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A decision support system for automatic screening of non-proliferative diabetic retinopathy

Reza AW, Eswaran C

J Med Syst, 2011 Feb;35(1):17-24.
PMID: 20703589 DOI: 10.1007/s10916-009-9337-y

The increasing number of diabetic retinopathy (DR) cases world wide demands the development of an automated decision support system for quick and cost-effective screening of DR. We present an automatic screening system for detecting the early stage of DR, which is known as non-proliferative diabetic retinopathy (NPDR). The proposed system involves processing of fundus images for extraction of abnormal signs, such as hard exudates, cotton wool spots, and large plaque of hard exudates. A rule based classifier is used for classifying the DR into two classes, namely, normal and abnormal. The abnormal NPDR is further classified into three levels, namely, mild, moderate, and severe. To evaluate the performance of the proposed decision support framework, the algorithms have been tested on the images of STARE database. The results obtained from this study show that the proposed system can detect the bright lesions with an average accuracy of about 97%. The study further shows promising results in classifying the bright lesions correctly according to NPDR severity levels.

Matched MeSH terms: Software
Optimization of bioresource material from oil palm trunk core drying using microwave radiation; a response surface methodology application

Amouzgar P, Khalil HP, Salamatinia B, Abdullah AZ, Issam AM

Bioresour Technol, 2010 Nov;101(21):8396-401.
PMID: 20639118 DOI: 10.1016/j.biortech.2010.05.061

In this study optimization of drying oil palm trunk core lumber (OPTCL) biomass using microwave radiation was reported. Optimizing of the drying conditions using microwave, avoid burning, shrinkage and increasing the permeability of OPT was aimed to develop a new value added material. A set of experiments was designed by central composite design using response surface methodology (RSM) to statistically evaluate the findings. Three independent process variables including time (2-10 min), sample weight (300-1000 g) and input power (660-3300 W) were studied under the given conditions designed by Design Expert software. The results showed the effectiveness of microwave drying in reducing the time and better removal of moisture as compared to that of oven drying with no significant changes. Employing optimum conditions at 6.89 min of time with a microwave power set at 4 for a sample of 1000 g, predicting 14.62% of moisture content.

Matched MeSH terms: Software
QSAR study of substituted 1,3,4-oxadiazole naphthyridines as HIV-1 integrase inhibitors

Ravichandran V, Shalini S, Sundram K, Sokkalingam AD

Eur J Med Chem, 2010 Jul;45(7):2791-7.
PMID: 20347187 DOI: 10.1016/j.ejmech.2010.02.062

A linear quantitative structure activity relationship (QSAR) model is presented for modeling and predicting the inhibition of HIV-1 integrase. The model was produced by using the stepwise multiple linear regression technique on a database that consists of 67 recently discovered 1,3,4-oxadiazole substituted naphthyridine derivatives. The developed QSAR model was evaluated for statistical significance and predictive power. The key conclusion of this study is that valence connectivity index order 1, lowest unoccupied molecular orbital and dielectric energy significantly affect the inhibition of HIV-1 integrase activity by 1,3,4-oxadiazole substituted naphthyridine derivatives. The selected physicochemical descriptors serve as a first guideline for the design of novel and potent antagonists of HIV-1 integrase.

Matched MeSH terms: Software
Deciphering the flexibility and dynamics of Geobacillus zalihae strain T1 lipase at high temperatures by molecular dynamics simulation

Abdul Rahman MB, Karjiban RA, Salleh AB, Jacobs D, Basri M, Thean Chor AL, et al.

Protein Pept Lett, 2009;16(11):1360-70.
PMID: 20001926

The stability of biocatalysts is an important criterion for a sustainable industrial operation economically. T1 lipase is a thermoalkalophilic enzyme derived from Geobacillus zalihae strain T1 (T1 lipase) that was isolated from palm oil mill effluent (POME) in Malaysia. We report here the results of high temperatures molecular dynamics (MD) simulations of T1 lipase in explicit solvent. We found that the N-terminal moiety of this enzyme was accompanied by a large flexibility and dynamics during temperature-induced unfolding simulations which preceded and followed by clear structural changes in two specific regions; the small domain (consisting of helices alpha3 and alpha5, strands beta1 and beta2, and connecting loops) and the main catalytic domain or core domain (consisting of helices alpha6- alpha9 and connecting loops which located above the active site) of the enzyme. The results suggest that the small domain of model enzyme is a critical region to the thermostability of this organism.

Matched MeSH terms: Software
Development and implementation of a web-based system to study children with malnutrition

Syed-Mohamad SM

Comput Methods Programs Biomed, 2009 Jan;93(1):83-92.
PMID: 18789553 DOI: 10.1016/j.cmpb.2008.07.011

To develop and implement a collective web-based system to monitor child growth in order to study children with malnutrition.

