BigraphER: rewriting and analysis engine for bigraphs

BigraphER is a suite of open-source tools providing an effi- cient implementation of rewriting, simulation, and visualisation for bigraphs, a universal formalism for modelling interacting systems that evolve in time and space and first introduced by Milner. BigraphER consists of an OCaml library that provides programming interfaces for the manipulation of bigraphs, their constituents and reaction rules, and a command-line tool capable of simulating Bigraphical Reactive Systems (BRSs) and computing their transition systems. Other features are native support for both bigraphs and bigraphs with sharing, stochastic reaction rules, rule priorities, instantiation maps, parameterised controls, predicate checking, graphical output and integration with the probabilistic model checker PRISM

Phylo-mLogo: an interactive and hierarchical multiple-logo visualization tool for alignment of many sequences

BACKGROUND: When aligning several hundreds or thousands of sequences, such as epidemic virus sequences or homologous/orthologous sequences of some big gene families, to reconstruct the epidemiological history or their phylogenies, how to analyze and visualize the alignment results of many sequences has become a new challenge for computational biologists. Although there are several tools available for visualization of very long sequence alignments, few of them are applicable to the alignments of many sequences. RESULTS: A multiple-logo alignment visualization tool, called Phylo-mLogo, is presented in this paper. Phylo-mLogo calculates the variabilities and homogeneities of alignment sequences by base frequencies or entropies. Different from the traditional representations of sequence logos, Phylo-mLogo not only displays the global logo patterns of the whole alignment of multiple sequences, but also demonstrates their local homologous logos for each clade hierarchically. In addition, Phylo-mLogo also allows the user to focus only on the analysis of some important, structurally or functionally constrained sites in the alignment selected by the user or by built-in automatic calculation. CONCLUSION: With Phylo-mLogo, the user can symbolically and hierarchically visualize hundreds of aligned sequences simultaneously and easily check the changes of their amino acid sites when analyzing many homologous/orthologous or influenza virus sequences. More information of Phylo-mLogo can be found at URL

Validation of a prognostic scoring system for locally recurrent nasopharyngeal carcinoma treated by stereotactic radiosurgery

<p>Abstract</p> <p>Background</p> <p>Selection of patients with local failure of nasopharyngeal carcinoma (NPC) for appropriate type of salvage treatment can be difficult due to the lack of data on comparative efficacy of different salvage treatments. The purpose of the present study was to validate a previously published prognostic scoring system for local failures of NPC treated by radiosurgery based on reported results in the literature.</p> <p>Methods</p> <p>A literature search yielded 3 published reports on the use of radiosurgery as salvage treatment of NPC that contained sufficient clinical information for validation of the scoring system. Prognostic scores of 18 patients from these reports were calculated and actuarial survival rates were estimated and compared to the original cohort used to design the prognostic scoring system. The area under the receiver operating characteristic curve was also determined and compared between the current and original patient groups.</p> <p>Results</p> <p>The calculated prognostic scores ranged from 0.32 to 1.21, with 15 patients assigned to the poor prognostic group and 3 to the intermediate prognostic group. The actuarial 3-year survival rates in the intermediate and poor prognostic groups were 67% and 0%, respectively. These results were comparable to the observed 3-year survival rates of 74% and 23% in the intermediate and poor prognostic group in the original reports. The area under the receiver operating characteristic curve for the current patient group was 0.846 which was similar to 0.841 in the original group.</p> <p>Conclusion</p> <p>The previously published prognostic scoring system demonstrated good prediction of treatment outcome after radiosurgery in a small group of NPC patients with poor prognosis. Prospective study to validate the scoring system is currently being carried out in our institution.</p

