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Files for evaluating FRC second test envelope, status June 2020
<p>Related to Description in QualyGridS publication "Finalized testing Protocol" DOI: 10.5281/zenodo.3912063</p> <p>Annex B3 refers to this data set which is too large to be reproduced in the testing protocols file.</p>
Interstate Transport of CO and BC and other relevant model evaluation data
<p>This zip file contains four sub-folders and 4 other files which are used in <strong>Bhardwaj et al., 2020</strong> submitted in <strong>JGR:Atmospheres</strong></p> <p><strong>1. bc_data</strong> : contains 15 files</p> <ul> <li>12 netcdf files (<strong>2014*_bc.nc</strong>) for each month having co-located WRF and observation data</li> <li>2 files (<strong>BC_seasonal_*.txt</strong>) which contains all BC surface observations over India from Kumar et al., (2015)</li> </ul> <p><strong>2. comp_MOPITT</strong> : contains 8 files</p> <ul> <li>4 netcdf files (<strong>wrf_mop_tc_co_*.nc</strong>; for four seasons defined in the paper) with WRF and MOPITT total CO column data</li> <li>4 netcdf files (<strong>wrf_mop_co_*.nc</strong>; for four seasons defined in the paper) with WRF and MOPITT CO profile data.</li> </ul> <p><strong>3. comp_TRMM</strong> contains 12 monthly netCDF files (<strong>comp_wrf_trmm_prec_2014*.nc</strong>) with WRF and TRMM data used in this study</p> <p><strong>4. NOAA_NCDC_ISD</strong> contains six netcdf files (<strong>wrf_obs_*.nc</strong>) for six regions (defined in this study) with co-located temperature and wind speed observations over India. The file also has WRF data for the same sites</p> <ul> <li>Two “<strong>wrfchemi_*z_d01</strong>” input emission files which are used for making emission flux (the above files) and mixing ratio plots (below files)</li> <li>Two files “<strong>state_contri_2014.nc</strong>” and “<strong>region_contri_2014.nc</strong>” have all information on interstate CO, BC for every six hours during 2014 from 30 states or six regions. These files are used for most plots in Bhardwaj et al., 2020.</li> </ul>
Using genomics to optimise and evaluate the performance of underwater forest restoration
<p>1. Restoration is an emerging intervention to reverse the degradation and loss of marine habitat-formers and the ecosystem services they underpin. Current best practice seeks to restore populations by transplanting donor individuals chosen to replicate genetic diversity and structure of extant, nearby populations. However, genetic characteristics are rarely empirically examined across generations, despite their potential role in influencing restoration success.</p> <p>2. We used genomics to design a restoration program for lost underwater forests of Phyllospora comosa, a dominant forest-forming macroalga that went locally extinct from reefs off Sydney, Australia. Population genetic diversity and structure of nearby extant populations informed choice of donor sites. We tested whether donor provenance influenced adult transplant survival, condition (via metrics of epibiosis) and the genetic characteristics of recruits at restoration sites.</p> <p>3. Extant populations of Phyllospora within a 100 km radius of Sydney comprised three distinct genetic clusters with similar levels of genetic diversity. We transplanted reproductive adults from two of these sites, with the aim of restoring five Phyllospora forests with levels of genetic structure and diversity similar to donor populations.</p> <p>4. Donor provenance influenced survival and condition of transplanted adults and recruitment levels varied significantly among restoration sites. Yet, recruitment was rapid and genetic diversity and structure of the F1 generation resembled extant populations. This likely occurred because transplanted individuals reproduced synchronously and rapidly post-transplantation, prior to mortality of adult donor transplants.</p> <p>5. Synthesis and applications: As restoration and the need to "future-proof" marine ecosystems increase globally, it will be critical to understand the role of genetic diversity and structure in restoration success. This study demonstrates that evidence-based selection of donor macroalgal forests for restoration using genomics can result in levels of genetic diversity and structure in the F1 generation that resemble extant populations. However, further refinement of transplantation techniques to maximise recruitment is also needed.02-Jun-2020</p>
Data from: Using a participatory impact assessment framework to evaluate a community-led mangrove and fisheries conservation approach in West Kalimantan, Indonesia
