Simulating topological domains in human chromosomes with a fitting-free model

We discuss a polymer model for the 3D organization of human chromosomes. A chromosome is represented by a string of beads, with each bead being "colored" according to 1D bioinformatic data (e.g., chromatin state, histone modification, GC content). Individual spheres (representing bi- and multi-valent transcription factors) can bind reversibly and selectively to beads with the appropriate color. During molecular dynamics simulations, the factors bind, and the string spontaneously folds into loops, rosettes, and topologically-associating domains (TADs). This organization occurs in the absence of any specified interactions between distant DNA segments, or between transcription factors. A comparison with Hi-C data shows that simulations predict the location of most boundaries between TADs correctly. The model is "fitting-free" in the sense that it does not use Hi-C data as an input; consequently, one of its strengths is that it can - in principle - be used to predict the 3D organization of any region of interest, or whole chromosome, in a given organism, or cell line, in the absence of existing Hi-C data. We discuss how this simple model might be refined to include more transcription factors and binding sites, and to correctly predict contacts between convergent CTCF binding sites.

Abstract P3-06-03: The short term effects of an AKT inhibitor (AZD5363) on biomarkers of the AKT pathway and anti-tumour activity in a breast cancer paired biopsy study (STAKT trial)

This abstract was withdrawn by the authors.

Liver abscess secondary to an endoscopic tattoo in the colon

Introduction Endoscopic tattooing of colonic lesions has been used safely for their localization. CASE HISTORY We report a 61-year-old female who had left hemicolectomy in 2006 for adenocarcinoma of the left colon (pT3, pN0, M0). Cancer in the transverse colon was discovered during annual colonoscopy surveillance. The lesion was tattooed 5cm proximal to the lesion. Twenty-four days after tattooing, she was admitted to the emergency department with increased levels of inflammatory markers. CT showed an abscess in the left lobe of the liver adjacent to the tattoo site. The abscess was drained under ultrasound guidance. She had antibiotic treatment for 3 weeks and made a full recovery. CONCLUSION Endoscopic tattooing of colonic lesions is safe but this case report highlights the possibility of a rare (but serious) complication that must be taken into consideration.

The significance of extramural venous invasion in R1 positive rectal cancer

BACKGROUND AND AIMS

Evidence has shown that a positive resection margin (R1) is a key determinant of subsequent local recurrence and a poor prognostic factor in rectal cancer. The aim of this study was to evaluate the outcomes and prognosticators in patients with R1 resection of rectal cancer.

MATERIAL AND METHODS

Retrospective study of all patients operatively managed within our institution between April 2008 and April 2013 for rectal cancer. Baseline demographics and multiple outcome measures recorded. Overall survival (OS), disease-free survival (DFS) and recurrence were the primary outcome measures.

RESULTS

Overall, there were 306 primary rectal cancers. Seventy-six percent were grade T3/4 tumours. OS was 30 months. R1 rate was 16 % (48 patients). Thirty-one patients underwent APR and 17 AR. In patients who responded to neoadjuvant chemotherapy (NAC), overall survival was 55 months, with no extramural venous invasion (EMV) seen in this cohort. In non-responders OS was 29 months, with EMV in 48 %. In patients who did not receive NAC, OS was 23 months, with EMV in 74 %. EMV is a strong predictor for poor survival following R1 (p = 0.001). We also found a correlation between number of positive nodes and OS/DFS (p = 0.004).

CONCLUSIONS

In this small cohort of patients with R1 positive rectal cancers, response to NAC is the strongest predictor of poor overall and disease-free survival. In patients who respond to NAC, OS and DFS has been shown to be positive, with a reduced rate of EMV.

Ethical issues and best practice in clinically based genomic research: Exeter Stakeholders Meeting Report

Current guidelines on consenting individuals to participate in genomic research are diverse. This creates problems for participants and also for researchers, particularly for clinicians who provide both clinical care and research to their patients. A group of 14 stakeholders met on 7 October 2015 in Exeter to discuss the ethical issues and the best practice arising in clinically based genomic research, with particular emphasis on the issue of returning results to study participants/patients in light of research findings affecting research and clinical practices. The group was deliberately multidisciplinary to ensure that a diversity of views was represented. This report outlines the main ethical issues, areas of best practice and principles underlying ethical clinically based genomic research discussed during the meeting. The main point emerging from the discussion is that ethical principles, rather than being formulaic, should guide researchers/clinicians to identify who the main stakeholders are to consult with for a specific project and to incorporate their voices/views strategically throughout the lifecycle of each project. We believe that the mix of principles and practical guidelines outlined in this report can contribute to current debates on how to conduct ethical clinically based genomic research.

