Browse publications by year: 2025

  1. Muhamad AN, Teh CSJ, Draman MR, Adnan YK, Abbas AA, Khong TL, et al.
    Antimicrob Resist Infect Control, 2025 Mar 13;14(1):22.
    PMID: 40082971 DOI: 10.1186/s13756-025-01537-2
    BACKGROUND: Surgical site infections (SSIs) are a persistent challenge in healthcare, contributing significantly to patient morbidity, mortality, and healthcare costs. Despite advancements in preventive measures, SSIs remain prevalent, especially in countries like Malaysia where rates are higher than in high-income nations.

    METHODS: A prospective, cohort study was conducted at the University Malaya Medical Center (UMMC), Malaysia, from November 2020 to May 2023. Clinical and microbiological data were collected, and logistic regression were performed to identify risk factors associated with SSIs.

    RESULTS: A total of 1,815 patients undergoing orthopedic, neurosurgical, and general surgical procedures were monitored for SSIs. The incidence rate of SSIs was 3.23 per 100 procedures (n = 71) with significant associations observed between SSI occurrence and prolonged surgical duration > 100 min, extended hospitalization > 5 days, trauma-to-surgery interval > 8 days, and presence of implants. Common pathogens isolated included Staphylococcus aureus, Klebsiella pneumoniae, and Pseudomonas aeruginosa. Multidrug-resistant organisms (MDROs) were identified in 42.1% of the total isolates.

    CONCLUSIONS: In this study, a high rate of MDRO and risk factors for SSI were identified. It emphasises the need for ongoing surveillance to guide infection prevention strategies and antimicrobial stewardship programs. Future research should prioritize evaluating the impact of targeted interventions tailored to identified risk factors to optimize surgical patient outcomes.

    MeSH terms: Adult; Aged; Female; Humans; Klebsiella pneumoniae/drug effects; Klebsiella pneumoniae/isolation & purification; Malaysia/epidemiology; Male; Middle Aged; Prospective Studies; Pseudomonas aeruginosa/drug effects; Pseudomonas aeruginosa/isolation & purification; Risk Factors; Staphylococcus aureus/drug effects; Staphylococcus aureus/isolation & purification; Incidence; Drug Resistance, Multiple, Bacterial*; Young Adult; Tertiary Care Centers*
  2. Knox-Brown B, Algharbi F, Mulhern O, Potts J, Harrabi I, Janson C, et al.
    EClinicalMedicine, 2025 Mar;81:103123.
    PMID: 40083442 DOI: 10.1016/j.eclinm.2025.103123
    BACKGROUND: Bronchodilator responsiveness testing is mainly used for diagnosing asthma. We aimed to investigate whether it is associated with progression to chronic airflow obstruction over time.

    METHODS: The multinational Burden of Obstructive Lung Disease cohort study surveyed adults, aged 40 years and above, at baseline and followed them up after a mean of 9.1 years. Recruitment took place between January 2, 2003 and December 26, 2016. Follow-up measurements were collected between January 29, 2019 and October 24, 2021. On both occasions, study participants provided information on respiratory symptoms, health status and several environmental and lifestyle exposures. They also underwent pre- and post-bronchodilator spirometry. We defined bronchodilator responsiveness at baseline using the American Thoracic Society and European Respiratory Society (ATS/ERS) 2022 definition, and the presence of chronic airflow obstruction at follow-up as a post-bronchodilator forced expiratory volume in 1 s to forced vital capacity ratio (FEV1/FVC) less than the lower limit of normal. We used multi-level regression models to estimate the association between baseline bronchodilator responsiveness and incident chronic airflow obstruction. We stratified analyses by gender and performed a sensitivity analysis in never smokers.

    FINDINGS: We analysed data from 3701 adults with 56% being women. Compared to those without bronchodilator responsiveness at baseline, those with bronchodilator responsiveness had 36% increased risk of developing chronic airflow obstruction (RR: 1.36, 95%CI 1.04, 1.80). This effect was stronger in women (RR: 1.45, 95%CI 1.09, 1.91) than men (RR: 1.07, 95%CI 0.51, 2.24). Never smokers with bronchodilator responsiveness also were at greater risk of incident chronic airflow obstruction (RR: 1.48, 95%CI 1.01, 2.20).

