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.

Factors influencing the recommendation of the Human Papillomavirus vaccine by South African doctors working in a tertiary hospital.

Background: In South Africa, HPV vaccination programme has been incorporated recently in the school health system. Since doctors are the most trusted people regarding health issues in general, their knowledge and attitudes regarding HPV infections and vaccination are very important for HPV vaccine program nationally. Objective: The objective of this study was to investigate factors contributing to recommendation of HPV vaccines to the patients. Methods: This was a quantitative cross-sectional study conducted among 320 doctors, using a self-administered anonymous questionnaire. Results: All the doctors were aware of HPV and knew that HPV is transmitted sexually. Their overall level of knowledge regarding HPV infections and HPV vaccine was poor. But the majority intended to prescribe the vaccine to their patients. It was found that doctors who knew that HPV 6 and 11 are responsible for >90% of anogenital warts, their patients would comply with the counselling regarding HPV vaccination, and received sufficient information about HPV vaccination were 5.68, 4.91 and 4.46 times respectively more likely to recommend HPV vaccination to their patients, compared to their counterparts (p<0.05). Conclusion: There was a knowledge gap regarding HPV infection and HPV vaccine among the doctors.

Diabetes mellitus among tuberculosis patients: a cross sectional study from Pakistan

Background: The co-occurrence of diabetes mellitus (DM) and tuberculosis (TB) is largely associated with high frequency of morbidity. Objective: To determine the prevalence of DM among TB patients and describe the socio-demographic and behavioral factors associated with TB-DM co-occurrence . Methods: We enrolled 500 TB patients from September, 2014 to August 2015 at four major public sector hospitals of Lahore, Pakistan. A questionnaire was used to collect information regarding associated socio-demographic and behavioral factors of the patients. We monitored the fasting blood sugar of each patient by using a semi automated clinical chemistry analyzer followed by an HbA1c level check of all hyperglycemic patients. Results: The prevalence of TB-DM co-occurrence was 14.8%. The prevalence of TB-DM was higher (62.2%) among males. The >57 year age group had the highest proportion of patients (35.1%), with co-existent TB-DM. Most were illiterate (73.0%) and unemployed (48%). Moreover, among the 74 patients positive for TB-DM had a history of smoking. Age and education level were significantly associated with DM-TB while gender, occupation and smoking were not associated. Conclusion: The study revealed a 14.8% prevalence of DM among TB patients. This was associated with several socio-demographic factors, including age, unemployment, literacy and polluted environment. Thus, poor and unhealthy lifestyles were the factors associated with DM among immunologically compromised individuals due to TB.

Late-stage disease at presentation to an HIV clinic in eastern Tanzania: A retrospective cross-sectional study

Background Late presentation and delayed treatment initiation is associated with poor outcomes in patients with HIV. Little is known about the stage at which HIV patients present at HIV clinics in Tanzania. Aim This study aimed at determining the proportion of HIV patients presenting with WHO clinical stages 3 and 4 disease, and the level of immunity at the time of enrollment at the care and treatment center. Methods A retrospective cross-sectional study was conducted among 366 HIVinfected adults attending HIV clinic at Mwananyamala Hospital in Dar es Salaam, Tanzania. Data were obtained from the care and treatment clinic database. Results Late stage disease at the time of presentation was found in 276 (75.4%) of the patients; out of whom 153 (41.8%) presented with CD4 count <200 cells/ul and 229 (62.6%) presented with WHO clinical stage 3 or 4 at the time of clinic enrollment. Strategies to improve early diagnosis and treatment initiation should be improved.