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2,129 results for “scores”
Assessment of Fast-Track pathway in hip and knee replacement surgery by propensity score matching on patient-reported outcomes
<p>This is the dataset accompanying the publication "Assessment of Fast-Track pathway in hip and knee replacement surgery by propensity score matching on patient-reported outcomes" published on the Diagnostics journal.</p>
Submitted Galaxy Scores to the Gravitational Wave Treasure Map for event TEST_EVENT Preliminary
Attached in a .json file is the ranked galaxy information within the contour region of the EM counterpart search associated with the gravitational wave event TEST_EVENT Preliminary. A reference to these calculations can be found here: https://ui.adsabs.harvard.edu/abs/2020arXivNicePaper
Cognitive scores of bees exposed to various environmental stressors
<p><span>Environmental stressors have sublethal consequences on animals, often affecting the mean of phenotypic traits in populations. However, effects on inter-individual variability are poorly understood. Since phenotypic variability is the basis for adaptation, any change due to stressors may have important implications for population resilience. </span></p> <p><span>Here we explored this possibility in bees by analysing raw datasets from 23 studies (5,618 bees) in which individuals were first exposed to stressors and then tested for cognitive tasks.</span></p> <p><span>While all types of stressors decreased the mean cognitive performance of bees, they increased cognitive variability. Focusing on 14 pesticide studies, we found that the mode of exposure to stressors and the dose were critical. <a>Mean</a></span> <span>cognitive performance was more affected by a chronic exposure than by an acute exposure. Yet, cognitive variability increased with increasing doses following both exposure durations.</span></p> <p><span>Policy implications: Current guidelines for the authorization of plant protection products on the European market prioritize acute over chronic toxicity assessments on non-target organisms. By overlooking the consequences of a chronic exposure, regulatory authorities may register new products or doses that are harmful to bee populations. </span><span>Our findings call for more research on stress-induced phenotypic variation and its incorporation to policy guidelines to help identify levels and modes of exposure animals can cope with.</span></p>
Submitted Galaxy Scores to the Gravitational Wave Treasure Map for event MS230322s Preliminary
Attached in a .json file is the ranked galaxy information within the contour region of the EM counterpart search associated with the gravitational wave event MS230322s Preliminary. A reference to these calculations can be found here: https://ui.adsabs.harvard.edu/abs/2020arXivNicePaper
Submitted Galaxy Scores to the Gravitational Wave Treasure Map for event MS230322s Preliminary
Attached in a .json file is the ranked galaxy information within the contour region of the EM counterpart search associated with the gravitational wave event MS230322s Preliminary. A reference to these calculations can be found here: https://ui.adsabs.harvard.edu/abs/2020arXivNicePaper
PASS - A SCORING SYSTEM TO EVALUATE PERSISTENT ACUTE KIDNEY INJURY IN CRITICALLY ILL ADULT ICU PATIENTS
<p>Acute Kidney Injury (AKI) and sepsis is highly prevalent in Intensive Care Units (ICU) and has direct effect on mortality and morbidity. We aimed to evaluate if course and recovery of sepsis-AKI can be predicted using variables collected at the time of admission, and to develop a formula - Persistent AKI Scoring System (PASS) to predict recovery.</p> <p>63 consecutive patients admitted for sepsis-AKI in our ICUs were evaluated over a period of 8 months. Baseline demographic and clinical/laboratory parameters ,including serum creatinine (SCr), Base Excess (BE), Plethysmographic Variability Index (PVI), Caval Index, R wave Variability (RVI), Mean Arterial Pressure (MAP) and Renal Resistivity Index (RI) using renal doppler and need for inotropes were assessed on admission. Patients were managed with standard protocols with fluid resuscitation and other specific therapy. After 6 of hours of fluid resuscitation, hemodynamic status and volume status of the patient was assessed. Patients were classified as Volume Responders or Non-responders depending on hemodynamic stabilization using parameters like MAP. Re- assessment of all the variables was done at 24 hours and 72 hours after admission. The primary outcome was persistent AKI after 72hrs. The secondary outcome was initiation of dialysis and death within 15 days of admission.</p> <p>34 subjects recovered from AKI. 32 patients showed volume response with respect to hemodynamic parameters and 31 patients were non-responders. Response to fluid, MAP at admission, MAP after 6 hours, BE at admission, inotrope requirement, and PVI at admission did not correlate with recovery of AKI. RI, RVI and S Cr at admission significantly correlated with recovery from AKI These 3 parameters were evaluated further to develop the model for predicting recovery from AKI.• Score> 7.8 predicted recovery from AKI with sensitivity of 79.4%, specificity of 72.4%. PPV 81.8% and NPV 76.7%. PASS Score>7.8 had AUROC of 0.85.</p> <p>Multiple logistic regression showed that SCr< 2.36 mg%, RVI > 14.45 and RI < 0.8 on admission correlated with recovery.</p> <p>PASS SCORE Formula was created using the same.</p> <p>CONCLUSION: PASS score can be a simple bed side method to reliably identify salvageable cases of sepsis-AKI, guiding fluid resuscitation and also aiding early referrals from rural to higher centers for better management.</p>
FUN-LDA scores for human genome assembly GRCh37
<p>FUN-LDA is based on a Latent Dirichlet Allocation (LDA) model for predicting functional effects of non-coding genetic variants in a cell type and tissue-specific way by integrating diverse epigenetic annotations for specific cell types and tissues from large-scale genomics projects such as ENCODE and Roadmap Epigenomics. Using this unsupervised approach, we predict tissue-specific functional effects for every position in the human genome for 127 tissues and cell types in ENCODE and Roadmap Epigenomics. This <a href="https://docs.google.com/spreadsheet/ccc?key=0Am6FxqAtrFDwdHU1UC13ZUxKYy1XVEJPUzV6MEtQOXc&usp=sharing">online spreadsheet</a> includes the information about the 127 Roadmap tissues in detail.</p> <p><strong>Format</strong></p> <p>The FUN-LDA scores are stored in the UCSC Genome Browser bigWig Track Format. </p> <p>To extract FUN-LDA scores, the bigWigAverageOverBed utility is required. It can be downloaded from the Genome Browser website at <a href="https://hgdownload.cse.ucsc.edu/admin/exe">https://hgdownload.cse.ucsc.edu/admin/exe</a>.</p> <p>User should prepare a UCSC Genome Browser bed file, a tab-separated four-column file. The first column is the chromosome; the second is the zero-based coordinate of the position of interest; the third is that zero-based coordinate plus one; and the fourth is a unique identifier for the position. The command below is an example of extracting FUN-LDA scores in tissue E007 for the positions defined in a bed file, "input.bed".</p> <pre><code class="language-bash">bigWigAverageOverBed E007.valley9.c89.bigwig input.bed output.tab</code></pre> <p>It produces a six-column file, output.tab. The first column includes the unique position id defined in the input bed file. The last column, average over the covered bases, is the score for this position.</p> <p><strong>Reference</strong></p> <p>Daniel Backenroth, Zihuai He, Krzysztof Kiryluk, Valentina Boeva, Lynn Pethukova, Ekta Khurana, Angela Christiano, Joseph Buxbaum, Iuliana Ionita-Laza. FUN-LDA: A latent Dirichlet allocation model for predicting tissue-specific functional effects of noncoding variation: Methods and applications. American Journal of Human Genetics, 2018.<br> </p> <p> </p>
Database Wine and Scores
<p>Database built from Wine Spectators' annual rankings for high-quality wines</p>
An unbiased, automated platform for scoring dopaminergic neurodegeneration in C. elegans
<p><em><span>Caenorhabditis elegans</span></em><span> (<em>C. elegans</em>) has served as a simple model organism to study dopaminergic neurodegeneration, as it enables quantitative analysis of cellular and sub-cellular morphologies in live animals. These isogenic nematodes have a rapid life cycle and transparent body, making high-throughput imaging and evaluation of fluorescently tagged neurons possible. However, the current state-of-the-art method for quantifying dopaminergic degeneration requires researchers to manually examine images and score dendrites into groups of varying levels of neurodegeneration severity, which is time-consuming, subject to bias, and limited in data sensitivity. We aim to overcome the pitfalls of manual neuron scoring by developing an automated, unbiased image processing algorithm to quantify dopaminergic neurodegeneration in <em>C. elegans</em>. The algorithm can be used on images acquired with different microscopy setups and only requires two inputs: a maximum projection image of the four cephalic neurons in the <em>C. elegans</em> head and the pixel size of the user's camera. We validate the platform by detecting and quantifying neurodegeneration in nematodes exposed to rotenone, cold shock, and 6-hydroxydopamine using 63x epifluorescence, 63x confocal, and 40x epifluorescence microscopy, respectively. Analysis of tubby mutant worms with altered fat storage showed that, contrary to our hypothesis, increased adiposity did not sensitize to stressor-induced neurodegeneration. We further verify the accuracy of</span><span> the</span><span> algorithm by comparing code-generated, categorical degeneration results with manually scored dendrites of the same experiments. The platform, which detects 19 different metrics of neurodegeneration, can provide comparative insight into how each exposure affects dopaminergic neurodegeneration patterns. </span></p>
Scores on independence, quality of life, and satisfaction on visual mapping software intervention in children with Down syndrome
<p>Enhancing independence and quality of life are key modifiable outcomes that are short- and long-term goals for children with Down syndrome and for their parents. Here we report the outcome of a 4-week feasibility study in a cohort of 26 children with Down Syndrome, 7–17 years old, who used an assistive technology approach that incorporated smart device software and <span>step-by-step</span> pictures (the MapHabit System). Parents reported improvements in children's activities of daily living, quality of life, and independence. They recommended this technology to other families. This report and its findings underscore the feasibility of using assistive technology in children with Down syndrome within home and family settings.</p> <p>The current findings that assistive technology can be used successfully and effectively in family and home settings set the stage for more informative systematic studies using assistive technology for this population.</p>
Dataset: Reliability of the domain authority scores calculated by Moz, Semrush, and Ahrefs
<p>This dataset contains the <em>Domain Authority</em>, <em>Authority Score</em>, and <em>Domain Rating </em>collected by using Moz, Semrush, and Ahrefs applications. By doing different searches, the data collection was conducted in Google using keywords selected in the most neutral way possible. The selection of keywords was made by applying two criteria: 1) Fifty words of four or more characters were selected from those identified as being the most frequently used on the web, according to the WordFrequency ranking, and 2) the eleven keywords used most during the previous six months to conduct searches on Google, according to Google Trends in November 2022, were added. The data collection was carried out between 11/03/2022 and 12/22/2022. In total, 16,937 results were obtained.</p> <p>All the searches were conducted simultaneously and in the same geographical location to avoid any potential bias. Subsequently, the URL information corresponding to the path, file name, and parameters was removed, resulting in 6,268 domains. All duplicates were then removed, leaving a final sample of 3,151 distinct domains.</p> <p>This data set accompanies the article entitled "Reliability of the domain authority scores calculated by Moz, Semrush, and Ahrefs".</p>
PASS: A scoring system to evaluate persistent kidney injury in critically ill ICU adult patients
<p>Acute Kidney Injury (AKI) and sepsis is highly prevalent in Intensive Care Units (ICU) and has direct effect on mortality and morbidity. We aimed to evaluate if course and recovery of sepsis-AKI can be predicted using variables collected at the time of admission, and to develop a formula - Persistent AKI Scoring System (PASS) to predict recovery.</p> <p>63 consecutive patients admitted for sepsis-AKI in our ICUs were evaluated over a period of 8 months. Baseline demographic and clinical/laboratory parameters ,including serum creatinine (SCr), Base Excess (BE), Plethysmographic Variability Index (PVI), Caval Index, R wave Variability (RVI), Mean Arterial Pressure (MAP) and Renal Resistivity Index (RI) using renal doppler and need for inotropes were assessed on admission. Patients were managed with standard protocols with fluid resuscitation and other specific therapy. After 6 of hours of fluid resuscitation, hemodynamic status and volume status of the patient was assessed. Patients were classified as Volume Responders or Non-responders depending on hemodynamic stabilization using parameters like MAP. Re- assessment of all the variables was done at 24 hours and 72 hours after admission. The primary outcome was persistent AKI after 72hrs. The secondary outcome was initiation of dialysis and death within 15 days of admission.</p> <p>34 subjects recovered from AKI. 32 patients showed volume response with respect to hemodynamic parameters and 31 patients were non-responders. Response to fluid, MAP at admission, MAP after 6 hours, BE at admission, inotrope requirement, and PVI at admission did not correlate with recovery of AKI. RI, RVI and S Cr at admission significantly correlated with recovery from AKI These 3 parameters were evaluated further to develop the model for predicting recovery from AKI.• Score> 7.8 predicted recovery from AKI with sensitivity of 79.4%, specificity of 72.4%. PPV 81.8% and NPV 76.7%. PASS Score>7.8 had AUROC of 0.85.</p> <p>Multiple logistic regression showed that SCr< 2.36 mg%, RVI > 14.45 and RI < 0.8 on admission correlated with recovery.</p> <p>PASS SCORE Formula was created using the same.</p> <p>CONCLUSION: PASS score can be a simple bed side method to reliably identify salvageable cases of sepsis-AKI, guiding fluid resuscitation and also aiding early referrals from rural to higher centers for better management.</p>
PIGNet2: A versatile deep learning-based protein-ligand interaction prediction model for accurate binding affinity scoring and virtual screening
<p>Training and test datasets of the paper "Improving the versatility of deep learning-based protein-ligand interaction prediction for accurate binding affinity scoring and virtual screening".</p>
A multi-model ensemble of baseline and process-based models improves the predictive skill of near-term lake forecasts: data, forecasts, and scores
<p>This data publication contains zipped parquet from the Falling Creek Reservoir multi-model ensemble (MME) forecasting work using the FLARE (Forecasting Lake And Reservoir Ecosystems) system and baseline models: drivers.zip contains NOAA driver forecast files, targets.zip contains in-situ water temperature observations, forecasts.zip contains forecast parquet files generated from the MME workflow (FLARE & baseline models), and scores.zip contains forecast skill metrics required for analysis.</p>
Generating VISA scores on glioma bulk RNAseq and single cell RNAseq glioma
<p>Tissue stiffness is collectively determined by the stiffness of ECM and cells. Gliomas are characterized by dysregulated expression of ECM proteins, ECM crosslinking enzymes, and aberrant cellular contractility.While The RNA sequencing datasets have been comprehensively analyzed to interrogate tumor genomes, epigenomes, and transcriptomes, we realized an untapped potential: using transcriptomic data coupled with analysis of gene expression associated with ECM and actomyosin contractility to establish a bioinformatic tool, which we named VIrtual Stiffness Algorithm (VISA), capable of inferring tissue stiffness.</p> <p>This data repository is for reproducing VISA scores on glioma bulk RNAseq and single cell RNAseq glioma.</p>
Thyroid cancer polygenic risk score improves classification of thyroid nodules as benign or malignant.
<p>Supplementary Data for the manuscript: Thyroid cancer polygenic risk score improves classification of thyroid nodules as benign or malignant. Nikita Pozdeyev, MD, PhD (ORCiD ID: 0000-0001-8574-1972), Manjiri Dighe, MD, Martin Barrio, MD, MS, Christopher Raeburn, MD, Harry Smith, MS, Matthew Fisher, MS, Sameer Chavan, MS, Nicholas Rafaels, MS, Jonathan A. Shortt, PhD, Meng Lin, PhD, Michael G. Leu, MD, Toshimasa Clark, MD, Carrie Marshall, MD, Bryan R. Haugen, MD, Devika Subramanian, PhD, Regeneron Genetics Center, Kristy Crooks, PhD, Christopher Gignoux, PhD, Trevor Cohen, MBChB, PhD, FACMI</p>
Genetic architecture and polygenic risk score prediction of degenerative suspensory ligament desmitis (DSLD) in the Peruvian Horse
<p class="MsoNormal"><strong>Introduction</strong>: Spontaneous rupture of tendons and ligaments is common in several species including humans. In horses, degenerative suspensory ligament desmitis (DSLD) is an important acquired idiopathic disease of a major energy-storing tendon-like structure. DSLD risk is increased in several breeds, including the Peruvian Horse. Affected horses have often been used for breeding before the disease is apparent. Breed predisposition suggests a substantial genetic contribution, but heritability and genetic architecture of DSLD have not been determined.</p> <p class="MsoNormal"><strong>Methods</strong>: To identify genomic regions associated with DSLD, we recruited a reference population of 183 Peruvian Horses, phenotyped as DSLD cases or controls, and undertook a genome-wide association study (GWAS), a regional window variance analysis using local genomic partitioning, a signatures of selection (SOS) analysis, and polygenic risk score (PRS) prediction of DSLD risk. We also estimated trait heritability from pedigrees.</p> <p class="MsoNormal"><strong>Results</strong>: Heritability was estimated in a population of 1,927 Peruvian horses at 0.22±0.08. After establishing a permutation-based threshold for genome-wide significance, 151 DSLD risk single nucleotide polymorphisms (SNPs) were identified by GWAS. Multiple regions of enriched local heritability were identified across the genome, with strong enrichment signals on chromosomes 1, 2, 6, 10, 13, 16, 18, 22, and the X chromosome. With SOS analysis, there were 66 genes with a selection signature in DSLD cases that was not present in the control group that included the <em>TGFB3</em> gene. Pathways enriched in DSLD cases included proteoglycan metabolism, extracellular matrix homeostasis, and signal transduction pathways that included the hedgehog signaling pathway. The best PRS predictive performance was obtained when we fitted 1% of top SNPs using a Bayesian Ridge Regression model which achieved the highest mean of R<sup>2</sup> on both the probit and logit liability scales, indicating a strong predictive performance.</p> <p><strong>Discussion</strong>: We conclude that within-breed GWAS of DSLD in the Peruvian Horse has further confirmed that moderate heritability and a polygenic architecture underlies the trait and identified multiple DSLD SNP associations in novel tendinopathy candidate genes influencing disease risk. Pathways enriched with DSLD risk variants include ones that influence glycosaminoglycan metabolism, extracellular matrix homeostasis, and signal transduction pathways.</p>
BioGraph Quality Score and Genotype Classifer Models
<p>BioGraph Quality Score and Genotype Classifer Models v7.1.0 for use with BioGraph software available at https://github.com/spiralgenetics/biograph</p>
Data from: Scoring thermal limits in small insects using open-source, computer assisted motion detection
<p>Scoring large amounts of thermal tolerance traits live or with recorded video can be time consuming and susceptible to investigator bias, and as with many physiological measurements, there can be trade-offs between accuracy and throughput. Recent studies show that particle tracking is a viable alternative to manually scoring videos, although it may not detect subtle movements, and many of the software options are proprietary and costly. In this study, we present a novel strategy for automated scoring of thermal tolerance videos by inferring motor activity with motion detection using an open-source Python command line application called DIME (Detector of Insect Motion Endpoint). We apply our strategy to both dynamic and static thermal tolerance assays, and our results indicate that DIME can accurately measure thermal acclimation responses, generally agrees with visual estimates of thermal limits, and can significantly increase the throughput over manual methods.</p>
Prediction of Individual Autism Diagnostic Observation Schedule (ADOS) scores based on neural responses during live eye-to-eye contact
<p>Social difficulties are impactful in autism spectrum disorder (ASD), and links between these difficulties and underlying neural processes are active research questions. We present a multivariate classification method for neural data acquired from 36 participants during a live eye-to-eye contact task. Participants were either typically developed (TD) or diagnosed as ASD through gold-standard Autism Diagnostic Observation Schedule (ADOS) evaluation. We hypothesized multivariate classification could discriminate TD vs. ASD based on neural responses. Support vector machine (SVM) classification was able to discriminate between groups during the eye-contact interaction. In addition, it was found that underlying neural patterns contributing to binary classification also predicted measured ADOS scores with high correlation even though ADOS scores were not used for training. The correlation between observed and predicted ADOS scores was 0.72 (p < 0.002) for eye-to-eye contact. These findings suggest neural responses to live eye-to-eye contact are predictive of social symptomatology in ASD.</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.