    INTERPRETATION: Bronchodilator responsiveness appears to be a risk factor for incident chronic airflow obstruction. It is important that future studies in other large population-based cohorts replicate these findings.

    FUNDING: National Heart and Lung Institute, UK Medical Research Council, and Wellcome Trust.

  3. Wan J, Wee LH, Siau CS, Wong YH
    Front Psychol, 2025;16:1473871.
    PMID: 40083756 DOI: 10.3389/fpsyg.2025.1473871
    INTRODUCTION: Psychological well-being refers to a mental state that allows an individual to achieve their full potential, be productive and innovative in their work, and manage everyday stressors. This study aims to assess university students' psychological well-being by examining its associations with demographic factors such as gender, only child status, family background, grade level, financial aid status, and household income.

    METHODS: This cross-sectional, online study utilized the EPOCH Measure of Adolescent Well-being to examine five positive well-being indicators: Engagement, Perseverance, Optimism, Connectedness and Happiness among Chinese university students aged 18-25 years (N = 4,911).

    RESULTS: The results showed that females, only children, first-year students, and urban students exhibited higher levels of psychological well-being. Additionally, students who received the highest level of financial assistance were significantly associated with lower levels of psychological well-being.

    CONCLUSION: Identifying the influence of these socioeconomic factors on psychological well-being allows for targeted interventions to improve the mental health and social well-being of at-risk groups.

