Browse publications by year: 2014

Evaluation of retinal nerve fiber layer thickness in eyes with hypertensive uveitis

Din NM, Taylor SR, Isa H, Tomkins-Netzer O, Bar A, Talat L, et al.

JAMA Ophthalmol, 2014 Jul;132(7):859-65.
PMID: 24789528 DOI: 10.1001/jamaophthalmol.2014.404

IMPORTANCE: Uveitic glaucoma is among the most common causes of irreversible visual loss in uveitis. However, glaucoma detection can be obscured by inflammatory changes.
OBJECTIVE: To determine whether retinal nerve fiber layer (RNFL) measurement can be used to detect glaucoma in uveitic eyes with elevated intraocular pressure (IOP).
DESIGN, SETTING, AND PARTICIPANTS: Comparative case series of RNFL measurement using optical coherence tomography performed from May 1, 2010, through October 31, 2012, at a tertiary referral center. We assigned 536 eyes with uveitis (309 patients) in the following groups: normal contralateral eyes with unilateral uveitis (n = 72), normotensive uveitis (Uv-N) (n = 143), raised IOP and normal optic disc and/or visual field (Uv-H) (n = 233), and raised IOP and glaucomatous disc and/or visual field (Uv-G) (n = 88).
EXPOSURES: Eyes with uveitis and elevated IOP (>21 mm Hg) on at least 2 occasions.
MAIN OUTCOMES AND MEASURES: Comparison of RNFL values between groups of eyes and correlation with clinical data; risk factors for raised IOP, glaucoma, and RNFL thinning.
RESULTS: Mean (SD) global RNFL was thicker in Uv-N (106.4 [21.4] µm) compared with control (96.0 [9.0] µm; P

MeSH terms: Adolescent; Adult; Age Factors; Aged; Aged, 80 and over; Female; Glaucoma, Open-Angle/diagnosis; Humans; Infant; Intraocular Pressure; Male; Middle Aged; Nerve Fibers/pathology*; Ocular Hypertension/diagnosis*; Optic Disk/pathology*; Optic Nerve Diseases/diagnosis*; Retinal Ganglion Cells/pathology*; Risk Factors; Sex Factors; Uveitis/diagnosis*; Visual Fields; Tomography, Optical Coherence; Young Adult
Fulltext Preparation and properties of poly(vinyl alcohol)/chitosan blend bionanocomposites reinforced with cellulose nanocrystals/ZnO-Ag multifunctional nanosized filler

Azizi S, Ahmad MB, Hussein MZ, Ibrahim NA, Namvar F

Int J Nanomedicine, 2014;9:1909-17.
PMID: 24790433 DOI: 10.2147/IJN.S60274

A series of novel bionanocomposites were cast using different contents of zinc oxide-silver nanoparticles (ZnO-AgNPs) stabilized by cellulose nanocrystals (CNC) as multifunctional nanosized fillers in poly(vinyl alcohol)/chitosan (PVA/Cs) matrices. The morphological structure, mechanical properties, ultraviolet-visible absorption, and antimicrobial properties of the prepared films were investigated as a function of their CNC/ZnO-AgNP content and compared with PVA/chitosan/CNC bionanocomposite films. X-ray diffraction and field emission scanning electron microscopic analyses showed that the CNC/ZnO-AgNPs were homogeneously dispersed in the PVA/Cs matrix and the crystallinity increased with increasing nanosized filler content. Compared with pure PVA/Cs, the tensile strength and modulus in the films increased from 0.055 to 0.205 GPa and from 0.395 to 1.20 GPa, respectively. Ultraviolet and visible light can be efficiently absorbed by incorporating ZnO-AgNPs into a PVA/Cs matrix, suggesting that these bionanocomposite films show good visibility and ultraviolet-shielding effects. The bionanocomposite films had excellent antimicrobial properties, killing both Gram-negative Salmonella choleraesuis and Gram-positive Staphylococcus aureus. The enhanced physical properties achieved by incorporating CNC/ZnO-AgNPs could be beneficial in various applications.

