Discovery of large genomic inversions using long range information.

BackgroundAlthough many algorithms are now available that aim to characterize different classes of structural variation, discovery of balanced rearrangements such as inversions remains an open problem. This is mainly due to the fact that breakpoints of such events typically lie within segmental duplications or common repeats, which reduces the mappability of short reads. The algorithms developed within the 1000 Genomes Project to identify inversions are limited to relatively short inversions, and there are currently no available algorithms to discover large inversions using high throughput sequencing technologies.ResultsHere we propose a novel algorithm, VALOR, to discover large inversions using new sequencing methods that provide long range information such as 10X Genomics linked-read sequencing, pooled clone sequencing, or other similar technologies that we commonly refer to as long range sequencing. We demonstrate the utility of VALOR using both pooled clone sequencing and 10X Genomics linked-read sequencing generated from the genome of an individual from the HapMap project (NA12878). We also provide a comprehensive comparison of VALOR against several state-of-the-art structural variation discovery algorithms that use whole genome shotgun sequencing data.ConclusionsIn this paper, we show that VALOR is able to accurately discover all previously identified and experimentally validated large inversions in the same genome with a low false discovery rate. Using VALOR, we also predicted a novel inversion, which we validated using fluorescent in situ hybridization. VALOR is available at https://github.com/BilkentCompGen/VALOR

Comparing performance of amoxicillin and intramuscular benzathine penicillin in relieving manifestations of Streptococcal pharyngitis in children

Objective: To compare clinical and bacteriologic responses to intramuscular benzathine penicillin G (BPG) and single dose of amoxicillin in Group A streptococcal (GAS) pharyngitis.Design: This study included 571 children from 6 to 15 years old age, with pharyngitis, who were admitted to 45 elementary and guidance schools from 7 regions of Education Organization in North-East of Iran, Mashhad. They were screened for enrollment and if he/she presented pharyngitis with clinical criteria of sore throat, erythema, exudate and tender or enlarged anterior cervical lymph nodes. Exclusion criteria included reports of antibiotic use, negative throat culture for GAS and history of allergy to the drugs. Clinical and bacteriologic responses to BPG and once daily orallyamoxicillin were considered and compared.Results: In the amoxicillin group, treatment failure was more than the penicillin group (18.9% vs. 6.4%, respectively) but the difference was not statistically significant (p < 0.05). Both drugs were significantly effective in reducing pharyngitis manifestations but penicillin was significantly more effective in reducing exudate than amoxicillin.Conclusion: Our study was in line with studies comparing the two drugs. The results show that once-daily therapy with amoxicillin is as effective as intramuscular benzathine penicillin G for the treatment of GAS pharyngitis, but penicillin was significantly more effective in reducing exudate and concurrent signs vs. amoxicillin.Keywords: Streptococcal Pharyngitis, Erythema, Lymph nodes, Amoxicillin, Penicilli

A CNN cascade for landmark guided semantic part segmentation

This paper proposes a CNN cascade for semantic part segmentation guided by pose-specifc information encoded in terms of a set of landmarks (or keypoints). There is large amount of prior work on each of these tasks separately, yet, to the best of our knowledge, this is the first time in literature that the interplay between pose estimation and semantic part segmentation is investigated. To address this limitation of prior work, in this paper, we propose a CNN cascade of tasks that firstly performs landmark localisation and then uses this information as input for guiding semantic part segmentation. We applied our architecture to the problem of facial part segmentation and report large performance improvement over the standard unguided network on the most challenging face datasets. Testing code and models will be published online at http://cs.nott.ac.uk/~psxasj/

Prevalence of ESBLs in Acinetobacter baumannii isolated from intensive care unit (ICU) of Ghaem hospital, Mashhad, Iran

Acinetobacter baumannii is an important opportunistic pathogen that mainly infects critically patients in intensive care units (ICU). The production of plasmid-mediated extended-spectrum b-lactamases (ESBLs) is one of the most important mechanisms of resistance against b-lactam antibiotics. This study aimed to evaluate the prevalence of ESBLs in A. baumannii isolated from ICU of Ghaem hospital, Mashhad, Iran. A total of 140 A. baumannii isolates recovered from hospitalized patients in ICU of Ghaem hospital in Mashhad city from December 2014 to March 2015. Identification of A. baumannii isolates carried out using biochemical laboratory methods and then confirmed by OXA-51 PCR screening. Susceptibility testing performed using disk diffusion (Kirby-Bauer) method as recommended by CLSI guidelines. A. baumannii isolates screened for production of ESBLs using combination disk test. blaPER, blaGES, blaTEM, blaSHV, blaCTX, blaVEB and blaOXA-10 beta-lactamase genes detected using conventional PCR. The most antibacterial resistance was against cefuroxime (­99.3%) and colistin was the most effective antibiotic. None of the isolates were ESBL producer by combination disk test. However, results of PCR revealed that the prevalence of blaPER, blaGES and blaTEM genes were 7.1%, 4.3% and 27.1%, respectively. blaCTX, blaVEB, and blaOXA-10 were not found in any of isolates. According to the results, the high resistance was seen against selected antibiotics and the phenotypic tests are not sufficient alone for determination of ESBLs producer of A. baumannii isolates. So, molecular tests are also necessary for detection of these enzymes