<ol> <li>Community-based conservation (CBC) has been identified as a solution to biodiversity loss, climate change, and the reduction of rural poverty. The heterogeneity in social and economic inequalities often acts as a barrier to community engagement in resource management and further inhibits the distributional equity of social and ecological outcomes.</li> <li>This study presents a participatory impact assessment (PIA) framework that evaluated the outcomes of a cross-sector community-led conservation initiative. Community members involved in the program identified activities and outcomes for the Conservation Cooperative (CC), ranking the influence of the former on the latter as well as their daily life through multiple focus group discussions (FGDs). Participants were asked to rank the impact of activities on outcomes and the scale of the outcome which was totaled to identify the most impactful program activities and outcomes during the project period.</li> <li>Community members reported improved income, health, education and the creation of a locally-led natural resource management system. Members also reported improved crab harvest rates and reduced mangrove deforestation. Environmental outcomes identified by community members through the PIA were verified through a secondary spatial analysis and mud-crab independent fisheries monitoring.</li> <li>The results support the hypothesis that environmental NGOs need to consider a multi-dimensional view of human well-being, and that cross-sector integrated interventions may be effective at improving multiple outcomes.</li> <li>Future steps should focus on spatial replication of the CC program which will provide further insights by testing for differences in outcomes between villages, how those are impacted by preexisting social and ecological systems, and comparing outcomes between control sites that did not receive interventions.</li> </ol>
Data from: Evaluation of the Laguerre-Gaussian mode purity produced by 3D-printed microwave spiral phase plates
Computer-aided design software and additive manufacturing provide flexibility in the direct fabrication of multi-material devices. This design and fabrication versatility has been investigated for the manufacture of dielectric spiral phase plates (SPP) to generate electromagnetic waves with helical wave-fronts. Three types of SPPs designed to produce an orbital angular momentum (OAM) mode number l=|1| were additively manufactured using multi-material extrusion and multijet fabrication methods. The phase mode and mode characteristics of transformed helical microwaves as a function of the SPP geometrical features was investigated experimentally in the 12 to 18 GHz frequency range, providing high purity at characteristic frequencies. The SPPs were further combined with an additively manufactured dielectric lens that provided a marked improvement in OAM mode purity. Finally, multiplexing and de-multiplexing of two OAM modes were demonstrated successfully using the optimum SPP geometry and design.
Data from: Evaluation of a pharmacist-led actionable audit and feedback intervention for improving medication safety in primary care: an interrupted time series analysis
<p><strong>Background</strong>. We evaluated the impact of a pharmacist-led Safety Medication dASHboard (SMASH) intervention on medication safety in primary care.<br> <strong>Methods and findings</strong>. SMASH comprised: (1) training of clinical pharmacists to deliver the intervention; (2) a web-based dashboard providing actionable, patient-level feedback; and (3) pharmacists reviewing individual at-risk patients, and initiating remedial actions or advising general practitioners on doing so. It was implemented in forty-three general practices covering a population of 235,595 people in Salford (Greater Manchester), UK. All practices started receiving the intervention between 18 April 2016 and 26 September 2017. We used an interrupted time series analysis of rates of potentially hazardous prescribing and inadequate blood-test monitoring, comparing observed rates post-intervention to extrapolations from a 24-month pre-intervention trend. The number of people registered to participating practices and having one or more risk factors for being exposed to hazardous prescribing or inadequate blood-test monitoring at the start of the intervention was 47,413 (males: 23,073 [48.7%]; mean age: 60 [standard deviation: 21]). At baseline, 95% of practices had rates of potentially hazardous prescribing (composite of 10 indicators) between 0.88% and 6.19%. The prevalence of potentially hazardous prescribing reduced by 27.9% (95% confidence interval [CI], 20.3% to 36.8%) at 24 weeks and by 40.7% (95% CI, 29.1% to 54.2%) at twelve months after introduction of SMASH. The rate of inadequate blood-test monitoring (composite of 2 indicators) reduced by 22.0% (95% CI, 0.2% to 50.7%) at 24 weeks and by 23.5% (95% CI, -4.5% to 61.6%) at 12 months. After 12 months, 95% of practices had rates of potentially hazardous prescribing between 0.74% and 3.02%. We did not randomise practices but enrolled them in a naturalistic fashion. All our measurements were based on routinely kept electronic health records.<br> <strong>Conclusions</strong>. The SMASH intervention was associated with reduced rates of potentially hazardous prescribing and inadequate blood-test monitoring in general practices. This reduction was sustained over 12 months after start of the intervention for prescribing but not for monitoring of medication. There was a marked reduction in the variation in rates of high-risk prescribing between practices.</p>
