18,674 research outputs found

    A cancer cell-line titration series for evaluating somatic classification.

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    BackgroundAccurate detection of somatic single nucleotide variants and small insertions and deletions from DNA sequencing experiments of tumour-normal pairs is a challenging task. Tumour samples are often contaminated with normal cells confounding the available evidence for the somatic variants. Furthermore, tumours are heterogeneous so sub-clonal variants are observed at reduced allele frequencies. We present here a cell-line titration series dataset that can be used to evaluate somatic variant calling pipelines with the goal of reliably calling true somatic mutations at low allele frequencies.ResultsCell-line DNA was mixed with matched normal DNA at 8 different ratios to generate samples with known tumour cellularities, and exome sequenced on Illumina HiSeq to depths of >300×. The data was processed with several different variant calling pipelines and verification experiments were performed to assay >1500 somatic variant candidates using Ion Torrent PGM as an orthogonal technology. By examining the variants called at varying cellularities and depths of coverage, we show that the best performing pipelines are able to maintain a high level of precision at any cellularity. In addition, we estimate the number of true somatic variants undetected as cellularity and coverage decrease.ConclusionsOur cell-line titration series dataset, along with the associated verification results, was effective for this evaluation and will serve as a valuable dataset for future somatic calling algorithm development. The data is available for further analysis at the European Genome-phenome Archive under accession number EGAS00001001016. Data access requires registration through the International Cancer Genome Consortium's Data Access Compliance Office (ICGC DACO)

    Resting-state abnormalities in amnestic mild cognitive impairment: a meta-analysis

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    Moderating Effects of Cortisol on Neural-Cognitive Association in Cognitively Normal Elderly Subjects

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    PHP12 THE PUBLIC'S PREFERENCE ON THE PRIORITIES IN HEALTH CARE

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    The use of nutritional guidance within chiropractic patient management: A survey of 333 chiropractors from the ACORN practice-based research network

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    © 2018 The Author(s). Background: Food consumption and nutritional status affect an individual's health throughout their life-course and an unhealthy diet is a major risk factor for the current global burden of chronic disease. The promotion of health and good nutrition through healthy eating requires the active involvement of all health professionals including chiropractors. This paper reports findings from the first nationally representative examination of the use of nutritional guidance within chiropractic patient management in Australia. Methods: A sample of 1000 practising chiropractors was randomly selected from the Australian Chiropractic Research Network (ACORN) practice-based research network database for a cross-sectional study and 33% participated in the online survey in November 2016. The questionnaire, based on previous designs used in similar surveys and nutrition resources developed by the National Health and Medical Research Council, was pretested prior to the survey. Pearson's Chi square and bivariate logistic regression were undertaken to explore relationships with variables of interest. Results: The demographic details of the respondents are similar to those of the chiropractic workforce registered in Australia. Most chiropractors provided nutritional advice as part of their patient care and around a quarter provided specific dietary advice to their patients, including the use of nutrition supplements. Nutrition-related conditions most commonly encountered by the chiropractors were musculoskeletal, usually inflammatory in origin. Common nutritional assessment methods used included questioning patients to assess their nutritional and health status and physical appearance. Most of the participants provided nutritional resources to their patients in their clinics. However, the Australian Dietary Guidelines and the accompanying Australian Guide to Healthy Eating were not well utilised by the respondents. Australian chiropractors often referred patients with nutrition issues to qualified dietitians and other health professionals when deemed necessary. Conclusions: Australian chiropractors regularly provide nutritional advice and appear to acknowledge the importance of nutrition in their clinical practice especially for patients presenting with chronic disease. If chiropractors are to fulfil their potential in providing such wider public health and preventative health advice to patients, further research examining the utilisation of evidence-based nutrition resources within chiropractic patient management is recommended

    Behaviour of engineered cementitious composite-encased stub concrete columns under axial compression

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    Although high-strength concrete (HSC) has higher compressive strength than normal-strength concrete (NSC), its application in column construction is often limited by its brittleness and limited post-peak ductility. In this preliminary study, hybrid fibre engineered cementitious composite (ECC) is proposed as a potential encasement material to confine the HSC core and to increase the column's ductility. The behaviours of the proposed ECC-encased concrete stub column under axial compression are studied experimentally. Thirty stub columns, including six NSC/HSC, six ECC and 18 ECC-encased NSC/HSC (ECC-NSC/HSC) are tested under axial compression. The effects of ECC strength, ECC encasement thickness, concrete strength and cross-section shapes (circular, square and rectangular) are then investigated and reported in terms of failure modes, strength ratios, post-peak ductility and energy dissipation capacity of the stub columns. It is found that, when comparing with NSC/HSC stub columns, although no significant improvement in the ultimate strength was observed, the ECC encasement improved the performance of ECC-NSC/HSC stub columns by reducing brittleness and improving the post-peak behaviour during failure
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