MeSH terms: Anti-Bacterial Agents/chemical synthesis; Anti-Bacterial Agents/pharmacology*; Anti-Bacterial Agents/chemistry*; Biocompatible Materials/administration & dosage; Biocompatible Materials/chemistry; Cellulose/chemistry*; Excipients/chemistry; Materials Testing; Particle Size; Polyvinyl Alcohol/chemistry; Salmonella/drug effects; Silver/pharmacology*; Silver/chemistry; Staphylococcus aureus/drug effects; Surface Properties; Tensile Strength; Zinc Oxide/pharmacology; Zinc Oxide/chemistry; Bacterial Physiological Phenomena/drug effects; Chitosan/chemistry*; Nanocomposites/administration & dosage*; Nanocomposites/chemistry*; Metal Nanoparticles/administration & dosage; Metal Nanoparticles/chemistry; Nanocapsules/administration & dosage; Nanocapsules/chemistry; Absorption, Physicochemical
Fulltext Accuracy enhancement for forecasting water levels of reservoirs and river streams using a multiple-input-pattern fuzzification approach

Valizadeh N, El-Shafie A, Mirzaei M, Galavi H, Mukhlisin M, Jaafar O

ScientificWorldJournal, 2014;2014:432976.
PMID: 24790567 DOI: 10.1155/2014/432976

Water level forecasting is an essential topic in water management affecting reservoir operations and decision making. Recently, modern methods utilizing artificial intelligence, fuzzy logic, and combinations of these techniques have been used in hydrological applications because of their considerable ability to map an input-output pattern without requiring prior knowledge of the criteria influencing the forecasting procedure. The artificial neurofuzzy interface system (ANFIS) is one of the most accurate models used in water resource management. Because the membership functions (MFs) possess the characteristics of smoothness and mathematical components, each set of input data is able to yield the best result using a certain type of MF in the ANFIS models. The objective of this study is to define the different ANFIS model by applying different types of MFs for each type of input to forecast the water level in two case studies, the Klang Gates Dam and Rantau Panjang station on the Johor river in Malaysia, to compare the traditional ANFIS model with the new introduced one in two different situations, reservoir and stream, showing the new approach outweigh rather than the traditional one in both case studies. This objective is accomplished by evaluating the model fitness and performance in daily forecasting.

MeSH terms: Algorithms; Forecasting*; Models, Theoretical*; Water*; Rivers*
Fulltext Heuristics for multiobjective optimization of two-sided assembly line systems

Jawahar N, Ponnambalam SG, Sivakumar K, Thangadurai V

ScientificWorldJournal, 2014;2014:458959.
PMID: 24790568 DOI: 10.1155/2014/458959

Products such as cars, trucks, and heavy machinery are assembled by two-sided assembly line. Assembly line balancing has significant impacts on the performance and productivity of flow line manufacturing systems and is an active research area for several decades. This paper addresses the line balancing problem of a two-sided assembly line in which the tasks are to be assigned at L side or R side or any one side (addressed as E). Two objectives, minimum number of workstations and minimum unbalance time among workstations, have been considered for balancing the assembly line. There are two approaches to solve multiobjective optimization problem: first approach combines all the objectives into a single composite function or moves all but one objective to the constraint set; second approach determines the Pareto optimal solution set. This paper proposes two heuristics to evolve optimal Pareto front for the TALBP under consideration: Enumerative Heuristic Algorithm (EHA) to handle problems of small and medium size and Simulated Annealing Algorithm (SAA) for large-sized problems. The proposed approaches are illustrated with example problems and their performances are compared with a set of test problems.

MeSH terms: Algorithms; Artificial Intelligence*; Efficiency*; Models, Theoretical
Fulltext Experimental study on tsunami risk reduction on coastal building fronted by sea wall

Rahman S, Akib S, Khan MT, Shirazi SM

ScientificWorldJournal, 2014;2014:729357.
PMID: 24790578 DOI: 10.1155/2014/729357

This experimental study was conducted to idealize the efficacy of sea wall in controlling the tsunami forces on onshore structures. Different types of sea walls were placed in front of the building model. The tsunami forces and the wave heights were measured with and without the sea wall conditions. Types of sea wall, wall height, and wall positions were varied simultaneously to quantify the force reductions. Maximum of 41% forces was reduced by higher sea wall, positioned closer proximity to the model whereas this reduction was about 27% when the wall height was half of the high wall. Experimental investigations revealed that wall with adequate height and placed closer to the structures enables a satisfactory predictor of the force reduction on onshore structures. Another set of tests were performed with perforated wall placing near the building model. Less construction cost makes the provision of perforated sea wall interesting. The overall results showed that the efficacy of perforated wall is almost similar to solid wall. Hence, it can be efficiently used instead of solid wall. Moreover, overtopped water that is stuck behind the wall is readily gone back to the sea through perforations releasing additional forces on the nearby structures.

