cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.1184/r1/5108716
title: Culture and Breaking Change: A Survey of Values and Practices in 18 Open Source Software Ecosystems

description: Software ecosystems have become one of the most important ways to organize software development, and to maintain and reuse code packages. But coordination can be a major challenge in software ecosystems when packages change, since packages tend to be highly interdependent yet independently maintained. The culture of an ecosystem includes those values and practices associated with managing change. We conducted a survey of thousands of developers in more than a dozen ecosystems, asking them about the values and practices that make up their communities' distinctive cultures; as well as the perceived power of different stakeholders and perceived health of the community. This dataset release shares anonymized data from the survey.
DOI: 10.6084/m9.figshare.5108737.v2
title: Direct Likelihood Evaluation for the Renewal Hawkes Process

description: An interesting extension of the widely applied Hawkes self-exiting point process, the renewal Hawkes (RHawkes) process, was recently proposed by Wheatley, Filimonov, and Sornette, which has the potential to significantly widen the application domains of the self-exciting point processes. However, they claimed that computation of the likelihood of the RHawkes process requires exponential time and therefore is practically impossible. They proposed two expectation–maximization (EM) type algorithms to compute the maximum likelihood estimator (MLE) of the model parameters. Because of the fundamental role of likelihood in statistical inference, a practically feasible method for likelihood evaluation is highly desirable. In this article, we provide an algorithm that evaluates the likelihood of the RHawkes process in quadratic time, a drastic improvement from the exponential time claimed by Wheatley, Filimonov, and Sornette. We demonstrate the superior performance of the resulting MLEs of the model relative to the EM estimators through simulations. We also present a computationally efficient procedure to calculate the Rosenblatt residuals of the process for goodness-of-fit assessment, and a simple yet efficient procedure for future event prediction. The proposed methodologies were applied on real data from seismology and finance. An R package implementing the proposed methodologies is included in the supplementary materials.
DOI: 10.1184/r1/5108716.v1
title: Culture and Breaking Change: A Survey of Values and Practices in 18 Open Source Software Ecosystems

description: Software ecosystems have become one of the most important ways to organize software development, and to maintain and reuse code packages. But coordination can be a major challenge in software ecosystems when packages change, since packages tend to be highly interdependent yet independently maintained. The culture of an ecosystem includes those values and practices associated with managing change. We conducted a survey of thousands of developers in more than a dozen ecosystems, asking them about the values and practices that make up their communities' distinctive cultures; as well as the perceived power of different stakeholders and perceived health of the community. This dataset release shares anonymized data from the survey.
DOI: 10.6084/m9.figshare.5108635
title: Statistical analysis of winter ozone exceedances in the Uintah Basin, Utah, USA

description: Because of the confluence of several factors (persistent multiday inversions, petroleum production, and snow cover), the Uintah Basin of eastern Utah, USA, exhibits high concentrations of winter ozone. A regression analysis is presented that successfully predicts daily ozone concentration with a standard error of about 11 ppb. It also predicts with 90% accuracy whether any given day will exceed the National Ambient Air Quality Standard for ozone, 70 ppb. An analysis is introduced for calculating a “pseudo-lapse rate,” a determination of inversion intensity in the absence of sounding data. By combining the model with historical meteorological data, it is possible to make long-range predictions about ozone formation. The odds of observing no exceedance days in any given season are 38%. The odds of only three or fewer exceedance days in any given season are 46%. <i>Implications</i>: This paper provides an improved understanding of the scientific underpinnings of the winter ozone phenomenon and an ability to make long-range predictions.
DOI: 10.6084/m9.figshare.5108737.v1
title: Direct Likelihood Evaluation for the Renewal Hawkes Process<sup>*</sup>

