Displaying publications 21 - 40 of 754 in total

Abstract:
Sort:
  1. NETASA: neural network based prediction of solvent accessibility
    Ahmad S, Gromiha MM
    Bioinformatics, 2002 Jun;18(6):819-24.
    PMID: 12075017
    MOTIVATION: Prediction of the tertiary structure of a protein from its amino acid sequence is one of the most important problems in molecular biology. The successful prediction of solvent accessibility will be very helpful to achieve this goal. In the present work, we have implemented a server, NETASA for predicting solvent accessibility of amino acids using our newly optimized neural network algorithm. Several new features in the neural network architecture and training method have been introduced, and the network learns faster to provide accuracy values, which are comparable or better than other methods of ASA prediction.

    RESULTS: Prediction in two and three state classification systems with several thresholds are provided. Our prediction method achieved the accuracy level upto 90% for training and 88% for test data sets. Three state prediction results provide a maximum 65% accuracy for training and 63% for the test data. Applicability of neural networks for ASA prediction has been confirmed with a larger data set and wider range of state thresholds. Salient differences between a linear and exponential network for ASA prediction have been analysed.

    AVAILABILITY: Online predictions are freely available at: http://www.netasa.org. Linux ix86 binaries of the program written for this work may be obtained by email from the corresponding author.

    Matched MeSH terms: Software
  2. Fulltext Developing an integrated data management system for general practice
    Doshi HK
    Asia Pac Fam Med, 2003;2(4):193-195.
    Developing a software program to manage data in a general practice setting is complicated. Vision Integrated Medical System is an example of a integrated management system that was developed by general practitioners, within a general practice, to offer a user friendly system with multi tasking capabilities. The present report highlights the reasons behind the development of this system and how it can assist day to day practice.
    Matched MeSH terms: Software
  3. DietPal: a Web-based dietary menu-generating and management system
    Noah SA, Abdullah SN, Shahar S, Abdul-Hamid H, Khairudin N, Yusoff M, et al.
    J Med Internet Res, 2004 Jan 30;6(1):e4.
    PMID: 15111270
    Attempts in current health care practice to make health care more accessible, effective, and efficient through the use of information technology could include implementation of computer-based dietary menu generation. While several of such systems already exist, their focus is mainly to assist healthy individuals calculate their calorie intake and to help monitor the selection of menus based upon a prespecified calorie value. Although these prove to be helpful in some ways, they are not suitable for monitoring, planning, and managing patients' dietary needs and requirements. This paper presents a Web-based application that simulates the process of menu suggestions according to a standard practice employed by dietitians.
    Matched MeSH terms: Software/trends*; Software Design
  4. A direction-sensitive underwater blast detector and its application for managing blast fishing
    Woodman GH, Wilson SC, Li VY, Renneberg R
    Mar Pollut Bull, 2004 Dec;49(11-12):964-73.
    PMID: 15556182
    Little is known about the spatial and temporal distribution of blast fishing which hampers enforcement against this activity. We have demonstrated that a triangular array of hydrophones 1 m apart is capable of detecting blast events whilst effectively rejecting other sources of underwater noise such as snapping shrimp and nearby boat propellers. A total of 13 blasts were recorded in Sepangor bay, North of Kota Kinabalu, Sabah, Malaysia from 7th to 15th July 2002 at distances estimated to be up to 20 km, with a directional uncertainty of 0.2 degrees . With such precision, a network of similar hydrophone arrays has potential to locate individual blast events by triangulation to within 30 m at a range of 10 km.
    Matched MeSH terms: Software*
  5. Phylogeny and phylogeography of Old World fruit bats in the Cynopterus brachyotis complex
    Campbell P, Schneider CJ, Adnan AM, Zubaid A, Kunz TH
    Mol Phylogenet Evol, 2004 Dec;33(3):764-81.
