cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.3708468
title: Artifacts: An Efficient Approach for Reviewing Security-Related Aspects in Agile Requirements Specifications of Web Applications

description: Defects in requirements specifications can have severe consequences during the software development lifecycle. Some of them result in overall project failure due to incorrect or missing quality characteristics, such as security. This characteristic requires special attention in web applications because they have become a target for manipulating sensible data. Several concerns make security difficult to deal with. For instance, (1) when stakeholders discuss general requirements they are often unaware that they should also discuss security-related aspects, because (2) they typically do not have enough expertise in security. This often leads to unspecified or ill-defined security requirements. These concerns become even more challenging in agile contexts, where lightweight documentation is typically produced. To tackle this problem, we designed an approach for reviewing security-related aspects in agile requirements specifications of web applications. Our proposal considers user stories and security specifications as inputs and relates those user stories to security properties via Natural Language Processing. Based on the related security properties, our approach identifies high-level security requirements from the Open Web Application Security Project (OWASP) to be verified, and generates a reading technique to support reviewers in detecting defects. We evaluate our approach via three experiment trials conducted with 56 novice software engineers, measuring effectiveness, efficiency, usefulness, and ease to use. We compare our approach against using: (1) OWASP high-level security requirements, and (2) the perspective-based approach as proposed in contemporary state of the art. The results strengthen our confidence that using our approach has a positive impact (with large effect size) on the performance of inspectors in terms of effectiveness and efficiency.
DOI: 10.5281/zenodo.3708404
title: Dataset related to article "p2PSA for predicting biochemical recurrence of prostate cancer earlier than total prostate-specific antigen after radical prostatectomy: an observational prospective cohort study."

description: BACKGROUND: There is an unmet clinical need for more biochemical specific tests that may detect clinically significant recurrent PCa at an early stage after radical prostatectomy (RP). Our purpose is to test the hypothesis that p2PSA (Index test) detects prostate cancer relapse (BCR) earlier than the current Reference Standard Test (total prostate-specific antigen [tPSA]) in patients who underwent RP for localized PCa. METHODS: This is an observational, prospective, cohort, follow-up study in patients subjected to RALP (robotic assisted laparoscopic radical prostatectomy) for clinically localized PCa from January 2013 to July 2013 at a high-volume Institution (450 average RP/year). A blood sample, for tPSA and p2PSA, was prospectively drawn after 3, 6, and 12 months and then every 6 months during the following two years. The primary outcome is to determine whether or not kinetics in rising of p2PSA significantly anticipates the tPSA kinetics. Exploratory data analysis was used to identify relationship between different variables. RESULTS: Over 134 patients 20 BCRs were detected according to tPSA cut-off. Five patients showed a contemporary increase of tPSA and p2PSA, 11 presented a p2PSA increase earlier than tPSA increase (13.9 months ±9.7). In four patients, the increase of PSA was not associated with a p2PSA&gt;0.8 pg/mL. The correlation between tPSA and p2PSA according to Sperman's rho coefficient was statistically significant at 3, 6, 18 and 30 months: 0.416 (P&lt;0.01), 0.255 (P&lt;0.01), 0.359 (P&lt;0.01) and 0.413 (P&lt;0.01) respectively. When subjects were stratified according to stage/grade and margins (positive vs. negative), patients with higher stage and positive surgical margins could be considered the target categories. The low rate of observed BCR and high rate of p2PSA false positive are the main limitations. CONCLUSIONS: The current findings showed that p2PSA might be more sensitive than tPSA in detecting earlier BCR within 3-year follow-up. Further studies with a longer follow-up and larger population remain mandatory before considering p2PSA for clinical decision-making.
DOI: 10.5281/zenodo.3708405
title: Dataset related to article "p2PSA for predicting biochemical recurrence of prostate cancer earlier than total prostate-specific antigen after radical prostatectomy: an observational prospective cohort study."

