Displaying publications 1 - 20 of 753 in total

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  1. Moradpour N, Karimova M, Pourafshary P, Zivar D
    ACS Omega, 2020 Jul 28;5(29):18155-18167.
    PMID: 32743190 DOI: 10.1021/acsomega.0c01766
    The results of many previous studies on low salinity/controlled ions water (CIW) flooding suggest that future laboratory and modeling investigations are required to comprehensively understand and interpret the achieved observations. In this work, the aim is co-optimization of the length of the injected slug and soaking time in the CIW flooding process. Furthermore, the possibility of the occurrence of several governing mechanisms is studied. Therefore, the experimental results were utilized to develop a compositional model, using CMG GEM software, in order to obtain the relative permeability curves by history matching. It was concluded that CIW slug injection, concentrated in the potential-determining ion, can increase oil recovery under a multi ion exchange (MIE) mechanism. The wettability of the carbonate rocks was changed from a mixed or oil wet state toward more water wetness. However, there is a CIW slug length, beyond which extending the length does not significantly improve the rock wettability, and consequently, the oil production, which is known as the optimum slug size. This implies that the optimization of the injection process, by minimizing the slug size, can decrease the need for the CIW supply, therefore lowering the process expenditure. Moreover, if the exposure time of the rock and CIW is increased (soaking), a higher level of ion substitution is probable, leading to more oil detachment and production. Rock dissolution/precipitation (leading to a pH change) was found to have a negligible contribution.
    Matched MeSH terms: Software
  2. Anuar MAM, Amran NA, Ruslan MSH
    ACS Omega, 2021 Feb 02;6(4):2707-2716.
    PMID: 33553888 DOI: 10.1021/acsomega.0c04897
    Oil and grease remain the dominant contaminants in the palm oil mill effluent (POME) despite the conventional treatment of POME. The removal of residual oil from palm oil-water mixture (POME model) using the progressive freezing process was investigated. An optimization technique called response surface methodology (RSM) with the design of rotatable central composite design was applied to figure out the optimum experimental variables generated by Design-Expert software (version 6.0.4. Stat-Ease, trial version). Besides, RSM also helps to investigate the interactive effects among the independent variables compared to one factor at a time. The variables involved are coolant temperature, XA (4-12 °C), freezing time, XB (20-60 min), and circulation flow, XC (200-600 rpm). The statistical analysis showed that a two-factor interaction model was developed using the obtained experimental data with a coefficient of determination (R2) value of 0.9582. From the RSM-generated model, the optimum conditions for extraction of oil from the POME model were a coolant temperature of 6 °C in 50 min freezing time with a circulation flowrate of 500 rpm. The validation of the model showed that the predicted oil yield and experimental oil yield were 92.56 and 93.20%, respectively.
    Matched MeSH terms: Software
  3. Supramani S, Ahmad R, Ilham Z, Annuar MSM, Klaus A, Wan-Mohtar WAAQI
    AIMS Microbiol, 2019;5(1):19-38.
    PMID: 31384700 DOI: 10.3934/microbiol.2019.1.19
    Wild-cultivated medicinal mushroom Ganoderma lucidum was morphologically identified and sequenced using phylogenetic software. In submerged-liquid fermentation (SLF), biomass, exopolysaccharide (EPS) and intracellular polysaccharide (IPS) production of the identified G.lucidum was optimised based on initial pH, starting glucose concentration and agitation rate parameters using response surface methodology (RSM). Molecularly, the G. lucidum strain QRS 5120 generated 637 base pairs, which was commensurate with related Ganoderma species. In RSM, by applying central composite design (CCD), a polynomial model was fitted to the experimental data and was found to be significant in all parameters investigated. The strongest effect (p < 0.0001) was observed for initial pH for biomass, EPS and IPS production, while agitation showed a significant value (p < 0.005) for biomass. By applying the optimized conditions, the model was validated and generated 5.12 g/L of biomass (initial pH 4.01, 32.09 g/L of glucose and 102 rpm), 2.49 g/L EPS (initial pH 4, 24.25 g/L of glucose and 110 rpm) and 1.52 g/L of IPS (and initial pH 4, 40.43 g/L of glucose, 103 rpm) in 500 mL shake flask fermentation. The optimized parameters can be upscaled for efficient biomass, EPS and IPS production using G. lucidum.
    Matched MeSH terms: Software
  4. Tan LK, Wong JH, Ng KH
    AJR Am J Roentgenol, 2006 Mar;186(3):898-901.
    PMID: 16498128
    The purpose of this article was to develop a low-cost method for high-quality remote capturing and recording of multimedia presentations.
