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Complete mitochondrial genome of Malaysian Mahseer (Tor tambroides)

Norfatimah MY, Teh LK, Salleh MZ, Mat Isa MN, SitiAzizah MN

Gene, 2014 Sep 15;548(2):263-9.
PMID: 25042454 DOI: 10.1016/j.gene.2014.07.044

This is the first documentation of the complete mitochondrial genome sequence of the Malaysian Mahseer, Tor tambroides. The 16,690 bp mitogenome with GenBank accession number JX444718 contains 13 protein genes, 22 tRNAs, two rRNAs, and a noncoding control region (D-loop) as is typical of most vertebrates. The phylogenomic reconstruction of this newly generated data with 21 Cypriniformes GenBank accession ID concurs with the recognized status of T. tambroides within the subfamily Cyprininae. This is in agreement with previous hypotheses based on morphological and partial mitochondrial analyses.
Fulltext The Relationship between the Neighborhood Safety and Nutritional Status of Children in Baghdad City, Iraq

Ghazi HF, Isa ZM, Shah SA, Abdal Qader MA, Hasan TN, Al-Abed AA

J Nutr Metab, 2014;2014:686934.
PMID: 25243083 DOI: 10.1155/2014/686934

Introduction. The neighborhoods where the children live play an important role in their development physically and mentally. The objective of this study was to assess the relationship between neighborhood safety and child nutritional status in Baghdad city, Iraq. Methods. A cross-sectional study was carried out in Baghdad city, Iraq, among 400 primary school children from 4 schools. BMI-for-age Z score was used to assess the nutritional status of the children. Newly developed questionnaires on neighborhood safety were distributed to the parents to answer them. Results. In this study, males were more predominant than females with 215 participants compared to 185 females. A total of 49% were normal weight, 38.8% either overweight or obese, and only 12.2% underweight. There was a significant relationship between father education, father and mother working status, family income, and children nutritional status (P = 0.10, 0.009, <0.001, 0.37), respectively. The association between neighborhood safety variables and child nutritional status was significant except for worrying about child safety and thinking of leaving the neighborhood (P = 0.082, 0.084), respectively. Conclusion. Nutritional status of school children continues to be a public health issue in Iraq especially Baghdad city. There was a significant association between neighborhood safety and children nutritional status.
Comparative analysis between multilevel sectioning with conventional haematoxylin and eosin staining and immunohistochemistry for detecting nodal micrometastases with stage I and II colorectal cancers

Wong YP, Shah SA, Shaari N, Mohamad Esa MS, Sagap I, Isa NM

Asian Pac J Cancer Prev, 2014;15(4):1725-30.
PMID: 24641399

Management of patients with stage II colorectal carcinomas remains challenging as 20 - 30% of them will develop recurrence. It is postulated that these patients may harbour nodal micrometastases which are imperceptible by routine histopathological evaluation. The aims of our study were to evaluate (1) the feasibility of multilevel sectioning method utilizing haematoxylin and eosin stain and immunohistochemistry technique with cytokeratin AE1/AE3, in detecting micrometastases in histologically-negative lymph nodes, and (2) correlation between nodal micrometastases with clinicopathological parameters. Sixty two stage I and II cases with a total of 635 lymph nodes were reviewed. Five-level haematoxylin and eosin staining and one-level cytokeratin AE1/AE3 immunostaining were performed on all lymph nodes retrieved. The findings were correlated with clinicopathological parameters. Two (3.2%) lymph nodes in two patients (one in each) were found to harbour micrometastases detected by both methods. With cytokeratin AE1/AE3, we successfully identified four (6.5%) patients with isolated tumour cells, but none through the multilevel sectioning method. Nodal micrometastases detected by both multilevel sectioning and immunohistochemistry methods were not associated with larger tumour size, higher depth of invasion, poorer tumour grade, disease recurrence or distant metastasis. We conclude that there is no difference between the two methods in detecting nodal micrometastases. Therefore it is opined that multilevel sectioning is a feasible and yet inexpensive method that may be incorporated into routine practice to detect nodal micrometastases in centres with limited resources.
Fulltext Multiple adaptive neuro-fuzzy inference system with automatic features extraction algorithm for cervical cancer recognition

