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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
Fulltext Rapid Determination of Major Compounds in the Ethanol Extract of Geopropolis from Malaysian Stingless Bees, Heterotrigona itama, by UHPLC-Q-TOF/MS and NMR

Zhao L, Yu M, Sun M, Xue X, Wang T, Cao W, et al.

Molecules, 2017 Nov 10;22(11).
PMID: 29125569 DOI: 10.3390/molecules22111935

A reliable, rapid analytical method was established for the characterization of constituents of the ethanol extract of geopropolis (EEGP) produced by Malaysian stingless bees-Heterotrigona itama-by combining ultra-high-performance liquid chromatography with quadruple time-of-flight mass spectrometry (UHPLC-Q-TOF/MS). Based on known standards, the online METLIN database, and published literature, 28 compounds were confirmed. Phenolic acids, flavones, triterpenes and phytosterol were identified or tentatively identified using characteristic diagnostic fragment ions. The results indicated that terpenoids were the main components of EEGP, accompanied by low levels of phenolic acids, flavonoids, and phytosterol. Two major components were further purified by preparative high-performance liquid chromatography (PHPLC) and identified by nuclear magnetic resonance (NMR) as 24(E)-cycloart-24-ene-26-ol-3-one and 20-hydroxy-24-dammaren-3-one. These two triterpenes, confirmed in this geopropolis for the first time, are potential chemical markers for the identification of geopropolis from Malaysian stingless bees, H. itama.

Matched MeSH terms: Software
Loxodonta Localizer: A Software Tool for Inferring the Provenance of African Elephants and Their Ivory Using Mitochondrial DNA

Zhao K, Ishida Y, Green CE, Davidson AG, Sitam FAT, Donnelly CL, et al.

J Hered, 2019 12 17;110(7):761-768.
PMID: 31674643 DOI: 10.1093/jhered/esz058

Illegal hunting is a major threat to the elephants of Africa, with more elephants killed by poachers than die from natural causes. DNA from tusks has been used to infer the source populations for confiscated ivory, relying on nuclear genetic markers. However, mitochondrial DNA (mtDNA) sequences can also provide information on the geographic origins of elephants due to female elephant philopatry. Here, we introduce the Loxodonta Localizer (LL; www.loxodontalocalizer.org), an interactive software tool that uses a database of mtDNA sequences compiled from previously published studies to provide information on the potential provenance of confiscated ivory. A 316 bp control region sequence, which can be readily generated from DNA extracted from ivory, is used as a query. The software generates a listing of haplotypes reported among 1917 African elephants in 24 range countries, sorted in order of similarity to the query sequence. The African locations from which haplotype sequences have been previously reported are shown on a map. We demonstrate examples of haplotypes reported from only a single locality or country, examine the utility of the program in identifying elephants from countries with varying degrees of sampling, and analyze batches of confiscated ivory. The LL allows for the source of confiscated ivory to be assessed within days, using widely available molecular methods that do not depend on a particular platform or laboratory. The program enables identification of potential regions or localities from which elephants are being poached, with capacity for rapid identification of populations newly or consistently targeted by poachers.

Matched MeSH terms: Software*
Fulltext Retrofitting ancient timber glulam mortise & tenon construction joints through computer-aided laser cutting

Zhan Z, Wang C, Yap JBH, Loi MS

Heliyon, 2020 Apr;6(4):e03671.
PMID: 32382668 DOI: 10.1016/j.heliyon.2020.e03671

This study is aimed to rationalise and demonstrate the efficacy of utilising laser cutting technique in the fabrication of glulam mortise & tenon joints in timber frame. Trial-and-error experiments aided by laser cutter were conducted to produce 3D timber mortise & tenon joints models. The two main instruments used were 3D modelling software and the laser cutter TH 1390/6090. Plywood was chosen because it could produce smooth and accurate cut edges whereby the surface could remain crack-free, and it could increase stability due to its laminated nature. Google SketchUp was used for modelling and Laser CAD v7.52 was used to transfer the 3D models to the laser cutter because it is compatible with AI, BMP, PLT, DXF and DST templates. Four models were designed and fabricated in which the trial-and-error experiments proved laser cutting could speed up the manufacturing process with superb quality and high uniformity. Precision laser cutting supports easy automation, produces small heat-affected zone, minimises deformity, relatively quiet and produces low amount of waste. The LaserCAD could not process 3D images directly but needed 2D images to be transferred, so layering and unfolding works were therefore needed. This study revealed a significant potential of rapid manufacturability of mortise & tenon joints with high-quality and high-uniformity through computer-aided laser cutting technique for wide applications in the built environment.