Matched MeSH terms: Software
Developing a Web 2.0 telemedical education system: the AJAX-Cocoon portal

Mohammed S, Orabi A, Fiaidhi J, Orabi M, R. Benlamri

Int J Electron Healthc, 2008;4(1):24-42.
PMID: 18583294

Web 2.0 technologies such as wikis, podcasts/vodcasting, blogs and semantic portals could be quite effective tools in e-learning for health professionals. If effectively deployed, such tools can offer a way to enhance students', clinicians' and patients' learning experiences, and deepens levels of learners' engagement and collaboration within medical learning environments. However, Web 2.0 requires simplicity of use as well as integration with modern web technologies. This article presents a Web 2.0 telemedical portal, which provides a social community-learning paradigm from the desk of the physician, the student, the hospital administrator, or the insurer. The presented portal utilises RESTful web services and techniques like content syndication, mushups and Asynchronous JavaScript API and XML (AJAX). The designed portal is based on the Apache Cocoon RESTful framework for sharing Digital Imaging and Communications in Medicine (DICOM) medical case studies. Central to this article is the integration between Cocoon and AJAX. The proposed AJAX-Cocoon portal utilises a JSP portlet architecture, which manages the interaction dynamics and overcomes the shortcomings of the JSR 168 and WSRP 1.0 standards.

Matched MeSH terms: Software
A visual probe localization and calibration system for cost-effective computer-aided 3D ultrasound

Ali A, Logeswaran R

Comput Biol Med, 2007 Aug;37(8):1141-7.
PMID: 17126314

The 3D ultrasound systems produce much better reproductions than 2D ultrasound, but their prohibitively high cost deprives many less affluent organization this benefit. This paper proposes using the conventional 2D ultrasound equipment readily available in most hospitals, along with a single conventional digital camera, to construct 3D ultrasound images. The proposed system applies computer vision to extract position information of the ultrasound probe while the scanning takes place. The probe, calibrated in order to calculate the offset of the ultrasound scan from the position of the marker attached to it, is used to scan a number of geometrical objects. Using the proposed system, the 3D volumes of the objects were successfully reconstructed. The system was tested in clinical situations where human body parts were scanned. The results presented, and confirmed by medical staff, are very encouraging for cost-effective implementation of computer-aided 3D ultrasound using a simple setup with 2D ultrasound equipment and a conventional digital camera.

Matched MeSH terms: Software Design
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
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
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
Stone detection in MRCP images using controlled region growing

Logeswaran R, Eswaran C

Comput Biol Med, 2007 Aug;37(8):1084-91.
PMID: 17112496

Stones in the biliary tract are routinely identified using MRCP (magnetic resonance cholangiopancreatography). The noisy nature of the images, as well as varying intensity, size and location of the stones, defeat most automatic detection algorithms, making computer-aided diagnosis difficult. This paper proposes a multi-stage segment-based scheme for semi-automated detection of choledocholithiasis and cholelithiasis in the MRCP images, producing good performance in tests, differentiating them from "normal" MRCP images. With the high success rate of over 90%, refinement of the scheme could be applicable in the clinical environment as a tool in aiding diagnosis, with possible applications in telemedicine.

Matched MeSH terms: Software Design
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
Meta-analysis: the association between HIV infection and extrapulmonary tuberculosis

Naing C, Mak JW, Maung M, Wong SF, Kassim AI

Lung, 2013 Feb;191(1):27-34.
PMID: 23180033 DOI: 10.1007/s00408-012-9440-6

BACKGROUND: Extrapulmonary tuberculosis has been an AIDS-defining condition. Individual studies that highlight the association between HIV and extrapulmonary TB are available. Our objectives were to synthesis evidence on the association between extrapulmonary tuberculosis and HIV and to explore the effective preventive measures of these two diseases.
METHODS: This is a meta-analysis of observational studies reporting effect estimates on how HIV is associated with extrapulmonary tuberculosis. We searched for the eligible studies in the electronic databases using search terms related to HIV and extrapulmonary tuberculosis. Where possible, we estimated the summary odds ratios using random effects meta-analysis. We stratified analysis by the type of study design. We assessed heterogeneity of effect estimates within each group of studies was assessed using I (2) test.
RESULTS: Nineteen studies (7 case control studies and 12 cohort studies) were identified for the present study. The pooled analysis shows a significant association between HIV and extrapulmonary tuberculosis (summary odds ratio: 1.3; 95 % confidence interval (CI) 1.05-1.6; I (2): 0 %). In a subgroup analysis with two studies, a significant association was found between CD4+ count less than 100 and the incidence of extrapulmonary tuberculosis (summary OR: 1.31; 95 % CI 1.02-1.68; I (2): 0 %).
CONCLUSIONS: Findings show evidence on the association between extrapulmonary tuberculosis and HIV, based on case control studies. Further studies to understand the mechanisms of interaction of the two pathogens are recommended.