    PMID: 15522802
    Taxonomic relationships within the Old World fruit bat genus, Cynopterus, have been equivocal for the better part of a century. While nomenclature has been revised multiple times on the basis of phenotypic characters, evolutionary relationships among taxa representing the entire geographic range of the genus have not been determined. We used mitochondrial DNA sequence data to infer phylogenetic relationships among the three most broadly distributed members of the genus: C. brachyotis, C. horsfieldi, and C. sphinx, and to assess whether C. brachyotis represents a single widespread species, or a complex of distinct lineages. Results clearly indicate that C. brachyotis is a complex of lineages. C. sphinx and C. horsfieldi haplotypes formed monophyletic groups nested within the C. brachyotis species complex. We identified six divergent mitochondrial lineages that are currently referred to C. brachyotis. Lineages from India, Myanmar, Sulawesi, and the Philippines are geographically well-defined, while in Malaysia two lineages, designated Sunda and Forest, are broadly sympatric and may be ecologically distinct. Demographic analyses of the Sunda and Forest lineages suggest strikingly different population histories, including a recent and rapid range expansion in the Sunda lineage, possibly associated with changes in sea levels during the Pleistocene. The resolution of the taxonomic issues raised in this study awaits combined analysis of morphometric characters and molecular data. However, since both the Indian and Malaysian Forest C. brachyotis lineages are apparently ecologically restricted to increasingly fragmented forest habitat, we suggest that reevaluation of the conservation status of populations in these regions should be an immediate goal.
    Matched MeSH terms: Software
  6. Integrated telehealth: putting it all together and addressing the challenges
    Harum H
    Stud Health Technol Inform, 2004;104:75-86.
    PMID: 15747966
    The Integrated Telehealth Project of Malaysia is considered a principal enabler for the nation's Vision 2020 as well as the National Health Vision. Being in such an unenviable position, of being not only the pioneer for such an integrated project, but also with no benchmark to compare with, the project implementers have faced manifold challenges along the way. This chapter deals with some of the challenges and lessons learnt that have accumulated as the project progressed.
    Matched MeSH terms: Software
  7. Comparison between field experiment and PERSIST model simulation: dissipation of fenvalerate in a Malaysian agricultural soil
    Ismail BS, Maznah Z
    Bull Environ Contam Toxicol, 2005 Jun;74(6):1143-50.
    PMID: 16158853
    Matched MeSH terms: Software
  8. Fulltext Is Profile Alone Sufficient To Remove Gutta-Percha During Endodontic Re-treatment?
    Lee, S.W., Tan, S.T., Che Ab Aziz, Z.A.
    Ann Dent, 2005;12(1):-.
    MyJurnal
    Thirty extracted mandibular premolars were randomly divided into 3 groups. Canals were cleaned, obturated and the teeth incubated. Guttapercha removal was performed using: Hedström files with xylene (Group 1); ProFile® alone (Group 2) and combination of both (Group 3). Time required to remove the gutta-percha was recorded. Postoperative radiographs were taken. Specimens were split longitudinally and photographed. Amount of gutta-percha left at coronal, middle and apical thirds was calculated by computer (QWIN software) and the photographs were also evaluated visually by two endodontists. Results showed that the combined technique was fastest in removing gutta-percha. Radiographically, more residual was left in Group 2. Although computer analysis also showed more residual was left in Group 2, they were in a small percentage and there were no significant differences (P>0.05, SPSS paired-samples T test) among groups. Although there were significant differences between the two evaluators in their scoring, both generally agreed (Kappa’s analysis= 0.64) there was more guttapercha residual in Group 2 compared to Group 3 in the apical thirds. Although the differences in efficacy of guttapercha removal among these techniques were not significant, the use of ProFile® increased the speed of the procedure. The combined technique showed the most superior efficacy in gutta-percha removal.
    Matched MeSH terms: Software
  9. Patients with congenital hypothyroidism demonstrate different altered expression of plasma fibrinogen and haptoglobin polypeptide chains
    Yong PH, Junit SM, Harun F, Hashim OH
    Clin Biochem, 2006 Feb;39(2):126-32.
    PMID: 16412408
    To compare the plasma protein profiles of treated and untreated congenital hypothyroidism (CH) patients with those of normal control infants.
    Matched MeSH terms: Software
  10. Singapore Human Mutation/Polymorphism Database: a country-specific database for mutations and polymorphisms in inherited disorders and candidate gene association studies
    Tan EC, Loh M, Chuon D, Lim YP
    Hum Mutat, 2006 Mar;27(3):232-5.
