cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3458996.v3
title: A Dissection of Test-Driven Development Process: Does It Really Matter to Test-First or to Test-Last?

description: A replication package for the study reported in the paper "A Dissection of Test-Driven Development Process: Does It Really Matter to Test-First or to Test-Last?"<br>Includes:- acceptance tests- Eclipse plugin for data recording- script for automated analysis of Eclipse plugin records- the programming tasks used in the study- a spreadsheet to report the metrics extracted- questionnaires- training material for participants- dataset analyzed in the study
DOI: 10.5517/ccdc.csd.cc25kw2q
title: CCDC 2013173: Experimental Crystal Structure Determination

description: Related Article: Nils L. Ahlburg, Peter G. Jones, Daniel B. Werz|2020|Org.Lett.|22|6404|doi:10.1021/acs.orglett.0c02210
DOI: 10.6084/m9.figshare.3458996.v4
title: A Dissection of Test-Driven Development Process: Does It Really Matter to Test-First or to Test-Last?

description: A replication package for the study reported in the paper "A Dissection of Test-Driven Development Process: Does It Really Matter to Test-First or to Test-Last?"<br>Includes:- acceptance tests- Eclipse plugin for data recording- script for automated analysis of Eclipse plugin records- the programming tasks used in the study- a spreadsheet to report the metrics extracted- questionnaires- training material for participants- dataset analyzed in the study
DOI: 10.5517/ccdc.csd.cc25kw3r
title: CCDC 2013174: Experimental Crystal Structure Determination

description: Related Article: Nils L. Ahlburg, Peter G. Jones, Daniel B. Werz|2020|Org.Lett.|22|6404|doi:10.1021/acs.orglett.0c02210
DOI: 10.6084/m9.figshare.3458954
title: Supplementary Material for: Berücksichtigung von Wechsel- und Nebenwirkungen bei pflanzlichen Arzneimitteln in deutschen S3-Leitlinien der AWMF

description: Herbal remedies have a long history in the medical care ofthe German-speaking regions but they are rarely taken intoaccount in the development of medical guidelines. In a prestudy,our working group analyzed as to how far herbalremedies were taken into consideration in the current interdisciplinaryevidence- and consensus-based S3 medicalguidelines established by the Association of the ScientificMedical Societies (AWMF) in Germany. The aim of thisstudy was to analyze to what extent possible side effectsand interactions of herbal remedies are mentioned in the S3medical guidelines. In January 2015, 134 S3 guidelines werecounted and analyzed. 27.6% (n = 37) of them show 194statements summarized under the term ‘phytotherapy’. Referencesto side effects and interactions can be found in28.4% of the statements (n = 55); 13.9% (n = 27) of thesereferences are backed by the literature. 14 of the statementsdeal with nutritional supplements, 11 are statements aboutphytotherapy in general, and 7 summarize at least 2 medicalplants in 1 statement. Hence, only 23 statements pay attentionto side effects and interactions of individual medicalplants; 14 of these are backed by the literature. These resultsdo not correspond to the standards required by theAWMF, which is due to imprecise terms as well as to theinsufficiently systematic approach in the search for scientificevidence for the safety of medical plants. Here, the Associationfor Phytotherapy may achieve an important contributionto quality improvement.
DOI: 10.5517/ccdc.csd.cc25kw4s
title: CCDC 2013175: Experimental Crystal Structure Determination

description: Related Article: Nils L. Ahlburg, Peter G. Jones, Daniel B. Werz|2020|Org.Lett.|22|6404|doi:10.1021/acs.orglett.0c02210
DOI: 10.6084/m9.figshare.3458936
title: Computational model of mesenchymal migration in 3D under chemotaxis

