Displaying publications 61 - 80 of 754 in total

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  1. Darawi MN, Ai-Vyrn C, Ramasamy K, Hua PP, Pin TM, Kamaruzzaman SB, et al.
    BMC Med Genet, 2013;14:27.
    PMID: 23419238 DOI: 10.1186/1471-2350-14-27
    The incidence of Alzheimer's disease, particularly in developing countries, is expected to increase exponentially as the population ages. Continuing research in this area is essential in order to better understand this disease and develop strategies for treatment and prevention. Genome-wide association studies have identified several loci as genetic risk factors of AD aside from apolipoprotein E such as bridging integrator (BIN1), clusterin (CLU), ATP-binding cassette sub-family A member 7 (ABCA7), complement receptor 1 (CR1) and phosphatidylinositol binding clathrin assembly protein (PICALM). However genetic research in developing countries is often limited by lack of funding and expertise. This study therefore developed and validated a simple, cost effective polymerase chain reaction based technique to determine these single nucleotide polymorphisms.
    Matched MeSH terms: Software*
  2. Hosseinpoor AR, Nambiar D, Schlotheuber A, Reidpath D, Ross Z
    BMC Med Res Methodol, 2016 10 19;16(1):141.
    PMID: 27760520
    BACKGROUND: It is widely recognised that the pursuit of sustainable development cannot be accomplished without addressing inequality, or observed differences between subgroups of a population. Monitoring health inequalities allows for the identification of health topics where major group differences exist, dimensions of inequality that must be prioritised to effect improvements in multiple health domains, and also population subgroups that are multiply disadvantaged. While availability of data to monitor health inequalities is gradually improving, there is a commensurate need to increase, within countries, the technical capacity for analysis of these data and interpretation of results for decision-making. Prior efforts to build capacity have yielded demand for a toolkit with the computational ability to display disaggregated data and summary measures of inequality in an interactive and customisable fashion that would facilitate interpretation and reporting of health inequality in a given country.

    METHODS: To answer this demand, the Health Equity Assessment Toolkit (HEAT), was developed between 2014 and 2016. The software, which contains the World Health Organization's Health Equity Monitor database, allows the assessment of inequalities within a country using over 30 reproductive, maternal, newborn and child health indicators and five dimensions of inequality (economic status, education, place of residence, subnational region and child's sex, where applicable).

    RESULTS/CONCLUSION: HEAT was beta-tested in 2015 as part of ongoing capacity building workshops on health inequality monitoring. This is the first and only application of its kind; further developments are proposed to introduce an upload data feature, translate it into different languages and increase interactivity of the software. This article will present the main features and functionalities of HEAT and discuss its relevance and use for health inequality monitoring.

    Matched MeSH terms: Software*
  3. Amin L, Hashim H, Mahadi Z, Ismail K
    BMC Med Res Methodol, 2018 12 05;18(1):163.
    PMID: 30518344 DOI: 10.1186/s12874-018-0619-2
    BACKGROUND: The demand in biobanking for the collection and maintenance of biological specimens and personal data from civilians to improve the prevention, diagnosis and treatment of diseases has increased notably. Despite the advancement, certain issues, specifically those related to privacy and data protection, have been critically discussed. The purposes of this study are to assess the willingness of stakeholders to participate in biobanking and to determine its predictors.

    METHODS: A survey of 469 respondents from various stakeholder groups in the Klang Valley region of Malaysia was carried out. Based on previous research, a multi-dimensional instrument measuring willingness to participate in biobanking, and its predictors, was constructed and validated. A single step Structural Equation Modelling was performed to analyse the measurements and structural model using the International Business Machines Corporation Software Package for Social Sciences, Analysis of Moment Structures (IBM SPSS Amos) version 20 with a maximum likelihood function.

