cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5057836.v1
title: Assessing nanomaterial exposures in aquatic ecotoxicological testing: Framework and case studies based on dispersion and dissolution

description: The unique behavior of engineered nanomaterials (ENM) in aqueous media and dynamic changes in particle settling, agglomeration and dissolution rates is a challenge to the consistency, reliability and interpretation of standard aquatic hazard bioassay results. While the toxicological endpoints (e.g., survival, growth, reproduction, etc.) in ecotoxicity bioassays are largely applicable to ENMs, the standard methods as written for dissolved substances are confounded by the dynamic settling, agglomeration and dissolution of particulate ENMs during the bioassay. A testing framework was designed to serve as a starting point to identify approaches for the consistent conduct of aquatic hazard tests that account for the behavior of ENMs in test media and suitable data collection to support representative exposure metrology. The framework was demonstrated by conducting three case studies testing ENMs with functionally distinct characteristics and behaviors. Pretests with a temporal sampling of particle concentration, agglomeration and dissolution were conducted on each ENM in test media. Results indicated that a silver nanoparticle (AgNP) powder was not dispersible, a nano-TiO<sub>2</sub> powder was dispersible but unstable, and a polyvinylpyrrolidinone-coated AgNP was relatively stable in test media. Based on these functional results, <i>Ceriodaphnia dubia</i> bioassays were conducted to compare different exposure summary methods (nominal, arithmetic average, geometric average, time-weighted average) for calculating and expressing toxicity endpoints. Results indicated that while arithmetic means were effective for expressing the toxicity of more stable materials, time-weighted averaged concentrations were appropriate for the unstable nano-TiO<sub>2</sub>.
DOI: 10.6084/m9.figshare.5057833.v1
title: Probabilistic risk assessment of emerging materials: case study of titanium dioxide nanoparticles

description: The development and use of emerging technologies such as nanomaterials can provide both benefits and risks to society. Emerging materials may promise to bring many technological advantages but may not be well characterized in terms of their production volumes, magnitude of emissions, behaviour in the environment and effects on living organisms. This uncertainty can present challenges to scientists developing these materials and persons responsible for defining and measuring their adverse impacts. Human health risk assessment is a method of identifying the intrinsic hazard of and quantifying the dose–response relationship and exposure to a chemical, to finally determine the estimation of risk. Commonly applied deterministic approaches may not sufficiently estimate and communicate the likelihood of risks from emerging technologies whose uncertainty is large. Probabilistic approaches allow for parameters in the risk assessment process to be defined by distributions instead of single deterministic values whose uncertainty could undermine the value of the assessment. A probabilistic approach was applied to the dose–response and exposure assessment of a case study involving the production of nanoparticles of titanium dioxide in seven different exposure scenarios. Only one exposure scenario showed a statistically significant level of risk. In the latter case, this involved dumping high volumes of nano-TiO<sub>2</sub> powders into an open vessel with no personal protection equipment. The probabilistic approach not only provided the likelihood of but also the major contributing factors to the estimated risk (e.g. emission potential).
DOI: 10.6084/m9.figshare.5057668
title: Supplementary Material for: Less Fibrotic Burden Differently Affects the Long-Term Outcomes of Hepatocellular Carcinoma after Curative Resection