Matched MeSH terms: Software
Fulltext Graphery: interactive tutorials for biological network algorithms

Zeng H, Zhang J, Preising GA, Rubel T, Singh P, Ritz A

Nucleic Acids Res, 2021 07 02;49(W1):W257-W262.
PMID: 34037782 DOI: 10.1093/nar/gkab420

Networks have been an excellent framework for modeling complex biological information, but the methodological details of network-based tools are often described for a technical audience. We have developed Graphery, an interactive tutorial webserver that illustrates foundational graph concepts frequently used in network-based methods. Each tutorial describes a graph concept along with executable Python code that can be interactively run on a graph. Users navigate each tutorial using their choice of real-world biological networks that highlight the diverse applications of network algorithms. Graphery also allows users to modify the code within each tutorial or write new programs, which all can be executed without requiring an account. Graphery accepts ideas for new tutorials and datasets that will be shaped by both computational and biological researchers, growing into a community-contributed learning platform. Graphery is available at https://graphery.reedcompbio.org/.

Matched MeSH terms: Software*
Molecular detection of Trypanosoma evansi based on ITS1 rDNA gene in Camelus dromedarius in Sistan Region, Iran

Zangooie F, Ganjali M, Keighobadi M, Nabavi R

Trop Biomed, 2018 Dec 01;35(4):1140-1147.
PMID: 33601861

Trypanosomiasis is a disease caused by a flagellate protozoon called Trypanosoma and can be mechanically transmitted by vectors to humans and animals. Various species of Trypanosoma are found in livestock and poultry, which include Trypanosoma evansi, T. brucei, T. vivax and T. congolense. The camel is the most sensitive livestock for T. evansi, so the exact identification of infection is very important for epidemiological studies and the design of control programs. The present study was conducted with the aim of molecular detection of camel trypanosomiasis in the Sistan region in 2015. Previous studies have shown that internal transcribed spacer one (ITS1) of the ribosomal DNA is a reliable genetic marker for carrying out systematic molecular studies of trypanosomes. In order to investigate infections of camels with T. evansi, a total of 113 blood samples were collected randomly and the presence of parasites in each sample was evaluated using the microscopic method and polymerase chain reaction (PCR) test. Genomic DNA was extracted and the ITS-1 was amplified by PCR. In comparison to the nucleotide sequence obtained with the sequences recorded in GenBank, it was determined that there is a 99% homology with the recorded sequence of T. evansi. The obtained sequence was registered in Gen Bank with kx900449 code. The T. evansi sequences from different countries such as India, Taiwan, Thailand, the Philippines, China and Argentina and etc., were extracted from the Gene bank and aligned using the ClustalW2 sequence alignment tool and MEGA software. In this study the prevalence of T. evansi infection using the molecular method was 6.19% and no positive samples were found by microscopic observation.

Matched MeSH terms: Software
Comparison of planned and measured rectal dose in-vivo during high dose rate Cobalt-60 brachytherapy of cervical cancer

Zaman ZK, Ung NM, Malik RA, Ho GF, Phua VC, Jamalludin Z, et al.

Phys Med, 2014 Dec;30(8):980-4.
PMID: 25086486 DOI: 10.1016/j.ejmp.2014.07.002

Cobalt-60 (Co-60) is a relatively new source for the application of high-dose rate (HDR) brachytherapy. Radiation dose to the rectum is often a limiting factor in achieving the full prescribed dose to the target during brachytherapy of cervical cancer. The aim of this study was to measure radiation doses to the rectum in-vivo during HDR Co-60 brachytherapy. A total of eleven HDR brachytherapy treatments of cervical cancer were recruited in this study. A series of diodes incorporated in a rectal probe was inserted into the patient's rectum during each brachytherapy procedure. Real-time measured rectal doses were compared to calculated doses by the treatment planning system (TPS). The differences between calculated and measured dose ranged from 8.5% to 41.2%. This corresponds to absolute dose differences ranging from 0.3 Gy to 1.5 Gy. A linear relationship was observed between calculated and measured doses with linear regression R(2) value of 0.88, indicating close association between the measured and calculated doses. In general, absorbed doses for the rectum as calculated by TPS were observed to be higher than the doses measured using the diode probe. In-vivo dosimetry is an important quality assurance method for HDR brachytherapy of cervical cancer. It provides information that can contribute to the reduction of errors and discrepancies in dose delivery. Our study has shown that in-vivo dosimetry is feasible and can be performed to estimate the dose to the rectum during HDR brachytherapy using Co-60.