Outcomes of a community-based weight management programme for morbidly obese populations

BACKGROUND

Morbid obesity is an ongoing concern worldwide. There is a paucity of research reporting primary care outcomes focussed on complex and morbidly obese populations. The National Institute for Health and Care Excellence (NICE) recommends a specialist, multidisciplinary weight management team for the successful management of such populations. This is the first service evaluation reporting both primary (weight change) and secondary [body mass index (BMI), waist circumference, physical activity levels, fruit and vegetable intake, Rosenberg self-esteem score] outcomes in these patients.

METHODS

The present study comprised a prospective observational study of a cohort data set for patients (n = 288) attending their 3-month and 6-month (n = 115) assessment appointments at a specialist community weight management programme.

RESULTS

Patients had a mean (SD) initial BMI of 45.5 (6.6) kg m^- ²; 66% were females. Over 80% of patients attending the service lost some weight by 3 months. Average absolute weight loss was 4.11 (4.95) kg at 3 months and 6.30 (8.41) kg at 6 months, equating to 3.28% (3.82%) and 4.90% (6.26%), respectively, demonstrating a statistically significant weight change at both time points (P < 0.001). This meets NICE best practice guidelines for the commissioning of services leading to a minimum of 3% average weight loss, with at least 30% of patients losing at ≥5% of their initial weight. Waist measurement and BMI were reduced significantly at 3 months. Improvements were also seen in physical activity levels, fruit and vegetable consumption, and self-esteem levels (P < 0.001).

CONCLUSIONS

This service was successful in aiding weight loss in morbidly obese populations. The findings of the present study support the view that weight-loss targets of 3% are realistic.

Atomic scale mobility of the volatile fission products Xe, Kr and I in cubic SiC

The migration barriers for the vacancy-assisted migration of fission products in 3C-SiC are reported and analysed in the context of the five frequency model, which enables one to calculate an effective diffusion coefficient from elementary mechanisms. Calculations were carried out using the nudged elastic band method (NEB) with interatomic forces determined from density functional theory (DFT). Justification for treating vacancy-assisted fission product migration as limited to the FCC carbon sublattice is based on the stability of carbon vacancies, unfavourable silicon vacancy formation and the accommodation of fission products on the carbon sublattice. Results show that for most Fermi levels within the band gap the activation energy for I exceeds that of Xe which exceeds that of Kr. Results also indicate that activation energies are higher near the conduction edge, thus, implying that enhanced fission product retention can be achieved through n-type doping of 3C-SiC, which limits the availability of the migration mediating carbon vacancies.

Subcortical brain volume abnormalities in 2028 individuals with schizophrenia and 2540 healthy controls via the ENIGMA consortium

The profile of brain structural abnormalities in schizophrenia is still not fully understood, despite decades of research using brain scans. To validate a prospective meta-analysis approach to analyzing multicenter neuroimaging data, we analyzed brain MRI scans from 2028 schizophrenia patients and 2540 healthy controls, assessed with standardized methods at 15 centers worldwide. We identified subcortical brain volumes that differentiated patients from controls, and ranked them according to their effect sizes. Compared with healthy controls, patients with schizophrenia had smaller hippocampus (Cohen's d=-0.46), amygdala (d=-0.31), thalamus (d=-0.31), accumbens (d=-0.25) and intracranial volumes (d=-0.12), as well as larger pallidum (d=0.21) and lateral ventricle volumes (d=0.37). Putamen and pallidum volume augmentations were positively associated with duration of illness and hippocampal deficits scaled with the proportion of unmedicated patients. Worldwide cooperative analyses of brain imaging data support a profile of subcortical abnormalities in schizophrenia, which is consistent with that based on traditional meta-analytic approaches. This first ENIGMA Schizophrenia Working Group study validates that collaborative data analyses can readily be used across brain phenotypes and disorders and encourages analysis and data sharing efforts to further our understanding of severe mental illness.