description: An interesting extension of the widely applied Hawkes self-exiting point process, the renewal Hawkes (RHawkes) process, was recently proposed by Wheatley et al., which has the potential to significantly widen the application domains of the self-exciting point processes. However, the authors claimed that computation of the likelihood of the RHawkes process requires exponential time and therefore is practically impossible. They proposed two Expectation-Maximization (EM) type algorithms to compute the maximum likelihood estimator (MLE) of the model parameters. Because of the fundamental role of likelihood in statistical inference, a practically feasible method for likelihood evaluation is highly desirable. In this article we provide an algorithm that evaluates the likelihood of the RHawkes process in quadratic time, a drastic improvement from the exponential time claimed by Wheatley et al. We demonstrate the superior performance of the resulting MLEs of the model relative to the EM estimators through simulations. We also present a computationally efficient procedure to calculate the Rosenblatt residuals of the process for goodness-of-fit assessment, and a simple yet efficient procedure for future event prediction. The proposed methodologies were applied on real data from seismology and finance. An R package implementing the proposed methodologies is included in the supplementary materials.
DOI: 10.6084/m9.figshare.5108620
title: Bayesian Fused Lasso Regression for Dynamic Binary Networks

description: We propose a multinomial logistic regression model for link prediction in a time series of directed binary networks. To account for the dynamic nature of the data, we employ a dynamic model for the model parameters that is strongly connected with the fused lasso penalty. In addition to promoting sparseness, this prior allows us to explore the presence of change points in the structure of the network. We introduce fast computational algorithms for estimation and prediction using both optimization and Bayesian approaches. The performance of the model is illustrated using simulated data and data from a financial trading network in the NYMEX natural gas futures market. Supplementary material containing the trading network dataset and code to implement the algorithms is available online.
DOI: 10.6084/m9.figshare.5108635.v2
title: Statistical analysis of winter ozone exceedances in the Uintah Basin, Utah, USA

description: Because of the confluence of several factors (persistent multiday inversions, petroleum production, and snow cover), the Uintah Basin of eastern Utah, USA, exhibits high concentrations of winter ozone. A regression analysis is presented that successfully predicts daily ozone concentration with a standard error of about 11 ppb. It also predicts with 90% accuracy whether any given day will exceed the National Ambient Air Quality Standard for ozone, 70 ppb. An analysis is introduced for calculating a “pseudo-lapse rate,” a determination of inversion intensity in the absence of sounding data. By combining the model with historical meteorological data, it is possible to make long-range predictions about ozone formation. The odds of observing no exceedance days in any given season are 38%. The odds of only three or fewer exceedance days in any given season are 46%. <i>Implications</i>: This paper provides an improved understanding of the scientific underpinnings of the winter ozone phenomenon and an ability to make long-range predictions.
DOI: 10.6084/m9.figshare.5108635.v1
title: Statistical Analysis of Winter Ozone Exceedances in the Uintah Basin, Utah, USA

description: Because of the confluence of several factors (persistent multi-day inversions, petroleum production, and snow cover) the Uintah Basin of eastern Utah, USA exhibits high concentrations of winter ozone. A regression analysis is presented that successfully predicts daily ozone concentration with a standard error of about 11 ppb. It also predicts with 90% accuracy whether any given day will exceed the National Ambient Air Quality Standard for ozone, 70 ppb. An analysis is introduced for calculating a “pseudo-lapse rate,” a determination of inversion intensity in the absence of sounding data. By combining the model with historical meteorological data it is possible to make long-range predictions about ozone formation. The odds of observing no exceedance days in any given season are 38%. The odds of only three or fewer exceedance days in any given season are 46%. Implications This paper provides an improved understanding of the scientific underpinnings of the winter ozone phenomenon and an ability to make long-range predictions.
DOI: 10.6084/m9.figshare.5108620.v2
title: Bayesian Fused Lasso Regression for Dynamic Binary Networks

description: We propose a multinomial logistic regression model for link prediction in a time series of directed binary networks. To account for the dynamic nature of the data, we employ a dynamic model for the model parameters that is strongly connected with the fused lasso penalty. In addition to promoting sparseness, this prior allows us to explore the presence of change points in the structure of the network. We introduce fast computational algorithms for estimation and prediction using both optimization and Bayesian approaches. The performance of the model is illustrated using simulated data and data from a financial trading network in the NYMEX natural gas futures market. Supplementary material containing the trading network dataset and code to implement the algorithms is available online.
DOI: 10.6084/m9.figshare.5108620.v1
title: Bayesian Fused Lasso regression for dynamic binary networks

