Displaying all 9 publications

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  1. Ahmed Tarajo Buba, Lee, Lai Soon
    MyJurnal
    The urban transit network design problem (UTNDP) involves the development of a transit route set and associated schedules for an urban public transit system. The design of efficient public transit systems is widely considered as a viable option for the economic, social, and physical structure of an urban setting. This paper reviews four well-known population-based metaheuristics that have been employed and deemed potentially viable for tackling the UTNDP. The aim is to give a thorough review of the algorithms and identify the gaps for future research directions.
    Matched MeSH terms: Knowledge Bases
  2. Lebedeva A, Timokhin G, Ignatova E, Kavun A, Veselovsky E, Sharova M, et al.
    Clin Exp Med, 2023 Oct;23(6):2663-2674.
    PMID: 36752890 DOI: 10.1007/s10238-023-01011-6
    With the growing use of comprehensive tumor molecular profiling (CTMP), the therapeutic landscape of cancer is rapidly evolving. NGS produces large amounts of genomic data requiring complex analysis and subsequent interpretation. We sought to determine the utility of publicly available knowledge bases (KB) for the interpretation of the cancer mutational profile in clinical practice. Analysis was performed across patients who previously underwent CTMP. Independent interpretation of the CTMP was performed manually, and then, the recommendations were compared to ones present in KBs (OncoKB, CIViC, CGI, CGA, VICC, MolecularMatch). A total of 222 CTMP reports from 222 patients with 932 genomic alterations (GA) were identified. For 368 targetable GA identified in 171 (77%) of the patients, 1381 therapy recommendations were compiled. Except for CGA, therapy ESCAT LOE I, II, IIIA and IIIB therapy options were equally represented in the majority of KB. Personalized treatment options with ESCAT LOE I-II were provided for 35 patients (16%); MolecularMatch/CIViC allowed to collect ESCAT I-II treatment options for 34 of them (97%), OncoKB/CGI-for 33 of them (94%). Employing VICC and CGA 6 (17%) and 20 (57%) of patients were left without ESCAT I or II treatment options. For 88 patients with ESCAT level III-B therapy recommendations: only 2 (2%), 3 (3%), 4 (5%) and 6 (7%) of patients were left without options with CIViC, MolecularMatch, CGI and OncoKB, and with VICC-12 (14%). Highest overlap ratio was observed for IIIA (0.81) biomarkers, with the comparable results for LOE I-II. Meanwhile, overlap ratio for ESCAT LOE IV was 0.22. Public KBs provide substantial information on ESCAT-I/R1 biomarkers, but the information on ESCAT II-IV and resistance biomarkers is underrepresented. Manual curation should be considered the gold standard for the CTMP interpretation.
    Matched MeSH terms: Knowledge Bases
  3. Lebedeva AA, Kavun AI, Veselovsky EM, Mileyko VA, Ivanov MV
    Sovrem Tekhnologii Med, 2022;14(6):15-23.
    PMID: 37181287 DOI: 10.17691/stm2022.14.6.02
    Multigene testing using NGS (next-generation sequencing) provides a large amount of information and can detect multiple molecular alterations. Subsequent clinical interpretation is a time-consuming process necessary to select a treatment strategy. Existing databases often contain inconsistent information and are not regularly updated. The use of ESCAT levels of evidence requires a deep understanding of the nature of alterations and does not answer the question of which therapy option to select when multiple biomarkers with the same level of evidence are detected. To address these issues, we created the Clinical Relevance of Alterations in Cancer (CRAC) database on the relevance of detected alterations in specific genes, which are often analyzed as part of NGS panels. The team of oncologists and biologists assigned a CRAC score from 1 to 10 to each biomarker (a type of genomic alteration characteristic of specific genes) for 15 malignancies; an average score was entered into the database. CRAC scores are a numerical reflection of the following factors: therapy availability and the prospects of drug treatment with experimental drugs for patients with a particular type of tumor. A total of 134 genes and 15 of the most common tumor types have been selected for CRAC. The biomarker-nosology associations with CRAC scores in the range of 1-3 are the most frequent (n=2719 out of 3495; 77.8%), the least frequent ones (n=52 out of 3495; 1.5%) are with the highest CRAC scores 9 and 10. To estimate the practical effectiveness of the CRAC database, 208 reports on comprehensive molecular profiling were retrospectively analyzed; the applicability of CRAC was compared with the ESCAT level of evidence system. The highest CRAC scores corresponded to the ESCAT maximum levels of evidence: the range of scores 8-10 corresponded to evidence levels I and II. No biomarker within the same level of evidence was represented by the same CRAC score; the largest range of CRAC scores was observed for biomarkers of levels evidence IIIA and IV - from 2 to 10 and from 1 to 9, respectively. The use of CRAC scores allowed to identify additional 95 alterations with CRAC scores of 1-5 in the studied patients. The developed database is available at: https://crac.oncoatlas.ru/.
    Matched MeSH terms: Knowledge Bases
  4. Poovaneswaran, Sangeetha, Khajotia, Rumi, Subramaniam, Thiruselvi
    MyJurnal
    The incidence of cancer in Malaysia is rising alarmingly and newly qualified doctors will be expected
    to be competent in the basic management of cancer patients. However, the opportunity to gain experience in oncology management will remain limited unless these students are stationed in an oncology unit which is solely dedicated to the treatment of such patients. Therefore, it is essential that undergraduate medical school training equips students with a sound knowledgebase, so that they can confidently manage basic oncological conditions appropriately. With the many private and local medical universities across the country, it is important that oncology training be standardized
    and reflective of the local resources available, and government health policies. As a result, having a
    standardized curriculum would help create a framework whereby competencies in cancer management would be accurately assessed.
    Matched MeSH terms: Knowledge Bases
  5. Abu A, Susan LL, Sidhu AS, Dhillon SK
    BMC Bioinformatics, 2013;14:48.
    PMID: 23398696 DOI: 10.1186/1471-2105-14-48
    Digitised monogenean images are usually stored in file system directories in an unstructured manner. In this paper we propose a semantic representation of these images in the form of a Monogenean Haptoral Bar Image (MHBI) ontology, which are annotated with taxonomic classification, diagnostic hard part and image properties. The data we used are basically of the monogenean species found in fish, thus we built a simple Fish ontology to demonstrate how the host (fish) ontology can be linked to the MHBI ontology. This will enable linking of information from the monogenean ontology to the host species found in the fish ontology without changing the underlying schema for either of the ontologies.
    Matched MeSH terms: Knowledge Bases
  6. Abdullah D, Soo SY, Kanagasingam S
    Singapore Dent J, 2016 Dec;37:21-26.
    PMID: 27916252 DOI: 10.1016/j.sdj.2016.01.001
    BACKGROUND: Dental and maxillofacial injuries are one of the areas of concern highlighted in the Malaysian National Oral Health Plan 2011-2020. General dental practitioners (GDPs) have the responsibility of diagnosing and assessing dental trauma and determining the prognosis and outcomes of trauma along with its management. The purpose of this study was to evaluate the knowledge base and preferred methods of general dental practitioners regarding the management of avulsed tooth.

