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Fulltext An automated materials and processes identification tool for material informatics using deep learning approach

Miah MSU, Sulaiman J, Sarwar TB, Ibrahim N, Masuduzzaman M, Jose R

Heliyon, 2023 Sep;9(9):e20003.
PMID: 37809409 DOI: 10.1016/j.heliyon.2023.e20003

This article reports a tool that enables Materials Informatics, termed as MatRec, via a deep learning approach. The tool captures data, makes appropriate domain suggestions, extracts various entities such as materials and processes, and helps to establish entity-value relationships. This tool uses keyword extraction, a document similarity index to suggest relevant documents, and a deep learning approach employing Bi-LSTM for entity extraction. For example, materials and processes for electrical charge storage under an electric double layer capacitor (EDLC) mechanism are demonstrated herewith. A knowledge graph approach finds and visualizes different latent knowledge sets from the processed information. The MatRec received an F1 score of 9̃6% for entity extraction, 8̃3% for material-value relationship extraction, and 8̃7% for process-value relationship extraction, respectively. The proposed MatRec could be extended to solve material selection issues for various applications and could be an excellent tool for academia and industry.
Fulltext Mitochondrial Dysfunction and Biogenesis in Neurodegenerative diseases: Pathogenesis and Treatment

Golpich M, Amini E, Mohamed Z, Azman Ali R, Mohamed Ibrahim N, Ahmadiani A

CNS Neurosci Ther, 2017 Jan;23(1):5-22.
PMID: 27873462 DOI: 10.1111/cns.12655

Neurodegenerative diseases are a heterogeneous group of disorders that are incurable and characterized by the progressive degeneration of the function and structure of the central nervous system (CNS) for reasons that are not yet understood. Neurodegeneration is the umbrella term for the progressive death of nerve cells and loss of brain tissue. Because of their high energy requirements, neurons are especially vulnerable to injury and death from dysfunctional mitochondria. Widespread damage to mitochondria causes cells to die because they can no longer produce enough energy. Several lines of pathological and physiological evidence reveal that impaired mitochondrial function and dynamics play crucial roles in aging and pathogenesis of neurodegenerative diseases. As mitochondria are the major intracellular organelles that regulate both cell survival and death, they are highly considered as a potential target for pharmacological-based therapies. The purpose of this review was to present the current status of our knowledge and understanding of the involvement of mitochondrial dysfunction in pathogenesis of neurodegenerative diseases including Alzheimer's disease (AD), Parkinson's disease (PD), Huntington's disease (HD), and amyotrophic lateral sclerosis (ALS) and the importance of mitochondrial biogenesis as a potential novel therapeutic target for their treatment. Likewise, we highlight a concise overview of the key roles of mitochondrial electron transport chain (ETC.) complexes as well as mitochondrial biogenesis regulators regarding those diseases.
Characterization of the root and canal anatomy of maxillary premolar teeth in an Iraqi subpopulation: a cone beam computed tomography study

Aljawhar AM, Ibrahim N, Abdul Aziz A, Ahmed HMA, Azami NH

Odontology, 2023 Nov 13.
PMID: 37957521 DOI: 10.1007/s10266-023-00870-5

This study aims to evaluate the number of roots and root canal morphology types of maxillary premolars in relation to a patient's gender and age in an Iraqi population using two classification systems. Cone beam computed tomography (CBCT) scans of 1116 maxillary premolars from 385 patients were evaluated for the number of roots and root canal morphology types according to Vertucci's classification and Ahmed et al. classification systems. Differences in the number of roots and root canal morphology types with regard to tooth type, patients' gender and age groups were evaluated and the degree of bilateral symmetry was determined. Chi-squared test was used for statistical analysis. About 51.1% of the 1st premolars were double rooted. The majority (87.9%) of the 2nd premolars were single rooted. The three-rooted form presented in only 1.2% and 0.7% of the 1st and 2nd premolars, respectively. Vertucci Type IV (Ahmed et al. code 2MaxP B1P1) and Vertucci Type I (Ahmed et al. code 1MaxP1) were the most common canal morphology types in the 1st and 2nd premolars, respectively. Females showed a lower number of roots and a higher prevalence of Vertucci Type I configuration (P
Fulltext The effects of psychosocial and economic factors on the quality of life of patients with end-stage renal disease and their caregivers in Klang Valley, Malaysia: protocol for a mixed-methods study

Ibrahim N, Chu SY, Siau CS, Amit N, Ismail R, Abdul Gafor AH

BMJ Open, 2022 Jun 03;12(6):e059305.
PMID: 36691236 DOI: 10.1136/bmjopen-2021-059305