  4. Shao J, Abdul Rabu SN, Chen C
    Front Psychol, 2025;16:1509549.
    PMID: 40083757 DOI: 10.3389/fpsyg.2025.1509549
    Bullying is increasingly prevalent in Chinese schools, contributing to a rise in associated criminal cases. A key factor in this trend is the lack of comprehensive understanding of bullying. Studies indicate a clear correlation between the level of understanding of bullying and its frequency. The adverse effects of bullying are expected to persist into adulthood, particularly during the crucial phase of behavioral and cognitive development in elementary school, when children are most receptive to changes in behavior and attitudes. Traditional lecture-based methods used to teach bullying awareness to Chinese primary school students often result in boredom and disengagement, reducing their ability to comprehend and address bullying effectively. This study developed a gamified interactive e-book (GIEB) aimed at enhancing the motivation and anti-bullying knowledge of Chinese primary school students. A quasi-experimental design with pretest and posttest assessments was employed to evaluate the approach's effectiveness. The study involved 60 third-grade students from a public primary school in Hefei, Anhui Province, China, who were randomly assigned to either an experimental group using the gamified interactive e-books (GIEB group) or a control group receiving traditional lectures (TL group). Findings indicated that the GIEB group showed significant improvements in motivation and understanding of bullying compared to the TL group. This research highlights the potential of gamified interactive e-books as effective educational tools for bullying prevention by making learning more engaging and effective. The practical implications of this study suggest that integrating gamified interactive e-books into the curriculum could significantly enhance students' motivation to learn about bullying and their anti-bullying knowledge, ultimately contributing to more effective bullying prevention in schools.
  5. Wu W, Kabilan MK
    Front Psychol, 2025;16:1551640.
    PMID: 40083763 DOI: 10.3389/fpsyg.2025.1551640
    Language classrooms are embedded with a wide range of emotions. Emotions play a significant role in affecting learners' language learning and academic performance. Yet, while the role of emotions in L2 classrooms has been recognized, very scant studies have investigated the underlying theoretical frameworks in great depth with regard to the conceptualization and causation of emotions. Moreover, very few review studies have paid sufficient attention to the antecedents or causes of emotions underpinned by certain theories in the field of SLA. Therefore, to offer a complementary review of emotion-related theories and provide fresh insights into the emotional research in SLA, the present study first explains the theoretical approaches of the conceptualization and causation of emotions, elucidates how these theories are applied into the emotional research in language learning, and identifies the effect of the interplay between cognitive, psychological, social, and contextual factors on the emotional development in the language learning. Finally, practical implications, like emotional regulation strategies for both language teachers and learners and future directions, like the integration with AI tools for L2 researchers, language teachers, and teacher educators who are interested in emotional research are also discussed.
  6. Alshajrawi OM, Tengku Din TADAATD, Marzuki SSB, Maulidiani M, Mohd Rusli NARB, Badrol Hisham NFAB, et al.
    Mol Clin Oncol, 2025 Apr;22(4):35.
    PMID: 40083862 DOI: 10.3892/mco.2025.2830
    An overview of metabolomics in cancer research, focusing on the identification of biomarkers, pharmacological targets and therapeutic agents, is provided in the present review. The fundamentals of metabolomics, the role of metabolites in cancer emergence and the methods used in metabolomic analysis, are reviewed. The applications of metabolomics in cancer therapy and diagnostics, as well as the challenges encountered in metabolomic research, are discussed. Finally, the potential clinical uses of metabolomics in cancer research and its future possibilities are explored, emphasising the importance of non-invasive diagnostic and monitoring techniques. The present review highlights the significance of metabolite-based metabolomics as a specialised tool for illuminating disease processes and identifying treatment potentials. The malfunctioning of metabolomic pathways and metabolite accumulation or depletion is caused by metabolomics abnormalities. Metabolite signatures close to a subject's phenotypic informative dimension can be used to monitor therapies and disease prediction diagnosis and prognosis. Non-invasive diagnostic and monitoring techniques with high specificity and selectivity are urgently needed. Metabolite-based metabolomics is a specialised metabolic biomarker and pathway-analysis technique, illuminating the putative processes of numerous human illnesses and determining treatment potentials. Locating biochemical pathway modifications that are early warning signs of pathological malfunction and illness is possible by identifying functional biomarkers linked to phenotypic variance. Scientists generated numerous metabolomics profiles to disclose the underlying processes and metabolomics networks for therapeutic target research in biomedicine. The metabolomic analysis of the potential utility of metabolites as biomarkers for clinical events is summarised in the present review. The significance of metabolite-based metabolomics as a specialised tool for illuminating disease processes and identifying treatment potentials is highlighted.
  7. Ali AS, Maelah R
    Heliyon, 2025 Feb 28;11(4):e42915.
    PMID: 40084032 DOI: 10.1016/j.heliyon.2025.e42915
    Shared service centre is a transformative organizational approach that fuels operational efficiency, cost reduction, and elevated service delivery across diverse industries. Technological innovation is paramount for driving organizational success, fostering competitive advantage, and enabling sustainable growth in today's dynamic business landscape. The purpose of this research article is to investigate the impact of technological innovations on the sustainability performance of shared service centers. Semi-structured email interviews were conducted with eleven practitioners from multinational shared services in Malaysia. The data was analyzed using structural and pattern coding, and six phases of thematic analysis were applied. The results reveal several themes related to innovative technologies in shared services, including robotic process automation, efficiency in service delivery, remote access, cost-effectiveness, customer satisfaction, and paper waste reduction, that practitioners consider relevant for sustainable performance in shared services. The findings have theoretical and managerial implications, emphasizing the significance of technological innovation approaches and sustainable performance in supporting technologies. This study provides insights for SSCs to adopt innovative technologies for improving their sustainability performance and achieving business goals.
  8. Low ZX, Kanauchi O, AbuBakar S, Tiong V, Hassandarvish P
    Bio Protoc, 2025 Mar 05;15(5):e5230.
    PMID: 40084071 DOI: 10.21769/BioProtoc.5230
    This protocol offers an ex vivo method for screening host-targeting antivirals (HTAs) using human peripheral blood mononuclear cells (PBMCs) or plasmacytoid dendritic cells (pDCs). Unlike virus-targeting antivirals (VTAs), HTAs provide advantages in overcoming drug resistance and offering broad-spectrum protection, especially against rapidly mutating or newly emerging viruses. By focusing on PBMCs or pDCs, known for their high production of humoral factors such as Type I interferons (IFNs), the protocol enables the screening of antivirals that modulate immune responses against viruses. Targeting host pathways, especially innate immunity, allows for species-independent antiviral activity, reducing the likelihood of viral escape mutations. Additionally, the protocol's versatility makes it a powerful tool for testing potential antivirals against various viral pathogens, including emerging viruses, positioning it as an essential resource in both pandemic preparedness and broad-spectrum antiviral research. This approach differentiates itself from existing protocols by focusing on host immune modulation through pDCs, offering a novel avenue for HTA discovery. Key features • Optimized protocol for screening HTAs against dengue virus (DENV), chikungunya virus (CHIKV), and Zika virus (ZIKV). • This protocol is ideal for screening soluble or intravenous-formulated compounds for evaluating their efficacy in experimental settings. • This protocol builds upon the method developed by Tsuji et al. [1] and extends its application to PBMCs and testing against DENV, CHIKV, and ZIKV.
  9. Sharma N, Khatib MN, Balaraman AK, Roopashree R, Kaur M, Srivastava M, et al.
    Int Urol Nephrol, 2025 Apr;57(4):1039-1049.
    PMID: 39495435 DOI: 10.1007/s11255-024-04266-4
    BACKGROUND: Prostate cancer is one of the most prevalent malignancies among men globally. Glucagon-like peptide 1 receptor agonists (GLP-1 RAs), primarily used for type 2 diabetes mellitus (T2DM) management, have been investigated for their potential effects on cancer risks. This systematic review and meta-analysis aimed to assess the association between GLP-1 RA use and risk reduction of prostate cancer.

