Shock dynamics of phase diagrams

A thermodynamic phase transition denotes a drastic change of state of a physical system due to a continuous change of thermodynamic variables, as for instance pressure and temperature. The classical van der Waals equation of state is the simplest model that predicts the occurrence of a critical point associated with the gas-liquid phase transition. Nevertheless, below the critical temperature, theoretical predictions of the van der Waals theory significantly depart from the observed physical behaviour. We develop a novel approach to classical thermodynamics based on the solution of Maxwell relations for a generalised family of nonlocal entropy functions. This theory provides an exact mathematical description of discontinuities of the order parameter within the phase transition region, it explains the universal form of the equations of state and the occurrence of triple points in terms of the dynamics of nonlinear shock wave fronts

Successful recruitment to trials : findings from the SCIMITAR+ Trial

BACKGROUND: Randomised controlled trials (RCT) can struggle to recruit to target on time. This is especially the case with hard to reach populations such as those with severe mental ill health. The SCIMITAR+ trial, a trial of a bespoke smoking cessation intervention for people with severe mental ill health achieved their recruitment ahead of time and target. This article reports strategies that helped us to achieve this with the aim of aiding others recruiting from similar populations. METHODS: SCIMITAR+ is a multi-centre pragmatic two-arm parallel-group RCT, which aimed to recruit 400 participants with severe mental ill health who smoke and would like to cut down or quit. The study recruited primarily in secondary care through community mental health teams and psychiatrists with a smaller number of participants recruited through primary care. Recruitment opened in October 2015 and closed in December 2016, by which point 526 participants had been recruited. We gathered information from recruiting sites on strategies which led to the successful recruitment in SCIMITAR+ and in this article present our approach to trial management along with the strategies employed by the recruiting sites. RESULTS: Alongside having a dedicated trial manager and trial management team, we identified three main themes that led to successful recruitment. These were: clinicians with a positive attitude to research; researchers and clinicians working together; and the use of NHS targets. The overriding theme was the importance of relationships between both the researchers and the recruiting clinicians and the recruiting clinicians and the participants. CONCLUSIONS: This study makes a significant contribution to the limited evidence base of real-world cases of successful recruitment to RCTs and offers practical guidance to those planning and conducting trials. Building positive relationships between clinicians, researchers and participants is crucial to successful recruitment

Acceptability of financial incentives for breastfeeding: thematic analysis of readers' comments to UK online news reports.

BACKGROUND: Whilst it is recommended that babies are breastfed exclusively for the first six months, many mothers do not maintain breastfeeding for this length of time. Previous research confirms that women and midwives value financial incentives for breastfeeding, but limited research has explored the wider acceptability of these interventions to the general public. This paper examines opinion towards financial incentives for breastfeeding using reader responses to UK on-line media coverage of a study undertaken in this area. METHODS: This study used netnography to undertake a thematic analysis of 3,373 reader comments posted in response to thirteen articles, published in November 2013, which reported findings from a feasibility study of financial incentives for breastfeeding. All articles were published on one of six UK news websites that achieved a monthly audience of at least five million viewers across laptop and desktop computers and mobile devices during April-May 2013. RESULTS: Nine analytical themes were identified, with a majority view that financial incentives for breastfeeding are unacceptable. These themes cover a range of opinions: from negligent parents unable to take responsibility for their own actions; through to psychologically vulnerable members of society who should be protected from coercion and manipulation; to capable and responsible women who can, and should be allowed to, make their own decisions. Many views focused on the immediate costs of the intervention, concluding that this was something that was currently unaffordable to fund (e.g. by the NHS). Others contrasted the value of the incentive against other 'costs' of breastfeeding. There was some consideration of the issue of cost-effectiveness and cost-saving, where the potential future benefit from initial investment was identified. Many commenters identified that financial incentives do not address the many structural and cultural barriers to breastfeeding. CONCLUSIONS: Overall, those commenting on the on-line UK news articles viewed financial incentives for breastfeeding as unacceptable and that alternative, structural, interventions were likely to be more effective. Further consideration of how best to conduct internet-based qualitative research to elicit opinion towards public health issues is required

A real-world approach to Evidence-Based Medicine in general practice: a competency framework derived from a systematic review and Delphi process

