cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6073/pasta/d64bad432c80ea84102ce90aef04dc9a
title: Ecosystem metabolism and associated environmental data for a forested, meadow and reforested reach of White Clay Creek, Chester Co., Pennsylvania; 1971-1975 and 1997-2010

description: Ecosystem metabolism data for a 3rd-order Piedmont stream were collected during two periods: P1- April 1971 – Dec 1975, and P2- May 1997 – January 2010. Measures were made in a meadow and a forested reach during each period and in a reforested (formerly meadow) reach during the latter years of P2. During P1, measures were made by transferring streambed substrata to chambers in water jackets located on the streambank and measuring dissolved oxygen changes over diel periods. During P2, open system measures of dissolved O2 change were made for several days in warm and cold seasons, with reaeration determined from a propane injection experiment. Metabolism estimates were determined from diel curves of dissolved O2 change. Photosynthetically active radiation (PAR) and chlorophyll were measured concurrent with many measurements in P1 and all measures during P2, and temperature with all measures. Water chemistry parameters (NH4-N, NO3-N, PO4-P, SiO2, Cl, SO4, total alkalinity, pH) associated with each run are included in the data set, as are days since storm of various thresholds. Field procedures, analytical methods and data analyses are detailed in Bott, T.L. & J. D. Newbold, 2023. A multi-year analysis of factors affecting ecosystem metabolism in forested and meadow reaches of a Piedmont Stream. Hydrobiologia
DOI: 10.6084/m9.figshare.22293163
title: Supplementary Material for: Nephropathy is aggravated by fatty acids in diabetic kidney disease through tubular epithelial cell necroptosis and is alleviated by an RIPK-1 inhibitor

description: Introduction: Diabetic kidney disease (DKD), one of the leading causes of end-stage renal disease, has complex pathogenic mechanisms and few effective clinical therapies. DKD progression is accompanied by the loss of renal resident cells, followed by chronic inflammation and extracellular matrix deposition. Necroptosis is a newly discovered form of regulated cell death and is a major form of intrinsic cell loss in certain diabetic complications such as cardiomyopathy, intestinal disease, and retinal neuropathy; however, its significance in DKD is largely unknown. Methods: In this study, the expression of necroptosis marker phosphorylated MLKL (p-MLKL) in renal biopsy tissues of patients with DKD was detected using immunofluorescence and semiquantified using immunohistochemistry. The effects of different disease-causing factors on necroptosis activation in human HK-2 cells were evaluated using immunofluorescence and western blotting. db/db diabetic mice were fed a high-fat diet to establish an animal model of DKD with significant renal tubule damage. Mice were treated with RIPK1 inhibitor RIPA-56 to evaluate its renal protective effects. mRNA transcriptome sequencing was used to explore the changes in signaling pathways after RIPA-56 treatment. Oil red O staining and electron macroscopy were used to observe lipid droplet accumulation in renal biopsy tissues and mouse kidney tissues. Results: Immunostaining of phosphorylated RIPK1/RIPK3/MLKL verified the occurrence of necroptosis in renal tubular epithelial cells (RTECs) of patients with DKD. The level of the necroptosis marker p-MLKL correlated positively with the severity of renal functional, pathological damages, and lipid droplet accumulation in patients with DKD. High glucose and fatty acids were the main factors causing necroptosis in human renal tubular HK-2 cells. Renal function deterioration and renal pathological injury were accelerated, and the necroptosis pathway was activated in db/db mice fed a high-fat diet. Application of RIPA-56 effectively reduced the degree of renal injury, inhibited the necroptosis pathway activation, and reduced necroinflammation and lipid droplet accumulation in the renal tissues of db/db mice fed a high-fat diet. Conclusion: The present study revealed the role of necroptosis in the progression of DKD and might provide a new therapeutic target for the treatment of DKD.
DOI: 10.6084/m9.figshare.22293163.v1
title: Supplementary Material for: Nephropathy is aggravated by fatty acids in diabetic kidney disease through tubular epithelial cell necroptosis and is alleviated by an RIPK-1 inhibitor