Matched MeSH terms: Software Design
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
Fulltext Computational discovery and RT-PCR validation of novel Burkholderia conserved and Burkholderia pseudomallei unique sRNAs

Khoo JS, Chai SF, Mohamed R, Nathan S, Firdaus-Raih M

BMC Genomics, 2012;13 Suppl 7:S13.
PMID: 23282220 DOI: 10.1186/1471-2164-13-S7-S13

The sRNAs of bacterial pathogens are known to be involved in various cellular roles including environmental adaptation as well as regulation of virulence and pathogenicity. It is expected that sRNAs may also have similar functions for Burkholderia pseudomallei, a soil bacterium that can adapt to diverse environmental conditions, which causes the disease melioidosis and is also able to infect a wide variety of hosts.

Matched MeSH terms: Software
Fulltext Diagnosis of Lung Cancer by Fractal Analysis of Damaged DNA

Namazi H, Kiminezhadmalaie M

Comput Math Methods Med, 2015;2015:242695.
PMID: 26539245 DOI: 10.1155/2015/242695

Cancer starts when cells in a part of the body start to grow out of control. In fact cells become cancer cells because of DNA damage. A DNA walk of a genome represents how the frequency of each nucleotide of a pairing nucleotide couple changes locally. In this research in order to study the cancer genes, DNA walk plots of genomes of patients with lung cancer were generated using a program written in MATLAB language. The data so obtained was checked for fractal property by computing the fractal dimension using a program written in MATLAB. Also, the correlation of damaged DNA was studied using the Hurst exponent measure. We have found that the damaged DNA sequences are exhibiting higher degree of fractality and less correlation compared with normal DNA sequences. So we confirmed this method can be used for early detection of lung cancer. The method introduced in this research not only is useful for diagnosis of lung cancer but also can be applied for detection and growth analysis of different types of cancers.

Matched MeSH terms: Software
Study on the performance of different craniofacial superimposition approaches (II): Best practices proposal

Damas S, Wilkinson C, Kahana T, Veselovskaya E, Abramov A, Jankauskas R, et al.

Forensic Sci Int, 2015 Dec;257:504-508.
PMID: 26482539 DOI: 10.1016/j.forsciint.2015.07.045

Craniofacial superimposition, although existing for one century, is still a controversial technique within the scientific community. Objective and unbiased validation studies over a significant number of cases are required to establish a more solid picture on the reliability. However, there is lack of protocols and standards in the application of the technique leading to contradictory information concerning reliability. Instead of following a uniform methodology, every expert tends to apply his own approach to the problem, based on the available technology and deep knowledge on human craniofacial anatomy, soft tissues, and their relationships. The aim of this study was to assess the reliability of different craniofacial superimposition methodologies and the corresponding technical approaches to this type of identification. With all the data generated, some of the most representative experts in craniofacial identification joined in a discussion intended to identify and agree on the most important issues that have to be considered to properly employ the craniofacial superimposition technique. As a consequence, the consortium has produced the current manuscript, which can be considered the first standard in the field; including good and bad practices, sources of error and uncertainties, technological requirements and desirable features, and finally a common scale for the craniofacial matching evaluation. Such a document is intended to be part of a more complete framework for craniofacial superimposition, to be developed during the FP7-founded project MEPROCS, which will favour and standardize its proper application.

Matched MeSH terms: Software
Fulltext NeisseriaBase: a specialised Neisseria genomic resource and analysis platform

Zheng W, Mutha NV, Heydari H, Dutta A, Siow CC, Jakubovics NS, et al.