    Matched MeSH terms: Software*
  5. Omar, N.Y.M., Rahman, N.A., Zain, S.M.
    ASM Science Journal, 2009;3(1):77-90.
    MyJurnal
    Computational chemistry is a discipline that concerns the computing of physical and chemical properties of atoms and molecules using the fundamentals of quantum mechanics. The expense of computational chemistry calculations is significant and limited by available computational capabilities. The use of high-performance computing clusters alleviate such calculations. However, as high-performance computing (HPC) clusters have always required a balance between four major factors: raw computing power, memory size, I/O capacity, and communication capacity. In this paper, we present the results of standard HPC benchmarks in order to help assess the performance characteristics of the various hardware and software components of a home-built commodity-class Linux cluster. We optimized a range of TCP/MPICH parameters and achieved a maximum MPICH bandwidth of 666 Mbps. The bandwidth and latency of GA put/get operations were better than the corresponding MPICH send/receive ones. We also examined the NFS, PVFS2, and Lustre parallel filesystems and Lustre provided the best read/write bandwidths with more than 90% of those of the local filesystem.
    Matched MeSH terms: Software
  6. Bong, C.H.J., Mah, D.Y.S, Putuhena, F.J., Said, S., Bustami, R.A.
    ASM Science Journal, 2012;6(1):47-60.
    MyJurnal
    Hydraulics simulation can be used as a supporting tool for planning and developing a framework, such as Integrated Flood Management for river management. To demonstrate this, a hydraulics model for the Sarawak River Basin was run using InfoWorks RS software by Wallingford Software, UK. InfoWorks River Simulation (RS) was chosen because its applicability has been proven and widely used to model Malaysian rivers. The extraction of computed floodwater level and flood maps for different time intervals would produce the rate of floodplain submergence from river bank level. This information could be incorporated into a logical framework to support decisions on flood management measures. Thus, hydraulics models can be used as tools to provide the necessary decision parameters for developing logical frameworks which would act as to guide the planning when it involved various stakeholders’ participation.
    Matched MeSH terms: Software
  7. Ngah, U.K., Aziz, S.A., Aziz, M.E., Murad, M., Mahdi, N.M.N., Shakaff, A.Y.M., et al.
    ASM Science Journal, 2008;2(1):1-11.
    MyJurnal
    The incidences of breast cancer have been rising at an alarming rate. Mass breast screening programmes involving mammography and ultrasound in certain parts of the world have also proven their benefits in early detection. However, radiologists may be confronted with increased workload. An attempt has been made in this paper to rectify part of the problems faced in this area. Expert systems based on the interpretation of mammographic and ultrasound images for classifying patient cases could be utilized by doctors (expert and non-expert) in screening. These softwares consist of MAMMEX (for mammogram) and SOUNDEX (for breast ultrasound) could be used to deduce cases according to Breast Imaging Recording and Data System (BI-RADS), based on patients’ history, physical and clinical assessment, mammograms and breast ultrasound images. A total of 179 retrospective cases from the Radiology Department, hospital of the University of Science Malaysia, Kubang Kerian, Kelantan were used in this study. A receiver operating characteristic (ROC) curve analysis was implemented, based on the usage of a two-class forced choice of classifying suspicious and malignant findings as positive with normal, benign and probably benign classified as negative. Results yielded an area under the curve (AUC) of 0.997 with the least standard error value of 0.003 for MAMMEX while an AUC of 0.996 with the least standard error of 0.004 was accomplished for SOUNDEX. A system which very closely simulated radiologists was also successfully developed in this study. The ROC curve analysis indicated that the expert systems developed were of high performance and reliability.
    Matched MeSH terms: Software
  8. Fauzi, R., Salazar, D.M., Kadzim, R.M., Hussin, A., Burbano, L.
    ASM Science Journal, 2009;3(2):161-167.
    MyJurnal
    In this project, a Geographic Information System (GIS) was used to collect and compile various field data in the Pedro Vicente Maldonado Ecuadorian Scientific Station Antarctica Base area. The main source of data was obtained from a global positioning system (GPS) survey using kinematic GPS (GPS-RTK) which allowed continuous point mapping in the terrain. GPS units were utilized in the collection of spatial data for all field work. The co-ordinates obtained were used to produce a point map which was then exported into GIS software where the proximity of cartographic phenomena and boundaries were mapped. All the collected data were subsequently gathered to develop the GIS database which was then used to generate and compile different maps to test for spatial and temporal relationships. The output of the project comprises a GIS database, spatial maps and 3D terrain model of the area. The developed GIS database can be used with other ecological datasets to provide biogeographical information, potential range distribution and sampling adequacy. The database is also applicable to geographical management and multi-disciplinary research projects.
