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Fulltext Eukaryotic pathways targeted by the type III secretion system effector protein, BipC, involved in the intracellular lifecycle of Burkholderia pseudomallei

Kang WT, Vellasamy KM, Vadivelu J

Sci Rep, 2016 09 16;6:33528.
PMID: 27634329 DOI: 10.1038/srep33528

Burkholderia pseudomallei, the etiological agent for melioidosis, is known to secrete a type III secretion system (TTSS) protein into the host's internal milieu. One of the TTSS effector protein, BipC, has been shown to play an important role in the B. pseudomallei pathogenesis. To identify the host response profile that was directly or indirectly regulated by this protein, genome-wide transcriptome approach was used to examine the gene expression profiles of infected mice. The transcriptome analysis of the liver and spleen revealed that a total of approximately 1,000 genes were transcriptionally affected by BipC. Genes involved in bacterial invasion, regulation of actin cytoskeleton, and MAPK signalling pathway were over-expressed and may be specifically regulated by BipC in vivo. These results suggest that BipC mainly targets pathways related to the cellular processes which could modulate the cellular trafficking processes. The host transcriptional response exhibited remarkable differences with and without the presence of the BipC protein. Overall, the detailed picture of this study provides new insights that BipC may have evolved to efficiently manipulate host-cell pathways which is crucial in the intracellular lifecycle of B. pseudomallei.

Matched MeSH terms: Software
Fulltext Three-dimensional facial analysis of Chinese children with repaired unilateral cleft lip and palate

Othman SA, Aidil Koay NA

Sci Rep, 2016 08 10;6:31335.
PMID: 27507713 DOI: 10.1038/srep31335

We analyzed the facial features of Chinese children with repaired unilateral cleft lip and palate (UCLP) and compared them with a normal control group using a three-dimensional (3D) stereophotogrammetry camera. This cross-sectional study examined 3D measurements of the facial surfaces of 20 Chinese children with repaired UCLP and 40 unaffected Chinese children aged 7 to 12 years old, which were captured using the VECTRA 3D five-pod photosystem and analyzed using Mirror software. Twenty-five variables and two ratios were compared between both groups using independent t-test. Intra- and inter-observer reliability was determined using ten randomly selected images and analyzed using intra-class correlation coefficient test (ICC). The level of significance was set at p

Matched MeSH terms: Software
Fulltext On the Stability of MHD Boundary Layer Flow over a Stretching/Shrinking Wedge

Awaludin IS, Ishak A, Pop I

Sci Rep, 2018 Sep 11;8(1):13622.
PMID: 30206256 DOI: 10.1038/s41598-018-31777-9

The steady two dimensional magnetohydrodynamic (MHD) boundary layer flow and heat transfer over a stretching/shrinking permeable wedge is numerically investigated. The partial differential equations governing the flow and heat transfer are transformed into a system of ordinary differential equations using a similarity transformation. These equations are then solved numerically using the boundary value problem solver, bvp4c in Matlab software. It is found that dual solutions exist for a certain range of the shrinking strength. A stability analysis is performed to identify which solution is stable and physically reliable.

Matched MeSH terms: Software
Fulltext Biomechanical System Versus Observational Rating Scale for Parkinson's Disease Tremor Assessment

Chan PY, Mohd Ripin Z, Abdul Halim S, Kamarudin MI, Ng KS, Eow GB, et al.

Sci Rep, 2019 05 31;9(1):8117.
PMID: 31148550 DOI: 10.1038/s41598-019-44142-1

There is a lack of evidence that either conventional observational rating scale or biomechanical system is a better tremor assessment tool. This work focuses on comparing a biomechanical system and the Movement Disorder Society-sponsored revision of the Unified Parkinson's Disease Rating Scale in terms of test-retest reliability. The Parkinson's disease tremors were quantified by biomechanical system in joint angular displacement and predicted rating, as well as assessed by three raters using observational ratings. Qualitative comparisons of the validity and function are made also. The observational rating captures the overall severity of body parts, whereas the biomechanical system provides motion- and joint-specific tremor severity. The tremor readings of the biomechanical system were previously validated against encoders' readings and doctors' ratings; the observational ratings were validated with previous ratings on assessing the disease and combined motor symptoms rather than on tremor specifically. Analyses show that the predicted rating is significantly more reliable than the average clinical ratings by three raters. The comparison work removes some of the inconsistent impressions of the tools and serves as guideline for selecting a tool that can improve tremor assessment. Nevertheless, further work is required to consider more variabilities that influence the overall judgement.