Baby Skyrmion chains

Previous results on multi-charged Baby Skyrmion solutions have pointed to a modular structure, comprised of charge two rings and single charge one Skyrmions, which combine to form higher charged structures. In this paper we present numerical evidence which shows an alternative finite chain, multi-charged global energy minimum Baby Skymion solution. We then proceed from the infinite plane, to Baby Skyrmions on a cylinder and then a torus, to obtain the solutions of periodic Baby Skyrmions, of which periodic segments will correspond to sections of large charge Baby Skyrmions in the plane

A survey of attitudes, practices, and knowledge regarding drug-drug interactions among medical residents in Iran

Background When prescribing medications, physicians should recognize clinically relevant potential drug–drug interactions (DDIs). To improve medication safety, it is important to understand prescribers’ knowledge and opinions pertaining to DDIs. Objective To determine the current DDI information sources used by medical residents, their knowledge of DDIs, their opinions about performance feedback on co-prescription of interacting drugs. Setting Academic hospitals of Mashhad University of Medical Sciences (MUMS) in Iran. Methods A questionnaire containing questions regarding demographic and practice characteristics, DDI information sources, ability to recognize DDIs, and opinions about performance feedback was distributed to medical residents of 22 specialties in eight academic hospitals in Iran. We analyzed their perception pertaining to DDIs, their performance on classifying drug pairs, and we used a linear regression model to assess the association of potential determinants on their DDI knowledge. Main Outcome Measure prescribers’ knowledge and opinions pertaining to DDIs. Results The overall response rate and completion rate for 315 distributed questionnaires were 90% (n = 295) and 86% (n = 281), respectively. Among DDI information sources, books, software on mobile phone or tablet, and Internet were the most commonly-used references. Residents could correctly classify only 41% (5.7/14) of the drug pairs. The regression model showed no significant association between residents’ characteristics and their DDI knowledge. An overwhelming majority of the respondents (n = 268, 95.4%) wished to receive performance feedback on co-prescription of interacting drugs in their prescriptions. They mostly selected information technology-based tools (i.e. short text message and email) as their preferred method of receiving feedback. Conclusion Our findings indicate that prescribers may have poor ability to prevent clinically relevant potential DDI occurrence, and they perceive the need for performance feedback. These findings underline the importance of well-designed computerized alerting systems and delivering performance feedback to improve patient safety

Effects of Computerized Decision Support Systems on Management of Atrial Fibrillation: A Scoping Review

Background: Potential role of computerized decision support system on management of atrial fibrillation is not well understood. Objectives: To systematically review studies that evaluate the effects of computerized decision support systems and decision aids on aspects pertaining to atrial fibrillation. Data sources: We searched Medline, Scopus and Cochrane database. Last date of search was 2016, January 10. Selection criteria: Computerized decision support systems that help manage atrial fibrillation and decision aids that provide useful knowledge for patients with atrial fibrillation and help them to self-care. Data collection and analysis: Two reviewers extracted data and summarized findings. Due to heterogeneity, meta-analysis was not feasible; mean differences of outcomes and confidence intervals for a difference between two Means were reported. Results: Seven eligible studies were included in the final review. There were one observational study without controls, three observational studies with controls, one Non-Randomized Controlled Trial and two Randomized Controlled Trials. The interventions were three decision aids that were used by patients and four computerized decision support systems. Main outcomes of studies were: stroke events and major bleeding (one article), Changing doctor-nurse behavior (three articles), Time in therapeutic International Normalized Ratio range (one article), decision conflict scale (two articles), patient knowledge and anxiety about stroke and bleeding (two articles). Conclusions: A computerized decision support system may decrease decision conflict and increase knowledge of patients with atrial fibrillation (AF) about risks of AF and AF treatments. Effect of computerized decision support system on outcomes such as changing doctor-nurse behavior, anxiety about stroke and bleeding and stroke events could not be shown.We need more studies to evaluate the role of computerized decision support system in patients with atrial fibrillation