Replication Package for the paper: Evaluating the Agreement among Technical Debt Measurement Tools: Building an Empirical Benchmark of Technical Debt Liabilities
<p>This is the replication package for the Archetypal Analysis conducted in the paper "Evaluating the Agreement among Technical Debt Measurement Tools: Building an Empirical Benchmark of Technical Debt Liabilities" accepted at Springer's EMSE Journal.</p> <p>It contains:</p> <ul> <li>The dataset with TD measurements from three TD tools for 25 Java projects</li> <li>The dataset with TD measurements from three TD tools for 25 JS projects</li> <li>The script to run the Archetypal Analysis on the two datasets</li> </ul>
Hakea vegetation dataset for training and evaluating segmentation network
<p>This dataset is the version used for both training and evaluation of the models discussed the (in press) publication in Methods in Ecology and Evolution, "Detecting plant species in the field with deep learning and drone technology".</p> <p>Also included in this upload, results_inference_images.tar includes the output predictions for each of the trained models on the unseen test set.</p>
Data for: Evaluating the impact of physical frailty during ageing in wild chimpanzees (Pan troglodytes schweinfurthii)
<p>While declining physical performance is an expected consequence of aging, human clinical research has placed increasing emphasis on physical frailty as a predictor of death and disability in the elderly. We examined non-invasive measures approximating frailty in a richly-sampled longitudinal dataset on wild chimpanzees. Using urinary creatinine to assess lean body mass, we demonstrated moderate but significant declines in physical condition with age in both sexes. While older chimpanzees spent less of their day in the trees and feeding, they did not alter activity budgets with respect to travel or resting. There was little evidence that declining lean body mass had negative consequences independent of age. Old chimpanzees with poor lean body mass rested more often but did not otherwise differ in activity. Males, but not females, in poor condition were more likely to exhibit respiratory illness. Poor muscle mass was associated acutely with death in males, but it did not predict future mortality in either sex. While there may be some reasons to suspect biological differences in the susceptibility to frailty in chimpanzees versus humans, our data are consistent with recent reports from humans that lean, physically active individuals can successfully combat frailty.</p>
Re-evaluating deep neural networks for phylogeny estimation: the issue of taxon sampling
Deep neural networks (DNNs) are powerful machine learning models that are widely used for classification problems, and have been recently proposed for quartet tree phylogeny estimation (Survorov et al. Systematic Biology 2020 and Zou et al. Molecular Biology and Evolution 2020). Here we present a study evaluating recently trained DNNs (from Zou et al., MBE 2020) in comparison to a collection of standard phylogeny estimation methods, including UPGMA, neighbor joining, maximum parsimony, and maximum likelihood, on a heterogeneous collection of 20-sequence datasets simulated under the same models that were used to train the DNNs, and also under similar conditions but with higher rates of evolution. Our study shows that using DNNs with quartet amalgamation (to combine quartet trees into a tree on the full dataset) is only more accurate than UPGMA, and otherwise is less accurate than all standard phylogeny estimation methods we explore (maximum likelihood, neighbor joining, and maximum parsimony). We further find that while DNNs can provide good quartet tree accuracy, some standard phylogeny estimation methods match or improve on DNNs for quartet accuracy, especially, but not exclusively, when used in a global manner (i.e., the tree on the full dataset is computed and then the induced quartet trees are extracted from the full tree). Thus, our study provides evidence that a major challenge impacting the utility of current DNNs for phylogeny estimation is their restriction to estimating quartet trees which must subsequently be combined into a tree on the full dataset: in contrast, global methods -- i.e., those that estimate trees from the full set of sequences -- are able to benefit from taxon sampling, and hence have higher accuracy on large datasets.
