Negative DNA supercoiling induces genome-wide Cas9 off-target activity

CRISPR-Cas9 is a powerful gene-editing technology; however, off-target activity remains an important consideration for therapeutic applications. We have previously shown that force-stretching DNA induces off-target activity and hypothesized that distortions of the DNA topology in vivo, such as negative DNA supercoiling, could reduce Cas9 specificity. Using single-molecule optical-tweezers, we demonstrate that negative supercoiling λ-DNA induces sequence-specific Cas9 off-target binding at multiple sites, even at low forces. Using an adapted CIRCLE-seq approach, we detect over 10,000 negative-supercoiling-induced Cas9 off-target double-strand breaks genome-wide caused by increased mismatch tolerance. We further demonstrate in vivo that directed local DNA distortion increases off-target activity in cells and that induced off-target events can be detected during Cas9 genome editing. These data demonstrate that Cas9 off-target activity is regulated by DNA topology in vitro and in vivo, suggesting that cellular processes, such as transcription and replication, could induce off-target activity at previously overlooked sites

Feasibility of a cognitive behavioural group intervention to reduce fear of falling and associated avoidance of activity in community-living older people: a process evaluation

BACKGROUND: Fear of falling and associated avoidance of activity are common among older people and may have negative consequences in terms of functional decline, quality of life and institutionalisation. We evaluated the effects of a cognitive behavioural group intervention to reduce fear of falling and associated avoidance of activity among older persons. This intervention showed favourable effects on fear of falling, avoidance of activity, daily activity, and several secondary outcomes. The aim of the present study is to assess the feasibility of this cognitive behavioural group intervention for participants and facilitators. METHODS: The intervention consisted of eight weekly group sessions lasting two hours each and a booster session after six months. Self-administered questionnaires, registration forms and interviews were used to collect data from participants (n = 168) and facilitators (n = 6) on the extent to which the intervention was performed according to protocol, participant attendance, participant adherence, and participants' and facilitators' opinion of the intervention. Quantitative data from the questionnaires and registration forms were analysed by means of descriptive statistics. Qualitative data were categorised based on matching contents of the answers. RESULTS: Facilitators reported no major protocol deviations. Twenty-six percent of the participants withdrew before the start of the programme. Of the persons who started the programme, 84% actually completed it. The participants reported their adherence as good, but facilitators had a less favourable opinion of this. The majority of participants still reported substantial benefits from the programme after six and twelve months of follow-up (71% and 61% respectively). Both participants and facilitators provided suggestions for improvement of the intervention. CONCLUSION: Results of this study show that the current cognitive behavioural group intervention is feasible for both participants and facilitators and fits in well with regular care. Minor refinement of the intervention, however, is warranted to further improve intervention effectiveness and efficiency. Based on these positive findings, we recommend implementing a refined version of this effective and feasible intervention in regular care. TRIAL REGISTRATION: ISRCTN43792817

Evaluating an intervention to reduce fear of falling and associated activity restriction in elderly persons: design of a randomised controlled trial [ISRCTN43792817]

BACKGROUND: Fear of falling and associated activity restriction is common in older persons living in the community. Adverse consequences of fear of falling and associated activity restriction, like functional decline and falls, may have a major impact on physical, mental and social functioning of these persons. This paper presents the design of a trial evaluating a cognitive behavioural group intervention to reduce fear of falling and associated activity restriction in older persons living in the community. METHODS/DESIGN: A two-group randomised controlled trial was developed to evaluate the intervention. Persons 70 years of age or over and still living in the community were eligible for study if they experienced at least some fear of falling and associated activity restriction. A random community sample of elderly people was screened for eligibility; those eligible for study were measured at baseline and were subsequently allocated to the intervention or control group. Follow-up measurements were carried out directly after the intervention period, and then at six months and 12 months after the intervention. People allocated to the intervention group were invited to participate in eight weekly sessions of two hours each and a booster session. This booster session was conducted before the follow-up measurement at six months after the intervention. People allocated to the control group received no intervention as a result of this trial. Both an effect evaluation and a process evaluation were performed. The primary outcome measures of the effect evaluation are fear of falling, avoidance of activity due to fear of falling, and daily activity. The secondary outcome measures are perceived general health, self-rated life satisfaction, activities of daily life, feelings of anxiety, symptoms of depression, social support interactions, feelings of loneliness, falls, perceived consequences of falling, and perceived risk of falling. The outcomes of the process evaluation comprise the performance of the intervention according to protocol, the attendance and adherence of participants, and the participants' and facilitators' opinion about the intervention. Data of the effect evaluation will be analysed according the intention-to-treat and on-treatment principle. Data of the process evaluation will be analysed using descriptive techniques