description: We propose a multinomial logistic regression model for link prediction in a time series of directed binary networks. To account for the dynamic nature of the data we employ a dynamic model for the model parameters that is strongly connected with the fused lasso penalty. In addition to promoting sparseness, this prior allows us to explore the presence of change points in the structure of the network. We introduce fast computational algorithms for estimation and prediction using both optimization and Bayesian approaches. The performance of the model is illustrated using simulated data and data from a financial trading network in the NYMEX natural gas futures market. Supplementary material containing the trading network data set and code to implement the algorithms is available online.
DOI: 10.6084/m9.figshare.5107771
title: Timelapse - Vernalization effect on flowering in Brachypodium

description: Timelapse of vernalized versus non-vernalized Brachypodium plants of the two accessions Bd1-1 and Bd21.
DOI: 10.6084/m9.figshare.5107777
title: Social policies during economic crises: an analysis of cross-national variation in coping strategies from 1980 to 2013

description: This paper provides a comprehensive analysis of the relationship between economic crises and social policy change for 13 European countries. Based on the degree of policy expansion and dismantling, we identify three potential crisis-coping strategies, namely ‘Muddling Through’, ‘Social Protectionism’ and ‘Austerity’. By means of multinomial logistic regression analysis, we test the effect of various factors on governments’ choice of crisis-coping strategies for 45 economic crises between 1980 and 2013. Our analysis reveals that Austerity becomes a more likely scenario in crisis times. Moreover, we demonstrate that governments in consensual systems do not deviate from their true policy preferences when facing economic hardship. In majoritarian systems, by contrast, this pattern is strikingly reversed. Here, left-wing governments resort to Austerity, while right-wing parties opt for Social Protectionism. This indicates that both blame avoidance and the capabilities to mediate unpopular reform decisions can convert political parties from ‘Saul to Paul’ and vice versa.
DOI: 10.6084/m9.figshare.5107777.v1
title: Social policies during economic crises: an analysis of cross-national variation in coping strategies from 1980 to 2013

description: This paper provides a comprehensive analysis of the relationship between economic crises and social policy change for 13 European countries. Based on the degree of policy expansion and dismantling, we identify three potential crisis-coping strategies, namely ‘Muddling Through’, ‘Social Protectionism’ and ‘Austerity’. By means of multinomial logistic regression analysis, we test the effect of various factors on governments’ choice of crisis-coping strategies for 45 economic crises between 1980 and 2013. Our analysis reveals that Austerity becomes a more likely scenario in crisis times. Moreover, we demonstrate that governments in consensual systems do not deviate from their true policy preferences when facing economic hardship. In majoritarian systems, by contrast, this pattern is strikingly reversed. Here, left-wing governments resort to Austerity, while right-wing parties opt for Social Protectionism. This indicates that both blame avoidance and the capabilities to mediate unpopular reform decisions can convert political parties from ‘Saul to Paul’ and vice versa.
DOI: 10.6084/m9.figshare.5107771.v1
title: Timelapse - Vernalization effect on flowering in Brachypodium

description: Timelapse of vernalized versus non-vernalized Brachypodium plants of the two accessions Bd1-1 and Bd21.
DOI: 10.6084/m9.figshare.5107711
title: Heagy et al 2017 Inversion of RESOLVE and SkyTEM data at Bookpurnong

description: Inversion of RESOLVE (2008) and SkyTEM (2006) data as presented in <br>Heagy, L.J., R. Cockett, S. Kang, G.K. Rosenkjaer, D.W. Oldenburg,2017 (in review), A framework for simulation and inversion in electromagnetics.Computers & Geosciences. <br>There are 3 scripts included: (1) plot_load_booky.py loads the RESOLVE and SkyTEM data and plots them. This produces resolve_skytem_data.png. (2) plot_booky_1D_time_freq_inv.py performs a 1D inversion for a single sounding from each of the RESOLVE and the SkyTEM data sets. This produces booky_1d_time_freq.png. (3) plot_booky_1Dstitched_resolve_inv.py performs a 1D stitched inversion of downsampled RESOLVE data. This produces the image resolve_cond_9m.png which shows a depth slice through the recovered model and predicted and observed data at 400Hz (real). <br>The RESOLVE and SkyTEM data collected over Bookpurnong have been made available with permission from CSIRO. Please acknowledge CSIRO if using these data in a presentation, publication, etc.
DOI: 10.6084/m9.figshare.5107672
title: Archive.zip

description: New indexes for GeCKOv2 libraries with only unique sgRNAs. In cases that an sgRNA targets more than one gene then it is indicated in the gene_name column.
DOI: 10.6084/m9.figshare.5107672.v1
title: Archive.zip

