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641 results for “data validation”
Sequencing data from validation experiment for base editing of SCN2A
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Supplemental data for: Development and validation of a polygenic risk score for stroke in the Chinese population
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Elbow and wrist range of motion assessment comparing inertial sensors against goniometry_Raw data clinical validation
<p>These data were taken during the validity and reliability analysis of inertial sensors (S) against goniometry (G) for the assessment of the elbow and wrist range of motion. To study the intra-inter-rater reliability, two physiotherapists (A and B) and a technician were in charge of taking the measurements. 29 subjects were evaluated in two different sessions (1 and 2). In the elbow assessment, the flexo-extension, pronation and supination movements were performed. For the wrist, flexo-extension and radial-ulnar deviation movements were evaluated.</p>
TTnet - Model validation data
<p>This repository contains the raw data collected to validate the <em>TTnet</em> time and energy model, which is described in</p> <ul> <li><strong>Time-Triggered Wireless Architecture</strong><br> Romain Jacob, Licong Zhang, Marco Zimmerling, Samarjit Chakraborty, Lothar Thiele <br> Accepted to ECRTS 2020 <br> <a href="https://arxiv.org/abs/2002.07491">arxiv.org/abs/2002.07491</a></li> <li><strong>Leveraging Synchronous Transmissions for the Design of Real-time Wireless Cyber-Physical Systems</strong><br> Romain Jacob<br> Doctoral dissertation , 2020<br> <a href="https://doi.org/10.5281/zenodo.3510184">10.5281/zenodo.3510184 </a>(Chapter 5)</li> </ul> <p>The processing of these data is described in detailed in the following GitHub repository:<br> <a href="https://github.com/romain-jacob/TTW-Artifacts">github.com/romain-jacob/TTW-Artifacts</a></p> <p><strong>Files description</strong></p> <ul> <li><strong>data_raw.zip</strong><br> Contains the serial logs and test configuration files, for all three test series</li> <li><strong>serieX_all_data.zip</strong><br> Contains all the test results (serial logs + GPIO traces + power traces) for the test of series X.<br> Missing for series 3 (we forgot to save it before it got deleted from the server... sorry about that)</li> </ul>
Data from: Identification of intraductal carcinoma of the prostate on tissue specimens using Raman micro-spectroscopy: A diagnostic accuracy case-control study with multicohort validation
<p class="AbstractSummary"><b>Background</b></p> <p class="AbstractSummary">Prostate cancer (PC) is the most frequently diagnosed cancer in North American men. Pathologists are in critical need of accurate biomarkers to characterize PC, particularly to confirm the presence of intraductal carcinoma of the prostate (IDC-P), an aggressive histopathological variant for which therapeutic options are now available. Our aim was to identify IDC-P with Raman micro-spectroscopy and machine learning technology following a protocol suitable for routine clinical histopathology laboratories.</p> <p class="AbstractSummary"><b>Methods and findings</b></p> <p class="AbstractSummary">We used Raman micro-spectroscopy to differentiate IDC-P from PC, as well as PC and IDC-P from benign tissue on formalin-fixed paraffin-embedded first-line radical prostatectomy specimens (embedded in tissue microarrays, TMAs) from 483 patients treated in three Canadian institutions between 1993 and 2013. The main measures were the presence or absence of IDC-P and of PC, regardless of the clinical outcomes. Most of the 483 patients were pT2 stage (44–69%), and pT3a (22–49%) was more frequent than pT3b (9–12%). After approval of the construction of the TMAs by local ethics review board, the diagnostic accuracy study was approved by the Centre hospitalier de l'Université de Montréal (CHUM) ethics review board. Briefly, two consecutive sections of each TMA block were cut. The first section was transferred onto a glass slide to perform immunohistochemistry with H&E counterstaining for cell identification. The second section was placed on an aluminum slide, dewaxed, and then used to acquire an average of 7 Raman spectra per specimen (between 4 and 24 Raman spectra, 4 acquisitions / TMA core). Raman spectra of each cell type were then analyzed to retrieve tissue-specific molecular information and to generate classification models using machine learning technology. <span>Models were trained and cross-validated using data from one institution. Accuracy, sensitivity and specificity were respectively of 87 ± 5%, 86 ± 6% and 89 ± 8% to differentiate PC from benign tissue, and of 95 ± 2%, 96 ± 4% and 94 ± 2% respectively to differentiate IDC-P from PC. The trained models were then tested on data from two independent institutions, reaching accuracies, sensitivities and specificities of 84 and 86%, 84 and 87%, and 81 and 82%, respectively</span><span> to diagnose PC, and of 85 and 91%, 85 and 88%, and 86 and 93% respectively for the identification of IDC-P.