Al-batah MS, Isa NA, Klaib MF, Al-Betar MA

Comput Math Methods Med, 2014;2014:181245.
PMID: 24707316 DOI: 10.1155/2014/181245

To date, cancer of uterine cervix is still a leading cause of cancer-related deaths in women worldwide. The current methods (i.e., Pap smear and liquid-based cytology (LBC)) to screen for cervical cancer are time-consuming and dependent on the skill of the cytopathologist and thus are rather subjective. Therefore, this paper presents an intelligent computer vision system to assist pathologists in overcoming these problems and, consequently, produce more accurate results. The developed system consists of two stages. In the first stage, the automatic features extraction (AFE) algorithm is performed. In the second stage, a neuro-fuzzy model called multiple adaptive neuro-fuzzy inference system (MANFIS) is proposed for recognition process. The MANFIS contains a set of ANFIS models which are arranged in parallel combination to produce a model with multi-input-multioutput structure. The system is capable of classifying cervical cell image into three groups, namely, normal, low-grade squamous intraepithelial lesion (LSIL) and high-grade squamous intraepithelial lesion (HSIL). The experimental results prove the capability of the AFE algorithm to be as effective as the manual extraction by human experts, while the proposed MANFIS produces a good classification performance with 94.2% accuracy.
Evaluation of retinal nerve fiber layer thickness in eyes with hypertensive uveitis

Din NM, Taylor SR, Isa H, Tomkins-Netzer O, Bar A, Talat L, et al.

JAMA Ophthalmol, 2014 Jul;132(7):859-65.
PMID: 24789528 DOI: 10.1001/jamaophthalmol.2014.404

IMPORTANCE: Uveitic glaucoma is among the most common causes of irreversible visual loss in uveitis. However, glaucoma detection can be obscured by inflammatory changes.
OBJECTIVE: To determine whether retinal nerve fiber layer (RNFL) measurement can be used to detect glaucoma in uveitic eyes with elevated intraocular pressure (IOP).
DESIGN, SETTING, AND PARTICIPANTS: Comparative case series of RNFL measurement using optical coherence tomography performed from May 1, 2010, through October 31, 2012, at a tertiary referral center. We assigned 536 eyes with uveitis (309 patients) in the following groups: normal contralateral eyes with unilateral uveitis (n = 72), normotensive uveitis (Uv-N) (n = 143), raised IOP and normal optic disc and/or visual field (Uv-H) (n = 233), and raised IOP and glaucomatous disc and/or visual field (Uv-G) (n = 88).
EXPOSURES: Eyes with uveitis and elevated IOP (>21 mm Hg) on at least 2 occasions.
MAIN OUTCOMES AND MEASURES: Comparison of RNFL values between groups of eyes and correlation with clinical data; risk factors for raised IOP, glaucoma, and RNFL thinning.
RESULTS: Mean (SD) global RNFL was thicker in Uv-N (106.4 [21.4] µm) compared with control (96.0 [9.0] µm; P
Fulltext Psychometric properties of the 'Skala Kepuasan Interaksi Perubatan-11' to measure patient satisfaction with physician-patient interaction in Malaysia

Abd Aziz A, Izyan Farhana Nordin N, Mohd Noor N, Bachok N, Nor Ismalina Isa S

Fam Pract, 2014 Apr;31(2):236-44.
PMID: 24317538 DOI: 10.1093/fampra/cmt062

Background. Patient satisfaction influences the outcomes of the patient-physician encounter.
Objective. The objective of this study was to validate the Malay version patient satisfaction
(MISS-21) questionnaire using a confirmatory validity approach.
Methods. A cross-sectional study was conducted involving 252 patients attending primary health
clinic, Hospital Universiti Sains Malaysia. Construct validity (convergent and discriminant) using
confirmatory factor analysis and internal consistency were performed after the translation, content
validity and face validity processes. Criterion validity was assessed using Pearson correlations
with the scale of shared decision making 9-item questionnaire (SDMQ-9). The data was
analysed using Analysis of Moment Structure version 19.
Results. A total of 252 (100%) outpatients responded to this study. The final model that consists
of three domains with 11 items had a good fit; (χ2
(df) = 65.805 (32), P
Fulltext Determination of important topographic factors for landslide mapping analysis using MLP network

