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8,038 results for “validation.”
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.
Data from: Towards the validation of endogenous steroid testing in wildlife hair
1. Hair is emerging as a popular tool to examine steroid hormone levels in wild mammals. The reliability of this approach, however, depends on an understanding of steroid hormone incorporation into hair as well as appropriate validations. 2. We reviewed studies that have examined steroid hormones in wildlife hair with the goal of summarizing the analytical, physiological, and biological evidence that this approach is meaningful. Accordingly, we differentiated among validations aimed at evaluating the reliability of the analytical method versus those designed to assess whether hormone levels in hair reflect physiologically meaningful processes in the target species. 3. Our literature survey revealed that endogenous steroids have been examined in hair from 42 species of non-human animals across 7 mammalian classes. Although the majority (85%) of 72 studies reported analytical validations of the method, physiological validations have only been reported for five species. Moreover, results of physiological validations were inconsistent among studies, highlighting the need for further research designed carefully to differentiate among the multiple purported models of steroid incorporation into hair in species with different types of hair and hair growth patterns. 4. To complement our review of published studies, we present new data supporting a positive relationship between levels of the steroid, cortisol, in hair and blood across eight mammalian species. In addition, we present novel results from a laboratory-based study showing variable hair growth in genetically identical laboratory mice that were kept under controlled conditions. 5. Synthesis and Applications: Collectively, this synthesis reveals substantial progress towards the validation of endocrine assays in hair from a variety of wildlife species. Further validations of other steroids, combined with appropriate physiological validations, would expand the potential applications of hair testing in wildlife research. As a key example, physiological data can provide mechanistic insight into species' responses to change and may therefore contribute to conservation planning.
Data from: An active-radio-frequency-identification system capable of identifying co-locations and social-structure: validation with a wild free-ranging animal
Behavioural events that are important for understanding sociobiology and movement ecology are often rare, transient and localised, but can occur at spatially distant sites e.g. territorial incursions and co-locating individuals. Existing animal tracking technologies, capable of detecting such events, are limited by one or more of: battery life; data resolution; location accuracy; data security; ability to co-locate individuals both spatially and temporally. Technology that at least partly resolves these limitations would be advantageous. European badgers (Meles meles L.), present a challenging test-bed, with extra-group paternity (apparent from genotyping) contradicting established views on rigid group territoriality with little social-group mixing. In a proof of concept study we assess the utility of a fully automated active-radio-frequency-identification (aRFID) system combining badger-borne aRFID-tags with static, wirelessly-networked, aRFID-detector base-stations to record badger co-locations at setts (burrows) and near notional border latrines. We summarise the time badgers spent co-locating within and between social-groups, applying network analysis to provide evidence of co-location based community structure, at both these scales. The aRFID system co-located animals within 31.5 m (adjustable) of base-stations. Efficient radio transmission between aRFIDs and base-stations enables a 20 g tag to last for 2–5 years (depending on transmission interval). Data security was high (data stored off tag), with remote access capability. Badgers spent most co-location time with members of their own social-groups at setts; remaining co-location time was divided evenly between intra- and inter-social-group co-locations near latrines and inter-social-group co-locations at setts. Network analysis showed that 20–100% of tracked badgers engaged in inter-social-group mixing per week, with evidence of trans-border super-groups, that is, badgers frequently transgressed notional territorial borders. aRFID occupies a distinct niche amongst established tracking technologies. We validated the utility of aRFID to identify co-locations, social-structure and inter-group mixing within a wild badger population, leading us to refute the conventional view that badgers (social-groups) are territorial and to question management strategies, for controlling bovine TB, based on this model. Ultimately aRFID proved a versatile system capable of identifying social-structure at the landscape scale, operating for years and suitable for use with a range of species.
