The accuracy of protein structure alignment servers

Background: Protein structural alignment is one of the most fundamental and crucial areas of research in the domain of computational structural biology. Comparison of a protein structure with known structures helps to classify it as a new or belonging to a known group of proteins. This, in turn, is useful to determine the function of protein, its evolutionary relationship with other protein molecules and grasping principles underlying protein architecture and folding. Results: A large number of protein structure alignment methods are available. Each protein structure alignment tool has its own strengths andweaknesses that need to be highlighted.We compared and presented results of six most popular and publically available servers for protein structure comparison. These web-based servers were compared with the respect to functionality (features provided by these servers) and accuracy (how well the structural comparison is performed). The CATH was used as a reference. The results showed that overall CE was top performer. DALI and PhyreStorm showed similar results whereas PDBeFold showed the lowest performance. In case of few secondary structural elements, CE, DALI and PhyreStorm gave 100% success rate. Conclusion: Overall none of the structural alignment servers showed 100% success rate. Studies of overall performance, effect of mainly alpha and effect of mainly beta showed consistent performance. CE, DALI, FatCat and PhyreStorm showed more than 90% success rate.

Five years retrospective cohort analysis of treatment outcomes of TB-HIV patients at a PEPFAR/DOTS Centre in South Eastern Nigeria.

Background: Human immunodeficiency virus (HIV) associated tuberculosis (TB) remains a major global public health challenge, with an estimated 1.4 million patients worldwide. Co-infection with HIV leads to challenges in the diagnosis and treatment of patients. Objectives: The aim of this study was to assess treatment outcomes of a cohort of smear positive TB-HIV co-infected patients over a five-year study period. Methods: A retrospective cohort study of 600 smear-positive tuberculosis patients registered at the chest unit of the University of Nigeria Teaching Hospital, Enugu from January 2008 to December 2012 was done. The data was analyzed using SPSS Version 17. Results: One hundred and three (17.2%) of the patients were co-infected with TB/HIV, while 398 (66.3%) and 99 (16.5%) were HIV negative and unknown respectively. Among the co-infected patients, 45(43.7%) were cured as against 222(55.8%) in the TBHIV negatives (Z=4.53, p=0.000, 95%CI= 0.12-0.34). Respectively in the TB-HIV co-infected and TB-HIV negative patients, treatment completed were 21(20.4%) and 71(17.8%) (Z=9.15, p=0.000, 95%= 0.4035-0.60); defaulted 19(18.5%) vs 70 (17.6%) (Z=9.29, p=0.000, 95%CI=0.42-0.60), died 10(9.7%) vs. 6(1.5%) (Z=1.22, p=0.224, 95%CI= -0.0286-0.1086), and failures were 1(0.9%) vs. 7(1.8%) (Z=2.48, p=0.013, 95%CI=0.04-0.10). Treatment success rate was lower in TB-HIV co-infected patients, 64.1% compared to TB-HIV negative patients with 73.6%. Also those that defaulted among the TB-HIV co-infected patients (18.5%) were higher than 17.6% among TB-HIV negative patients, a difference of 0.9%. Conclusion: Findings demonstrate that HIV co-infection affects TB treatment outcomes adversely. Treatment adherence, timely and sustained access to antiretroviral therapy for TB/HIV co-infected patients are important.

Profile and treatment outcomes of patients with tuberculosis in Northeastern Ethiopia: a cross sectional study.

Background: Data on the epidemiology of tuberculosis and its treatment outcomes were incomplete in the study area and this study was done to fill this gap. Methods: Institution based cross sectional study was conducted from January 2011 to December 2014. A total of 949 TB patients who were on treatment in North Eastern Ethiopia, Eastern Amhara region were included. Data was analyzed using SPSS version 20. Frequency, percentages and means were used to present data. To assess the associations of treatment outcomes with sex, age, type of TB and human immunodeficiency virus (HIV), logistic regression was used. Results: The proportion of smear positive and negative pulmonary TB, and extra pulmonary TB were 187/949 (19.7%), 322/949 (33.9%) and 440/949 (46.4%), respectively. Treatment success rate was 853/949 (89.9%). Smear positive pulmonary TB and TB/HIV co-infections were significantly associated with unsuccessful treatment outcome, P≤ 0.002. Conclusion: Extra pulmonary TB was the most prevalent types of TB followed by smear negative pulmonary TB. Treatment success rate was above the WHO target of 85%. The causes for the high proportion of smear negative PTB and EPTB should be further investigated. Special emphasis should be put on smear positive PTB patients and TB/HIV co-infected patients to decrease unsuccessful treatment outcome and TB transmissions.

