cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5023592.v1
title: ESM 1 from Depth-dependent effects of culling—do mesophotic lionfish populations undermine current management?

description: <b>GPS locations of lionfish abundance survey locations around Utila, Honduras</b>.
DOI: 10.17608/k6.auckland.5023580
title: Variable-width lines in R

description: This document describes the ‘vwline’ package, which provides an R interface for drawing variable-width curves. The package provides functions to draw line segments through a set of locations, or a smooth curve relative to a set of control points, with the width of the line allowed to vary along the length of the line.
DOI: 10.6084/m9.figshare.5023256
title: GOAJ2: Gold Open Access Journals 2011-2016

description: A sequel to Gold Open Access Journals 2011-2015, this dataset reflects the state of DOAJ as of the very start of 2017. <br>
DOI: 10.6084/m9.figshare.5023232
title: Data and code to reproduce Dallas, Decker, Hastings. "Species are not most abundant in the center of their geographic range or climatic niche"

description: This repository contains the code and data to reproduce the analyses and figures from:<br>Dallas, T., R. Decker, and AM Hastings. 2017. "Species are not most abundant in the center of their geographic range or climatic niche" <i>Ecology Letters</i><br><br>Note that these data sources are published elsewhere, and if these data used, the original data sources should be cited. <br><br>
DOI: 10.6084/m9.figshare.5021297
title: R code

description: R code used for each data set to perform negative binomial regression, calculate overdispersion statistic, generate summary statistics, remove outliers
DOI: 10.6084/m9.figshare.5021327
title: Raw data spreadsheets (Excel)

description: Raw field data collected from 11 experiments
DOI: 10.6084/m9.figshare.5021429
title: Preliminary data from the Dyad-Adaptive PASAT

description: The Paced Auditory Serial Addition Test (PASAT) is a neuropsychological assessment that is widely used to evaluate processing speed and executive function in patients with multiple sclerosis, traumatic brain injury, and other neuropsychiatric disorders. In the PASAT, subjects listen to sequences of digits while continuously reporting the sum of the last two digits presented. Four different stimulus onset asynchronies (SOAs) are usually tested, with difficulty increasing as SOAs are reduced. Ceiling effects are common at long SOAs. In contrast, the digit delivery rate often exceeds the subject’s processing capacity at short SOAs, resulting in frustration and stress and causing some subjects to stop performing altogether. In addition, subjects may adopt an “alternate answer” strategy at short SOAs, which reduces the test’s demands on working-memory and processing speed. Consequently, studies have shown that the number of dyads (consecutive correct answers) is a more sensitive measure of PASAT performance than the overall number of correct sums. Here, we describe a 2.5-minute computerized test, the Dyad-Adaptive PASAT (DA-PASAT), where stimulus onset asynchronies (SOAs) are adjusted based on dyad accuracy and processing capacity is reflected in the minimum SOA (minSOA) achieved in 54 trials. Experiment 1 gathered normative data in two large populations: 1617 subjects in New Zealand ranging in age from 18 to 65 years, and 214 Californians ranging in age from 18 to 82 years. Minimum SOAs were influenced by age, education, and daily hours of computer-use. Minimum SOA z-scores, calculated after factoring out the influence of these factors, were virtually identical in the two control groups, as were response times (RTs). The dyad ratio (the proportion of hits occurring in dyads) averaged 0.93 in both experiments. Experiment 2 measured the test-retest reliability of the DA-PASAT in 44 young subjects who underwent three test sessions at weekly intervals. High intraclass correlation coefficients (ICCs) were found for minSOAs (0.87), response times (0.76), and dyad ratios (0.87). Performance improved across test sessions for all measures. Experiment 3 investigated the effects of simulated malingering in 50 subjects: 42% of simulated malingerers produced abnormal (p&lt; 0.05) minSOA z-scores. Simulated malingerers with abnormal scores were distinguished with 87% sensitivity and 69% specificity from control subjects with abnormal scores by differences between performance during training and during the actual test. Experiment 4 investigated patients with traumatic brain injury (TBI): patients with mild TBI performed within the normal range while patients with severe TBI showed deficits. The DA-PASAT reduces the time and stress of PASAT assessment while gathering sensitive measures of dyad processing that reveal the effects of aging, malingering, and traumatic brain injury on performance.
DOI: 10.6084/m9.figshare.5021429.v2
title: Preliminary data from the Dyad-Adaptive PASAT