MeSH terms: Civil Defense*; Disasters*; Models, Theoretical; Tsunamis*
Fulltext Support vector machine based on adaptive acceleration particle swarm optimization

Abdulameer MH, Sheikh Abdullah SN, Othman ZA

ScientificWorldJournal, 2014;2014:835607.
PMID: 24790584 DOI: 10.1155/2014/835607

Existing face recognition methods utilize particle swarm optimizer (PSO) and opposition based particle swarm optimizer (OPSO) to optimize the parameters of SVM. However, the utilization of random values in the velocity calculation decreases the performance of these techniques; that is, during the velocity computation, we normally use random values for the acceleration coefficients and this creates randomness in the solution. To address this problem, an adaptive acceleration particle swarm optimization (AAPSO) technique is proposed. To evaluate our proposed method, we employ both face and iris recognition based on AAPSO with SVM (AAPSO-SVM). In the face and iris recognition systems, performance is evaluated using two human face databases, YALE and CASIA, and the UBiris dataset. In this method, we initially perform feature extraction and then recognition on the extracted features. In the recognition process, the extracted features are used for SVM training and testing. During the training and testing, the SVM parameters are optimized with the AAPSO technique, and in AAPSO, the acceleration coefficients are computed using the particle fitness values. The parameters in SVM, which are optimized by AAPSO, perform efficiently for both face and iris recognition. A comparative analysis between our proposed AAPSO-SVM and the PSO-SVM technique is presented.

MeSH terms: Algorithms; Face*; Pattern Recognition, Automated*; Support Vector Machine*
Fulltext Antibiofilm activity, compound characterization, and acute toxicity of extract from a novel bacterial species of paenibacillus

Alasil SM, Omar R, Ismail S, Yusof MY

Int J Microbiol, 2014;2014:649420.
PMID: 24790603 DOI: 10.1155/2014/649420

The effectiveness of many antimicrobial agents is currently decreasing; therefore, it is important to search for alternative therapeutics. Our study was carried out to assess the in vitro antibiofilm activity using microtiter plate assay, to characterize the bioactive compounds using Ultra Performance Liquid Chromatography-Diode Array Detection and Liquid Chromatography-Mass Spectrometry and to test the oral acute toxicity on Sprague Dawley rats of extract derived from a novel bacterial species of Paenibacillus strain 139SI. Our results indicate that the crude extract and its three identified compounds exhibit strong antibiofilm activity against a broad range of clinically important pathogens. Three potential compounds were identified including an amino acid antibiotic C8H20N3O4P (MW 253.237), phospholipase A2 inhibitor C21H36O5 (MW 368.512), and an antibacterial agent C14H11N3O2 (MW 253.260). The acute toxicity test indicates that the mortality rate among all rats was low and that the biochemical parameters, hematological profile, and histopathology examination of liver and kidneys showed no significant differences between experimental groups (P > 0.05). Overall, our findings suggest that the extract and its purified compounds derived from novel Paenibacillus sp. are nontoxic exhibiting strong antibiofilm activity against Gram-positive and Gram-negative pathogens that can be useful towards new therapeutic management of biofilm-associated infections.