INTRODUCTION: The number of patients in Malaysia requiring dialysis is expected to rise substantially in the future due to the ageing population and increasing prevalence of diabetes mellitus and hypertension. Hence, more individuals will be expected to adopt the role of caregivers in the future. The upward trend of end-stage renal disease (ESRD) and caregiving for dialysis patients has detrimental consequences for both patients and caregivers in terms of their psychological well-being and quality of life. Despite the current circumstances, there are very few studies in Malaysia that have explored the psychosocial factors, specifically on the economic impact of the management of ESRD.
METHODS AND ANALYSIS: This two-phase sequential explanatory mixed-methods design, incorporating a quantitative design (phase I) and a qualitative study (phase II), is to be conducted in 4 government hospitals and 10 other non-governmental organisations or private dialysis centres within Klang Valley, Malaysia. A cross-sectional survey (phase I) will include 236 patient-caregiver dyads, while focus group discussions (phase II) will include 30 participants. The participants for both phases will be recruited purposively. Descriptive statistics, independent sample t-tests and multiple regression analysis will be used for analyses in phase I, and thematic analysis will be used in phase II.
ETHICS AND DISSEMINATION: Approval for the study has been obtained from the National Medical Research and Ethics Committee (MREC) (NMRR-21-1012-59714) and the Research Ethics Committee of Hospital Canselor Tuanku Muhriz UKM (UKM PPI/111/8/JEP-2021-078) and University of Malaya Medical Centre (MREC ID NO: 2 02 178-10346). Informed consent of the participants will be obtained beforehand, and no personal identifiers will be obtained from the participants to protect their anonymity. The findings will be published in peer-reviewed scientific journals and presented at national or international conferences with minimal anonymised data.
Fulltext Improving the clinical recognition, prognosis, and treatment of melioidosis through epidemiology and clinical findings: The Sabah perspective

Hussin A, Nor Rahim MY, Dalusim F, Shahidan MA, Nathan S, Ibrahim N

PLoS Negl Trop Dis, 2023 Oct;17(10):e0011696.
PMID: 37844130 DOI: 10.1371/journal.pntd.0011696

INTRODUCTION: Melioidosis is a deadly endemic disease in northern Australia and Southeast Asia, including Sabah, Malaysia, which is caused by the bacterium Burkholderia pseudomallei. It contributes to high fatality rates, mainly due to misdiagnosis leading to the wrong treatment being administered to the patients. Local epidemiology and data on clinical features could assist clinicians during diagnosis and treatment. However, these details are still scarce, particularly in Sabah.
METHODS: A retrospective study of 246 culture-confirmed melioidosis cases in Queen Elizabeth Hospital, Sabah, Malaysia was performed between 2016 and 2018. The epidemiological data and clinical and laboratory findings were extracted and analysed.
RESULTS: The annual incidence of culture-confirmed melioidosis cases was estimated to be 4.97 per 100,000 people. The mean age of the patients was 50±15 years. Males and members of the Kadazan-Dusun ethnic group accounted for the majority of the melioidosis cases. The odds ratio analysis indicated that bacteraemic melioidosis in this region was significantly associated with fever (76%), and patients having at least one underlying illness (43%), including diabetes mellitus (32%). Sixty-eight patients (28%) succumbed to melioidosis. Contrary to what is known regarding factors that promote bacteraemic melioidosis, neither patients with fever nor patients with at least one comorbid disease, including diabetes mellitus, were significantly associated with death from melioidosis. There was no statistically significant difference between patients without comorbidities (24, 27%) and those with at least one comorbid disease (26, 25%), including diabetes mellitus (18, 23%). The odds ratios indicate that melioidosis mortality in this region is related to patients showing respiratory organ-associated symptoms (29%), bacteraemia (30%), and septic shock (47%). Burkholderia pseudomallei isolates in this study were highly susceptible to ceftazidime (100%), imipenem (100%), and trimethoprim-sulfamethoxazole (98%).
CONCLUSIONS: Information obtained from this study can be used by clinicians to recognise individuals with the highest risk of acquiring melioidosis, estimate an accurate prognosis, and provide effective treatment for melioidosis patients to reduce death from melioidosis.
Fulltext Effects of a Community-Based Healthy Lifestyle Intervention Program (Co-HELP) among Adults with Prediabetes in a Developing Country: A Quasi-Experimental Study