description: The Paced Auditory Serial Addition Test (PASAT) is a neuropsychological assessment that is widely used to evaluate processing speed and executive function in patients with multiple sclerosis, traumatic brain injury, and other neuropsychiatric disorders. In the PASAT, subjects listen to sequences of digits while continuously reporting the sum of the last two digits presented. Four different stimulus onset asynchronies (SOAs) are usually tested, with difficulty increasing as SOAs are reduced. Ceiling effects are common at long SOAs. In contrast, the digit delivery rate often exceeds the subject’s processing capacity at short SOAs, resulting in frustration and stress and causing some subjects to stop performing altogether. In addition, subjects may adopt an “alternate answer” strategy at short SOAs, which reduces the test’s demands on working-memory and processing speed. Consequently, studies have shown that the number of dyads (consecutive correct answers) is a more sensitive measure of PASAT performance than the overall number of correct sums. Here, we describe a 2.5-minute computerized test, the Dyad-Adaptive PASAT (DA-PASAT), where stimulus onset asynchronies (SOAs) are adjusted based on dyad accuracy and processing capacity is reflected in the minimum SOA (minSOA) achieved in 54 trials. Experiment 1 gathered normative data in two large populations: 1617 subjects in New Zealand ranging in age from 18 to 65 years, and 214 Californians ranging in age from 18 to 82 years. Minimum SOAs were influenced by age, education, and daily hours of computer-use. Minimum SOA z-scores, calculated after factoring out the influence of these factors, were virtually identical in the two control groups, as were response times (RTs). The dyad ratio (the proportion of hits occurring in dyads) averaged 0.93 in both experiments. Experiment 2 measured the test-retest reliability of the DA-PASAT in 44 young subjects who underwent three test sessions at weekly intervals. High intraclass correlation coefficients (ICCs) were found for minSOAs (0.87), response times (0.76), and dyad ratios (0.87). Performance improved across test sessions for all measures. Experiment 3 investigated the effects of simulated malingering in 50 subjects: 42% of simulated malingerers produced abnormal (p&lt; 0.05) minSOA z-scores. Simulated malingerers with abnormal scores were distinguished with 87% sensitivity and 69% specificity from control subjects with abnormal scores by differences between performance during training and during the actual test. Experiment 4 investigated patients with traumatic brain injury (TBI): patients with mild TBI performed within the normal range while patients with severe TBI showed deficits. The DA-PASAT reduces the time and stress of PASAT assessment while gathering sensitive measures of dyad processing that reveal the effects of aging, malingering, and traumatic brain injury on performance.
DOI: 10.6084/m9.figshare.5021429.v1
title: Data from the Dyad-Adaptive PASAT