    Matched MeSH terms: Software
  9. Kamal, Z.Z., Daud, A.H.M., Ashidi, M.I.N., Fadel, J.K.M.
    ASM Science Journal, 2007;1(2):87-100.
    MyJurnal
    Covering as much as 25% to 35% of the development cost, software testing is an integral part of the software development lifecycle. Despite its importance, the current software testing practice is still based on highly manual processes from the generation of test cases (i.e. from specifications) up to the actual execution of the test. These manually generated tests are sometimes executed using ad hoc approaches, typically requiring the construction of a test driver for the particular application under test. In addition, test engineers are also under pressure to test increasing lines of code in order to meet market demands for more software functionalities. While there are significant proliferations of helpful testing tools or research prototypes in the market, much of them do not adequately provide the right level of abstraction and automation as required by test engineers. In order to facilitate and address some of the aforementioned issues, an automated testing tool was developed, called SFIT, based on Java® technology. This paper describes the development, implementation and evaluation of SFIT. Two case studies involving the robustness assessment of an adder module and a Linda-based distributed shared memory implementation are described in order to demonstrate the applicability of SFIT as a helpful automated testing tool.
    Matched MeSH terms: Software
  10. Manley S
    Account Res, 2023 May;30(4):219-245.
    PMID: 34569370 DOI: 10.1080/08989621.2021.1986018
    Popular text-matching software generates a percentage of similarity - called a "similarity score" or "Similarity Index" - that quantifies the matching text between a particular manuscript and content in the software's archives, on the Internet and in electronic databases. Many evaluators rely on these simple figures as a proxy for plagiarism and thus avoid the burdensome task of inspecting the longer, detailed Similarity Reports. Yet similarity scores, though alluringly straightforward, are never enough to judge the presence (or absence) of plagiarism. Ideally, evaluators should always examine the Similarity Reports. Given the persistent use of simplistic similarity score thresholds at some academic journals and educational institutions, however, and the time that can be saved by relying on the scores, a method is arguably needed that encourages examining the Similarity Reports but still also allows evaluators to rely on the scores in some instances. This article proposes a four-band method to accomplish this. Used together, the bands oblige evaluators to acknowledge the risk of relying on the similarity scores yet still allow them to ultimately determine whether they wish to accept that risk. The bands - for most rigor, high rigor, moderate rigor and less rigor - should be tailored to an evaluator's particular needs.
    Matched MeSH terms: Software*
  11. Abu Hassan MA, Kamaruddin MI, Pharo HJ
    Acta Vet Scand Suppl, 1988;84:110-2.
    PMID: 3232593
    Matched MeSH terms: Software*
  12. Jamaluddin AA, Chang KW, Johar MS, Yaacob H
    Acta Vet Scand Suppl, 1988;84:194-6.
    PMID: 3232606
    Matched MeSH terms: Software
  13. Rai NP, Kumar P, Mustafa SM, Divakar DD, Kheraif AA, Ramakrishnaiah R, et al.
    Adv Clin Exp Med, 2016 Jul-Aug;25(4):763-6.
    PMID: 27629852 DOI: 10.17219/acem/59014
    BACKGROUND: Oral lichen planus (OLP) is a common chronic mucocutaneous disease mostly seen in middle aged and elderly females. Oral lichen planus can occur in different oral sites such as gingiva, labial, buccal mucosa and on the tongue. And can have an indirect effect on initiating periodontitis.
    OBJECTIVES: The purpose of the study was to evaluate the periodontal status of OLP patients and compare it with that of healthy controls. The presence of erosive lesions among gingival tissues makes oral hygiene procedures difficult to perform for obvious reasons. Plaque control and rigorous oral hygiene are primary requisites for the treatment of any oro-mucosal disease.
    MATERIAL AND METHODS: Thirty patients with the erosive and reticular form of OLP as a study group and 30 healthy subjects as a control group were selected. The periodontal status of all subjects including gingival index (GI), Russell's periodontal index (PI) and bleeding on probing (BOP) were evaluated in both groups. Finally, the data was analyzed by a paired t-test using SPSS software v. 22.
    RESULTS: The mean values of GI, PI and BOP were observed to be higher in the study group compared to the control group, and this was statistically significant (p < 0.05). The results shown are suggestive that periodontal status was poor in the study group as compared to the control group.
    CONCLUSIONS: Further studies need to investigate periodontal status in oral lichen planus patients with larger sample size, and careful follow-up of these will assure an increase in the quality of life of these patients. The patient should be informed regarding the risk of periodontal problems in OLP and should be advised to have regular dental checkups to avoid a worsening of the conditio.