Matched MeSH terms: Software
Fulltext A Methodology on the Impact of Different Teamwork Skill Levels on the Efficiency of the Software Development Workflow Based on Malaysia Industry

Zairina Ibrahim, Md Gapar Md Johar

Journal of Management & Science, 2018;16(2):1-10.
MyJurnal

The process of software development life cycle (SDLC) is an important element of development phases to develop the application. In fact, there are needs to upgrade the sequence of methodology in software development. Thus, the SDLC is very crucial in order for them to ensure the quality of skills is placed accordingly in the workflow. This research contributes to the development of a new approach in system development workflow with the aim to properly manage system development projects. It started by providing some background data related to the previous mode of operation in the teamwork samples as shared by the stakeholders of the transformation projects and the new proposed Analysis System Development Framework (ASDF) method team members. Then, the key findings related to steps of software development such as (1) input for User Requirement Specification (URS) and (2) System Requirement Specification (SRS), (3) process for module, (4) process for database, (5) process for User Acceptance Testing (UAT) (6) output for Final Acceptance Testing (FAT) and empowerment for the whole level based on ASDF method. This paper contribution significantly to support the perception of high quality of skills in a teamwork, results in better performance of software development.

Matched MeSH terms: Software
Fulltext Flexible model-based clustering of mixed binary and continuous data: application to genetic regulation and cancer

Zainul Abidin FN, Westhead DR

Nucleic Acids Res, 2017 04 20;45(7):e53.
PMID: 27994031 DOI: 10.1093/nar/gkw1270

Clustering is used widely in 'omics' studies and is often tackled with standard methods, e.g. hierarchical clustering. However, the increasing need for integration of multiple data sets leads to a requirement for clustering methods applicable to mixed data types, where the straightforward application of standard methods is not necessarily the best approach. A particularly common problem involves clustering entities characterized by a mixture of binary data (e.g. presence/absence of mutations, binding, motifs and epigenetic marks) and continuous data (e.g. gene expression, protein abundance, metabolite levels). Here, we present a generic method based on a probabilistic model for clustering this type of data, and illustrate its application to genetic regulation and the clustering of cancer samples. We show that the resulting clusters lead to useful hypotheses: in the case of genetic regulation these concern regulation of groups of genes by specific sets of transcription factors and in the case of cancer samples combinations of gene mutations are related to patterns of gene expression. The clusters have potential mechanistic significance and in the latter case are significantly linked to survival. The method is available as a stand-alone software package (GNU General Public Licence) from http://github.com/BioToolsLeeds/FlexiCoClusteringPackage.git.

Matched MeSH terms: Software
Fulltext PC based DAQ & control for nuclear counting system

Zainudin Jaafar, Mukhlis Mokhtar, Abu Bakar Mhd Ghazali

Journal of Nuclear and Related Technologies, 2010;2010(2):89-101.
MyJurnal

Personal computer (PC) based user interface for equipment control and data acquisition from the nuclear counting system to count nuclear radiation energy from radioactive sources have been developed at Malaysian Nuclear Agency. Effort is made to ensure a good reliability of the system for nuclear counting, especially neutrons particles and gamma rays. It will be used in laboratory for testing and maintenance of nuclear spectrometry instruments. Personal computer is used to control the operation of equipment and data acquisition from counter/timer module. Control and data communication between PC and the Counter/ Timer is made through the USB' to RS 232 converter terminal. The program for this system was written using Labview 8.6 software on Windows XP environment. This system has been successfully tested using a pulse generator to simulate the detector signal for calibration and then followed by actual measurement using HE-3 detector.

