cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1568328.v2
title: Bayesian Model Fusion for Forecasting Civil Unrest

description: With the rapid rise in social media, alternative news sources, and blogs, ordinary citizens have become information producers as much as information consumers. Highly charged prose, images, and videos spread virally, and stoke the embers of social unrest by alerting fellow citizens to relevant happenings and spurring them into action. We are interested in using Big Data approaches to generate forecasts of civil unrest from open source indicators. The heterogenous nature of data coupled with the rich and diverse origins of civil unrest call for a multi-model approach to such forecasting. We present a modular approach wherein a collection of models use overlapping sources of data to independently forecast protests. Fusion of alerts into one single alert stream becomes a key system informatics problem and we present a statistical framework to accomplish such fusion. Given an alert from one of the numerous models, the decision space for fusion has two possibilities: (i) release the alert or (ii) suppress the alert. Using a Bayesian decision theoretical framework, we present a fusion approach for releasing or suppressing alerts. The resulting system enables real-time decisions and more importantly tuning of precision and recall. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.1568329.v2
title: Blocking Orthogonal Designs With Mixed Integer Linear Programming

description: We present a mixed integer linear programming approach to orthogonally block two-level, multilevel, and mixed-level orthogonal designs. The approach involves an exact optimization technique which guarantees an optimal solution. It can be applied to many problems where combinatorial methods for blocking orthogonal designs cannot be used. By means of 54-run and 64-run examples, we demonstrate that our approach outperforms two benchmark techniques in terms of the number of estimable two-factor interaction contrasts and in terms of the D-efficiency for models with main effects and some two-factor interaction contrasts. We demonstrate the generic nature of our approach by applying it to the most challenging instances in a catalog of all orthogonal designs of strength 3 with up to 81 runs as well as a small catalog of strength-4 designs. The approach can also be applied to strength-2 designs, but, for these cases, alternative methods described in the literature may perform equally well. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.1568322
title: Relationships between dose to the gastro-intestinal tract and patient-reported symptom domains after radiotherapy for localized prostate cancer

description: ABSTRACT<b>Background.</b> Gastrointestinal (GI) morbidity after radiotherapy (RT) for prostate cancer is typically addressed by studying specific single symptoms. The aim of this study was to explore the interplay between domains of patient- reported outcomes (PROs) on GI morbidity, and to what extent these are explained by RT dose to the GI tract.<b>Material and methods.</b> The study included men from two Scandinavian studies (N = 211/277) who had undergone primary external beam radiotherapy (EBRT) for localized prostate cancer to 70–78 Gy (2 Gy/fraction). Factor analysis was applied to previously identified PRO-based symptom domains from two study-specific questionnaires. Number of questions: 43; median time to follow-up: 3.6–6.4 years) and dose-response outcome variables were defined from these domains. Dose/volume parameters of the anal sphincter (AS) or the rectum were tested as predictors for each outcome variable using logistic regression with 10-fold cross-validation. Performance was assessed using area under the receiver operating characteristic curve (A<sub>z</sub>) and model frequency.<b>Results.</b> Outcome variables from <i>Defecation urgency</i> (number of symptoms: 2–3), <i>Fecal leakage</i> (4–6), <i>Mucous</i> (4), and <i>Pain</i> (3–6) were defined. In both cohorts, intermediate rectal doses predicted <i>Defecation urgency</i> (mean A<sub>z</sub>: 0.53–0.54; Frequency: 70–75%), and near minimum and low AS doses predicted <i>Fecal leakage</i> (mean A<sub>z</sub>: 0.63–0.67; Frequency: 83–99%). In one cohort, high AS doses predicted <i>Mucous</i> (mean A<sub>z</sub>: 0.54; Frequency: 96%), whereas in the other, low AS doses and intermediate rectal doses predicted <i>Pain</i> (mean A<sub>z</sub>: 0.69; Frequency: 28–82%).<b>Conclusion.</b> We have demonstrated that <i>Defecation urgency, Fecal leakage, Mucous</i>, and <i>Pain</i> following primary EBRT for localized prostate cancer primarily are predicted by intermediate rectal doses, low AS doses, high AS doses, or a combination of low AS and intermediate rectal doses, respectively. This suggests that there is a domain-specific dose-response for the GI tract. To reduce risk of GI morbidity, dose distributions of both the AS region and the rectum should, therefore, be considered when prescribing prostate cancer RT.
DOI: 10.6084/m9.figshare.1568327.v2
title: Cokriging-Based Sequential Design Strategies Using Fast Cross-Validation Techniques for Multi-Fidelity Computer Codes

