A new species of the cheilostome bryozoan Chiastosella in the Southern Ocean, past and present

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Calculation of a subject specific adaptive motion correction factor for improved real-time navigator echo gated MR coronary angiography

There has been conflicting data in the literature regarding the use of wide navigator echo (NE) acceptance windows in combination with adaptive motion correction for magnetic resonance coronary angiography (MRCA). This in part may be due to the use of a fixed correction factor when applying the adaptive motion-correction algorithm, which may potentially result in miscorrection of the imaging slice in subjects whose correction factor differs widely from the mean. We have addressed this issue by measuring the superior/inferior correction factor in 25 subjects and assessing the effect of using a subject-specific correction factor (CFss) for MRCA in comparison with no adaptive motion correction (CF,) and erroneous adaptive motion correction with a correction factor of 1.0 (CF,). There was a wide variation in the correction factor between subjects (proximal right coronary artery, 0.49 2 0.15, range 0.20-0.70; proximal left coronary artery, mean 0.59 ? 0.I5, range 0.20-0.85). The subject-specific correction factor was accurately calculated from motion of the aortic root in the coronal plane between expiratory and inspiratory breathhold (correction factor calculated from coronal image versus correction factor calculated after localization of coronary arteries, r = 0.92, p < 0.001). MRCA image quality was improved using a subject-specific correction factor, for both a 6-mm NE acceptance window (CF, versus CF,, p = 0.008; CF, versus CF,, p = 0.02) and a 16- mm NE window (CFss versus CF,, p = 0.01; CF, versus CF,, p = 0.007). Furthermore, image quality was maintained between the two NE windows if the subjects-specific correction factor was used (6 versus 16 mm, p = 0.21), with an improvement in scan efficiency (6 versus 16 mm, 49 5 17% versus 81 & 22% respectively, p < 0.001). Thus, for adaptive motion correction to be implemented, a subject- specific correction factor should be used and calculated from simple coronal expiratory and inspiratory breathholds. For real-time NE-gated cardiac MR with adaptive motion correction, the NE window can be widened to reduce the acquisition period without loss of image quality

Phases of one dimensional large N gauge theory in a 1/D expansion

We consider large N Yang Mills theory with D adjoint scalar fields in d dimensions for d=0 or 1. We show the existence of a non-trivial saddle point of the functional integral at large D which is characterized by a mass gap for the adjoint scalars. We integrate out the adjoint scalars in a 1/D expansion around the saddle point. In case of one dimension which is regarded as a circle, this procedure leads to an effective action for the Wilson line. We find an analogue of the confinement/deconfinement transition which consists of a second order phase transition from a uniform to a non-uniform eigenvalue distribution of the Wilson line, closely followed by a Gross-Witten-Wadia transition where a gap develops in the eigenvalue distribution. The phase transition can be regarded as a continuation of a Gregory-Laflamme transition. Our methods involve large values of the dimensionless 'tHooft coupling. The analysis in this paper is quantitatively supported by earlier numerical work for D=9.Comment: 27 pages + 21 pages of Appendix; 8 figures, v2:some comments are added in sec.4.3, minor corrections, one reference added, v3: minor corrections, one reference added, version to be published in JHE

Increase in circulating Th17 cells during anti-TNF therapy is associated with ultrasonographic improvement of synovitis in rheumatoid arthritis

Background Anti-TNF agents have revolutionised rheumatoid arthritis (RA) treatment; however, a third of patients fail to achieve therapeutic responses. Unexpectedly, studies in murine and human arthritis have indicated that anti-TNF treatment can increase circulating T helper 17 (Th17) cells, but the relationship to treatment response is unclear. To identify immune correlates of anti-TNF treatment response, we conducted a longitudinal study using clinical, ultrasound and T cell assessments. Methods Patients with RA (n = 25) were studied at protocol visits during the initial 12 weeks of anti-TNF treatment. Improvement in the disease activity score of 28 joints (DAS28) >1.2 defined treatment responders (n = 16) and non-responders (n = 9). Changes in synovial thickening and vascularity of 10 metacarpophalangeal joints were quantitatively assessed by grey scale and power Doppler ultrasound. The frequency of circulating Th17 cells was determined by IL17 enzyme-linked immunospot assay (Elispot) and flow cytometry (fluorescence-activated cell sorting (FACS)). Results The frequency of circulating IL17-producing cells increased significantly 12 weeks after anti-TNF initiation (Elispot median (range) specific spot forming cells (spSFC)/106 360 (280–645) vs 632 (367 − 1167), p = 0.003). The increase in CD4 + IL17+ cells at 12 weeks was confirmed by FACS (median (range) %, 0.7 (0.5–0.9) vs 1.05 (0.6–1.3); p = 0.01). The increase in circulating Th17 cells inversely correlated with reduction in synovial vascularity (r = -0.68, p = 0.007) and thickening (r = -0.39; p = 0.04). Higher frequencies of circulating Th17 cells at baseline were associated with poorer anti-TNF treatment response defined by ultrasonographic measures. Conclusions These results demonstrate a link between changes in circulating Th17 cells with resolution of ultrasonographic features of synovial inflammation and vascularity during anti-TNF treatment. The findings may reflect redistribution of Th17 cells from inflamed joints or TNF-driven regulation of Th17 cell production. Trial Registration ClinicalTrials.gov: NCT01060098. Registered 29 January 2010