Data from: Female assortative mate choice functionally validates synthesized male odors of evolving river-lake stickleback ecotypes
During mate choice decisions, females of many vertebrates use male olfactory cues to achieve immunogenetic optimality of their offspring. Three-spined sticklebacks (Gasterosteus aculeatus) populating habitats that differ in their parasite communities evolve locally adapted combinations of genetic variants encoded at the Major Histocompatibility Complex (MHC). Such adaptation confers optimal resistance to the local parasite fauna. Immunogenetic signatures co-evolved with local parasites favor population-specific assortative mate choice behaviour. Previous studies have shown that female sticklebacks evaluate male MHC-associated olfactory cues during the process of mate choice, but how habitat-specific information is exchanged between males and females has remained elusive. Here, we directly demonstrate the molecular nature of the olfactory cue providing habitat-specific information. Under controlled laboratory conditions females that are ready to mate prefer mixtures of synthetic MHC peptide ligands mimicking the optimal allele number of their original population. These results imply that female sticklebacks can determine the number of MHC alleles of their prospective mates, compare it to their own immunogenetic status, and, if optimal with respect to the immunogenetic complementarity, accept the male as mate. Our results suggest a potentially common mechanism of ecological speciation in vertebrates that is based on the olfactory assessment of habitat-specific immunogenetic diversity.
Data from: Development and validation of a score to detect paroxysmal atrial fibrillation after stroke
Objective: Prolonged monitoring times (72h) are recommended to detect paroxysmal atrial fibrillation (pAF) after ischemic stroke, but not yet clinical practice; therefore, an individual patient selection for prolonged ECG monitoring might increase the diagnostic yield of pAF in a resource-saving manner. Methods: We used individual patient data from three prospective studies (ntotal=1556) performing prolonged Holter ECG monitoring (at least 72h) and centralized data evaluation after TIA or stroke in patients with sinus rhythm. Based on the TRIPOD guideline, a clinical score was developed on one cohort, internally validated by bootstrapping and externally validated on two other studies. Results: pAF was detected in 77 (4.9%) of 1556 patients during 72h-Holter monitoring. After logistic regression analysis with variable selection, age and the qualifying stroke event (categorised as stroke severity with NIH-SS≤5 (OR 2.4 vs. TIA; 95%CI0.8-6.9,p=0.112) or stroke with NIH-SS>5 (OR 7.2 vs. TIA; 95%CI 2.4-21.8,p<0.001)) were found to be predictive for the detection of pAF within 72h-Holter monitoring and included in the final score (Age: 0.76 points/year, Stroke Severity NIH-SS≤5 = 9 points, NIH-SS>5 = 21 points; to Find AF, AS5F). The high risk group defined by AS5F is characterized by a predicted risk between 5.2% and 40.8% for detection of pAF with a number needed to screen of 3 for the highest observed AS5F points within the study population. Regarding the low number of outcomes before generalization of AS5F the results need replication. Conclusion: The AS5F score can select patients for prolonged ECG monitoring after ischemic stroke to detect pAF.
Data from: Field validation of radar systems for monitoring bird migration
1. Advances in information technology are increasing the use of radar as a tool to investigate and monitor bird migration movements. We set up a field campaign to compare and validate outputs from different radar systems. 2. Here we compare the pattern of nocturnal bird migration movements recorded by four different radar systems at a site in southern Sweden. Within the range of the weather radar (WR) Ängelholm, we operated a "BirdScan" (BS) dedicated bird radar, a standard marine radar (MR), and a tracking radar (TR). 3. The measures of nightly migration intensities, provided by three of the radars (WR, BS, MR), corresponded well with respect to the relative seasonal course of migration, while absolute migration intensity agreed reasonably only between WR and BS. Flight directions derived from WR, BS and TR corresponded very well, despite very different sample sizes. Estimated mean ground speeds differed among all four systems. The correspondence among systems was highest under clear sky conditions and at high altitudes. 4. Synthesis and applications. While different radar systems can provide useful information on nocturnal bird migration, they have distinct strengths and weaknesses, and all require supporting data to allow for species level inference. Weather radars continuously detect avian biomass flows across a wide altitude band, making them a useful tool for monitoring and predictive applications at regional to continental scales that do not rely on resolving individuals. BirdScan and marine radar's strengths are in local and low altitude applications, such as collision risks with man-made structures and airport safety, although marine radars should not be trusted for absolute intensities of movement. In quantifying flight behaviour of individuals, tracking radars are the most informative.
