25 results on '"Shuib, S."'
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2. Evolution of the leading-edge vortex over a flapping wing mechanism
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Arifin, Muhamad Ridzuan, primary, Yusoff, H., additional, Yamin, A.F.M., additional, Abdullah, A.S., additional, Zakaryia, M.F., additional, Shuib, S., additional, and Suhaimi, S., additional
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- 2020
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3. Anatomical modelling and simplified modelling in total hip replacement: difference in contact mechanics perspective
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Manap, M F A, primary, Shuib, S, additional, Yamin, A F M, additional, and Shokri, A A, additional
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- 2020
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4. The Effect of Magnetic Field on the Correlation Between Current Gain and on -to-off Current Ratio in a Nonmagnetic Organic Transistor With P36HCTPSi:FIrpic as Double Emitter
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Schulz, D., primary, Holz, E., additional, Yusoff, Abd R. B. M., additional, Song, Y., additional, and Shuib, S. A., additional
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- 2012
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5. Multilayer n-Type Organic Metal-Base Transistor
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Yusoff, Abd R. B. M., primary, Song, Y., additional, Schulz, D., additional, Holz, E., additional, and Shuib, S. A., additional
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- 2011
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6. Mutation analysis of hypoxia-inducible factors HIF1A and HIF2A in renal cell carcinoma
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Morris, M. R., Hughes, D. J., Tian, Y. -M, Ricketts, C. J., Lau, K. W., Gentle, D., Shuib, S., Serrano-Fernandez, P., Jan Lubinski, Wiesener, M. S., Pugh, C. W., Latif, F., Ratcliffe, P. J., and Maher, E. R.
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urologic and male genital diseases ,neoplasms ,female genital diseases and pregnancy complications - Abstract
BACKGROUND: Inactivation of the Von Hippel-Lindau (VHL) tumour suppressor gene leading to overexpression of hypoxia-inducible transcription factors (HIF)-1alpha and -2alpha is a critical event in the pathogenesis of most clear cell renal cell carcinomas (RCC). HIF-1alpha and HIF-2alpha share significant homology and regulate overlapping repertoires of hypoxia-inducible target genes but may have differing effects on RCC cell growth. Loss of HIF-1alpha expression has been described in RCC cell lines and primary tumours. Whether mutations in the alpha-subunits of HIF-1alpha and HIF-2alpha contribute to renal tumourigenesis was investigated here. MATERIALS AND METHODS: Mutation analysis of the complete coding sequence of HIF-1alpha and HIF-2alpha was carried out in primary RCC (n=40). RESULTS: The analysis revealed a somatic HIF1A missense substitution, p.Val116Glu, in a single RCC. Functional studies demonstrated that p.Val116Glu impaired HIF-1alpha transcriptional activity. Genotyping of HIF1A variants p.Pro582Ser and p.Ala588Thr demonstrated no significant differences between RCC patients and controls. CONCLUSION: The detection of a loss-of-function HIF1A mutation in a primary RCC is consistent with HIF-1 and HIF-2 having different roles in renal tumourigenesis, However, somatic mutations of HIF1A are not frequently implicated in the pathogenesis of RCC.
7. Diagnostic Utility of TSSC3 and RB1 Immunohistochemistry in Hydatidiform Mole.
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Chia WK, Chia PY, Abdul Aziz NH, Shuib S, Mustangin M, Cheah YK, Khong TY, Wong YP, and Tan GC
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- Animals, Female, Humans, Pregnancy, Antibodies metabolism, Cyclin-Dependent Kinase Inhibitor p57 genetics, Cyclin-Dependent Kinase Inhibitor p57 metabolism, Immunohistochemistry, Placenta metabolism, Retinoblastoma Binding Proteins metabolism, Ubiquitin-Protein Ligases metabolism, Hydatidiform Mole diagnosis, Hydatidiform Mole genetics, Moles metabolism
- Abstract
The general notion of complete hydatidiform moles is that most of them consist entirely of paternal DNA; hence, they do not express p57, a paternally imprinted gene. This forms the basis for the diagnosis of hydatidiform moles. There are about 38 paternally imprinted genes. The aim of this study is to determine whether other paternally imprinted genes could also assist in the diagnostic approach of hydatidiform moles. This study comprised of 29 complete moles, 15 partial moles and 17 non-molar abortuses. Immunohistochemical study using the antibodies of paternal-imprinted (RB1, TSSC3 and DOG1) and maternal-imprinted (DNMT1 and GATA3) genes were performed. The antibodies' immunoreactivity was evaluated on various placental cell types, namely cytotrophoblasts, syncytiotrophoblasts, villous stromal cells, extravillous intermediate trophoblasts and decidual cells. TSSC3 and RB1 expression were observed in all cases of partial moles and non-molar abortuses. In contrast, their expression in complete moles was identified in 31% (TSSC3) and 10.3% (RB1), respectively ( p < 0.0001). DOG1 was consistently negative in all cell types in all cases. The expressions of maternally imprinted genes were seen in all cases, except for one case of complete mole where GATA3 was negative. Both TSSC3 and RB1 could serve as a useful adjunct to p57 for the discrimination of complete moles from partial moles and non-molar abortuses, especially in laboratories that lack comprehensive molecular service and in cases where p57 staining is equivocal.
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- 2023
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8. Systematic Review on Multilevel Analysis of Radiation Effects on Bone Microarchitecture.