description: The Paced Auditory Serial Addition Test (PASAT) is a neuropsychological assessment that is widely used to evaluate processing speed and executive function in patients with multiple sclerosis, traumatic brain injury, and other neuropsychiatric disorders. In the PASAT, subjects listen to sequences of digits while continuously reporting the sum of the last two digits presented. Four different stimulus onset asynchronies (SOAs) are usually tested, with difficulty increasing as SOAs are reduced. Ceiling effects are common at long SOAs. In contrast, the digit delivery rate often exceeds the subject’s processing capacity at short SOAs, resulting in frustration and stress and causing some subjects to stop performing altogether. In addition, subjects may adopt an “alternate answer” strategy at short SOAs, which reduces the test’s demands on working-memory and processing speed. Consequently, studies have shown that the number of dyads (consecutive correct answers) is a more sensitive measure of PASAT performance than the overall number of correct sums. Here, we describe a 2.5-minute computerized test, the Dyad-Adaptive PASAT (DA-PASAT), where stimulus onset asynchronies (SOAs) are adjusted based on dyad accuracy and processing capacity is reflected in the minimum SOA (minSOA) achieved in 54 trials. Experiment 1 gathered normative data in two large populations: 1617 subjects in New Zealand ranging in age from 18 to 65 years, and 214 Californians ranging in age from 18 to 82 years. Minimum SOAs were influenced by age, education, and daily hours of computer-use. Minimum SOA z-scores, calculated after factoring out the influence of these factors, were virtually identical in the two control groups, as were response times (RTs). The dyad ratio (the proportion of hits occurring in dyads) averaged 0.93 in both experiments. Experiment 2 measured the test-retest reliability of the DA-PASAT in 44 young subjects who underwent three test sessions at weekly intervals. High intraclass correlation coefficients (ICCs) were found for minSOAs (0.87), response times (0.76), and dyad ratios (0.87). Performance improved across test sessions for all measures. Experiment 3 investigated the effects of simulated malingering in 50 subjects: 42% of simulated malingerers produced abnormal (p&lt; 0.05) minSOA z-scores. Simulated malingerers with abnormal scores were distinguished with 87% sensitivity and 69% specificity from control subjects with abnormal scores by differences between performance during training and during the actual test. Experiment 4 investigated patients with traumatic brain injury (TBI): patients with mild TBI performed within the normal range while patients with severe TBI showed deficits. The DA-PASAT reduces the time and stress of PASAT assessment while gathering sensitive measures of dyad processing that reveal the effects of aging, malingering, and traumatic brain injury on performance.
DOI: 10.6084/m9.figshare.5018810
title: ASANTE INDIGENOUS KNOWLEDGE SYSTEMS: REPOSITORIES OF CONSERVATION ETHICS FOR GHANA’S BIODIVERSITY

description: The indigenous knowledge systems of the Asantes handed down to them by their past but active forebears carries a lot of weight in biodiversity conservation discussions. This is promulgated by the numerous conservation ethics hidden in the cultural and artistic practices of the people. Using the Asante Bekwai Traditional Area and it’s Protected Areas as a case study, the researcher accentuates the enormous conservation ethics in the Asante indigenous knowledge particularly cosmological beliefs, taboos and totems. Data analysis spiral was implemented for the interpretation of the data accrued via focus group interviews and non- participant observations. The study revealed that the Asante indigenous knowledge systems were and is still instrumental in conserving the biodiversity resources by regulating the residents’ behaviours towards the biodiversity resources in the environment. The research contends that the conservation ethics of Asante indigenous knowledge transcends time and must be utilized in contemporary conservation strategies for biodiversity. The study advocates for a renaissance and factorization of Asante indigenous knowledge in various developmental projects in Ghana. It tasks developers of conservation strategies and projects in Ghana to tactfully synergize the Asante indigenous knowledge with the Western scientific knowledge to aid in conserving and arresting the deficiencies in Ghana’s biodiversity.
DOI: 10.6084/m9.figshare.5018810.v1
title: ASANTE INDIGENOUS KNOWLEDGE SYSTEMS: REPOSITORIES OF CONSERVATION ETHICS FOR GHANA’S BIODIVERSITY