Data from: Compromised external validity: federally produced cannabis does not reflect legal markets
As the most widely used illicit drug worldwide, and as a source of numerous under-studied pharmacologically-active compounds, a precise understanding of variability in psychological and physiological effects of Cannabis varieties is essential. The National Institute on Drug Abuse (NIDA) is designated as the sole legal producer of Cannabis for use in US research studies. We sought to compare the chemical profiles of Cannabis varieties that are available to consumers in states that have state-legalized use versus what is available to researchers interested in studying the plant and its effects. Our results demonstrate that the federally-produced Cannabis has significantly less variety and lower concentrations of cannabinoids than are observed in state-legal U.S. dispensaries. Most dramatically, NIDA's varieties contain only 27% of the THC levels and as much as 11–23 times the Cannabinol (CBN) content compared to what is available in the state-legal markets. Research restricted to using the current range of federally-produced Cannabis thus may yield limited insights into the chemical, biological and pharmacological properties, and medical potential of material that is available in the state markets. Investigation is urgently needed on the full diversity of Cannabis chemotypes known to be available to the public.
Data from: Fluorescent sperm in a transparent worm: validation of a GFP marker to study sexual selection
Background: Sexual selection has initially been thought to occur exclusively at the precopulatory stage in terms of contests among males and female mate choice, but research over the last four decades revealed that it often continues after copulation through sperm competition and cryptic female choice. However, studying these postcopulatory processes remains challenging because they occur internally and therefore are often difficult to observe. In the transparent free-living flatworm Macrostomum lignano, a recently established transgenic line that expresses green fluorescent protein (GFP) in all cell types, including sperm, offers a unique opportunity to non-invasively visualise and quantify the sperm of a GFP-expressing donor inside the reproductive tract of wild-type recipients in vivo. We here test several aspects of the reproductive performance of the transgenic individuals and the accuracy of the techniques involved in assessing the GFP-expressing worms and their sperm. We then show the usefulness of these methods in a study on sperm displacement. Results: GFP-expressing worms do not differ from wild-type worms in terms of morphology, mating rate and reproductive success. In addition, we show that the GFP signal is reliably and unequivocally expressed by all GFP-expressing individuals observed under epifluorescence illumination. However, the intensity of the GFP signal emitted by sperm of GFP expressing donors can vary (which we show to be at least in part due to sperm ageing) and the GFP marker is inherited according to Mendel's laws in most, but not all, of the individuals. Nevertheless, we argue these two issues can be addressed with an appropriate experimental design. Finally, we demonstrate the value of the GFP-techniques by comparing the number of GFP-expressing sperm in a wild-type recipient before and after mating with a competing sperm donor, providing clear experimental evidence for sperm displacement in M. lignano. This result suggests that sperm donors can displace previously stored sperm and replace it with their own. Conclusion: The availability of the GFP-techniques in a transparent organism provide unique opportunities to visualise and quantify internal processes in the female reproductive tract after mating, which opens new avenues in the study of sexual selection.