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Bakar AAA, Mohamad NS, Mahmud MH, Razak HRA, Sudin AELT, and Shuib S
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- Animals, Cortical Bone, Humans, Mice, Multilevel Analysis, Osteoblasts radiation effects, Bone and Bones, Radiation Injuries
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Introduction: Modern radiation therapy has become an effective method to treat and monitor tumour growth in cancer patients. It has proved to be a successful way to minimise mortality rates. However, the adverse effects of radiation have been historical evidence in the clinical environment involving diminishing the quality and density of bone and causing fragility fracture to the bone in the long run. This systematic review was aimed at identifying and evaluating the effects of irradiation on morphology and mechanical properties of murine model bone in previous publications., Methods: A systematic literature review was undertaken following the Preferred Reporting Items for Systemic Reviews and Meta-analysis (PRISMA) guidelines. A comprehensive literature search was performed using Scopus, Web of Science, and Science Direct databases (English only studies published between 2015 and 2020). The selected studies were evaluated according to three criteria: (1) criteria for study sample selection; (2) criteria for methodological procedures; and (3) criteria for detection and evaluation., Results: The initial search strategy identified 1408 related studies, 8 of were included based on inclusion and exclusion criteria. This review revealed an association between bone destruction and the magnitude of time and dose postirradiation. We agreed that the effect of radiation on bone morphology and strength primarily is a later stage event but noticeable in both low (1 Gy) and high dose (30 Gy) radiation. Trabecular and cortical bone microstructures were significantly altered at irradiation and contralateral sites. Besides, the mechanical strength was significantly impacted in both shorter and longer periods., Conclusion: Overall, the radiotherapy altered bone microstructures and substantially decreases bone mechanical properties. The alteration was related to quantity and the activity of the osteoblast and osteoclast. Early detection of those most at risk for radiation-induced bone alterations could lead to better prophylactic intervention decisions., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2022 Ayuni Amalina Abu Bakar et al.)
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- 2022
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9. Rare but Potentially Fatal Presentations of Diffuse Large B-cell Lymphoma: Leukemic Phase or Hemophagocytic Syndrome in Bone Marrow.
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Wan Mohd Zohdi WA, Ismail AZ, Yusof N, Ithnin A, Shuib S, Masir N, Palaniappan S, and Tumian NR
- Abstract
Diffuse large B-cell lymphoma (DLBCL) is a type of non-Hodgkin Lymphoma commonly presenting as a solid tumor either by nodal or extra-nodal manifestations. Here we describe two atypical presentations of lymphoma, finally resulting in the diagnosis of DLBCL. Case 1: A 53-year-old man with a previous history of nasopharyngeal carcinoma presented with a two-week history of B-symptoms and hyperleukocytosis. Peripheral blood film showed 78% abnormal mononuclear cells. Immunohistochemical stain showing Ki-67 of 90%, negative c-myc, BCL2 and BCL6, and negative c-MYC with fluorescence in-situ hybridization studies on the trephine biopsy, concluded the diagnosis of CD5+ DLBCL of ABC subtype. He received intravenous cyclophosphamide and oral prednisolone for cytoreduction, followed by 6 cycles of chemo-immunotherapy. However, he succumbed due to severe sepsis after the completion of therapy. Case 2: A 56-year-old lady who was initially investigated for pyrexia of unknown origin was noted to have hemophagocytosis upon bone marrow aspirate examination. The bone marrow trephine biopsy revealed some atypical clusters of B-cells positive for CD20 which was inconclusive. PET-CT scan noted an enlarged hypermetabolic spleen without lymphadenopathy. Splenic biopsy with immunohistochemical studies revealed DLBCL of ABC subtype. The diagnosis was consistent with primary splenic DLBCL. She became unwell post splenic biopsy and was admitted to the intensive care unit where she passed away 2 weeks later from Candida and Sternotrophomonas septicemia. These cases highlight the atypical presentations of a common subtype of NHL in our center. Arriving at the definitive diagnosis can be difficult especially when patients are acutely ill, hampering the necessary invasive procedures for diagnosis. The outcomes of both cases are briefly discussed hoping to spread awareness among clinicians on the rare and acutely critical presentations of DLBCL., Competing Interests: Declaration of conflicting interests: The author(s) declared no potential conflicts of interest with respect to the research, authorship, and/or publication of this article., (© The Author(s) 2022.)
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- 2022
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10. A Novel Rank Aggregation-Based Hybrid Multifilter Wrapper Feature Selection Method in Software Defect Prediction.
