cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4836884.v1
title: Safety and effectiveness of high-dose methotrexate (over 8 mg/week) in 2838 Japanese patients with rheumatoid arthritis: A postmarketing surveillance report

description: <b>Objectives:</b> To confirm the safety and effectiveness of high-dose (&gt;8 mg/week) methotrexate (MTX) for the treatment of rheumatoid arthritis in Japan. <b>Methods:</b> A postmarketing surveillance program enrolled Japanese patients with rheumatoid arthritis starting on high-dose MTX followed up for either 24- or 52-weeks. Analyses for safety, risk factors affecting safety, and effectiveness were conducted. <b>Results:</b> The safety/effectiveness analysis sets included 2838/2779 and 335/326 patients in the 24-weeks and 52-weeks follow-up groups, respectively. Incidence rates of adverse drug reactions (ADRs) and serious ADRs were 21.42% and 1.66% in the 24-weeks, and 35.52% and 2.69% in the 52-weeks groups, respectively. The Disease Activity Score in 28 Joints (DAS28) was significantly decreased as early as four weeks from the start of high-dose MTX; after 24-weeks (4.09–3.21) and 52-weeks of treatment (3.91–2.80; both <i>p</i> <b>Conclusions:</b> High-dose MTX was well tolerated in Japanese patients, resulted in improved disease control, and can be considered a step forward in achieving treat-to-target goals.
DOI: 10.6084/m9.figshare.4836890.v1
title: Lateral roots dataset

description: The measured lateral root information of maize(ZD958 and XY335) was presented with a standard format (RSML).
DOI: 10.6084/m9.figshare.4836890.v2
title: Lateral roots dataset

description: The measured lateral root information of maize(ZD958 and XY335) was presented with a standard format (RSML).
DOI: 10.6084/m9.figshare.4836836
title: Structure identification and variable selection in geographically weighted regression models

description: Geographically weighted regression (GWR) is an important tool for exploring spatial non-stationarity of a regression relationship, in which whether a regression coefficient really varies over space is especially important in drawing valid conclusions on the spatial variation characteristics of the regression relationship. This paper proposes a so-called GWGlasso method for structure identification and variable selection in GWR models. This method penalizes the loss function of the local-linear estimation of the GWR model by the coefficients and their partial derivatives in the way of the adaptive group lasso and can simultaneously identify spatially varying coefficients, nonzero constant coefficients and zero coefficients. Simulation experiments are further conducted to assess the performance of the proposed method and the Dublin voter turnout data set is analysed to demonstrate its application.
DOI: 10.6084/m9.figshare.4836890.v3
title: Lateral roots dataset

description: The measured lateral root information of maize(ZD958 and XY335) was presented with a standard format (RSML).
DOI: 10.6084/m9.figshare.4836836.v1
title: Structure identification and variable selection in geographically weighted regression models

description: Geographically weighted regression (GWR) is an important tool for exploring spatial non-stationarity of a regression relationship, in which whether a regression coefficient really varies over space is especially important in drawing valid conclusions on the spatial variation characteristics of the regression relationship. This paper proposes a so-called GWGlasso method for structure identification and variable selection in GWR models. This method penalizes the loss function of the local-linear estimation of the GWR model by the coefficients and their partial derivatives in the way of the adaptive group lasso and can simultaneously identify spatially varying coefficients, nonzero constant coefficients and zero coefficients. Simulation experiments are further conducted to assess the performance of the proposed method and the Dublin voter turnout data set is analysed to demonstrate its application.
DOI: 10.6084/m9.figshare.4836839.v1
title: Pfiles

description: <strong><strong>Diffraction pattern of </strong></strong><strong><strong>P1-P5 </strong></strong><b>Incidence angle and rotation angle of slit are changed.</b><strong><strong>See </strong></strong><strong><strong>A READMEPx-xsxbk.jpg</strong></strong><br>
DOI: 10.6084/m9.figshare.4836827
title: Supplementary Material for: Predictive Value of Second-Trimester Biomarkers and Maternal Features for Adverse Pregnancy Outcomes

