ± 29.0 months, <i>p</i> = 0.03). After transplantation, UP KT patients presented longer hospital stay (29.3 ± 35.7 vs. 18.5 ± 19.5 days, <i>p</i> = 0.003) and inferior death-censored graft survival at 3 years (82 vs. 95.8%, log rank = 0.016), with 33.3% of graft losses due to vascular thrombosis. In PS-matched multivariable analysis, UP status hazard ratios (HR 4.791, 95% CI 1.052–21.722, <i>p</i> = 0.042) and donor age (HR 1.071, 95% CI 1.003–1.145, <i>p</i> = 0.041) were independent risk factors for death-censored graft loss. <b><i>Conclusion:</i></b> Patients transplanted under UP status remained a longer time on dialysis off the WL, suggesting that long-term dialysis led to exhaustion of accesses. After transplantation, outcomes are inferior and UP status was a risk factor for graft loss. These results point to the need for local policies to encourage and monitor the early referral to KT.
DOI: 10.7284/123795
title: Meteorological Station data collected during research cruise AT37-06 using a Vaisala WXT520 instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7687778
title: winnersLosersMeta.xlsx

description: The file includes all data used in "A balance of winners and losers in the Anthropocene"<br>It is composed of two spreadsheets in a single file: the first includes links to relevant urls to access all data used in the paper, and the second relevant citations for each of the datasets.<br>
DOI: 10.7284/123800
title: Meteorological Station data collected during research cruise AT37-06 using a Vaisala WXT520 instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7687775
title: Supplementary Material for: The Role of Extracellular Phosphate Levels on Kidney Disease Progression in a Podocyte Injury Mouse Model

description: <b><i>Background:</i></b> Hyperphosphatemia is a major accelerator of complications in chronic kidney disease and dialysis, and phosphate (Pi) binders have been shown to regulate extracellular Pi levels. Research on hyperphosphatemia in mouse models is scarce, and few models display hyperphosphatemia induced by glomerular injury, despite its relevance to human glomerular disease conditions. In this study, we investigated the involvement of hyperphosphatemia in kidney disease progression using a mouse model in which hyperphosphatemia is induced by focal segmental glomerulosclerosis (FSGS). <b><i>Methods:</i></b> We established the NEP25 mouse model in which FSGS-hyperphosphatemia is induced by podocyte injury and evaluated the effect of a Pi binder, sevelamer. <b><i>Results:</i></b> After disease induction, we confirmed a gradual increase in serum Pi accompanied by reduced renal function and observed increases in serum FGF23 and PTH. Treatment with sevelamer significantly reduced serum Pi and urinary Pi fractional excretion and suppressed increases in serum FGF23 and PTH. A high dose improved serum creatinine and tubular injury markers, and pathological analysis confirmed amelioration of glomerular and tubular damage. Gene expression and marker analysis suggested protective effects on tubular epithelial cells in the diseased kidney. Compared to disease control, NEP25 mice treated with sevelamer retained their mRNA expression of Klotho, a known FGF23 co-receptor and renoprotective factor. <b><i>Conclusions:</i></b> Hyperphosphatemia caused by renal function decline was observed in a FSGS-induced NEP25 mouse model. Studies using this model showed that Pi regulation had a positive impact on kidney disease progression, and notably on tubular epithelial cell injury, which indicates the importance of Pi regulation in the treatment of kidney disease progression.
DOI: 10.6084/m9.figshare.7687823.v1
title: LSR_data abstraction form_20190129.xlsx

description: This is a pilot-tested standardized data extraction form with detailed instructions.
DOI: 10.6084/m9.figshare.7687778.v1
title: winnersLosersMeta.xlsx

description: The file includes all data used in "A balance of winners and losers in the Anthropocene"<br>It is composed of two spreadsheets in a single file: the first includes links to relevant urls to access all data used in the paper, and the second relevant citations for each of the datasets.<br>
DOI: 10.6084/m9.figshare.7687739
title: ITEM 5 -- Class corpora per project

description: * One zip file per application domain* application domains contain the zip's for each project
DOI: 10.6084/m9.figshare.7687775.v1
title: Supplementary Material for: The Role of Extracellular Phosphate Levels on Kidney Disease Progression in a Podocyte Injury Mouse Model