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Balogun AO, Basri S, Mahamad S, Capretz LF, Imam AA, Almomani MA, Adeyemo VE, and Kumar G
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- Area Under Curve, Bayes Theorem, Algorithms, Software
- Abstract
The high dimensionality of software metric features has long been noted as a data quality problem that affects the performance of software defect prediction (SDP) models. This drawback makes it necessary to apply feature selection (FS) algorithm(s) in SDP processes. FS approaches can be categorized into three types, namely, filter FS (FFS), wrapper FS (WFS), and hybrid FS (HFS). HFS has been established as superior because it combines the strength of both FFS and WFS methods. However, selecting the most appropriate FFS (filter rank selection problem) for HFS is a challenge because the performance of FFS methods depends on the choice of datasets and classifiers. In addition, the local optima stagnation and high computational costs of WFS due to large search spaces are inherited by the HFS method. Therefore, as a solution, this study proposes a novel rank aggregation-based hybrid multifilter wrapper feature selection (RAHMFWFS) method for the selection of relevant and irredundant features from software defect datasets. The proposed RAHMFWFS is divided into two stepwise stages. The first stage involves a rank aggregation-based multifilter feature selection (RMFFS) method that addresses the filter rank selection problem by aggregating individual rank lists from multiple filter methods, using a novel rank aggregation method to generate a single, robust, and non-disjoint rank list. In the second stage, the aggregated ranked features are further preprocessed by an enhanced wrapper feature selection (EWFS) method based on a dynamic reranking strategy that is used to guide the feature subset selection process of the HFS method. This, in turn, reduces the number of evaluation cycles while amplifying or maintaining its prediction performance. The feasibility of the proposed RAHMFWFS was demonstrated on benchmarked software defect datasets with Naïve Bayes and Decision Tree classifiers, based on accuracy, the area under the curve (AUC), and F-measure values. The experimental results showed the effectiveness of RAHMFWFS in addressing filter rank selection and local optima stagnation problems in HFS, as well as the ability to select optimal features from SDP datasets while maintaining or enhancing the performance of SDP models. To conclude, the proposed RAHMFWFS achieved good performance by improving the prediction performances of SDP models across the selected datasets, compared to existing state-of-the-arts HFS methods., Competing Interests: The authors declare that they have no conflicts of interest., (Copyright © 2021 Abdullateef O. Balogun et al.)
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- 2021
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11. Outpatient vs inpatient Foley catheter induction of labor in multiparas with unripe cervixes: A randomized trial.
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Hamdan M, Shuhaina S, Hong JGS, Vallikkannu N, Zaidi SN, Tan YP, and Tan PC
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- Adult, Cervical Ripening, Female, Humans, Inpatients, Length of Stay statistics & numerical data, Malaysia, Outpatients, Parity, Patient Satisfaction, Pregnancy, Pregnancy Outcome, Labor, Induced methods, Urinary Catheterization
- Abstract
Introduction: Multiparous labor inductions are typically successful, and the process can be rapid, starting from a ripened cervix with a predictable response to amniotomy and oxytocin infusion. Outpatient Foley catheter labor induction in multiparas with unripe cervixes is a feasible option as the mechanical process of ripening is usually without significant uterine contractions and well tolerated. Labor contractions can be initiated by amniotomy and titrated oxytocin infusion in the hospital for well-timed births during working hours as night birth are associated with adverse events. We sought to evaluate outpatient compared with inpatient Foley catheter induction of labor in multiparas for births during working hours and maternal satisfaction., Material and Methods: A randomized trial was conducted in the University of Malaya Medical Center. A total of 163 term multiparas (no dropouts) with unripe cervixes (Bishop score ≤5) scheduled for labor induction were randomized to outpatient or inpatient Foley catheter. Primary outcomes were delivery during "working hours" 08:00-18:00 h and maternal satisfaction on allocated care (assessed by 11-point visual numerical rating score 0-10, with higher score indicating more satisfied)., Clinical Trial Registration: ISRCTN13534944., Results: Comparing outpatient and inpatient arms, delivery during working hours were 54/82 (65.9%) vs. 48/81 (59.3%) (relative risk 1.1, 95% CI 0.9-1.4, p = 0.421) and median maternal satisfaction visual numerical rating score was 9 (interquartile range 9-9) vs. 9 (interquartile range 8-9, p = 0.134), repectively. Duration of hospital stay and membrane rupture to delivery interval were significantly shorter in the outpatient arm: 35.8 ± 20.2 vs. 45.2 ± 16.2 h (p = 0.001) and 4.1 ± 2.9 vs. 5.3 ± 3.6 h (p = 0.020), respectively. Other maternal and neonatal secondary outcomes were not significantly different., Conclusions: The trial failed to demonstrate the anticipated increase in births during working hours with outpatient compared with inpatient induction of labor with Foley catheter in parous women with an unripe cervix. Hospital stay and membrane rupture to delivery interval were significantly shortened in the outpatient group. The rate of maternal satisfaction was high in both groups and no significant differences were found., (© 2021 The Authors. Acta Obstetricia et Gynecologica Scandinavica published by John Wiley & Sons Ltd on behalf of Nordic Federation of Societies of Obstetrics and Gynecology (NFOG).)
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- 2021
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12. An Adaptive Rank Aggregation-Based Ensemble Multi-Filter Feature Selection Method in Software Defect Prediction.
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Balogun AO, Basri S, Capretz LF, Mahamad S, Imam AA, Almomani MA, Adeyemo VE, and Kumar G
- Abstract
Feature selection is known to be an applicable solution to address the problem of high dimensionality in software defect prediction (SDP). However, choosing an appropriate filter feature selection (FFS) method that will generate and guarantee optimal features in SDP is an open research issue, known as the filter rank selection problem. As a solution, the combination of multiple filter methods can alleviate the filter rank selection problem. In this study, a novel adaptive rank aggregation-based ensemble multi-filter feature selection (AREMFFS) method is proposed to resolve high dimensionality and filter rank selection problems in SDP. Specifically, the proposed AREMFFS method is based on assessing and combining the strengths of individual FFS methods by aggregating multiple rank lists in the generation and subsequent selection of top-ranked features to be used in the SDP process. The efficacy of the proposed AREMFFS method is evaluated with decision tree (DT) and naïve Bayes (NB) models on defect datasets from different repositories with diverse defect granularities. Findings from the experimental results indicated the superiority of AREMFFS over other baseline FFS methods that were evaluated, existing rank aggregation based multi-filter FS methods, and variants of AREMFFS as developed in this study. That is, the proposed AREMFFS method not only had a superior effect on prediction performances of SDP models but also outperformed baseline FS methods and existing rank aggregation based multi-filter FS methods. Therefore, this study recommends the combination of multiple FFS methods to utilize the strength of respective FFS methods and take advantage of filter-filter relationships in selecting optimal features for SDP processes.