    METHODS: A comprehensive literature search was conducted across PubMed, Embase, and Web of Science up to July 30, 2024. Studies that met the inclusion criteria randomized controlled trials, cohort studies, case-control studies, and observational studies assessing the incidence of prostate cancer in GLP-1 RA-treated patients were included. The quality of studies was evaluated using the Newcastle-Ottawa Scale and the Cochrane Risk of Bias tool. Meta-analysis was performed using a random effects model.

    RESULTS: A total of five studies were included, analyzing data from diverse international contexts. The included studies showed a reduced risk of prostate cancer with both adjusted and unadjusted effect estimates with GLP-1 RAs. The meta-analysis revealed an RR of 0.72 (95% CI: 0.610 to 0.832), indicating a statistically significant 28% reduction in prostate cancer risk associated with GLP-1 RA use compared to placebo or other antidiabetic drugs. Moderate heterogeneity was observed (I2 = 51%). Sensitivity analysis confirmed the results.

    CONCLUSION: The findings suggest a significant protective association between GLP-1 RA use and reduced prostate cancer risk in men, particularly those with T2DM. This supports the potential of GLP-1 RAs not only in diabetes management but also as a strategy to mitigate cancer risk. Further research is required to confirm these findings and explore the underlying mechanisms, considering different dosages, durations of therapy, and patient subgroups based on demographic and metabolic characteristics.

    MeSH terms: Glucagon-Like Peptide-1 Receptor*; Diabetes Mellitus, Type 2/drug therapy; Humans; Hypoglycemic Agents/therapeutic use; Male
  10. Karunaithas S, Chaibun T, Chatchawal P, Promptmas C, Buajeeb W, Yin LS, et al.
    J Med Virol, 2025 Mar;97(3):e70299.
    PMID: 40071579 DOI: 10.1002/jmv.70299
    Human papillomavirus type 16 (HPV-16) is a key driver in the development of cervical carcinoma, with the integration of its genome into the host DNA marking a critical step in disease progression. Monitoring the physical state of HPV-16, particularly the transition from episomal to integrated forms, is essential for evaluating the risk of malignancy development in cervix. This study presents the development of a duplex electrochemical biosensor for the simultaneous detection of the E2 and E6 genes of HPV-16. Using a one-step sandwich hybridization assay, the biosensor was able to detect HPV-16 E2 and E6 genes with a sensitivity of 8 copies/mL and 12 copies/mL respectively and distinguish between the episomal and integrated forms based on the E2/E6 ratio (cut-off 0.77, 100% sensitivity/specificity). The sensor was validated with 30 clinical cervical tissue samples, providing results comparable to qPCR method. This novel biosensor offers a rapid and efficient platform for the detection and monitoring of HPV-16, with potential applications in cervical cancer screening and prognosis.
    MeSH terms: DNA, Viral/genetics; Female; Humans; Sensitivity and Specificity
  11. Morgan P, Zanudin A
    J Prim Care Community Health, 2025;16:21501319251320160.
    PMID: 40071833 DOI: 10.1177/21501319251320160
    BACKGROUND: Individuals with cerebral palsy (CP) experience acute and chronic health issues requiring lifespan primary care. This review aimed to investigate characteristics and utilization of general practitioner (GP) access by adults with CP. Secondary aims included exploring reasons prompting access, identifying interventions provided, and personal features affecting access.