Matched MeSH terms: Software
Application of acid-modified Imperata cylindrica powder for latent fingerprint development

Low WZ, Khoo BE, Aziz ZB, Low LW, Teng TT, bin Abdullah AF

Sci Justice, 2015 Sep;55(5):347-54.
PMID: 26385718 DOI: 10.1016/j.scijus.2015.04.008

A novel powdering material that utilizes acid-modified Imperata cylindrica (IC) powder for the development of fingermarks was studied. Experiments were carried out to determine the suitability, adherence quality and sensitivity of the acid-modified IC powder. Fingermarks of different constituents (eccrine, sebaceous and natural fingermarks) on different types of surfaces were used. Acid-modified IC powder was also used to develop fingermarks of different ages as well as aged fingermarks recovered from the water. From the visual inspection, acid-modified IC powder was able to interact with different fingermark constituents and produced distinct ridge details on the examined surfaces. It was also able to develop aged fingermarks and fingermarks that were submerged in water. A statistical comparison was made against the Sirchie® Hi-Fi black powder in terms of the powders' sensitivity and quality of the developed natural fingermarks. The image quality was analyzed using MITRE's Image Quality of Fingerprint (IQF) software. From the experiments, acid-modified IC powder has the potential as a fingermark development powder, although natural fingermarks developed by Sirchie® black powder showed better quality and sensitivity based on the results of the statistical comparison.

Matched MeSH terms: Software
Multi stakeholders of health and industries perspectives on medicine price transparency initiative in private health care settings in Malaysia

Sufiza Ahmad N, Makmor-Bakry M, Hatah E

Saudi Pharm J, 2020 Jul;28(7):850-858.
PMID: 32647487 DOI: 10.1016/j.jsps.2020.06.003

Introduction: Medicine price transparency initiatives provide public or government on information about the product's prices and the components that may influence the prices, such as volume and product quality. In Malaysia, medicine price transparency has become part of the government's strategies in ensuring adequate, continuous and equitable access to quality, safe, effective and affordable medicines. Since the effect of medicine price transparency depend critically on how prices are presented, this study aims to evaluate the stakeholders' perspective of medicine price transparency practice in the private healthcare system in Malaysia.
Methods: This study was conducted as face-to-face, semi-structured interview. Respondents from private pharmaceutical industries, community pharmacists, general practitioners, private hospital pharmacists, governments, academicians and senior pharmacist were recruited using purposive sampling. Using phenomenological study approach, interviews were conducted, and audio recorded with their consent. Data were transcribed verbatim and analysed using thematic analysis with Atlas.ti 8 software and categorised as strengths, weaknesses, opportunities and threats (SWOT).
Results: A total of 28 respondents were interviewed. There was a mixed perception regarding the price transparency implementation in Malaysia's private healthcare settings. The potential strengths include it will provide price standardization, reduce price manipulation and competition, hence allowing the industry players to focus more on patient-care services. Moreover, the private stakeholders were concerned that the practice may affect stakeholders' business and marketing strategy, reduce profit margin, increase general practitioner's consultation fees and causing impact on geographical discrepancies. The practice was viewed as an opportunity to disseminate the truth price information to consumer and strengthen collaboration between healthcare industries and Ministry of Health although this may become a threat that affect the business survival.
Conclusion: Price transparency initiatives would benefit the pharmaceutical industries, consumer and countries, but it needs to be implemented appropriately to prevent price manipulation, market monopoly, and business closure. Future study may want to evaluate the impact of the initiatives on the business in the industry.