description: Cokriging-based surrogate models have become popular in recent decades to approximate a computer code output from a few simulations using both coarse and more complex versions of the code. In practical applications, it is common to sequentially add new simulations to obtain more accurate approximations. We propose a method of cokriging-based sequential design, which combines both the error evaluation provided by the cokriging model and the observed errors of a leave-one-out cross-validation procedure. This method is proposed in two versions, the first one selects points one at a time. The second one allows us to parallelize the simulations and to add several design points at a time. The main advantage of the suggested strategies is that at a new design point they choose which code versions should be simulated (i.e., the complex code or one of its fast approximations). A multifidelity application is used to illustrate the efficiency of the proposed approaches. In this example, the accurate code is a two-dimensional finite element model and the less accurate one is a one-dimensional approximation of the system. This article has supplementary material online.
DOI: 10.6084/m9.figshare.1568322.v2
title: Relationships between dose to the gastro-intestinal tract and patient-reported symptom domains after radiotherapy for localized prostate cancer

description: ABSTRACT<b>Background.</b> Gastrointestinal (GI) morbidity after radiotherapy (RT) for prostate cancer is typically addressed by studying specific single symptoms. The aim of this study was to explore the interplay between domains of patient- reported outcomes (PROs) on GI morbidity, and to what extent these are explained by RT dose to the GI tract.<b>Material and methods.</b> The study included men from two Scandinavian studies (N = 211/277) who had undergone primary external beam radiotherapy (EBRT) for localized prostate cancer to 70–78 Gy (2 Gy/fraction). Factor analysis was applied to previously identified PRO-based symptom domains from two study-specific questionnaires. Number of questions: 43; median time to follow-up: 3.6–6.4 years) and dose-response outcome variables were defined from these domains. Dose/volume parameters of the anal sphincter (AS) or the rectum were tested as predictors for each outcome variable using logistic regression with 10-fold cross-validation. Performance was assessed using area under the receiver operating characteristic curve (A<sub>z</sub>) and model frequency.<b>Results.</b> Outcome variables from <i>Defecation urgency</i> (number of symptoms: 2–3), <i>Fecal leakage</i> (4–6), <i>Mucous</i> (4), and <i>Pain</i> (3–6) were defined. In both cohorts, intermediate rectal doses predicted <i>Defecation urgency</i> (mean A<sub>z</sub>: 0.53–0.54; Frequency: 70–75%), and near minimum and low AS doses predicted <i>Fecal leakage</i> (mean A<sub>z</sub>: 0.63–0.67; Frequency: 83–99%). In one cohort, high AS doses predicted <i>Mucous</i> (mean A<sub>z</sub>: 0.54; Frequency: 96%), whereas in the other, low AS doses and intermediate rectal doses predicted <i>Pain</i> (mean A<sub>z</sub>: 0.69; Frequency: 28–82%).<b>Conclusion.</b> We have demonstrated that <i>Defecation urgency, Fecal leakage, Mucous</i>, and <i>Pain</i> following primary EBRT for localized prostate cancer primarily are predicted by intermediate rectal doses, low AS doses, high AS doses, or a combination of low AS and intermediate rectal doses, respectively. This suggests that there is a domain-specific dose-response for the GI tract. To reduce risk of GI morbidity, dose distributions of both the AS region and the rectum should, therefore, be considered when prescribing prostate cancer RT.
DOI: 10.6084/m9.figshare.1568321.v1
title: Modifications of membrane lipids in response to wounding of <i>Arabidopsis thaliana</i> leaves

description: Mechanical wounding of <i>Arabidopsis thaliana</i> leaves results in modifications of most membrane lipids within 6 hours. Here, we discuss the lipid changes, their underlying biochemistry, and possible relationships among activated pathways. New evidence is presented supporting the role of the processive galactosylating enzyme SENSITIVE TO FREEZING2 in the wounding response.
DOI: 10.6084/m9.figshare.1568322.v1
title: Relationships between dose to the gastro-intestinal tract and patient-reported symptom domains after radiotherapy for localized prostate cancer