    PMID: 16429432
    There is a need for country/population-specific databases because the existence of population-specific mutations for single gene disorders is well documented, and there is also good evidence for ethnic differences in the frequencies of genetic variations involved in complex disorders. Thus the Singapore Human Mutation/Polymorphism Database (SHMPD) was created to provide clinicians and scientists access to a central genetic database for the Singapore population. The data catalogued in the database include mutations identified in Singapore for Mendelian diseases, and frequencies of polymorphisms that have been investigated in either healthy controls or samples associated with specific phenotypes. Data from journal articles identified by searches in PubMed and other online resources, and via personal communications with researchers were compiled and assembled into a single database. Genes are categorized alphabetically and are also searchable by name and disease. The information provided for each variant of the gene includes the protein encoded, phenotype association, gender, size, and ethnic origin of the sample, as well as the reported genotype and allele frequencies, and direct links to the corresponding abstracts on PubMed. Our database will facilitate molecular diagnosis of Mendelian disorders and improve study designs for complex traits. It will be useful not only for researchers in Singapore, but also for those in countries with similar ethnic backgrounds, such as China, Taiwan, Hong Kong, Indonesia, and Malaysia.
    Matched MeSH terms: Software
  11. A low-cost, high-quality method for remote recording of presentations
    Tan LK, Wong JH, Ng KH
    AJR Am J Roentgenol, 2006 Mar;186(3):898-901.
    PMID: 16498128
    The purpose of this article was to develop a low-cost method for high-quality remote capturing and recording of multimedia presentations.
    Matched MeSH terms: Software*
  12. Model-based compression for 3D medical images stored in the DICOM format
    Logeswaran R, Eswaran C
    J Med Syst, 2006 Apr;30(2):133-8.
    PMID: 16705998
    Many medical examinations involve acquisition of a large series of slice images for 3D reconstruction of the organ of interest. With the paperless hospital concept and telemedicine, there is very heavy utilization of limited electronic storage and transmission bandwidth. This paper proposes model-based compression to reduce the load on such resources, as well as aid diagnosis through the 3D reconstruction of the structures of interest, for images acquired by various modalities, such as MRI, Ultrasound, CT, PET etc. and stored in the DICOM file format. An example implementation for the biliary track in MRCP images is illustrated in the paper. Significant compression gains may be derived from the proposed method, and a suitable mixture of the models and raw images would enhance the patient medical history archives as the models may be stored in the DICOM file format used in most medical archiving systems.
    Matched MeSH terms: Software
  13. Structural analysis of peptides that interact with Newcastle disease virus
    Chia SL, Tan WS, Shaari K, Abdul Rahman N, Yusoff K, Satyanarayanajois SD
    Peptides, 2006 Jun;27(6):1217-25.
    PMID: 16377031
    A peptide with the sequence CTLTTKLYC has previously been identified to inhibit the propagation of Newcastle disease virus (NDV) in embryonated chicken eggs and tissue culture. NDV has been classified into two main groups: the velogenic group, and mesogenic with lentogenic strains as the other group based on its dissociation constants. In this study the peptide, CTLTTKLYC, displayed on the pIII protein of a filamentous M13 phage was synthesized and mutated in order to identify the amino acid residues involved in the interactions with NDV. Mutations of C1 and K6 to A1 and A6 did not affect the binding significantly, but substitution of Y8 with A8 dramatically reduced the interaction. This suggests that Y8 plays an important role in the peptide-virus interaction. The three-dimensional structure of the peptide was determined using circular dichroism (CD), nuclear magnetic resonance (NMR), and molecular modeling. The peptide exhibited two possible conformers. One that consists of consecutive beta-turns around T2-L3-T4-T5 and K6-L7-Y8-C9. The other conformer exhibited a beta-hairpin bend type of structure with a bend around L3-T4-T5-K6.
    Matched MeSH terms: Software
  14. Isolated hypertriglyceridemia: an insulin-resistant state with or without low HDL cholesterol
    Al-Mahmood A, Ismail A, Rashid F, Mohamed W
    J Atheroscler Thromb, 2006 Jun;13(3):143-8.