Matched MeSH terms: Software
Fulltext Efficacy of choline and DHA supplements or enriched environment exposure during early adult obesity in mitigating its adverse impact through aging in rats

Prabhu GS, Prasad K, K G MR, Rai KS

Saudi J Biol Sci, 2021 Apr;28(4):2396-2407.
PMID: 33911955 DOI: 10.1016/j.sjbs.2021.01.037

Introduction: The aim of this study was to assess the efficacy of choline and DHA or exposure to environmental enrichment in obese adult and aging rats on alterations in body mass index, serum lipid profile and arterial wall changes, despite stopping high fat diet consumption and interventions during adulthood.
Methods: 21 day old male Sprague Dawley rats were assigned as Experiment-1 & 2 - PND rats were divided into 4 groups with interventions for 7 months (n = 8/group). NC- Normal control fed normal chow diet; OB- Obese group, fed high fat diet; OB + CHO + DHA- fed high fat diet and oral supplementation of choline, DHA. OB + EE- fed high fat diet along with exposure to enriched environment .Experiment-2 had similar groups and interventions as experiment 1 but for next 5 months were fed normal chow diet without any interventions. Body mass index was assessed and blood was analyzed for serum lipid profile. Common Carotid Artery (CCA) was processed for Haematoxylin and eosin, Verhoff Vangeison stains. Images of tissue sections were analyzed and quantified using image J and tissue quant software.
Results: In experiment.1, mean body mass index (p

Matched MeSH terms: Software
Fulltext Geographic Information System (GIS) modeling approach to determine the fastest delivery routes

Abousaeidi M, Fauzi R, Muhamad R

Saudi J Biol Sci, 2016 Sep;23(5):555-64.
PMID: 27579003 DOI: 10.1016/j.sjbs.2015.06.004

This study involves the adoption of the Geographic Information System (GIS) modeling approach to determine the quickest routes for fresh vegetable delivery. During transport, fresh vegetables mainly deteriorate on account of temperature and delivery time. Nonetheless, little attention has been directed to transportation issues in most areas within Kuala Lumpur. In addition, perishable food normally has a short shelf life, thus timely delivery significantly affects delivery costs. Therefore, selecting efficient routes would consequently reduce the total transportation costs. The regression model is applied in this study to determine the parameters that affect route selection with respect to the fastest delivery of fresh vegetables. For the purpose of this research, ArcGIS software with network analyst extension is adopted to solve the problem of complex networks. The final output of this research is a map of quickest routes with the best delivery times based on all variables. The variables tested from regression analysis are the most effective parameters to make the flow of road networks slower. The objective is to improve the delivery services by achieving the least drive time. The main findings of this research are that Land use such as residential area and population as variables are the effective parameters on drive time.

Matched MeSH terms: Software
The influence of geometrical shapes of stenosis on the blood flow in stenosed artery

Kamangar S, Nik-Ghazali N, Badarudin A, Ameer Ahamad N, Irfan Anjum Badruddin, Govindaraju K, et al.

Sains Malaysiana, 2017;46:1923-1933.

The present work was carried out to investigate the blood flow behavior and the severity of blockage caused in the
arterial passage due to the different geometries such as elliptical, trapezium and triangular shapes of stenosis. The study
was conducted with respect to various sizes of stenosis in terms of 70%, 80% and 90% area blockage of the arterial
blood flow. The study was carried out numerically with the help of advance computational fluid dynamic software. It
was found that the shape of the stenosis plays an important role in overall pressure drop across the blockage region
of artery. The highest level of pressure drop was observed for trapezoidal shape of stenosis followed by elliptical and
then by triangular shaped stenosis. The wall shear stress across the stenosis is great for trapezoidal shape followed by
triangular and elliptical stenosis for same blockage area in the artery.

Matched MeSH terms: Software
MHD stagnation-point flow over a stretching/shrinking sheet in a micropolar fluid with a slip boundary

Siti Khuzaimah Soid, Anuar Ishak, Ioan Pop

Sains Malaysiana, 2018;47:2907-2916.