    KEYWORDS: gingivitis; oral lichen planus; periodontitis; pre-cancerous condition
    Matched MeSH terms: Software
  14. Shanmugapriya, Huda HA, Vijayarathna S, Oon CE, Chen Y, Kanwar JR, et al.
    Adv Exp Med Biol, 2018 9 28;1087:95-105.
    PMID: 30259360 DOI: 10.1007/978-981-13-1426-1_8
    Circular RNAs characterize a class of widespread and diverse endogenous RNAs which are non-coding RNAs that are made by back-splicing events and have covalently closed loops with no polyadenylated tails. Various indications specify that circular RNAs (circRNAs) are plentiful in the human transcriptome. However, their participation in biological processes remains mostly undescribed. To date thousands of circRNAs have been revealed in organisms ranging from Drosophila melanogaster to Homo sapiens. Functional studies specify that these transcripts control expression of protein-coding linear transcripts and thus encompass a key component of gene expression regulation. This chapter provide a comprehensive overview on functional validation of circRNAs. Furthermore, we discuss the recent modern methodologies for the functional validation of circRNAs such as RNA interference (RNAi) gene silencing assay, luciferase reporter assays, circRNA gain-of-function investigation via overexpression of circular transcript assay, RT-q-PCR quantification, and other latest applicable assays. The methods described in this chapter are demonstrated on the cellular model.
    Matched MeSH terms: Software
  15. Goh HH, Ng CL, Loke KK
    Adv Exp Med Biol, 2018 11 2;1102:11-30.
    PMID: 30382566 DOI: 10.1007/978-3-319-98758-3_2
    Functional genomics encompasses diverse disciplines in molecular biology and bioinformatics to comprehend the blueprint, regulation, and expression of genetic elements that define the physiology of an organism. The deluge of sequencing data in the postgenomics era has demanded the involvement of computer scientists and mathematicians to create algorithms, analytical software, and databases for the storage, curation, and analysis of biological big data. In this chapter, we discuss on the concept of functional genomics in the context of systems biology and provide examples of its application in human genetic disease studies, molecular crop improvement, and metagenomics for antibiotic discovery. An overview of transcriptomics workflow and experimental considerations is also introduced. Lastly, we present an in-house case study of transcriptomics analysis of an aromatic herbal plant to understand the effect of elicitation on the biosynthesis of volatile organic compounds.
    Matched MeSH terms: Software
  16. Wan Hassan WN, Othman SA, Chan CS, Ahmad R, Ali SN, Abd Rohim A
    Am J Orthod Dentofacial Orthop, 2016 Nov;150(5):886-895.
    PMID: 27871715 DOI: 10.1016/j.ajodo.2016.04.021
    INTRODUCTION: In this study we aimed to compare measurements on plaster models using a digital caliper, and on 3-dimensional (3D) digital models, produced using a structured-light scanner, using 3D software.

    METHODS: Fifty digital models were scanned from the same plaster models. Arch and tooth size measurements were made by 2 operators, twice. Calibration was done on 10 sets of models and checked using the Pearson correlation coefficient. Data were analyzed by error variances, repeatability coefficient, repeated-measures analysis of variance, and Bland-Altman plots.

    RESULTS: Error variances ranged between 0.001 and 0.044 mm for the digital caliper method, and between 0.002 and 0.054 mm for the 3D software method. Repeated-measures analysis of variance showed small but statistically significant differences (P <0.05) between the repeated measurements in the arch and buccolingual planes (0.011 and 0.008 mm, respectively). There were no statistically significant differences between methods and between operators. Bland-Altman plots showed that the mean biases were close to zero, and the 95% limits of agreement were within ±0.50 mm. Repeatability coefficients for all measurements were similar.

    CONCLUSIONS: Measurements made on models scanned by the 3D structured-light scanner were in good agreement with those made on conventional plaster models and were, therefore, clinically acceptable.

    Matched MeSH terms: Software
  17. Ibrahim A, Alias A, Nor FM, Swarhib M, Abu Bakar SN, Das S
    Anat Cell Biol, 2017 Jun;50(2):86-92.
    PMID: 28713610 DOI: 10.5115/acb.2017.50.2.86
    Sex determination is one of the main steps in the identification of human skeletal remains. It constitutes an initial step in personal identification from the skeletal remains. The aim of the present study was to provide the population-specific sex discriminating osteometric standards to aid human identification. The present study was conducted on 87 (174 sides) slices of crania using postmortem computed tomography in 45 males and 42 females, aged between 18 and 75 years. About 22 parameters of crania were measured using Osirix software 3-D Volume Rendering. Results showed that all parameters were significantly higher in males than in females except for orbital height of the left eye by independent t test (P<0.01). By discriminant analysis, the classification accuracy was 85.1%, and by regression, the classification accuracy ranged from 78.2% to 86.2%. In conclusion, cranium can be used to distinguish between males and females in the Malaysian population. The results of the present study can be used as a forensic tool for identification of unknown crania.