MeSH terms: Amino Acids; Animals; Anti-Infective Agents; Anti-Bacterial Agents; Blood Proteins; Chromatography, Liquid; Liver; Mass Spectrometry; Rats, Sprague-Dawley; Biofilms; Toxicity Tests, Acute; Complex Mixtures; Rats; Paenibacillus
Fulltext Pathological conditions associated with the male reproductive tract of the sahel bucks

Abba Y, Simon S, Idris Gambo H, Onyebuchi Igbokwe I, Iliyasu Y

Vet Med Int, 2014;2014:406431.
PMID: 24790768 DOI: 10.1155/2014/406431

The study of pathological conditions of the male reproductive system is paramount to understanding reproductive inefficiency in the Sahel goat. In this study, 1048 Sahel bucks presented for slaughter at the Maiduguri metropolitan abattoir were evaluated for the presence of various pathological abnormalities of the reproductive system. A total incidence of 15.08% was recorded for various pathological conditions, with testicular, penile, and scrotal conditions having incidences of 7.82%, 4.80 and 2.50%, respectively. Bilateral testicular hypoplasia and atrophy and unilateral cryptorchidism accounted for incidences of 4.10%, 2.38%, and 1.24%, respectively, while paraphimosis and scrotal laceration had incidences of 1.72% and 1.05%, respectively. Age specific incidence of pathological conditions were not significant (P > 0.05) between bucks aged <1-1.5 and 2-2.5 years. However, bucks aged 3-3.5 year a had lower (P < 0.05) incidence of pathological conditions than other age groups. Histopathological evidence of inflammation, degeneration, and atrophy was observed in the testes, while inflammatory changes were observed in the prepuce.
Fulltext A new nested allele-specific multiplex polymerase chain reaction method for haplotyping of VKORC1 gene to predict warfarin sensitivity

Chua YA, Abdullah WZ, Yusof Z, Gan SH

Biomed Res Int, 2014;2014:316310.
PMID: 24790995 DOI: 10.1155/2014/316310

The vitamin K epoxide reductase complex 1 gene (VKORC1) is commonly assessed to predict warfarin sensitivity. In this study, a new nested allele-specific multiplex polymerase chain reaction (PCR) method that can simultaneously identify single nucleotide polymorphisms (SNPs) at VKORC1 381, 861, 5808, and 9041 for haplotype analysis was developed and validated. Extracted DNA was amplified in the first PCR DNA, which was optimized by investigating the effects of varying the primer concentrations, annealing temperature, magnesium chloride concentration, enzyme concentration, and the amount of DNA template. The amplification products produced from the first round of PCR were used as templates for a second PCR amplification in which both mutant and wild-type primers were added in separate PCR tubes, followed by optimization in a similar manner. The final PCR products were resolved by agarose gel electrophoresis and further analysed by using a VKORC1 genealogic tree to infer patient haplotypes. Fifty patients were identified to have H1H1, one had H1H2, one had H1H7, 31 had either H1H7 or H1H9, one had H1H9, eight had H7H7, and one had H8H9 haplotypes. This is the first method that is able to infer VKORC1 haplotypes using only conventional PCR methods.

MeSH terms: Adult; Aged; Aged, 80 and over; Alleles; Drug Resistance/genetics; Female; Haplotypes/genetics*; Humans; Male; Metabolism, Inborn Errors/genetics*; Middle Aged; Sensitivity and Specificity; Reproducibility of Results; Genetic Predisposition to Disease/genetics*; Precision Medicine/methods; Multiplex Polymerase Chain Reaction/methods*; Vitamin K Epoxide Reductases/genetics*
Fulltext Anti-proliferative effect and phytochemical analysis of Cymbopogon citratus extract

Halabi MF, Sheikh BY

Biomed Res Int, 2014;2014:906239.
PMID: 24791006 DOI: 10.1155/2014/906239

The antiproliferative and antioxidant potential of Cymbopogon citratus (Lemon grass) extracts were investigated. The extracts were isolated by solvent maceration method and thereafter subjected to antiproliferative activity test on five different cancer cells: human colon carcinoma (HCT-116), breast carcinoma (MCF-7 and MDA-MB 231), ovarian carcinoma (SKOV-3 and COAV), and a normal liver cell line (WRL 68). The cell viability was determined using MTT assay. The DPPH radical scavenging assay revealed a concentration dependent trend. A maximum percentage inhibition of 45% and an IC50 of 278 μg/mL were observed when aqueous extract was evaluated. In contrast, 48.3% and IC50 of 258.9 μg/mL were observed when 50% ethanolic extract was evaluated. Both extracts at concentration of 50 to 800 μg/mL showed appreciative metal chelating activity with IC50 value of 172.2 ± 31 μg/mL to 456.5 ± 30 μg/mL. Depending on extraction solvent content, extract obtained from 50% ethanolic solvent proved to be more potent on breast cancer MCF-7 cell line (IC50 = 68 μg/mL). On the other hand, 90% ethanolic extract showed a moderate potency on the ovarian cancer (COAV) and MCF-7 cells having an IC50 of 104.6 μg/mL each. These results suggested antiproliferative efficacy of C. citratus ethanolic extract against human cancer cell lines.