description: <b><i>Background:</i></b> The clinical features of hepatocellular carcinoma (HCC) differ in patients with and without cirrhosis. <b><i>Objective:</i></b> We aimed to investigate the long-term outcomes of noncirrhotic HCC patients after curative resection. <b><i>Methods:</i></b> We retrospectively examined 649 consecutive patients with HCC who underwent curative resection from 1996 to 2012; 387 (59.6%) were cirrhotic and 262 (40.4%) were noncirrhotic. <b><i>Results:</i></b> The mean age was 54.7 years, and 511 (78.7%) of the study participants were men. The most common cause of HCC was hepatitis B virus (<i>n</i> = 419, 64.6%). Noncirrhotic tumors were larger and more advanced than cirrhotic tumors. However, the noncirrhotic group showed better disease-free survival (DFS) and overall survival (OS) after resection than the cirrhotic group (median 64.0 vs. 56.0 months for OS and 48.0 vs. 31.0 months for DFS, <i>p</i> &lt; 0.05). The predictors for HCC recurrence were cirrhosis, tumor number, portal vein invasion, and major surgery. <b><i>Conclusions:</i></b> Noncirrhotic HCC showed better DFS and OS after resection than cirrhotic HCC, although noncirrhotic HCC presented more aggressively.
DOI: 10.6084/m9.figshare.5057668.v1
title: Supplementary Material for: Less Fibrotic Burden Differently Affects the Long-Term Outcomes of Hepatocellular Carcinoma after Curative Resection

description: <b><i>Background:</i></b> The clinical features of hepatocellular carcinoma (HCC) differ in patients with and without cirrhosis. <b><i>Objective:</i></b> We aimed to investigate the long-term outcomes of noncirrhotic HCC patients after curative resection. <b><i>Methods:</i></b> We retrospectively examined 649 consecutive patients with HCC who underwent curative resection from 1996 to 2012; 387 (59.6%) were cirrhotic and 262 (40.4%) were noncirrhotic. <b><i>Results:</i></b> The mean age was 54.7 years, and 511 (78.7%) of the study participants were men. The most common cause of HCC was hepatitis B virus (<i>n</i> = 419, 64.6%). Noncirrhotic tumors were larger and more advanced than cirrhotic tumors. However, the noncirrhotic group showed better disease-free survival (DFS) and overall survival (OS) after resection than the cirrhotic group (median 64.0 vs. 56.0 months for OS and 48.0 vs. 31.0 months for DFS, <i>p</i> &lt; 0.05). The predictors for HCC recurrence were cirrhosis, tumor number, portal vein invasion, and major surgery. <b><i>Conclusions:</i></b> Noncirrhotic HCC showed better DFS and OS after resection than cirrhotic HCC, although noncirrhotic HCC presented more aggressively.
DOI: 10.6084/m9.figshare.5057557
title: Supplementary Material for: Remotely Programmed Deep Brain Stimulation of the Bilateral Subthalamic Nucleus for the Treatment of Primary Parkinson Disease: A Randomized Controlled Trial Investigating the Safety and Efficacy of a Novel Deep Brain Stimulation System

description: <b><i>Background:</i></b> Deep brain stimulation (DBS) is the most commonly performed surgery for the debilitating symptoms of Parkinson disease (PD). However, DBS systems remain largely unaffordable to patients in developing countries, warranting the development of a safe, economically viable, and functionally comparable alternative. <b><i>Objective:</i></b> To investigate the efficacy and safety of wirelessly programmed DBS of bilateral subthalamic nucleus (STN) in patients with primary PD. <b><i>Methods:</i></b> Sixty-four patients with primary PD were randomly divided into test and control groups (1:1), where DBS was initiated at either 1 month or 3 months, respectively, after surgery. Safety and efficacy of the treatment were compared between on- and off-medication states 3 months after surgery. Outcome measures included analysis of Unified Parkinson's Disease Rating Scale (UPDRS) scores, duration of “on” periods, and daily equivalent doses of levodopa. All patients were followed up both 6 and 12 months after surgery. <b><i>Results:</i></b> Three months after surgery, significant decrease in the UPDRS motor scores were observed for the test group in the off-medication state (25.08 ± 1.00) versus the control group (4.20 ± 1.99). <b><i>Conclusions:</i></b> Bilateral wireless programming STN-DBS is safe and effective for patients with primary PD in whom medical management has failed to restore motor function.
DOI: 10.15131/shef.data.5057527
title: Shear database of RC FRP beams without shear reinforcement