description: New indexes for GeCKOv2 libraries with only unique sgRNAs. In cases that an sgRNA targets more than one gene then it is indicated in the gene_name column.
DOI: 10.6084/m9.figshare.5107552
title: Supplementary Material for: Compact Intraoperative MRI: Stereotactic Accuracy and Future Directions

description: <b><i>Background:</i></b> Intraoperative imaging must supply data that can be used for accurate stereotactic navigation. This information should be at least as accurate as that acquired from diagnostic imagers. <b><i>Objectives:</i></b> The aim of this study was to compare the stereotactic accuracy of an updated compact intraoperative MRI (iMRI) device based on a 0.15-T magnet to standard surgical navigation on a 1.5-T diagnostic scan MRI and to navigation with an earlier model of the same system. <b><i>Methods:</i></b> The accuracy of each system was assessed using a water-filled phantom model of the brain. Data collected with the new system were compared to those obtained in a previous study assessing the older system. The accuracy of the new iMRI was measured against standard surgical navigation on a 1.5-T MRI using T1-weighted (W) images. <b><i>Results:</i></b> The mean error with the iMRI using T1W images was lower than that based on images from the 1.5-T scan (1.24 vs. 2.43 mm). T2W images from the newer iMRI yielded a lower navigation error than those acquired with the prior model (1.28 vs. 3.15 mm). <b><i>Conclusions:</i></b> Improvements in magnet design can yield progressive increases in accuracy, validating the concept of compact, low-field iMRI. Avoiding the need for registration between image and surgical space increases navigation accuracy.
DOI: 10.6084/m9.figshare.5107561
title: Supplementary Material for: The Novel Ser18del AVP Variant Causes Inherited Neurohypophyseal Diabetes Insipidus by Mechanisms Shared with Other Signal Peptide Variants

description: <b><i>Background/Aim:</i></b> Variability in the severity and age at onset of autosomal dominant familial neurohypophyseal diabetes insipidus (adFNDI) may be associated with certain types of variants in the arginine vasopressin (<i>AVP</i>) gene. In this study, we aimed to describe a large family with an apparent predominant female occurrence of polyuria and polydipsia and to determine the underlying cause. <b><i>Methods:</i></b> The family members reported their family demography and symptoms. Two subjects were diagnosed by fluid deprivation and dDAVP challenge tests. Eight subjects were tested genetically. The identified variant along with 3 previously identified variants in the <i>AVP</i> gene were investigated by heterologous expression in a human neuronal cell line (SH-SY5Y). <b><i>Results:</i></b> Both subjects investigated clinically had a partial neurohypophyseal diabetes insipidus phenotype. A g.276_278delTCC variant in the <i>AVP</i> gene causing a Ser18del deletion in the signal peptide (SP) of the AVP preprohormone was perfectly co-segregating with the disease. When expressed in SH-SY5Y cells, the Ser18del variant along with 3 other SP variants (g.227G&gt;A, Ser17Phe, and Ala19Thr) resulted in reduced <i>AVP</i> mRNA, impaired AVP secretion, and partial AVP prohormone degradation and retention in the endoplasmic reticulum. Impaired SP cleavage was demonstrated directly in cells expressing the Ser18del, g.227G&gt;A, and Ala19Thr variants, using state-of-the-art mass spectrometry. <b><i>Conclusion:</i></b> Variants affecting the SP of the AVP preprohormone cause adFNDI with variable phenotypes by a mechanism that may involve impaired SP cleavage combined with effects at the mRNA, protein, and cellular level.
DOI: 10.6084/m9.figshare.5107561.v1
title: Supplementary Material for: The Novel Ser18del AVP Variant Causes Inherited Neurohypophyseal Diabetes Insipidus by Mechanisms Shared with Other Signal Peptide Variants