description: <b>Background.</b> Gastrointestinal (GI) morbidity after radiotherapy (RT) for prostate cancer is typically addressed by studying specific single symptoms. The aim of this study was to explore the interplay between domains of patient- reported outcomes (PROs) on GI morbidity, and to what extent these are explained by RT dose to the GI tract.<b>Material and methods.</b> The study included men from two Scandinavian studies (N = 211/277) who had undergone primary external beam radiotherapy (EBRT) for localized prostate cancer to 70–78 Gy (2 Gy/fraction). Factor analysis was applied to previously identified PRO-based symptom domains from two study-specific questionnaires. Number of questions: 43; median time to follow-up: 3.6–6.4 years) and dose-response outcome variables were defined from these domains. Dose/volume parameters of the anal sphincter (AS) or the rectum were tested as predictors for each outcome variable using logistic regression with 10-fold cross-validation. Performance was assessed using area under the receiver operating characteristic curve (A<sub>z</sub>) and model frequency.<b>Results.</b> Outcome variables from <i>Defecation urgency</i> (number of symptoms: 2–3), <i>Fecal leakage</i> (4–6), <i>Mucous</i> (4), and <i>Pain</i> (3–6) were defined. In both cohorts, intermediate rectal doses predicted <i>Defecation urgency</i> (mean A<sub>z</sub>: 0.53–0.54; Frequency: 70–75%), and near minimum and low AS doses predicted <i>Fecal leakage</i> (mean A<sub>z</sub>: 0.63–0.67; Frequency: 83–99%). In one cohort, high AS doses predicted <i>Mucous</i> (mean A<sub>z</sub>: 0.54; Frequency: 96%), whereas in the other, low AS doses and intermediate rectal doses predicted <i>Pain</i> (mean A<sub>z</sub>: 0.69; Frequency: 28–82%).<b>Conclusion.</b> We have demonstrated that <i>Defecation urgency, Fecal leakage, Mucous</i>, and <i>Pain</i> following primary EBRT for localized prostate cancer primarily are predicted by intermediate rectal doses, low AS doses, high AS doses, or a combination of low AS and intermediate rectal doses, respectively. This suggests that there is a domain-specific dose-response for the GI tract. To reduce risk of GI morbidity, dose distributions of both the AS region and the rectum should, therefore, be considered when prescribing prostate cancer RT.
DOI: 10.6084/m9.figshare.1568321.v2
title: Modifications of membrane lipids in response to wounding of <i>Arabidopsis thaliana</i> leaves

description: Mechanical wounding of <i>Arabidopsis thaliana</i> leaves results in modifications of most membrane lipids within 6 hours. Here, we discuss the lipid changes, their underlying biochemistry, and possible relationships among activated pathways. New evidence is presented supporting the role of the processive galactosylating enzyme SENSITIVE TO FREEZING2 in the wounding response.
DOI: 10.6084/m9.figshare.1568327.v3
title: Cokriging-Based Sequential Design Strategies Using Fast Cross-Validation Techniques for Multi-Fidelity Computer Codes

description: Cokriging-based surrogate models have become popular in recent decades to approximate a computer code output from a few simulations using both coarse and more complex versions of the code. In practical applications, it is common to sequentially add new simulations to obtain more accurate approximations. We propose a method of cokriging-based sequential design, which combines both the error evaluation provided by the cokriging model and the observed errors of a leave-one-out cross-validation procedure. This method is proposed in two versions, the first one selects points one at a time. The second one allows us to parallelize the simulations and to add several design points at a time. The main advantage of the suggested strategies is that at a new design point they choose which code versions should be simulated (i.e., the complex code or one of its fast approximations). A multifidelity application is used to illustrate the efficiency of the proposed approaches. In this example, the accurate code is a two-dimensional finite element model and the less accurate one is a one-dimensional approximation of the system. This article has supplementary material online.
DOI: 10.6084/m9.figshare.1568327.v5
title: Cokriging-Based Sequential Design Strategies Using Fast Cross-Validation Techniques for Multi-Fidelity Computer Codes