description: <b><i>Background:</i></b> Hyperphosphatemia is a major accelerator of complications in chronic kidney disease and dialysis, and phosphate (Pi) binders have been shown to regulate extracellular Pi levels. Research on hyperphosphatemia in mouse models is scarce, and few models display hyperphosphatemia induced by glomerular injury, despite its relevance to human glomerular disease conditions. In this study, we investigated the involvement of hyperphosphatemia in kidney disease progression using a mouse model in which hyperphosphatemia is induced by focal segmental glomerulosclerosis (FSGS). <b><i>Methods:</i></b> We established the NEP25 mouse model in which FSGS-hyperphosphatemia is induced by podocyte injury and evaluated the effect of a Pi binder, sevelamer. <b><i>Results:</i></b> After disease induction, we confirmed a gradual increase in serum Pi accompanied by reduced renal function and observed increases in serum FGF23 and PTH. Treatment with sevelamer significantly reduced serum Pi and urinary Pi fractional excretion and suppressed increases in serum FGF23 and PTH. A high dose improved serum creatinine and tubular injury markers, and pathological analysis confirmed amelioration of glomerular and tubular damage. Gene expression and marker analysis suggested protective effects on tubular epithelial cells in the diseased kidney. Compared to disease control, NEP25 mice treated with sevelamer retained their mRNA expression of Klotho, a known FGF23 co-receptor and renoprotective factor. <b><i>Conclusions:</i></b> Hyperphosphatemia caused by renal function decline was observed in a FSGS-induced NEP25 mouse model. Studies using this model showed that Pi regulation had a positive impact on kidney disease progression, and notably on tubular epithelial cell injury, which indicates the importance of Pi regulation in the treatment of kidney disease progression.
DOI: 10.6084/m9.figshare.7687724
title: Table S6 from Hidden in plain sight: what remains to be discovered in the eukaryotic proteome?

description: The first decade of genome sequencing stimulated an explosion in the characterization of unknown proteins. More recently, the pace of functional discovery has slowed, leaving around 20% of the proteins even in well-studied model organisms without informative descriptions of their biological roles. Remarkably, many uncharacterized proteins are conserved from yeasts to human, suggesting that they contribute to fundamental biological processes (BP). To fully understand biological systems in health and disease, we need to account for every part of the system. Unstudied proteins thus represent a collective blind spot that limits the progress of both basic and applied biosciences. We use a simple yet powerful metric based on gene ontology BP terms to define characterized and uncharacterized proteins for human, budding yeast and fission yeast. We then identify a set of conserved but unstudied proteins in <i>S. pombe</i>, and classify them based on a combination of orthogonal attributes determined by large-scale experimental and comparative methods. Finally, we explore possible reasons why these proteins remain neglected, and propose courses of action to raise their profile and thereby reap the benefits of completing the catalogue of proteins’ biological roles.
DOI: 10.6084/m9.figshare.7687739.v1
title: ITEM 5 -- Class corpora per project

description: * One zip file per application domain* application domains contain the zip's for each project
DOI: 10.7284/123798
title: Radiometer data collected during research cruise AT37-06 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.7687721
title: Table S1 from Hidden in plain sight: what remains to be discovered in the eukaryotic proteome?

description: The first decade of genome sequencing stimulated an explosion in the characterization of unknown proteins. More recently, the pace of functional discovery has slowed, leaving around 20% of the proteins even in well-studied model organisms without informative descriptions of their biological roles. Remarkably, many uncharacterized proteins are conserved from yeasts to human, suggesting that they contribute to fundamental biological processes (BP). To fully understand biological systems in health and disease, we need to account for every part of the system. Unstudied proteins thus represent a collective blind spot that limits the progress of both basic and applied biosciences. We use a simple yet powerful metric based on gene ontology BP terms to define characterized and uncharacterized proteins for human, budding yeast and fission yeast. We then identify a set of conserved but unstudied proteins in <i>S. pombe</i>, and classify them based on a combination of orthogonal attributes determined by large-scale experimental and comparative methods. Finally, we explore possible reasons why these proteins remain neglected, and propose courses of action to raise their profile and thereby reap the benefits of completing the catalogue of proteins’ biological roles.
DOI: 10.6084/m9.figshare.7687724.v1
title: Table S6 from Hidden in plain sight: what remains to be discovered in the eukaryotic proteome?

description: The first decade of genome sequencing stimulated an explosion in the characterization of unknown proteins. More recently, the pace of functional discovery has slowed, leaving around 20% of the proteins even in well-studied model organisms without informative descriptions of their biological roles. Remarkably, many uncharacterized proteins are conserved from yeasts to human, suggesting that they contribute to fundamental biological processes (BP). To fully understand biological systems in health and disease, we need to account for every part of the system. Unstudied proteins thus represent a collective blind spot that limits the progress of both basic and applied biosciences. We use a simple yet powerful metric based on gene ontology BP terms to define characterized and uncharacterized proteins for human, budding yeast and fission yeast. We then identify a set of conserved but unstudied proteins in <i>S. pombe</i>, and classify them based on a combination of orthogonal attributes determined by large-scale experimental and comparative methods. Finally, we explore possible reasons why these proteins remain neglected, and propose courses of action to raise their profile and thereby reap the benefits of completing the catalogue of proteins’ biological roles.
DOI: 10.6084/m9.figshare.7687742.v1
title: Motivational Interviewing Process

description: MI communication approach including the MI spirit, MI processes and basic communication methods<br><br>
DOI: 10.7284/123802
title: Water Temperature data collected during research cruise AT37-06 using a Sea-Bird SBE-48 instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition