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7,518 results for “screenings”
Screening the Sigma LOPAC®1280 library of compounds for protective effects against cisplatin-induced oto- and nephrotoxicity
<p>Dose-limiting toxicities for cisplatin administration, including ototoxicity and nephrotoxicity, impact the clinical utility of this effective chemotherapy agent and lead to lifelong complications, particularly in pediatric cancer survivors. Using a two-pronged drug screen employing the zebrafish lateral line as an <i>in vivo</i> readout for ototoxicity and kidney cell-based nephrotoxicity assay, we screened 1280 compounds and identified 22 that were both oto- and nephroprotective. Of these, dopamine and L-mimosine, a plant-based amino acid active in the dopamine pathway, were further investigated. Dopamine and L-mimosine protected the hair cells in the zebrafish otic vesicle from cisplatin-induced damage and preserved zebrafish larval glomerular filtration. Importantly, these compounds did not abrogate the cytotoxic effects of cisplatin on human cancer cells. This study provides insights into the mechanisms underlying cisplatin-induced oto- and nephrotoxicity and compelling preclinical evidence for the potential utility of dopamine and L-mimosine in the safer administration of cisplatin.</p>
Screening for functional transcriptional and splicing regulatory variants with GenIE
<p>Here we provide data used in the analysis for our paper introducing the GenIE method (Genome engineering-based Interrogation of Enhancers).</p> <p><strong>Abstract</strong></p> <p>Genome-wide association studies (GWAS) have identified numerous genetic loci underlying human diseases, but a fundamental challenge remains to accurately identify the underlying causal genes and variants. Here we describe an arrayed CRISPR screening method, Genome engineering-based Interrogation of Enhancers (GenIE), which assesses the effects of defined alleles on transcription or splicing when introduced in their endogenous genomic location. We use this sensitive assay to validate the activity of transcriptional enhancers and splice regulatory elements in human induced pluripotent stem cells (hiPSCs), and develop a software package (rgenie) to analyse the data. We screen the 99% credible set of Alzheimer’s disease (AD) GWAS variants identified at the clusterin (CLU) locus to identify a subset of likely causal variants, and employ GenIE to understand the impact of specific mutations on splicing efficiency. We thus establish GenIE as an efficient tool to rapidly screen for the role of transcribed variants on gene expression.</p>
Data from: Brief in-hospital cognitive screening detects dementia and anticipates complex admissions
<p><strong>Objective</strong>: With the goal of improving community health by screening for dementia, we tested the utility of integrating the Six-Item Screener (SIS) into our emergency room neurology consultations.</p> <p><strong>Methods</strong>: In this cross-sectional observational study, we measured SIS performance within 24 hours of hospital arrival in one hundred consecutive English-speaking patients aged ≥ 45 years. Performance was compared to patient age, previously-charted cognitive impairment, and proxies for in-hospital complexity: whether or not a patient was admitted to the hospital and the number of medical studies ordered.</p> <p><strong>Results</strong>: Those with poor SIS performance were older (<em>p</em> = 0.02), more likely to have previously-charted cognitive impairment (<em>p</em> < 0.01; sensitivity 86%, specificity 77%). Poor performers were more likely to be admitted to the hospital (<em>p</em> = 0.04; odds ratio = 3.6) and were subjected to more tests once admitted (<em>p</em> < 0.01). These findings persisted after accounting for age and history of cognitive impairment.</p> <p><strong>Conclusions</strong>: Poor performance on the SIS was associated with previously charted cognitive impairment, justifying future study of its ability to detect unrecognized dementia cases. Until then, its ability to inexpensively anticipate medically complex hospital admissions motivates broader emergency department use of the SIS.</p>
Comparing three screen-based sedentary behaviours' effect upon adolescents' participation in physical activity: The ESSENS study
<p class="Arthurstyle1">Background: Literature focusing on the association between sedentary behaviours and physical activity has provided equivocal results and has been dominated by TV viewing as the indicator of sedentary behaviour. There is a need for more studies exploring the association between contemporary screen activities and physical activity among youth.</p> <p class="Arthurstyle1">Methods: A cross-sectional study including 742 adolescents was conducted in 2016. Data were collected at school through an online questionnaire. Regression analyses were used to explore the association between different screen-based sedentary behaviours and participation in physical activity.</p> <p class="Arthurstyle1">Results: The results showed that those with lower (vs higher) time spent on TV/movie streaming and electronic game playing both on weekdays and weekend days had significantly higher odds of participating in physical activity. There were no significant associations between socializing/surfing online both on weekdays and weekend days and physical activity in adjusted models.</p> <p class="Arthurstyle1">Conclusions: TV/movie streaming and electronic game playing during both weekdays and weekend days were significantly inversely related with participating in physical activity. Initiatives aimed at reducing screen-based sedentary activities might result in favourable effects on physical activity levels among adolescents.</p>
Screening and microsatellite data for Varroa infesting resistant honey bee pupae
<p>We investigated how the evolution of host resistance could affect the infesting population of Varroa mites. We screened a Varroa-resistant honey bee population near Toulouse, France, for a Varroa resistance trait: the inhibition of Varroa's reproduction in drone pupae. We then genotyped Varroa which had co-infested a cell using microsatellites. Across all resistant honey bee colonies, Varroa's reproductive success was significantly higher in co-infested cells but the distribution of Varroa between singly and multiply infested cells was not different from random. While there was a trend for increased reproductive success when Varroa of differing haplotypes co-infested a cell, this was not significant. This dataset may be useful to anybody interested in the evolution of host-resistance on the parasitic mite Varroa destructor. There were no legal or ethical considerations associated with this study.</p>
Virtual screening for functional foods against the main protease of 2019 novel coronavirus
<p>Design and development of an effective method or technologyto combat the 2019 novel coronavirus remains a challenge. In this work, the special attention was paid on the interaction between functional foods and the main protease of 2019-nCoV. Here, 10870 ligands were employed and screened by the molecular docking, which involved 12 kinds of functional foods (carbohydrates, fat acids, phospholipids, vitamin, β-sitosterol, flavonoids, nordihydroguaiaretic acid, curcumin, nookatone, β-pinene, tincturoid, and their isomers/analogs/derivatives). Then, 60 ligands were obtained with the good docking affinity. Most of them belong to quercetin and its isomers/analogs/derivatives, which also showed the highest affinity for the main protease of 2019-nCoV. The dynamic simulation indicated that quercetin-protease and quercetin-analog-protease showed the excellent stability. Thus, quercetin may be the best candidate to prevent or inhibit the main protease of 2019-nCoV. Considering the green and white tea are rich in quercetin and its isomers/analogs/derivatives, tea and relative beverages may become a good option to regulate our metabolism and help us to overcome this special time.</p>
Data from: Cost effectiveness of the New Zealand diabetes in pregnancy guideline screening recommendations
Objective: To compare the cost-effectiveness of 2 possible screening strategies for gestational diabetes mellitus (GDM) from the perspective of the New Zealand health system, developed as part of a gestational diabetes guideline. Design: A decision analytic model was built comparing 2-step screening (glycated haemoglobin (HbA1c) test at first booking and a 2 h 75 g oral glucose tolerance test (OGTT) as a single test at 24–28 weeks) with 3-step screening (HbA1c test at first booking and a 1 h glucose challenge test (GCT) followed by a 2 h 75 g OGTT when indicated from 24–28 weeks) using a 9-month time horizon. Setting: A hypothetical cohort of 62 000 pregnant women in New Zealand. Methods: Probabilities, costs and benefits were derived from the literature, and supplementary data was obtained from National Women's Annual Clinical Reports. Main outcome measures, screening and treatment costs (NZ$2013) and effect on health outcomes (incidence of complications). Results: The total cost for both strategies under baseline assumptions shows that the 2-step screening strategy would cost NZ$1.38 m more than the 3-step screening strategy overall. The additional cost per case detected was NZ$12 460 per case. The model found that the 2-step screening strategy identifies 12 more women with diabetes and 111 more women with GDM when compared against the 3-step screening strategy. We assessed the effect of changing the sensitivity and specificity of the OGTT. The baseline model assumed that the 2 h 75 g OGTT has a sensitivity and specificity of 95%. The 2-step strategy becomes more cost-effective when the diagnostic accuracy measures are improved. Conclusions: Adopting a 2-step strategy would moderately increase the number of GDM cases detected at the same time as moderately increasing the number of women with false negatives at a significant cost to the health system. Further evidence on the benefits of the 2 different approaches would be welcome.
Parallel CRISPR-Cas9 screens clarify impacts of p53 on screen performance
<p>CRISPR-Cas9 genome engineering has revolutionised high-throughput functional genomic screens. However, recent work has raised concerns regarding the performance of CRISPR-Cas9 screens using <i>TP53</i> wild-type human cells due to a p53-mediated DNA damage response (DDR) limiting the efficiency of generating viable edited cells. To directly assess the impact of cellular p53 status on CRISPR-Cas9 screen performance, we carried out parallel CRISPR-Cas9 screens in wild-type and <i>TP53</i> knockout human retinal pigment epithelial cells using a focused dual guide RNA library targeting 852 DDR-associated genes. Our work demonstrates that although functional p53 status negatively affects identification of significantly depleted genes, optimal screen design can nevertheless enable robust screen performance. Through analysis of our own and published screen data, we highlight key factors for successful screens in both wild-type and p53-deficient cells.</p>
Data from: Exploitation of a turbot (Scophthalmus maximus L.) immune-related expressed sequence tag (EST) database for microsatellite screening and validation
In this study, we identified and characterized 160 microsatellite loci from an expressed sequence tag (EST) database generated from immune-related organs of turbot (Scophthalmus maximus). A final set of 83 new polymorphic microsatellites were validated after the analysis of 40 individuals from Atlantic origin including both wild and farmed individuals. The allele number and the expected heterozygosity ranged from 2 to 18 and from 0.021 to 0.951, respectively. Evidences of null alleles at moderate-high frequencies were detected at six loci using population data. None of the analyzed loci showed deviations from Mendelian segregation after analysis of five full-sib families including ~92 individuals/family. The markers are used to consolidate the turbot genetic map and, since they are mostly EST-derived, they will be very useful for comparative genomic studies within flatfishes and with model fish species. Using an in silico approach, we detected significant homologies of microsatellite sequences with the EST databases of the flatfish species with highest genomic resources (Senegalese sole, Atlantic halibut, bastard halibut) at 31% of these turbot markers. The conservation of these microsatellites within Pleuronectiformes will pave the way for anchoring genetic maps of different species and identifying genomic regions related to productive traits.
Data from: Development of a genotype-by-sequencing immunogenetic assay as exemplified by screening for variation in red fox with and without endemic rabies exposure
Pathogens are recognized as major drivers of local adaptation in wildlife systems. By determining which gene variants are favored in local interactions among populations with and without disease, spatially explicit adaptive responses to pathogens can be elucidated. Much of our current understanding of host responses to disease comes from a small number of genes associated with an immune response. High-throughput sequencing (HTS) technologies, such as genotype-by-sequencing (GBS), facilitate expanded explorations of genomic variation among populations. Hybridization-based GBS techniques can be leveraged in systems not well characterized for specific variants associated with disease outcome to "capture" specific genes and regulatory regions known to influence expression and disease outcome. We developed a multiplexed, sequence capture assay for red foxes to simultaneously assess ~300-kbp of genomic sequence from 116 adaptive, intrinsic, and innate immunity genes of predicted adaptive significance and their putative upstream regulatory regions along with 23 neutral microsatellite regions to control for demographic effects. The assay was applied to 45 fox DNA samples from Alaska, where three arctic rabies strains are geographically restricted and endemic to coastal tundra regions, yet absent from the boreal interior. The assay provided 61.5% on-target enrichment with relatively even sequence coverage across all targeted loci and samples (mean = 50×), which allowed us to elucidate genetic variation across introns, exons, and potential regulatory regions (4,819 SNPs). Challenges remained in accurately describing microsatellite variation using this technique; however, longer-read HTS technologies should overcome these issues. We used these data to conduct preliminary analyses and detected genetic structure in a subset of red fox immune-related genes between regions with and without endemic arctic rabies. This assay provides a template to assess immunogenetic variation in wildlife disease systems.
Data from: Screening of duplicated loci reveals hidden divergence patterns in a complex salmonid genome
A whole-genome duplication (WGD) doubles the entire genomic content of a species and is thought to have catalysed adaptive radiation in some polyploid-origin lineages. However, little is known about general consequences of a WGD because gene duplicates (i.e., paralogs) are commonly filtered in genomic studies; such filtering may remove substantial portions of the genome in data sets from polyploid-origin species. We demonstrate a new method that enables genome-wide scans for signatures of selection at both nonduplicated and duplicated loci by taking locus-specific copy number into account. We apply this method to RAD sequence data from different ecotypes of a polyploid-origin salmonid (Oncorhynchus nerka) and reveal signatures of divergent selection that would have been missed if duplicated loci were filtered. We also find conserved signatures of elevated divergence at pairs of homeologous chromosomes with residual tetrasomic inheritance, suggesting that joint evolution of some nondiverged gene duplicates may affect the adaptive potential of these genes. These findings illustrate that including duplicated loci in genomic analyses enables novel insights into the evolutionary consequences of WGDs and local segmental gene duplications.
Data from: Screening primary-care patients forgoing health care for economic reasons
Background: Growing social inequities have made it important for general practitioners to verify if patients can afford treatment and procedures. Incorporating social conditions into clinical decision-making allows general practitioners to address mismatches between patients' health-care needs and financial resources. Objectives: Identify a screening question to, indirectly, rule out patients' social risk of forgoing health care for economic reasons, and estimate prevalence of forgoing health care and the influence of physicians' attitudes toward deprivation. Design: Multicenter cross-sectional survey. Participants: Forty-seven general practitioners working in the French–speaking part of Switzerland enrolled a random sample of patients attending their private practices. Main Measures: Patients who had forgone health care were defined as those reporting a household member (including themselves) having forgone treatment for economic reasons during the previous 12 months, through a self-administered questionnaire. Patients were also asked about education and income levels, self-perceived social position, and deprivation levels. Key Results: Overall, 2,026 patients were included in the analysis; 10.7% (CI95% 9.4-12.1) reported a member of their household to have forgone health care during the 12 previous months. The question "Did you have difficulties paying your household bills during the last 12 months" performed better in identifying patients at risk of forgoing health care than a combination of four objective measures of socio-economic status (gender, age, education level, and income) (R2=0.184 vs. 0.083). This question effectively ruled out that patients had forgone health care, with a negative predictive value of 96%. Furthermore, for physicians who felt powerless in the face of deprivation, we observed an increase in the odds of patients forgoing health care of 1.5 times. Conclusion: General practitioners should systematically evaluate the socio-economic status of their patients. Asking patients whether they experience any difficulties in paying their bills is an effective means of identifying patients who might forgo health care.
Data from: Systematic review on barriers and enablers for access to diabetic retinopathy screening services in different income settings
Background: Diabetic retinopathy (DR) can lead to visual impairment and blindness if not detected and treated in time. Knowing the barriers/enablers in advance in contrasting different country income settings may accelerate development of a successful DR screening (DRS) program. This would be especially applicable in the low-income settings with the rising prevalence of DR. Objectives: The aim of this systematic review is to identify and contrast the barriers/enablers to DRS for different contexts using both consumers i.e., people with diabetes (PwDM) and provider perspectives and system level factors in different country income settings. Methods: We searched MEDLINE, Embase, CENTRAL in the Cochrane Library from the databases start date to December 2018. We included the studies reported on barriers and enablers to access DRS services based at health care facilities. We categorised and synthesized themes related to the consumers (individuals), providers and the health systems (environment) as main dimensions according to the constructs of social cognitive theory, supported by the quantitative measures i.e., odds ratios as reported by each of the study authors. Main Results: We included 77 studies primarily describing the barriers and enablers. Most of the studies were from high income settings (72.7%, 56/77) and cross sectional in design (76.6%, 59/77). From the perspectives of consumers, lack of knowledge, attitude, awareness and motivation were identified as major barriers. The enablers were fear of blindness, proximity of screening facility, experiences of vision loss and being concerned of eye complications. In providers' perspectives, lack of skilled human resources, training programs, infrastructure of retinal imaging and cost of services were the main barriers. Higher odds of uptake of DRS services was observed when PwDM were provided health education (odds ratio (OR) 4.3) and having knowledge on DR (OR range 1.3-19.7). Conclusion: Knowing the barriers to access DRS is a pre-requisite in development of a successful screening program. The awareness, knowledge and attitude of the consumers, availability of skilled human resources and infrastructure emerged as the major barriers to access to DRS in any income setting.
Assessing the feasibility of a rapid, high-volume cervical cancer screening program using HPV self-sampling and digital colposcopy in rural regions of Yunnan, China
<p>Objective: Implementation of a novel, rapid, high-volume, see-and-treat cervical cancer screening program utilizing self-swab HPV testing and digital colposcopy in underserved regions of Yunnan China.</p> <p>Design: 500-1000 women per day self-swabbed for high-risk HPV (hrHPV+). Four careHPVTM machines (Qiagen) were run simultaneously to test the specimens. All hrHPV+ patients were contacted the same day and digital colposcopy (DC) was performed with the EVA system (MobileODT). Digital images were obtained, and all suspected lesions were biopsied and then treated.</p> <p>Setting: Rural and underserved areas of the Yunnan province, Kunming municipality.</p> <p>Participants: 3600 women, mean age 50.2 years, who had never been screened for cervical cancer. The women were of the Yi, Hui, Dai, and Han ethnicities.</p> <p>Interventions: Cryotherapy was performed on all lesions suspicious for CIN1 and LEEP was performed on all lesions suspicious CIN2+. ECC was performed if the transformation zone was not fully visualized.</p> <p>Results: 216 women (6%) were hrHPV+. 168 underwent same-day colposcopy (23 CIN1, 17 CIN2+). DC was able to identify 15 of 16 (93.8%) CIN2+ lesions.</p> <p>Conclusions: Currently, China does not have national screening guidelines or services for cervical cancer. Only 20.7% of Chinese women reported having ever been screened.</p> <p>This study illustrates a cost- effective, rapid and practical strategy that can be used to screen-and-treat 400+ million Chinese women for cervical cancer. First, HPV self-sampling allows large numbers of women to be screened rapidly and inexpensively and only +hrHPV women require further evaluation. Digital colposcopy is then performed on +hrHPV women with a portable digital colposcope. The high-resolution images obtained during DC then facilitates appropriate same-day treatment as they are able to accurately distinguish between CIN1 and CIN2+ lesions. Additionally, DC adds little to the time and cost of screening and produces permanent images that can be used for documentation, quality control, and expert consultation via a secure cloud-based portal.</p>
Setaria viridis images used in the paper entitled "Led Color Gradient As A New Screening Tool For Rapid Phenotyping Of Plant Responses To Light Quality" by Pierre LEJEUNE et al.