    METHODS: A random convenient sampling methodology was employed for sample selection. A pre-tested 11-item questionnaire was validated on the dental officers. The survey was distributed to 182 GDPs attending the annual Malaysian Dental Association conference in January 2010. The data obtained was statistically analyzed using descriptive analysis and logistic regression was employed to predict the probability of achieving high scores.

    RESULTS: A total of 182 general dental practitioners participated in the study, with the majority being female (n=153, 75%). The place of practice significantly affected the knowledge score. In the group that scored more than 80 points (n=84, 46%), 76% of them worked with government hospitals. Age, work duration and number of traumatised teeth previously treated had no significant effect. The odds ratio for place of practice indicates that respondents who work in government hospitals are 3.6 times more likely to score more than 80 points compared to those who worked in private clinics (OR=3.615, P=0.001).

    CONCLUSION: The knowledge level on the management of avulsed tooth among general dental practitioners in Malaysia needs to be improved. Strategies in improvement of the Malaysian dental educational system, continuous dental educational activities and utilisation of guidelines on trauma management should be recommended to increase the knowledge level of avulsed tooth management to ensure good treatment outcomes.

    CLINICAL IMPLICATION: Trauma prevention and further education regarding the management of avulsed tooth is an essential requirement to improve general dental practitioners knowledge and clinical skills.