description: <b><i>Background/Aim:</i></b> Variability in the severity and age at onset of autosomal dominant familial neurohypophyseal diabetes insipidus (adFNDI) may be associated with certain types of variants in the arginine vasopressin (<i>AVP</i>) gene. In this study, we aimed to describe a large family with an apparent predominant female occurrence of polyuria and polydipsia and to determine the underlying cause. <b><i>Methods:</i></b> The family members reported their family demography and symptoms. Two subjects were diagnosed by fluid deprivation and dDAVP challenge tests. Eight subjects were tested genetically. The identified variant along with 3 previously identified variants in the <i>AVP</i> gene were investigated by heterologous expression in a human neuronal cell line (SH-SY5Y). <b><i>Results:</i></b> Both subjects investigated clinically had a partial neurohypophyseal diabetes insipidus phenotype. A g.276_278delTCC variant in the <i>AVP</i> gene causing a Ser18del deletion in the signal peptide (SP) of the AVP preprohormone was perfectly co-segregating with the disease. When expressed in SH-SY5Y cells, the Ser18del variant along with 3 other SP variants (g.227G&gt;A, Ser17Phe, and Ala19Thr) resulted in reduced <i>AVP</i> mRNA, impaired AVP secretion, and partial AVP prohormone degradation and retention in the endoplasmic reticulum. Impaired SP cleavage was demonstrated directly in cells expressing the Ser18del, g.227G&gt;A, and Ala19Thr variants, using state-of-the-art mass spectrometry. <b><i>Conclusion:</i></b> Variants affecting the SP of the AVP preprohormone cause adFNDI with variable phenotypes by a mechanism that may involve impaired SP cleavage combined with effects at the mRNA, protein, and cellular level.
DOI: 10.6084/m9.figshare.5107498
title: Supplementary Material for: Drug Discovery to Halt the Progression of Acute Kidney Injury to Chronic Kidney Disease: A Case for Phenotypic Drug Discovery in Acute Kidney Injury

description: The cellular responses that occur following acute kidney injury (AKI) are complex and dynamic, involving multiple cells types and molecular pathways. For this reason, early selection of defined molecular targets for therapeutic intervention is unlikely to be effective in complex in vivo models of AKI, let alone Phase 3 clinical trials in patients with even more complex AKI pathobiology. Phenotypic screening using zebrafish provides an attractive alternative that does not require prior knowledge of molecular targets and may identify compounds that modify multiple targets that might be missed in more traditional target-based screens. In this review, we discuss results of an academic drug discovery campaign that used zebrafish as a primary screening tool to discover compounds with favorable absorption, metabolism, and toxicity that enhance repair when given late after injury in multiple models of AKI. We discuss how this screening campaign is being integrated into a more comprehensive, phenotypic, and target-based screen for lead compound optimization.
DOI: 10.6084/m9.figshare.5107501
title: Raw Data TRAIL.xlsx

description: Cp raw data from real time RT-PCR experiments are included in this excel file<br>
DOI: 10.6084/m9.figshare.5107510
title: Supplementary Material for: Visual Evaluation of Medial Temporal Lobe Atrophy as a Clinical Marker of Conversion from Mild Cognitive Impairment to Dementia and for Predicting Progression in Patients with Mild Cognitive Impairment and Mild Alzheimer's Disease

description: <b><i>Background/Aims:</i></b> To evaluate whether visual assessment of medial temporal lobe atrophy (vaMTA) can predict 2-year conversion from mild cognitive impairment (MCI) to dementia and progression of MCI and Alzheimer's disease dementia as measured by the Clinical Dementia Rating Scale Sum of Boxes score (CDR-SB). <b><i>Methods:</i></b> vaMTA was performed in 94 patients with MCI according to the Winblad criteria and in 124 patients with AD according to ICD-10 and NINCDS-ADRDA criteria. Demographic data, the Consortium to Establish a Registry for Alzheimer's Disease 10-word delayed recall, APOE ɛ4 status, Cornell Scale for Depression in Dementia, and comorbid hypertension were used as covariates. <b><i>Results:</i></b> vaMTA was associated with MCI conversion in an unadjusted model but not in an adjusted model (<i>p</i> = 0.075), where delayed recall and APOE ɛ4 status were significant predictors. With CDR-SB change as the outcome, an interaction between vaMTA and diagnosis was found, but in the adjusted model only delayed recall and age were significant predictors. For vaMTA below 2, the association between vaMTA and CDR-SB change differed between diagnostic groups. Similar results were found based on a trajectory analysis. <b><i>Conclusion:</i></b> In adjusted models, memory function, APOE ɛ4 status and age were significant predictors of disease progression, not vaMTA. The association between vaMTA and CDR-SB change was different in patients with MCI and Alzheimer's disease dementia.