Alkhasawneh MSh, Ngah UK, Tay LT, Mat Isa NA, Al-batah MS

ScientificWorldJournal, 2013;2013:415023.
PMID: 24453846 DOI: 10.1155/2013/415023

Landslide is one of the natural disasters that occur in Malaysia. Topographic factors such as elevation, slope angle, slope aspect, general curvature, plan curvature, and profile curvature are considered as the main causes of landslides. In order to determine the dominant topographic factors in landslide mapping analysis, a study was conducted and presented in this paper. There are three main stages involved in this study. The first stage is the extraction of extra topographic factors. Previous landslide studies had identified mainly six topographic factors. Seven new additional factors have been proposed in this study. They are longitude curvature, tangential curvature, cross section curvature, surface area, diagonal line length, surface roughness, and rugosity. The second stage is the specification of the weight of each factor using two methods. The methods are multilayer perceptron (MLP) network classification accuracy and Zhou's algorithm. At the third stage, the factors with higher weights were used to improve the MLP performance. Out of the thirteen factors, eight factors were considered as important factors, which are surface area, longitude curvature, diagonal length, slope angle, elevation, slope aspect, rugosity, and profile curvature. The classification accuracy of multilayer perceptron neural network has increased by 3% after the elimination of five less important factors.
Antenatal calcium intake in Malaysia

Mahdy ZA, Basri H, Md Isa Z, Ahmad S, Shamsuddin K, Mohd Amin R

J Obstet Gynaecol Res, 2014 Apr;40(4):983-7.
PMID: 24320794 DOI: 10.1111/jog.12277

To determine the adequacy of antenatal calcium intake in Malaysia, and the influencing factors.
Fulltext Draft Genome Sequence of Pasteurella multocida subsp. multocida Strain PMTB, Isolated from a Buffalo

Yap HY, Ghazali K, Wan Mohamad Nazarie WF, Mat Isa MN, Zakaria Z, Omar AR

Genome Announc, 2013;1(5).
PMID: 24136854 DOI: 10.1128/genomeA.00872-13

Pasteurella multocida serotypes B:2 and E:2 are the main causative agents of ruminant hemorrhagic septicemia in Asia and Africa, respectively. Pasteurella multocida strain PMTB was isolated from a buffalo with hemorrhagic septicemia and has been determined to be serotype B:2. Here we report the draft genome sequence of strain PMTB.
Investigating metal removal potential by Effective Microorganisms (EM) in alginate-immobilized and free-cell forms

Ting ASY, Rahman NHA, Isa MIHM, Tan WS

Bioresour Technol, 2013 Nov;147:636-639.
PMID: 24001691 DOI: 10.1016/j.biortech.2013.08.064

Metal removal potential of both alginate-immobilized and free-cells of Effective Microorganisms (EM-1™ Inoculant) was investigated in this study. Results revealed that removal of Cr(III), Cu(II) and Pb(II) followed a similar trend where alginate-immobilized EM were more efficient compared to free-cells of EM. For these metals, 0.940, 2.695 and 4.011 mg g(-1) of Cr(III), Cu(II) and Pb(II) were removed compared to only 0.160, 0.859 and 0.755 mg ml(-1) removed by free-cells, respectively. The higher efficiency of alginate-immobilized EM was primarily attributed to the alginate matrix. This was evident when both alginate-immobilized EM and plain alginate beads (without EM), were not significantly different in their removal efficacies. Presence of alginate also enhanced the use of the biosorbents as maximum metal sorption was achieved after 120 min as opposed to only 60 min for free-cells. EM per se in immobilized or free-cell forms did not enhance metal removal efficacy.
Polycyclic aromatic hydrocarbon removal from petroleum sludge cake using thermal treatment with additives