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- 2021
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13. Clastogenicity and Aneugenicity of 1,4-Benzoquinone in Different Lineages of Mouse Hematopoietic Stem/Progenitor Cells.
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Chow PW, Abd Hamid Z, Mathialagan RD, Rajab NF, Shuib S, and Sulong S
- Abstract
Previous reports on hematotoxicity and leukemogenicity related to benzene exposure highlighted its adverse effects on hematopoiesis. Despite the reported findings, studies concerning the mechanism of benzene affecting chromosomal integrity in lineage-committed hematopoietic stem/progenitor cells (HSPCs) remain unclear. Here, we studied the clastogenicity and aneugenicity of benzene in lineage-committed HSPCs via karyotyping. Isolated mouse bone marrow cells (MBMCs) were exposed to the benzene metabolite 1,4-benzoquinone (1,4-BQ) at 1.25, 2.5, 5, 7, and 12 μM for 24 h, followed by karyotyping. Then, the chromosomal aberration (CA) in 1,4-BQ-exposed hematopoietic progenitor cells (HPCs) comprising myeloid, Pre-B lymphoid, and erythroid lineages were evaluated following colony-forming cell (CFC) assay. Percentage of CA, predominantly via Robertsonian translocation (Rb), was increased significantly ( p < 0.05) in MBMCs and all progenitors at all concentrations. As a comparison, Pre-B lymphoid progenitor demonstrated a significantly higher percentage of CA ( p < 0.05) than erythroid progenitor at 1.25, 2.5, and 7 μM as well as a significantly higher percentage ( p < 0.05) than myeloid progenitor at 7 μM of 1,4-BQ. In conclusion, 1,4-BQ induced CA, particularly via Rb in both MBMCs and HPCs, notably via a lineage-dependent response. The role of lineage specificity in governing the clastogenicity and aneugenicity of 1,4-BQ deserves further investigation.
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- 2021
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14. A Review of Placenta and Umbilical Cord-Derived Stem Cells and the Immunomodulatory Basis of Their Therapeutic Potential in Bronchopulmonary Dysplasia.
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Chia WK, Cheah FC, Abdul Aziz NH, Kampan NC, Shuib S, Khong TY, Tan GC, and Wong YP
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Bronchopulmonary dysplasia (BPD) is a devastating lung disorder of preterm infants as a result of an aberrant reparative response following exposures to various antenatal and postnatal insults. Despite sophisticated medical treatment in this modern era, the incidence of BPD remains unabated. The current strategies to prevent and treat BPD have met with limited success. The emergence of stem cell therapy may be a potential breakthrough in mitigating this complex chronic lung disorder. Over the last two decades, the human placenta and umbilical cord have gained increasing attention as a highly potential source of stem cells. Placenta-derived stem cells (PDSCs) and umbilical cord-derived stem cells (UCDSCs) display several advantages such as immune tolerance and are generally devoid of ethical constraints, in addition to their stemness qualities. They possess the characteristics of both embryonic and mesenchymal stromal/stem cells. Recently, there are many preclinical studies investigating the use of these cells as therapeutic agents in neonatal disease models for clinical applications. In this review, we describe the preclinical and clinical studies using PDSCs and UCDSCs as treatment in animal models of BPD. The source of these stem cells, routes of administration, and effects on immunomodulation, inflammation and regeneration in the injured lung are also discussed. Lastly, a brief description summarized the completed and ongoing clinical trials using PDSCs and UCDSCs as therapeutic agents in preventing or treating BPD. Due to the complexity of BPD, the development of a safe and efficient therapeutic agent remains a major challenge to both clinicians and researchers., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Chia, Cheah, Abdul Aziz, Kampan, Shuib, Khong, Tan and Wong.)
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- 2021
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15. Sensitivities of Rheological Properties of Magnetoactive Foam for Soft Sensor Technology.
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Norhaniza R, Mazlan SA, Ubaidillah U, Sedlacik M, Aziz SAA, Nazmi N, Homma K, and Rambat S
- Abstract
Magnetoactive (MA) foam, with its tunable mechanical properties and magnetostriction, has the potential to be used for the development of soft sensor technology. However, researchers have found that its mechanical properties and magnetostriction are morphologically dependent, thereby limiting its capabilities for dexterous manipulation. Thus, in this work, MA foam was developed with additional capabilities for controlling its magnetostriction, normal force, storage modulus, shear stress and torque by manipulating the concentration of carbonyl iron particles (CIPs) and the magnetic field with regard to morphological changes. MA foams were prepared with three weight percentages of CIPs, namely, 35 wt.%, 55 wt.% and 75 wt.%, and three different modes, namely, zero shear, constant shear and various shears. The results showed that the MA foam with 75 wt.% of CIPs enhanced the normal force sensitivity and positive magnetostriction sensitivity by up to 97% and 85%, respectively. Moreover, the sensitivities of the storage modulus, torque and shear stress were 8.97 Pa/mT, 0.021 µN/mT, and 0.0096 Pa/mT, respectively. Meanwhile, the magnetic dipolar interaction between the CIPs was capable of changing the property of MA foam from a positive to a negative magnetostriction under various shear strains with a low loss of energy. Therefore, it is believed that this kind of highly sensitive MA foam can potentially be implemented in future soft sensor systems.