MeSH terms: Antineoplastic Agents/pharmacology; Antineoplastic Agents/chemistry; Antioxidants/pharmacology; Antioxidants/chemistry; Humans; Plant Extracts/pharmacology*; Plant Extracts/chemistry*; Cymbopogon/chemistry*; Cell Line, Tumor; Cell Proliferation/drug effects*
Evaluation of metabolic and immunological changes in streptozotocin-nicotinamide induced diabetic rats

Mojani MS, Sarmadi VH, Vellasamy S, Sandrasaigaran P, Rahmat A, Peng LS, et al.

Cell Immunol, 2014 May-Jun;289(1-2):145-9.
PMID: 24791700 DOI: 10.1016/j.cellimm.2014.04.004

Type 2 diabetes is a chronic disease with growing public health concern globally. Finding remedies to assist this health issue requires recruiting appropriate animal model for experimental studies. This study was designated to evaluate metabolic and immunologic changes in streptozotocin-nicotinamide induced diabetic rats as a model of type 2 diabetes. Male rats were induced diabetes using nicotinamide (110 mg/kg) and streptozotocin (65 mg/kg). Following 42 days, biochemical and immunological tests showed that diabetic rats had higher levels of blood glucose, WBC, certain abnormalities in lipid profile and insufficient mitogenic responses of lymphocytes (p<0.05). However, the status of the total antioxidant, inflammatory biomarkers and other parameters of full blood count (except HCT) were not significantly altered. Phenotyping assay indicated insignificant lymphocyte subtype imbalances excluding a significant rise in the level of CD4+CD25+ marker (p<0.05). This model of diabetic animals may represent some but not all symptoms of human type 2 diabetes.

MeSH terms: Animals; Antioxidants/analysis; Blood Glucose/analysis; C-Reactive Protein/analysis; Diabetes Mellitus, Experimental/chemically induced; Diabetes Mellitus, Experimental/immunology*; Diabetes Mellitus, Experimental/metabolism*; Diabetes Mellitus, Type 2/immunology*; Diabetes Mellitus, Type 2/metabolism*; T-Lymphocytes, Helper-Inducer; Lipids/blood; Male; Niacinamide; Streptozocin; Antigens, CD4/blood; Rats, Sprague-Dawley; Lymphocyte Count; Rats; Interleukin-2 Receptor alpha Subunit/blood
Fulltext AP1S3 mutations are associated with pustular psoriasis and impaired Toll-like receptor 3 trafficking

Setta-Kaffetzi N, Simpson MA, Navarini AA, Patel VM, Lu HC, Allen MH, et al.

Am J Hum Genet, 2014 May 01;94(5):790-7.
PMID: 24791904 DOI: 10.1016/j.ajhg.2014.04.005

Adaptor protein complex 1 (AP-1) is an evolutionary conserved heterotetramer that promotes vesicular trafficking between the trans-Golgi network and the endosomes. The knockout of most murine AP-1 complex subunits is embryonically lethal, so the identification of human disease-associated alleles has the unique potential to deliver insights into gene function. Here, we report two founder mutations (c.11T>G [p.Phe4Cys] and c.97C>T [p.Arg33Trp]) in AP1S3, the gene encoding AP-1 complex subunit σ1C, in 15 unrelated individuals with a severe autoinflammatory skin disorder known as pustular psoriasis. Because the variants are predicted to destabilize the 3D structure of the AP-1 complex, we generated AP1S3-knockdown cell lines to investigate the consequences of AP-1 deficiency in skin keratinocytes. We found that AP1S3 silencing disrupted the endosomal translocation of the innate pattern-recognition receptor TLR-3 (Toll-like receptor 3) and resulted in a marked inhibition of downstream signaling. These findings identify pustular psoriasis as an autoinflammatory phenotype caused by defects in vesicular trafficking and demonstrate a requirement of AP-1 for Toll-like receptor homeostasis.