    RESULTS: Malaysian stakeholders in the Klang Valley were found to be cautious of biobanks. Although they perceived the biobanks as moderately beneficial (mean score of 4.65) and were moderately willing to participate in biobanking (mean score of 4.10), they professed moderate concern about data and specimen protection issues (mean score of 4.33). Willingness to participate in biobanking was predominantly determined by four direct predictors: specific application-linked perceptions of their benefits (β = 0.35, p 
    Matched MeSH terms: Software
  4. Masri A, Khan NA, Zoqratt MZHM, Ayub Q, Anwar A, Rao K, et al.
    BMC Microbiol, 2021 Feb 17;21(1):51.
    PMID: 33596837 DOI: 10.1186/s12866-021-02097-2
    BACKGROUNDS: Escherichia coli K1 causes neonatal meningitis. Transcriptome studies are indispensable to comprehend the pathology and biology of these bacteria. Recently, we showed that nanoparticles loaded with Hesperidin are potential novel antibacterial agents against E. coli K1. Here, bacteria were treated with and without Hesperidin conjugated with silver nanoparticles, and silver alone, and 50% minimum inhibitory concentration was determined. Differential gene expression analysis using RNA-seq, was performed using Degust software and a set of genes involved in cell stress response and metabolism were selected for the study.

    RESULTS: 50% minimum inhibitory concentration with silver-conjugated Hesperidin was achieved with 0.5 μg/ml of Hesperidin conjugated with silver nanoparticles at 1 h. Differential genetic analysis revealed the expression of 122 genes (≥ 2-log FC, P

    Matched MeSH terms: Software
  5. Khan IM, Mani SA, Doss JG, Danaee M, Kong LYL
    BMC Oral Health, 2021 Jun 02;21(1):283.
    PMID: 34078349 DOI: 10.1186/s12903-021-01643-8
    BACKGROUND: Toothbrushing is an important yet neglected behaviour that affects the oral health of preschool children. Little is reported on parental supervision, an essential aspect of routine effective toothbrushing in this age group. The aim of this study was to evaluate pre-schoolers' toothbrushing behaviour including parental involvement and its association with their oral health.

    METHODS: This was a cross-sectional study. A total of 92 preschool children (4-6 years) were invited to participate with their parents/guardians. Nine parameters of toothbrushing behaviour were assessed from parental responses (questionnaire) and observation of child and parents/guardians (video recording). Oral examination included recording plaque, gingival and dental caries indices. BORIS software was used to assess toothbrushing parameters and Smart PLS was used to perform association with a second-generation multivariate analysis to create models with and without confounding factors.

    RESULTS: Girls were slightly more (53%) than boys (47%). Children aged 4 years were slightly more in number (38%), followed by 6-year-olds and 5-year-olds. Nearly, 90% parents had tertiary education and 46% had more than 2 children. Differences were recorded in the reported and observed behaviour. Thirty-five percent parents/guardians reported using pea-size toothpaste amount but only 28% were observed. Forty percent reported to brush for 30 s-1 min, however 51% were observed to brush for 1-2 min. Half the children were observed to use fluoridated toothpaste (F 

    Matched MeSH terms: Software
  6. Muhammad AMA, Ibrahim N, Ahmad R, Asif MK, Radzi Z, Zaini ZM, et al.
    BMC Oral Health, 2020 02 10;20(1):48.
    PMID: 32041589 DOI: 10.1186/s12903-020-1035-7
    BACKGROUND: Cone Beam Computed Tomography (CBCT) is a reliable radiographic modality to assess trabecular bone microarchitecture. The aim of this study was to determine the effect of CBCT image reconstruction parameters, namely, the threshold value and reconstruction voxel size, on trabecular bone microstructure assessment.

    METHODS: Five sectioned maxilla of adult Dorper male sheep were scanned using a CBCT system with a resolution of 76 μm3 (Kodak 9000). The CBCT images were reconstructed using different reconstruction parameters and analysed. The effect of reconstruction voxel size (76, 100 and 200 μm3) and threshold values (±15% from the global threshold value) on trabecular bone microstructure measurement was assessed using image analysis software (CT analyser version 1.15).