Data from: Evaluating tooth strontium and barium as indicators of weaning age in Pacific walruses
<p>A dataset of calcium-normalized <sup>88</sup>Sr and <sup>137</sup>Ba concentrations from laser ablation transects across the cementum layer of 107 (female: n = 84, male: n = 23) Pacific walrus (Odobenus rosmarus divergens) teeth. Dataset includes spreadsheets containing elapsed time of laser ablation transect in seconds (ElapsedTime_s; laser transect speed = 5μm/s), calcium-normalized strontium concentrations (Sr_ppm_m88; values below limit of detection replaced with 1/2*limit of detection, see methods), and calcium-normalized barium concentrations (Ba_ppm_m137; values below limit of detection replaced with 0.5*limit of detection). Photos (in .tif format) of tooth cementum used to estimate the positions of cementum growth layer groups are included for each animal. For teeth where more than one laser ablation scar is visible in the photo, an arrow is included to indicate the laser ablation scar that corresponds with the included trace element data. Finally, a Word document containing metadata (Catalog Number/ID, Sex, Median Age Est., Coll. Year, Est. Birth Year), weaning age estimates produced by both a visual and mathematical method (Sr Vis. Est., Sr Math. Est., Ba Vis. Est., Ba Math. Est.), and a descriptive grouping of the patterns of accumulation of Sr and Ba (Sr Pat., Ba Pat.) are included. See methods and accompanying paper in Methods in Ecology and Evolution for more details.</p>
Data from: Evaluating the taxa that provide shared pollination services across multiple crops and regions
Many pollinator species visit multiple crops in multiple regions, yet we know little about their pollination service provisioning at local and regional scales. We investigated the floral visitors (n = 13,200), their effectiveness (n = 1718 single visits) and response to landscape composition across three crops avocado, mango and macadamia within a single growing region (1 year), a single crop (3 years) and across different growing regions in multiple years. In total, eight wild visitor groups were shared across all three crops. The network was dominated by three pollinators, two bees (Apis mellifera and Tetragonula spp.) and a fly, Stomorhina discolour. The visitation network for the three crops was relatively generalised but with the addition of pollen deposition data, specialisation increased. Sixteen managed and wild taxa were consistently present across three years in avocado, yet their contribution to annual network structure varied. Node specialisation (d') analyses indicated many individual orchard sites across each of the networks were significantly more specialised compared to that predicted by null models, suggesting the presence of site-specific factors driving these patterns. Identifying the taxa shared across multiple crops, regions and years will facilitate the development of specific pollinator management strategies to optimize crop pollination services in horticultural systems.
Which pitfall traps and sampling effort to choose to evaluate cropping system effects on spider and carabid assemblages?
<p>Dataset and example of the script (R) used in the simulation approach.</p>
Evaluation of IDEAL-CT test in Utah for Balanced Mix Design
<p>The data contained herein are the results of asphalt mixtures tested at 25 C using the indirect tensile configuration based on the IDEAL tests developed by Zhou et al. (Zhou, F., Newcomb, D., Gurganus, C., Banihashemrad, S., Park, E., Sakheeifar, M., and Lytton, R.: Experimental Design for Field Validation of Laboratory Tests to Assess Cracking Resistance of Asphalt Mixtures. Final Project Report, NCHRP project 9-57. April 2016)</p> <p>The work was performed in the State of Utah as part of a research contract between the Department of Transportation and the University of Utah. PEPG, LLC., a consulting lab was also involved. The complete report can be found at the Utah Department of Transportation website (<a href="http://www.udot.utah.edu">www.udot.utah.edu</a>), Research and Innovation Division.</p>
Data and code for training and evaluating machine learning models for thunderstorm prediction from reanalysis data
<p>FIXED Data and Python code for training and evaluating machine learning models for predicting thunderstorms, associated with the paper:</p> <p>"Evaluation of machine learning classifiers for predicting deep convection"</p> <p>by Peter Ukkonen and Antti Mäkelä (to appear in JAMES)</p> <p>The data (preprocessed inputs and outputs) is stored as netCDF files and .mat files which can be loaded with Python. </p>
An Empirical Evaluation about Using Models to Improve Preliminary Safety Analysis