The problem of stagnation point flow over a stretching/shrinking sheet immersed in a micropolar fluid is analyzed
numerically. The governing partial differential equations are transformed into a system of ordinary (similarity) differential
equation and are then solved numerically using the boundary value problem solver (bvp4c) in Matlab software. The
effects of various parameters on the velocity and the angular velocity as well as the skin friction coefficient and the couple
stress are shown in tables and graphs. The noticeable results are found that the micropolar and the slip parameters
decrease the skin friction coefficient and the couple stress in the existence of magnetic field. Dual solutions appear for
certain range of the shrinking strength. A stability analysis is performed to determine which one of the solutions is stable.
Practical applications include polymer extrusion, where one deals with stretching of plastic sheets and in metallurgy
that involves the cooling of continuous strips.

Matched MeSH terms: Software
Application of a simple mono window land surface temperature algorithm from Landsat ETM+ over Al Qassim, Saudi Arabia

Lim H, Mat Jafri M, Abdullah K, Sultan Alsultan

Sains Malaysiana, 2012;41:841-846.

This study was conducted to retrieve the land surface temperature (LST) from Landsat ETM+ data for Al Qassim, Saudi Arabia. The proposed technique employed a mono window LST algorithm for retrieving surface temperature from Landsat ETM+. The land surface emissivity and solar angle values were needed in order to apply these in the proposed algorithm. The surface emissivity values were computed based on the NDVI values. The LST values derived from ATCOR2_T in the PCI Geomatica image processing software was used for algorithm calibration. The results showed a high correlation
coefficient (R) and low root-mean-square error (RMS) between the LST values retrieved from the proposed algorithm and ATCOR2_T. This study indicated that the proposed algorithm is capable of retrieving accurate LST values and the derived information can be used in the environmental impact assessment for Al Qassim area.

Matched MeSH terms: Software
A view from a different angle: investigating the significance of rattan spines from a small mammals’ visual point of view using imageJ

Nik Fadzly, Asyraf Mansor, Rahmad Zakaria, Syed Ahmad Edzham

Sains Malaysiana, 2014;43:973-976.

Rattans are one of the most unique and economically important plants for most tropical countries. There is however, a lack of interest in the specific study of the rattan spines. In this paper, we tested a new hypothesis concerning the functional role of rattan spines. We proposed that rattan spines also serve as a visual deterrent against herbivores or seed predators. In our proposed method we used an Imaging software, ImageJ, to measure the spine area of four species of rattan (Calamus insignis, Myrialepis schortechinii, Plectocomiopsis geminiflorus and Calamus caesius) from two different orientations (root to shoot and vice versa). Our results showed that rattan spines were very heterogeneous and highly variable between different species. One common trait that the rattan spines share is that spine area measurements of shoot to root (ShR) are larger than root to shoot (RH) orientation. We propose that the downwards spine angle might be specifically designed to discourage climbing leaf and seed predators.

Matched MeSH terms: Software
Molecular characterization of Malaysian marine fish species using partial sequence of mitochondrial DNA 12S and 16S rRNA markers

Nur Haslindawaty Abd Rashid, Siti Farah Quraisha, Sundararajulu Panneerchelvam, Zafarina Zainuddin

Sains Malaysiana, 2015;44:1119-1123.

This study was conducted to characterize the selected marine fish species using partial sequence of mtDNA 12S and 16S rRNA gene. PCR amplification of 12S and 16S rRNA generated PCR amplicons at 350 and 440 bp lengths, respectively. Sequence analysis was performed using BioEdit software. Phylogenetic tree was constructed using MEGA software. Two reference species have been used namely Gobio gobio (AB239596 and EF112528) and Pentapodus caninus (DQ533268 and DQ532933). Based on the result obtained, mtDNA 12S and 16S rRNA were found to be useful as molecular markers for fish species identification. These markers will provide correct identification of fish species when considered along with morphological characteristics.

Matched MeSH terms: Software
Calculation of Mean Kidney Dose for a Co-57 External Radiation Source

Supian Samat

Sains Malaysiana, 1996;25.

A description is given of the numerical integration method for the calculation of the mean kidney dose for a Co-57 external radiation source. Based on this theory, a computer program was written. Initial calculation of the kidney volume shows that the method has a good accuracy. For the mean kidney dose, this method gives a satisfactory result, since the calculated value lies within the acceptable range of the central axis depth dose.
Satu huraian diberikan tentang kaedah pengkamiran berangka untuk mengira dos buah pinggang purata untuk satu sumber sinaran luar Co-57. Berdasarkan teori ini, satu program komputer ditulis. Pengiraan awal isipadu buah pinggang menunjukkan yang kaedah ini mempunyai ketepatan yang baik. Untuk dos buah pinggang purata, kaedah ini memberikan keputusan yang baik, kerana nilai kiraan terletak diantara julat dos kedalaman paksi pusat yang diterima.

Matched MeSH terms: Software
Status Kegiatan Pembangunan Perisian di Malaysia (Status of Software Development in Malaysia)

Aziz Bin Deraman, Ahmad Shukri Bin Yahaya

Sains Malaysiana, 1997;26.

A study was conducted to examine the usage of application software and its development practices in Malaysia. The study has shown that the use of application software is greatly emphasized by organizations in their respective businesses. And for most organizations, the application software is supplied by a vendor or through in house development. For the software development practices, the deployment of a current technique and technology is still inadequate. Therefore, most of the existing information technology practitioners should be given additional training on the latest techniques of software development. Other aspect of improvement on software development practices is also discussed.
Satu kajian terhadap status pemakaian dan kegiatan pembangunan perisian gunaan di Malaysia telah dijalankan. Kajian ini menunjukkan yang aspek pemakaian sangat diberi penekanan oleh organisasi. Manakala proses perolehan perisian gunaan pula terbahagi secara setara di antara buat sendiri dengan menggunakan pihak ketiga. Namun begitu yang ketara ialah kadar penggunaan teknologi dan teknik terkini dalam kegiatan pembangunan perisian masih berkurangan. Oleh itu disarankan supaya aspek latihan teknik kakitangan teknologi maklumat organisasi perlu dipertingkatkan secara berterusan. Di samping itu kajian ini memaparkan beberapa aspek amalan pembangunan perisian yang boleh diperbaiki lagi.

Matched MeSH terms: Software
Response surface methodology models of processing parameters for high performance phenolic compreg wood

Zaidon A, Kim G, Bakar E, Rasmina H

Sains Malaysiana, 2014;43:775-782.

The aim of the study was to develop response surface methodology (RSM) models for polymer loading, density, dimensional stability, strength and stiffness of compressed wood of sesenduk (Endospermum diadenum) treated with phenol formaldehyde (PF). Central composite design (CCD) using RSM with three processing parameters was studied in their specific ranges: PF concentration (PC) from 24-40%, pre-curing time (PCT), 3-9 h and compression ratio (CR), 70-90%. The experimental design was analysed and interpreted using the Design Expert Software (Stat Ease version 8) and the responses of 3d plots were built using the same software. Quadratic models in terms of PC, PCT and CR were developed for polymer loading, density, reduction in water absorption and modulus of rupture in static bending. Multiple linear equations were developed for anti-swelling efficiency and modulus of elasticity. The experimental values were in good agreement with predicted ones and the models were highly significant with correlation coefficients between 0.626 and 0.926. PC and CR had significant effects on the responses. The range of PCT used did not significantly affect the responses. It was also found that the improvement of properties ranged from moderately to highly correlated with the polymer loading in the compreg wood.

Matched MeSH terms: Software Design
Fulltext GIS based assessment on landslide hazard zonation: case study of Cameron Highlands – Gua Musang road Kelantan, Malaysia

Mohamed M. GahGah, Juhari Mat Akhir, Abdul Ghani M. Rafek, Ibrahim Abdullah

Sains Malaysiana, 2009;38(6):827-833.