description: This database collects the main experimental results form the tests performed on the FRP reinforced concrete beams without shear reinforcement.<br>Note: A description of each spreadsheet column is available as a comment, on downloading and opening the excel file.<br>
DOI: 10.6084/m9.figshare.5057518
title: Numerical simulation of 4-step facilitated diffusion model from A facilitated diffusion model constrained by the probability isotherm: a pedagogical exercise in intuitive non-equilibrium thermodynamics

description: Filename "INET.xlsx"
DOI: 10.6084/m9.figshare.5057518.v1
title: Numerical simulation of 4-step facilitated diffusion model from A facilitated diffusion model constrained by the probability isotherm: a pedagogical exercise in intuitive non-equilibrium thermodynamics

description: Filename "INET.xlsx"
DOI: 10.6084/m9.figshare.5057515
title: Phylogenetic characters from Taxonomic review of the Late Cenozoic megapodes (Galliformes: Megapodiidae) of Australia

description: List of character codes used in the phylogenetic analysis
DOI: 10.6084/m9.figshare.5057503
title: Dataset for: Peptide Microarray Analysis of the Cross-talk Between O-GlcNAcylation and Tyrosine Phosphorylation

description: O-GlcNAcylation of proteins regulates important cellular processes. A few reports noted that O-GlcNAcylation exhibits cross-talk with tyrosine phosphorylation. With an activity-based microarray analysis of 256 tyrosine kinase peptide substrates, we found that phosphorylation of 6 peptides by Jak2 inhibited their subsequent O-GlcNAcylation. However, O-GlcNAcylation had no detectable effect on their subsequent phosphorylation. A specific peptide (ZO3_357_371), derived from the ZO-3 protein, was studied in detail. Kinetic results showed that the presence of a phosphate at Tyr364 of ZO3_357_371 slowed the O-GlcNAcylation of nearby Ser369, while the presence of a GlcNAc at Ser369 had no significant effect on the phosphorylation of this peptide at Tyr364. These findings provide a glimpse into the new paradigm for cellular signaling control by cross-talk.
DOI: 10.6084/m9.figshare.5057515.v1
title: Phylogenetic characters from Taxonomic review of the Late Cenozoic megapodes (Galliformes: Megapodiidae) of Australia

description: List of character codes used in the phylogenetic analysis
DOI: 10.6084/m9.figshare.5057497
title: vdfvdfv

description: vdvdv
DOI: 10.6084/m9.figshare.5057479
title: Supplementary Material for: Elevated Preoperative CA125 or CA19-9 in Borderline Ovarian Tumors: Could It Be Suggestive of Advanced Stage or a Poor Prognosis?

description: <b><i>Objectives:</i></b> To investigate whether elevated levels of CA125 (≥35 U/mL) and CA19-9 (≥37 U/mL) suggest advanced-stage disease (defined as stage II or higher) or poor prognosis in patients with borderline ovarian tumors (BOTs). <b><i>Study Design:</i></b> We retrospectively identified 591 patients with BOTs. Multivariate logistic regressions and Cox proportional hazard regressions were used to determine the clinicopathologic factors associated with the presence of advanced-stage disease and the prognostic factors associated with recurrence-free survival. <b><i>Results:</i></b> CA125 was elevated more often in serous than in mucinous tumors (50.6 vs. 35.5%; <i>p</i> = 0.003), whereas CA19-9 was elevated more often in mucinous than serous tumors (33.6 vs. 15.3%; <i>p</i> = 0.001). An elevated CA125 level was independently associated with the presence of advanced-stage disease in serous (<i>p</i> = 0.005) and in mucinous BOTs (<i>p</i> = 0.015). However, preoperative elevation of CA19-9, unlike CA125, was not associated with the advanced-stage disease. Elevated preoperative CA125 level (<i>p</i> = 0.037) was an independent prognostic factor for recurrence-free survival in patients with serous BOTs. However, neither CA125 nor CA19-9 had prognostic significance in mucinous BOTs. <b><i>Conclusions:</i></b> Elevated preoperative CA125, unlike CA19-9, is a diagnostic and prognostic biomarker associated with the presence of advanced-stage disease and risk of relapse in patients with serous BOTs.
DOI: 10.6084/m9.figshare.5057482
title: Charge redistribution in QM:QM ONIOM model systems: a constrained density functional theory approach