    METHODS: Using systematic review methodology, 5 databases were searched using keywords relating to adults, CP, and primary care, relating to quantitative studies (January 2000-July 2024). Data was extracted, collated, and analyzed descriptively, with additional meta-analyses to estimate proportion of GP visits.

    RESULTS: Fifteen studies were included describing GP access by 6231 adults with CP. The proportion annually accessing a GP was 78% (95% CI = 69%-85%). The frequency of GP access ranged from 1.76 to 11.7 visits per year, increased with advancing age and disability severity. Comorbid intellectual disability and pain also increased GP attendance. Limited data was available reporting healthcare needs prompting GP access, and no interventions were described.

    CONCLUSIONS: Advancing age, greater disability severity, comorbid intellectual disability, and pain may prompt increased GP access by adults with CP. Identification of reasons for seeking primary care, and interventions provided are required through data linkage studies to enhance lifespan care.

    MeSH terms: Adult; Age Factors; Humans; Primary Health Care/statistics & numerical data
  12. Figueras MM, Okada N, Tan CK, Aquino MC, Tan MCJ, Lun KW, et al.
    J Glaucoma, 2025 Mar 13.
    PMID: 40071977 DOI: 10.1097/IJG.0000000000002564
    PRCIS: In this retrospective cohort study, the 1-year cumulative probability of failure was comparable, achieving 52.20% in the phacoemulsification-iStent inject W (phaco/iStent) group and 47.80% in the phacoemulsification-micropulse transscleral laser therapy (phaco/MPTLT) group (P=0.994).

    PURPOSE: To compare the 1-year efficacy and safety of phacoemulsification combined with iStent Inject W (phaco/iStent) and phacoemulsification combined with micropulse transscleral laser therapy (phaco/MPTLT).

    METHODS: Retrospective cohort study that included patients with mild-moderate open angle glaucoma (OAG) and cataract who underwent either phaco/iStent or phaco/MPTLT in a tertiary hospital in Singapore between August 1, 2016 and December 31, 2022. The primary outcome measures were cumulative probabilities of failure between the two groups with failure defined as disease progression by Ocular Coherence Tomography (OCT-RNFL) or Visual Field Test (VFT), repeat glaucoma surgery, and inability to maintain intraocular pressure (IOP) lower than pre-operative baseline or the use of glaucoma medications for 2 consecutive visits after 1 month post-operatively. Additionally, post-operative mean IOP, average number of IOP lowering medications, visual acuity, and complications were analyzed.

    RESULTS: Forty-six patients were included. 23 eyes underwent phaco/iStent and 23 had phaco/MPTLT. The two groups had comparable cumulative probabilities of failure (52.20% phaco/iStent, 47.80% phaco/MPTLT; P=0.994) and mean IOP (15.57+2.95 mmHg phaco /iStent, 14.39+2.25 mmHg phaco/MPTLT; P=0.136) after 1 year. The change in IOP before surgery to 12 months is -1.04+3.07 mmHg in the phaco/iStent group (P=0.593) and -2.43+4.12 mmHg in the phaco/MPTLT group (P=0.022). Both achieved significant medication reduction burden (P<0.05). Intra-operative and post-operative complication rates were similar.

    CONCLUSION: Both groups showed comparable surgical efficacy and safety after 1 year. The phaco/MPTLT group demonstrated sustained IOP reduction 1 year post-operatively.