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- 2021
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16. Bone Marrow Oxidative Stress and Acquired Lineage-Specific Genotoxicity in Hematopoietic Stem/Progenitor Cells Exposed to 1,4-Benzoquinone.
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Mathialagan RD, Abd Hamid Z, Ng QM, Rajab NF, Shuib S, and Binti Abdul Razak SR
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- Animals, Benzoquinones toxicity, Bone Marrow Cells, Mice, Bone Marrow, DNA Damage drug effects, Hematopoietic Stem Cells drug effects, Oxidative Stress
- Abstract
Hematopoietic stem/progenitor cells (HSPCs) are susceptible to benzene-induced genotoxicity. However, little is known about the mechanism of DNA damage response affecting lineage-committed progenitors for myeloid, erythroid, and lymphoid. Here, we investigated the genotoxicity of a benzene metabolite, 1,4-benzoquinone (1,4-BQ), in HSPCs using oxidative stress and lineage-directed approaches. Mouse bone marrow cells (BMCs) were exposed to 1,4-BQ (1.25-12 μM) for 24 h, followed by oxidative stress and genotoxicity assessments. Then, the genotoxicity of 1,4-BQ in lineage-committed progenitors was evaluated using colony forming cell assay following 7-14 days of culture. 1,4-BQ exposure causes significant decreases ( p < 0.05) in glutathione level and superoxide dismutase activity, along with significant increases ( p < 0.05) in levels of malondialdehyde and protein carbonyls. 1,4-BQ exposure induces DNA damage in BMCs by significantly ( p < 0.05) increased percentages of DNA in tail at 7 and 12 μM and tail moment at 12 μM. We found crucial differences in genotoxic susceptibility based on percentages of DNA in tail between lineage-committed progenitors. Myeloid and pre-B lymphoid progenitors appeared to acquire significant DNA damage as compared with the control starting from a low concentration of 1,4-BQ exposure (2.5 µM). In contrast, the erythroid progenitor showed significant damage as compared with the control starting at 5 µM 1,4-BQ. Meanwhile, a significant ( p < 0.05) increase in tail moment was only notable at 7 µM and 12 µM 1,4-BQ exposure for all progenitors. Benzene could mediate hematological disorders by promoting bone marrow oxidative stress and lineage-specific genotoxicity targeting HSPCs.
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- 2020
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17. Association of CD58 polymorphism and multiple sclerosis in Malaysia: a pilot study.
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Ching YM, Viswanathan S, Mohamed Nor N, Shuib S, Kamarudin B, Mansor S, Yusof AY, and Arip M
- Abstract
Background: Multiple sclerosis is an immune mediated disease targeting the central nervous system. Association of non-human leukocyte antigen gene, CD58 , with multiple sclerosis has been reported in several populations but is unclear among Southeast Asians. This pilot study was conducted to explore the association between CD58 polymorphism and multiple sclerosis among the Malay population in Malaysia., Methods: Blood samples were collected from 27 multiple sclerosis patients, and compared with 58 age- and gender matched healthy individuals. All patients were tested negative for anti-aquaporin 4. DNA was extracted from the blood and genotyped for 3 single nucleotide polymorphisms rs12044852, rs2300747 and rs1335532 of gene CD58 by real-time PCR., Results: The majority of multiple sclerosis patients were female (85.2%). The general mean age of onset was 30.5 years. Genotyping results showed that frequencies of the alleles were between 40 and 50% for MS patients and healthy individuals. Association (allelic model) between multiple sclerosis and CD58 gene polymorphism alleles rs12044852 (p = 0.410), rs2300747 (p = 0.881) and rs1335532 (p = 0.407) were indistinct., Conclusions: The impact of the CD58 gene polymorphism was not prominent in this pilot study, implying that genetic composition contributing to multiple sclerosis may be different between different populations, thus results in a heterogeneity of disease manifestation and distribution., Competing Interests: Competing interestThe authors declare that they have no competing interest., (© The Author(s) 2019.)
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- 2019
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18. Optimization of Culture Conditions for Enhanced Growth, Lipid and Docosahexaenoic Acid (DHA) Production of Aurantiochytrium SW1 by Response Surface Methodology.