Ibrahim N, Ming Moy F, Awalludin IA, Mohd Ali Z, Ismail IS

PLoS One, 2016;11(12):e0167123.
PMID: 27935988 DOI: 10.1371/journal.pone.0167123

BACKGROUND: The prevalence of type 2 diabetes among Malaysian adults has increased by more than two folds over the past two decades. Strategies to collaborate with the existing community partners may become a promising channel for wide-scale dissemination of diabetes prevention in the country. The objectives of this study were to determine the effects of community-based lifestyle interventions delivered to adults with prediabetes and their health-related quality of life as compared to the usual care group.
METHODS: This was a quasi-experimental study conducted in two sub-urban communities in Seremban, Malaysia. A total of 268 participants with prediabetes aged between 18 to 65 years old were assigned to either the community-based lifestyle intervention (Co-HELP) (n = 122) or the usual care (n = 146) groups. The Co-HELP program was delivered in partnership with the existing community volunteers to incorporate diet, physical activity, and behaviour modification strategies. Participants in the Co-HELP group received twelve group-based sessions and two individual counselling to reinforce behavioural change. Participants in the usual care group received standard health education from primary health providers in the clinic setting. Primary outcomes were fasting blood glucose, 2-hour plasma glucose, and HbA1C. Secondary outcomes included weight, BMI, waist circumference, total cholesterol, triglyceride, LDL cholesterol, HDL cholesterol, systolic and diastolic blood pressure, physical activity, diet, and health-related quality of life (HRQOL).
RESULTS: An intention-to-treat analysis of between-groups at 12-month (mean difference, 95% CI) revealed that the Co-HELP participants' mean fasting plasma glucose reduced by -0.40 mmol/l (-0.51 to -0.28, p<0.001), 2-hour post glucose by -0.58 mmol/l (-0.91 to -0.24, p<0.001), HbA1C by -0.24% (-0.34 to -0.15, p<0.001), diastolic blood pressure by -2.63 mmHg (-3.79 to -1.48, p<0.01), and waist circumference by -2.44 cm (-4.75 to -0.12, p<0.05) whereas HDL cholesterol increased by 0.12 mmol/l (0.05 to 0.13, p<0.01), compared to the usual care group. Significant improvements were also found in HRQOL for both physical component (PCS) by 6.51 points (5.21 to 7.80, p<0.001) and mental component (MCS) by 7.79 points (6.44 to 9.14, p<0.001). Greater proportion of participants from the Co-HELP group met the clinical recommended target of 5% or more weight loss from the initial weight (24.6% vs 3.4%, p<0.001) and physical activity of >600 METS/min/wk (60.7% vs 32.2%, p<0.001) compared to the usual care group.
CONCLUSIONS: This study provides evidence that a culturally adapted diabetes prevention program can be implemented in the community setting, with reduction of several diabetes risk factors and improvement of HRQOL. Collaboration with existing community partners demonstrated a promising channel for the wide-scale dissemination of diabetes prevention at the community level. Further studies are required to determine whether similar outcomes could be achieved in communities with different socioeconomic backgrounds and geographical areas.
TRIAL REGISTRATION: IRCT201104106163N1.
Phenotyping of lymphocytes expressing regulatory and effector markers in infiltrating ductal carcinoma of the breast

Leong PP, Mohammad R, Ibrahim N, Ithnin H, Abdullah M, Davis WC, et al.

Immunol Lett, 2006 Feb 15;102(2):229-36.
PMID: 16246429

Dysfunction of the host immune system in cancer patients can be due to a number of reasons including suppression of tumour associated antigen reactive lymphocytes by regulatory T (Treg) cells. In this study, we used flow cytometry to determine the phenotype and relative abundance of the tumour infiltrating lymphocytes (TILs) from 47 enzymatically dissociated tumour specimens from patients with infiltrating ductal carcinoma (IDC) of the breast. The expression of both effector and regulatory markers on the TILs were determined by using a panel of monoclonal antibodies. Analysis revealed CD8(+) T cells (23.4+/-2.1%) were predominant in TILs, followed by CD4(+) T cells (12.6+/-1.7%) and CD56(+) natural killer cells (6.4+/-0.7%). The CD4(+)/CD8(+) ratio was 0.8+/-0.9%. Of the CD8(+) cells, there was a higher number (68.4+/-3.5%) that expressed the effector phenotype, namely, CD8(+)CD28(+) and about 46% of this subset expressed the activation marker, CD25. Thus, a lower number of infiltrating CD8(+) T cells (31.6+/-2.8%) expressed the marker for the suppressor phenotype, CD8(+)CD28(-). Of the CD4(+) T cells, 59.6+/-3.9% expressed the marker for the regulatory phenotype, CD4(+)CD25(+). About 43.6+/-3.8% CD4(+)CD25(+) subset co-expressed both the CD152 and FOXP3, the Treg-associated molecules. A positive correlation was found between the presence of CD4(+)CD25(+) subset and age (> or =50 years old) (r=0.51; p=0.045). However, no significant correlation between tumour stage and CD4(+)CD25(+) T cells was found. In addition, we also found that the CD4(+)CD25(-) subset correlated with the expression of the nuclear oestrogen receptor (ER)-alpha in the tumour cells (r=0.45; p=0.040). In conclusion, we detected the presence of cells expressing the markers for Tregs (CD4(+)CD25(+)) and suppressor (CD8(+)CD28(-)) in the tumour microenvironment. This is the first report of the relative abundance of Treg co-expressing CD152 and FOXP3 in breast carcinoma.
Application of two systems to classify the root and canal morphology in the human dentition: A national survey in India