description: Cell chemotaxis is an important characteristic of cellular migration, which takes part in crucial aspects of life and development. In this work, we propose a novel <i>in silico</i> model of mesenchymal 3D migration with competing protrusions under a chemotactic gradient. Based on recent experimental observations, we identify three main stages that can regulate mesenchymal chemotaxis: chemosensing, dendritic protrusion dynamics and cell–matrix interactions. Therefore, each of these features is considered as a different module of the main regulatory computational algorithm. The numerical model was particularized for the case of fibroblast chemotaxis under a PDGF-bb gradient. Fibroblasts migration was simulated embedded in two different 3D matrices – collagen and fibrin – and under several PDGF-bb concentrations. Validation of the model results was provided through qualitative and quantitative comparison with <i>in vitro</i> studies. Our numerical predictions of cell trajectories and speeds were within the measured <i>in vitro</i> ranges in both collagen and fibrin matrices. Although in fibrin, the migration speed of fibroblasts is very low, because fibrin is a stiffer and more entangling matrix. Testing PDGF-bb concentrations, we noticed that an increment of this factor produces a speed increment. At 1 ng mL<sup>−1</sup> a speed peak is reached after which the migration speed diminishes again. Moreover, we observed that fibrin exerts a dampening behavior on migration, significantly affecting the migration efficiency.
DOI: 10.6084/m9.figshare.3458936.v1
title: Computational model of mesenchymal migration in 3D under chemotaxis

description: Cell chemotaxis is an important characteristic of cellular migration, which takes part in crucial aspects of life and development. In this work, we propose a novel <i>in silico</i> model of mesenchymal 3D migration with competing protrusions under a chemotactic gradient. Based on recent experimental observations, we identify three main stages that can regulate mesenchymal chemotaxis: chemosensing, dendritic protrusion dynamics and cell–matrix interactions. Therefore, each of these features is considered as a different module of the main regulatory computational algorithm. The numerical model was particularized for the case of fibroblast chemotaxis under a PDGF-bb gradient. Fibroblasts migration was simulated embedded in two different 3D matrices – collagen and fibrin – and under several PDGF-bb concentrations. Validation of the model results was provided through qualitative and quantitative comparison with <i>in vitro</i> studies. Our numerical predictions of cell trajectories and speeds were within the measured <i>in vitro</i> ranges in both collagen and fibrin matrices. Although in fibrin, the migration speed of fibroblasts is very low, because fibrin is a stiffer and more entangling matrix. Testing PDGF-bb concentrations, we noticed that an increment of this factor produces a speed increment. At 1 ng mL<sup>−1</sup> a speed peak is reached after which the migration speed diminishes again. Moreover, we observed that fibrin exerts a dampening behavior on migration, significantly affecting the migration efficiency.
DOI: 10.6084/m9.figshare.3458921
title: Documentation of Information (Forms)

description: The establishment and maintenance of relevant documentation and reports are necessary to facilitate an effective and efficient operation.
DOI: 10.6084/m9.figshare.3458921.v3
title: Documentation of Information (Forms)

description: The establishment and maintenance of relevant documentation and reports are necessary to facilitate an effective and efficient operation.
DOI: 10.6084/m9.figshare.3458918
title: Supplementary Material for: A Novel Phytase Derived from an Acidic Peat-Soil Microbiome Showing High Stability under Acidic Plus Pepsin Conditions

description: Four novel phytases of the histidine acid phosphatase family were identified in two publicly available metagenomic datasets of an acidic peat-soil microbiome in northeastern Bavaria, Germany. These enzymes have low similarity to all the reported phytases. They were overexpressed in <i>Escherichia coli</i> and purified. Catalytic efficacy in simulated gastric fluid was measured and compared among the four candidates. The phytase named rPhyPt4 was selected for its high activity. It is the first phytase identified from unculturable Acidobacteria. The phytase showed a longer half-life than all the gastric-stable phytases that have been reported to date, suggesting a strong resistance to low pH and pepsin. A wide pH profile was observed between pH 1.5 and 5.0. At the optimum pH (2.5) the activity was 2,790 μmol/min/mg at the physiological temperature of 37°C and 3,989 μmol/min/mg at the optimum temperature of 60°C. Due to the competent activity level as well as the high gastric stability, the phytase could be a potential candidate for practical use in livestock and poultry feeding
DOI: 10.6084/m9.figshare.3458912
title: Supplementary Material for: Phenotyping Adults with Non-Cystic Fibrosis Bronchiectasis: A 10-Year Cohort Study in a French Regional University Hospital Center