Matched MeSH terms: Software
Fulltext House building tips (HBT) corpus dataset as a resource to discover Malay architectural ingenuity and identity

Zaini MF, Sarudin A, Muhammad MM, Osman Z, Mohamed Redzwan HF, Al-Muhsin MA

Data Brief, 2021 Jun;36:107013.
PMID: 33898671 DOI: 10.1016/j.dib.2021.107013

House Building Tips is the title of a classic text containing historical information on early house construction in Malay communities. These tips were written by a scholar with knowledge of house construction through observation of the surrounding environment. In Malaysia, written sources or records of house construction are scarce and underexposed. As such, this research was conducted to guarantee the written legacy of the construction of Malay houses. The purpose of this paper is to introduce a statistical data source of house building tips that is laden with Malay ingenuity and identity. The wordlists generated from this study can become a source of reference for the field of Malay architecture. Accordingly, this study utilises the quantitative method by applying the Linguistic Corpus Statistical Approach; these data utilise specific corpus development procedures, beginning with text collection, scanning and cleaning processes, text annotation, and data storing in plain text. Next, the data analysis procedure utilises a corpus software, LancsBox, to generate specialised wordlists. The bubble graphs are developed based on these wordlists through the Tableau software, and illustrate the most used lexical items with the raw and relative frequency values. This facilitates searches for, and the reading of, architectural words and architectural word references. These data represent written sources that need to be preserved and become points of reference concerning Malay architectural ingenuity and identity.

Matched MeSH terms: Software
Fulltext Method development for determination of sodium, potassium and calcium ions concentrations in hot springs water using EDXRF

Zaini Hamzah, Nurul Latiffah Abd Rani, Ahmad Saat

Journal of Nuclear and Related Technologies, 2013;2013(2):59-64.
MyJurnal

Measurement of major cation such as Na+, K+, and Ca2+ in water are normally carried out using
AAS, ICP-OES or flame photometry. In this study, an attempt was made to measure these cations
using Energy Dispersive X-ray Fluorescent Spectrometry (EDXRF). Hot spring s water was taken from varies hot spring in Selangor and divided into two portions that is filtered and unfiltered. 5 mL of water samples were pipette into a special liquid cups (sample holders) which has a thin mylar film underneath. The MiniPal4 XRF instrument was used in this study. The resolution for the instrument use is 145 keV with energy resolution at 5.9 keV. The spectrum of cations were analysed by using MiniPal/MiniMate software to determine the cations concentration. For K+ and Ca2+, Al-thin filter was used and default filter was used for Na+. The concentration of Na+ obtained for filtered and unfiltered samples were ranged from 38.00 to 66.05 and 43.26 to 76.95 ppm. Meanwhile, concentrations of K+ for filtered and unfiltered samples were ranged from 2.42 to 8.07 and 6.18 to 29.28 ppm. Concentrations of Ca2+ for filtered and unfiltered samples were ranged from 2.59 to 10.94 and 3.18 to 12.99 ppm.

Matched MeSH terms: Software
Fulltext Assessment of 137 Cs activity concentration in soil from tea plantantion areas in Cameron Highlands

Zaini Hamzah, Che Yasmin Amirudin, Seh Datul Riduan, Ahmad Saat

Journal of Nuclear and Related Technologies, 2012;9(1):1-5.
MyJurnal

137 Cs is well known man-made radionuclide produced from nuclear industry. Nuclear weapon tests and nuclear accidents had contributed to presence of 137 Cs into the worldwide environment including Malaysia. It has spread out to the entire world through the air and water current. Since Cameron Highlands is located at high altitude, there is a better chance of the 137 Cs to settle down on the trees and later the soil underneath. In this study, the soil samples were taken at the slopes of two different tea plantation areas namely A and B. The soil samples were oven dried, ground, sieved and packed and sealed properly in plastic containers before measurement. Each plastic container contains around 450 g of sample. The measurement of 137 Cs activity concentration was done using HPGe detector gamma spectrometer. The spectrum was analyzed using Gamma Vision software to calculate the activity concentration of 137 Cs with energy peak of 661.66 keV. The activity concentration of 137 Cs found in the samples ranged from 0.23 to 1.90 and 0.11 to 3.01 Bq/kg for tea plantation A and tea plantation B, respectively. From the activity concentration of 137 Cs result, it was comparable to the others research regarding to 137 Cs in the soil around Asian.

Matched MeSH terms: Software
Fulltext Simulation of galvanic corrosion using boundary element method

Zaifol Samsu, Muhamad Daud, Siti Radiah Mohd Kamarudin, Nur Ubaidah Saidin, Abdul Aziz Mohamed, Mohd Sa’ari Ripin, et al.

