Studies on distributed approaches for large scale multi-criteria protein structure comparison and analysis

Protein Structure Comparison (PSC) is at the core of many important structural biology problems. PSC is used to infer the evolutionary history of distantly related proteins; it can also help in the identification of the biological function of a new protein by comparing it with other proteins whose function has already been annotated; PSC is also a key step in protein structure prediction, because one needs to reliably and efficiently compare tens or hundreds of thousands of decoys (predicted structures) in evaluation of 'native-like' candidates (e.g. Critical Assessment of Techniques for Protein Structure Prediction (CASP) experiment). Each of these applications, as well as many others where molecular comparison plays an important role, requires a different notion of similarity, which naturally lead to the Multi-Criteria Protein Structure Comparison (MC-PSC) problem. ProCKSI (www.procksi.org), was the first publicly available server to provide algorithmic solutions for the MC-PSC problem by means of an enhanced structural comparison that relies on the principled application of information fusion to similarity assessments derived from multiple comparison methods (e.g. USM, FAST, MaxCMO, DaliLite, CE and TMAlign). Current MC-PSC works well for moderately sized data sets and it is time consuming as it provides public service to multiple users. Many of the structural bioinformatics applications mentioned above would benefit from the ability to perform, for a dedicated user, thousands or tens of thousands of comparisons through multiple methods in real-time, a capacity beyond our current technology. This research is aimed at the investigation of Grid-styled distributed computing strategies for the solution of the enormous computational challenge inherent in MC-PSC. To this aim a novel distributed algorithm has been designed, implemented and evaluated with different load balancing strategies and selection and configuration of a variety of software tools, services and technologies on different levels of infrastructures ranging from local testbeds to production level eScience infrastructures such as the National Grid Service (NGS). Empirical results of different experiments reporting on the scalability, speedup and efficiency of the overall system are presented and discussed along with the software engineering aspects behind the implementation of a distributed solution to the MC-PSC problem based on a local computer cluster as well as with a GRID implementation. The results lead us to conclude that the combination of better and faster parallel and distributed algorithms with more similarity comparison methods provides an unprecedented advance on protein structure comparison and analysis technology. These advances might facilitate both directed and fortuitous discovery of protein similarities, families, super-families, domains, etc, and also help pave the way to faster and better protein function inference, annotation and protein structure prediction and assessment thus empowering the structural biologist to do a science that he/she would not have done otherwise

Studies on distributed approaches for large scale multi-criteria protein structure comparison and analysis

Protein Structure Comparison (PSC) is at the core of many important structural biology problems. PSC is used to infer the evolutionary history of distantly related proteins; it can also help in the identification of the biological function of a new protein by comparing it with other proteins whose function has already been annotated; PSC is also a key step in protein structure prediction, because one needs to reliably and efficiently compare tens or hundreds of thousands of decoys (predicted structures) in evaluation of 'native-like' candidates (e.g. Critical Assessment of Techniques for Protein Structure Prediction (CASP) experiment). Each of these applications, as well as many others where molecular comparison plays an important role, requires a different notion of similarity, which naturally lead to the Multi-Criteria Protein Structure Comparison (MC-PSC) problem. ProCKSI (www.procksi.org), was the first publicly available server to provide algorithmic solutions for the MC-PSC problem by means of an enhanced structural comparison that relies on the principled application of information fusion to similarity assessments derived from multiple comparison methods (e.g. USM, FAST, MaxCMO, DaliLite, CE and TMAlign). Current MC-PSC works well for moderately sized data sets and it is time consuming as it provides public service to multiple users. Many of the structural bioinformatics applications mentioned above would benefit from the ability to perform, for a dedicated user, thousands or tens of thousands of comparisons through multiple methods in real-time, a capacity beyond our current technology. This research is aimed at the investigation of Grid-styled distributed computing strategies for the solution of the enormous computational challenge inherent in MC-PSC. To this aim a novel distributed algorithm has been designed, implemented and evaluated with different load balancing strategies and selection and configuration of a variety of software tools, services and technologies on different levels of infrastructures ranging from local testbeds to production level eScience infrastructures such as the National Grid Service (NGS). Empirical results of different experiments reporting on the scalability, speedup and efficiency of the overall system are presented and discussed along with the software engineering aspects behind the implementation of a distributed solution to the MC-PSC problem based on a local computer cluster as well as with a GRID implementation. The results lead us to conclude that the combination of better and faster parallel and distributed algorithms with more similarity comparison methods provides an unprecedented advance on protein structure comparison and analysis technology. These advances might facilitate both directed and fortuitous discovery of protein similarities, families, super-families, domains, etc, and also help pave the way to faster and better protein function inference, annotation and protein structure prediction and assessment thus empowering the structural biologist to do a science that he/she would not have done otherwise

An Assessment of Public Opinion in Balochistan about Federal Form of Government in Pakistan

Almost every state or society particularly a pluralistic one is composed of various nationalities or sub-national groups whereas every segment has its own distinct identity being a source of pride and strength for its survival. In relatively homogenous societies, the process of nation-building though not easy is at least less cumbersome whereas in pluralistic societies this process demands a lot of hard work on the part of the elite who must exhibit vision, wisdom, foresight and patience; because such societies are always fraught with the danger that any of the nationalities or sub-national group may dominate the others. The societies having a considerable level of social, cultural and linguistic heterogeneity hence horizontally/vertically divided and cross-divided in the pursuit of their distinct preferences and priorities can hardly be united under a single administrative structure nevertheless they can be persuaded to form a union under some common government.  For this purpose, a federal arrangement may be suitable option because it provides for unity in diversity rather than unity in its absolute terms. The federation of Pakistan, since its vey inception, is struggling to create the said unity particularly with reference to the situation in Balochistan which is facing a long and multi-faceted unrest posing a substantial challenge for the federation. The present study empirically explores the nature of grievances of the people of Balochistan with respect to the federation of Pakistan by conducting a field survey and establishes that majority of the people of Balochistan do not believe that the federal design in Pakistan is functioning in its true letter and spirit with reference to Balochistan