Fracture Propagation Driven by Fluid Outflow from a Low-permeability Aquifer

Deep saline aquifers are promising geological reservoirs for CO2 sequestration if they do not leak. The absence of leakage is provided by the caprock integrity. However, CO2 injection operations may change the geomechanical stresses and cause fracturing of the caprock. We present a model for the propagation of a fracture in the caprock driven by the outflow of fluid from a low-permeability aquifer. We show that to describe the fracture propagation, it is necessary to solve the pressure diffusion problem in the aquifer. We solve the problem numerically for the two-dimensional domain and show that, after a relatively short time, the solution is close to that of one-dimensional problem, which can be solved analytically. We use the relations derived in the hydraulic fracture literature to relate the the width of the fracture to its length and the flux into it, which allows us to obtain an analytical expression for the fracture length as a function of time. Using these results we predict the propagation of a hypothetical fracture at the In Salah CO2 injection site to be as fast as a typical hydraulic fracture. We also show that the hydrostatic and geostatic effects cause the increase of the driving force for the fracture propagation and, therefore, our solution serves as an estimate from below. Numerical estimates show that if a fracture appears, it is likely that it will become a pathway for CO2 leakage.Comment: 21 page

Delayed treatment of basilar thrombosis in a patient with a basilar aneurysm: a case report

<p>Abstract</p> <p>Introduction</p> <p>Acute occlusion of the basilar artery is a neurological emergency that has a high risk of severe disability and mortality. Delayed thrombolysis or endovascular therapy has been performed with some success in patients who present after 3 hours of symptom onset. Here we present the first case of delayed intra-arterial thrombolysis of a basilar artery thrombosis associated with a large saccular aneurysm.</p> <p>Case presentation</p> <p>A 73-year-old Caucasian man with a history of smoking and alcohol abuse presented to the Emergency Department complaining of diplopia and mild slurred speech and who progressed over 12 hours to coma and quadriparesis. He was found to have a large basilar tip aneurysm putting him at high risk for hemorrhage with lytic treatment.</p> <p>Conclusion</p> <p>The treatment options for basilar thrombosis are discussed. Aggressive treatment options should be considered despite long durations of clinical symptoms in basilar thrombosis, even in extremely high risk patients.</p

Investigating outcome inequalities in osteoarthritis management programmes: an analysis of registry data from the good life with osteoarthritis in Denmark (GLA:D®) programme using tapered balancing

Purpose: The burden of osteoarthritis (OA) is often greater among disadvantaged people and communities, prompting calls for more attention to equity-focussed research and policy. A specific concern is whether healthcare interventions may inadvertently widen health inequalities. OA management programmes (OAMP) have emerged in the past decade in a major international effort to improve provision of core non-surgical care for people with OA. Recent studies have focussed on equity of access. We address a complementary issue: having gained access, do people from socially disadvantaged groups have poorer outcomes than their advantaged counterparts, and if so, what might determine this? Methods: The study population was consecutive adults with knee OA attending the 8-week GLA:D® supervised exercise and education programme in Denmark between Oct 2014-Feb 2018. We defined a ‘multiple social disadvantage’ group based on primary/secondary school education and being either born outside Denmark or not having Danish citizenship. Their outcomes were compared with those of native Danish citizens with higher education. Outcomes of interest were pain intensity (0-100 VAS), KOOS Quality of Life subscale (QOL 0-100), EQ-5D-5L health utility (-0.624-1.0) at 3 and 12 months. Missing data were imputed using multiple imputation with chained equations. We used Coarsened Exact Matching (CEM) to restrict group comparisons to areas of common support, i.e. sufficient overlap on key prognostic factors (age, sex, body mass index, baseline value of the outcome measure of interest). We then used Entropy Balancing to sequentially control for differences between disadvantaged and advantaged groups in: (1) baseline value of the outcomes of interest (2) type of treatment centre, enrollment year (3) age, sex (4) BMI, previous knee injury, previous knee surgery (5) no. of selected comorbidities, no. of other non-knee pain sites (6) self-efficacy score, self-reported presence of depression (7) previous/current tailored exercise advice, weight loss counselling, analgesia/natural remedies (8) attendance at GLA:D® education and exercise sessions. Mean differences in outcomes between disadvantaged and advantaged groups were then estimated by weighted linear regression without balancing and then with entropy balancing weights from steps 1-8. Results: Of 18,448 eligible participants, 250 (1.4%) were classed as disadvantaged. Compared with advantaged participants, they were younger, less likely to have attended GLA:D® in a private physiotherapy clinic, reported more comorbidity, pain sites, depression, lower self-efficacy, and lower attendance on GLA:D® sessions. Both groups showed overall improvements over baseline in mean pain VAS, KOOS QOL and EQ5D scores at 3 months, typically maintained at 12 months. Before covariate balancing, disadvantaged participants had substantially worse scores than advantaged participants on each measure at both follow-up points (e.g. crude between-group mean differences (95%CI) in pain VAS at 12 months: 8.6 (4.5, 12.6) respectively: Table 1). Balancing for differences on baseline score, comorbidity, self-efficacy, and depression had the greatest effect on reducing differences in outcomes. Conclusions: Both disadvantaged and advantaged adults with knee OA reported improvements in key outcomes up to 12 months after OAMP attendance. However, compared with more advantaged adults, disadvantaged adults typically began the OAMP with more severe pain and poorer quality of life. This gap in outcomes was not reduced following OAMP attendance: for generic health-related quality of life in particular the gap widened slightly. Low self-efficacy, depression and other comorbidities may be potential determinants. Our analysis is of observed outcomes in a relatively small group with multiple disadvantage attending one OAMP. We encourage further work in other settings and groups. If confirmed, our findings suggest that while improving access to OAMPs for socially disadvantaged people with OA is important, additional actions may be needed to reduce outcome inequalities