MeSH terms: Amino Acid Sequence; Cell Line; Female; Humans; Male; Molecular Sequence Data; Protein Conformation; Psoriasis/genetics*; Psoriasis/metabolism*; Amino Acid Substitution; Protein Transport/genetics; Adaptor Protein Complex 1/genetics*; Adaptor Protein Complex 1/chemistry; Toll-Like Receptor 3/metabolism*; Gene Knockdown Techniques
Fulltext "Why do I always see double?" A misdiagnosed case of ocular myasthenia gravis for 10 years

Yousuf UA, Yashodhara BM, Thanigasalam T, Ting HS

BMJ Case Rep, 2014 May 02;2014.
PMID: 24792021 DOI: 10.1136/bcr-2013-203488

A 58-year-old man presented with diplopia and partial ptosis for 10 years. It was non-progressive in nature, despite inadequate medical attention the patient received from non-specialists/general practitioners. He did not have fatigability or diurnal variation in weakness and was clinically stable without exacerbations of disease for a decade. He did not have features of Graves's disease, oculopharyngeal dystrophy, cranial nerve paralysis, polymyositis and stroke. The possibility of an atypical presentation of myasthenia gravis (MG) was considered and the patient was evaluated. Ice pack test was negative, Cogan's lid twitch (CLT) test was positive and high titres of acetylcholine receptor antibodies (AChR Ab) suggestive of MG were found. He was treated accordingly with a very good response.

MeSH terms: Anti-Inflammatory Agents/therapeutic use; Blepharoptosis/drug therapy; Blepharoptosis/etiology; Cholinesterase Inhibitors/therapeutic use; Diagnosis, Differential; Diagnostic Errors*; Diplopia/drug therapy; Diplopia/etiology; Humans; Male; Middle Aged; Myasthenia Gravis/complications; Myasthenia Gravis/diagnosis*; Myasthenia Gravis/drug therapy; Prednisolone/therapeutic use; Pyridostigmine Bromide/therapeutic use; Oculomotor Nerve Diseases/diagnosis*
Fulltext Unilateral striatal CT and MRI changes secondary to non-ketotic hyperglycaemia

Johari B, Hanafiah M, Shahizon AM, Koshy M

BMJ Case Rep, 2014;2014.
PMID: 24792025 DOI: 10.1136/bcr-2014-204053

A 62-year-old man presented with a right-sided hemichorea-hemiballismus secondary to underlying non-ketotic hyperglycaemia. This condition is recognised to have a unique finding of unilateral basal ganglia lesion, which is hyperdense on CT and hyperintense on T1-weighted MRI. The clinical course of this condition is benign and has a good prognosis with early correction of the hyperglycaemia.

MeSH terms: Basal Ganglia/pathology; Basal Ganglia/radiography; Humans; Hyperglycemia/complications*; Hyperglycemia/drug therapy; Hypoglycemic Agents/therapeutic use; Insulin/therapeutic use; Magnetic Resonance Imaging; Male; Middle Aged; Tomography, X-Ray Computed; Neostriatum/pathology*; Neostriatum/radiography; Dyskinesias/etiology; Dyskinesias/pathology*; Dyskinesias/radiography
Biologic valved conduits in infants

Corno AF

Ann Thorac Surg, 2014 May;97(5):1853.
PMID: 24792290 DOI: 10.1016/j.athoracsur.2013.12.010
MeSH terms: Blood Vessel Prosthesis*; Heart Defects, Congenital/surgery*; Humans; Pulmonary Artery/surgery*
Active incremental Support Vector Machine for oil and gas pipeline defects prediction system using long range ultrasonic transducers

Akram NA, Isa D, Rajkumar R, Lee LH

Ultrasonics, 2014 Aug;54(6):1534-44.
PMID: 24792683 DOI: 10.1016/j.ultras.2014.03.017