description: Introduction: Diabetic kidney disease (DKD), one of the leading causes of end-stage renal disease, has complex pathogenic mechanisms and few effective clinical therapies. DKD progression is accompanied by the loss of renal resident cells, followed by chronic inflammation and extracellular matrix deposition. Necroptosis is a newly discovered form of regulated cell death and is a major form of intrinsic cell loss in certain diabetic complications such as cardiomyopathy, intestinal disease, and retinal neuropathy; however, its significance in DKD is largely unknown. Methods: In this study, the expression of necroptosis marker phosphorylated MLKL (p-MLKL) in renal biopsy tissues of patients with DKD was detected using immunofluorescence and semiquantified using immunohistochemistry. The effects of different disease-causing factors on necroptosis activation in human HK-2 cells were evaluated using immunofluorescence and western blotting. db/db diabetic mice were fed a high-fat diet to establish an animal model of DKD with significant renal tubule damage. Mice were treated with RIPK1 inhibitor RIPA-56 to evaluate its renal protective effects. mRNA transcriptome sequencing was used to explore the changes in signaling pathways after RIPA-56 treatment. Oil red O staining and electron macroscopy were used to observe lipid droplet accumulation in renal biopsy tissues and mouse kidney tissues. Results: Immunostaining of phosphorylated RIPK1/RIPK3/MLKL verified the occurrence of necroptosis in renal tubular epithelial cells (RTECs) of patients with DKD. The level of the necroptosis marker p-MLKL correlated positively with the severity of renal functional, pathological damages, and lipid droplet accumulation in patients with DKD. High glucose and fatty acids were the main factors causing necroptosis in human renal tubular HK-2 cells. Renal function deterioration and renal pathological injury were accelerated, and the necroptosis pathway was activated in db/db mice fed a high-fat diet. Application of RIPA-56 effectively reduced the degree of renal injury, inhibited the necroptosis pathway activation, and reduced necroinflammation and lipid droplet accumulation in the renal tissues of db/db mice fed a high-fat diet. Conclusion: The present study revealed the role of necroptosis in the progression of DKD and might provide a new therapeutic target for the treatment of DKD.
DOI: 10.6084/m9.figshare.22434493
title: Supplementary Material for: Senescent tumor cells are frequently present at the invasion front - implications for improving disease control in patients with locally advanced prostate cancer

description: Introduction: Local tumor invasion is a critical factor for the outcome of men with prostate cancer. In particular seminal vesicle invasion (SVI) has been reported to be associated with a more unfavorable prognosis. A better understanding of the functional state of invading prostate cancer cells is crucial to develop novel therapeutic strategies for patients with locally advanced disease. Methods: The prognostic impact of local tumor progression was ascertained in over 1,000 men with prostate cancer. Prostate cancer specimens were stained by double-immunohistochemistry for the proliferation marker Ki-67 and the senescence marker p16INK4A. The migratory properties of senescent prostate cancer cells were analyzed in vitro using a wound healing assay and immunofluorescence microscopy for p16INK4A. Results: We confirm the notion that patients with SVI have a more unfavorable prognosis than patients with extraprostatic extension alone. Surprisingly, we found that the tumor invasion front frequently harbors p16INK4A positive and Ki-67 negative i.e., senescent, tumor cells. While the intraprostatic tumor periphery was a hotspot for both proliferation and expression of p16INK4A, the area of SVI showed less proliferative activity but was at the same time a hotspot of cells with increased nuclear p16INK4A expression. Senescence was associated with an accelerated migration of prostate cancer cells in vitro. Discussion/Conclusion: This proof-of-concept study shows that invading prostate cancer cells frequently show signs of cellular senescence. This finding may open new avenues for neoadjuvant and adjuvant treatment concepts in men with locally advanced prostate cancer.
DOI: 10.4121/21502338
title: Data underlying the paper: "Development and experimental testing of a collaborative design rationale method for early stage ship layout design"

description: This data set comprises the data underlying the case study in the paper "Development and experimental testing of a collaborative design rationale method for early- stage ship layout design". Specifically, the data underlying the figures in the paper is provided.It comprises 1) a questionnaire, 2) all responses to the questionnaire, and 3) all tracked data from the experiment described in the paper.
DOI: 10.4121/21502338.v1
title: Data underlying the paper: "Development and experimental testing of a collaborative design rationale method for early stage ship layout design"

description: This data set comprises the data underlying the case study in the paper "Development and experimental testing of a collaborative design rationale method for early- stage ship layout design". Specifically, the data underlying the figures in the paper is provided.It comprises 1) a questionnaire, 2) all responses to the questionnaire, and 3) all tracked data from the experiment described in the paper.
DOI: 10.23636/kvwc-ty06
title: UK Doctoral Thesis Metadata from EThOS