</span> IDC-P could further be differentiated from high-grade prostatic intraepithelial neoplasia (HGPIN), a pre-malignant intraductal proliferation which can be mistaken as IDC-P, with accuracies, sensitivities and specificities >95% in both training and testing cohorts. As we used stringent criteria to diagnose IDC-P, the main limitation of our study is the exclusion of borderline, difficult to classify lesions from our datasets.</p> <p class="AbstractSummary"><b>Conclusions</b></p> <p>In this study, we developed classification models for the analysis of Raman micro-spectroscopy data to differentiate IDC-P, PC and benign tissue, including HGPIN. Raman micro-spectroscopy could be a next-generation histopathological technique used to <span>reinforce the identification of high-risk PC patients and lead to more precise diagnosis of IDC-P.</span></p>
Data from: Intra-Rater reliability and validity of outcome measures in Myotonic Dystrophy Type 1
<p>Objective</p> <p>To investigate intra-rater reliability, concurrent- and construct validity of muscle strength, balance, and functional mobility measures in individuals with non-congenital DM1.</p> <p>Methods</p> <p><a name="_Hlk4397329">Seventy-eight adults with non-congenital DM1 participated in visit 1 and 73 of the subjects participated in visit 2 separated by 1-2 weeks. The assessments consisted of </a>muscle strength tests with Hand-Held Dynamometry (HHD) and Stationary Dynamometry in the lower limb. The balance tests comprised of Step Test, Timed Up and Go test, Feet-Together stance, Tandem-Stance, One-Leg-Stance, and modified Clinical Test of Sensory Integration and Balance on a balance platform. The functional mobility tests consisted of the 10-meter Walk Test (10mWT) and 10-times Sit-To-Stand test.</p> <p><a name="_Hlk14169462">Results</a></p> <p>The HHD and Stationary Dynamometry were sufficiently intra-rater reliable for most muscle groups on a group- (SEM<sub>%</sub>≤15%) and individual level (MDD<sub>95%</sub>≤30%), but HHD was most reliable. Stationary Dynamometry measured a higher torque than HHD for all extensor muscles, but for single individuals none of the devices were favored. Overall, intra-rater reliability and validity were only sufficient for the dynamic balance tests and not the static balance tests. Both functional mobility tests were sufficiently reliable and valid, but the 10mWT was most reliable.</p> <p>Conclusion</p> <p>Overall, HHD is recommended as a reliable and valid tool for single individuals and for flexor muscles on a group level. For balance assessments, the dynamic balance tests are recommended as the most valid and reliable balance tests. Both functional mobility tests are recommended for valid and reliable outcomes, but the 10mWT was superior for reliability.</p>
Data from: Validation of a simple extraction procedure for bisphenol A identification from human plasma
The general population is exposed to bisphenol A (BPA) orally, parenterally, transdermally, and environmentally as a result of the use of BPA in food packaging, plastics, and personal care products. The majority of the population nowadays (91–99%) has detectable levels of BPA inside their body. In this study, we successfully performed an inexpensive, rapid, and simple protein precipitation procedure for extraction of BPA from human plasma, followed by analysis by LC-MS/MS. This method was specifically developed for handling large numbers of samples with minimum cost and volume of sample. The developed method was accurate, precise, and reproducible for quantification of BPA from human plasma samples in the concentration range of 10–2000 ng/mL. The method was performed on samples from 150 healthy volunteers who were enrolled in the study. The mean of observed BPA level was 2.22 ± 9.91 ng/mL. Higher BPA levels were observed for females compare to that of males (p-value = 0.002), the BPA levels were higher in participants 33 years of age and older compared to those less than 33 years of age (p-value = 0.000), then the BPA levels higher in subjects with tap water as source of drinking (p-value = 0.005). This method may be valuable for general risk assessment of BPA for a large and varied population because of its efficiency and economical aspects.