DVT presentations to an Emergency Department: A study of guideline based care and decision making

Pre-test probability scoring and blood tests for deep venous thrombosis (DVT) assessment are sensitive but not specific leading to increased demands on radiology services. 385 patients presenting to an Emergency Department with suspected DVT were studied to explore our actual work up of patients with possible DVT relating to risk stratification, further investigation and follow up. Of the 205 patients with an initially negative scan, 36 (17.6%) were brought for review to the Emergency Department Consultant clinic. 34 (16.6%) patients underwent repeat compression ultrasound with 5 (2.4%) demonstrating a DVT on the second scan. Repeat compression ultrasound scans were performed on 34 (16.6%) of patients with an initially negative scan with essentially the same diagnostic yield as other larger studies where 100% of such patients had repeat scanning. Where there is ongoing concern, repeat above knee compression ultrasound within one week will pick up a small number of deep venous thromboses.

Factors Associated With Increased Rates of Caesarean Section in Women of Advanced Maternal Age

OBJECTIVE

To compare rates of Caesarean section between mothers of advanced age (35 to 40, and over 40 years) and those aged 20 to 34, using the Robson classification system to examine additional maternal factors.

METHODS

A total of 134 088 hospital deliveries in Ontario between April 1, 2011, and March 31, 2012, were grouped into Robson's 10 mutually exclusive and totally inclusive classification categories. Records from the three Robson groups that made the greatest contribution to the overall CS rate were stratified by maternal age, health condition, obstetrical complication, assisted reproductive technology usage, smoking during pregnancy, and socioeconomic status.

RESULTS

Rates of CS increased with advancing maternal age; in women aged 20 to 34, 35 to 40, and over 40, the rates were 26.2%, 35.9%, and 43.1%, respectively. The top three Robson groups by contribution to CS rates involved women who had one or more of the following factors: previous Caesarean section, primiparity, conception by means of assisted reproductive technology, chronic hypertension, gestational diabetes, diabetes mellitus, preeclampsia, placenta previa, placental abruption, or large for gestational age infants. The prevalence of these factors increased with advancing maternal age, yet mothers aged ≥ 35 with one or more health conditions or obstetrical complications had higher CS rates than mothers aged 20 to 34 with the same condition(s) or complication(s).

CONCLUSION

Health conditions and obstetrical complications alone in older women do not account for increased rates of CS. The preferences of the individual care provider and the mother on CS rates may play a key role and require further investigation.

Who dares, wins : Heroism versus altruism in women's mate choice

Heroism is apparently nonadaptive in Darwinian terms, so why does it exist at all? Risk-taking and heroic behavior are predominantly male tendencies, and literature and legend reflect this. This study explores the possibility that heroism persists in many human cultures owing to a female preference for risk-prone rather than risk-averse males as sexual partners, and it suggests that such a preference may be exploited as a male mating strategy. It also attempts to quantify the relative influences of altruism and bravery in the evolution of heroism. Our study found that females do prefer risk-prone brave males to risk-averse non-brave males, and that men are aware of this preference. Bravery in a male was shown to be the stronger factor influencing female choice of short-term partners, long-term partners, and male friends, with altruism playing a lesser part in their choice. Altruism was deemed important in long-term relationships and friendships, but for short-term liaisons, non-altruists were preferred to altruists. Heroism may therefore have evolved owing to a female preference for brave, risk-prone males because risk-taking acts as an honest cue for "good genes." Altruism was judged to be a less influential factor in the evolution of heroism than bravery and a demonstrated willingness to take risks.

Defining response to anti-VEGF therapies in neovascular AMD

The introduction of anti-vascular endothelial growth factor (anti-VEGF) has made significant impact on the reduction of the visual loss due to neovascular age-related macular degeneration (n-AMD). There are significant inter-individual differences in response to an anti-VEGF agent, made more complex by the availability of multiple anti-VEGF agents with different molecular configurations. The response to anti-VEGF therapy have been found to be dependent on a variety of factors including patient's age, lesion characteristics, lesion duration, baseline visual acuity (VA) and the presence of particular genotype risk alleles. Furthermore, a proportion of eyes with n-AMD show a decline in acuity or morphology, despite therapy or require very frequent re-treatment. There is currently no consensus as to how to classify optimal response, or lack of it, with these therapies. There is, in particular, confusion over terms such as 'responder status' after treatment for n-AMD, 'tachyphylaxis' and 'recalcitrant' n-AMD. This document aims to provide a consensus on definition/categorisation of the response of n-AMD to anti-VEGF therapies and on the time points at which response to treatment should be determined. Primary response is best determined at 1 month following the last initiation dose, while maintained treatment (secondary) response is determined any time after the 4th visit. In a particular eye, secondary responses do not mirror and cannot be predicted from that in the primary phase. Morphological and functional responses to anti-VEGF treatments, do not necessarily correlate, and may be dissociated in an individual eye. Furthermore, there is a ceiling effect that can negate the currently used functional metrics such as >5 letters improvement when the baseline VA is good (ETDRS>70 letters). It is therefore important to use a combination of both the parameters in determining the response.The following are proposed definitions: optimal (good) response is defined as when there is resolution of fluid (intraretinal fluid; IRF, subretinal fluid; SRF and retinal thickening), and/or improvement of >5 letters, subject to the ceiling effect of good starting VA. Poor response is defined as <25% reduction from the baseline in the central retinal thickness (CRT), with persistent or new IRF, SRF or minimal or change in VA (that is, change in VA of 0+4 letters). Non-response is defined as an increase in fluid (IRF, SRF and CRT), or increasing haemorrhage compared with the baseline and/or loss of >5 letters compared with the baseline or best corrected vision subsequently. Poor or non-response to anti-VEGF may be due to clinical factors including suboptimal dosing than that required by a particular patient, increased dosing intervals, treatment initiation when disease is already at an advanced or chronic stage), cellular mechanisms, lesion type, genetic variation and potential tachyphylaxis); non-clinical factors including poor access to clinics or delayed appointments may also result in poor treatment outcomes. In eyes classified as good responders, treatment should be continued with the same agent when disease activity is present or reactivation occurs following temporary dose holding. In eyes that show partial response, treatment may be continued, although re-evaluation with further imaging may be required to exclude confounding factors. Where there is persistent, unchanging accumulated fluid following three consecutive injections at monthly intervals, treatment may be withheld temporarily, but recommenced with the same or alternative anti-VEGF if the fluid subsequently increases (lesion considered active). Poor or non-response to anti-VEGF treatments requires re-evaluation of diagnosis and if necessary switch to alternative therapies including other anti-VEGF agents and/or with photodynamic therapy (PDT). Idiopathic polypoidal choroidopathy may require treatment with PDT monotherapy or combination with anti-VEGF. A committee comprised of retinal specialists with experience of managing patients with n-AMD similar to that which developed the Royal College of Ophthalmologists Guidelines to Ranibizumab was assembled. Individual aspects of the guidelines were proposed by the committee lead (WMA) based on relevant reference to published evidence base following a search of Medline and circulated to all committee members for discussion before approval or modification. Each draft was modified according to feedback from committee members until unanimous approval was obtained in the final draft. A system for categorising the range of responsiveness of n-AMD lesions to anti-VEGF therapy is proposed. The proposal is based primarily on morphological criteria but functional criteria have been included. Recommendations have been made on when to consider discontinuation of therapy either because of success or futility. These guidelines should help clinical decision-making and may prevent over and/or undertreatment with anti-VEGF therapy.

Ivacaftor as salvage therapy in a patient with cystic fibrosis genotype F508del/R117H/IVS8-5T

Ivacaftor is a novel CFTR potentiator that increases CFTR activity and improves clinical outcomes in cystic fibrosis (CF) patients with at least one copy of CFTR-G551D. Clinical trials have shown an improvement in lung function, weight and CF pulmonary exacerbation in adults with CFTR-G551D leading to the approval of ivacaftor as a novel CF therapy [1]. In vitro studies of ivacaftor have also shown significant improvements in CFTR chloride channel opening time in other non-G551D CFTR mutations suggesting that ivacaftor may be of benefit to patients with mutations other than gating mutations [2]. R117H-CFTR is a relatively common CFTR mutation that demonstrates an in-vitro response to ivacaftor [2,3]. A clinical trial has suggested that there may be a role for ivacaftor in older patients with R117H-CFTR although this trial did not include patients with very severe CF lung disease [4]. In 2014, ivacaftor was approved in the United States as a treatment for CF subjects aged greater than 6 years old with a copy of R117H-CFTR. We present a case demonstrating a substantial therapeutic effect of ivacaftor in a CF patient with genotype F508del/R117H and advanced lung disease.

Editor's choice--Angulation of the C-arm during complex endovascular aortic procedures increases radiation exposure to the head

OBJECTIVES/BACKGROUND

The increased complexity of endovascular aortic repair necessitates longer procedural time and higher radiation exposure to the operator, particularly to exposed body parts. The aims were to measure directly exposure to radiation of the bodies and heads of the operating team during endovascular repair of thoracoabdominal aortic aneurysms (TAAA), and to identify factors that may increase exposure.

METHODS

This was a single-centre prospective study. Between October 2013 and July 2014, consecutive elective branched and fenestrated TAAA repairs performed in a hybrid operating room were studied. Electronic dosimeters were used to measure directly radiation exposure to the primary (PO) and assistant (AO) operator in three different areas (under-lead, over-lead, and head). Fluoroscopy and digital subtraction angiography (DSA) acquisition times, C-arm angulation, and PO/AO height were recorded.

RESULTS

Seventeen cases were analysed (Crawford II-IV), with a median operating time of 280 minutes (interquartile range 200-330 minutes). Median age was 76 years (range 71-81 years); median body mass index was 28 kg/m(2) (25-32 kg/m(2)). Stent-grafts incorporated branches only, fenestrations only, or a mixture of branches and fenestrations. A total of 21 branches and 38 fenestrations were cannulated and stented. Head dose was significantly higher in the PO compared with the AO (median 54 μSv [range 24-130 μSv] vs. 15 μSv [range 7-43 μSv], respectively; p = .022), as was over-lead body dose (median 80 μSv [range 37-163 μSv] vs. 32 μSv [range 6-48 μSv], respectively; p = .003). Corresponding under-lead doses were similar between operators (median 4 μSv [range 1-17 μSv] vs. 1 μSv [range 1-3 μSv], respectively; p = .222). Primary operator height, DSA acquisition time in left anterior oblique (LAO) position, and degrees of LAO angulation were independent predictors of PO head dose (p < .05).

CONCLUSIONS

The head is an unprotected area receiving a significant radiation dose during complex endovascular aortic repair. The deleterious effects of exposure to this area are not fully understood. Vascular interventionalists should be cognisant of head exposure increasing with C-arm angulation, and limit this manoeuvre.

Measuring quality in maternal-newborn care: developing a clinical dashboard

Pregnancy, birth, and the early newborn period are times of high use of health care services. As well as opportunities for providing quality care, there are potential missed opportunities for health promotion, safety issues, and increased costs for the individual and the system when quality is not well defined or measured. There has been a need to identify key performance indicators (KPIs) to measure quality care within the provincial maternal-newborn system. We also wanted to provide automated audit and feedback about these KPIs to support quality improvement initiatives in a large Canadian province with approximately 140 000 births per year. We therefore worked to develop a maternal-newborn dashboard to increase awareness about selected KPIs and to inform and support hospitals and care providers about areas for quality improvement. We mapped maternal-newborn data elements to a quality domain framework, sought feedback via survey for the relevance and feasibility of change, and examined current data and the literature to assist in setting provincial benchmarks. Six clinical performance indicators of maternal-newborn quality care were identified and evidence-informed benchmarks were set. A maternal-newborn dashboard with "drill down" capacity for detailed analysis to enhance audit and feedback is now available for implementation. While audit and feedback does not guarantee individuals or institutions will make practice changes and move towards quality improvement, it is an important first step. Practice change and quality improvement will not occur without an awareness of the issues.