    RESULTS: There was no significant difference in trabecular bone microstructure measurement between the reconstruction voxel sizes, but a significant difference (Tb.N = 0.03, Tb.Sp = 0.04, Tb.Th = 0.01, BV/TV = 0.00) was apparent when the global threshold value was decreased by 15%.

    CONCLUSIONS: Trabecular bone microstructure measurements are not compromised by changing the CBCT reconstruction voxel size. However, measurements can be affected when applying a threshold value of less than 15% of the recommended global value.

    Matched MeSH terms: Software
  7. Aggarwal A, Court LE, Hoskin P, Jacques I, Kroiss M, Laskar S, et al.
    BMJ Open, 2023 Dec 07;13(12):e077253.
    PMID: 38149419 DOI: 10.1136/bmjopen-2023-077253
    INTRODUCTION: Fifty per cent of patients with cancer require radiotherapy during their disease course, however, only 10%-40% of patients in low-income and middle-income countries (LMICs) have access to it. A shortfall in specialised workforce has been identified as the most significant barrier to expanding radiotherapy capacity. Artificial intelligence (AI)-based software has been developed to automate both the delineation of anatomical target structures and the definition of the position, size and shape of the radiation beams. Proposed advantages include improved treatment accuracy, as well as a reduction in the time (from weeks to minutes) and human resources needed to deliver radiotherapy.

    METHODS: ARCHERY is a non-randomised prospective study to evaluate the quality and economic impact of AI-based automated radiotherapy treatment planning for cervical, head and neck, and prostate cancers, which are endemic in LMICs, and for which radiotherapy is the primary curative treatment modality. The sample size of 990 patients (330 for each cancer type) has been calculated based on an estimated 95% treatment plan acceptability rate. Time and cost savings will be analysed as secondary outcome measures using the time-driven activity-based costing model. The 48-month study will take place in six public sector cancer hospitals in India (n=2), Jordan (n=1), Malaysia (n=1) and South Africa (n=2) to support implementation of the software in LMICs.

    ETHICS AND DISSEMINATION: The study has received ethical approval from University College London (UCL) and each of the six study sites. If the study objectives are met, the AI-based software will be offered as a not-for-profit web service to public sector state hospitals in LMICs to support expansion of high quality radiotherapy capacity, improving access to and affordability of this key modality of cancer cure and control. Public and policy engagement plans will involve patients as key partners.