Journal of Nuclear and Related Technologies, 2011;2011(2):78-84.
MyJurnal

Boundary element method (BEM) is a numerical technique that used for modeling infinite domain as is the case for galvanic corrosion analysis. The use of boundary element analysis system (BEASY) has allowed cathodic protection (CP) interference to be assessed in terms of the normal current density, which is directly proportional to the corrosion rate. This paper was present the analysis of the galvanic corrosion between Aluminium and Carbon Steel in natural sea water. The result of experimental was validated with computer simulation like BEASY program. Finally, it can conclude that the BEASY software is a very helpful tool for
future planning before installing any structure, where it gives the possible CP interference on any nearby unprotected metallic structure.

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 Evaluation and selection of open-source EMR software packages based on integrated AHP and TOPSIS

Zaidan AA, Zaidan BB, Al-Haiqi A, Kiah ML, Hussain M, Abdulnabi M

J Biomed Inform, 2015 Feb;53:390-404.
PMID: 25483886 DOI: 10.1016/j.jbi.2014.11.012

Evaluating and selecting software packages that meet the requirements of an organization are difficult aspects of software engineering process. Selecting the wrong open-source EMR software package can be costly and may adversely affect business processes and functioning of the organization. This study aims to evaluate and select open-source EMR software packages based on multi-criteria decision-making. A hands-on study was performed and a set of open-source EMR software packages were implemented locally on separate virtual machines to examine the systems more closely. Several measures as evaluation basis were specified, and the systems were selected based a set of metric outcomes using Integrated Analytic Hierarchy Process (AHP) and TOPSIS. The experimental results showed that GNUmed and OpenEMR software can provide better basis on ranking score records than other open-source EMR software packages.

Matched MeSH terms: Software; Software Design
Algorithms that eliminate the effects of calibration artefact and trial-imposed offsets of Masimo oximeter in BOOST-NZ trial

Zahari M, Lee DS, Darlow BA

J Clin Monit Comput, 2016 Oct;30(5):669-78.
PMID: 26282827 DOI: 10.1007/s10877-015-9752-1

The displayed readings of Masimo pulse oximeters used in the Benefits Of Oxygen Saturation Targeting (BOOST) II and related trials in very preterm babies were influenced by trial-imposed offsets and an artefact in the calibration software. A study was undertaken to implement new algorithms that eliminate the effects of offsets and artefact. In the BOOST-New Zealand trial, oxygen saturations were averaged and stored every 10 s up to 36 weeks' post-menstrual age. Two-hundred and fifty-seven of 340 babies enrolled in the trial had at least two weeks of stored data. Oxygen saturation distribution patterns corresponding with a +3 % or -3 % offset in the 85-95 % range were identified together with that due to the calibration artefact. Algorithms involving linear and quadratic interpolations were developed, implemented on each baby of the dataset and validated using the data of a UK preterm baby, as recorded from Masimo oximeters with the original software and a non-offset Siemens oximeter. Saturation distributions obtained were compared for both groups. There were a flat region at saturations 85-87 % and a peak at 96 % from the lower saturation target oximeters, and at 93-95 and 84 % respectively from the higher saturation target oximeters. The algorithms lowered the peaks and redistributed the accumulated frequencies to the flat regions and artefact at 87-90 %. The resulting distributions were very close to those obtained from the Siemens oximeter. The artefact and offsets of the Masimo oximeter's software had been addressed to determine the true saturation readings through the use of novel algorithms. The implementation would enable New Zealand data be included in the meta-analysis of BOOST II trials, and be used in neonatal oxygen studies.

Matched MeSH terms: Software
Mutational Profiles of F8 and F9 in a Cohort of Haemophilia A and Haemophilia B Patients in the Multi-ethnic Malaysian Population

Zahari M, Sulaiman SA, Othman Z, Ayob Y, Karim FA, Jamal R

Mediterr J Hematol Infect Dis, 2018;10(1):e2018056.
PMID: 30210749 DOI: 10.4084/MJHID.2018.056