The aim of this study is to investigate the factors that cause landslides in the area along the new road between Cameron Highlands and Gua Musang. Landslide factors such as lineaments have been extracted from remote sensing data (Landsat TM image) using ERDAS software. A soil map has been produced using field work and laboratory analysis, and the lithology, roads, drainage pattern and rainfall have been digitized using ILWIS software together with the slope angle and elevation from the Digital Elevation Model (DEM). All these parameters, which are vital for landslide hazard assessment, have been integrated into the geographical information system (GIS) for further data processing. Weightage for these landslide relevant factors related to their influence in landslide occurrence using the heuristic method has been carried out. The results from this combination through a modified ‘index overlay with multi class maps’ model was used to produce a landslide hazard zonation map. Five classes of potential landslide hazard have been derived as the following: very low hazard zone 17.27%, low hazard zone 39.35%, medium hazard zone 25.1%, high hazard zone 15.35% and very high hazard zone 2.93%. The results from this work have been checked through the landslide inventory using available aerial photos interpretation and field work, and show that the slope and elevation have the most direct affect on landslide occurrence.

Matched MeSH terms: Software
A fourth-order compact finite difference scheme for the goursat problem

Mohd Agos Salim Nasir, Ahmad Izani Md Ismail

Sains Malaysiana, 2013;42:341-346.

A high-order uniform Cartesian grid compact finite difference scheme for the Goursat problem is developed. The basic idea of high-order compact schemes is to find the compact approximations to the derivatives terms by differentiating centrally the governing equations. Our compact scheme will approximate the derivative terms by involving the higher terms and reducing the number of grid points. The compact finite difference scheme is given for general form of the Goursat problem in uniform domain and illustrates the performance by applying a linear problem. Numerical experiments have been conducted with the new scheme and encouraging results have been obtained. In this paper we present the compact finite difference scheme for the Goursat problem. With the aid of computational software the scheme was programmed for determining the relative errors of linear Goursat problem.

Matched MeSH terms: Software
Prediction of tool life in end milling of Ti-6A1-4V alloy using artificial neural network and multiple regression models

SALAH AL-ZUBAIDI, JAHARAH A. GHANI, CHE HASSAN CHE HARON

Sains Malaysiana, 2013;42:1735-1741.

Tool life of the cutting tools is considered as one of the factors which has effects on machining costs and the quality of machined parts. The topic of tool life prediction has been an interesting and important research topic attracting the attention of a wide number of researchers in this particular area. In terms of the suitable methods used in this research topic, it is stated that both statistical and artificial intelligence (AI) approaches can be employed to model tool life. For further justifying the capability of the ANN model in predicting tool life, the current study was based on conducting experimental work for collecting the experimental data. After carrying out the experiment, 17 data sets were collected and they were divided into two subsets; the first one for training and the second for testing. Since the data sets seemed to be lower than the number of data sets used in previous studies, we attempted to make verification of the ability of the ANN model in learning and adapting with low training and testing data. Diverse topologies accompanied with single and two hidden layers were created for modeling the tool life. For choosing the best and most effective network, the study adopted the mean square error function as criteria for the evaluation of the network selection. Thus, based on the data generated from the same experiment, a regression model (RM) was constructed employing the SPSS software. A comparison between the ANN model and RMs in terms of their accuracy was carried out and the findings revealed that the accuracy of the ANN was higher than that of the RM.

Matched MeSH terms: Software
The use of inter-conversion equations on bituminous binder data

NUR IZZI MD.YUSOFF, MOHD ROSLI HAININ, MOUNIER D, AIREY GD

Sains Malaysiana, 2013;42:1647-1654.

According to the classical theory of viscoelasticity, a linear viscoelastic (LVE) function can be converted into another viscoelastic function even though they emphasize different information. In this study, dynamic tests were conducted on different conventional penetration grade bitumens using a dynamic shear rheometer (DSR) in the LVE region. The results showed that the dynamic data in the frequency domain can be converted into the time domain functions using a numerical technique. This was done with the aid of the non-linear regularization (NLREG) computer program. The NLREG software is a computer program for solving nonlinear ill-posed problem and is based on non-linear Tikhonov regularization method. The use of data interconversion equation is found suitable for converting from the frequency domain into the time domain of conventional penetration grade bitumens.

Matched MeSH terms: Software

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