Background Evidence-Based Medicine (EBM) skills have been included in general practice curricula and competency frameworks. However, GPs experience numerous barriers to developing and maintaining EBM skills, and some GPs feel the EBM movement misunderstands, and threatens their traditional role. We therefore need a new approach that acknowledges the constraints encountered in real-world general practice. The aim of this study was to synthesise from empirical research a real-world EBM competency framework for general practice, which could be applied in training, in the individual pursuit of continuing professional development, and in routine care. We sought to integrate evidence from the literature with evidence derived from the opinions of experts in the fields of general practice and EBM. Methods We synthesised two sets of themes describing the meaning of EBM in general practice. One set of themes was derived from a mixed-methods systematic review of the literature; the other set was derived from the further development of those themes using a Delphi process among a panel of EBM and general practice experts. From these two sets of themes we constructed a real-world EBM competency framework for general practice. Results A simple competency framework was constructed, that acknowledges the constraints of real-world general practice: (1) mindfulness - in one’s approach towards EBM itself, and to the influences on decision-making; (2) pragmatism – in one’s approach to finding and evaluating evidence; and (3) knowledge of the patient – as the most useful resource in effective communication of evidence. We present a clinical scenario to illustrate how a GP might demonstrate these competencies in their routine daily work. Conclusion We have proposed a real-world EBM competency framework for general practice, derived from empirical research, which acknowledges the constraints encountered in modern general practice. Further validation of these competencies is required, both as an educational resource and as a strategy for actual practice.</p

Development and validation of a targeted gene sequencing panel for application to disparate cancers

Next generation sequencing has revolutionised genomic studies of cancer, having facilitated the development of precision oncology treatments based on a tumour’s molecular profile. We aimed to develop a targeted gene sequencing panel for application to disparate cancer types with particular focus on tumours of the head and neck, plus test for utility in liquid biopsy. The final panel designed through Roche/Nimblegen combined 451 cancer-associated genes (2.01 Mb target region). 136 patient DNA samples were collected for performance and application testing. Panel sensitivity and precision were measured using well-characterised DNA controls (n = 47), and specificity by Sanger sequencing of the Aryl Hydrocarbon Receptor Interacting Protein (AIP) gene in 89 patients. Assessment of liquid biopsy application employed a pool of synthetic circulating tumour DNA (ctDNA). Library preparation and sequencing were conducted on Illumina-based platforms prior to analysis with our accredited (ISO15189) bioinformatics pipeline. We achieved a mean coverage of 395x, with sensitivity and specificity of >99% and precision of >97%. Liquid biopsy revealed detection to 1.25% variant allele frequency. Application to head and neck tumours/cancers resulted in detection of mutations aligned to published databases. In conclusion, we have developed an analytically-validated panel for application to cancers of disparate types with utility in liquid biopsy

A bespoke smoking cessation service compared with treatment as usual for people with severe mental ill health: the SCIMITAR+ RCT

BackgroundThere is a high prevalence of smoking among people with severe mental ill health (SMI). Helping people with SMI to quit smoking could improve their health and longevity, and reduce health inequalities. However, those with SMI are less likely to access and engage with routine smoking cessation services than the general population.ObjectivesTo compare the clinical effectiveness and cost-effectiveness of a bespoke smoking cessation (BSC) intervention with usual stop smoking services for people with SMI.DesignA pragmatic, two-arm, individually randomised controlled trial.SettingPrimary care and secondary care mental health services in England.ParticipantsSmokers aged ≥ 18 years with SMI who would like to cut down on or quit smoking.InterventionsA BSC intervention delivered by mental health specialists trained to deliver evidence-supported smoking cessation interventions compared with usual care.Main outcome measuresThe primary outcome was self-reported, CO-verified smoking cessation at 12 months. Smoking-related secondary outcomes were self-reported smoking cessation, the number of cigarettes smoked per day, the Fagerström Test for Nicotine Dependence and the Motivation to Quit questionnaire. Other secondary outcomes were Patient Health Questionnaire-9 items, Generalised Anxiety Disorder Assessment-7 items and 12-Item Short-Form Health Survey, to assess mental health and body mass index measured at 6 and 12 months post randomisation.ResultsThe trial randomised 526 people (265 to the intervention group, 261 to the usual-care group) aged 19 to 72 years (mean 46 years). About 60% of participants were male. Participants smoked between 3 and 100 cigarettes per day (mean 25 cigarettes per day) at baseline. The intervention group had a higher rate of exhaled CO-verified smoking cessation at 6 and 12 months than the usual-care group [adjusted odds ratio (OR) 12 months: 1.6, 95% confidence interval (CI) 0.9 to 2.8; adjusted OR 6 months: 2.4, 95% CI 1.2 to 4.7]. This was not statistically significant at 12 months (p = 0.12) but was statistically significant at 6 months (p = 0.01). In total, 111 serious adverse events were reported (69 in the BSC group and 42 in the usual-care group); the majority were unplanned hospitalisations due to a deterioration in mental health (n = 98). The intervention is likely (57%) to be less costly but more effective than usual care; however, this result was not necessarily associated with participants’ smoking status.LimitationsFollow-up was not blind to treatment allocation. However, the primary outcome included a biochemically verified end point, less susceptible to observer biases. Some participants experienced difficulties in accessing nicotine replacement therapy because of changes in service provision. Efforts were made to help participants access nicotine replacement therapy, but this may have affected participants’ quit attempt.ConclusionsPeople with SMI who received the intervention were more likely to have stopped smoking at 6 months. Although more people who received the intervention had stopped smoking at 12 months, this was not statistically significant.Future workFurther research is needed to establish how quitting can be sustained among people with SMI.Trial registrationCurrent Controlled Trials ISRCTN72955454.FundingThis project was funded by the National Institute for Health Research (NIHR) Health Technology Assessment programme and will be published in full in Health Technology Assessment; Vol. 23, No. 50. See the NIHR Journals Library website for further project information