<p><em>Setaria viridis</em> images used in the paper entitled "Led Color Gradient As A New Screening Tool For Rapid Phenotyping Of Plant Responses To Light Quality" by Pierre LEJEUNE, Anthony FRATAMICO, Frédéric BOUCHÉ, Samuel HUERGA-FERNÁNDEZ, Pierre TOCQUIN, Claire PÉRILLEUX</p>
Results of preliminary screening tests for all participants (ACI experiment)
<p>Participants' gender, ages, handedness. Results of Raven's test, Reading test, Memory span test, ANT test, and audiogram</p>
PanDDA analysis of JMJD2D screened against Zenobia Fragment Library
<p>De-methylase JMJD2D screened against the Zenobia Fragment Library by X-ray Crystallography.</p>
PanDDA analysis of BAZ2B screened against Zenobia Fragment Library
<p>Bromodomain BAZ2B screened against the Zenobia Fragment Library by X-ray Crystallography.</p>
Video Figure: Intelligent Agents and Networked Buttons Improve Free-Improvised Ensemble Music-Making on Touch-Screens
<p>This video figure is an overview of our study comparing two designs for network communications between touch-screen musical instruments played in free-improvised ensemble performances.</p> <p>The video shows an overview of the touch-screen app (PhaseRings) used in the study and each of the interface conditions.</p> <p>The abstract of the paper relating to this figure is as follows:</p> <p>We present the results of two controlled studies of free-improvised ensemble music-making on touch-screens. In our system, updates to an interface of harmonically-selected pitches are broadcast to every touch-screen in response to either a performer pressing a GUI button, or to interventions from an intelligent agent. In our first study, analysis of survey results and performance data indicated significant effects of the button on performer preference, but of the agent on performance length. In the second follow-up study, a mixed-initiative interface, where the presence of the button was interlaced with agent interventions, was developed to leverage both approaches. Comparison of this mixed-initiative interface with the always-on button-plus-agent condition of the first study demonstrated significant preferences for the former. The different approaches were found to shape the creative interactions that take place. Overall, this research offers evidence that an intelligent agent and a networked GUI both improve aspects of improvised ensemble music-making.</p>
Supplemental Data for "Modeled Fetal Risk of Genetic Diseases Identified by Expanded Carrier Screening"
<p>Data file accompanying: Haque IS, Lazarin GA, Kang HP, Evans EA, Goldberg JD, Wapner RJ. Modeled Fetal Risk of Genetic Diseases Identified by Expanded Carrier Screening. <em>JAMA. </em>2016;316(7):734-742. doi:10.1001/jama.2016.11139</p> <p>(SRC = self-reported racial/ethnic category; TG = targeted genotyping; NGS = next-generation sequencing)</p> <p>Data file includes:</p> <ul> <li><strong>Couple Data: </strong>Number of self-identified reproductive couples, separated by tandem or sequential screening status and by (mother SRC, father SRC)</li> <li><strong>Disease Severity</strong>: List of all diseases tested with severity rating as used in the manuscript.</li> <li><strong>Allele Data</strong>: Listing of all alleles considered pathogenic in manuscript's data analysis, with number of observations and number of tested chromosomes in each SRC.</li> <li><strong>Chromosome Frequencies</strong>: for each disease in each SRC: <ul> <li>Effective total chromosome count (effective sample size after integrating TG and NGS-only alleles).</li> <li>Beta posterior a,b: parameters a, b for the best-fit beta distribution approximating the probability that a random chromosome in this SRC carries a pathogenic allele (integrating both TG and NGS alleles).</li> <li># Chromosomes total/positive for TG alleles</li> <li># Chromosomes total/positive for NGS alleles</li> <li># Chromosomes total/positive for individuals tested by TG</li> <li># Chromosomes total/positive for individuals tested by NGS</li> </ul> </li> <li><strong>Disease Risks</strong>: for each disease in each pairing of SRCs <ul> <li>Father/Mother computed carrier frequency: probability that a random individual from father/mother's SRC is a carrier for the given disease</li> <li>Computed risk of affected conceptus (mean, 2.5, 97.5 percentiles): mean and CI of the posterior distribution over the probability that a random conceptus arising from the racial/ethnic pairing indicated would be homozygous or compound heterozygous for pathogenic alleles for the indicated disease.</li> <li>Computed carrier couple frequency: probability that a random couple from the given SRCs would be a carrier couple for the indicated disease (ie, that both members of the couple would be carriers for the indicated disease)</li> <li>Total couples: number of tandemly-tested couples of the indicated SRC pairing who both had the "routine carrier testing" indication for testing and were both tested for the given disease</li> <li>Number of carrier couple: from the set of "Total couples", the number of couples in which both members were carriers for the indicated disease</li> <li>Number of carrier couples expected: based on computed carrier couple frequency and number of tested couples, the expected number of carrier couples under the model described in sections 4.3.2 and 4.4 of the supplement.</li> <li>P-value: probability that the number of observed carrier couples or a more extreme count would have occurred by chance, given the posterior distribution over carrier couple counts (see section 4.4 of the supplement). One-tailed p-value.</li> </ul> </li> </ul>
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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.