Pakpahan EN, Isa MH, Kutty SR, Chantara S, Wiriya W

Environ Technol, 2013 Jan-Feb;34(1-4):407-16.
PMID: 23530354

Petroleum sludge is a hazardous waste that contains various organic compounds including polycyclic aromatic hydrocarbons (PAHs) which have carcinogenic-mutagenic and toxic characteristics. This study focuses on the thermal treatment (indirect heating) of petroleum sludge cake for PAH degradation at 250, 450, and 650 degrees C using Ca(OH)2 + NaHCO3 as an additive. The treatment was conducted in a rotary drum electric heater. All experiments were carried out in triplicate. Concentrations of the 16 priority PAHs in gas (absorbed on Amberlite XAD-4 adsorbent), particulate (on quartz filter) and residue phases were determined using gas chromatography-mass spectrometry (GC-MS). The samples were extracted with acetonitrile by ultra-sonication prior to GC-MS analysis. The use of additive was beneficial and a temperature of 450 degrees C was suitable for PAH degradation. Low levels of PAH emissions, particularly carcinogenic PAH and toxic equivalent concentration (sigma TEC), were observed in gas, particulate and residue phases after treatment.
Impact of applied progressive deep muscle relaxation training on the level of depression, anxiety and stress among prostate cancer patients: a quasi-experimental study

Isa MR, Moy FM, Abdul Razack AH, Zainuddin ZM, Zainal NZ

Asian Pac J Cancer Prev, 2013;14(4):2237-42.
PMID: 23725119

BACKGROUND: The aim of this study was to determine the impact of applied progressive muscle relaxation training on the levels of depression, anxiety and stress among prostate cancer patients.
MATERIALS AND METHODS: A quasi-experimental study was conducted at the University Malaya Medical Centre (UMMC) and Universiti Kebangsaan Malaysia Medical Centre (UKMMC) over six months. Prostate cancer patients from UMMC received the intervention and patients from UKMMC were taken as controls. The level of depression, anxiety and stress were measured using Depression, Anxiety Stress Scales - 21 (DASS-21).
RESULTS: A total of 77 patients from the UMMC and 78 patients from the UKMMC participated. At the end of the study, 90.9% and 87.2% of patients from the UMMC and UKMMC groups completed the study respectively. There were significant improvements in anxiety (p<0.001, partial ?2=0.198) and stress (p<0.001, partial ?2=0.103) at the end of the study in those receiving muscle training. However, there was no improvement in depression (p=0.956).
CONCLUSIONS: The improvement in anxiety and stress showed the potential of APMRT in the management of prostate cancer patients. Future studies should be carried out over a longer duration to provide stronger evidence for the introduction of relaxation therapy among prostate cancer patients as a coping strategy to improve their anxiety and stress.
Application of geoaccumulation index and enrichment factors on the assessment of heavy metal pollution in the sediments

Shafie NA, Aris AZ, Zakaria MP, Haris H, Lim WY, Isa NM

J Environ Sci Health A Tox Hazard Subst Environ Eng, 2013;48(2):182-90.
PMID: 23043340 DOI: 10.1080/10934529.2012.717810

An investigative study was carried out in Langat River to determine the heavy metal pollution in the sediment with 22 sampling stations selected for the collection of sediment samples. The sediment samples were digested and analyzed for extractable metal ((48)Cd, (29)Cu, (30)Zn, (33)As, (82)Pb) using the Inductively Coupled Plasma-Mass Spectrometry (ICP-MS). Parameters, such as pH, Eh, electrical conductivity (EC), salinity, cation exchange capacity (CEC) and loss on ignition (LOI) were also determined. The assessment of heavy metal pollution was derived using the enrichment factors (EF) and geoaccumulation index (I(geo)). This study revealed that the sediment is predominantly by As > Cd > Pb > Zn > Cu. As recorded the highest EF value at 187.45 followed by Cd (100.59), Pb (20.32), Zn (12.42) and Cu (3.46). This is similar to the I(geo), which indicates that the highest level goes to As (2.2), exhibits moderately polluted. Meanwhile, Cd recorded 1.8 and Pb (0.23), which illustrates that both of these elements vary from unpolluted to moderately polluted. The Cu and Zn levels are below 0, which demonstrates background concentrations. The findings are expected to update the current status of the heavy metal pollution as well as creating awareness concerning the security of the river water as a drinking water source.
Outbreaks of foot-and-mouth disease in Peninsular Malaysia from 2001 to 2007

Ramanoon SZ, Robertson ID, Edwards J, Hassan L, Isa KM

Trop Anim Health Prod, 2013 Feb;45(2):373-7.
PMID: 22826115 DOI: 10.1007/s11250-012-0226-x

This is a retrospective study of the outbreaks of foot-and-mouth disease (FMD) in Peninsular Malaysia between 2001 and May 2007. In total, 270 outbreaks of FMD were recorded. Serotype O virus (89.95 %) and serotype A (7.7 %) had caused the outbreaks. Significant differences on the occurrence of FMD were found between the years (t = 5.73, P = 0.000, df = 11), months (t = 4.7, P = 0.000, df = 11), monsoon season (t = 2.63, P = 0.025, df = 10) and states (t = 4.84, P = 0.001, df = 10). A peak of outbreaks observed in 2003 could be due to increased animal movement and the other peak in 2006 could be due to a compromised FMD control activities due to activities on the eradication of highly pathogenic avian influenza. Cattle (86 % of outbreaks) suffered the most. However, no difference in disease occurrence between species was observed. The populations of cattle (r = 0.672, P = 0.023) and sheep (r = 0.678, P = 0.022) were significantly correlated with occurrence of FMD. Movement of animals (66 % of outbreaks) was the main source for outbreaks. A combination of control measures were implemented during outbreaks. In conclusion, the findings of this study show that FMD is endemic in Peninsular Malaysia, and information gained could be used to improve the existing control strategy.
Association of Malaysian Helicobacter pylori virulence polymorphisms with severity of gastritis and patients' ethnicity

Alfizah H, Ramelah M, Rizal AM, Anwar AS, Isa MR

Helicobacter, 2012 Oct;17(5):340-9.
PMID: 22967117 DOI: 10.1111/j.1523-5378.2012.00956.x

Polymorphisms of Helicobacter pylori cagA and vacA genes do exist and may contribute to differences in H. pylori infection and gastroduodenal diseases among races in the Malaysian population. This study was conducted to characterize the polymorphisms in H. pylori cagA and vacA in Malaysian population.
Fulltext The negative impact of living environment on intelligence quotient of primary school children in Baghdad City, Iraq: a cross-sectional study

Ghazi HF, Isa ZM, Aljunid S, Shah SA, Tamil AM, Abdalqader MA

BMC Public Health, 2012;12:562.
PMID: 22839101 DOI: 10.1186/1471-2458-12-562

Environmental factors play a very important role in the child development process, especially in a situation like that of Iraq. Thirteen years of economic sanctions followed by the 2003 war and 8 years of unstable security have affected the daily life of Iraqi families and children. The objective of this study was to assess the associations between living environment domains and child intelligence quotient (IQ) score.
General health related quality of life and associated factors among prostate cancer patients in two tertiary medical centers in Kuala Lumpur, Malaysia: a cross-sectional study