description: The ONIOM hybrid method has found considerable success in QM:QM studies designed to approximate a high level of theory at a significantly reduced cost. This cost reduction is achieved by treating only a small model system with the target level of theory and the rest of the system with a low, inexpensive, level of theory. However, the choice of an appropriate model system is a limiting factor in ONIOM calculations and effects such as charge redistribution across the model system boundary must be considered as a source of error. In an effort to increase the general applicability of the ONIOM model, a method to treat the charge redistribution effect is developed using constrained density functional theory (CDFT) to constrain the charge experienced by the model system in the full calculation to the link atoms in the truncated model system calculations. Two separate CDFT-ONIOM schemes are developed and tested on a set of 20 reactions with eight combinations of levels of theory. It is shown that a scheme using a scaled Lagrange multiplier term obtained from the low-level CDFT model calculation outperforms ONIOM at each combination of levels of theory from 32% to 70%.
DOI: 10.6084/m9.figshare.5057488
title: vdfvdfv

description: fdvdfvdfv
DOI: 10.6084/m9.figshare.5057497.v1
title: vdfvdfv

description: vdvdv
DOI: 10.6084/m9.figshare.5057503.v1
title: Dataset for: Peptide Microarray Analysis of the Cross-talk Between O-GlcNAcylation and Tyrosine Phosphorylation

description: O-GlcNAcylation of proteins regulates important cellular processes. A few reports noted that O-GlcNAcylation exhibits cross-talk with tyrosine phosphorylation. With an activity-based microarray analysis of 256 tyrosine kinase peptide substrates, we found that phosphorylation of 6 peptides by Jak2 inhibited their subsequent O-GlcNAcylation. However, O-GlcNAcylation had no detectable effect on their subsequent phosphorylation. A specific peptide (ZO3_357_371), derived from the ZO-3 protein, was studied in detail. Kinetic results showed that the presence of a phosphate at Tyr364 of ZO3_357_371 slowed the O-GlcNAcylation of nearby Ser369, while the presence of a GlcNAc at Ser369 had no significant effect on the phosphorylation of this peptide at Tyr364. These findings provide a glimpse into the new paradigm for cellular signaling control by cross-talk.
DOI: 10.6084/m9.figshare.5057473
title: Supplementary Material for: Impact of Diabetes on Extracellular Volume Status in Patients Initiating Peritoneal Dialysis

description: <b><i>Background:</i></b> Recent reports have highlighted that diabetic patients with kidney failure are at increased risk of technique failure and transfer to haemodialysis within 90 days of initiating peritoneal dialysis (PD). We wished to determine whether there were differences between diabetic and non-diabetic patients within the first 3 months of starting PD. <b><i>Methods:</i></b> We reviewed results of corresponding bioimpedance and the 1st test of peritoneal membrane function (PET) in consecutive patients, 6-10 weeks after initiating PD electively. <b><i>Results:</i></b> Adult patients numbering 386 - 230 males (59.6%), 152 (39.4%) diabetic, 188 (48.7%) white, mean age 57.3 ±16.9 years - were studied. Although weight, residual renal function and peritoneal clearances were not different, diabetic patients had greater extracellular water to total body water (ECW/TBW; 40.4 ± 1.1 vs. 39.2 ± 1.4) and % ECW excess (9.6 [6.3-12.3] vs. 4.9 [0.7-8.9]), lower serum albumin (35.2 ± 4.7 vs. 37.8 ± 4.9 g/L), greater fat mass index (9.5 ± 4.2 vs. 7.7 ± 4.2), and although mean arterial blood pressure was similar, arterial pulse pressure was greater (66.9 ± 10.8 vs. 54.3 ± 17.3 mm Hg, all <i>p</i> &lt; 0.001). On multivariate analysis, glycated haemoglobin was associated with pulse pressure (standardised β 0.24, <i>p</i> &lt; 0.001), N terminal brain natriuretic peptide (β 0.24, <i>p</i> &lt; 0.001), ECW/TBW (β 0.19, <i>p</i> = 0.012) and negatively with serum albumin (β -0.14, <i>p</i> = 0.033) and creatinine (β -0.18, <i>p</i> = 0.02). <b><i>Conclusion:</i></b> Diabetic patients electively starting PD were found to have greater ECW/TBW ratios and ECW excess 6-10 weeks after starting PD compared to non-diabetics, despite similar PET. Increased ECW could predispose diabetic patients to be at greater risk of volume overload.
DOI: 10.6084/m9.figshare.5057482.v1
title: Charge redistribution in QM:QM ONIOM model systems: a constrained density functional theory approach