Data from: Both trait-neutrality and filtering effects are validated by the vegetation patterns detected in the functional recovery of sand grasslands
Neutral theory of species assembly means that species assembly is governed by stochastic dispersal processes and fluctuations in established populations. An alternative theory suggests that assembly is strongly determined by functional trait filtering governed by abiotic and biotic filtering selecting species from the local species pool. To test these assumptions, in the current paper we analysed vegetation changes in the first 12 years of succession after heavy goose grazing on acidic sand. With trait-based analyses using permanent plots we addressed the following hypotheses: (i) High fluctuations in the trait values are typical in the first years; later a temporally divergent change in the trait patterns of sites with different vertical position became characteristic. (ii) In the functional diversity of regenerative and vegetative traits we expected different temporal patterns. We confirmed the first hypothesis, as in the first few years most traits displayed high fluctuations with no clear patterns. Our findings weakly supported the second hypothesis; while there were distinct patterns detected in the functional richness of traits, functional divergence and evenness displayed no clear distinctive patterns. We can conclude that both trait neutrality and filtering effects operate in the vegetation changes of the first period of secondary succession.
Data from: A draft fur seal genome provides insights into factors affecting SNP validation and how to mitigate them
Custom genotyping arrays provide a flexible and accurate means of genotyping single nucleotide polymorphisms (SNPs) in a large number of individuals of essentially any organism. However, validation rates, defined as the proportion of putative SNPs that are verified to be polymorphic in a population, are often very low. A number of potential causes of assay failure have been identified, but none have been explored systematically. In particular, as SNPs are often developed from transcriptomes, parameters relating to the genomic context are rarely taken into account. Here, we assembled a draft Antarctic fur seal (Arctocephalus gazella) genome (assembly size: 2.41Gb; scaffold/contig N50: 3.1Mb/27.5kb). We then used this resource to map the probe sequences of 144 putative SNPs genotyped in 480 individuals. The number of probe-to-genome mappings and alignment length together explained almost a third of the variation in validation success, indicating that sequence uniqueness and proximity to intron-exon boundaries play an important role. The same pattern was found after mapping the probe sequences to the Walrus and Weddell seal genomes, suggesting that the genomes of species divergent by as much as 23 million years can hold information relevant to SNP validation outcomes. Additionally, re-analysis of genotyping data from seven previous studies found the same two variables to be significantly associated with SNP validation success across a variety of taxa. Finally, our study reveals considerable scope for validation rates to be improved, either by simply filtering for SNPs whose flanking sequences align uniquely and completely to a reference genome, or through predictive modeling.
Supplemental figures and tables of a European multicenter validation study of the External Genitalia Score
<p><b>Context: </b>Standardized description of external genitalia is needed in the assessment of children with atypical genitalia.</p> <p><b>Objectives:<i> </i></b>To validate the External Genitalia Score (EGS), to present reference values for preterm and term babies up to 24 months and correlate obtained scores with anogenital distances (AGDs).</p> <p><b>Design, Setting: </b>A<b> </b>European multicentre (n=8) validation study was conducted from 07/2016 until 07/2018.</p> <p><b>Patients and Methods: </b>EGS is based on the external masculinization score but uses a gradual scale from female to male (range 0-12) and terminology appropriate for both sexes. The reliability of EGS and AGD's were determined by the interclass correlation coefficient (ICC). Cross-sectional data were obtained in 686 term (0-24 months), and 181 preterm babies and 111 babies with atypical genitalia.</p> <p><b>Results:<i> </i></b>ICC of EGS in typical and atypical genitalia is excellent and good. Median EGS (10<sup>th </sup>-<sup> </sup>90<sup>th </sup>centile) in males < 28 weeks gestation is 10 (8.6-11.5); in males 28-32 weeks 11.5 (9.2-12); in males 33-36 weeks 11.5 (10.5-12) and in full-term males 12 (10.5-12). In all female babies, EGS is 0 (0-0). The mean (SD) AGDl/u is 0.45 (0.1), with significant difference between AGDl/u in males 0.49 (0.1) and females 0.39 (0.1) and in-between values in DSD 0.43 (0.1). AGDl/u correlates with EGS in males with typical genitalia and in atypical genitalia.</p> <p><b>Conclusions: </b>EGS is a reliable and valid tool to describe external genitalia in premature and term babies up to 24 months. EGS correlates with AGDl/u in males. It facilitates standardized assessment, clinical decision-making and multicenter research.</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.