2,455 research outputs found

    Predicting deleterious nsSNPs: an analysis of sequence and structural attributes

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    BACKGROUND: There has been an explosion in the number of single nucleotide polymorphisms (SNPs) within public databases. In this study we focused on non-synonymous protein coding single nucleotide polymorphisms (nsSNPs), some associated with disease and others which are thought to be neutral. We describe the distribution of both types of nsSNPs using structural and sequence based features and assess the relative value of these attributes as predictors of function using machine learning methods. We also address the common problem of balance within machine learning methods and show the effect of imbalance on nsSNP function prediction. We show that nsSNP function prediction can be significantly improved by 100% undersampling of the majority class. The learnt rules were then applied to make predictions of function on all nsSNPs within Ensembl. RESULTS: The measure of prediction success is greatly affected by the level of imbalance in the training dataset. We found the balanced dataset that included all attributes produced the best prediction. The performance as measured by the Matthews correlation coefficient (MCC) varied between 0.49 and 0.25 depending on the imbalance. As previously observed, the degree of sequence conservation at the nsSNP position is the single most useful attribute. In addition to conservation, structural predictions made using a balanced dataset can be of value. CONCLUSION: The predictions for all nsSNPs within Ensembl, based on a balanced dataset using all attributes, are available as a DAS annotation. Instructions for adding the track to Ensembl are a

    Kolping house, shelter for mothers with children, to prevent social exclusion

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    Bakalářská práce - Kolpingův dům, azylový dům pro matky s dětmi, jako prevence sociálního vyloučení, pojednává o společenském jevu - o sociálním vyloučení. Zvláště o jeho příčinách a problémech, které se k tomu vztahují. Sociální vyloučení se týká i osamocených rodičů a tato práce se zaměřuje převážně na tuto skupinu. Následující část práce je o úloze státních organizacích, které sociálně vyloučené osoby podporují finančně a prostřednictvím sociálních služeb zaměřených na prevenci. Praktická část práce je věnována Kolpingovu domu - azylovému domu pro matky s dětmi, kterým hrozí riziko sociálního vyloučení. Představuji zde cíle organizace, podmínky pobytu v Kolpingově domě a pro koho je pobyt v Kolpingově domě prioritně určen. Práce obsahuje popis sociální práce v Kolpingově domě, především informace o službě pod názvem videotrénink interakcí, kasuistiku neboli příběh typické klientky, se kterou jsem delší dobu v kontaktu, rozhovor se sociální pracovnicí Kolpingova domu a dotazník zjišťující spokojenost a kvalitu poskytovaných sociálních služeb v Kolpingově domě. Součást práce je osm příloh, např. aktuální seznam azylových domů pro matky s dětmi v České republice, týdenní program Kolpingova domu a představení ostatních projektů Kolpingova díla. Powered by TCPDF (www.tcpdf.org)Bachelor's thesis - Kolping house, shelter for mothers with children, to prevent social exclusion, deals with the social phenomenon - social exclusion. Especially on the causes and issues that relate to this. Social exclusion also applies to lonely parents and this work focuses mainly on this group. The following is part of the work on the role of state organizations that promote socially excluded persons through financial and social services aimed at prevention. Practical work is given Kolping house - the house of asylum for mothers with children, who risk social exclusion. I present here the objectives of the organization, the conditions of stay in Kolping house and who is resident in the house Kolpingově primarily intended. The work contains a description of social work in Kolping house, especially information about the service under the name video interaction guidance, the story - case study of typical clients with I have a longer time in contact, interview with social worker Kolping house, questionnaire and providing satisfaction and quality of social services in Kolping house. Part of the work are eight annexes, such as the current list of shelters house for mothers with children in the Czech Republic, a weekly program Kolpingova house and other projects Kolping work. Powered by TCPDF (www.tcpdf.org)JabokJabokProtestant Theological FacultyEvangelická teologická fakult

    Knowledge graph prediction of unknown adverse drug reactions and validation in electronic health records

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    Abstract Unknown adverse reactions to drugs available on the market present a significant health risk and limit accurate judgement of the cost/benefit trade-off for medications. Machine learning has the potential to predict unknown adverse reactions from current knowledge. We constructed a knowledge graph containing four types of node: drugs, protein targets, indications and adverse reactions. Using this graph, we developed a machine learning algorithm based on a simple enrichment test and first demonstrated this method performs extremely well at classifying known causes of adverse reactions (AUC 0.92). A cross validation scheme in which 10% of drug-adverse reaction edges were systematically deleted per fold showed that the method correctly predicts 68% of the deleted edges on average. Next, a subset of adverse reactions that could be reliably detected in anonymised electronic health records from South London and Maudsley NHS Foundation Trust were used to validate predictions from the model that are not currently known in public databases. High-confidence predictions were validated in electronic records significantly more frequently than random models, and outperformed standard methods (logistic regression, decision trees and support vector machines). This approach has the potential to improve patient safety by predicting adverse reactions that were not observed during randomised trials

    Male-biased autosomal effect of 16p13.11 copy number variation in neurodevelopmental disorders.

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    Copy number variants (CNVs) at chromosome 16p13.11 have been associated with a range of neurodevelopmental disorders including autism, ADHD, intellectual disability and schizophrenia. Significant sex differences in prevalence, course and severity have been described for a number of these conditions but the biological and environmental factors underlying such sex-specific features remain unclear. We tested the burden and the possible sex-biased effect of CNVs at 16p13.11 in a sample of 10,397 individuals with a range of neurodevelopmental conditions, clinically referred for array comparative genomic hybridisation (aCGH); cases were compared with 11,277 controls. In order to identify candidate phenotype-associated genes, we performed an interval-based analysis and investigated the presence of ohnologs at 16p13.11; finally, we searched the DECIPHER database for previously identified 16p13.11 copy number variants. In the clinical referral series, we identified 46 cases with CNVs of variable size at 16p13.11, including 28 duplications and 18 deletions. Patients were referred for various phenotypes, including developmental delay, autism, speech delay, learning difficulties, behavioural problems, epilepsy, microcephaly and physical dysmorphisms. CNVs at 16p13.11 were also present in 17 controls. Association analysis revealed an excess of CNVs in cases compared with controls (OR = 2.59; p = 0.0005), and a sex-biased effect, with a significant enrichment of CNVs only in the male subgroup of cases (OR = 5.62; p = 0.0002), but not in females (OR = 1.19, p = 0.673). The same pattern of results was also observed in the DECIPHER sample. Interval-based analysis showed a significant enrichment of case CNVs containing interval II (OR = 2.59; p = 0.0005), located in the 0.83 Mb genomic region between 15.49-16.32 Mb, and encompassing the four ohnologs NDE1, MYH11, ABCC1 and ABCC6. Our data confirm that duplications and deletions at 16p13.11 represent incompletely penetrant pathogenic mutations that predispose to a range of neurodevelopmental disorders, and suggest a sex-limited effect on the penetrance of the pathological phenotypes at the 16p13.11 locus.South London and Maudsley Trust NIHR specialist Biomedical Research Centre Guys and St Thomas Trust NIHR comprehensive Biomedical Research Centre European Commission Seventh Framework project PsychCNVs info:eu-repo/grantAgreement/EC/FP7/223423 Wellcome Trust (Wellcome Trust Case control consortium; WTCCC2

    A model for permeability evolution during volcanic welding

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    Volcanic ash and pyroclasts can weld when deposited hot by pyroclastic density currents, in near-vent fall deposits, or in fractures in volcano interiors. Welding progressively decreases the permeability of the particle packs, influencing a range of magmatic and volcanic processes, including magma outgassing, which is an important control on eruption dynamics. Consequently, there is a need for a quantitative model for permeability evolution during welding of ash and pyroclasts under the range of conditions encountered in nature. Here we present in situ experiments in which hydrous, crystal-free, glassy pyroclasts are imaged via x-ray tomography during welding at high temperature. For each 3D dataset acquired, we determine the porosity, Darcian gas permeability, specific surface area, and pore connectivity. We find that all of these quantities decrease as a critical percolation threshold is approached. We develop a constitutive mathematical model for the evolution of permeability in welding volcanic systems based on percolation theory, and validate the model against our experimental data. Importantly, our model accounts for polydispersivity of the grainsize in the particle pack, the pressures acting on the pack, and changes in particle viscosity arising from degassing of dissolved H2O during welding. Our model is theoretically grounded and has no fitting parameters, hence it should be valid across all magma compositions. The model can be used to predict whether a cooling pyroclast pack will have sufficient time to weld and to degas, the scenarios under which a final deposit will retain a permeable network, the timescales over which sealing occurs, and whether a welded deposit will have disequilibrium or equilibrium H2O content. A user-friendly implementation of the model is provided

    EDIFY (Eating disorders: delineating illness and recovery trajectories to inform personalised prevention and early intervention in young people):Project outline