    PMID: 16835469
    There are numerous reports on insulin resistance in subjects with hypertriglyceridemia but most of the studies involved obese or diabetic subjects. We were interested to study such events but in a population free from other confounders influencing insulin sensitivity (i.e., obesity, glucose intolerance and hypertension). From the population of a cross-sectional study we obtained 12 subjects with isolated hypertriglyceridemia and compared their insulin sensitivity with that of normolipidemic subjects in that study. Insulin sensitivity and secretory status were computed using homeostasis model assessment (HOMA) software. The insulin sensitivity of hypertriglyceridemic subjects was found to be lower than in normolipidemic subjects. For the hypertriglyceridemic subjects, insulin sensitivity (HOMA%S) was 60.07% (values adjusted for age, BMI, waist circumference, and cholesterol levels), which was substantially lower than that of normolipidemic subjects (150.03%; p<0.001). The insulin secretory status (HOMA%B) of the two groups was 248.17% and 124.63%, respectively, and significantly different (p<0.001). Relative insulin resistance, HOMA-IR, of the two groups was 4.90 and 1.54, respectively. We therefore concluded that in comparison with normolipidemic subjects, the insulin sensitivity of otherwise healthy non-obese hypertriglyceridemic subjects was lower, and that B cells had to work harder to compensate for the lowered insulin sensitivity.
    Matched MeSH terms: Software
  15. Fulltext Insulin sensitivity and secretory status of a healthy malay population
    Al-Mahmood AK, Ismail AA, Rashid FA, Wan Bebakar WM
    Malays J Med Sci, 2006 Jul;13(2):37-44.
    PMID: 22589603 MyJurnal
    Insulin insensitivity is a common finding in several metabolic disorders including glucose intolerance, dyslipidemia, hyperuricemia and hypertension. Most of the previous studies on insulin sensitivity were performed on diabetic or obese population. So our knowledge about insulin sensitivity of healthy population remains limited. Rising prevalence of obesity, diabetes and metabolic syndrome is a serious issue in Malaysia and some other rapidly developing countries. So it is important to look at the insulin sensitivity status of healthy Malaysian subjects and to compare it in future with those of diabetic, obese or metabolic syndrome patients. In this study we sampled subjects who were independent of confounding factors such as obesity (including abdominal obesity), hypertension and glucose intolerance (diabetes, IGT or IFG) which may influence insulin sensitivity. Fasting plasma glucose, fasting insulin and lipid profile were determined. Insulin sensitivity and secretory status were calculated using the homeostasis model assessment (HOMA) software (HOMA%S, HOMA%B and HOMA-IR). The insulin sensitivity (HOMA%S) of healthy Malay subjects aged between 30-60 years was 155.17%, HOMA-IR was 1.05 and HOMA%B was 116.65% (values adjusted for age, sex, BMI and waist circumference). It was seen that non-obese Malaysians can prevent age related lowering of insulin sensitivity if they can retain their BMI within limit.
    Study site: 7 schools and 2 public offices in Kota Bharu, Kelantan, Malaysia
    Matched MeSH terms: Software
  16. The hyoid bone in malay infants with cleft lip and palate
    Rajion ZA, Townsend GC, Netherway DJ, Anderson PJ, Hughes T, Shuaib IL, et al.
    Cleft Palate Craniofac J, 2006 Sep;43(5):532-8.
    PMID: 16986987
    To compare morphological and positional variations of the hyoid bone in unoperated infants with cleft lip and palate (CL/P) with those in noncleft infants.
    Matched MeSH terms: Software*
  17. Fulltext Impact of pre-dilution and flushing on continuous renal replacement therapy
    Koh KH
    Singapore Med J, 2006 Sep;47(9):785-95.
    PMID: 16924361
    Infusing the replacement solution before the filter (pre-dilution) and regular flushing have not been accounted for in conventional mathematical equations. Their effects on various continuous renal replacement therapy (CRRT) parameters, such as ultrafiltration fraction and urea clearance, have not been well studied. We incorporated these parameters into mathematical equations to help in understanding and prescribing CRRT.
    Matched MeSH terms: Software
  18. Quantitative assessment of breast density from digitized mammograms into Tabar's patterns
    Jamal N, Ng KH, Looi LM, McLean D, Zulfiqar A, Tan SP, et al.
    Phys Med Biol, 2006 Nov 21;51(22):5843-57.