  13. Wang Y, Li Y, Wang X, Gao Y, Li C, Meng T, et al.
    Adv Mater, 2025 Mar 12.
    PMID: 40072325 DOI: 10.1002/adma.202420373
    Anode-free lithium metal batteries are promising toward high-energy-density power sources with low-cost, but their practical applications are challenged by poor cycling stability and low rate capability. Herein, a shape change-free and lithium-free anode that well controls the reversible Li plating-stripping is reported, which is composed of a highly-ordered hollow ZnO matrix with a surface-coated lithium-phosphorus-oxynitride (LiPON) layer. The ZnO matrix supplies sufficient cavities and lithiophilic sites to facilitate uniform Li plating/stripping within the hollow cavity, while the LiPON layer maintains stable solid-electrolyte interphase from mechanical and electrochemical damage. As a result, lithium is constrained within the cavity and the overall anode shape is effectively controlled during long-term and high-rate cycling. The assembled half-cell stably works at 1.2 mA cm-2 for 335 cycles with Coulombic efficiency of 98.8%. Without Li pre-deposition, full-cells using modified-LiFePO4 and LiNi0.5Co0.2Mn0.3O2 cathodes demonstrate 150-cycles lifespan and high energy density of 617 Wh kg-1 at 2C rate.
  14. Kok SHW, Chong WK, Khor J, Liu R, Tan LS, Low J, et al.
    Small, 2025 Mar 12.
    PMID: 40072339 DOI: 10.1002/smll.202501119
    The design of highly efficient photocatalysts to photoreduce nitrogen (N2) to ammonia (NH3) under mild conditions is extremely challenging. In this work, various molar ratio of molybdenum (Mo) is incorporated into Bi12O17Cl2 via a hydrothermal process. The resulting Mo-doped Bi12O17Cl2 exhibits remarkable solar-driven activity for N2 photo fixation without any scavengers or sacrificial agents. The optimal sample with 5% Mo dopants displays an NH3 yield of 39.83 µmol g-1 h-1, a 1.6-fold improvement over undoped pristine Bi12O17Cl2. The impressive performance is attributed to the synergistic effects of oxygen vacancies (OVs) and Mo-loading, enhancing light absorption and extending photo-response through band gap reduction. Additional contributions arise from the enriched active sites, facilitating N2 adsorption and electron transport to the reactants. Density functional theory calculations reveal that Mo integration induces significant charge redistribution around the active sites, thereby reducing the energy barrier associated with N2 activation and protonation. In-depth investigation into the reaction pathway unravels the step-by-step reaction process which further elucidates the beneficial role of Mo loading in the overall N2 photoconversion process. As a whole, this work promotes a simple and effective engineering approach based on heteroatom doping as an efficacious strategy to design highly active photocatalysts toward N2 photo fixation.
  15. Tan AZL, Ho WS, Hassim MH, Abdullah F, Lim LY
    Environ Monit Assess, 2025 Mar 12;197(4):385.
    PMID: 40072627 DOI: 10.1007/s10661-025-13797-x
    In industrialized areas, air pollution is a recurring problem, especially in areas with high manufacturing and energy-intensive businesses. The challenge lies in the tension between industrial growth and environmental protection, as these sectors significantly contribute to pollution, resource depletion, and climate change. The objectives of the study were (1) to assess the contribution of each industrial group to the air quality in and around the Pasir Gudang industrial area, Malaysia, and (2) to evaluate the Air Pollution Index (API). Industrial emission sources were grouped into 10 specific groups, namely (1) biomass energy plants, (2) ceramic and mineral, (3) chemical, (4) electrical, (5) food and beverage, (6) metal industries, (7) paint, (8) rubber product, (9) waste recovery, and (10) wood respectively. For this, hourly, daily, and annual modelling of pollutant gases and particulate matter (SO2, NO2, and PM10) for 3 years (2019 to 2021) were conducted using the AERMOD dispersion model. The maximum hourly, daily, and annual average ground level concentrations of SO2 and PM10 were mainly contributed by Wood industry group emissions, while NO2 was dominated by metal industry group emissions. It was observed that the average hourly and daily NO2 levels exceeded Malaysia's standard limits. The API during the study period was 146.97, contributed by NO2, which indicates unhealthy conditions for sensitive groups. Therefore, NO2 pollutant control measures from the Metal industry group should be prioritized in this industrial area.
    MeSH terms: Environmental Monitoring*; Industry*; Malaysia; Nitrogen Dioxide/analysis; Sulfur Dioxide/analysis
  16. Westaway JAF, Diez Benavente E, Auburn S, Kucharski M, Aranciaga N, Nayak S, et al.
    PLoS Negl Trop Dis, 2025 Mar;19(3):e0012885.
    PMID: 40072967 DOI: 10.1371/journal.pntd.0012885