This work proposes a long range ultrasonic transducers technique in conjunction with an active incremental Support Vector Machine (SVM) classification approach that is used for real-time pipeline defects prediction and condition monitoring. Oil and gas pipeline defects are detected using various techniques. One of the most prevalent techniques is the use of "smart pigs" to travel along the pipeline and detect defects using various types of sensors such as magnetic sensors and eddy-current sensors. A critical short coming of "smart pigs" is the inability to monitor continuously and predict the onset of defects. The emergence of permanently installed long range ultrasonics transducers systems enable continuous monitoring to be achieved. The needs for and the challenges of the proposed technique are presented. The experimental results show that the proposed technique achieves comparable classification accuracy as when batch training is used, while the computational time is decreased, using 56 feature data points acquired from a lab-scale pipeline defect generating experimental rig.
Fast decision tree-based method to index large DNA-protein sequence databases using hybrid distributed-shared memory programming model

Jaber KM, Abdullah R, Rashid NA

Int J Bioinform Res Appl, 2014;10(3):321-40.
PMID: 24794073 DOI: 10.1504/IJBRA.2014.060765

In recent times, the size of biological databases has increased significantly, with the continuous growth in the number of users and rate of queries; such that some databases have reached the terabyte size. There is therefore, the increasing need to access databases at the fastest rates possible. In this paper, the decision tree indexing model (PDTIM) was parallelised, using a hybrid of distributed and shared memory on resident database; with horizontal and vertical growth through Message Passing Interface (MPI) and POSIX Thread (PThread), to accelerate the index building time. The PDTIM was implemented using 1, 2, 4 and 5 processors on 1, 2, 3 and 4 threads respectively. The results show that the hybrid technique improved the speedup, compared to a sequential version. It could be concluded from results that the proposed PDTIM is appropriate for large data sets, in terms of index building time.

MeSH terms: Algorithms*; Computer Storage Devices*; Sequence Analysis/methods*; Systems Integration; Databases, Genetic*; Data Mining/methods*
Fulltext Metabolically-healthy obesity and coronary artery calcification

Chang Y, Kim BK, Yun KE, Cho J, Zhang Y, Rampal S, et al.

J Am Coll Cardiol, 2014 Jun 24;63(24):2679-86.
PMID: 24794119 DOI: 10.1016/j.jacc.2014.03.042

The purpose of this study was to compare the coronary artery calcium (CAC) scores of metabolically-healthy obese (MHO) and metabolically healthy normal-weight individuals in a large sample of apparently healthy men and women.

MeSH terms: Adult; Coronary Artery Disease/diagnosis*; Coronary Artery Disease/metabolism*; Coronary Artery Disease/epidemiology; Cross-Sectional Studies; Female; Health Status; Humans; Male; Middle Aged; Obesity/diagnosis*; Obesity/metabolism*; Obesity/epidemiology; Republic of Korea/epidemiology; Vascular Calcification/diagnosis*; Vascular Calcification/metabolism*; Vascular Calcification/epidemiology
Medium-term (5-year) comparison of the functional outcomes of combined anterior cruciate ligament and posterolateral corner reconstruction compared with isolated anterior cruciate ligament reconstruction

Cartwright-Terry M, Yates J, Tan CK, Pengas IP, Banks JV, McNicholas MJ

Arthroscopy, 2014 Jul;30(7):811-7.
PMID: 24794571 DOI: 10.1016/j.arthro.2014.02.039

To present a 5-year comparison of the functional outcomes of combined anterior cruciate ligament (ACL) and posterolateral corner (PLC) reconstruction with those of isolated ACL reconstruction.

MeSH terms: Adult; Athletic Injuries/surgery; Female; Humans; Knee Injuries/surgery*; Knee Joint/surgery; Longitudinal Studies; Male; Middle Aged; Osteoarthritis/surgery; Postoperative Complications; Surveys and Questionnaires; Case-Control Studies; Anterior Cruciate Ligament/surgery; Posterior Cruciate Ligament/injuries*; Posterior Cruciate Ligament/surgery; Treatment Outcome; Outcome Assessment (Health Care); Recovery of Function; Osteoarthritis, Knee/surgery; Tenodesis/methods*; Young Adult; Anterior Cruciate Ligament Reconstruction/adverse effects; Anterior Cruciate Ligament Reconstruction/methods*
Fulltext The causal role between phasic midbrain dopamine signals and learning

Aquili L

Front Behav Neurosci, 2014;8:139.
PMID: 24795588 DOI: 10.3389/fnbeh.2014.00139

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