description: The ONIOM hybrid method has found considerable success in QM:QM studies designed to approximate a high level of theory at a significantly reduced cost. This cost reduction is achieved by treating only a small model system with the target level of theory and the rest of the system with a low, inexpensive, level of theory. However, the choice of an appropriate model system is a limiting factor in ONIOM calculations and effects such as charge redistribution across the model system boundary must be considered as a source of error. In an effort to increase the general applicability of the ONIOM model, a method to treat the charge redistribution effect is developed using constrained density functional theory (CDFT) to constrain the charge experienced by the model system in the full calculation to the link atoms in the truncated model system calculations. Two separate CDFT-ONIOM schemes are developed and tested on a set of 20 reactions with eight combinations of levels of theory. It is shown that a scheme using a scaled Lagrange multiplier term obtained from the low-level CDFT model calculation outperforms ONIOM at each combination of levels of theory from 32% to 70%.
DOI: 10.6084/m9.figshare.5057470
title: Supplementary Material for: Hemophagocytic Lymphohistiocytosis in Adults with Intraocular Involvement: Clinicopathologic Features of 3 Cases

description: <b><i>Background/Aims:</i></b> Hemophagocytic lymphohistiocytosis (HLH) is an infrequent inflammatory multisystemic syndrome. Only rare cases with ophthalmic involvement describing their pathologic features have been previously reported. <b><i>Methods:</i></b> We report 3 cases of adult-onset HLH with bilateral ocular involvement and describe their clinicopathologic features. <b><i>Results:</i></b> Three adult males - 2 with a history of viral infection - developed persistent fever, fatigue, bone marrow abnormalities, and irreversible multiorgan failure. Visual impairment was also documented in 2 cases. Complete autopsies were performed. Ophthalmic pathology demonstrated a bilateral histiocytic infiltrate with scant lymphocytes affecting the uvea. Focal extension to the retina, optic nerve, and trabecular meshwork were also identified, as well as hemophagocytosis in 1 case. Macrophages showed strong immunoreactivity for CD163 antibody and lacked BRAF p.V600E mutant protein. <b><i>Conclusion:</i></b> HLH is an unusual disorder associated with several systemic conditions. Histologic features in the eye are poorly documented, with prior reports restricted to children. Our 3 adult cases are reported using updated criteria and, despite the difference in age, show changes similar to those observed in the pediatric population.
DOI: 10.6084/m9.figshare.5057488.v1
title: vdfvdfv

description: fdvdfvdfv
DOI: 10.6084/m9.figshare.5057464
title: Supplementary Material for: High-Dose Cannabidiol-Induced Hypotension after Global Hypoxia-Ischemia in Piglets