description: The indigenous knowledge systems of the Asantes handed down to them by their past but active forebears carries a lot of weight in biodiversity conservation discussions. This is promulgated by the numerous conservation ethics hidden in the cultural and artistic practices of the people. Using the Asante Bekwai Traditional Area and it’s Protected Areas as a case study, the researcher accentuates the enormous conservation ethics in the Asante indigenous knowledge particularly cosmological beliefs, taboos and totems. Data analysis spiral was implemented for the interpretation of the data accrued via focus group interviews and non- participant observations. The study revealed that the Asante indigenous knowledge systems were and is still instrumental in conserving the biodiversity resources by regulating the residents’ behaviours towards the biodiversity resources in the environment. The research contends that the conservation ethics of Asante indigenous knowledge transcends time and must be utilized in contemporary conservation strategies for biodiversity. The study advocates for a renaissance and factorization of Asante indigenous knowledge in various developmental projects in Ghana. It tasks developers of conservation strategies and projects in Ghana to tactfully synergize the Asante indigenous knowledge with the Western scientific knowledge to aid in conserving and arresting the deficiencies in Ghana’s biodiversity.
DOI: 10.25392/leicester.data.12859853
title: Critical closing pressure dynamic response

description: Continuous recordings of bilateral cerebral blood flow velocity with transcranial Doppler ultrasound, arterial blood pressure, with finger volume clamping, end-tidal carbon dioxide with infra-red capnography, and electrocardiogram for heart rate.
DOI: 10.6084/m9.figshare.5018774
title: Using AmgX to Accelerate PETSc-Based CFD Codes

description: [This file set supplements the presentation by Pi-Yueh Chuang at 2016 GPU Technology Conference, on Thu. April 7th: see session S6355.]<br>Please cite as:<br>Chuang, Pi-Yueh; Barba, Lorena A. (2017): Using AmgX to Accelerate PETSc-Based CFD Codes. figshare.https://doi.org/10.6084/m9.figshare.5018774.v1<br>The file set includes a Jupyter notebook that reports how we accelerated our PETSc-based CFD solver, PetIBM, with multi-GPU capability enabled through AmgX library. PETSc, developed by Argonne National Laboratory, is a toolkit for parallel scientific computing. AmgX is an NVIDIA library providing multigrid preconditioners and Krylov linear solvers. It features the capability of multi-GPU computing through MPI. We developed AmgXWrapper to couple PETSc and AmgX, so that we can easily integrate AmgX into PetIBM with less than 10 lines of code modification.<br>The links in references are:* Video record of GTC 2016 presentation* Rendered version of the notebook viewed on nbviewer* GitHub repository of AmgXWrapper* GitHub repository of PetIBM<br>
DOI: 10.25392/leicester.data.12859853.v1
title: Critical closing pressure dynamic response

description: Continuous recordings of bilateral cerebral blood flow velocity with transcranial Doppler ultrasound, arterial blood pressure, with finger volume clamping, end-tidal carbon dioxide with infra-red capnography, and electrocardiogram for heart rate.
DOI: 10.6084/m9.figshare.5017154
title: PowerPoint Slides for: Donor-Specific Anti-Human Leukocyte Antigens Antibodies, Acute Rejection, Renal Function, and Histology in Kidney Transplant Recipients Receiving Tacrolimus and Everolimus