description: This dataset has been superseded by a more recent version: https://doi.org/10.23636/vtpx-we51. If you require access to an earlier version, please email openaccess@bl.uk, including the dataset title, date, and DOI in your request. The data in this collection comprises the bibliographic metadata for all UK doctoral theses listed in EThOS, the UK's national thesis service. We estimate the data covers around 98% of all PhDs ever awarded by UK Higher Education institutions, dating back to 1787. Thesis metadata from every PhD-awarding university in the UK is included. You can investigate and re-use this unique collection of UK universities' PhD thesis data to analyse trends in postgraduate research, make connections between researchers, apply large data analysis, improve citation of theses and many more applications.
description: UK
DOI: 10.6084/m9.figshare.22272031
title: Supplementary Material for: Association of four types of vascular access including arterial superficialization with mortality in maintenance hemodialysis patients: a nationwide cohort study in Japan

description: Introduction: Vascular access usage varies widely across countries. Previous studies have evaluated the association of clinical outcomes with the three types of vascular access, namely arteriovenous fistula (AVF), arteriovenous graft (AVG), and tunneled and cuffed central venous catheter (TC-CVC). However, little is known regarding the association between arterial superficialization (AS) and the mortality of patients. Methods: A nationwide cohort study was conducted using data from the Japanese Society for Dialysis Therapy Renal Data Registry (2006–2007). We included patients aged ≥20 years undergoing hemodialysis with a dialysis vintage ≥6 months. The exposures of interest were the four types of vascular access: AVF, AVG, AS, and TC-CVC. Cox proportional hazards models were used to evaluate the associations of vascular access types with 1-year all-cause and cause-specific mortality. Results: A total of 183,490 maintenance hemodialysis patients were included: 90.7% with AVF, 6.9% with AVG, 2.0% with AS, and 0.4% with TC-CVC. During the 1-year follow-up period, 13,798 patients died. Compared to patients with AVF, those with AVG, AS, and TC-CVC had a significantly higher risk of all-cause mortality after adjustment for confounding factors; adjusted hazard ratios (95% confidence intervals): 1.30 (1.20–1.41), 1.56 (1.39–1.76), and 2.15 (1.77–2.61), respectively. Similar results were obtained for infection-related and cardiovascular mortality. Conclusion: This nationwide cohort study conducted in Japan suggested that AVF usage may have the lowest risk of all-cause mortality. The study also suggested that the usage of AS may be associated with better survival rates compared to those of TC-CVC in patients who are not suitable for AVF or AVG.
DOI: 10.6084/m9.figshare.22272031.v1
title: Supplementary Material for: Association of four types of vascular access including arterial superficialization with mortality in maintenance hemodialysis patients: a nationwide cohort study in Japan

description: Introduction: Vascular access usage varies widely across countries. Previous studies have evaluated the association of clinical outcomes with the three types of vascular access, namely arteriovenous fistula (AVF), arteriovenous graft (AVG), and tunneled and cuffed central venous catheter (TC-CVC). However, little is known regarding the association between arterial superficialization (AS) and the mortality of patients. Methods: A nationwide cohort study was conducted using data from the Japanese Society for Dialysis Therapy Renal Data Registry (2006–2007). We included patients aged ≥20 years undergoing hemodialysis with a dialysis vintage ≥6 months. The exposures of interest were the four types of vascular access: AVF, AVG, AS, and TC-CVC. Cox proportional hazards models were used to evaluate the associations of vascular access types with 1-year all-cause and cause-specific mortality. Results: A total of 183,490 maintenance hemodialysis patients were included: 90.7% with AVF, 6.9% with AVG, 2.0% with AS, and 0.4% with TC-CVC. During the 1-year follow-up period, 13,798 patients died. Compared to patients with AVF, those with AVG, AS, and TC-CVC had a significantly higher risk of all-cause mortality after adjustment for confounding factors; adjusted hazard ratios (95% confidence intervals): 1.30 (1.20–1.41), 1.56 (1.39–1.76), and 2.15 (1.77–2.61), respectively. Similar results were obtained for infection-related and cardiovascular mortality. Conclusion: This nationwide cohort study conducted in Japan suggested that AVF usage may have the lowest risk of all-cause mortality. The study also suggested that the usage of AS may be associated with better survival rates compared to those of TC-CVC in patients who are not suitable for AVF or AVG.
DOI: 10.5281/zenodo.7930360
title: Low-Cost Sustainable Engineered Geopolymer Composites (EGCs) for Repair and New Construction of Transportation Infrastructure