description: <b><i>Background:</i></b> Cannabidiol (CBD) is considered a promising neuroprotectant after perinatal hypoxia-ischemia (HI). We have previously studied the effects of CBD 1 mg/kg in the early phase after global HI in piglets. In contrast to prior studies, we found no evidence of neuroprotection and hypothesized that higher doses might be required to demonstrate efficacy in this animal model. <b><i>Objective:</i></b> To assess the safety and potential neuroprotective effects of high-dose CBD. <b><i>Methods:</i></b> Anesthetized newborn piglets underwent global HI by ventilation with 8% O<sub>2</sub> until the point of severe metabolic acidosis (base excess -20 mmol/L) and/or hypotension (mean arterial blood pressure ≤20 mm Hg). Piglets were randomized to intravenous treatment with vehicle (<i>n</i> = 9) or CBD (<i>n</i> = 13). The starting dose, CBD 50 mg/kg, was reduced if adverse effects occurred. The piglets were euthanized 9.5 h after HI and tissue was collected for analysis. <b><i>Results:</i></b> CBD 50 mg/kg (<i>n</i> = 4) induced significant hypotension in 2 out of 4 piglets, and 1 out of 4 piglets suffered a fatal cardiac arrest. CBD 25 mg/kg (<i>n</i> = 4) induced significant hypotension in 1 out of 4 piglets, while 10 mg/kg (<i>n</i> = 5) was well tolerated. A significant negative correlation between the plasma concentration of CBD and hypotension during drug infusion was observed (<i>p</i> &lt; 0.005). Neuroprotective effects were evaluated in piglets that did not display significant hypotension (<i>n</i> = 9) and CBD did not alter the degree of neuronal damage as measured by a neuropathology score, levels of the astrocytic marker S100B in CSF, magnetic resonance spectroscopy markers (Lac/NAA and Glu/NAA ratios), or plasma troponin T. <b><i>Conclusions:</i></b> High-dose CBD can induce severe hypotension and did not offer neuroprotection in the early phase after global HI in piglets.
DOI: 10.6084/m9.figshare.5057473.v1
title: Supplementary Material for: Impact of Diabetes on Extracellular Volume Status in Patients Initiating Peritoneal Dialysis

description: <b><i>Background:</i></b> Recent reports have highlighted that diabetic patients with kidney failure are at increased risk of technique failure and transfer to haemodialysis within 90 days of initiating peritoneal dialysis (PD). We wished to determine whether there were differences between diabetic and non-diabetic patients within the first 3 months of starting PD. <b><i>Methods:</i></b> We reviewed results of corresponding bioimpedance and the 1st test of peritoneal membrane function (PET) in consecutive patients, 6-10 weeks after initiating PD electively. <b><i>Results:</i></b> Adult patients numbering 386 - 230 males (59.6%), 152 (39.4%) diabetic, 188 (48.7%) white, mean age 57.3 ±16.9 years - were studied. Although weight, residual renal function and peritoneal clearances were not different, diabetic patients had greater extracellular water to total body water (ECW/TBW; 40.4 ± 1.1 vs. 39.2 ± 1.4) and % ECW excess (9.6 [6.3-12.3] vs. 4.9 [0.7-8.9]), lower serum albumin (35.2 ± 4.7 vs. 37.8 ± 4.9 g/L), greater fat mass index (9.5 ± 4.2 vs. 7.7 ± 4.2), and although mean arterial blood pressure was similar, arterial pulse pressure was greater (66.9 ± 10.8 vs. 54.3 ± 17.3 mm Hg, all <i>p</i> &lt; 0.001). On multivariate analysis, glycated haemoglobin was associated with pulse pressure (standardised β 0.24, <i>p</i> &lt; 0.001), N terminal brain natriuretic peptide (β 0.24, <i>p</i> &lt; 0.001), ECW/TBW (β 0.19, <i>p</i> = 0.012) and negatively with serum albumin (β -0.14, <i>p</i> = 0.033) and creatinine (β -0.18, <i>p</i> = 0.02). <b><i>Conclusion:</i></b> Diabetic patients electively starting PD were found to have greater ECW/TBW ratios and ECW excess 6-10 weeks after starting PD compared to non-diabetics, despite similar PET. Increased ECW could predispose diabetic patients to be at greater risk of volume overload.