    Matched MeSH terms: Software
  8. Vasudevan R, Ismail P, Jaafar N, Mohamad N, Etemad E, Wan Aliaa W, et al.
    Balkan J. Med. Genet., 2014 Jun;17(1):37-40.
    PMID: 25741213 DOI: 10.2478/bjmg-2014-0023
    The aim of this study was to determine the association of the c.894G>T; p.Glu298Asp polymorphism and the variable number tandem repeat (VNTR) polymorphism of the endothelial nitric oxide synthase (eNOS) gene and c.181C>T polymorphism of the bradykinin type 2 receptor gene (B2R) in Malaysian end-stage renal disease (ESRD) subjects. A total of 150 ESRD patients were recruited from the National Kidney Foundation's (NKF)dialysis centers in Malaysia and compared with 150 normal healthy individuals. Genomic DNA was extracted from buccal cells of all the subjects. The polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method was carried out to amplify the products and the restricted fragments were separated by agarose gel electrophoresis. Statistical analyses were carried out using software where a level of p <0.05 was considered to be statistically significant. The genotypic and allelic frequencies of the B2R gene (c.181C>T, 4b/a) and eNOS gene (c.894G>T) polymorphisms were not statistically significant (p >0.05) when compared to the control subjects. The B2R and eNOS gene polymorphisms may not be considered as genetic susceptibility markers for Malaysian ESRD subjects.
    Matched MeSH terms: Software
  9. Amir Hashim NA, Ab-Rahim S, Wan Ngah WZ, Nathan S, Ab Mutalib NS, Sagap I, et al.
    Bioimpacts, 2021;11(1):33-43.
    PMID: 33469506 DOI: 10.34172/bi.2021.05
    Introduction:
    The serum metabolomics approach has been used to identify metabolite biomarkers that can diagnose colorectal cancer (CRC) accurately and specifically. However, the biomarkers identified differ between studies suggesting that more studies need to be performed to understand the influence of genetic and environmental factors. Therefore, this study aimed to identify biomarkers and affected metabolic pathways in Malaysian CRC patients.
    Methods:
    Serum from 50 healthy controls and 50 CRC patients were collected at UKM Medical Centre. The samples were deproteinized with acetonitrile and untargeted metabolomics profile determined using liquid chromatography-quadrupole time-of-flight mass spectrometry (LC-QTOFMS, Agilent USA). The data were analysed using Mass Profiler Professional (Agilent, USA) software. The panel of biomarkers determined were then used to identify CRC from a new set of 20 matched samples.
    Results:
    Eleven differential metabolites were identified whose levels were significantly different between CRC patients compared to normal controls. Based on the analysis of the area under the curve, 7 of these metabolites showed high sensitivity and specificity as biomarkers. The use of the 11 metabolites on a new set of samples was able to differentiate CRC from normal samples with 80% accuracy. These metabolites were hypoxanthine, acetylcarnitine, xanthine, uric acid, tyrosine, methionine, lysoPC, lysoPE, citric acid, 5-oxoproline, and pipercolic acid. The data also showed that the most perturbed pathways in CRC were purine, catecholamine, and amino acid metabolisms.
    Conclusion:
    Serum metabolomics profiling can be used to identify distinguishing biomarkers for CRC as well as to further our knowledge of its pathophysiological mechanisms.
    Matched MeSH terms: Software
  10. Chong ETJ, Kuok SSE, Lee PC
    Bioimpacts, 2018;8(3):159-165.
    PMID: 30211075 DOI: 10.15171/bi.2018.18
    Introduction:
    Obesity is commonly linked up with several life-threatening diseases. This study aims to investigate the association of fatty acid synthase (FASN) rs4246445, rs2229425, rs2228305, and rs2229422 single nucleotide polymorphisms (SNPs) with the risk of overweight and obesity in the Malaysian population.
    Methods:
    Blood samples were collected from 1030 individuals who were grouped into normal, overweight, and obese categories. Blood biochemistry test and lipid profiling were performed and genomic DNA was extracted. Genotyping was performed using hydrolysis probes and odd ratio with 95% CI was calculated for risk association analysis. Linkage disequilibrium and haplotypes analyses were carried out using SHEsis software.
    Results:
    We found that the hemoglobin and white blood cell counts were significantly high in the obese subjects. There is a lack of evidence to link the FASN SNPs with the risk of overweight and obesity in the population. All 4 SNPs were seemed to be in linkage equilibrium. Five common haplotypes were identified in this study but none of them was significantly associated with overweight and obesity in the population.
    Conclusion:
    Our findings suggest a lack of evidence to associate the FASN rs4246445, rs2229425, rs2228305, and rs2229422 SNPs with the risk of overweight and obesity in the Malaysian population. All 4 SNPs were independent of each other and not all identified haplotypes were significantly associated with overweight and obesity in this study.
    Matched MeSH terms: Software
  11. Tan CS, Ting WS, Mohamad MS, Chan WH, Deris S, Shah ZA
    Biomed Res Int, 2014;2014:213656.
    PMID: 25250315 DOI: 10.1155/2014/213656
    When gene expression data are too large to be processed, they are transformed into a reduced representation set of genes. Transforming large-scale gene expression data into a set of genes is called feature extraction. If the genes extracted are carefully chosen, this gene set can extract the relevant information from the large-scale gene expression data, allowing further analysis by using this reduced representation instead of the full size data. In this paper, we review numerous software applications that can be used for feature extraction. The software reviewed is mainly for Principal Component Analysis (PCA), Independent Component Analysis (ICA), Partial Least Squares (PLS), and Local Linear Embedding (LLE). A summary and sources of the software are provided in the last section for each feature extraction method.
    Matched MeSH terms: Software*; Software Design
  12. Saleh MA, Solayman M, Paul S, Saha M, Khalil MI, Gan SH
    Biomed Res Int, 2016;2016:9142190.
    PMID: 27294143 DOI: 10.1155/2016/9142190
    Despite the reported association of adiponectin receptor 1 (ADIPOR1) gene mutations with vulnerability to several human metabolic diseases, there is lack of computational analysis on the functional and structural impacts of single nucleotide polymorphisms (SNPs) of the human ADIPOR1 at protein level. Therefore, sequence- and structure-based computational tools were employed in this study to functionally and structurally characterize the coding nsSNPs of ADIPOR1 gene listed in the dbSNP database. Our in silico analysis by SIFT, nsSNPAnalyzer, PolyPhen-2, Fathmm, I-Mutant 2.0, SNPs&GO, PhD-SNP, PANTHER, and SNPeffect tools identified the nsSNPs with distorting functional impacts, namely, rs765425383 (A348G), rs752071352 (H341Y), rs759555652 (R324L), rs200326086 (L224F), and rs766267373 (L143P) from 74 nsSNPs of ADIPOR1 gene. Finally the aforementioned five deleterious nsSNPs were introduced using Swiss-PDB Viewer package within the X-ray crystal structure of ADIPOR1 protein, and changes in free energy for these mutations were computed. Although increased free energy was observed for all the mutants, the nsSNP H341Y caused the highest energy increase amongst all. RMSD and TM scores predicted that mutants were structurally similar to wild type protein. Our analyses suggested that the aforementioned variants especially H341Y could directly or indirectly destabilize the amino acid interactions and hydrogen bonding networks of ADIPOR1.
    Matched MeSH terms: Software
  13. Al-Absi AA, Al-Sammarraie NA, Shaher Yafooz WM, Kang DK
    Biomed Res Int, 2018;2018:7501042.
    PMID: 30417014 DOI: 10.1155/2018/7501042
    MapReduce is the preferred cloud computing framework used in large data analysis and application processing. MapReduce frameworks currently in place suffer performance degradation due to the adoption of sequential processing approaches with little modification and thus exhibit underutilization of cloud resources. To overcome this drawback and reduce costs, we introduce a Parallel MapReduce (PMR) framework in this paper. We design a novel parallel execution strategy of Map and Reduce worker nodes. Our strategy enables further performance improvement and efficient utilization of cloud resources execution of Map and Reduce functions to utilize multicore environments available with computing nodes. We explain in detail makespan modeling and working principle of the PMR framework in the paper. Performance of PMR is compared with Hadoop through experiments considering three biomedical applications. Experiments conducted for BLAST, CAP3, and DeepBind biomedical applications report makespan time reduction of 38.92%, 18.00%, and 34.62% considering the PMR framework against Hadoop framework. Experiments' results prove that the PMR cloud computing platform proposed is robust, cost-effective, and scalable, which sufficiently supports diverse applications on public and private cloud platforms. Consequently, overall presentation and results indicate that there is good matching between theoretical makespan modeling presented and experimental values investigated.
    Matched MeSH terms: Software
  14. Tiong KH, Chang JK, Pathmanathan D, Hidayatullah Fadlullah MZ, Yee PS, Liew CS, et al.
    Biotechniques, 2018 12;65(6):322-330.
    PMID: 30477327 DOI: 10.2144/btn-2018-0072