Family physicians' perceptions of academic detailing: a quantitative and qualitative study

<p>Abstract</p> <p>Background</p> <p>The efficacy of academic detailing in changing physicians' knowledge and practice has been the subject of many primary research publications and systematic reviews. However, there is little written about the features of academic detailing that physicians find valuable or that affect their use of it. The goal of our project was to explore family physicians' (FPs) perceptions of academic detailing and the factors that affect their use of it.</p> <p>Methods</p> <p>We used 2 methods to collect data, a questionnaire and semi-structured telephone interviews. We mailed questionnaires to all FPs in the Dalhousie Office of Continuing Medical Education database and analyzed responses of non-users and users of academic detailing. After a preliminary analysis of questionnaire data, we conducted semi-structured interviews with 7 FPs who did not use academic detailing and 17 who did use it.</p> <p>Results</p> <p>Overall response rate to the questionnaire was 33% (289/869). Response rate of non-users of academic detailing was 15% (60/393), of users was 48% (229/476). The 3 factors that most encouraged use of academic detailing were the topics selected, the evidence-based approach adopted, and the handout material. The 3 factors that most discouraged the use of academic detailing were spending office time doing CME, scheduling time to see the academic detailer, and having CME provided by a non-physician. Users of academic detailing rated it as being more valuable than other forms of CME. Generally, interview data confirmed questionnaire data with the exception that interview informants did not view having CME provided by a non-physician as a barrier. Interview informants mentioned that the evidence-based approach adopted by academic detailing had led them to more critically evaluate information from other CME programs, pharmaceutical representatives, and journal articles, but not advice from specialists.</p> <p>Conclusion</p> <p>Users of academic detailing highly value its educational value and tend to view information from other sources more critically because of its evidence-based approach. Non-users are unlikely to adopt academic detailing despite its high educational value because they find using office time for CME too much of a barrier. To reach these physicians with academic detailing messages, we will have to find other CME formats.</p

Process factors explaining the ineffectiveness of a multidisciplinary fall prevention programme: A process evaluation

<p>Abstract</p> <p>Background</p> <p>Falls are a major health threat to older community-living people, and initiatives to prevent falls should be a public health priority. We evaluated a Dutch version of a successful British fall prevention programme. Results of this Dutch study showed no effects on falls or daily functioning. In parallel to the effect evaluation, we carried out a detailed process evaluation to assess the feasibility of our multidisciplinary fall prevention programme. The present study reports on the results of this process evaluation.</p> <p>Methods</p> <p>Our fall prevention programme comprised a medical and occupational-therapy assessment, resulting in recommendations and/or referrals to other services if indicated. We used self-administered questionnaires, structured telephone interviews, structured recording forms, structured face-to-face interviews and a plenary group discussion to collect data from participants allocated to the intervention group (n = 166) and from all practitioners who performed the assessments (n = 8). The following outcomes were assessed: the extent to which the multidisciplinary fall prevention programme was performed according to protocol, the nature of the recommendations and referrals provided to the participants, participants' self-reported compliance and participants' and practitioners' opinions about the programme.</p> <p>Results</p> <p>Both participants and practitioners judged the programme to be feasible. The programme was largely performed according to protocol. The number of referrals and recommendations ensuing from the medical assessment was relatively small. Participants' self-reported compliance as regards contacting their GP to be informed of the recommendations and/or referrals was low to moderate. However, self-reported compliance with such referrals and recommendations was reasonable to good. A large majority of participants reported they had benefited from the programme.</p> <p>Conclusion</p> <p>The results of the present study show that the programme was feasible for both practitioners and participants. Main factors that seem to be responsible for the lack of effectiveness are the relatively low number of referrals and recommendations ensuing from the medical assessments and participants' low compliance as regards contacting their GP about the results of the medical assessment. We do not recommend implementing the programme in its present form in regular care.</p> <p>Trial registration</p> <p>ISRCTN64716113</p

To what extent does IQ 'explain' socio-economic variations in function?