description: BACKGROUND: There is an unmet clinical need for more biochemical specific tests that may detect clinically significant recurrent PCa at an early stage after radical prostatectomy (RP). Our purpose is to test the hypothesis that p2PSA (Index test) detects prostate cancer relapse (BCR) earlier than the current Reference Standard Test (total prostate-specific antigen [tPSA]) in patients who underwent RP for localized PCa. METHODS: This is an observational, prospective, cohort, follow-up study in patients subjected to RALP (robotic assisted laparoscopic radical prostatectomy) for clinically localized PCa from January 2013 to July 2013 at a high-volume Institution (450 average RP/year). A blood sample, for tPSA and p2PSA, was prospectively drawn after 3, 6, and 12 months and then every 6 months during the following two years. The primary outcome is to determine whether or not kinetics in rising of p2PSA significantly anticipates the tPSA kinetics. Exploratory data analysis was used to identify relationship between different variables. RESULTS: Over 134 patients 20 BCRs were detected according to tPSA cut-off. Five patients showed a contemporary increase of tPSA and p2PSA, 11 presented a p2PSA increase earlier than tPSA increase (13.9 months ±9.7). In four patients, the increase of PSA was not associated with a p2PSA&gt;0.8 pg/mL. The correlation between tPSA and p2PSA according to Sperman's rho coefficient was statistically significant at 3, 6, 18 and 30 months: 0.416 (P&lt;0.01), 0.255 (P&lt;0.01), 0.359 (P&lt;0.01) and 0.413 (P&lt;0.01) respectively. When subjects were stratified according to stage/grade and margins (positive vs. negative), patients with higher stage and positive surgical margins could be considered the target categories. The low rate of observed BCR and high rate of p2PSA false positive are the main limitations. CONCLUSIONS: The current findings showed that p2PSA might be more sensitive than tPSA in detecting earlier BCR within 3-year follow-up. Further studies with a longer follow-up and larger population remain mandatory before considering p2PSA for clinical decision-making.
DOI: 10.5281/zenodo.3708427
title: OCRed text of the Allgemeine musikalische Zeitung (ALTO format) from 1798-1848 and 1863-1965

description: Dataset as used in the LREC 2020 publication '<em>Allgemeine Musikalische Zeitung</em> as a Searchable Online Corpus'.
DOI: 10.18112/openneuro.ds002634.v1.0.0
title: Project_larynx
DOI: 10.5281/zenodo.3708426
title: OCRed text of the Allgemeine musikalische Zeitung (ALTO format) from 1798-1848 and 1863-1965

description: Dataset as used in the LREC 2020 publication '<em>Allgemeine Musikalische Zeitung</em> as a Searchable Online Corpus'.
DOI: 10.5281/zenodo.3708487
title: Embedding Metadata Shex and Example RDF

description: Vector Embedding Metadata Example: TransE embeddings for DrugBank computed using TransE.
DOI: 10.6084/m9.figshare.3761562.v1417
title: Online Labour Index: Measuring the Online Gig Economy for Policy and Research

description: Data repository for the data underlying the Online Labour Index. See http://ilabour.oii.ox.ac.uk online-labour-index/ for details.
DOI: 10.5281/zenodo.3708416
title: Dataset related to article "Psychological Characteristics of Inflammatory Bowel Disease Patients: A Comparison Between Active and Nonactive Patients."

description: BACKGROUND AND AIMS: The role of new psychological factors such as psychopathological patterns and defense mechanisms in the care of inflammatory bowel disease (IBD) has been poorly investigated. We aimed to assess the psychological characteristics and defense mechanisms of IBD patients. METHODS: This was a single-center, observational, cross-sectional study. Consecutive adult IBD patients were enrolled and stratified according to disease activity. Sociodemographic and clinical data were collected, and validated questionnaires (Symptom Checklist-90-R [SCL-90-R]) for psychological distress, Defense Mechanism Inventory (DMI) for psychological defense mechanisms, and Inflammatory Bowel Disease Questionnaire (IBDQ) for quality of life (QoL) were administered. RESULTS: Two hundred one patients were enrolled: 101 in remission and 100 with active disease. The mean score for IBDQ was below the cutoff level (156.8 ± 37.8), with a significantly greater impairment of QoL in subjects with flares (136.5 vs 177.5, P &lt; 0.001). Lower scores were associated with female gender. No patients had psychological scores above the cutoff for normality. Statistically higher SCL-90-R scores were found in active patients for obsessive-compulsive disorder (P = 0.026), depression (P = 0.013), anxiety (P = 0.013), phobic anxiety (P = 0.002), psychoticism (P = 0.007), global severity index (GSI) (P = 0.005) and positive symptom total (PST) (P = 0.001). A significantly increased probability of higher global indexes was associated with Crohn's disease and disease flares. None of the defensive Defense Mechanism Inventory (DMI) styles resulted above the cutoff in our cohort. CONCLUSIONS: Further data are needed to demonstrate the potential key role of psychological intervention in the therapeutic strategies utilized for IBD patients, and the identification of specific psychological patterns based on the patients profile is necessary to optimize psychological intervention.
DOI: 10.5281/zenodo.3708417
title: Dataset related to article "Psychological Characteristics of Inflammatory Bowel Disease Patients: A Comparison Between Active and Nonactive Patients."