PeerJ, 2016;4:e1698.
PMID: 27017950 DOI: 10.7717/peerj.1698

Background. The gram-negative Neisseria is associated with two of the most potent human epidemic diseases: meningococcal meningitis and gonorrhoea. In both cases, disease is caused by bacteria colonizing human mucosal membrane surfaces. Overall, the genus shows great diversity and genetic variation mainly due to its ability to acquire and incorporate genetic material from a diverse range of sources through horizontal gene transfer. Although a number of databases exist for the Neisseria genomes, they are mostly focused on the pathogenic species. In this present study we present the freely available NeisseriaBase, a database dedicated to the genus Neisseria encompassing the complete and draft genomes of 15 pathogenic and commensal Neisseria species. Methods. The genomic data were retrieved from National Center for Biotechnology Information (NCBI) and annotated using the RAST server which were then stored into the MySQL database. The protein-coding genes were further analyzed to obtain information such as calculation of GC content (%), predicted hydrophobicity and molecular weight (Da) using in-house Perl scripts. The web application was developed following the secure four-tier web application architecture: (1) client workstation, (2) web server, (3) application server, and (4) database server. The web interface was constructed using PHP, JavaScript, jQuery, AJAX and CSS, utilizing the model-view-controller (MVC) framework. The in-house developed bioinformatics tools implemented in NeisseraBase were developed using Python, Perl, BioPerl and R languages. Results. Currently, NeisseriaBase houses 603,500 Coding Sequences (CDSs), 16,071 RNAs and 13,119 tRNA genes from 227 Neisseria genomes. The database is equipped with interactive web interfaces. Incorporation of the JBrowse genome browser in the database enables fast and smooth browsing of Neisseria genomes. NeisseriaBase includes the standard BLAST program to facilitate homology searching, and for Virulence Factor Database (VFDB) specific homology searches, the VFDB BLAST is also incorporated into the database. In addition, NeisseriaBase is equipped with in-house designed tools such as the Pairwise Genome Comparison tool (PGC) for comparative genomic analysis and the Pathogenomics Profiling Tool (PathoProT) for the comparative pathogenomics analysis of Neisseria strains. Discussion. This user-friendly database not only provides access to a host of genomic resources on Neisseria but also enables high-quality comparative genome analysis, which is crucial for the expanding scientific community interested in Neisseria research. This database is freely available at http://neisseria.um.edu.my.

Matched MeSH terms: Software
Development, feasibility, and validity of a computer-based utility assessment tool for measuring asthma-specific health utilities in Malaysia using the standard gamble method

Yong YV, Shafie AA

J Asthma, 2016 10;53(8):835-42.
PMID: 27049693 DOI: 10.3109/02770903.2016.1156694

OBJECTIVES: To develop and test the feasibility and validity of a computer-based utility assessment tool that used standard gamble (SG) method for measuring asthma-specific health utilities.
METHODS: A computer-based SG (CBSG) tool was developed using Microsoft® PowerPoint 2007 to value asthma-specific health states in Malaysia. Eight hypothetical health states were considered, including two anchor states (healthy and dead), three chronic (C) states and three temporary (T) states (each numbered 1 through 3, with increasing severity) in addition to the subject's current health state. Twenty adult asthma patients completed the CBSG tool in addition to paper-based Asthma Control Test, three health status measures (EQ-5D, EQ-VAS, and Mini Asthma Quality of Life Questionnaire (MiniAQLQ)), and VAS utility assessment tool. Patients and interviewers rated the difficulty of the VAS and CBSG tools. Correlations between current health state values derived from the various measures were determined.
RESULTS: The SG and the VAS received similar difficulty ratings. 17 patients completed the CBSG tool within 30 minutes. The mean utilities determined by the CBSG tool for the T1-T3 asthma health states met the expected logical order of 1>2>3, but those for the C1-C3 states did not. Correlation between current health state values derived from the CBSG tool and other measurement tools was poor.
CONCLUSION: The CBSG tool developed for measuring utilities of asthma health states showed acceptable feasibility and overall validity.

Matched MeSH terms: Software
Fulltext The prevalence of dental fluorosis and its associated factors in Salem district

Ramesh M, Narasimhan M, Krishnan R, Chalakkal P, Aruna RM, Kuruvilah S

Contemp Clin Dent, 2016 6 17;7(2):203-8.
PMID: 27307668 DOI: 10.4103/0976-237X.183061

CONTEXT: There are various regions in India that have high levels of fluoride in drinking water sources. Many people residing in such places suffer from dental fluorosis (DF).
AIMS: To evaluate the prevalence of DF in children residing in Salem and also to find any correlation between DF and other related factors.
MATERIALS AND METHODS: One school from each block of Salem (total 21 blocks) was selected for the study. A single examiner had evaluated untreated caries, lesions, and DF (for permanent anterior teeth and molars) using the Dean's fluorosis index, in all children. Water fluoride level determination at each school was done using the Tamil Nadu Water Fluoridation and Drainage Board field kit. Other factors that may have contributed to DF were assessed using a questionnaire, which was provided to each student. The data obtained were statistically analyzed using the SPSS software version 11.5.
STATISTICAL ANALYSIS: Chi-square test was used for statistical analysis.
RESULTS: DF was present in 56.9% of the children examined. It was mostly seen in 9 years old (72%) and male (59%) children. A positive correlation was found between the occurrence of DF and the duration of residence in a place with high water fluoride content, consumption of borewell water (64%), the parts per million of fluoride in drinking water, consumption of black tea (59%). However, no correlation was found between DF, dental caries, consumption of milk, or consumption of foods cooked in aluminum vessels.
CONCLUSION: There was a correlation between DF and factors such as male gender, bore well water consumption, black tea consumption and the duration of residence in a place with high water fluoride content.

Matched MeSH terms: Software

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