description: <b><i>Background:</i></b> This analysis compared efficacy, renal function, and histology in kidney transplant recipients receiving tacrolimus (TAC) combined with everolimus (EVR) or mycophenolate (MPS). <b><i>Methods:</i></b> This was a retrospective analysis from a randomized trial in kidney transplant recipients who received a single 3 mg/kg dose of rabbit antithymocyte globulin (r-ATG), TAC, EVR, and prednisone (PRED; r-ATG/EVR, <i>n</i> = 85), basiliximab (BAS), TAC, EVR, and PRED (BAS/EVR, <i>n</i> = 102) or BAS, TAC, MPS, and PRED (BAS/MPS, <i>n</i> = 101). We evaluated the incidence of de novo donor-specific anti-human leukocyte antigens antibodies (DSA) and histology on protocol biopsies at 12 months, and the incidence of acute rejection, estimated glomerular filtration rate (eGFR) and proteinuria at 36 months. <b><i>Results:</i></b> At 12 months, there were no differences in de novo DSA (6.4 vs. 3.4 vs. 5.5%) or in subclinical inflammation (2.0 vs. 4.8 vs. 10.2%), interstitial fibrosis/tubular atrophy (57.1 vs. 58.5 vs. 53.8%) and C4d deposition (2.0 vs. 7.3 vs. 2.6%). At 36 months, there were no differences in the incidence of treatment failure (19.0 vs. 27.7 vs. 27.7%, <i>p</i> = 0.186), first biopsy-proven acute rejection (9.5 vs. 21.8 vs. 16.8%, <i>p</i> = 0.073), and urine protein/creatinine ratios (0.53 ± 1.05 vs. 0.62 ± 0.75 vs. 0.71 ± 1.24). eGFR was lower in the BAS/EVR compared to that in the BAS/MPS group (53.4 ± 20.9 vs. 50.8 ± 19.5 vs. 60.7 ± 21.2 mL/min/1.73 m<sup>2</sup>, <i>p</i> = 0.017) but comparable using a sensitive analysis (49.5 ± 23 vs. 47.5 ± 22.6 vs. 53.6 ± 27.8 mL/min/1.73 m<sup>2</sup>, <i>p</i> = 0.207). <b><i>Conclusion:</i></b> In this cohort, the use of EVR and reduced TAC concentrations were associated with comparable efficacy, renal function, and histological parameters compared to the standard-of-care immunosuppressive regimen.
DOI: 10.17028/rd.lboro.5017130
title: Tyre cavity noise simulation results

description: Individual data runs for simulation of the tyre cavity noise in a rotating wheel assembly.Matlab v 2011 has been used to save the individual data files.
DOI: 10.6084/m9.figshare.5017127
title: PowerPoint Slides for: Effect of Febuxostat on the Endothelial Dysfunction in Hemodialysis Patients: A Randomized, Placebo-Controlled, Double-Blinded Study

description: <b><i>Background:</i></b> Endothelial dysfunction is an important risk factor for cardiovascular diseases to occur in end-stage renal disease patients. Febuxostat, being a novel xanthine oxidase inhibitor, is apparently having a beneficial role in improving the endothelial dysfunction; however, data among hemodialysis patients are still limited. <b><i>Methods:</i></b> A prospective, placebo-controlled, block-randomized, double-blinded study was carried out to evaluate the effect of oral febuxostat on the endothelial dysfunction in hemodialysis patients. Fifty-seven eligible hemodialysis patients were randomly assigned to either the drug group (40 mg thrice weekly) or the placebo group. Serum Asymmetric dimethylarginine (ADMA), Serum uric acid (UA), and serum high sensitivity C-reactive protein (hsCRP) were measured at baseline and at the end of a 2-month study. Serum alanine aminotransferase (ALT), serum aspartate aminotransferase (AST), and the occurrence of pancytopenia were tested as safety parameters at baseline and at the end of study. <b><i>Results:</i></b> Serum UA significantly decreased from 7.5 ± 0.8 to 5.1 ± 1.2 mg/dL in the febuxostat group, while it did not change significantly in the placebo group. Treatment with febuxostat resulted in a significant decrease in the serum ADMA level from 1.027 ± 0.116 to 0.944 ± 0.104 µmol/L and the serum hsCRP level from 12.5 ± 1.65 to 12.1 ± 1.70 mg/L. Testing of serum ALT, serum AST, and pancytopenia revealed no significant difference in both groups. <b><i>Conclusion:</i></b> Febuxostat appears to improve hyperuricemia and endothelial dysfunction and ameliorate inflammation in hemodialysis patients with no safety concerns.
DOI: 10.6084/m9.figshare.5017145
title: PowerPoint Slides for: Pre-End-Stage Renal Disease Care and Early Survival among Incident Dialysis Patients in the US Military Health System