Karobari MI, Ahmed HMA, Khamis MFB, Ibrahim N, Noorani TY

J Dent Educ, 2023 Aug;87(8):1089-1098.
PMID: 37164913 DOI: 10.1002/jdd.13236

PURPOSE: To assess the application and accuracy of two systems (Vertucci et al. 1974 and Ahmed et al. 2017) in classifying the root and canal morphology of human dentition among final-year undergraduates, interns, and postgraduate dental students in India.
METHODS: The survey was conducted using physical and online presentation modes in two phases. Phase 1; PowerPoint presentation (PPT), describing the most used classification system (Vertucci et al. 1974) and its supplementary types and Ahmed et al. (2017) classification. A single presenter delivered the PPT to participants, using either a projector in an auditorium/seminar hall (face-to-face) or an online platform (zoom meeting software). Phase 2 involved determining the students' responses. A questionnaire was distributed amongst the participants after the lecture and collected for analysis. Fisher's exact test was used to analyze the data statistically, and the significance level was set at 0.05 (p
Fulltext Astaxanthin as a Potent Antioxidant for Promoting Bone Health: An Up-to-Date Review

Davan I, Fakurazi S, Alias E, Ibrahim N', Hwei NM, Hassan H

Antioxidants (Basel), 2023 Jul 24;12(7).
PMID: 37508018 DOI: 10.3390/antiox12071480

In recent years, bone loss and its associated diseases have become a significant public health concern due to increased disability, morbidity, and mortality. Oxidative stress and bone loss are correlated, where oxidative stress suppresses osteoblast activity, resulting in compromised homeostasis between bone formation and resorption. This event causes upregulation of bone remodeling turnover rate with an increased risk of fractures and bone loss. Therefore, supplementation of antioxidants can be proposed to reduce oxidative stress, facilitate the bone remodeling process, suppress the initiation of bone diseases, and improve bone health. Astaxanthin (3,3'-dihydroxy-4-4'-diketo-β-β carotene), a potent antioxidant belonging to the xanthophylls family, is a potential ROS scavenger and could be a promising therapeutic nutraceutical possessing various pharmacological properties. In bone, astaxanthin enhances osteoblast differentiation, osteocytes numbers, and/or differentiation, inhibits osteoclast differentiation, cartilage degradation markers, and increases bone mineral density, expression of osteogenic markers, while reducing bone loss. In this review, we presented the up-to-date findings of the potential anabolic effects of astaxanthin on bone health in vitro, animal, and human studies by providing comprehensive evidence for its future clinical application, especially in treating bone diseases.
Fulltext Comparison of cooling methods on denture base adaptation of rapid heat-cured acrylic using a three-dimensional superimposition technique

May LW, John J, Seong LG, Abidin ZZ, Ibrahim N, Danaee M, et al.

J Indian Prosthodont Soc, 2021 5 4;21(2):198-203.
PMID: 33938871 DOI: 10.4103/jips.jips_41_21

Aim: To investigate the effect of different cooling methods on denture base adaptation of rapid heat-cured acrylic resin using 3D superimposition technique.
Setting and Design: In vitro - Comparative study.
Materials and Methods: Denture base adaptation of two different rapid heat-cured polymethyl methacrylate acrylic resins using five different cooling methods were compared. Forty maxillary edentulous stone cast were prepared to produce the denture bases with standardized thickness. The specimens were divided into five groups (n = 8) according to type of materials and cooling methods. The master stone cast and all forty denture bases were scanned with 3Shape E1 laboratory scanner. The scanned images of each of the denture bases were superimposed over the scanned image of the master cast using Materialize 3-matic software. Three dimensional differences between the two surfaces were calculated and color surface maps were generated for visual qualitative assessment.
Statistical Analysis Used: Generalized Linear Model Test, Bonferroni Post Hoc Analysis.
Results: All bench-cooled specimens showed wide green-colored area in the overall palatal surface, while the rapid cooled specimens presented with increased red color areas especially at the palate and post dam area. Generalized Linear Model test followed by Bonferroni post hoc analysis showed significant difference in the root mean square values among the specimen groups.
Conclusion: Samples that were bench cooled, demonstrated better overall accuracy compared to the rapid cooling groups. Regardless of need for shorter denture processing time, bench cooling of rapid heat-cured PMMA is essential for acceptable denture base adaptation.
Fulltext Therapeutic Potential of Polyphenol and Nanoparticles Mediated Delivery in Periodontal Inflammation: A Review of Current Trends and Future Perspectives