Smoking cessation for people with severe mental illness (SCIMITAR+) : a pragmatic randomised controlled trial

BACKGROUND: People with severe mental illnesses such as schizophrenia are three times more likely to smoke than the wider population, contributing to widening health inequalities. Smoking remains the largest modifiable risk factor for this health inequality, but people with severe mental illness have not historically engaged with smoking cessation services. We aimed to test the effectiveness of a combined behavioural and pharmacological smoking cessation intervention targeted specifically at people with severe mental illness. METHODS: In the smoking cessation intervention for severe mental illness (SCIMITAR+) trial, a pragmatic, randomised controlled study, we recruited heavy smokers with bipolar disorder or schizophrenia from 16 primary care and 21 community-based mental health sites in the UK. Participants were eligible if they were aged 18 years or older, and smoked at least five cigarettes per day. Exclusion criteria included substantial comorbid drug or alcohol problems and people who lacked capacity to consent at the time of recruitment. Using computer-generated random numbers, participants were randomly assigned (1:1) to a bespoke smoking cessation intervention or to usual care. Participants, mental health specialists, and primary care physicians were unmasked to assignment. The bespoke smoking cessation intervention consisted of behavioural support from a mental health smoking cessation practitioner and pharmacological aids for smoking cessation, with adaptations for people with severe mental illness-such as, extended pre-quit sessions, cut down to quit, and home visits. Access to pharmacotherapy was via primary care after discussion with the smoking cessation specialist. Under usual care participants were offered access to local smoking cessation services not specifically designed for people with severe mental illnesses. The primary endpoint was smoking cessation at 12 months ascertained via carbon monoxide measurements below 10 parts per million and self-reported cessation for the past 7 days. Secondary endpoints were biologically verified smoking cessation at 6 months; number of cigarettes smoked per day, Fagerström Test for Nicotine Dependence (FTND) and Motivation to Quit (MTQ) questionnaire; general and mental health functioning determined via the Patient Health Questionnaire-9 (PHQ-9), the Generalised Anxiety Disorder-7 (GAD-7) questionnaire, and 12-Item Short Form Health Survey (SF-12); and body-mass index (BMI). This trial was registerd with the ISRCTN registry, number ISRCTN72955454, and is complete. FINDINGS: Between Oct 7, 2015, and Dec 16, 2016, 526 eligible patients were randomly assigned to the bespoke smoking cessation intervention (n=265) or usual care (n=261). 309 (59%) participants were male, median age was 47·2 years (IQR 36·3-54·5), with high nicotine dependence (mean 24 cigarettes per day [SD 13·2]), and the most common severe mental disorders were schizophrenia or other psychotic illness (n=343 [65%]), bipolar disorder (n=115 [22%]), and schizoaffective disorder (n=66 [13%]). 234 (88%) of intervention participants engaged with the treatment programme and attended 6·4 (SD 3·5) quit smoking sessions, with an average duration of 39 min (SD 17; median 35 min, range 5-120). Verified quit data at 12 months were available for 219 (84%) of 261 usual care and 223 (84%) of 265 intervention participants. The proportion of participants who had quit at 12 months was higher in the intervention group than in the usual care group, but non-significantly (34 [15%] of 223 [13% of those assigned to group] vs 22 [10%] of 219 [8% of those assigned to group], risk difference 5·2%, 95% CI -1·0 to 11·4; odds ratio [OR] 1·6, 95% CI 0·9 to 2·9; p=0·10). The proportion of participants who quit at 6 months was significantly higher in the intervention group than in the usual care group (32 [14%] of 226 vs 14 [6%] of 217; risk difference 7·7%, 95% CI 2·1 to 13·3; OR 2·4, 95% CI 1·2 to 4·6; p=0·010). The incidence rate ratio for number of cigarettes smoked per day at 6 months was 0·90 (95% CI 0·80 to 1·01; p=0·079), and at 12 months was 1·00 (0·89 to 1·13; p=0·95). At both 6 months and 12 months, the intervention group was non-significantly favoured in the FTND (adjusted mean difference 6 months -0·18, 95% CI -0·53 to 0·17, p=0·32; and 12 months -0·01, -0·39 to 0·38, p=0·97) and MTQ questionnaire (adjusted mean difference 0·58, -0·01 to 1·17, p=0·056; and 12 months 0·64, 0·04 to 1·24, p=0·038). The PHQ-9 showed no difference between the groups (adjusted mean difference at 6 months 0·20, 95% CI -0·85 to 1·24 vs 12 months -0·12, -1·18 to 0·94). For the SF-12 survey, we saw evidence of improvement in physical health in the intervention group at 6 months (adjusted mean difference 1·75, 95% CI 0·21 to 3·28), but this difference was not evident at 12 months (0·59, -1·07 to 2·26); and we saw no difference in mental health between the groups at 6 or 12 months (adjusted mean difference at 6 months -0·73, 95% CI -2·82 to 1·36, and 12 months -0·41, -2·35 to 1·53). The GAD-7 questionnaire showed no difference between the groups (adjusted mean difference at 6 months -0·32 95% CI -1·26 to 0·62 vs 12 months -0·10, -1·05 to 0·86). No difference in BMI was seen between the groups (adjusted mean difference 6 months 0·16, 95% CI -0·54 to 0·85; 12 months 0·25, -0·62 to 1·13). INTERPRETATION: This bespoke intervention is a candidate model of smoking cessation for clinicians and policy makers to address high prevalence of smoking. The incidence of quitting at 6 months shows that smoking cessation can be achieved, but the waning of this effect by 12 months means more effort is needed for sustained quitting. FUNDING: National Institute for Health Research Health Technology Assessment Programme