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    EDIFY (Eating Disorders: Delineating Illness and Recovery Trajectories to Inform Personalised Prevention and Early Intervention in Young People) is an ambitious research project aiming to revolutionise how eating disorders are perceived, prevented and treated. Six integrated workstreams will address key questions, including: What are young people's experiences of eating disorders and recovery? What are the unique and shared risk factors in different groups? What helps or hinders recovery? How do the brain and behaviour change from early- to later-stage illness? How can we intervene earlier, quicker and in a more personalised way? This 4-year project, involving over 1000 participants, integrates arts, design and humanities with advanced neurobiological, psychosocial and bioinformatics approaches. Young people with lived experience of eating disorders are at the heart of EDIFY, serving as advisors and co-producers throughout. Ultimately, this work will expand public and professional perceptions of eating disorders, uplift under-represented voices and stimulate much-needed advances in policy and practice

    UK phenomics platform for developing and validating electronic health record phenotypes: CALIBER

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    Objective: Electronic health records (EHRs) are a rich source of information on human diseases, but the information is variably structured, fragmented, curated using different coding systems, and collected for purposes other than medical research. We describe an approach for developing, validating, and sharing reproducible phenotypes from national structured EHR in the United Kingdom with applications for translational research. Materials and Methods: We implemented a rule-based phenotyping framework, with up to 6 approaches of validation. We applied our framework to a sample of 15 million individuals in a national EHR data source (population-based primary care, all ages) linked to hospitalization and death records in England. Data comprised continuous measurements (for example, blood pressure; medication information; coded diagnoses, symptoms, procedures, and referrals), recorded using 5 controlled clinical terminologies: (1) read (primary care, subset of SNOMED-CT [Systematized Nomenclature of Medicine Clinical Terms]), (2) International Classification of Diseases–Ninth Revision and Tenth Revision (secondary care diagnoses and cause of mortality), (3) Office of Population Censuses and Surveys Classification of Surgical Operations and Procedures, Fourth Revision (hospital surgical procedures), and (4) DMþD prescription codes. Results: Using the CALIBER phenotyping framework, we created algorithms for 51 diseases, syndromes, biomarkers, and lifestyle risk factors and provide up to 6 validation approaches. The EHR phenotypes are curated in the open-access CALIBER Portal (https://www.caliberresearch.org/portal) and have been used by 40 national and international research groups in 60 peer-reviewed publications. Conclusions: We describe a UK EHR phenomics approach within the CALIBER EHR data platform with initial evidence of validity and use, as an important step toward international use of UK EHR data for health research

    Modelling Transmission of Vector-Borne Pathogens Shows Complex Dynamics When Vector Feeding Sites Are Limited

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    The relationship between species richness and the prevalence of vector-borne disease has been widely studied with a range of outcomes. Increasing the number of host species for a pathogen may decrease infection prevalence (dilution effect), increase it (amplification), or have no effect. We derive a general model, and a specific implementation, which show that when the number of vector feeding sites on each host is limiting, the effects on pathogen dynamics of host population size are more complex than previously thought. The model examines vector-borne disease in the presence of different host species that are either competent or incompetent (i.e. that cannot transmit the pathogen to vectors) as reservoirs for the pathogen. With a single host species present, the basic reproduction ratio R0 is a non-monotonic function of the population size of host individuals (H), i.e. a value exists that maximises R0. Surprisingly, if a reduction in host population size may actually increase R0. Extending this model to a two-host species system, incompetent individuals from the second host species can alter the value of which may reverse the effect on pathogen prevalence of host population reduction. We argue that when vector-feeding sites on hosts are limiting, the net effect of increasing host diversity might not be correctly predicted using simple frequency-dependent epidemiological models

    Automatic assessment of the 2-minute walk distance for remote monitoring of people with multiple sclerosis

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    The aim of this study was to investigate the feasibility of automatically assessing the 2-Minute Walk Distance (2MWD) for monitoring people with multiple sclerosis (pwMS). For 154 pwMS, MS-related clinical outcomes as well as the 2MWDs as evaluated by clinicians and derived from accelerometer data were collected from a total of 323 periodic clinical visits. Accelerometer data from a wearable device during 100 home-based 2MWD assessments were also acquired. The error in estimating the 2MWD was validated for walk tests performed at hospital, and then the correlation (r) between clinical outcomes and home-based 2MWD assessments was evaluated. Robust performance in estimating the 2MWD from the wearable device was obtained, yielding an error of less than 10% in about two-thirds of clinical visits. Correlation analysis showed that there is a strong association between the actual and the estimated 2MWD obtained either at hospital (r = 0.71) or at home (r = 0.58). Furthermore, the estimated 2MWD exhibits moderate-to-strong correlation with various MS-related clinical outcomes, including disability and fatigue severity scores. Automatic assessment of the 2MWD in pwMS is feasible with the usage of a consumer-friendly wearable device in clinical and non-clinical settings. Wearable devices can also enhance the assessment of MS-related clinical outcomes
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