Pilot implementation, monitoring, co-evaluation and validation data_v2
<p>These data have been collected in the context of monitoring and assessing the pilot operation of the INVITE project (H2020 GA 763651) and its OI2Lab platform during their 2nd deployment round.</p>
University of Denver Collections as Data - HTR Train and Validation Set JCRS_2020_5_27
<p><a href="https://zenodo.org/api/files/333ecb88-1f48-4ffd-b39e-5e70b800c276/HTR_Train_Set_JCRS_2020_5_27.zip">HTR_Train_Set_JCRS_2020_5_27.zip</a> <br> Description</p>
Dataset for "Validation of the Astro dataset clustering solutions with external data"
<p><strong>Validation data for the <em>Astro</em> scientific publication clustering benchmark dataset</strong></p> <p>This is the dataset used in the publication Donner, P. "Validation of the Astro dataset clustering solutions with external data", Scientometrics, DOI 10.1007/s11192-020-03780-3</p> <p>Certain data included herein are derived from Clarivate Web of Science. © Copyright Clarivate 2020. All rights reserved.</p> <p>Published with permission from Clarivate.</p> <p>The original <em>Astro</em> dataset is not contained in this data. It can be obtained from http://topic-challenge.info/ and requires permission from Clarivate Analytics for use.</p> <p> </p> <p>This dataset collection consists of four files. Each file contains an independent dataset that relates to the Astro dataset via Web of Science (WoS) record identifiers. These identifiers are called UTs. All files are tabular data in CSV format. In each, at least one column contains UT data. This should be used to link to the <em>Astro </em>dataset or other WoS data. The datasets are discussed in detail in the journal publication.</p> <p> </p>
Data from: Mapping and validation of a major QTL affecting resistance to pancreas disease (salmonid alphavirus) in Atlantic salmon (Salmo salar)
Pancreas disease (PD), caused by a salmonid alphavirus (SAV), has a large negative economic and animal welfare impact on Atlantic salmon aquaculture. Evidence for genetic variation in host resistance to this disease has been reported, suggesting that selective breeding may potentially form an important component of disease control. The aim of this study was to explore the genetic architecture of resistance to PD, using survival data collected from two unrelated populations of Atlantic salmon; one challenged with SAV as fry in freshwater (POP 1) and one challenged with SAV as post-smolts in sea water (POP 2). Analyses of the binary survival data revealed a moderate-to-high heritability for host resistance to PD in both populations (fry POP 1 h2~0.5; post-smolt POP 2 h2~0.4). Subsets of both populations were genotyped for single nucleotide polymorphism markers, and six putative resistance quantitative trait loci (QTL) were identified. One of these QTL was mapped to the same location on chromosome 3 in both populations, reaching chromosome-wide significance in both the sire- and dam-based analyses in POP 1, and genome-wide significance in a combined analysis in POP 2. This independently verified QTL explains a significant proportion of host genetic variation in resistance to PD in both populations, suggesting a common underlying mechanism for genetic resistance across lifecycle stages. Markers associated with this QTL are being incorporated into selective breeding programs to improve PD resistance.
Data from: Validation of a non-invasive method for the early detection of metabolic syndrome: a diagnostic accuracy test in a working population
Objectives. A non-invasive method for the early detection of Metabolic Syndrome (NIN-MetS) using only Waist to Height Ratio (WHtR) and Blood Pressure (BP) has recently been published, with fixed cut-off values for gender and age. The aim of this study was to validate this method in a large sample of Spanish workers. Design. A diagnostic test accuracy to assess the validity of the method was performed. Setting. Occupational Health Services. Participants. The studies were conducted in 2012-2016 on a sample of 60,799 workers from the Balearic Islands (Spain). Interventions. The NCEP-ATP III criteria were used as the gold standard. NIM-MetS has been devised using classification trees (the CHAID, Chi-squared Automatic Interaction Detection method). Main outcome measures. Anthropometric and biochemical variables to diagnose MetS. Sensitivity, specificity, validity index and Youden Index were determined to analyse the accuracy of the diagnostic test (NIM-MetS). Results. Regarding the validation of the method, sensitivity was 54.7%, specificity 94.9% and validity index 91.2%. The cut-off value for WHtR was 0.54, ranging from 0.51 (lower age group) to 0.56 (higher) in the age groups. Variables more closely associated with MetS were WHtR (AUC=0.85; 95% CI: 0.84-0.86) and Systolic Blood Pressure (AUC=0.79; 95% CI: 0.78-0.80). The final cut-off values for the non-invasive method were WHtR≥0.56 and BP≥128/80 mmHg, which includes four levels of MetS risk (very low, low, moderate and high). Conclusions. The analysed method has shown a high validity index (higher than 91%) for the early detection of MetS. It is a non-invasive method easy to apply and interpret in any health care setting. This method provides a scale of MetS risk which allows a more accurate detection and a more effective intervention.