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Nazir Y, Shuib S, Kalil MS, Song Y, and Hamid AA
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In this study, optimization of growth, lipid and DHA production of Aurantiochytrium SW1 was carried out using response surface methodology (RSM) in optimizing initial fructose concentration, agitation speed and monosodium glutamate (MSG) concentration. Central composite design was applied as the experimental design and analysis of variance (ANOVA) was used to analyze the data. ANOVA analysis revealed that the process which adequately represented by quadratic model was significant (p < 0.0001) for all the response. All the three factors were significant (p < 0.005) in influencing the biomass and lipid data while only two factors (agitation speed and MSG) gave significant effect on DHA production (p < 0.005). The estimated optimal conditions for enhanced growth, lipid and DHA production were 70 g/L fructose, 250 rpm agitation speed and 10 g/L MSG. Consequently, the quadratic model was validated by applying the estimated optimum conditions, which confirmed the model validity where 19.0 g/L biomass, 9.13 g/L lipid and 4.75 g/L of DHA were produced. The growth, lipid and DHA were 28, 36 and 35% respectively higher than that produced in the original medium prior to optimization.
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- 2018
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19. First evidence for a multienzyme complex of lipid biosynthesis pathway enzymes in Cunninghamella bainieri.
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Shuib S, Ibrahim I, Mackeen MM, Ratledge C, and Hamid AA
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- ATP Citrate (pro-S)-Lyase metabolism, Acetyl-CoA Carboxylase metabolism, Chromatography, Liquid methods, Fatty Acid Synthase, Type II metabolism, Fatty Acid Synthases metabolism, Fatty Acids metabolism, Lipid Metabolism physiology, Lipogenesis physiology, Malate Dehydrogenase metabolism, Malates metabolism, Pyruvate Carboxylase metabolism, Tandem Mass Spectrometry methods, Cunninghamella enzymology, Cunninghamella metabolism, Lipids biosynthesis
- Abstract
Malic enzyme (ME) plays a vital role in determining the extent of lipid accumulation in oleaginous fungi being the major provider of NADPH for the activity of fatty acid synthase (FAS). We report here the first direct evidence of the existence of a lipogenic multienzyme complex (the lipid metabolon) involving ME, FAS, ATP: citrate lyase (ACL), acetyl-CoA carboxylase (ACC), pyruvate carboxylase (PC) and malate dehydrogenase (MDH) in Cunninghamella bainieri 2A1. Cell-free extracts prepared from cells taken in both growth and lipid accumulation phases were prepared by protoplasting and subjected to Blue Native (BN)-PAGE coupled with liquid chromatography-tandem mass spectrometry (LC-MS/MS). A high molecular mass complex (approx. 3.2 MDa) consisting of the above enzymes was detected during lipid accumulation phase indicating positive evidence of multienzyme complex formation. The complex was not detected in cells during the balanced phase of growth or when lipid accumulation ceased, suggesting that it was transiently formed only during lipogenesis.
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- 2018
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20. Multiplexed automated digital quantification of fusion transcripts: comparative study with fluorescent in-situ hybridization (FISH) technique in acute leukemia patients.
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Akhter A, Mughal MK, Elyamany G, Sinclair G, Azma RZ, Masir N, Shuib S, Rashid-Kolvear F, Shabani-Rad MT, Stewart DA, and Mansoor A
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- Adolescent, Adult, Aged, Aged, 80 and over, Automation, Laboratory, Biopsy, Bone Marrow Examination, Child, Child, Preschool, Female, High-Throughput Nucleotide Sequencing, Humans, Karyotyping, Leukemia, Myeloid, Acute diagnosis, Male, Middle Aged, Precursor Cell Lymphoblastic Leukemia-Lymphoma diagnosis, Predictive Value of Tests, Reproducibility of Results, Young Adult, Biomarkers, Tumor genetics, Gene Fusion, In Situ Hybridization, Fluorescence, Leukemia, Myeloid, Acute genetics, Multiplex Polymerase Chain Reaction, Precursor Cell Lymphoblastic Leukemia-Lymphoma genetics, RNA, Messenger genetics, Translocation, Genetic
- Abstract
Background: The World Health Organization (WHO) classification system defines recurrent chromosomal translocations as the sole diagnostic and prognostic criteria for acute leukemia (AL). These fusion transcripts are pivotal in the pathogenesis of AL. Clinical laboratories universally employ conventional karyotype/FISH to detect these chromosomal translocations, which is complex, labour intensive and lacks multiplexing capacity. Hence, it is imperative to explore and evaluate some newer automated, cost-efficient multiplexed technologies to accommodate the expanding genetic landscape in AL., Methods: "nCounter® Leukemia fusion gene expression assay" by NanoString was employed to detect various fusion transcripts in a large set samples (n = 94) utilizing RNA from formalin fixed paraffin embedded (FFPE) diagnostic bone marrow biopsy specimens. This series included AL patients with various recurrent translocations (n = 49), normal karyotype (n = 19), or complex karyotype (n = 21), as well as normal bone marrow samples (n = 5). Fusion gene expression data were compared with results obtained by conventional karyotype and FISH technology to determine sensitivity/specificity, as well as positive /negative predictive values., Results: Junction probes for PML/RARA; RUNX1-RUNX1T1; BCR/ABL1 showed 100 % sensitivity/specificity. A high degree of correlation was noted for MLL/AF4 (85 sensitivity/100 specificity) and TCF3-PBX1 (75 % sensitivity/100 % specificity) probes. CBFB-MYH11 fusion probes showed moderate sensitivity (57 %) but high specificity (100 %). ETV6/RUNX1 displayed discordance between fusion transcript assay and FISH results as well as rare non-specific binding in AL samples with normal or complex cytogenetics., Conclusions: Our study presents preliminary data with high correlation between fusion transcript detection by a throughput automated multiplexed platform, compared to conventional karyotype/FISH technique for detection of chromosomal translocations in AL patients. Our preliminary observations, mandates further vast validation studies to explore automated molecular platforms in diagnostic pathology.