description: Cokriging-based surrogate models have become popular in recent decades to approximate a computer code output from a few simulations using both coarse and more complex versions of the code. In practical applications, it is common to sequentially add new simulations to obtain more accurate approximations. We propose a method of cokriging-based sequential design, which combines both the error evaluation provided by the cokriging model and the observed errors of a leave-one-out cross-validation procedure. This method is proposed in two versions, the first one selects points one at a time. The second one allows us to parallelize the simulations and to add several design points at a time. The main advantage of the suggested strategies is that at a new design point they choose which code versions should be simulated (i.e., the complex code or one of its fast approximations). A multifidelity application is used to illustrate the efficiency of the proposed approaches. In this example, the accurate code is a two-dimensional finite element model and the less accurate one is a one-dimensional approximation of the system. This article has supplementary material online.
DOI: 10.6084/m9.figshare.1568321.v3
title: Modifications of membrane lipids in response to wounding of <i>Arabidopsis thaliana</i> leaves

description: Mechanical wounding of <i>Arabidopsis thaliana</i> leaves results in modifications of most membrane lipids within 6 hours. Here, we discuss the lipid changes, their underlying biochemistry, and possible relationships among activated pathways. New evidence is presented supporting the role of the processive galactosylating enzyme SENSITIVE TO FREEZING2 in the wounding response.
DOI: 10.6084/m9.figshare.1568327.v4
title: Cokriging-Based Sequential Design Strategies Using Fast Cross-Validation Techniques for Multi-Fidelity Computer Codes

description: Cokriging-based surrogate models have become popular in recent decades to approximate a computer code output from a few simulations using both coarse and more complex versions of the code. In practical applications, it is common to sequentially add new simulations to obtain more accurate approximations. We propose a method of cokriging-based sequential design, which combines both the error evaluation provided by the cokriging model and the observed errors of a leave-one-out cross-validation procedure. This method is proposed in two versions, the first one selects points one at a time. The second one allows us to parallelize the simulations and to add several design points at a time. The main advantage of the suggested strategies is that at a new design point they choose which code versions should be simulated (i.e., the complex code or one of its fast approximations). A multifidelity application is used to illustrate the efficiency of the proposed approaches. In this example, the accurate code is a two-dimensional finite element model and the less accurate one is a one-dimensional approximation of the system. This article has supplementary material online.
DOI: 10.6084/m9.figshare.1568321.v4
title: Modifications of membrane lipids in response to wounding of <i>Arabidopsis thaliana</i> leaves

description: Mechanical wounding of <i>Arabidopsis thaliana</i> leaves results in modifications of most membrane lipids within 6 hours. Here, we discuss the lipid changes, their underlying biochemistry, and possible relationships among activated pathways. New evidence is presented supporting the role of the processive galactosylating enzyme SENSITIVE TO FREEZING2 in the wounding response.
DOI: 10.6084/m9.figshare.1568321.v6
title: Modifications of membrane lipids in response to wounding of <i>Arabidopsis thaliana</i> leaves

description: Mechanical wounding of <i>Arabidopsis thaliana</i> leaves results in modifications of most membrane lipids within 6 hours. Here, we discuss the lipid changes, their underlying biochemistry, and possible relationships among activated pathways. New evidence is presented supporting the role of the processive galactosylating enzyme SENSITIVE TO FREEZING2 in the wounding response.
DOI: 10.6084/m9.figshare.1568321
title: Modifications of membrane lipids in response to wounding of <i>Arabidopsis thaliana</i> leaves

description: Mechanical wounding of <i>Arabidopsis thaliana</i> leaves results in modifications of most membrane lipids within 6 hours. Here, we discuss the lipid changes, their underlying biochemistry, and possible relationships among activated pathways. New evidence is presented supporting the role of the processive galactosylating enzyme SENSITIVE TO FREEZING2 in the wounding response.
DOI: 10.6084/m9.figshare.1568321.v5
title: Modifications of membrane lipids in response to wounding of <i>Arabidopsis thaliana</i> leaves

