1,107 research outputs found

    INTEGRATE-Neo: A pipeline for personalized gene fusion neoantigen discovery

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    Abstract Motivation While high-throughput sequencing (HTS) has been used successfully to discover tumor-specific mutant peptides (neoantigens) from somatic missense mutations, the field currently lacks a method for identifying which gene fusions may generate neoantigens. Results We demonstrate the application of our gene fusion neoantigen discovery pipeline, called INTEGRATE-Neo, by identifying gene fusions in prostate cancers that may produce neoantigens. Availability and Implementation INTEGRATE-Neo is implemented in C ++ and Python. Full source code and installation instructions are freely available from https://github.com/ChrisMaherLab/INTEGRATE-Neo. Supplementary information Supplementary data are available at Bioinformatics online. </jats:sec

    NMR study of paramagnetic nano-checkerboard superlattices

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    With the ubiquity of electronic devices, finding ways to improve quality or fabrication methods of components is an important area of study. This dissertation looks at two sets of materials that may be used to address this need. The first is a series of disordered perovskites of the form Nd&frac23;xLi3 xTiO3. These materials are notable for the way the lithium becomes spontaneously patterned during synthesis into square planar regions, the dimensions of which are only dependent upon the initial concentration of lithium. Through the use of point-charge calculations, the paramagnetic and first-order quadrupole interaction tensors for each of the 28 unique lithium sites of the x = 0.083 concentration were calculated and used to accurately simulate the experimental spectra. From this, it was observed that the 28 crystallographically distinct sites present in that particular concentration could be grouped into three sets based on the principal values of the paramagnetic interaction tensors. Qualitative analysis of spectra from the other concentrations suggests that this grouping holds for other concentrations, with only the relative number of sites in each group changing. Additionally, jump dynamics were incorporated into the simulations of one of the sites in order to explain the broadening that occurs at lower temperatures.;The second study included in this dissertation is focused on lithium in a pair of high-dielectric microwave ceramics, Ca(Li1/3Nb 2/3)O3 and (Ca2/3La1/3)(Li1/3 Nb2/3)O3. Experimental results are reported for the temperature-dependence of both the spin-lattice relaxation rate and the isotropic chemical shift for each material. For both samples, the isotropic shift was linear with temperature, with the isotropic shift of Ca(Li 1/3Nb2/3)O3 having a stronger temperature dependence (3.53 Hz??K-1 compared to 2.65 Hz??K -1). The spin-lattice relaxation rates of both samples follow an Arrhenius relationship with temperature, with Ca(Li1/3Nb 2/3)O3 sample having an activation energy of 5.08 kJ ?? (mol ?? K)-1 and (Ca2/3La1/3)(Li 1/3Nb2/3)O3 having an activation energy of 2.21kJ ?? (mol ?? K)-1. In addition to the lithium study, there were also spectra acquired that observed the niobium nucleus in each material, which has a noticeably more complex spectrum. For the (Ca2/3 La1/3)(Li1/3Nb2/3)O3 sample, a double-quantum satellite-transition magic angle spinning pulse sequence was used to determine the isotropic chemical shift as well as the quadrupole product of each of the five resolved sites

    Role of English in medicine and medical education in Japan

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    Shared decision making in Australian physiotherapy practice: A survey of knowledge, attitudes, and self-reported use

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    OBJECTIVE: To assess Australian physiotherapists’ knowledge about, attitudes towards, and self-reported use of shared decision making, as well as perceived barriers to its implementation in practice. METHODS: Physiotherapists registered for a national Australian physiotherapy conference were invited via email and the conference app to complete a self-administered online questionnaire about shared decision making, including: a) knowledge, b) attitude to and reported approach in practice, c) behaviours used, d) barriers, e) previous training and future training interest. Responses were analysed descriptively and open-ended questions synthesised narratively. RESULTS: 372 physiotherapists (71% female, mean age 45 years, mean experience 23 years) completed the survey. Respondents had a good level of knowledge on most questions, with correct responses ranging from 39.5% to 98.5% of participants, and a generally positive attitude towards shared decision making, believing it useful to most practice areas. Sixty percent indicated they make decisions with their patients and there was general agreement between how decisions should be made and how they are actually made. The behaviour with the lowest reported occurrence was explaining the relevant research evidence about the benefits and harms of the options. The main perceived barriers were patient knowledge and confidence, consequent fewer physiotherapy sessions, and time constraints. Most (79%) were keen to learn more about shared decision making. CONCLUSIONS: Shared decision making is of growing importance to all health professions and rarely studied in physical therapy. This sample of Australian physiotherapists had a generally positive attitude to shared decision making and learning more about it. Opportunities for providing such skills training at the undergraduate level and in continuing professional development should be explored. This training should ensure that the communicating evidence component of shared decision making is addressed as well as debunking myths about perceived barriers to its implementation

    Can nudge-interventions address health service overuse and underuse? Protocol for a systematic review

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    IntroductionNudge-interventions aimed at health professionals are proposed to reduce the overuse and underuse of health services. However, little is known about their effectiveness at changing health professionals’ behaviours in relation to overuse or underuse of tests or treatments.ObjectiveThe aim of this study is to systematically identify and synthesise the studies that have assessed the effect of nudge-interventions aimed at health professionals on the overuse or underuse of health services.Methods and analysisWe will perform a systematic review. All study designs that include a control comparison will be included. Any qualified health professional, across any specialty or setting, will be included. Only nudge-interventions aimed at altering the behaviour of health professionals will be included. We will examine the effect of choice architecture nudges (default options, active choice, framing effects, order effects) and social nudges (accountable justification and pre-commitment or publicly declared pledge/contract). Studies with outcomes relevant to overuse or underuse of health services will be included. Relevant studies will be identified by a computer-aided search of the Cochrane Central Register of Controlled Trials (CENTRAL) (The Cochrane Library), MEDLINE, CINAHL, Embase and PsycINFO databases. Two independent reviewers will screen studies for eligibility, extract data and perform the risk of bias assessment using the criteria recommended by the Cochrane Effective Practice and Organisation of Care (EPOC) group. We will report our results in a structured synthesis format, as recommended by the Cochrane EPOC group.Ethics and disseminationNo ethical approval is required for this study. Results will be presented at relevant scientific conferences and in peer-reviewed literature

    Prescription of activity for low back pain: What works?

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    This paper provides evidence-based guidelines for the prescription of activity in the management of non-specific low back pain (NSLBP). The 62 clinical trials published between 1966 and 1997, identified by a search of the Medline and Cinahl databases, were reviewed to provide the basis for the guidelines. The available evidence suggests that physiotherapists should advise patients with acute and sub-acute NSLBP to avoid bed rest and to return to normal activity using time rather than pain as the guide to activity resumption. While structured exercise programs have not been shown to provide a benefit for acute NSLBP, there is strong evidence to support their use for patients with sub-acute and chronic NSLBP and in the prevention of NSLBP
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