Data from: Validation of the Regicor short physical activity questionnaire for the adult population
Objective: To develop and validate a short questionnaire to estimate physical activity (PA) practice and sedentary behavior for the adult population. Methods: The short questionnaire was developed using data from a cross-sectional population-based survey (n=6352) that included the Minnesota leisure-time PA questionnaire. Activities that explained a significant proportion of the variability of population PA practice were identified. Validation of the short questionnaire included a cross-sectional component to assess validity with respect to the data collected by accelerometers and a longitudinal component to assess reliability and sensitivity to detect changes (n=114, aged 35 to 74 years). Results: Six types of activities that accounted for 87% of population variability in PA estimated with the Minnesota questionnaire were selected. The short questionnaire estimates energy expenditure in total PA and by intensity (light, moderate, vigorous), and includes 2 questions about sedentary behavior and a question about occupational PA. The short questionnaire showed high reliability, with intraclass correlation coefficients ranging between 0.79 to 0.95. The Spearman correlation coefficients between estimated energy expenditure obtained with the questionnaire and the number of steps detected by the accelerometer were as follows: 0.36 for total PA, 0.40 for moderate intensity, and 0.26 for vigorous intensity. The questionnaire was sensitive to detect changes in moderate and vigorous PA (correlation coefficients ranging from 0.26 to 0.34). Conclusion: The REGICOR short questionnaire is reliable, valid, and sensitive to detect changes in moderate and vigorous PA. This questionnaire could be used in daily clinical practice and epidemiological studies.
Data from: Validating two-dimensional leadership models on three-dimensionally structured fish schools
Identifying leader-follower interactions is crucial for understanding how a group decides where or when to move, and how this information is transferred between members. Although many animal groups have a three-dimensional structure, previous studies investigating leader-follower interactions have often ignored vertical information. This raises the question whether commonly used two-dimensional leader-follower analyses can be used justifiably on groups that interact in three dimensions. To address this we quantified the individual movements of banded tetra fish (Astyanax mexicanus) within shoals by computing the three-dimensional trajectories of all individuals using a stereo-camera technique. We used these data firstly to identify and compare leader-follower interactions in two and three dimensions, and secondly to analyse leadership with respect to an individual's spatial position in three dimensions. We show that for 95% of all pairwise interactions leadership identified through two-dimensional analysis matches that identified through three-dimensional analysis, and we reveal that fish attend to the same shoalmates for vertical information as they do for horizontal information. Our results therefore highlight that three-dimensional analyses are not always required to identify leader-follower relationships in species that move freely in three-dimensions. We discuss our results in terms of the importance of taking species' sensory capacities into account when studying interaction networks within groups.
Data from: Validation of network communicability metrics for the analysis of brain structural networks.
Computational network analysis provides new methods to analyze the brain's structural organization based on diffusion imaging tractography data. Networks are characterized by global and local metrics that have recently given promising insights into diagnosis and the further understanding of psychiatric and neurologic disorders. Most of these metrics are based on the idea that information in a network flows along the shortest paths. In contrast to this notion, communicability is a broader measure of connectivity which assumes that information could flow along all possible paths between two nodes. In our work, the features of network metrics related to communicability were explored for the first time in the healthy structural brain network. In addition, the sensitivity of such metrics was analysed using simulated lesions to specific nodes and network connections. Results showed advantages of communicability over conventional metrics in detecting densely connected nodes as well as subsets of nodes vulnerable to lesions. In addition, communicability centrality was shown to be widely affected by the lesions and the changes were negatively correlated with the distance from lesion site. In summary, our analysis suggests that communicability metrics that may provide an insight into the integrative properties of the structural brain network and that these metrics may be useful for the analysis of brain networks in the presence of lesions. Nevertheless, the interpretation of communicability is not straightforward; hence these metrics should be used as a supplement to the more standard connectivity network metrics.
Data from: Adiposity, compared with masculinity, serves as a more valid cue to immunocompetence in human mate choice
According to the "good genes" hypothesis, females choose males based on traits that indicate the male's genetic quality in terms of disease resistance. The "immunocompetence handicap hypothesis (ICHH)" proposed that secondary sexual traits serve as indicators of male genetic quality because they indicate that males can contend with the immunosuppressive effects of testosterone. Masculinity is commonly assumed to serve as such a secondary sexual trait. Yet women do not consistently prefer masculine looking men, nor is masculinity consistently related to health across studies. Here we show that adiposity, but not masculinity, significantly mediates the relationship between a direct measure of immune response (Hepatitis B antibody response) and attractiveness for both body and facial measurements. In addition, we show that circulating testosterone is more closely associated with adiposity than masculinity. These findings indicate that adiposity, compared to masculinity, serves as a more important cue to immunocompetence in female mate choice.