description: This study evaluated the use of cost-effective alternative materials in the formulation of novel low-cost Engineered Geopolymer Composite (EGC) materials for repair and new construction of transportation infrastructure in Region 6. Previous studies and reports have shown that EGCs have excellent mechanical properties, which makes them an eco-friendly and more sustainable alternative to Engineered Cementitious Composites (ECCs). However, the mass adoption of these emerging composites is expected to be hindered by their cost, which is mainly driven by the use of PVA reinforcing fibers, silica fume (SF), and manufactured microsilica sand (MS). To address this key shortcoming, novel low-cost EGC materials for repair and new construction of transportation infrastructure in Region 6 were developed by: (1) metakaolin (MK) and fly ash (FA) as replacements of commonly used SF for GP binders; (2) low-cost PP fiber, PVA fiber, and hybrid systems of PP and PVA fiber; and (3) natural sand instead of commonly used manufactured MS. The MK-FA GP binders were tested for compressive strength and characterized with scanning electron microscopy (SEM) and energy-dispersive X-ray spectroscopy (EDS), while the MK-FA GP composites were tested for workability, compressive strength, and uniaxial tensile strength (UTT). Based on the experimental findings, it was concluded that 20-40 wt% of FA replacement was the optimal range for Na-based MK-FA GP with the strength values of ~12-14 MPa, while 50 wt% of FA replacement had the highest strength for K-based MK-FA GP of 17.2 MPa at 90-day. For composites, the mortar with the highest compressive strength reached a value of 10.6 MPa with 45% of river sand, and with 4 wt% SF and 1.5% PVA+0.25% PP fibers, it reached 21 MPa as a fiber-reinforced composite at 28-day. The composite with 10 wt% SF and 1.75% PE had the highest UTT of 3.97 MPa and a strain capacity of 1.78%. All the slant shear test specimens meet the 28-day shear bond strength requirement according to ASTM C882.
description: Tran-SET Project: 21CLSU19
DOI: 10.5281/zenodo.7930359
title: Low-Cost Sustainable Engineered Geopolymer Composites (EGCs) for Repair and New Construction of Transportation Infrastructure

description: This study evaluated the use of cost-effective alternative materials in the formulation of novel low-cost Engineered Geopolymer Composite (EGC) materials for repair and new construction of transportation infrastructure in Region 6. Previous studies and reports have shown that EGCs have excellent mechanical properties, which makes them an eco-friendly and more sustainable alternative to Engineered Cementitious Composites (ECCs). However, the mass adoption of these emerging composites is expected to be hindered by their cost, which is mainly driven by the use of PVA reinforcing fibers, silica fume (SF), and manufactured microsilica sand (MS). To address this key shortcoming, novel low-cost EGC materials for repair and new construction of transportation infrastructure in Region 6 were developed by: (1) metakaolin (MK) and fly ash (FA) as replacements of commonly used SF for GP binders; (2) low-cost PP fiber, PVA fiber, and hybrid systems of PP and PVA fiber; and (3) natural sand instead of commonly used manufactured MS. The MK-FA GP binders were tested for compressive strength and characterized with scanning electron microscopy (SEM) and energy-dispersive X-ray spectroscopy (EDS), while the MK-FA GP composites were tested for workability, compressive strength, and uniaxial tensile strength (UTT). Based on the experimental findings, it was concluded that 20-40 wt% of FA replacement was the optimal range for Na-based MK-FA GP with the strength values of ~12-14 MPa, while 50 wt% of FA replacement had the highest strength for K-based MK-FA GP of 17.2 MPa at 90-day. For composites, the mortar with the highest compressive strength reached a value of 10.6 MPa with 45% of river sand, and with 4 wt% SF and 1.5% PVA+0.25% PP fibers, it reached 21 MPa as a fiber-reinforced composite at 28-day. The composite with 10 wt% SF and 1.75% PE had the highest UTT of 3.97 MPa and a strain capacity of 1.78%. All the slant shear test specimens meet the 28-day shear bond strength requirement according to ASTM C882.
description: Tran-SET Project: 21CLSU19
DOI: 10.23636/j278-4b96
title: UK Doctoral Thesis Metadata from EThOS