description: <b><i>Background:</i></b> Data concerning phenotypes in bronchiectasis are scarce. <b><i>Objective:</i></b> The aim of this study was to describe the clinical, functional and microbiological phenotypes of patients with bronchiectasis. <b><i>Methods:</i></b> A monocentric retrospective study in a university hospital in France was conducted over 10 years (2002-2012). Non-cystic fibrosis patients with tomographic confirmation of bronchiectasis were included. The clinical, functional and microbiological data of patients were analyzed relying on the underlying etiology. <b><i>Results:</i></b> Of the<b> </b>311 included patients, an etiology was found for 245 of them. At the time of diagnosis, the median age was 61 years and the mean FEV<sub>1</sub> was 63% of predicted. The main causes of bronchiectasis were post-infectious (50%, mostly related to tuberculosis), chronic obstructive pulmonary disease (COPD; 13%) and idiopathic (11%). Other causes were immune deficiency (6%), asthma (4%), autoimmunity (3%), tumor (2%) and other causes (4%). The comparison of phenotypic traits shows significant differences between COPD, congenital and idiopathic groups in term of sex (p = 0.0175), tobacco status (p &lt; 0.0001), FEV<sub>1</sub> (p = 0.0412) and age at diagnosis (p &lt; 0.001), <i>Pseudomonas aeruginosa</i> (PA) colonization (p = 0.0276) and lobectomy (0.0093). Functional follow-up was available in 30% of patients with a median duration of 2.7 years. Presence of PA was associated with a lower median FEV<sub>1</sub> at diagnosis (43% p &lt; 0.003) but not with a faster rate of decline in FEV<sub>1</sub>. <b><i>Conclusion:</i></b> Distinctive clinical, functional and microbiological features were found for idiopathic, congenital and COPD-related bronchiectasis. A prospective follow-up of these subgroups is necessary to validate their relevance in the management of bacterial colonization and specific complications of these bronchiectases.
DOI: 10.6084/m9.figshare.3458837
title: AHOI v18.11

description: AHOI (Adjusted Hydrography Optimal Interpolation) is a simple physical-statistical model developed in the Thünen Institute of Sea Fisheries to produce monthly gridded in situ hydrography through various decades.The present data set for the North Sea, version 18.11, was used in the study Akimova et al, submitted to PLOSONE in 2016 and is shared here as part of PLOSONE data policy. The data is in netCDF format, one file per month.<br>
DOI: 10.6084/m9.figshare.3458834
title: DataMatrixOrussidae2016

description: <br>data matrix used when describing new species of Ophrella (Orussidae)
DOI: 10.6084/m9.figshare.3458834.v1
title: DataMatrixOrussidae2016

description: <br>data matrix used when describing new species of Ophrella (Orussidae)
DOI: 10.6084/m9.figshare.3458828
title: Annotated Bombus terrestris transcriptome

description: This data was first used in Riddell et al 2014 BMC Genomics http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-15-1031<br>
DOI: 10.6084/m9.figshare.3458807
title: Treatment of genetic defects of thiamine transport and metabolism

description: <b>Introduction</b>: Thiamine is a key cofactor for energy metabolism in brain tissue. There are four major genetic defects (<i>SLC19A2, SLC19A3, SLC25A19</i> and <i>TPK1</i>) involved in the metabolism and transport of thiamine through cellular and mitochondrial membranes. Neurological involvement predominates in three of them (<i>SLC19A3, SCL25A19</i> and <i>TPK1</i>), whereas patients with <i>SLC19A2</i> mutations mainly present extra-neurological features (e.g. diabetes mellitus, megaloblastic anaemia and sensori-neural hearing loss). These genetic defects may be amenable to therapeutic intervention with vitamins supplementation and hence, constitutes a main area of research. <b>Areas covered</b>: We conducted a literature review of all reported cases with these genetic defects, and focused our paper on treatment efficacy and safety, adverse effects, dosing and treatment monitoring. <b>Expert commentary</b>: Doses of thiamine vary according to the genetic defect: for <i>SLC19A2</i>, the usual dose is 25–200 mg/day (1–4 mg/kg per day), for <i>SLC19A3</i>, 10–40 mg/kg per day, and for <i>TPK1</i>, 30 mg/kg per day. Thiamine supplementation in <i>SLC19A3</i>-mutated patients restores CSF and intracellular thiamine levels, resulting in successful clinical benefits. In conclusion, evidence collected so far suggests that the administration of thiamine improves outcome in <i>SLC19A-2, SLC19A3-</i> and <i>TPK1</i>-mutated patients, so most efforts should be aimed at early diagnosis of these disorders.
DOI: 10.6084/m9.figshare.3458807.v1
title: Treatment of genetic defects of thiamine transport and metabolism