Jayusman PA, Nasruddin NS, Mahamad Apandi NI, Ibrahim N, Budin SB

Front Pharmacol, 2022;13:847702.
PMID: 35903322 DOI: 10.3389/fphar.2022.847702

Periodontitis is an oral inflammatory process involving the periodontium, which is mainly caused by the invasion of periodontopathogenic microorganisms that results in gingival connective tissue and alveolar bone destruction. Metabolic products of the oral pathogens and the associated host immune and inflammatory responses triggered are responsible for the local tissue destruction. Numerous studies in the past decades have demonstrated that natural polyphenols are capable of modulating the host inflammatory responses by targeting multiple inflammatory components. The proposed mechanism by which polyphenolic compounds exert their great potential is by regulating the immune cell, proinflammatory cytokines synthesis and gene expression. However, due to its low absorption and bioavailability, the beneficial effects of these substances are very limited and it hampers their use as a therapeutic agent. To address these limitations, targeted delivery systems by nanoencapsulation techniques have been explored in recent years. Nanoencapsulation of polyphenolic compounds with different carriers is an efficient and promising approach to boost their bioavailability, increase the efficiency and reduce the degradability of natural polyphenols. In this review, we focus on the effects of different polyphenolic substances in periodontal inflammation and to explore the pharmaceutical significance of polyphenol-loaded nanoparticles in controlling periodontitis, which may be useful for further enhancement of their efficacy as therapeutic agents for periodontal disease.
Fulltext Facile Synthesis of Nitrogen-Doped Carbon Dots from Lignocellulosic Waste

Abdullah Issa M, Z Abidin Z, Sobri S, Rashid S, Adzir Mahdi M, Azowa Ibrahim N, et al.

Nanomaterials (Basel), 2019 Oct 22;9(10).
PMID: 31652527 DOI: 10.3390/nano9101500

The current research mainly focuses on transforming low-quality waste into value-added nanomaterials and investigating various ways of utilising them. The hydrothermal preparation of highly fluorescent N-doped carbon dots (N-CDs) was obtained from the carboxymethylcellulose (CMC) of oil palm empty fruit bunches and linear-structured polyethyleneimines (LPEI). Transmission electron microscopy (TEM) analysis showed that the obtained N-CDs had an average size of 3.4 nm. The N-CDs were monodispersed in aqueous solution and were strongly fluorescent under the irradiation of ultra-violet light. A detailed description of the morphology and shape was established using Fourier transform infrared (FTIR) spectroscopy and X-ray photoelectron spectroscopy (XPS). It was shown that LPEI were successfully tuned the fluorescence (PL) properties of CDs in both the intrinsic and surface electronic structures, and enhanced the quantum yield (QY) up to 44%. The obtained N-CDs exhibited remarkable PL stability, long lifetime and pH-dependence behaviour, with the excitation/emission maxima of 350/465.5 nm. Impressively, PL enhancement and blue-shifted emission could be seen with the dilution of the original N-CDs solution. The obtained N-CDs were further applied as fluorescent probe for the identification of Cu2+ in aqueous media. The mechanism could be attributed to the particularly high thermodynamic affinity of Cu2+ for the N-chelate groups over the surface of N-CDs and the fast metal-to-ligand binding kinetics. The linear relationship between the relative quenching rate and the concentration of Cu2+ were applied between 1-30 µM, with a detection limit of 0.93 µM. The fluorescent probe was successfully applied for the detection of Cu2+ in real water. Moreover, a solid-state film of N-CDs was prepared in the presence of poly (vinyl alcohol) (PVA) polymer and found to be stable even after 72-h of continuous irradiation to UV-lamp. In contrast to the aqueous N-CDs, the composite film showed only an excitation independent property, with enhanced PL QY of around 47%. Due to the strong and stable emission nature of N-CDs in both aqueous and solid conditions, the obtained N-CDs are ideal for reducing the overall preparation costs and applying them for various biological and environmental applications in the future.
Fulltext Effects of a school-based intervention to reduce cardiovascular disease risk factors among secondary school students: A cluster-randomized, controlled trial

Amoah J, Said S, Rampal L, Manaf R, Ibrahim N, Owusu-Agyei S, et al.