    PMID: 17068368
    We describe a semi-automated technique for the quantitative assessment of breast density from digitized mammograms in comparison with patterns suggested by Tabar. It was developed using the MATLAB-based graphical user interface applications. It is based on an interactive thresholding method, after a short automated method that shows the fibroglandular tissue area, breast area and breast density each time new thresholds are placed on the image. The breast density is taken as a percentage of the fibroglandular tissue to the breast tissue areas. It was tested in four different ways, namely by examining: (i) correlation of the quantitative assessment results with subjective classification, (ii) classification performance using the quantitative assessment technique, (iii) interobserver agreement and (iv) intraobserver agreement. The results of the quantitative assessment correlated well (r2 = 0.92) with the subjective Tabar patterns classified by the radiologist (correctly classified 83% of digitized mammograms). The average kappa coefficient for the agreement between the readers was 0.63. This indicated moderate agreement between the three observers in classifying breast density using the quantitative assessment technique. The kappa coefficient of 0.75 for intraobserver agreement reflected good agreement between two sets of readings. The technique may be useful as a supplement to the radiologist's assessment in classifying mammograms into Tabar's pattern associated with breast cancer risk.
    Matched MeSH terms: Software
  19. Fulltext A novel and improved method of predicting hand grip strength in the adult Malaysian population
    Kamarul T, Ahmad TS, Loh WY
    Med J Malaysia, 2006 Dec;61 Suppl B:37-44.
    PMID: 17600991
    Hand grip strength measurement is a recognized part of hand function assessment. The standard measurement using the Jamar dynamometer and comparing these results to the recommended normal values suggested by the manufacturers of the Jamar was questioned as these values were based on Western population. A study comparing a novel method of predicting grip strength using our software was conducted on 25 normal subjects using the LIDO kinetic workset (Group A and B ). These results were then compared against our predictive software (Group A) and the expected values supplied together with the Jamar Dynamometer (Group B). In another group, 22 normal subjects were tested using the Jamar (Group C and D) and then matched against the predicted values using their recommended chart (Group C). The last group (Group D) was tested using the Jamar but the values attained were compared to the results from our software. In group A, the predictability of our predictive method was 100% (both R & L) as compared to (R = 64%, L = 68%) in group B, (R = 27.3%, L = 59.1%) in group C and (R = 81.8%, L = 86.4%) in group D. The differences between the predictability of both methods were statistically significant. The data collected using both the Jamar and the LIDO kinetic workset correlated well to the data from our software but not to the values suggested by the manufacturers of Jamar. We conclude that our method of predicting hand grip values are superior to that suggested by the manufacturers of dynamometers. The standard reference for hand grip strength provided by the manufacturers is less accurate in predicting the grip strength of our local population.
    Matched MeSH terms: Software
  20. In silico analysis of Burkholderia pseudomallei genome sequence for potential drug targets
    Chong CE, Lim BS, Nathan S, Mohamed R
    In Silico Biol. (Gedrukt), 2006;6(4):341-6.
    PMID: 16922696
    Recent advances in DNA sequencing technology have enabled elucidation of whole genome information from a plethora of organisms. In parallel with this technology, various bioinformatics tools have driven the comparative analysis of the genome sequences between species and within isolates. While drawing meaningful conclusions from a large amount of raw material, computer-aided identification of suitable targets for further experimental analysis and characterization, has also led to the prediction of non-human homologous essential genes in bacteria as promising candidates for novel drug discovery. Here, we present a comparative genomic analysis to identify essential genes in Burkholderia pseudomallei. Our in silico prediction has identified 312 essential genes which could also be potential drug candidates. These genes encode essential proteins to support the survival of B. pseudomallei including outer-inner membrane and surface structures, regulators, proteins involved in pathogenenicity, adaptation, chaperones as well as degradation of small and macromolecules, energy metabolism, information transfer, central/intermediate/miscellaneous metabolism pathways and some conserved hypothetical proteins of unknown function. Therefore, our in silico approach has enabled rapid screening and identification of potential drug targets for further characterization in the laboratory.
    Matched MeSH terms: Software
Related Terms
Filters
Contact Us

Please provide feedback to Administrator (afdal@afpm.org.my)

External Links