description: <i>Objective:</i> To establish the predictive probability for placenta-associated morbidities using second-trimester α-fetoprotein (AFP), human chorionic gonadotropin (HCG), and maternal features. <i>Patients and Methods:</i> A retrospective database of all singleton deliveries with available second-trimester HCG and AFP results from 2005 to 2012 was built and divided into 0, 1, or 2 elevated markers (defined as ≥2 multiples of the median [MoM]). For each group, we analyzed the risk for adverse obstetric outcome - comprising preeclampsia, placental abruption, and birth weight below the 10th percentile - and the time of delivery in those pregnancies. Additionally, prediction models for adverse obstetric outcome, using logistic regression incorporating AFP, HCG, and other maternal characteristics, were calculated. <i>Results:</i> Among 22,124 women who delivered, 16,197 (73%) had AFP and HCG results. Compared with the group with normal markers, the adverse obstetric outcome rate was mildly increased with elevated HCG or AFP, but it was markedly increased when both markers were elevated (13 vs. 31%, OR 2.9, 95% CI 2.0-4.3). Delivery of newborns with adverse obstetric outcome was earlier with each additional elevated marker. The accuracy of predicting adverse obstetric outcome was improved by using prediction models for women with HCG or AFP ≥1.2 MoM that incorporated maternal age, BMI, parity, and chronic hypertension (C-statistic 61-75%). <i>Conclusion:</i> HCG and AFP combined with other maternal characteristics are useful tools for predicting the risk for adverse obstetric outcome.
DOI: 10.6084/m9.figshare.4836830
title: Supplementary Material for: Serum Lymphocyte-Associated Cytokine Concentrations Change More Rapidly over Time in Multiple System Atrophy Compared to Parkinson Disease

description: <i>Objective:</i> Chronic inflammatory processes contribute to the eventual death of motor neurons and the development of symptoms in both idiopathic Parkinson disease (PD) and multiple system atrophy (MSA). Given the faster rate of progression and more severe symptoms associated with MSA, we hypothesized that markers of inflammation would be more evident in the peripheral blood of MSA than PD patients, and that evidence of this inflammation might assist early diagnosis of MSA versus PD. <i>Methods:</i>We performed multiplex analysis to determine the concentrations of 37 immune-associated cytokines and chemokines isolated from the plasma of patients with PD (<i>n</i> = 25) and MSA (<i>n</i> = 14) and compared our results to those of age-matched controls (<i>n</i> = 15). We then applied a mixed-effect multiple regression model to determine if the concentration of cytokines in the plasma of patients with PD and MSA changed significantly over time. <i>Results:</i> Patients with MSA had a trend towards overall lower levels of immune-associated cytokines, while serum cytokine levels were increased in patients with PD. Statistically adjusted comparisons of overall changes in cytokine concentrations between the PD and MSA groups revealed higher concentrations of T-cell-associated cytokines TNFβ and IL-7 in PD. Comparison of samples taken over time revealed significantly faster rates of change in 4 different cytokine concentrations (IL-4, IL-15, IL-2, and IL-9) in patients with MSA versus patients with PD. <i>Conclusions:</i> Our results suggest that single measurements of plasma concentrations of inflammation-associated cytokines cannot be used to distinguish disease states. However, measurements made over time may correlate with pathogenesis. The significant changes in T-cell-associated cytokines may shed light on immune mechanisms that contribute to PD and MSA disease progression.
DOI: 10.6084/m9.figshare.4836890.v4
title: Lateral roots dataset

description: The measured lateral root information of maize(ZD958 and XY335) was presented with a standard format (RSML).
DOI: 10.6084/m9.figshare.4836827.v1
title: Supplementary Material for: Predictive Value of Second-Trimester Biomarkers and Maternal Features for Adverse Pregnancy Outcomes