An in-house real-time polymerase chain reaction: standardisation and comparison with the Cobas Amplicor HBV monitor and Cobas AmpliPrep/Cobas TaqMan HBV tests for the quantification of hepatitis B virus DNA

This study aimed to standardise an in-house real-time polymerase chain reaction (rtPCR) to allow quantification of hepatitis B virus (HBV) DNA in serum or plasma samples, and to compare this method with two commercial assays, the Cobas Amplicor HBV monitor and the Cobas AmpliPrep/Cobas TaqMan HBV test. Samples from 397 patients from the state of São Paulo were analysed by all three methods. Fifty-two samples were from patients who were human immunodeficiency virus and hepatitis C virus positive, but HBV negative. Genotypes were characterised, and the viral load was measure in each sample. The in-house rtPCR showed an excellent success rate compared with commercial tests; inter-assay and intra-assay coefficients correlated with commercial tests (r = 0.96 and r = 0.913, p < 0.001) and the in-house test showed no genotype-dependent differences in detection and quantification rates. The in-house assay tested in this study could be used for screening and quantifying HBV DNA in order to monitor patients during therapy.

Analysis of Outcome of Intraplueral Streptokinase in Pediatric Empyema Thoracis even in Advanced Stages: A Prospective Study

Background: Empyema thoracis in children causes significant morbidity. Standard treatment of Empyema thoracis includes tube drainage and antibiotics. But the tube drainage often fails. Intrapleural Streptokinase has been used in empyema thoracis with good success rate. Objectives: We evaluated the efficacy of intra-pleural Streptokinase in management of empyema thoracis even in advanced stages. Patients and Methods: A total of 28 patients with empyema thoracis requiring intercostal tube drainage aged zero to twelve years were included in the study who were admitted in Pediatric intensive care unit. 15,000 units/kg of Streptokinase was instilled into the pleural cavity. Response was assessed by clinical outcome, after unclamping and subsequent chest radiography and serial chest ultrasounds. Results: Streptokinase enhanced drainage in all patients with complete resolution of empyema thoracis in 26 patients. Two patients were referred for surgery. Only 7.2% required surgery. Streptokinase was equally effective if started before or after seven days. Conclusions: Intrapleural Streptokinase is the preferred treatment for treating pediatric empyema thoracis even in advanced stages and can avoid surgery.

Different Aspects of General Anesthesia in Pediatric Dentistry: A Review

Context:Most child population is able to undergo dental treatment in the conventional setting. However, some children fail to cope with in-office conscious state and cannot respond to usual management modalities. This review aims to discuss the topic further. Evidence Acquisition: A computerized search in databases PubMed, MEDLINE, EMBASE, Google Scholar and Google were performed using dental general anesthesia related keywords. Original and review English-written articles that were limited to child population were retrieved without any limitation of publication date. The suitable papers were selected and carefully studied. A data form designed by author was used to write relevant findings. Results: Preoperative oral examination and comprehensive evaluation of treatment needs is only possible after clinical and radiographic oral examination. Effective collaboration in dental GA team should be made to minimize psychological trauma of children who undergo dental GA. Before conducting comprehensive dental treatment under GA, the general health of the child and the success rate of procedures provided needs to be accurately evaluated. It is noteworthy that determination of the optimal timing for GA dental operation is of great importance. Providing safety with pediatric dental rehabilitation under GA is critical. Conclusions: Besides criteria for case selection of dental GA, some degree of dental practitioner’s judgment is required to make decision. Pre- and post-operative instructions to parents or caregiver decrease the risk of complications. However, trained resuscitation providers, careful monitoring and advanced equipment minimize adverse outcomes.