PLoS One, 2021;16(11):e0259581.
PMID: 34762713 DOI: 10.1371/journal.pone.0259581

BACKGROUND: Cardiovascular diseases (CVDs) are the number cause of death worldwide. In Ghana CVD has been the leading cause of death since 2001. The prevalence of CVD risk factors among adolescents in Ghana has been increasing. This study seeks to develop, implement and evaluate the effects of a behavioral modification intervention program to reduce CVD risk factors among secondary school students in Brong Ahafo, Ghana.
METHODS: A cluster-randomized controlled trial was conducted with schools as clusters over a period of six-months with pre and post intervention evaluations. Participants were public secondary school students (14-19 years) from four schools in Brong Ahafo, Ghana. Students in the intervention group were trained by the researchers whereas those of the control group received no intervention. The intervention included health education and physical activity modules. Follow-up data using same questionnaire were collected within two weeks after the intervention was completed. Intention-to-treat analysis was performed after replacing missing values using the multiple imputation method. The generalized linear mixed model (GLMM) was used to assess the effects of the intervention study.
RESULTS: The GLMM analyses showed the intervention was effective in attaining 0.77(p<0.001), 0.72(p<0.001), 0.47(p<0.001), 0.56(p<0.001), and 0.39(p = 0.045) higher total physical activity, fruits, vegetables, seafood, and water scores respectively for the intervention group over the control group. The intervention was also significant in reducing -0.15(p<0.001),-0.23(p<0.001),-0.50(p<0.001),-0.32(p<0.001),-0.90(p<0.001),-0.87(p<0.001),-0.38(p<0.001), -0.63(p<0.001), -1.63(p<0.001), 0.61(p<0.001), and -1.53(p = 0.005) carbohydrates, fats and oils, fried eggs, fried chicken, carbonated drinks, sugar, sweet snacks, salted fish, weight, BMI, and diastolic BP. The odds of quitting alcohol use in the intervention group were 1.06 times more than the control group. There was no significant effect on reducing smoking and systolic BP.
CONCLUSION: There is an urgent need for the intervention program to be integrated into the existing curriculum structure of secondary school schools. Implementing the intervention will allow for longer and more consistent impact on the reduction of CVD risk factors among secondary school students.
Histological and proteome analyses of Microbacterium foliorum-mediated decrease in arsenic toxicity in Melastoma malabathricum

Alka S, Shahir S, Ibrahim N, Rahmad N, Haliba N, Abd Manan F

3 Biotech, 2021 Jul;11(7):336.
PMID: 34221807 DOI: 10.1007/s13205-021-02864-y

Arsenic (As) is an increasing threat across the globe, widely known as a non-threshold carcinogen, and it is reaching harmful values in several areas of the world. In this study, the effect of plant growth promoting bacteria (Microbacterium foliorum) on inorganic arsenic (Arsenate) phytoremediation by Melastoma malabathricum plants was investigated through histological analysis and proteome profiling of the M. malabathricum plants. Two-dimensional gel electrophoresis and transmission electron microscopy were used to conduct the proteome and histological analysis. When arsenic-treated cells were compared to untreated cells, substantial changes were found (1) severely altered the morphology of the cells, intensely disturbed; (2) the cell wall was thicker; (3) drastically changed the cytoplasm, the cells were polygonal in shape, different in size (scattered), and relatively dense. Compared to the control group, the ultra-structure of the root cells of the control group revealed intact cytoplasm, vacuole, and cell wall under exposure to As + bacteria that had a minor effect on the cell form. To further understand As + bacteria interaction, proteome profiling of the root cell was analyzed. The As-induced oxidative stress enrichment was confirmed by the up-regulation of tubulin, nucleoside diphosphate kinase, and major allergen during As + bacteria exposure It was observed that the profusion of proteins involved in defence, protein biogenesis, signaling, photosynthesis, nucleoside and energy metabolism was greater in As + bacteria as compared to the rooting out of As only. Overall, it can be obviously seen that the current study demonstrates the effectiveness of phytoremediation by M. foliorum on proteins involved and responsive pathways in dealing with As toxicity in M. malabathricum plant.
Prevalence of depression and clinical depressive symptoms in community-dwelling older adults with cognitive frailty

Mohd Safien A, Ibrahim N, Subramaniam P, Singh DKA, Mat Ludin AF, Chin AV, et al.

Geriatr Gerontol Int, 2024 Feb;24(2):225-233.
PMID: 38199952 DOI: 10.1111/ggi.14801