Quantifying single nucleotide variant detection sensitivity in exome sequencing

BACKGROUND: The targeted capture and sequencing of genomic regions has rapidly demonstrated its utility in genetic studies. Inherent in this technology is considerable heterogeneity of target coverage and this is expected to systematically impact our sensitivity to detect genuine polymorphisms. To fully interpret the polymorphisms identified in a genetic study it is often essential to both detect polymorphisms and to understand where and with what probability real polymorphisms may have been missed. RESULTS: Using down-sampling of 30 deeply sequenced exomes and a set of gold-standard single nucleotide variant (SNV) genotype calls for each sample, we developed an empirical model relating the read depth at a polymorphic site to the probability of calling the correct genotype at that site. We find that measured sensitivity in SNV detection is substantially worse than that predicted from the naive expectation of sampling from a binomial. This calibrated model allows us to produce single nucleotide resolution SNV sensitivity estimates which can be merged to give summary sensitivity measures for any arbitrary partition of the target sequences (nucleotide, exon, gene, pathway, exome). These metrics are directly comparable between platforms and can be combined between samples to give “power estimates” for an entire study. We estimate a local read depth of 13X is required to detect the alleles and genotype of a heterozygous SNV 95% of the time, but only 3X for a homozygous SNV. At a mean on-target read depth of 20X, commonly used for rare disease exome sequencing studies, we predict 5–15% of heterozygous and 1–4% of homozygous SNVs in the targeted regions will be missed. CONCLUSIONS: Non-reference alleles in the heterozygote state have a high chance of being missed when commonly applied read coverage thresholds are used despite the widely held assumption that there is good polymorphism detection at these coverage levels. Such alleles are likely to be of functional importance in population based studies of rare diseases, somatic mutations in cancer and explaining the “missing heritability” of quantitative traits

Psychosocial stress and strategies for managing adversity: measuring population resilience in New South Wales, Australia

<p>Abstract</p> <p>Background</p> <p>Populations around the world are facing an increasing number of adversities such as the global financial crisis, terrorism, conflict, and climate change. The aim of this paper was to investigate self-reported strategies and sources of support used to get through "tough times" in an Australian context and to identify patterns of response in the general population and differences in potentially vulnerable subgroups.</p> <p>Methods</p> <p>Data were collected through a cross-sectional survey of the New South Wales population in Australia. The final sample consisted of 3,995 New South Wales residents aged 16 years and above who responded to the question: "What are the things that get you through tough times?"</p> <p>Results</p> <p>Respondents provided brief comments that were coded into 14 main subject-area categories. The most frequently reported responses were family and self (52%); friends and neighbors (21%); use of positive emotional and philosophical strategies (17%), such as sense of humor, determination, and the belief that things would get better; and religious beliefs (11%). The responses of four population subgroups were compared, based on gender, household income, level of psychological distress, and whether a language other than English was spoken at home. Women reported greater use of friends and neighbors and religious or spiritual beliefs for support, whereas men reported greater use of drinking/smoking and financial supports. Those with lower incomes reported greater reliance on positive emotional and philosophical strategies and on religious or spiritual beliefs. Those with high levels of psychological distress reported greater use of leisure interests and hobbies, drinking/smoking, and less use of positive lifestyle strategies, such as adequate sleep, relaxation, or work/life balance. Those who spoke a language other than English at home were less likely to report relying on self or others (family/friends) or positive emotional and philosophical strategies to get through tough times.</p> <p>Conclusions</p> <p>Understanding strategies and sources of support used by the population to get through adversity is the first step toward identifying the best approaches to build and support strengths and reduce vulnerabilities. It is also possible to reflect on how large-scale threats such as pandemics, disasters, conflict, bereavement, and loss could impact individual and population resilience.</p

Trichotillometry: the reliability and practicality of hair pluckability as a method of nutritional assessment

<p>Abstract</p> <p>Background</p> <p>A nutritional assessment method that is quick and easy to conduct would be extremely useful in a complex emergency, where currently there is no agreed practical and acceptable method. Hair pluckability has been suggested to be a useful method of assessing protein nutritional status. The aim was to investigate the reliability of the trichotillometer and to explore the effects of patient characteristics on hair epilation force.</p> <p>Methods</p> <p>Three observers plucked hair from twelve participants to investigate the within- and between-observer reliability. To investigate the effect of patient characteristics on hair pluckability, 12 black African and 12 white volunteers were recruited. Participants completed a short questionnaire to provide basic information on their characteristics and hair.</p> <p>Results</p> <p>Mean hair pluckability measurements for the 12 participants obtained by the three observers (39.5 g, 41.2 g and 32.7 g) were significantly different (p < 0.001). Significant variation between patients was also found (p < 0.001). None of the patient characteristics significantly affected hair pluckability, with the exception of age, although this relationship was not consistent.</p> <p>Conclusion</p> <p>Due to significant variation in measurements, hair pluckability does not appear to be a reliable method for assessing adult nutritional status. Hair pluckability could be a useful method of nutritional assessment in complex humanitarian emergencies but only if the reliability was improved.</p

Jejunal perforation in gallstone ileus – a case series

<p>Abstract</p> <p>Introduction</p> <p>Gallstone ileus is an uncommon complication of cholelithiasis but an established cause of mechanical bowel obstruction in the elderly. Perforation of the small intestine proximal to the obstructing gallstone is rare, and only a handful of cases have been reported. We present two cases of perforation of the jejunum in gallstone ileus, and remarkably in one case, the gallstone ileus caused perforation of a jejunal diverticulum and is to the best of our knowledge the first such case to be described.</p> <p>Case presentations</p> <p><b>Case 1</b></p> <p>A 69 year old man presented with two days of vomiting and central abdominal pain. He underwent laparotomy for small bowel obstruction and was found to have a gallstone obstructing the mid-ileum. There was a 2 mm perforation in the anti-mesenteric border of the dilated proximal jejunum. The gallstone was removed and the perforated segment of jejunum was resected.</p> <p><b>Case 2</b></p> <p>A 68 year old man presented with a four day history of vomiting and central abdominal pain. Chest and abdominal radiography were unremarkable however a subsequent CT scan of the abdomen showed aerobilia. At laparotomy his distal ileum was found to be obstructed by an impacted gallstone and there was a perforated diverticulum on the mesenteric surface of the mid-jejunum. An enterolithotomy and resection of the perforated small bowel was performed.</p> <p>Conclusion</p> <p>Gallstone ileus remains a diagnostic challenge despite advances in imaging techniques, and pre-operative diagnosis is often delayed. Partly due to the elderly population it affects, gallstone ileus continues to have both high morbidity and mortality rates. On reviewing the literature, the most appropriate surgical intervention remains unclear.</p> <p>Jejunal perforation in gallstone ileus is extremely rare. The cases described illustrate two quite different causes of perforation complicating gallstone ileus. In the first case, perforation was probably due to pressure necrosis caused by the gallstone. The second case was complicated by the presence of a perforated jejunal diverticulum, which was likely to have been secondary to the increased intra-luminal pressure proximal to the obstructing gallstone.</p> <p>These cases should raise awareness of the complications associated with both gallstone ileus, and small bowel diverticula.</p

Dynamic SU(2) Structure from Seven-branes

We obtain a family of supersymmetric solutions of type IIB supergravity with dynamic SU(2) structure, which describe the local geometry near a stack of four D7-branes and one O7-plane wrapping a rigid four-cycle. The deformation to a generalized complex geometry is interpreted as a consequence of nonperturbative effects in the seven-brane gauge theory. We formulate the problem for seven-branes wrapping the base of an appropriate del Pezzo cone, and in the near-stack limit in which the four-cycle is flat, we obtain an exact solution in closed form. Our solutions serve to characterize the local geometry of nonperturbatively-stabilized flux compactifications.Comment: 49 pages, 2 figures; v2: minor corrections, references adde