    Matched MeSH terms: Software
  18. Osman NA, Abdul-Latiff MAB, Mohd-Ridwan AR, Yaakop S, Nor SM, Md-Zain BM
    Animals (Basel), 2020 Nov 26;10(12).
    PMID: 33255964 DOI: 10.3390/ani10122215
    Understanding dietary diversity is a fundamental task in the study of stump-tailed macaque, Macaca arctoides in its natural habitat. However, direct feeding observation and morphological identification using fecal samples are not effective and nearly impossible to obtain in natural habitats because this species is sensitive to human presence. As ecological methods are challenging and time-consuming, DNA metabarcoding offers a more powerful assessment of the diet. We used a chloroplast tRNL DNA metabarcoding approach to identify the diversity of plants consumed by free-ranging M. arctoides in the Malaysia-Thailand border region located in Perlis State Park, Peninsular Malaysia. DNA was extracted from three fecal samples, and chloroplast tRNL DNA was amplified and sequenced using the Illumina MiniSeq platform. Sequences were analyzed using the CLC Genomic Workbench software. A total of 145 plant species from 46 families were successfully identified as being consumed by M. arctoides. The most abundant species were yellow saraca, Saraca thaipingensis (11.70%), common fig, Ficus carica (9.33%), aramata, Clathrotropis brachypetala (5.90%), sea fig, Ficus superba (5.44%), and envireira, Malmea dielsiana (1.70%). However, Clathrotropis and Malmea are not considered Malaysian trees because of limited data available from Malaysian plant DNA. Our study is the first to identify plant taxa up to the species level consumed by stump-tailed macaques based on a DNA metabarcoding approach. This result provides an important understanding on diet of wild M. arctoides that only reside in Perlis State Park, Malaysia.
    Matched MeSH terms: Software
  19. Nurul Farahah Bahari, Nur Iffah Izzaty Jamal, John, Jacob
    Ann Dent, 2019;26(1):8-14.
    MyJurnal
    This cross sectional study investigated the clinical and radiographic status of crowned teeth with and without root canal treatment. The study used secondary data from records of patients who received crown treatment at the Faculty of Dentistry, University of Malaya before 2015 and walk-in patients attending the primary care clinic between July - December 2016. The inclusion criterion was crown fitted for more than 12 months. Once identified, the patients were assessed for clinical and radiographic status. Data were entered into and analysed using SPSS Version 20 software. A total of 66 crowns [35 root canal treated (RCT) and 31 non-root canal treated (n-RCT)] were identified. Chi-square test was carried out to determine the health of crowned teeth and for its longevity in the oral cavity. There were 43 crowns (46.5% RCT; 53.5% n-RCT) with plaque accumulation, 15 (66.7% RCT; 33.3% n-RCT) with gingival swelling/recession, 17 (46.5% RCT; 53.5% n-RCT) with widening of the periodontal ligament, 13 (53.8% RCT; 46.2% n-RCT) with bone loss and 5 (60% RCT; 40% n-RCT) crowns with periapical lesion. There was no statistically significant difference except for poorer alveolar bone condition for crowns that have been in the mouth for >10 years. Based on the study, no significant adverse pulpal involvement between crown with RCT and crown without RCT was observed.
    Matched MeSH terms: Software
  20. Yahya, N.A., Youngson, C.C.
    Ann Dent, 2007;14(1):7-13.
    MyJurnal
    The purpose of this study were to compare the emergence profiles of crowns with their contralateral tooth, in vitro, and to determine if there is any association between the design of tooth preparations and the resultant emergence profile. 50 working models used for single crown construction were examined. Measurements of the faciolingual width of the crowns and contralateral teeth were taken using digital calipers. Internal line angles and the margin width of dies and the emergence profile of the corresponding crowns were measured from longitudinally sectioned polyvinylsiloxane indices mounted on a flat-bed scanner using image analysis software. Using Students t tests, no statistically significant differences (p>0.05) were found for shoulder width (mean 0.94 ± 0.23mm), internal line angle (mean 105.83 ± 13.57°) or emergence profiles (28.56 ± 12.95°) in the different (anterior, premolar or molar) preparations or crowns. The mean emergence profiles for all crowns was statistically significantly greater (p
    Matched MeSH terms: Software
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