description: <b>Introduction</b>: Thiamine is a key cofactor for energy metabolism in brain tissue. There are four major genetic defects (<i>SLC19A2, SLC19A3, SLC25A19</i> and <i>TPK1</i>) involved in the metabolism and transport of thiamine through cellular and mitochondrial membranes. Neurological involvement predominates in three of them (<i>SLC19A3, SCL25A19</i> and <i>TPK1</i>), whereas patients with <i>SLC19A2</i> mutations mainly present extra-neurological features (e.g. diabetes mellitus, megaloblastic anaemia and sensori-neural hearing loss). These genetic defects may be amenable to therapeutic intervention with vitamins supplementation and hence, constitutes a main area of research. <b>Areas covered</b>: We conducted a literature review of all reported cases with these genetic defects, and focused our paper on treatment efficacy and safety, adverse effects, dosing and treatment monitoring. <b>Expert commentary</b>: Doses of thiamine vary according to the genetic defect: for <i>SLC19A2</i>, the usual dose is 25–200 mg/day (1–4 mg/kg per day), for <i>SLC19A3</i>, 10–40 mg/kg per day, and for <i>TPK1</i>, 30 mg/kg per day. Thiamine supplementation in <i>SLC19A3</i>-mutated patients restores CSF and intracellular thiamine levels, resulting in successful clinical benefits. In conclusion, evidence collected so far suggests that the administration of thiamine improves outcome in <i>SLC19A-2, SLC19A3-</i> and <i>TPK1</i>-mutated patients, so most efforts should be aimed at early diagnosis of these disorders.
DOI: 10.6084/m9.figshare.3458756
title: Coronary artery disease genetic risk awareness motivates heart health behaviors in the Coriell Personalized Medicine Collaborative

description: <b>Objective</b>: The Coriell Personalized Medicine Collaborative (CPMC) research study is designed to evaluate the potential contributions of common genetic risk factors to complex disease prevention, screening, and management. Here we have focused on the impact of personalized risk reports including genetic and non-genetic risk factors for coronary artery disease (CAD) on heart health behaviors. <b>Methods</b>: We analyzed self-reported behavioral outcome data from 683 CPMC participants who received personalized CAD risk reports including: genetic risk, family history risk, and self-reported non-genetic risks based on smoking and diabetes status. <b>Results</b>: Participants with awareness of increased genetic risk for CAD were significantly more likely to report increases in heart health behaviors after viewing their personalized risk report (F-value=14.11, p-value=9.92 x 10<sup>−7</sup>). This result remained significant after controlling for BMI and gender (eta=0.58, p-value = 6.91 x 10<sup>−7</sup>). <b>Conclusion</b>: Our study indicates that individuals who are aware of their genetic risk for CAD may have higher motivation to increase heart health behaviors.
DOI: 10.6084/m9.figshare.3458756.v1
title: Coronary artery disease genetic risk awareness motivates heart health behaviors in the Coriell Personalized Medicine Collaborative

description: <b>Objective</b>: The Coriell Personalized Medicine Collaborative (CPMC) research study is designed to evaluate the potential contributions of common genetic risk factors to complex disease prevention, screening, and management. Here we have focused on the impact of personalized risk reports including genetic and non-genetic risk factors for coronary artery disease (CAD) on heart health behaviors. <b>Methods</b>: We analyzed self-reported behavioral outcome data from 683 CPMC participants who received personalized CAD risk reports including: genetic risk, family history risk, and self-reported non-genetic risks based on smoking and diabetes status. <b>Results</b>: Participants with awareness of increased genetic risk for CAD were significantly more likely to report increases in heart health behaviors after viewing their personalized risk report (F-value=14.11, p-value=9.92 x 10<sup>−7</sup>). This result remained significant after controlling for BMI and gender (eta=0.58, p-value = 6.91 x 10<sup>−7</sup>). <b>Conclusion</b>: Our study indicates that individuals who are aware of their genetic risk for CAD may have higher motivation to increase heart health behaviors.
DOI: 10.6084/m9.figshare.3458753
title: Machine learning approaches in MALDI-MSI: clinical applications