description: Mechanical wounding of <i>Arabidopsis thaliana</i> leaves results in modifications of most membrane lipids within 6 hours. Here, we discuss the lipid changes, their underlying biochemistry, and possible relationships among activated pathways. New evidence is presented supporting the role of the processive galactosylating enzyme SENSITIVE TO FREEZING2 in the wounding response.
DOI: 10.6084/m9.figshare.1568313
title: DNA barcoding of Jamaican bats: implications to Neotropical biodiversity

description: We report on the first comprehensive DNA barcoding survey of bats from Jamaica and compare the genetic variation to similar species on South America and Central America. Bats comprise the majority of mammalian diversity in typical lowland forest in the Neotropics, but the Caribbean is one noticeable geographic gap in the International Barcode of Life reference database. Of the 20 known species reported from Jamaica, half were DNA barcoded and were genetically distinct with interspecific variation ranging from 17 to 33%. By contrast, intraspecific variation ranged from 0 to 0.5% indicating that the barcode gap was sufficient in differentiating bat species diversity in Jamaica. The low levels of intraspecific divergence indicate that the populations within each species are relatively homogeneous across the island. There were, however, several cases of high sequence divergence for widely distributed species that occur on both the Caribbean islands and the continental mainland, which warrant further taxonomic study.
DOI: 10.6084/m9.figshare.1568313.v2
title: DNA barcoding of Jamaican bats: implications to Neotropical biodiversity

description: We report on the first comprehensive DNA barcoding survey of bats from Jamaica and compare the genetic variation to similar species on South America and Central America. Bats comprise the majority of mammalian diversity in typical lowland forest in the Neotropics, but the Caribbean is one noticeable geographic gap in the International Barcode of Life reference database. Of the 20 known species reported from Jamaica, half were DNA barcoded and were genetically distinct with interspecific variation ranging from 17 to 33%. By contrast, intraspecific variation ranged from 0 to 0.5% indicating that the barcode gap was sufficient in differentiating bat species diversity in Jamaica. The low levels of intraspecific divergence indicate that the populations within each species are relatively homogeneous across the island. There were, however, several cases of high sequence divergence for widely distributed species that occur on both the Caribbean islands and the continental mainland, which warrant further taxonomic study.
DOI: 10.6084/m9.figshare.1568310
title: The accuracy of self-reported adherence to an activity advice

description: <i>Objective</i>. The aim of this cross-sectional observational study was to investigate whether patients referred for non-specific low back pain accurately report whether they follow home-based activity advice. Research suggests that inadequate adherence to home-based activity advice during an intervention period might diminish the effectiveness of an intervention. Insight into patient adherence to home-based activity advice is hindered by a lack of objective data. Most data consist of self-reporting and interviews. <i>Methods</i>. Participants were advised to complete a home-based activity for 1 week. We validated self-reporting of home-based activity with data obtained from an activity monitor worn by 51 patients who reported non-specific low back pain. The proportion of accurate self-reporting and kappa values were calculated to determine the level of accuracy of self-reporting. <i>Results</i>. An analysis of 357 (51 × 7) walking days found accurate participant reports on 233 days; only 22% of the participants reported accurately on all 7 consecutive days. Low kappa scores between the barrier list and the activity monitor show the poor reliability of participants’ self-reporting. <i>Conclusion</i>. Self-reporting about the performance of advised home-based activity for the management of non-specific low back pain in a physiotherapy practice setting is rather inaccurate.
DOI: 10.6084/m9.figshare.1568311
title: An RNA-based approach to sequence the mitogenome of <i>Hypoptopoma incognitum</i> (Siluriformes: Loricariidae)

description: <i>Hypoptopoma incognitum</i> is a fish of the fifth most species-rich family of vertebrates and abundant in rivers from the Brazilian Amazon. Only two species of Loricariidae fish have their complete mitogenomes sequence deposited in the Genbank. An innovative RNA-based approach was used to assemble the complete mitogenome of <i>H. incognitum</i> with an average coverage depth of 5292×. The typical vertebrate mitochondrial features were found; 22 tRNA genes, two rRNA genes, 13 protein-coding genes, and a non-coding control region. Moreover, the use of this approach allowed the measurement of mtRNA expression levels, the punctuation pattern of editing, and the detection of heteroplasmies.