Non-Operative Management of Acute Uncomplicated Appendicitis in Children

Objective: To compare the efficacy of non-surgical conservative management with surgical management in cases of uncomplicated acute appendicitis in children. Study design: Prospective comparative study. Settings: Pediatric surgery Department, --removed for blind review---- Study duration: 1st February 2020 to 31st May 2021. Methodology: Ninety patients of either gender with age range from 5-12 years, diagnosed as uncomplicated acute appendicitis, were divided in two groups. Group C patients were managed conservatively with antibiotics (ceftriaxone 100 mg/kg/day, amikacin 10mg/kg/day and metronidazole 22.5 mg/kg/day) and maintenance fluids were started. Patients were observed for improvement or any signs of deterioration. Those who deteriorated within 24 hours were management with surgical management immediately. Follow ups were carried out after discharge at 7th day, 1 month and six months. Patients reporting with recurrence of symptoms were managed with appendicectomy. Group S patients were managed with appendicectomy with open technique. Patients were observed for post-operative complications. Results: Demographic data of both groups was comparable. In group C, 34 (75.56%) patients were successfully treated with conservative management, whereas in group S, 39 (86.67%) were successfully treated with surgical management. The difference was insignificant with a p-value of 0.114. In group C, 5 (11.11%) patients did not respond to conservative management and they were managed with appendicectomy and recurrence of symptoms was seen in 6 (13.33%) patients in group C, they were also managed with appendicectomy. In group S, 6 (13.33%) patients suffered post-operative complications. Mean length of stay in hospital was 4.31±1.20 and 4.09±1.12 days in group C and S respectively. This difference was statistically insignificant with a p-value of 0.368. Conclusion:     It is concluded in our study that uncomplicated acute appendicitis in children can be successfully managed with non-surgical conservative management. Keywords: Acute appendicitis, Appendicectomy, Conservative management, Non-surgical management, Pediatric surgery, Uncomplicated acute appendicitis

Non-Operative Management of Acute Uncomplicated Appendicitis in Children

Objective: To compare the efficacy of non-surgical conservative management with surgical management in cases of uncomplicated acute appendicitis in children. Study design: Prospective comparative study. Settings: Pediatric surgery Department, --removed for blind review---- Study duration: 1st February 2020 to 31st May 2021. Methodology: Ninety patients of either gender with age range from 5-12 years, diagnosed as uncomplicated acute appendicitis, were divided in two groups. Group C patients were managed conservatively with antibiotics (ceftriaxone 100 mg/kg/day, amikacin 10mg/kg/day and metronidazole 22.5 mg/kg/day) and maintenance fluids were started. Patients were observed for improvement or any signs of deterioration. Those who deteriorated within 24 hours were management with surgical management immediately. Follow ups were carried out after discharge at 7th day, 1 month and six months. Patients reporting with recurrence of symptoms were managed with appendicectomy. Group S patients were managed with appendicectomy with open technique. Patients were observed for post-operative complications. Results: Demographic data of both groups was comparable. In group C, 34 (75.56%) patients were successfully treated with conservative management, whereas in group S, 39 (86.67%) were successfully treated with surgical management. The difference was insignificant with a p-value of 0.114. In group C, 5 (11.11%) patients did not respond to conservative management and they were managed with appendicectomy and recurrence of symptoms was seen in 6 (13.33%) patients in group C, they were also managed with appendicectomy. In group S, 6 (13.33%) patients suffered post-operative complications. Mean length of stay in hospital was 4.31±1.20 and 4.09±1.12 days in group C and S respectively. This difference was statistically insignificant with a p-value of 0.368. Conclusion:     It is concluded in our study that uncomplicated acute appendicitis in children can be successfully managed with non-surgical conservative management. Keywords: Acute appendicitis, Appendicectomy, Conservative management, Non-surgical management, Pediatric surgery, Uncomplicated acute appendicitis

Surgical Site Infection with and without Prophylatic Antibiotic in Children undergoing Elecltive Inguinal Herniotomy

Objective: This study was aimed at determining the frequency of surgical site infection in children undergoing elective inguinal herniotomy with and without prophylactic antibiotic. Study design: Prospective comparative study. Settings: Pediatric surgery Department, Ghulam Muhammad Mahar Medical College Sukkur. Study duration: From 1st February 2020 to 31th March 2021. Methodology: One hundred and sixty patients selected for this study and were equally divided into two groups. Group A received antibiotic prophylaxis (Injection ceftriaxone 50mg/kg) before the induction of general anesthesia, whereas Group P received placebo before the induction of general anesthesia. Demographic data and duration of surgery was noted on a proforma. Surgical procedure was carried out following standard surgical protocols. Post-operatively all patients were observed by an independent observer. Patients were observed for post-operative fever, inflammation of the surgical site and discharge from the site of incision. Wound was examined on 1st, 3rd, 7th and 30th post-operative day. For labeling Surgical Site Infection, Center of Disease criteria was followed. Results: Demographic data of both groups was comparable. Mean duration of surgery in group A was 29.61±7.47 minutes, while it was 32.97±8.73 minutes in group P with p-value of 0.08. Out of 160 patients, thirteen patients developed surgical site infection; 5 (6.25%) patients belonged to group A, while 8 (10%) belonged to group P with a p-value of 0.385. Conclusion: It is concluded in our study that use of prophylactic antibiotics in elective herniotomy cases performed in pediatric patients do not significantly decrease the incidence of Surgical Site Infection