description: <i>Objective:</i> To establish the predictive probability for placenta-associated morbidities using second-trimester α-fetoprotein (AFP), human chorionic gonadotropin (HCG), and maternal features. <i>Patients and Methods:</i> A retrospective database of all singleton deliveries with available second-trimester HCG and AFP results from 2005 to 2012 was built and divided into 0, 1, or 2 elevated markers (defined as ≥2 multiples of the median [MoM]). For each group, we analyzed the risk for adverse obstetric outcome - comprising preeclampsia, placental abruption, and birth weight below the 10th percentile - and the time of delivery in those pregnancies. Additionally, prediction models for adverse obstetric outcome, using logistic regression incorporating AFP, HCG, and other maternal characteristics, were calculated. <i>Results:</i> Among 22,124 women who delivered, 16,197 (73%) had AFP and HCG results. Compared with the group with normal markers, the adverse obstetric outcome rate was mildly increased with elevated HCG or AFP, but it was markedly increased when both markers were elevated (13 vs. 31%, OR 2.9, 95% CI 2.0-4.3). Delivery of newborns with adverse obstetric outcome was earlier with each additional elevated marker. The accuracy of predicting adverse obstetric outcome was improved by using prediction models for women with HCG or AFP ≥1.2 MoM that incorporated maternal age, BMI, parity, and chronic hypertension (C-statistic 61-75%). <i>Conclusion:</i> HCG and AFP combined with other maternal characteristics are useful tools for predicting the risk for adverse obstetric outcome.
DOI: 10.6084/m9.figshare.4836830.v1
title: Supplementary Material for: Serum Lymphocyte-Associated Cytokine Concentrations Change More Rapidly over Time in Multiple System Atrophy Compared to Parkinson Disease

description: <i>Objective:</i> Chronic inflammatory processes contribute to the eventual death of motor neurons and the development of symptoms in both idiopathic Parkinson disease (PD) and multiple system atrophy (MSA). Given the faster rate of progression and more severe symptoms associated with MSA, we hypothesized that markers of inflammation would be more evident in the peripheral blood of MSA than PD patients, and that evidence of this inflammation might assist early diagnosis of MSA versus PD. <i>Methods:</i>We performed multiplex analysis to determine the concentrations of 37 immune-associated cytokines and chemokines isolated from the plasma of patients with PD (<i>n</i> = 25) and MSA (<i>n</i> = 14) and compared our results to those of age-matched controls (<i>n</i> = 15). We then applied a mixed-effect multiple regression model to determine if the concentration of cytokines in the plasma of patients with PD and MSA changed significantly over time. <i>Results:</i> Patients with MSA had a trend towards overall lower levels of immune-associated cytokines, while serum cytokine levels were increased in patients with PD. Statistically adjusted comparisons of overall changes in cytokine concentrations between the PD and MSA groups revealed higher concentrations of T-cell-associated cytokines TNFβ and IL-7 in PD. Comparison of samples taken over time revealed significantly faster rates of change in 4 different cytokine concentrations (IL-4, IL-15, IL-2, and IL-9) in patients with MSA versus patients with PD. <i>Conclusions:</i> Our results suggest that single measurements of plasma concentrations of inflammation-associated cytokines cannot be used to distinguish disease states. However, measurements made over time may correlate with pathogenesis. The significant changes in T-cell-associated cytokines may shed light on immune mechanisms that contribute to PD and MSA disease progression.
DOI: 10.6084/m9.figshare.4836680
title: Mapping of tissue names to Brenda Tissue Ontology

description: These files contain the mapping from tissue names to Brenda Tissue Ontology terms for the tissue expression datasets used in the publication.
DOI: 10.6084/m9.figshare.4836680.v1
title: Mapping of tissue names to Brenda Tissue Ontology

description: These files contain the mapping from tissue names to Brenda Tissue Ontology terms for the tissue expression datasets used in the publication.
DOI: 10.6084/m9.figshare.4836749.v1
title: School of Social Sciences - availability via Google Scholar

description: This are sampled citations from the SMU school of social sciences papers published in 2015. Each citation is check for availability of free copy via GS in June 2016. The available copy is then "Carbon dated" to obtain the earliest date it was made available.
DOI: 10.6084/m9.figshare.4836749.v2
title: School of Social Sciences/Economics - availability via Google Scholar