AIM: The present study determines the prevalence of depression and the extent of clinical depression symptoms among community-dwelling older adults with cognitive frailty and its associated factors.
METHODS: A total of 755 older adults aged ≥60 years were recruited. Their cognitive performance was determined using the Clinical Dementia Rating. Fried's criteria was applied to identify physical frailty, and the Beck Depression Inventory assessed their mental states.
RESULTS: A total of 39.2% (n = 304) of the participants were classified as cognitive frail. In this cognitive frail subpopulation, 8.6% (n = 26) had clinical depressive symptoms, which were mostly somatic such as disturbance in sleep pattern, work difficulty, fatigue, and lack of appetite. Older adults with cognitive frailty also showed significantly higher depression levels as compared with the noncognitive frail participants (t (622.06) = -3.38; P = 0.001). There are significant associations between depression among older adults with cognitive frailty and multimorbidity (P = 0.009), polypharmacy (P = 0.009), vision problems (P = 0.046), and hearing problems (P = 0.047). The likelihood of older adults with cognitive frailty who experience impairments to their vision and hearing, polypharmacy, and multimorbidity to be depressed also increased by 2, 3, 5, and 7-fold.
CONCLUSIONS: The majority of the Malaysian community-dwelling older adults were in a good mental state. However, older adults with cognitive frailty are more susceptible to depression due to impairments to their hearing and vision, multimorbidity, and polypharmacy. As common clinical depressive symptoms among older adults with cognitive frailty are mostly somatic, it is crucial for health professionals to recognize these and not to disregard them as only physical illness. Geriatr Gerontol Int 2024; 24: 225-233.
Fulltext Column-based removal of high concentration microplastics in synthetic wastewater using granular activated carbon

Amirah Mohd Napi NN, Ibrahim N, Adli Hanif M, Hasan M, Dahalan FA, Syafiuddin A, et al.

Bioengineered, 2023 Dec;14(1):2276391.
PMID: 37942779 DOI: 10.1080/21655979.2023.2276391

Microplastic (MP) is an emerging contaminant of concern due to its abundance in the environment. Wastewater treatment plant (WWTP) can be considered as one of the main sources of microplastics in freshwater due to its inefficiency in the complete removal of small MPs. In this study, a column-based MP removal which could serve as a tertiary treatment in WWTPs is evaluated using granular activated carbon (GAC) as adsorbent/filter media, eliminating clogging problems commonly caused by powder form activated carbon (PAC). The GAC is characterized via N2 adsorption-desorption isotherm, field emission scanning electron microscopy, and contact angle measurement to determine the influence of its properties on MP removal efficiency. MPs (40-48 μm) removal up to 95.5% was observed with 0.2 g/L MP, which is the lowest concentration tested in this work, but still higher than commonly used MP concentration in other studies. The performance is reduced with further increase in MP concentration (up to 1.0 g/L), but increasing the GAC bed length from 7.5 to 17.5 cm could lead to better removal efficiencies. MP particles are immobilized by the GAC predominantly by filtration process by being entangled with small GAC particles/chips or stuck between the GAC particles. MPs are insignificantly removed by adsorption process through entrapment in GAC porous structure or attachment onto the GAC surface.
Three-dimensional surface area analyses of developing maxillary second premolar root apices for age estimation using CBCT images

Gohain M, Asif MK, Nambiar P, Mohd Noor NS, Hidayah Reduwan N, Ibrahim N

Leg Med (Tokyo), 2024 Feb;66:102391.
PMID: 38211402 DOI: 10.1016/j.legalmed.2024.102391

Three-dimensional surface area analyses of developing root apices for age estimation in children and young adults have shown promising results. The current study aimed to apply this three-dimensional method to develop a regression model for estimating age in Malaysian children aged 7 to 14 using developing maxillary second premolars. A training sample of 155 cone-beam computed tomography scans (83 Malays and 72 Chinese) was analysed, and the formula was subsequently validated on an independent sample of 92 cone-beam computed tomography scans (45 Malays and 47 Chinese). The results showed a strong correlation (r = 94 %) between the chronological age as a dependent variable and the predictor variables, including root surface area of the apex, sex, ethnicity, and root development status (open/closed apices). For this model, the predictor variables accounted for 88.4 % of the variation in age except sex and ethnicity. A mean absolute error value of 0.42 indicated that this model can be reliably used for Malaysian children. In conclusion, this study recognises the method of three-dimensional surface area analyses as a valuable tool for age estimation in forensic and clinical practice. Further studies are highly recommended to assess its effectiveness across different demographic groups.
A novel method of age estimation in children using three-dimensional surface area analyses of maxillary canine apices

Asif MK, Ibrahim N, Al-Amery SM, Muhammad AMA, Khan AA, Nambiar P

Leg Med (Tokyo), 2020 Feb 24;44:101690.
PMID: 32135489 DOI: 10.1016/j.legalmed.2020.101690