Background: Haemophilia A (HA) and Haemophilia B (HB) are X-linked blood disorders that are caused by various mutations in the factor VIII (F8) and factor IX (F9) genes respectively. Identification of mutations is essential as some of the mutations are associated with the development of inhibitors. This study is the first comprehensive study of the F8 mutational profile in Malaysia.
Materials and methods: We analysed 100 unrelated HA and 15 unrelated HB patients for genetic alterations in the F8 and F9 genes by using the long-range PCR, DNA sequencing, and the multiplex-ligation-dependent probe amplification assays. The prediction software was used to confirm the effects of these mutations on factor VIII and IX proteins.
Results: 44 (53%) of the severe HA patients were positive for F8 intron 22 inversion, and three (3.6%) were positive for intron one inversion. There were 22 novel mutations in F8, including missense (8), frameshift (9), splice site (3), large deletion (1) and nonsense (1) mutations. In HB patients, four novel mutations were identified including the splice site (1), small deletion (1), large deletion (1) and missense (1) mutation.
Discussion: The mutational spectrum of F8 in Malaysian patients is heterogeneous, with a slightly higher frequency of intron 22 inversion in these severe HA patients when compared to other Asian populations. Identification of these mutational profiles in F8 and F9 genes among Malaysian patients will provide a useful reference for the early detection and diagnosis of HA and HB in the Malaysian population.

Matched MeSH terms: Software
Fulltext The Acquisition, Analyses and Interpretation of fMRI Data: A Study on Functional Specialisation in Primary Auditory Cortices

Yusuf, A.N., Abdul Hamid, K., Mohamad, M., Abd hamid, A.I.

Medicine & Health, 2008;3(2):300-317.
MyJurnal

In this study, functional magnetic resonance imaging (fMRI) is used to investigate func-tional specialisation in human auditory cortices during listening. A silent fMRI paradigm was used to reduce the scanner sound artefacts on functional images. The subject was instructed to pay attention to the white noise stimulus binaurally given at an inten-sity level of 70 dB higher than the hearing level for normal people. Functional speciali-sation was studied using the Matlab-based Statistical Parametric Mapping (SPM5) software by means of fixed effects (FFX), random effects (RFX) and conjunction analyses. Individual analyses on all subjects indicated asymmetrical bilateral activation of the left and right hemispheres in Brodmann areas (BA) 22, 41 and 42, involving the primary and secondary auditory cortices. The percentage of signal change is larger in the BA22, 41 and 42 on the right as compared to the ones on the left (p>0.05). The average number of activated voxels in all the respective Brodmann areas are higher in the right hemisphere than in the left (p>0.05). FFX results showed that the point of maximum intensity was in the right BA41 whereby 599±1 activated voxels were ob-served in the right temporal lobe as compared to 485±1 in the left temporal lobe. The RFX results were consistent with that of FFX. The analysis of conjunction which fol-lowed, showed that the right BA41 and left BA22 as the common activated areas in all subjects. The results confirmed the specialisation of the right auditory cortices in pro-cessing non verbal stimuli.

Matched MeSH terms: Software
Fulltext Using computational fluid dynamics in the determination of solar collector orientation and stack height of a solar induced ventilation prototype

Yusoff, W. F. M., Sapian, A. R., Salleh, E., Adam, N. M., Hamzah, Z., Mamat, M. H. H.

Pertanika Journal of Science & Technology, 2014;22(1):273-288.
MyJurnal

Stack ventilation in the hot and humid climate is inherently inefficient due to minimal air temperature differences between indoor and outdoor environment of a naturally ventilated building. Solar induced ventilation is a viable alternative in enhancing this stack ventilation. This paper aims to demonstrate investigations on the effective solar collector orientation and stack height for a solar induced ventilation prototype that utilizes roof solar collector and vertical stack. The orientation of the solar collector is significant as it determines the amount of solar radiation absorbed by the solar collector. Meanwhile, the height of the vertical stack influences the creation of the stack pressure in inducing air movement. Investigations were executed using a simulation modelling software called FloVENT. The validation of the simulation modelling against physical experiment indicated a good agreement between these two results. Analyses were executed on the air temperature increments inside the solar collector. A high increment of the air temperature resulted in the effective orientation. Meanwhile, the air temperature and mass flow rate of the various heights of the vertical stack were also analyzed. The findings concluded that the recommended orientation for the prototype’s solar collector is the west-facing orientation. It was also found that the higher the vertical stack, the lower the air temperature inside the stack would be, but with greater induced mass flow rate.

Matched MeSH terms: Software

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