description: This are sampled citations from the SMU school of social sciences and School of economics papers published in 2015. Each citation is check for availability of free copy via GS in June 2016. The available copy is then "Carbon dated" to obtain the earliest date it was made available.
DOI: 10.6084/m9.figshare.4836749.v3
title: School of Social Sciences/Economics - availability via Google Scholar

description: This are sampled citations from the SMU school of social sciences and School of economics papers published in 2015. Each citation is check for availability of free copy via GS in June 2016. The available copy is then "Carbon dated" to obtain the earliest date it was made available.
DOI: 10.6084/m9.figshare.4836413
title: The CompTox Chemistry Dashboard Content File: Versioned by date 2015_10_19

description: US EPA DSSTox DATA RELEASE OCTOBER 2015<br>DSSTox is an effort to collect and curate chemical information from across the web with a special focus on chemicals and substances of interest to the EPA. Curation effort is focused on ensuring accurate linkage of substance identifiers (names and registry numbers) with structural identifiers (SMILES and InChI).<br>DOWNLOAD CONTENT:This DSSTox_All download contains all DSSTox content that is considered high enough in quality to be beneficial to external scientists. It includes the top 4 QC-Levels of content from within DSSTox. <br>INCLUDED DSSTox STANDARD FIELDS:<br><br>DSSTox_Substance_IdDSSTox_Structure_IdDSSTox_QC-LevelSubstance_Name Substance_CASRN Substance_Type Substance_Note Structure_SMILESStructure_InChI Structure_InChIKeyStructure_Formula Structure_MolWt
DOI: 10.6084/m9.figshare.4836407
title: PaperBLAST_Apr2017.tar.gz

description: This the April 2017 version of the PaperBLAST database, a collection of protein sequences that are linked to scientific articles.<br>
DOI: 10.6084/m9.figshare.4836395
title: Data.csv

description: Significant increases in tree mortality due to drought-induced physiological stress have been documented worldwide. This trend is likely to continue with increased frequency and severity of extreme drought events in the future. Therefore, understanding the factors that influence variability in drought responses among trees will be critical to predicting ecosystem responses to climate change and developing effective management actions. In this study, we used hierarchical mixed-effects models to analyze drought responses of <i>Pseudotsuga menziesii</i> in 20 unmanaged forests stands across a broad range of environmental conditions in northeastern Washington, USA. We aimed to 1) identify the biotic and abiotic attributes most closely associated with the responses of individual trees to drought and 2) quantify the variability in drought responses at different spatial scales. We found that growth rates and competition for resources significantly affected resistance to a severe drought event in 2001: slow-growing trees and trees growing in subordinate canopy positions and/or with more neighbors suffered greater declines in radial growth during the drought event. In contrast, the ability of a tree to return to normal growth when climatic conditions improved (resilience) was unaffected by competition or relative growth rates. Drought responses were significantly influenced by tree age: older trees were more resistant but less resilient than younger trees. Finally, we found differences between resistance and resilience in spatial scale: a significant proportion (approximately 50%) of the variability in drought resistance across the study area was at broad spatial scales (i.e. among different forest types), most likely due to differences in the total amount of precipitation received at different elevations; in contrast, variation in resilience was overwhelmingly (82%) at the level of individual trees within stands and there was no difference in drought resilience among forest types. Our results suggest that for <i>Pseudotsuga menziesii</i> resistance and resilience to drought are driven by different factors and vary at different spatial scales.
DOI: 10.6084/m9.figshare.4836395.v1
title: Data.csv