<p>Abstract</p> <p>Background</p> <p>The aims of this study were to examine the extent to which higher intellectual abilities protect higher socio-economic groups from functional decline and to examine whether the contribution of intellectual abilities is independent of childhood deprivation and low birth weight and other socio-economic and developmental factors in early life.</p> <p>Methods</p> <p>The Maastricht Aging Study (MAAS) is a prospective cohort study based upon participants in a registration network of general practices in The Netherlands. Information was available on 1211 men and women, 24 – 81 years old, who were without cognitive impairment at baseline (1993 – 1995), who ever had a paid job, and who participated in the six-year follow-up. Main outcomes were longitudinal decline in important components of quality of life and successful aging, i.e., self-reported physical, affective, and cognitive functioning.</p> <p>Results</p> <p>Persons with a low occupational level at baseline showed more functional decline than persons with a high occupational level. Socio-economic and developmental factors from early life hardly contributed to the adult socio-economic differences in functional decline. Intellectual abilities, however, took into account more than one third of the association between adult socio-economic status and functional decline. The contribution of the intellectual abilities was independent of the early life factors.</p> <p>Conclusion</p> <p>Rather than developmental and socio-economic characteristics of early life, the findings substantiate the importance of intellectual abilities for functional decline and their contribution – as potential, but neglected confounders – to socio-economic differences in functioning, successful aging, and quality of life. The higher intellectual abilities in the higher socio-economic status groups may also underlie the higher prevalences of mastery, self-efficacy and efficient coping styles in these groups.</p

Colorectal carcinomas in MUTYH-associated polyposis display histopathological similarities to microsatellite unstable carcinomas

<p>Abstract</p> <p>Background</p> <p>MUTYH-associated polyposis (MAP) is a recessively inherited disorder which predisposes biallelic carriers for a high risk of polyposis and colorectal carcinoma (CRC). Since about one third of the biallelic MAP patients in population based CRC series has no adenomas, this study aimed to identify specific clinicopathological characteristics of MAP CRCs and compare these with reported data on sporadic and Lynch CRCs.</p> <p>Methods</p> <p>From 44 MAP patients who developed ≥ 1 CRCs, 42 of 58 tumours were analyzed histologically and 35 immunohistochemically for p53 and beta-catenin. Cell densities of CD3, CD8, CD57, and granzyme B positive lymphocytes were determined. <it>KRAS2</it>, the mutation cluster region (MCR) of <it>APC, p53</it>, and <it>SMAD4 </it>were analyzed for somatic mutations.</p> <p>Results</p> <p>MAP CRCs frequently localized to the proximal colon (69%, 40/58), were mucinous in 21% (9/42), and had a conspicuous Crohn's like infiltrate reaction in 33% (13/40); all of these parameters occurred at a higher rate than reported for sporadic CRCs. Tumour infiltrating lymphocytes (TILs) were also highly prevalent in MAP CRCs. Somatic <it>APC </it>MCR mutations occurred in 14% (5/36) while 64% (23/36) had <it>KRAS2 </it>mutations (22/23 c.34G>T). G>T tranversions were found in <it>p53 </it>and <it>SMAD4</it>, although the relative frequency compared to other mutations was low.</p> <p>Conclusion</p> <p>MAP CRCs show some similarities to micro-satellite unstable cancers, with a preferential proximal location, a high rate of mucinous histotype and increased presence of TILs. These features should direct the practicing pathologist towards a MAP aetiology of CRC as an alternative for a mismatch repair deficient cause. High frequent G>T transversions in <it>APC </it>and <it>KRAS2 </it>(mutated in early tumour development) but not in <it>P53 </it>and <it>SMAD4 </it>(implicated in tumour progression) might indicate a predominant MUTYH effect in <it>early </it>carcinogenesis.</p

Syndromic approach to arboviral diagnostics for global travelers as a basis for infectious disease surveillance

Background Arboviruses have overlapping geographical distributions and can cause symptoms that coincide with more common infections. Therefore, arbovirus infections are often neglected by travel diagnostics. Here, we assessed the potential of syndrome-based approaches for diagnosis and surveillance of neglected arboviral diseases in returning travelers. Method To map the patients high at risk of missed clinical arboviral infections we compared the quantity of all arboviral diagnostic requests by physicians in the Netherlands, from 2009 through 2013, with a literature-based assessment of the travelers’ likely exposure to an arbovirus. Results 2153 patients, with travel and clinical history were evaluated. The diagnostic assay for dengue virus (DENV) was the most commonly requested (86%). Of travelers returning from Southeast Asia with symptoms compatible with chikungunya virus (CHIKV), only 55% were tested. For travelers in Europe, arbovirus diagnostics were rarely requested. Over all, diagnostics for most arboviruses were requested only on severe clinical presentation. Conclusion Travel destination and syndrome were used inconsistently for triage of diagnostics, likely resulting in vast under-diagnosis of arboviral infections of public health significance. This study shows the need for more awareness among physicians and standardization of syndromic diagnostic algorithm

The effect of monthly sulfadoxine-pyrimethamine, alone or with azithromycin, on pcr-diagnosed malaria at delivery: A randomized controlled trial

10.1371/journal.pone.0041123PLoS ONE77