description: BACKGROUND AND AIMS: The role of new psychological factors such as psychopathological patterns and defense mechanisms in the care of inflammatory bowel disease (IBD) has been poorly investigated. We aimed to assess the psychological characteristics and defense mechanisms of IBD patients. METHODS: This was a single-center, observational, cross-sectional study. Consecutive adult IBD patients were enrolled and stratified according to disease activity. Sociodemographic and clinical data were collected, and validated questionnaires (Symptom Checklist-90-R [SCL-90-R]) for psychological distress, Defense Mechanism Inventory (DMI) for psychological defense mechanisms, and Inflammatory Bowel Disease Questionnaire (IBDQ) for quality of life (QoL) were administered. RESULTS: Two hundred one patients were enrolled: 101 in remission and 100 with active disease. The mean score for IBDQ was below the cutoff level (156.8 ± 37.8), with a significantly greater impairment of QoL in subjects with flares (136.5 vs 177.5, P &lt; 0.001). Lower scores were associated with female gender. No patients had psychological scores above the cutoff for normality. Statistically higher SCL-90-R scores were found in active patients for obsessive-compulsive disorder (P = 0.026), depression (P = 0.013), anxiety (P = 0.013), phobic anxiety (P = 0.002), psychoticism (P = 0.007), global severity index (GSI) (P = 0.005) and positive symptom total (PST) (P = 0.001). A significantly increased probability of higher global indexes was associated with Crohn's disease and disease flares. None of the defensive Defense Mechanism Inventory (DMI) styles resulted above the cutoff in our cohort. CONCLUSIONS: Further data are needed to demonstrate the potential key role of psychological intervention in the therapeutic strategies utilized for IBD patients, and the identification of specific psychological patterns based on the patients profile is necessary to optimize psychological intervention.
DOI: 10.5281/zenodo.3708436
title: Dataset related to article "Linac-based stereotactic body radiation therapy vs moderate hypofractionated radiotherapy in prostate cancer: propensity-score based comparison of outcome and toxicity."

description: OBJECTIVE: Prostate cancer represents the second most common malignancy in the world and majority of patients have diagnosis of localized disease. The aim of the present study was to compare two cohorts of patients treated with moderate hypofractionation (MHRT) or stereotactic body radiation therapy (SBRT). METHODS: We included patients treated between 2010 and 2015. Inclusion criteria were: adenocarcinoma of the prostate; class risks low or intermediate; WHO performance status 0-2. We evaluated rectal, gastrointestinal toxicity and genitourinary. Measures of outcome were biochemical disease-free survival and overall survival. Propensity score was used to approximate the balance in covariates. RESULTS: 209 patients were included, treated with MHRT (<em>n</em> = 109) or SBRT (<em>n</em> = 100). Median follow-up time was 37.4 months. Rates of biochemical disease-free survival at 1- and 3 years were 100 and 95%, respectively. There was no significant difference between the two groups (<em>p</em> = 0.868). Rates of overall survival at 1- and 3 years were 100 and 97.1%, respectively with no differences between the two groups (<em>p</em> = 0.312). After propensity scoring matching, no differences were observed in terms of acute and late rectal and gastrointestinal toxicity. While mild genitourinary side-effects were more common in SBRT group (45.5% <em>vs</em> 19.5 %), Grade 2 and 3 toxicity was increased after MHRT (11.7% <em>vs</em> 2.6 %; <em>p</em> = 0.029). CONCLUSIONS: Moderate hypofractionation and SBRT are two effective and safe options for the treatment of low- and intermediate-risk prostate cancer. The analysis showed no difference in terms of disease's control and survival but increased moderate and severe toxicity after MHRT. ADVANCES IN KNOWLEDGE: Moderate hypofractionation and SBRT are comparable in terms of efficacy while moderate and severe toxicity is more common in the first one.
DOI: 10.5281/zenodo.3708437
title: Dataset related to article "Linac-based stereotactic body radiation therapy vs moderate hypofractionated radiotherapy in prostate cancer: propensity-score based comparison of outcome and toxicity."