Data from: Prospective validation of the PML risk biomarker L-Selectin and influence of natalizumab extended intervals
Low L-selectin (CD62L) on CD4+ T cells after cryopreservation has been introduced in 2013 as a risk biomarker for the development of progressive multifocal leukoencephalopathy (PML) during natalizumab treatment1 or HIV infection.2 The biomarker has been reproduced retrospectively in some international cohorts,3,4 but not in others,5 potentially because of its sensitivity to biomaterial quality, assay protocols, and the time point of testing. With regard to current approaches to PML risk reduction, natalizumab extended interval dosing is thought to improve immune surveillance and reduce PML risk, whereas clinical efficacy seems unaffected.6
Data from: Forward genetic screening for regulators involved in cholesterol synthesis using validation-based insertional mutagenesis
Somatic cell genetics is a powerful approach for unraveling the regulatory mechanism of cholesterol metabolism. However, it is difficult to identify the mutant gene(s) due to cells are usually mutagenized chemically or physically. To identify important genes controlling cholesterol biosynthesis, an unbiased forward genetics approach named validation-based insertional mutagenesis (VBIM) system was used to isolate and characterize the 25-hydroxycholesterol (25-HC)-resistant and SR-12813-resisitant mutants. Here we report that five mutant cell lines were isolated. Among which, four sterol-resistant mutants either contain a truncated NH2-terminal domain of sterol regulatory element-binding protein (SREBP)-2 terminating at amino acids (aa) 400, or harbor an overexpressed SREBP cleavage-activating protein (SCAP). Besides, one SR-12813 resistant mutant was identified to contain a truncated COOH-terminal catalytic domain of 3-hydroxy-3-methylglutaryl-coenzyme A reductase (HMG-CoA reductase). This study demonstrates that the VBIM system can be a powerful tool to screen novel regulatory genes in cholesterol biosynthesis.
Data from: Logical validation and evaluation of practical feasibility for the SCRuM (School Clinical Rugby Measure) test battery developed for young adolescent rugby players in a resource-constrained environment
There is a growing impetus towards usage of test batteries in talent identification (TID) programmes in rugby. Consequently, there are many test batteries in existence profiling anthropometric, physiological characteristics and rugby-specific skills. There is no consensus in the literature on the constituent variables and corresponding tests required to inform TID programs. Following development of a new test battery called the SCRuM (School Clinical Rugby Measure), this study aimed at establishing face, logical validity and practical feasibility of included tests. The test battery, initially comprised of 23 items, had its face and logical validity evaluated by five (5) adolescent rugby coaches and 20 rugby experts, respectively. Logical validation was conducted in two questionnaire-based rounds with Content Validity Index (I-CVI) calculated for each variable. Subsequently, a cross-sectional study targeting 30 local rugby coaches was conducted to determine the perceived practical feasibility of each test item. The results showed excellent I-CVI (>0.78) for 17 variables (speed, weight, height and skin fold measures, repeated high-intensity exercise performance ability, prolonged high-intensity intermittent running ability, change of direction speed, anaerobic capacity, lower-and upper body muscular power and strength, muscular flexibility, reactive agility, passing for accuracy, tackling proficiency, and catching). However, three tests, namely, Reactive Agility, One Repetition Maximum Back Squat and One Repetition Maximum Bench Press had low test-feasibility indices (T-FI< 35) suggesting practicality concerns with implementation in the Zimbabwean context. Thus, these findings suggest the need for substitution or development of new practically feasible tests for upper-and lower body muscular strength and reactive agility.
Data from: Comparison of the validity of the checklist assessment in the cardiac arrest simulations with the app in an academic hospital in Taiwan: a retrospective observational study
Background: Robust assessment is a crucial component in Advanced Cardiac Life Support (ACLS) training to determine whether participants have achieved learning objectives with little or no variation in their overall outcomes. This study aimed to evaluate resuscitation performance by real-time logs. We hypothesized that instructors may not be able to evaluate time-sensitive parameters, namely, chest compression fraction, time to initiating chest compression, and time to initiating defibrillation efficiently in a subjective manner. Methods: Video records and formal checklist-based test results of Megacode scenarios for the ACLS certification examination at several hospitals in Taipei were examined. For the study interest, three time-sensitive parameters were measured via video review assisted by a mobile phone application, and were used for evaluation. We evaluated if the pass/fail results made by instructors via checklists were correlated with these parameters. Results: A total of 185 Megacode scenarios were eligible for the final analysis. Among the three parameters, good chest compression fraction was statistically significant with higher odds ratio (OR) of passing (OR = 3.65; 95% confidence interval [CI]: 1.36-9.91; P = 0.01). In 112 participants with one parameter that did not meet the criteria, 25 were graded as fail, making the specificity 22.3% (95% CI: 15.0-31.2%). Conclusions: Visual observation of cardiopulmonary resuscitation performance is not accurate when evaluating time-sensitive parameters. Objective results should be offered for training outcome evaluation, and also for feedback to participants.
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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.