<p>Video presentation of the paper "<em>An Empirical Evaluation about Using Models to Improve Preliminary Safety Analysis</em>" to appear at <strong>II Workshop de Modelagem e Simulação de sistemas intensivos em Software (II MSSiS) </strong>2020 co-located with CBSOFT 2020.</p> <p><strong>Abstract.</strong> <strong>Context</strong>: Safety analysis is an activity of fundamental importance in the development of safety-critical systems (SCS) to ensure that hazardous situations are properly found and mitigated. Such analysis is performed after a system requirements specification is available. Therefore, it is then worthwhile to investigate specification techniques to detect their strengths and weaknesses with respect to discovering hazards early in the development process. <strong>Objective</strong>: In this paper, we investigate similarities and differences in the results of a preliminary safety analysis from requirements specified using models in Business Process Modeling Notation (BPMN) and Textual Use Cases (TUC). <strong>Method</strong>: We adopted a controlled experiment as research method using computer engineering students as subjects. <strong>Results</strong>: The subjects of BPMN group found more accidents, hazards as well as more causes of hazards. Moreover, they have a higher preference for the template used for safety analysis documentation. <strong>Conclusions</strong>: The use of BPMN to represent the interactions among actors in a system probably lead to the discovery of more accidents and hazards, but more experiments are necessary to test this hypothesis since the results are not statistically significant.</p>
Software Product Quality Evaluation Guide for Electronic Health Record Systems
<p>Apresentação do artigo "Software Product Quality Evaluation Guide for Electronic Health Record Systems".</p> <p>SBES 2020 - Trilha de Ideias Inovadoras e Resultados Emergentes.</p>
Evaluating usefulness, ease of use and usability of an UML-based Software Product Line Tool
<p>Vídeo de apresentação do artigo "Evaluating usefulness, ease of use and usability of an UML-based Software Product Line Tool" para o 34° Simpósio Brasileiro de Engenharia de Software (SBES'20), 21-23 de Outubro de 2020, Natal, RN, Brasil. Autores: Leandro F. da Silva e Edson OliveiraJr.</p>
An Empirical Evaluation about Using Models to Improve Preliminary Safety Analysis - MSSIS 2020
<p>Video presentation of the paper "<em>An Empirical Evaluation about Using Models to Improve Preliminary Safety Analysis</em>" to appear at <strong>II Workshop de Modelagem e Simulação de sistemas intensivos em Software (II MSSiS) </strong>2020 co-located with CBSOFT 2020.</p> <p><strong>Abstract.</strong> <strong>Context</strong>: Safety analysis is an activity of fundamental importance in the development of safety-critical systems (SCS) to ensure that hazardous situations are properly found and mitigated. Such analysis is performed after a system requirements specification is available. Therefore, it is then worthwhile to investigate specification techniques to detect their strengths and weaknesses with respect to discovering hazards early in the development process. <strong>Objective</strong>: In this paper, we investigate similarities and differences in the results of a preliminary safety analysis from requirements specified using models in Business Process Modeling Notation (BPMN) and Textual Use Cases (TUC). <strong>Method</strong>: We adopted a controlled experiment as research method using computer engineering students as subjects. <strong>Results</strong>: The subjects of BPMN group found more accidents, hazards as well as more causes of hazards. Moreover, they have a higher preference for the template used for safety analysis documentation. <strong>Conclusions</strong>: The use of BPMN to represent the interactions among actors in a system probably lead to the discovery of more accidents and hazards, but more experiments are necessary to test this hypothesis since the results are not statistically significant.</p>
Re-evaluating phoneme frequencies: Supplementary materials S6–S7
<p>Supplementary materials (Sections S6–S7) for the paper <em>Re-evaluating phoneme frequencies</em><em> </em>(<a href="https://www.frontiersin.org/articles/10.3389/fpsyg.2020.570895/full">Macklin-Cordes & Round, 2020</a>)</p> <p>These materials include:</p> <ul> <li>S6: Data viewer app</li> <li>S7: Code, data and results</li> </ul> <p>Usage instructions for the code and app can be found in S1 of the paper's <a href="https://www.frontiersin.org/articles/10.3389/fpsyg.2020.570895/full#supplementary-material">Supplementary Materials</a> and in the readme file contained here.</p>
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.