description: OBJECTIVE: Prostate cancer represents the second most common malignancy in the world and majority of patients have diagnosis of localized disease. The aim of the present study was to compare two cohorts of patients treated with moderate hypofractionation (MHRT) or stereotactic body radiation therapy (SBRT). METHODS: We included patients treated between 2010 and 2015. Inclusion criteria were: adenocarcinoma of the prostate; class risks low or intermediate; WHO performance status 0-2. We evaluated rectal, gastrointestinal toxicity and genitourinary. Measures of outcome were biochemical disease-free survival and overall survival. Propensity score was used to approximate the balance in covariates. RESULTS: 209 patients were included, treated with MHRT (<em>n</em> = 109) or SBRT (<em>n</em> = 100). Median follow-up time was 37.4 months. Rates of biochemical disease-free survival at 1- and 3 years were 100 and 95%, respectively. There was no significant difference between the two groups (<em>p</em> = 0.868). Rates of overall survival at 1- and 3 years were 100 and 97.1%, respectively with no differences between the two groups (<em>p</em> = 0.312). After propensity scoring matching, no differences were observed in terms of acute and late rectal and gastrointestinal toxicity. While mild genitourinary side-effects were more common in SBRT group (45.5% <em>vs</em> 19.5 %), Grade 2 and 3 toxicity was increased after MHRT (11.7% <em>vs</em> 2.6 %; <em>p</em> = 0.029). CONCLUSIONS: Moderate hypofractionation and SBRT are two effective and safe options for the treatment of low- and intermediate-risk prostate cancer. The analysis showed no difference in terms of disease's control and survival but increased moderate and severe toxicity after MHRT. ADVANCES IN KNOWLEDGE: Moderate hypofractionation and SBRT are comparable in terms of efficacy while moderate and severe toxicity is more common in the first one.
DOI: 10.6073/pasta/1c7b4eb4e9723e059426bb37ca1e5eff
title: Santa Barbara Channel Marine BON Darwin Core Archive: Nearshore kelp forest integrated benthic cover, 1980-ongoing

description: The Santa Barbara Channel Marine Biodiversity Observation Network (SBCMBON) tracks long-term patterns in species abundance and diversity. This dataset contains cover of kelp forest sessile invertebrates, understory macroalgae, and substrate types by integrating data from four contributing projects working in the kelp forests of the Santa Barbara Channel, USA. Divers collect data on using either uniform point contact (UPC) or random point contact (RPC) methods. The four contributing projects are two research projects: The Santa Barbara Coastal LTER (SBC LTER) and the Partnership for Interdisciplinary Studies of Coastal Oceans (PISCO), the kelp forest monitoring program of the Santa Barbara Channel National Park, and the San Nicolas Island monitoring program supported by USGS. Together, these projects have recorded data for more than 200 species at approximately 100 sites on both the mainland coast and on the Santa Barbara Channel Islands. Sampling began in 1982 and is ongoing. Data were collected by human observation (divers using SCUBA) during regular surveys. Percent cover is recorded for taxa where individuals cannot be counted. Cover can be calculated from the data here as the fraction of total points at which the taxon was present x 100. With UPC and RPC methods, multiple species can be recorded at any given point. The total percent cover of all species combined using this method can exceed 100%; however, the percent cover of any single species cannot exceed 100%. See Methods for information on integration and data processing. MBON is funded by National Aeronautics and Space Administration (NASA), Bureau of Ocean Energy Management (BOEM), and National Oceanic and Atmospheric Administration (NOAA). This dataset is formatted as a Darwin Core Archive (DwC-A, occurrence core). This is a derived data product and see provenance for the source data. For users who are interested in using all or part of this integrated datasets, please contact data owners to discuss your research interests, data-related issues or any other questions. A recommended citation for the data package is available from the download page. In addition, any manuscript generated using this dataset is expected to be sent to the data owners before publication so we can be sure the data is used in the proper context and methods are reported accurately: Santa Barbara Coastal LTER (LTER): Dan Reed dan.reed@lifesci.ucsb.edu Robert Miller miller@msi.ucsb.edu Partnership for Interdisciplinary Studies of Coastal Oceans (PISCO): Jenn Caselle caselle@ucsb.edu Kelp forest monitoring (KFM): David Kushner david_kushner@nps.gov Joshua Sprague joshua_sprague@nps.gov San Nicolas Island monitoring (SNI): Kevin Lafferty Klafferty@usgs.gov Mike Kenner mkenner@ucsc.edu
DOI: 10.5281/zenodo.3708512
title: Input data of phylogenetic field analysis for exotic seed plants in Japan

