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This abstract was withdrawn by the authors.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.