Genetic polymorphisms of DNA double strand break gene Ku70 and gastric cancer in Taiwan

<p>Abstract</p> <p>Background and aim</p> <p>The DNA repair gene <it>Ku70</it>, an important member of non-homologous end-joining repair system, is thought to play an important role in the repairing of DNA double strand breaks. It is known that defects in double strand break repair capacity can lead to irreversible genomic instability. However, the polymorphic variants of <it>Ku70</it>, have never been reported about their association with gastric cancer susceptibility.</p> <p>Methods</p> <p>In this hospital-based case-control study, the associations of <it>Ku70 </it>promoter T-991C (rs5751129), promoter G-57C (rs2267437), promoter A-31G (rs132770), and intron 3 (rs132774) polymorphisms with gastric cancer risk in a Taiwanese population were investigated. In total, 136 patients with gastric cancer and 560 age- and gender-matched healthy controls recruited from the China Medical Hospital in Taiwan were genotyped.</p> <p>Results</p> <p>As for <it>Ku70 </it>promoter T-991C, the ORs after adjusted by age and gender of the people carrying TC and CC genotypes were 2.41 (95% CI = 1.53-3.88) and 3.21 (95% CI = 0.96-9.41) respectively, compared to those carrying TT wild-type genotype. The <it>P </it>for trend was significant (<it>P </it>< 0.0001). In the dominant model (TC plus CC versus TT), the association between <it>Ku70 </it>promoter T-991C polymorphism and the risk for gastric cancer was also significant (adjusted OR = 2.48, 95% CI = 1.74-3.92). When stratified by age and gender, the association was restricted to those at the age of 55 or elder of age (TC vs TT: adjusted OR = 2.52, 95% CI = 1.37-4.68, <it>P </it>= 0.0139) and male (TC vs TT: adjusted OR = 2.58, 95% CI = 1.33-4.47, <it>P </it>= 0.0085). As for the other three polymorphisms, there was no difference between both groups in the distributions of their genotype frequencies.</p> <p>Conclusion</p> <p>In conclusion, the <it>Ku70 </it>promoter T-991C (rs5751129), but not the <it>Ku70 </it>promoter C-57G (rs2267437), promoter A-31G (rs132770) or intron 3 (rs132774), is associated with gastric cancer susceptibility. This polymorphism may be a novel useful marker for gastric carcinogenesis.</p

Evaluation of the Osteogenic Potential of Growth Factorâ Rich Demineralized Bone Matrix In Vivo

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/141502/1/jper0036.pd