description: Significant increases in tree mortality due to drought-induced physiological stress have been documented worldwide. This trend is likely to continue with increased frequency and severity of extreme drought events in the future. Therefore, understanding the factors that influence variability in drought responses among trees will be critical to predicting ecosystem responses to climate change and developing effective management actions. In this study, we used hierarchical mixed-effects models to analyze drought responses of <i>Pseudotsuga menziesii</i> in 20 unmanaged forests stands across a broad range of environmental conditions in northeastern Washington, USA. We aimed to 1) identify the biotic and abiotic attributes most closely associated with the responses of individual trees to drought and 2) quantify the variability in drought responses at different spatial scales. We found that growth rates and competition for resources significantly affected resistance to a severe drought event in 2001: slow-growing trees and trees growing in subordinate canopy positions and/or with more neighbors suffered greater declines in radial growth during the drought event. In contrast, the ability of a tree to return to normal growth when climatic conditions improved (resilience) was unaffected by competition or relative growth rates. Drought responses were significantly influenced by tree age: older trees were more resistant but less resilient than younger trees. Finally, we found differences between resistance and resilience in spatial scale: a significant proportion (approximately 50%) of the variability in drought resistance across the study area was at broad spatial scales (i.e. among different forest types), most likely due to differences in the total amount of precipitation received at different elevations; in contrast, variation in resilience was overwhelmingly (82%) at the level of individual trees within stands and there was no difference in drought resilience among forest types. Our results suggest that for <i>Pseudotsuga menziesii</i> resistance and resilience to drought are driven by different factors and vary at different spatial scales.
DOI: 10.6084/m9.figshare.4836110
title: A Novel Approach for Markov Random Field With Intractable Normalizing Constant on Large Lattices

description: The pseudo likelihood method of Besag (1974) has remained a popular method for estimating Markov random field on a very large lattice, despite various documented deficiencies. This is partly because it remains the only computationally tractable method for large lattices. We introduce a novel method to estimate Markov random fields defined on a regular lattice. The method takes advantage of conditional independence structures and recursively decomposes a large lattice into smaller sublattices. An approximation is made at each decomposition. Doing so completely avoids the need to compute the troublesome normalizing constant. The computational complexity is <i>O</i>(<i>N</i>), where <i>N</i> is the number of pixels in the lattice, making it computationally attractive for very large lattices. We show through simulations, that the proposed method performs well, even when compared with methods using exact likelihoods. Supplementary material for this article is available online.
DOI: 10.6084/m9.figshare.4836146
title: SMS - RE for Robotic Systems

description: Requirements Engineering for Robotic System: A Systematic Mapping Study<br>
DOI: 10.6084/m9.figshare.4836188
title: TABLES FOR DATA ACCESIBILITY.xlsx

description: Data for Wiley et al. in Journal of Ecology from: "Effects of biological legacies and herbivory on fuels and flammability traits: A long-term experimental study of alternative stable states"
DOI: 10.6084/m9.figshare.4836104
title: A Nonparametric Adaptive Sampling Strategy for Online Monitoring of Big Data Streams

description: With the rapid advancement of sensor technology, a huge amount of data is generated in various applications, which poses new and unique challenges for statistical process control (SPC). In this article, we propose a nonparametric adaptive sampling (NAS) strategy to online monitor nonnormal big data streams in the context of limited resources, where only a subset of observations are available at each acquisition time. In particular, this proposed method integrates a rank-based CUSUM scheme and an innovative idea that corrects the anti-rank statistics with partial observations, which can effectively detect a wide range of possible mean shifts when data streams are exchangeable and follow arbitrary distributions. Two theoretical properties on the sampling layout of the proposed NAS algorithm are investigated when the process is in control and out of control. Both simulations and case studies are conducted under different scenarios to illustrate and evaluate the performance of the proposed method. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.4836146.v1
title: SMS - RE for Robotic Systems

description: Requirements Engineering for Robotic System: A Systematic Mapping Study<br>
DOI: 10.6084/m9.figshare.4836191.v1
title: Outcomes of experimenting RASH Javascript Editor (RAJE)

description: Outcomes of experimenting RASH Javascript Editor (RAJE)<br><br>These are the outcome results of the first RAJE test. All testers are anonymous.<br><br>Content of the archive:<br>1. <b>background.csv</b> It contains the answers from testers about own background experience<br>2. <b>sus.csv</b> It contains the answers of SUS questions<br>3. <b>grounded_analysis.ods</b> It contains the raw-text answers to capture feedback and produce the grounded analysis, and the result tables (with micro and macro cateogries).<br>4. <b>result_screens/</b> It is a folder containing the screenshots of the result scripts.<br><br>