    We describe a novel automated cell detection and counting software, QuickCount® (QC), designed for rapid quantification of cells. The Bland-Altman plot and intraclass correlation coefficient (ICC) analyses demonstrated strong agreement between cell counts from QC to manual counts (mean and SD: -3.3 ± 4.5; ICC = 0.95). QC has higher recall in comparison to ImageJauto, CellProfiler and CellC and the precision of QC, ImageJauto, CellProfiler and CellC are high and comparable. QC can precisely delineate and count single cells from images of different cell densities with precision and recall above 0.9. QC is unique as it is equipped with real-time preview while optimizing the parameters for accurate cell count and needs minimum hands-on time where hundreds of images can be analyzed automatically in a matter of milliseconds. In conclusion, QC offers a rapid, accurate and versatile solution for large-scale cell quantification and addresses the challenges often faced in cell biology research.
    Matched MeSH terms: Software*
  15. Yeo BPH, Foong LC, Tam SM, Lee V, Hwang SS
    Biochem Mol Biol Educ, 2018 01;46(1):47-53.
    PMID: 29131478 DOI: 10.1002/bmb.21089
    Structures and functions of protein motifs are widely included in many biology-based course syllabi. However, little emphasis is placed to link this knowledge to applications in biotechnology to enhance the learning experience. Here, the conserved motifs of nucleotide binding site-leucine rich repeats (NBS-LRR) proteins, successfully used for the isolation and characterization of many plant resistance gene analogues (RGAs), is featured in the development of a series of laboratory experiments using important molecular biology techniques. A set of previously isolated RGA sequences is used as the model for performing sequence alignment and visualising 3D protein structure using current bioinformatics programs (Clustal Omega and Argusdock software). A pair of established degenerate primer sequences is provided for the prediction of targeted amino acids sequences in the RGAs. Reverse transcription-polymerase chain reaction (RT-PCR) is used to amplify RGAs from total RNA samples extracted from the tropical wild relative of black pepper, Piper colubrinum (Piperaceae). This laboratory exercise enables students to correlate specific DNA sequences with respective amino acid codes and the interaction between conserved motifs of resistance genes with putatively targeted proteins. © 2017 by The International Union of Biochemistry and Molecular Biology, 46(1):47-53, 2018.
    Matched MeSH terms: Software
  16. Navien TN, Thevendran R, Hamdani HY, Tang TH, Citartan M
    Biochimie, 2020 Oct 18;180:54-67.
    PMID: 33086095 DOI: 10.1016/j.biochi.2020.10.005
    Aptamers are single-stranded DNA or RNA oligonucleotides generated by SELEX that exhibit binding affinity and specificity against a wide variety of target molecules. Compared to RNA aptamers, DNA aptamers are much more stable and therefore are widely adopted in a number of applications especially in diagnostics. The tediousness and rigor associated with certain steps of the SELEX intensify the efforts to adopt in silico molecular docking approaches together with in vitro SELEX procedures in developing DNA aptamers. Inspired by these endeavors, we carry out an overview of the in silico molecular docking approaches in DNA aptamer generation, by detailing the stepwise procedures as well as shedding some light on the various softwares used. The in silico maturation strategy and the limitations of the in silico approaches are also underscored.
    Matched MeSH terms: Software
  17. Chew TH, Joyce-Tan KH, Akma F, Shamsir MS
    Bioinformatics, 2011 May 1;27(9):1320-1.
    PMID: 21398666 DOI: 10.1093/bioinformatics/btr109
    birgHPC, a bootable Linux Live CD has been developed to create high-performance clusters for bioinformatics and molecular dynamics studies using any Local Area Network (LAN)-networked computers. birgHPC features automated hardware and slots detection as well as provides a simple job submission interface. The latest versions of GROMACS, NAMD, mpiBLAST and ClustalW-MPI can be run in parallel by simply booting the birgHPC CD or flash drive from the head node, which immediately positions the rest of the PCs on the network as computing nodes. Thus, a temporary, affordable, scalable and high-performance computing environment can be built by non-computing-based researchers using low-cost commodity hardware.
    Matched MeSH terms: Software*
  18. 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
  19. Cheong WH, Tan YC, Yap SJ, Ng KP
    Bioinformatics, 2015 Nov 15;31(22):3685-7.
    PMID: 26227146 DOI: 10.1093/bioinformatics/btv433
    : We present ClicO Free Service, an online web-service based on Circos, which provides a user-friendly, interactive web-based interface with configurable features to generate Circos circular plots.
    Matched MeSH terms: Software*
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