    Sabah, Malaysia, has amongst the highest burden of human Plasmodium knowlesi infection in the world, associated with increasing encroachment on the parasite's macaque host habitat. However, the genomic make-up of P. knowlesi in Sabah was previously poorly understood. To inform on local patterns of transmission and putative adaptive drivers, we conduct population-level genetic analyses of P. knowlesi human infections using 52 new whole genomes from Sabah, Malaysia, in combination with publicly available data. We identify the emergence of distinct geographical subpopulations within the macaque-associated clusters using identity-by-descent-based connectivity analysis. Secondly, we report on introgression events between the clusters, which may be linked to differentiation of the subpopulations, and that overlap genes critical for survival in human and mosquito hosts. Using village-level locations from P. knowlesi infections, we also identify associations between several introgressed regions and both intact forest perimeter-area ratio and mosquito vector habitat suitability. Our findings provide further evidence of the complex role of changing ecosystems and sympatric macaque hosts in Malaysia driving distinct genetic changes seen in P. knowlesi populations. Future expanded analyses of evolving P. knowlesi genetics and environmental drivers of transmission will be important to guide public health surveillance and control strategies.
    MeSH terms: Adaptation, Physiological/genetics; Animals; Humans; Malaysia/epidemiology; Ecosystem; Genome, Protozoan; Genomics; Mosquito Vectors/genetics; Mosquito Vectors/parasitology
  17. Patil SM, Ramu R, Goh KW
    STAR Protoc, 2025 Mar 21;6(1):103657.
    PMID: 40073020 DOI: 10.1016/j.xpro.2025.103657
    Colostrum and milk from dairy sources consist of whey, casein, and fat, which have notable pharmacological properties due to their proteins and peptides. Here, we present a protocol for isolating, simulating in vitro gastrointestinal digestion, and fractionating colostrum and milk hydrolysates from any dairy source. We also describe steps for nano-liquid chromatography-electrospray ionization-tandem mass spectrometry (nano-LC-ESI-MS/MS) identification of proteins and peptides and in silico system biology-based profiling of the proteins and peptides present in the hydrolysates.
    MeSH terms: Animals; Chromatography, Liquid/methods; Digestion/physiology; Female; Milk Proteins/analysis; Milk Proteins/isolation & purification; Milk Proteins/metabolism; Spectrometry, Mass, Electrospray Ionization/methods; Proteomics/methods; Gastrointestinal Tract/metabolism; Gastrointestinal Tract/chemistry; Systems Biology/methods
  18. Srivastava A, Idriss H, Das G, Abedrabbo S, Shamsir MS, Homouz D
    PLoS One, 2025;20(3):e0318614.
    PMID: 40073046 DOI: 10.1371/journal.pone.0318614
    DNA polymerase β, a member of the X-family of DNA polymerases, undergoes complex regulations both in vitro and in vivo through various posttranslational modifications, including phosphorylation and methylation. The impact of these modifications varies depending on the specific amino acid undergoing alterations. In vitro, methylation of DNA polymerase β with the enzyme protein arginine methyltransferase 6 (PRMT6) at R83 and R152 enhances polymerase activity by improving DNA binding and processivity. Although these studies have shown that methylation improves DNA binding, the underlying mechanism of enhancement of polymerase activity in terms of structure and dynamics remains poorly understood. To address this gap, we modeled the methylated enzyme/DNA complex and conducted a microsecond-long simulation in the presence of Mg ions. Our results revealed significant structural changes induced by methylating both R83 and R152 sites in the enzyme. Specifically, these changes caused the DNA fragment to move closer to the C- and N-subdomains, forming additional hydrogen bonds. Furthermore, the cross-correlation map demonstrated that methylation enhanced long-range correlations within the domains/subdomains of DNA polymerase β, along with an increase in the linear mutual information value between the domains/subdomains and DNA fragments. The graph connectivity network also illustrated that methylation modulates the information pathway and identifies residues exhibiting long-distance coupling with the methylated sites. Our results provide an atomic-level understanding of the structural transition induced by methylation, shedding light on the mechanisms underlying the methylation-induced enhancement of activity in DNA polymerase β.
    MeSH terms: DNA/metabolism; DNA/chemistry; Humans; Hydrogen Bonding; Methylation; Models, Molecular; Protein-Arginine N-Methyltransferases/genetics; Protein-Arginine N-Methyltransferases/metabolism; Protein-Arginine N-Methyltransferases/chemistry; Protein Binding; Molecular Dynamics Simulation
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