Isa MR, Ming MF, Abdul Razack AH, Zainuddin ZM, Zainal NZ

Asian Pac J Cancer Prev, 2012;13(12):5999-6004.
PMID: 23464393

Measurement of quality of life among prostate cancer patients helps the health care providers to understand the impact of the disease in the patients' own perspective. The main aim of this study is to measure the quality of life among prostate cancer patients at University Malaya Medical Center (UMMC) and Universiti Kebangsaan Malaysia Medical Centre (UKMMC) and to ascertain the association factors for physical coefficient summary (PCS) and mental coefficient summary (MCS). A hospital based, cross sectional study using the Short Form-36 (SF-36) questionnaire was conducted over a period of 6 months. A total of 193 respondents were recruited. Their total quality of life score was 70.1± 14.7 and the PCS score was lower compared to MCS. The factors associated for PCS were: age, living partner, renal problem, urinary problem of intermittency, dysuria and hematuria. Factors associated for MCS were: age, living partner, renal problem, presenting prostatic specific antigen and urinary problem of intermittency and dysuria. Our prostate cancer patients had moderate quality of life in the physical health components but their mental health was less affected.
A novel shape representation of the dental arch and its applications in some dentistry problems

Rijal OM, Abdullah NA, Isa ZM, Davaei FA, Noor NM, Tawfiq OF

Annu Int Conf IEEE Eng Med Biol Soc, 2011;2011:5092-5.
PMID: 22255484 DOI: 10.1109/IEMBS.2011.6091261

Standardized digital images of maxillary dental casts of 47 subjects were analyzed using MATLAB software whereby the two hamular notches and the incisive papilla defines the Cartesian vertical and horizontal axes, as well as the origin. The angle and length of the midpoints of the anterior teeth, mesiobuccal and distobuccal cusp of the posterior teeth were measured from the origin and denoted as θ(1), …, θ(18) and l(1), …, l(18) respectively. These values were collectively used to represent the shape of each dental cast. Clustering and principal component analyses were employed to find possible groups of dental arches using the above measure of shape. The main result of this study is that the 3 groups of dental arch shape may be represented by the novel feature vector v(k) = (θ(k)(1), l(k)(1), θ(k)(3), l(k)(3), θ(k)(5), l(k)(5), θ(k)(13), l(k)(13)), k = 1, 2, 3. Knowledge of v(k) implies three impression trays should be sufficient in a particular prosthetic dentistry application for Malaysian patients. Further, given that v(k) are accurately measured they may be potential candidates as evidence in specific application of forensic dentistry.
Synovial sarcoma: a rare presentation of parapharyngeal mass

Shaariyah MM, Mazita A, Masaany M, Razif MY, Isa MR, Asma A

Chin J Cancer, 2010 Jun;29(6):631-3.
PMID: 20507738

Synovial sarcoma is a rare soft tissue sarcoma of the head and neck region involving the parapharyngeal space. The diagnosis of synovial sarcoma can be very challenging to the pathologists. We present a rare case of parapharyngeal synovial sarcoma in a young female patient who had a two-month history of left cervical intumescent mass at level II. The fine needle aspiration cytology of the mass was proved inconclusive. Transcervical excision of the mass was performed and the first case of parapharyngeal sarcoma was identified in our center by fluorescence in situ hybridization (FISH) technique. Repeat imaging revealed residual tumor. The patient successfully underwent a second excision of the residual tumor and received adjuvant radiotherapy.
Response surface analysis and modeling of n-alkanes removal through bioremediation of weathered crude oil

Mohajeri L, Abdul Aziz H, Ali Zahed M, Mohajeri S, Mohamed Kutty SR, Hasnain Isa M

Water Sci Technol, 2011;63(4):618-26.
PMID: 21330705 DOI: 10.2166/wst.2011.211

Central composite design (CCD) and response surface methodology (RSM) were employed to optimize four important variables, i.e. amounts of oil, bacterial inoculum, nitrogen and phosphorus, for the removal of selected n-alkanes during bioremediation of weathered crude oil in coastal sediments using laboratory bioreactors over a 60 day experimentation period. The reactors contained 1 kg soil with different oil, microorganisms and nutrients concentrations. The F Value of 26.89 and the probability value (P < 0.0001) demonstrated significance of the regression model. For crude oil concentration of 2, 16 and 30 g per kg sediments and under optimized conditions, n-alkanes removal was 97.38, 93.14 and 90.21% respectively. Natural attenuation removed 30.07, 25.92 and 23.09% n-alkanes from 2, 16 and 30 g oil/kg sediments respectively. Excessive nutrients addition was found to inhibit bioremediation.

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