description: This release includes the dataset for evaluating phylogenetic fields of exotic plant species in Japan: co-occurrence matrices between Japanese native species (exotic vs all native seed plants at 10 km grid cells; exotic vs endemic native seed plants at 10 km grid cells; exotic vs all native seed plants at vegetation plots; exotic vs endemic native seed plants at vegetation plots), exotic species list with their species attributes (geographical extent within Japan, climatic niche widths, minimum residential time, disturbance dependency, origin place, and mean phylogenetic distance from their native recipients), and phylogenetic tree for native and exotic seed plants.
description: Fixed a bug in ExoticSpeciesList_Japan.csv on 13 Mar 2020
DOI: 10.25345/c5gt38
title: MassIVE MSV000085093 - Proteomic analysis of the contribution of SH3 domains positioning to NCK2 interactome
title: This submission contains the mass spectrometry files for the manuscript by Ugo Dionne et al. that describes the functional characterization of NCK2 SH3 domains positions. To determine the contribution of NCK2 SH3 domains positioning to the protein interactions, we inter-changed the positions of its three SH3 domains. The interactome of each NCK2 chimeras was determined and compared to the WT or to a SH3 dead negative control. AP-MS experiments were performed from HEK293T cells and 36 MS files were acquired on a TripleTOF 5600+ mass spectrometer in data dependent and independent acquisition modes. Only the DDA files are associated with this deposition. Please refer to the individual Tables 1 for additional details of submitted files. For questions, please contact Jean-Philippe Lambert (Jean-Philippe.Lambert@crchudequebec.ulaval.ca) or Nicolas Bisson (nick.bisson@crchudequebec.ulaval.ca).
DOI: 10.5281/zenodo.3708450
title: Artifacts: An Efficient Approach for Reviewing Security-Related Aspects in Agile Requirements Specifications of Web Applications

description: Defects in requirements specifications can have severe consequences during the software development lifecycle. Some of them result in overall project failure due to incorrect or missing quality characteristics, such as security. This characteristic requires special attention in web applications because they have become a target for manipulating sensible data. Several concerns make security difficult to deal with. For instance, (1) when stakeholders discuss general requirements they are often unaware that they should also discuss security-related aspects, because (2) they typically do not have enough expertise in security. This often leads to unspecified or ill-defined security requirements. These concerns become even more challenging in agile contexts, where lightweight documentation is typically produced. To tackle this problem, we designed an approach for reviewing security-related aspects in agile requirements specifications of web applications. Our proposal considers user stories and security specifications as inputs and relates those user stories to security properties via Natural Language Processing. Based on the related security properties, our approach identifies high-level security requirements from the Open Web Application Security Project (OWASP) to be verified, and generates a reading technique to support reviewers in detecting defects. We evaluate our approach via three experiment trials conducted with 56 novice software engineers, measuring effectiveness, efficiency, usefulness, and ease to use. We compare our approach against using: (1) OWASP high-level security requirements, and (2) the perspective-based approach as proposed in contemporary state of the art. The results strengthen our confidence that using our approach has a positive impact (with large effect size) on the performance of inspectors in terms of effectiveness and efficiency.