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- 2016
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21. Strategic feeding of ammonium and metal ions for enhanced GLA-rich lipid accumulation in Cunninghamella bainieri 2A1.
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Shuib S, Nawi WN, Taha EM, Omar O, Kader AJ, Kalil MS, and Hamid AA
- Subjects
- Cunninghamella drug effects, Fatty Acids, Unsaturated analysis, Lipid Metabolism drug effects, Ammonium Compounds administration & dosage, Cunninghamella metabolism, Fatty Acids, Unsaturated metabolism, Lipid Metabolism physiology, Metals administration & dosage
- Abstract
Strategic feeding of ammonium and metal ions (Mg(2+), Mn(2+), Fe(3+), Cu(2+), Ca(2+), Co(2+), and Zn(2+)) for enhanced GLA-rich lipid accumulation in C. bainieri 2A1 was established. When cultivated in nitrogen-limited medium, the fungus produced up to 30% lipid (g/g biomass) with 12.9% (g/g lipid) GLA. However, the accumulation of lipid stopped at 48 hours of cultivation although glucose was abundant. This event occurred in parallel to the diminishing activity of malic enzyme (ME), fatty acid synthase (FAS), and ATP citrate lyase (ACL) as well as the depletion of metal ions in the medium. Reinstatement of the enzymes activities was achieved by feeding of ammonium tartrate, but no increment in the lipid content was observed. However, increment in lipid content from 32% to 50% (g/g biomass) with 13.2% GLA was achieved when simultaneous feeding of ammonium, glucose, and metal ions was carried out. This showed that the cessation of lipid accumulation was caused by diminishing activities of the enzymes as well as depletion of the metal ions in the medium. Therefore, strategic feeding of ammonium and metal ions successfully reinstated enzymes activities and enhanced GLA-rich lipid accumulation in C. bainieri 2A1.
- Published
- 2014
- Full Text
- View/download PDF
22. Methylation profiling and evaluation of demethylating therapy in renal cell carcinoma.
- Author
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Ricketts CJ, Morris MR, Gentle D, Shuib S, Brown M, Clarke N, Wei W, Nathan P, Latif F, and Maher ER
- Abstract
Background: Despite therapeutic advances in targeted therapy, metastatic renal cell carcinoma (RCC) remains incurable for the vast majority of patients. Key molecular events in the pathogenesis of RCC include inactivation of the VHL tumour suppressor gene (TSG), inactivation of chromosome 3p TSGs implicated in chromatin modification and remodelling and de novo tumour-specific promoter methylation of renal TSGs. In the light of these observations it can be proposed that, as in some haematological malignancies, demethylating agents such as azacitidine might be beneficial for the treatment of advanced RCC., Results: Here we report that the treatment of RCC cell lines with azacitidine suppressed cell proliferation in all 15 lines tested. A marked response to azacitidine therapy (>50% reduction in colony formation assay) was detected in the three cell lines with VHL promoter methylation but some RCC cell lines without VHL TSG methylation also demonstrated a similar response suggesting that multiple methylated TSGs might determine the response to demethylating therapies. To identify novel candidate methylated TSGs implicated in RCC we undertook a combined analysis of copy number and CpG methylation array data. Candidate novel epigenetically inactivated TSGs were further prioritised by expression analysis of RCC cell lines pre and post-azacitidine therapy and comparative expression analysis of tumour/normal pairs. Thus, with subsequent investigation two candidate genes were found to be methylated in more than 25% of our series and in the TCGA methylation dataset for 199 RCC samples: RGS7 (25.6% and 35.2% of tumours respectively) and NEFM in (25.6% and 30.2%). In addition three candidate genes were methylated in >10% of both datasets (TMEM74 (15.4% and 14.6%), GCM2 (41.0% and 14.6%) and AEBP1 (30.8% and 13.1%)). Methylation of GCM2 (P = 0.0324), NEFM (P = 0.0024) and RGS7 (P = 0.0067) was associated with prognosis., Conclusions: These findings provide preclinical evidence that treatment with demethylating agents such as azacitidine might be useful for the treatment of advanced RCC and further insights into the role of epigenetic changes in the pathogenesis of RCC.