description: <b><i>Background:</i></b> Previous reports showed an increased early mortality after chronic dialysis initiation among the end-stage renal disease (ESRD) population. We hypothesized that ESRD patients in the Military Health System (MHS) would have greater access to pre-ESRD care and hence better survival rates during this early high-risk period. <b><i>Methods:</i></b> In this retrospective cohort study, using the US Renal Data System database, we identified 1,256,640 patients initiated on chronic dialysis from January 2, 2004 through December 31, 2014, from which a bootstrap sample of 3,984 non-MHS incident dialysis patients were compared with 996 MHS patients. We assessed care by a nephrologist and dietitian, erythropoietin administration, and vascular access use at dialysis initiation as well as all-cause mortality as outcome variables. <b><i>Results:</i></b> MHS patients were significantly more likely to have had pre-ESRD nephrology care (adjusted OR [aOR] 2.9; 95% CI 2.3-3.7) and arteriovenous fistula used at dialysis initiation (aOR 2.2; 95% CI 1.7-2.7). Crude mortality rates peaked between the 4th and the 8th week for both cohorts but were reduced among MHS patients. The baseline adjusted Cox model showed significantly lower death rates among MHS vs. non-MHS patients at 6, 9, and 12 months. This survival advantage among MHS patients was attenuated after further adjustment for pre-ESRD nephrology care and dialysis vascular access. <b><i>Conclusions:</i></b> MHS patients had improved survival within the first 12 months compared to the general ESRD population, which may be explained in part by differences in pre-ESRD nephrology care and vascular access types.
DOI: 10.6084/m9.figshare.5017154.v1
title: PowerPoint Slides for:Donor-Specific Anti-Human Leukocyte Antigens Antibodies, Acute Rejection, Renal Function, and Histology in Kidney Transplant Recipients Receiving Tacrolimus and Everolimus

description: <b><i>Background:</i></b> This analysis compared efficacy, renal function, and histology in kidney transplant recipients receiving tacrolimus (TAC) combined with everolimus (EVR) or mycophenolate (MPS). <b><i>Methods:</i></b> This was a retrospective analysis from a randomized trial in kidney transplant recipients who received a single 3 mg/kg dose of rabbit antithymocyte globulin (r-ATG), TAC, EVR, and prednisone (PRED; r-ATG/EVR, <i>n</i> = 85), basiliximab (BAS), TAC, EVR, and PRED (BAS/EVR, <i>n</i> = 102) or BAS, TAC, MPS, and PRED (BAS/MPS, <i>n</i> = 101). We evaluated the incidence of de novo donor-specific anti-human leukocyte antigens antibodies (DSA) and histology on protocol biopsies at 12 months, and the incidence of acute rejection, estimated glomerular filtration rate (eGFR) and proteinuria at 36 months. <b><i>Results:</i></b> At 12 months, there were no differences in de novo DSA (6.4 vs. 3.4 vs. 5.5%) or in subclinical inflammation (2.0 vs. 4.8 vs. 10.2%), interstitial fibrosis/tubular atrophy (57.1 vs. 58.5 vs. 53.8%) and C4d deposition (2.0 vs. 7.3 vs. 2.6%). At 36 months, there were no differences in the incidence of treatment failure (19.0 vs. 27.7 vs. 27.7%, <i>p</i> = 0.186), first biopsy-proven acute rejection (9.5 vs. 21.8 vs. 16.8%, <i>p</i> = 0.073), and urine protein/creatinine ratios (0.53 ± 1.05 vs. 0.62 ± 0.75 vs. 0.71 ± 1.24). eGFR was lower in the BAS/EVR compared to that in the BAS/MPS group (53.4 ± 20.9 vs. 50.8 ± 19.5 vs. 60.7 ± 21.2 mL/min/1.73 m<sup>2</sup>, <i>p</i> = 0.017) but comparable using a sensitive analysis (49.5 ± 23 vs. 47.5 ± 22.6 vs. 53.6 ± 27.8 mL/min/1.73 m<sup>2</sup>, <i>p</i> = 0.207). <b><i>Conclusion:</i></b> In this cohort, the use of EVR and reduced TAC concentrations were associated with comparable efficacy, renal function, and histological parameters compared to the standard-of-care immunosuppressive regimen.