    Matched MeSH terms: Knowledge Bases
  7. Liu C, Kanazawa T, Tian Y, Mohamed Saini S, Mancuso S, Mostaid MS, et al.
    Transl Psychiatry, 2019 08 27;9(1):205.
    PMID: 31455759 DOI: 10.1038/s41398-019-0532-4
    Over 3000 candidate gene association studies have been performed to elucidate the genetic underpinnings of schizophrenia. However, a comprehensive evaluation of these studies' findings has not been undertaken since the decommissioning of the schizophrenia gene (SzGene) database in 2011. As such, we systematically identified and carried out random-effects meta-analyses for all polymorphisms with four or more independent studies in schizophrenia along with a series of expanded meta-analyses incorporating published and unpublished genome-wide association (GWA) study data. Based on 550 meta-analyses, 11 SNPs in eight linkage disequilibrium (LD) independent loci showed Bonferroni-significant associations with schizophrenia. Expanded meta-analyses identified an additional 10 SNPs, for a total of 21 Bonferroni-significant SNPs in 14 LD-independent loci. Three of these loci (MTHFR, DAOA, ARVCF) had never been implicated by a schizophrenia GWA study. In sum, the present study has provided a comprehensive summary of the current schizophrenia genetics knowledgebase and has made available all the collected data as a resource for the research community.
    Matched MeSH terms: Knowledge Bases
  8. Maimaiti N, Ahmed Z, Md Isa Z, Ghazi HF, Aljunid S
    Value Health Reg Issues, 2013 09 13;2(2):259-263.
    PMID: 29702874 DOI: 10.1016/j.vhri.2013.07.003
    OBJECTIVE: To measure the clinical burden of invasive pneumococcal disease (IPD) in selected developing countries.

    METHODS: This is an extensive literature review of published articles on IPD in selected developing countries from East Asia, South Asia, Middle East, sub-Saharan Africa, and Latin America. We reviewed all the articles retrieved from the knowledge bases that were published between the years 2000 and 2010.

    RESULTS: After applying the inclusion, exclusion, and quality criteria, the comprehensive review of the literature yielded 10 articles with data for pneumococcal meningitis, septicemia/bacteremia, and pneumonia. These selected articles were from 10 developing countries from five different regions. Out of the 10 selected articles, 8 have a detailed discussion on IPD, one of them has s detailed discussion on bacteremia and meningitis, and another one has discussed pneumococcal bacteremia. Out of these 10 articles, only 5 articles discussed the case-fatality ratio (CFR). In our article review, the incidence of IPD ranged from less than 5/100,000 to 416/100,000 population and the CFR ranged from 12.2% to 80% in the developing countries.

    CONCLUSIONS: The review demonstrated that the clinical burden of IPD was high in the developing countries. The incidence of IPD and CFR varies from region to region and from country to country. The IPD burden was highest in sub-Saharan African countries followed by South Asian countries. The CFR was low in high-income countries than in low-income countries.

    Matched MeSH terms: Knowledge Bases
  9. Salizar Mohamed Ludin
    MyJurnal
    Objective: In 2014, Malaysia suffered a severe flood disaster and many people lost their home and belongings. Despite regular flooding in this area, the status of community disaster resilience (CDR) is unknown. This paper thus aims to assess the association between demographic characteristics and community disaster resilience factors.

    Methods: A cross-sectional study was completed using the Conjoint Community Resiliency Assessment Measure (CCRAM28) questionnaire six months after the flood event occurred. All selected respondents who met the inclusion criteria were recruited, and IBM SPSS software was used to undertake descriptive and inferential analysis.

    Results: A total of 386 respondents completed the questionnaires. Respondents were mostly female (57%); married (83.9%); with children under 17 years old (58.8%); from villages or rural area (97.2%); living in basic housing (95.6%); of average income; Muslim (97.5%); educated to primary or secondary level (81.1%); and not involved with any community organizations (95.1%), including volunteering, emergency teams, or military service. The mean age was 49 years, and length of time living in the area ranged from 1 to 85 years. CDR scores ranged between medium (2.34- 3.66) and high (3.67- 5.00). An analysis of the results showed that only gender (p = 0.003) and education (p = 0.001) were significantly related to CDR level. Positive and strong correlations were seen between resilience factors, however, particularly leadership (p = 0.001), collective efficacy (p = 0.001); preparedness (p = 0.001); place attachment (p = 0.001); and social trust (p = 0.001).

    Conclusion: The study provides a timely insight into the impact of demographic characteristics and resilience factors in Kelantan, developing the knowledge base needed to create comprehensive, improved community-relevant strategies for the future. This assessment enables top-down initiatives to better understand resilience levels, and this could act as tool to enable the government to prepare communities for future disasters or emergency events.
    Matched MeSH terms: Knowledge Bases
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