description: This dataset has been superseded by a more recent version: https://doi.org/10.23636/kvwc-ty06. If you require access to an earlier version, please email openaccess@bl.uk, including the dataset title, date, and DOI in your request. The data in this collection comprises the bibliographic metadata for all UK doctoral theses listed in EThOS, the UK's national thesis service. We estimate the data covers around 98% of all PhDs ever awarded by UK Higher Education institutions, dating back to 1787. Thesis metadata from every PhD-awarding university in the UK is included. You can investigate and re-use this unique collection of UK universities' PhD thesis data to analyse trends in postgraduate research, make connections between researchers, apply large data analysis, improve citation of theses and many more applications.
description: UK
DOI: 10.6084/m9.figshare.22580311
title: Q-Chem OT-SRSH TDDFT Spectra 23k

description: Q-Chem 5 output files time-dependent density functional theory calculations for 23,619 small organic molecules. Each file corresponds to one molecule calculates the energies and oscillator strengths of the 20 lowest electronic excitations computed using an optimally tuned and screened range-separated hybrid functional.
DOI: 10.6084/m9.figshare.22580311.v2
title: Q-Chem OT-SRSH TDDFT Spectra 23k

description: Q-Chem 5 output files time-dependent density functional theory calculations for 23,619 small organic molecules. Each file corresponds to one molecule calculates the energies and oscillator strengths of the 20 lowest electronic excitations computed using an optimally tuned and screened range-separated hybrid functional.
DOI: 10.6084/m9.figshare.22580311.v1
title: qchem.tar.gz

description: Q-Chem 5 output files time-dependent density functional theory calculations for 23,619 small organic molecules. Each file corresponds to one molecule calculates the energies and oscillator strengths of the 20 lowest electronic excitations computed using an optimally tuned and screened range-separated hybrid functional.
DOI: 10.6084/m9.figshare.22580308
title: Molecular Graphs & OT-SRSH TDDFT Spectra 23k

description: Numpy arrays containing molecular graph and spectral data for 23,619 small organic molecules. Each entry corresponds to one molecule and has five array-valued fields: "nodes" (atomic feature vectors), "edges" (bond feature vectors), "edge_index" (bond indices), "u" (molecular feature vector), and "y" (the energies in eV and oscillator strengths of the 20 lowest electronic excitations computed using time-dependent density functional theory).
DOI: 10.6084/m9.figshare.22580308.v2
title: Molecular Graphs & OT-SRSH TDDFT Spectra 23k

description: Numpy arrays containing molecular graph and spectral data for 23,619 small organic molecules. Each entry corresponds to one molecule and has five array-valued fields: "nodes" (atomic feature vectors), "edges" (bond feature vectors), "edge_index" (bond indices), "u" (molecular feature vector), and "y" (the energies in eV and oscillator strengths of the 20 lowest electronic excitations computed using time-dependent density functional theory).
DOI: 10.6084/m9.figshare.22580308.v1
title: numpy.tar.gz

description: Numpy arrays containing molecular graph and spectral data for 23,619 small organic molecules. Each entry corresponds to one molecule and has five array-valued fields: "nodes" (atomic feature vectors), "edges" (bond feature vectors), "edge_index" (bond indices), "u" (molecular feature vector), and "y" (the energies in eV and oscillator strengths of the 20 lowest electronic excitations computed using time-dependent density functional theory).
DOI: 10.5281/zenodo.7828084
title: Test version (delete)

description: 4 scenarios: DE, GA, DEE, DEG Countries included: BE, DE etc. Scenario years: 2030, 2035, 2040, 2045, 2050 Energetic scope: Electricity, hydrogen demand and supply per sector/subsector/application/technology Units: annual volumes in TWh, installed capacities in GW.
DOI: 10.5281/zenodo.7828085
title: Test version (delete)

description: 4 scenarios: DE, GA, DEE, DEG Countries included: BE, DE etc. Scenario years: 2030, 2035, 2040, 2045, 2050 Energetic scope: Electricity, hydrogen demand and supply per sector/subsector/application/technology Units: annual volumes in TWh, installed capacities in GW.