The study aimed to develop a novel and reliable age estimation method using three-dimensional surface area analyses of maxillary canine apices among Malaysian children using CBCT data. A validated regression equation for age estimation was derived and correlation between chronological age and the surface areas of the developing maxillary canine's apices were investigated. Variations based on ethnicities, gender and status of root development were also investigated in terms of fit to the age estimation model. CBCT images of the patients ranging in age from 7 to 14 years were included in the study. Training sample of 191 intact permanent maxillary canines was selected from 191 CBCT images belonging to 100 Malays and 91 Chinese. Moreover, an independent validation sample of 96 permanent maxillary canines was selected from 96 CBCT images belonging to 48 Malays and 48 Chinese. Three-dimensional image modeling and surface area analyses of the developing canine's apices were performed using Mimics and 3-Matics software. A strong correlation (r = 0.978) was observed between chronological age and surface area of the developing maxillary canine's apices. 95.6% of the variation in age can be explained by surface area of canine's apices, gender and status of the root development (open/closed apices). However, ethnicity did not contributed to the fit of age estimation model. Female showed advanced development as compared to male. Mean absolute error values indicated that this newly developed 3D surface area analyses of canine apex can be used as a reliable method for age estimation among Malaysian children.
Identification and mechanism determination of the efflux pump subunit amrB gene mutations linked to gentamicin susceptibility in clinical Burkholderia pseudomallei from Malaysian Borneo

Hussin A, Nathan S, Shahidan MA, Nor Rahim MY, Zainun MY, Khairuddin NAN, et al.

Mol Genet Genomics, 2024 Feb 21;299(1):12.
PMID: 38381232 DOI: 10.1007/s00438-024-02105-w

The bacterium Burkholderia pseudomallei is typically resistant to gentamicin but rare susceptible strains have been isolated in certain regions, such as Thailand and Sarawak, Malaysia. Recently, several amino acid substitutions have been reported in the amrB gene (a subunit of the amrAB-oprA efflux pump gene) that confer gentamicin susceptibility. However, information regarding the mechanism of the substitutions conferring the susceptibility is lacking. To understand the mechanism of amino acid substitution that confers susceptibility, this study identifies the corresponding mutations in clinical gentamicin-susceptible B. pseudomallei isolates from the Malaysian Borneo (n = 46; Sarawak: 5; Sabah: 41). Three phenotypically confirmed gentamicin-susceptible (GENs) strains from Sarawak, Malaysia, were screened for mutations in the amrB gene using gene sequences of gentamicin-resistant (GENr) strains (QEH 56, QEH 57, QEH20, and QEH26) and publicly available sequences (AF072887.1 and BX571965.1) as the comparator. The effect of missense mutations on the stability of the AmrB protein was determined by calculating the average energy change value (ΔΔG). Mutagenesis analysis identified a polymorphism-associated mutation, g.1056 T > G, a possible susceptible-associated in-frame deletion, Delta V412, and a previously confirmed susceptible-associated amino acid substitution, T368R, in each of the three GENs isolates. The contribution of Delta V412 needs further confirmation by experimental mutagenesis analysis. The mechanism by which T368R confers susceptibility, as elucidated by in silico mutagenesis analysis using AmrB-modeled protein structures, is proposed to be due to the location of T368R in a highly conserved region, rather than destabilization of the AmrB protein structure.
Fulltext MicroRNAs and Target Genes As Biomarkers for the Diagnosis of Early Onset of Parkinson Disease

Arshad AR, Sulaiman SA, Saperi AA, Jamal R, Mohamed Ibrahim N, Abdul Murad NA

Front Mol Neurosci, 2017;10:352.
PMID: 29163029 DOI: 10.3389/fnmol.2017.00352

Among the neurodegenerative disorders, Parkinson's disease (PD) ranks as the second most common disorder with a higher prevalence in individuals aged over 60 years old. Younger individuals may also be affected with PD which is known as early onset PD (EOPD). Despite similarities between the characteristics of EOPD and late onset PD (LODP), EOPD patients experience much longer disease manifestations and poorer quality of life. Although some individuals are more prone to have EOPD due to certain genetic alterations, the molecular mechanisms that differentiate between EOPD and LOPD remains unclear. Recent findings in PD patients revealed that there were differences in the genetic profiles of PD patients compared to healthy controls, as well as between EOPD and LOPD patients. There were variants identified that correlated with the decline of cognitive and motor symptoms as well as non-motor symptoms in PD. There were also specific microRNAs that correlated with PD progression, and since microRNAs have been shown to be involved in the maintenance of neuronal development, mitochondrial dysfunction and oxidative stress, there is a strong possibility that these microRNAs can be potentially used to differentiate between subsets of PD patients. PD is mainly diagnosed at the late stage, when almost majority of the dopaminergic neurons are lost. Therefore, identification of molecular biomarkers for early detection of PD is important. Given that miRNAs are crucial in controlling the gene expression, these regulatory microRNAs and their target genes could be used as biomarkers for early diagnosis of PD. In this article, we discussed the genes involved and their regulatory miRNAs, regarding their roles in PD progression, based on the findings of significantly altered microRNAs in EOPD studies. We also discussed the potential of these miRNAs as molecular biomarkers for early diagnosis.

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