The FANCM:p.Arg658* truncating variant is associated with risk of triple-negative breast cancer

Abstract: Breast cancer is a common disease partially caused by genetic risk factors. Germline pathogenic variants in DNA repair genes BRCA1, BRCA2, PALB2, ATM, and CHEK2 are associated with breast cancer risk. FANCM, which encodes for a DNA translocase, has been proposed as a breast cancer predisposition gene, with greater effects for the ER-negative and triple-negative breast cancer (TNBC) subtypes. We tested the three recurrent protein-truncating variants FANCM:p.Arg658*, p.Gln1701*, and p.Arg1931* for association with breast cancer risk in 67,112 cases, 53,766 controls, and 26,662 carriers of pathogenic variants of BRCA1 or BRCA2. These three variants were also studied functionally by measuring survival and chromosome fragility in FANCM−/− patient-derived immortalized fibroblasts treated with diepoxybutane or olaparib. We observed that FANCM:p.Arg658* was associated with increased risk of ER-negative disease and TNBC (OR = 2.44, P = 0.034 and OR = 3.79; P = 0.009, respectively). In a country-restricted analysis, we confirmed the associations detected for FANCM:p.Arg658* and found that also FANCM:p.Arg1931* was associated with ER-negative breast cancer risk (OR = 1.96; P = 0.006). The functional results indicated that all three variants were deleterious affecting cell survival and chromosome stability with FANCM:p.Arg658* causing more severe phenotypes. In conclusion, we confirmed that the two rare FANCM deleterious variants p.Arg658* and p.Arg1931* are risk factors for ER-negative and TNBC subtypes. Overall our data suggest that the effect of truncating variants on breast cancer risk may depend on their position in the gene. Cell sensitivity to olaparib exposure, identifies a possible therapeutic option to treat FANCM-associated tumors

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead