Molecular Simulations of the Ribosome and Associated Translation Factors

The ribosome is a macromolecular complex which is responsible for protein synthesis in all living cells according to their transcribed genetic information. Using X-ray crystallography and, more recently, cryo-electron microscopy (cryo-EM), the structure of the ribosome was resolved at atomic resolution in many functional and conformational states. Molecular dynamics simulations have added information on dynamics and energetics to the available structural information, thereby have bridged the gap to the kinetics obtained from single-molecule and bulk experiments. Here, we review recent computational studies that brought notable insights into ribosomal structure and function.Comment: 11 pages, 3 figures, to be published in Current Opinion in Structural Biolog

Risk assessment of failure of outdoor high voltage polluted insulators under combined stresses near shoreline

The aim of this paper is to investigate the various effects of climate conditions on outdoor insulators in coastal areas as a result of saline contamination under acidic and normal cold fog, determining significant electrical and physico-chemical changes on the insulator surface and considering the effect of discharge current, electric field distribution and surface roughness. To replicate similar conditions near the shoreline, experimental investigations have been carried out on insulation materials with the combined application of saline contamination and acidic or normal cold fog. The test samples included silicone rubber (SiR), ethylene propylene diene monomer (EPDM) and high-density polyethylene (HDPE), which were used as reference. The materials are of the same composition as those used in real-life outdoor high voltage insulators. All samples were aged separately in an environmental chamber for 150 h for various saline contaminations combined with acidic and normal cold fog, and were generated by means of the adopted experimental setup. This analysis represented conditions similar to those existing near the shoreline exposed to saline and acid spray during winter and early spring. Electric field and discharge current along polymeric samples were examined under acidic and normal cold fog. Fourier transform infrared (FTIR) spectroscopy and scanning electron microscopic (SEM) were used to probe the physico-chemical changes on the samples surface and investigate the hydrophobicity recovery property after aging tests. Finally, a comparative study was carried out on polymeric samples before and after being exposed to the acidic and normal cold fog based on the results obtained from the experiment. Research data may provide references for the better prediction of surface degradation as well as for the better material coating and design of external insulation

Algoritma Genetika Ganda (AGG) untuk Capacitated Vehicle Routing Problem (CVRP)

Capacitated vehicle routing problem (CVRP) merupakan suatu permasalahan penyaluran barang, dengan kendaraan berkapasitas tertentu, dari satu depot ke beberapa pelanggan, yang bertujuan untuk mencari rute yang meminimalkan total jarak yang ditempuh. Contoh nyata CVRP adalah permasalahan penyaluran bahan bakar minyak ke Stasiun Pengisian Bahan Bakar Umum (SPBU). Ada banyak metode yang telah dipakai untuk menyelesaikan CVRP, namun penggunaan algoritma genetika (AG) masih belum memberikan hasil yang memuaskan. Namun keberhasilan AG untuk menyelesaikan banyak permasalahan lain menunjukkan bahwa penggunaan AG akan memberikan hasil yang semakin baik apabila terus diteliti. Untuk mempermudah menyelesaikan CVRP, dapat dilakukan dekomposisi agar CVRP terbagi menjadi beberapa permasalahan yang lebih sederhana yang dapat diselesaikan secara independen. Berdasarkan hal tersebut, dirumuskan algoritma genetika ganda (AGG) yang terlebih dahulu berusaha untuk mendekomposisi CVRP dan kemudian mencari rute terpendek pada setiap permasalahan dengan menggunakan dua algoritma genetika sederhana berbeda. Untuk mengetahui seberapa baik AGG dalam menyelesaikan CVRP, dilakukan pembandingan antara AGG dengan AG. Pembandingan AGG dengan AG dilihat dari tiga segi, yaitu jarak, waktu komputasi, dan total generasi. Agar mendapatkan hasil yang akurat, pembandingan dilakukan dengan membuat empat permasalahan yaitu P50, P75, P100, dan P125, dan untuk setiap permasalahan digunakan empat belas variasi kapasitas kendaraan yang berbeda. Didapatkan hasil bahwa untuk segi waktu komputasi dan total generasi, AGG lebih baik dari AG. Sedangkan dari segi jarak, AGG juga lebih baik dari AG kecuali untuk beberapa kapasitas kendaraan yang kecil pada permasalahan P50 dan P75. Hasil juga menunjukkan bahwa penambahan kapasitas kendaraan mengakibatkan AGG menjadi jauh lebih baik dibandingkan dengan AG. Kata kunci: algoritma genetika (AG), algoritma genetika g anda (AGG), capacitated vehicle routing problem (CVRP

Frequency of NSAID induced peptic ulcer disease

Objective: To determine the frequency of peptic ulcer disease in patients on nonsteroidal anti-inflammatory drugs (NSAID). Methods: Record of eight hundred and twenty consecutive patients undergoing upper gastrointestinal (GI) endoscopy; from January 1998 to December 2000 were reviewed. The endoscopic diagnosis varied from gastritis, peptic ulcer to duodenitis. The use of NSAID was documented by reviewing medical records of patients with peptic ulcer. Results: Peptic ulcers were found in 43% (353/820) patients. NSAID associated peptic ulcers were identified in 14.7% (52/353) patients. Diclofenac and aspirin were most common NSAIDs associated with peptic ulcers in 32.7% (17/52) and 30.7% (16/52) patients, respectively. Duodenal ulcer was more common than gastric ulcer 65.3% (34/52) and 42.3% (22/52), respectively. H. pylori infection was present in 46% (24/52) of the cases. NSAIDs treatment and / or H. pylori infection compared to non NSAIDs and non H. pylori infected peptic ulcer disease were significantly associated with gastric ulcer (p = 0.004) and duodenal ulcer (p = 0.009) respectively. Conclusion: NSAID-associated peptic ulcer disease is common in Pakistan and most frequently associated with gastric and duodenal ulcer. H. pylori infection is common in association with NSAID related peptic ulcers (JPMA 56:218;2006

Giardiasis in patients with dyspeptic symptoms

AIM: To investigate the prevalence of giardiasis in patients with dyspeptic symptoms. METHODS: Clinical records of consecutive patients who attended Gastroenterology Department at Aga Khan University Hospital from January 2000 to June 2003 and had esophagogastroduodenoscopy (EGD) with duodenal biopsies and international classification of diseases 9th revision with clinical modifications (ICD-9-CM) coded with giardiasis were studied. RESULTS: Two hundred and twenty patients fulfilled the above criteria. There were 44% (96/220) patients who were giardiasis positive, 72% (69/96) of them were males and 28% (27/96) of them were females. There were 65% (81/124) males and 35% (43/124) females who were giardiasis negative. The mean age of patients with giardiasis was 28+/-17 years, while that of giardiasis negative patients was 40+/-18 years (P\u3c0.001). In patients with giardiasis, abdominal pain was present in 71% (68/96) of patients (P = 0.02) and diarrhea in 29% (28/96) (P = 0.005); duodenitis in 25% (24/96) on EGD (P = 0.006) and in 68% (65/96) on histopathology (P = 0.002). CONCLUSION: Giardiasis occurs significantly in young people with abdominal pain, while endoscopic duodenitis is seen in only 25% of giardiasis positive cases, which supports routine duodenal biopsy

Efficacy of L-ornithine-L-aspartate as an adjuvant therapy in cirrhotic patients with hepatic encephalopathy

OBJECTIVE: To evaluate the efficacy of L-ornithine-L-aspartate (LOLA) as an adjuvant therapy in cirrhotic patients with hepatic encephalopathy (HE). STUDY DESIGN: Randomized placebo controlled study. PLACE AND DURATION OF STUDY: The Aga Khan University Hospital, Karachi in the year 2003-2004. METHODOLOGY: Patients with HE were randomized to receive LOLA or placebo medicine as an adjuvant to treatment of HE. Number connection test-A (NCT-A), ammonia level, clinical grade of HE and duration of hospitalization were assessed. RESULTS: Out of 120 patients, there were 62 males with mean age of 57 11 years. Improvement in HE was higher (n=40, 66.7%) in LOLA group as compared to the placebo group (n=28, 46.7%, p=0.027). In patients with grade I or less encephalopathy, improvement was seen in 6 (35.3%) and 3 (20%) patients in LOLA and placebo groups respectively (p=0.667). Patients with HE grade II and above showed improvement in 34 (79.1%) and 25 (55.6%) cases in LOLA and placebo group respectively (p=0.019). On multivariate analysis patients with HE of grade II and above showed prothrombin time, creatinine level and use of LOLA influencing the outcome. Duration of hospitalization was 93.6 25.7 hours and 135.2 103.5 hours in LOLA and placebo groups respectively (p=0.025). No side effects were observed in either groups. CONCLUSION: In cirrhotic patients with advanced hepatic encephalopathy treatment with LOLA was safe and associated with relatively rapid improvement and shorter hospital stay

Multiple Sequence Alignment Menggunakan Nature-Inspired Metaheuristic Algorithms

Multiple sequence alignment adalah proses dasar yang sering dibutuhkan dalam mengolah beberapa sequence yang berhubungan dengan bioinformatika. Apabila multiple sequence alignment telah selesai dikerjakan, maka dapat dilakukan analisis-analisis lain yang lebih jauh, seperti analisis filogenetik atau prediksi struktur protein. Banyaknya kegunaan dari multiple sequence alignment mengakibatkannya menjadi salah satu permasalahan yang banyak diteliti. Banyak algoritma-algoritma metaheuristic yang berdasar pada kejadian-kejadian alami, yang biasa disebut dengan nature-inspired metaheuristic algorithms. Beberapa algoritma baru dalam nature-inspired metaheuristic algorithms yang dianggap cukup efisien antara lain adalah firefly algorithm, cuckoo search, dan flower pollination algorithm. Dalam penelitian ini dipaparkan modified Needleman-Wunsch alignment. Didapatkan hasil bahwa modified Needleman-Wunsch alignment adalah metode yang cukup bagus. Modified Needleman-Wunsch alignment tersebut digunakan untuk membentuk solusi awal dari firefly algorithm, cuckoo search, dan flower pollination algorithm. Didapatkan hasil bahwa firefly algorithm, cuckoo search, dan flower pollination algorithm dapat menghasilkan solusi-solusi baru yang lebih baik. Secara keseluruhan, firefly algorithm adalah algoritma yang terbaik dari tiga algoritma tersebut dalam segi skor alignment, namun membutuhkan waktu komputasi yang lebih besar. ======================================================================================== Multiple sequence alignment is a fundamental tool that often needed to process bioinformatic sequences. If multiple sequence alignment is completed, we can process other further analysis, such as phylogenetic analysis or protein structure prediction. The versatility of multiple sequence alignment led it to be the one of the problems that studied continously. Many metaheuristic algorithms are based on natural events, with the so called nature-inspired metaheuristic algorithms. Algorithms in nature-inspired metaheuristic algorithms that considered to be good are firefly algorithm, cuckoo search, and flower pollination algorithm. In this research, we propose modified Needleman-Wunsch alignment. The results show that modified Needleman-Wunsch alignment is a good method. Modified Needleman-Wunsch alignment is used to create initial solution of firefly algorithm, cuckoo search, and flower pollination algorithm. The results show that firefly algorithm, cuckoo search, and flower pollination algorithm can produce new better solution. Overall, firefly algorithm is the best algorithm among the others in alignment score, but need large computation time

Methodology for Designing and Evaluating Chemical Systems for Improved Oil Recovery

The purpose of this research was to demonstrate the methodology for development of high performance chemical systems for improved oil recovery (IOR). Previous studies have shown that high performing surfactant formulations can be quickly identified and optimized by assessing the microemulsion phase behavior and aqueous phase homogeneity. Similarly, in this research, extensive phase behavior assessments were performed for many combinations of chemical slug components that included various surfactants, co-surfactants, co-solvents, alkali and polymers. Methodical planning, preparation, execution, observations and recording of phase behavior experiments and results enabled selection of the best performing chemical components and their concentrations were optimized. A total of five formulations showed good microemulsion phase behavior but only three passed the aqueous stability requirement. These three formulations were then evaluated in core floods. Out of the three formulations, one consistently gave high residual oil recovery ranging between 86%-91% at reservoir temperature with both soft brine (NaCl only) and synthetic formation brine. Synthetic formation brine for Trembley contained a high concentration of divalent cations in addition to monovalent yet it had a minimal effect on oil recovery, proving that the formulation was robust at even high salinity contrast with formation brine. The formulation was therefore recommended for further studies on limestone cores. Pressures across the sandstone cores and its subsections, and effluent's microemulsion and aqueous phase properties were utilized to explain the performance of formulations and oil displacement process in the sandstone cores. Corefloods showed that slug size, surfactant concentration, salinity and viscosity of chemical systems were important chemical flood design parameters that also impacted the oil recovery

Candida esophagitis: Risk factors in non-HIV population in Pakistan

AIM: Candida esophagitis is a frequent infection in immunocompromised patients. This study was designed to determine its characteristics in non- human immune deficiency virus (HIV) infected patients attending a teaching hospital. METHODS: Clinical records of all patients coded by international classification of diseases 9th revision with clinical modifications\u27 (ICD-9-CM), with candida esophagitis diagnosed by esophagogastroduodenoscopy (EGD) and histopathology over a period of 5 years were studied. RESULTS: Fifty-one patients (27 males, 24 females, range 21-77 years old and mean age 52.9 years) fulfilled the criteria (0.34% of the EGD). The common predisposing factors were carcinoma (OR 3.87, CI 1.00-14.99) and diabetes mellitus (OR 4.39, CI 1.34-14.42). The frequent clinical symptoms were retrosternal discomfort, dysphagia and epigastric abdominal pain with endoscopic appearance of scattered mucosal plaques. Another endoscopic lesion was associated with candida esophagitis in 15% patients. CONCLUSION: Carcinomas, diabetes mellitus, corticosteroid and antibiotic therapy are major risk factors for candida esophagitis in Pakistan. It is an easily managed complication that responds to treatment with nystatin