- Published
- 2013
- Full Text
- View/download PDF
23. Phospholipase C beta 1 deficiency is associated with early-onset epileptic encephalopathy.
- Author
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Kurian MA, Meyer E, Vassallo G, Morgan NV, Prakash N, Pasha S, Hai NA, Shuib S, Rahman F, Wassmer E, Cross JH, O'Callaghan FJ, Osborne JP, Scheffer IE, Gissen P, and Maher ER
- Subjects
- Electroencephalography, Epilepsy physiopathology, Failure to Thrive physiopathology, Fatal Outcome, Humans, Infant, Male, Mutation, Phenotype, Polymerase Chain Reaction, Epilepsy genetics, Failure to Thrive genetics, Phospholipase C beta genetics
- Abstract
The epileptic encephalopathies of infancy and childhood are a collection of epilepsy disorders characterized by refractory, severe seizures and poor neurological outcome, in which the mechanism of disease is poorly understood. We report the clinical presentation and evolution of epileptic encephalopathy in a patient, associated with a loss-of-function mutation in the phospholipase C-β 1 gene. We ascertained a consanguineous family containing a male infant who presented with early-onset epileptic encephalopathy for detailed clinical phenotyping and molecular genetic investigation. In addition, a cohort of 12 consanguineous families of children with infantile spasms were analysed for linkage to the phospholipase C-β 1 gene locus. The male infant presented with tonic seizures in early infancy and subsequently developed infantile spasms. Over time, he developed drug-resistant epilepsy associated with severe neurological regression and failure to thrive. Molecular genetic investigation revealed a homozygous loss-of-function 0.5-Mb deletion, encompassing the promoter element and exons 1, 2 and 3 of phospholipase C-β 1 in the index case. Linkage to the phospholipase C-β 1 locus was excluded in the 12 other consanguineous families, consistent with genetic heterogeneity in this disorder. Although phospholipase C-β 1 deficiency has not previously been reported in humans, the Plcb1 homozygote knockout mouse displays early-onset severe tonic seizures and growth retardation, thus recapitulating the human phenotype. Phospholipase C-β 1 has important functions in both hippocampal muscarinic acetylcholine receptor signalling and in cortical development. Thus, the discovery of a phospholipase C-β 1 mutation allows us to propose a novel potential underlying mechanism in early-onset epileptic encephalopathy.
- Published
- 2010
- Full Text
- View/download PDF
24. Mutation analysis of hypoxia-inducible factors HIF1A and HIF2A in renal cell carcinoma.
- Author
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Morris MR, Hughes DJ, Tian YM, Ricketts CJ, Lau KW, Gentle D, Shuib S, Serrano-Fernandez P, Lubinski J, Wiesener MS, Pugh CW, Latif F, Ratcliffe PJ, and Maher ER
- Subjects
- Case-Control Studies, DNA Mutational Analysis, Genetic Predisposition to Disease, Germ-Line Mutation, Humans, Mutation, Missense, Polymorphism, Single Nucleotide, Basic Helix-Loop-Helix Transcription Factors genetics, Carcinoma, Renal Cell genetics, Hypoxia-Inducible Factor 1, alpha Subunit genetics, Kidney Neoplasms genetics
- Abstract
Background: Inactivation of the Von Hippel-Lindau (VHL) tumour suppressor gene leading to overexpression of hypoxia-inducible transcription factors (HIF)-1alpha and -2alpha is a critical event in the pathogenesis of most clear cell renal cell carcinomas (RCC). HIF-1alpha and HIF-2alpha share significant homology and regulate overlapping repertoires of hypoxia-inducible target genes but may have differing effects on RCC cell growth. Loss of HIF-1alpha expression has been described in RCC cell lines and primary tumours. Whether mutations in the alpha-subunits of HIF-1alpha and HIF-2alpha contribute to renal tumourigenesis was investigated here., Materials and Methods: Mutation analysis of the complete coding sequence of HIF-1alpha and HIF-2alpha was carried out in primary RCC (n=40)., Results: The analysis revealed a somatic HIF1A missense substitution, p.Val116Glu, in a single RCC. Functional studies demonstrated that p.Val116Glu impaired HIF-1alpha transcriptional activity. Genotyping of HIF1A variants p.Pro582Ser and p.Ala588Thr demonstrated no significant differences between RCC patients and controls., Conclusion: The detection of a loss-of-function HIF1A mutation in a primary RCC is consistent with HIF-1 and HIF-2 having different roles in renal tumourigenesis, However, somatic mutations of HIF1A are not frequently implicated in the pathogenesis of RCC.
- Published
- 2009
25. Utility of Ki-67 and p53 in distinguishing cervical intraepithelial neoplasia 3 from squamous cell carcinoma of the cervix.
- Author
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Tan GC, Sharifah NA, Shiran MS, Salwati S, Hatta AZ, and Paul-Ng HO
- Subjects
- Adult, Aged, Biopsy, Needle, Carcinoma, Squamous Cell pathology, Cohort Studies, Diagnosis, Differential, Female, Humans, Immunohistochemistry, Malaysia, Middle Aged, Neoplasm Staging, Prognosis, Retrospective Studies, Risk Assessment, Sensitivity and Specificity, Uterine Cervical Neoplasms pathology, Uterine Cervical Dysplasia pathology, Biomarkers, Tumor analysis, Carcinoma, Squamous Cell chemistry, Ki-67 Antigen analysis, Tumor Suppressor Protein p53 analysis, Uterine Cervical Neoplasms chemistry, Uterine Cervical Dysplasia chemistry
- Abstract
The differentiation between cervical intraepithelial neoplasia 3 (CIN 3) and early squamous cell carcinoma (SCC) of the cervix may be difficult in certain situations. Identification of invasion beyond the basement membrane is the gold standard for the diagnosis of the latter. The objective of this study was to determine whether the use of Ki-67 and p53 could help in solving the above dilemma. This was a retrospective study on 61 cases of cervical neoplasms comprising of 25 cases of CIN 3 and 36 SCC. All cases were evaluated by immunohistochemistry using Ki-67 and p53 monoclonal antibodies. Results showed that the differences of Ki-67 and p53 expression between CIN 3 and SCC were statistically significant. In conclusion, Ki-67 and p53 may serve as helpful adjuncts to routinely-stained histological sections in differentiating between CIN 3 and SCC.
- Published
- 2008
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