description: <b>Introduction:</b> Despite the unquestionable advantages of Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Imaging in visualizing the spatial distribution and the relative abundance of biomolecules directly <i>on-tissue</i>, the yielded data is complex and high dimensional. Therefore, analysis and interpretation of this huge amount of information is mathematically, statistically and computationally challenging. <b>Areas covered:</b> This article reviews some of the challenges in data elaboration with particular emphasis on <i>machine learning</i> techniques employed in clinical applications, and can be useful in general as an entry point for those who want to study the computational aspects. Several characteristics of data processing are described, enlightening advantages and disadvantages. Different approaches for data elaboration focused on clinical applications are also provided. Practical tutorial based upon Orange Canvas and Weka software is included, helping familiarization with the data processing. <b>Expert commentary:</b> Recently, MALDI-MSI has gained considerable attention and has been employed for research and diagnostic purposes, with successful results. Data dimensionality constitutes an important issue and statistical methods for information-preserving data reduction represent one of the most challenging aspects. The most common data reduction methods are characterized by collecting independent observations into a single table. However, the incorporation of relational information can improve the discriminatory capability of the data.
DOI: 10.6084/m9.figshare.3458753.v1
title: Machine learning approaches in MALDI-MSI: clinical applications

description: <b>Introduction:</b> Despite the unquestionable advantages of Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Imaging in visualizing the spatial distribution and the relative abundance of biomolecules directly <i>on-tissue</i>, the yielded data is complex and high dimensional. Therefore, analysis and interpretation of this huge amount of information is mathematically, statistically and computationally challenging. <b>Areas covered:</b> This article reviews some of the challenges in data elaboration with particular emphasis on <i>machine learning</i> techniques employed in clinical applications, and can be useful in general as an entry point for those who want to study the computational aspects. Several characteristics of data processing are described, enlightening advantages and disadvantages. Different approaches for data elaboration focused on clinical applications are also provided. Practical tutorial based upon Orange Canvas and Weka software is included, helping familiarization with the data processing. <b>Expert commentary:</b> Recently, MALDI-MSI has gained considerable attention and has been employed for research and diagnostic purposes, with successful results. Data dimensionality constitutes an important issue and statistical methods for information-preserving data reduction represent one of the most challenging aspects. The most common data reduction methods are characterized by collecting independent observations into a single table. However, the incorporation of relational information can improve the discriminatory capability of the data.
DOI: 10.6084/m9.figshare.3458738
title: Health facility Inspection

description: Contains data from checklists used for supportive supervision of health facilities of Punjab, North India.<br>
DOI: 10.6084/m9.figshare.3458738.v1
title: Health facility Inspection

description: Contains data from checklists used for supportive supervision of health facilities of Punjab, North India.<br>
DOI: 10.6084/m9.figshare.3458720
title: data_for_PLoS_June2016.sav

description: Using mixed design analysis of variance (ANOVA), this research investigates the effects of a subtle simulated increase in adiposity on women’s employment chances in the service sector. Employing a unique simulation of altering individuals’ BMIs and the literature on ‘aesthetic labour’, the study suggests that, especially for women, being heavier, but still within a healthy BMI, deleteriously impacts on hireability ratings. The research explores the gendered dimension of this prejudice by asking whether female employees at the upper end of a healthy BMI range are likely to be viewed more negatively than their overtly overweight male counterparts. The study concludes by considering the implications of these findings.
DOI: 10.6084/m9.figshare.3458717
title: Slides for "The Information Revolution and the Pacification of the World " (APSA 2016)

description: Slides for the 2016 conference of the American Political Science Association in Philadelphia.
DOI: 10.6084/m9.figshare.3458717.v1
title: Murphy_Pacification_EPSA_2016.pdf

description: Slides from EPSA 2016.
DOI: 10.6084/m9.figshare.3458717.v2
title: Mass Media and the Pacification of Anti-Systemic Political Contention

description: Slides from 2016 conference of the European Political Science Association.
DOI: 10.6084/m9.figshare.3458717.v7
title: Slides for "The Information Revolution and the Pacification of the World " (APSA 2016)

description: Slides for the 2016 conference of the American Political Science Association in Philadelphia.