MyMedR

Using GWAS top hits to inform priors in Bayesian fine-mapping association studies

Walters K, Cox A, Yaacob H

Genet Epidemiol, 2019 Sep;43(6):675-689.

The default causal single-nucleotide polymorphism (SNP) effect size prior in Bayesian fine-mapping studies is usually the Normal distribution. This choice is often based on computational convenience, rather than evidence that it is the most suitable prior distribution. The choice of prior is important because previous studies have shown considerable sensitivity of causal SNP Bayes factors to the form of the prior. In some well-studied diseases there are now considerable numbers of genome-wide association study (GWAS) top hits along with estimates of the number of yet-to-be-discovered causal SNPs. We show how the effect sizes of the top hits and estimates of the number of yet-to-be-discovered causal SNPs can be used to choose between the Laplace and Normal priors, to estimate the prior parameters and to quantify the uncertainty in this estimation. The methodology can readily be applied to other priors. We show that the top hits available from breast cancer GWAS provide overwhelming support for the Laplace over the Normal prior, which has important consequences for variant prioritisation. This work in this paper enables practitioners to derive more objective priors than are currently being used and could lead to prioritisation of different variants.

Bayesian multivariant fine mapping using the Laplace prior

Walters K, Yaacob H

Genet Epidemiol, 2023 Apr;47(3):249-260.

PMID: 36739616 DOI: 10.1002/gepi.22517

Currently, the only effect size prior that is routinely implemented in a Bayesian fine-mapping multi-single-nucleotide polymorphism (SNP) analysis is the Gaussian prior. Here, we show how the Laplace prior can be deployed in Bayesian multi-SNP fine mapping studies. We compare the ranking performance of the posterior inclusion probability (PIP) using a Laplace prior with the ranking performance of the corresponding Gaussian prior and FINEMAP. Our results indicate that, for the simulation scenarios we consider here, the Laplace prior can lead to higher PIPs than either the Gaussian prior or FINEMAP, particularly for moderately sized fine-mapping studies. The Laplace prior also appears to have better worst-case scenario properties. We reanalyse the iCOGS case-control data from the CASP8 region on Chromosome 2. Even though this study has a total sample size of nearly 90,000 individuals, there are still some differences in the top few ranked SNPs if the Laplace prior is used rather than the Gaussian prior. R code to implement the Laplace (and Gaussian) prior is available at https://github.com/Kevin-walters/lapmapr.

Fulltext The radiographic appearance of ameloblastoma in Malaysians

Yaacob H

Singapore Med J, 1991 Feb;32(1):70-2.

PMID: 2017711

The radiographs of fifteen Malaysian patients with presenting ameloblastoma aged between 20-55 years (average 35 years) were studied for any peculiar local features. The most common features were cortical plate expansion (80%), corticated scalloped margin (67%), multiloculation (87%), and resorption of tooth roots (47%). The latter two features are constantly found in advanced tumour stage. As pain was not a frequent complaint, many Malaysian patients seek treatment only at a very late stage after the tumours have reached large dimensions. Although ameloblastomas may be diagnosed often through radiographs, it should not be relied upon solely.

Pathogenic microbes of the oral environment

Park AW, Yaacob HB

J Nihon Univ Sch Dent, 1994 Mar;36(1):1-33.

PMID: 8207501

Detection of human herpesvirus 7 in salivary glands

Yadav M, Nambiar S, Khoo SP, Yaacob HB

Arch Oral Biol, 1997 Aug;42(8):559-67.

PMID: 9347118

The prevalence and cellular distribution of human herpesvirus 7 (HHV-7) in archival labial salivary glands was analysed for virus-specific DNA sequences by polymerase chain reaction (PCR) and in situ hybridization signals. In addition, the cellular expression of HHV-7-encoded protein was detected by immunohistochemical staining with a virus-specific monoclonal antibody. Eleven of 20 samples were positive for the HHV-7 DNA sequence by PCR. Eighteen of 20 tissues analysed by in situ hybridization showed signals in ductal, serous and mucous cells. Some nuclei of these cells and also the myoepithelial population were positive. In immunolocalization studies, all 20 salivary glands consistently showed HHV-7-expressed protein in the cytoplasm of ductal cuboidal and columnar cells. The protein was also found in the cytoplasm of mucous and serous acinar cells that were immunopositive for HHV-7. The observations are consistent with the suggestion that the labial salivary gland is a site for virus replication, potential persistence and a source of infective HHV-7 in saliva.

A synopsis of the origins and function of dental plaque and pellicle

Park AW, Yaacob HB

J Nihon Univ Sch Dent, 1994 Sep;36(3):157-74.

PMID: 7989958

Electrophoretic detection of salivary alpha-amylase activity

Rahim ZH, Yaacob HB

J Nihon Univ Sch Dent, 1992 Dec;34(4):273-7.

PMID: 1283755

Fresh samples of human whole saliva containing approximately 20-40 micrograms protein were analyzed using SDS-polyacrylamide slab gel electrophoresis systems. More than 20 protein bands were revealed by Coomassie Brilliant Blue R 250 staining. Some of the protein bands were shown to be glycoprotein-positive with PAS (periodic acid-Schiff) reagent. The protein bands with alpha-Amylase activity appeared within a molecular weight range of 120,000-180,000, which is 2 to 2.8 times higher than the normal molecular weight reported for alpha-Amylase from parotid saliva, and showed positive staining with PAS reagent. These results show that the alpha-Amylase in whole saliva appears to exist in a macromolecular form which is not dissociated in the presence of sodium dodecyl sulfate (SDS).

The ancient origins of oral pathology

Park AW, Yaacob HB

J Nihon Univ Sch Dent, 1991 Dec;33(4):211-43.

PMID: 1787417

Belief in a golden age has provided mankind with solace in times of despair and with élan during the expansive periods of history. Dreamers imagine the golden age in the remote past, in paradise lost, free from toil and grief. Optimists put their faith in the future and believe that mankind, Prometheus-like, will master the arts of life through power and knowledge. Thus, the golden age means different things to different men, but the very belief in its existence implies the conviction that perfect health and happiness are birthrights of men. Yet, in reality, complete freedom from disease and from struggle is almost incompatible with the process of living.

Effects of fasting on saliva composition

Rahim ZH, Yaacob HB

J Nihon Univ Sch Dent, 1991 Dec;33(4):205-10.

PMID: 1787416

The concentrations of calcium, phosphate, protein and nitrite in whole unstimulated saliva, and the salivary flow rate under fasting conditions (saliva collected at least after 6 h without food and water) were compared with those under control conditions (saliva collected within 30 min to 1 h after food). The flow rate of fasting saliva was half that of control (0.098 ml/min vs 0.208 ml/min) and no significant differences in the flow rate were observed between sexes. The concentration of nitrite under fasting conditions was 50% higher than that in control saliva (p less than 0.05). The protein concentration was decreased, but not significantly, under fasting conditions. The composition of fasting saliva with regard to calcium and phosphate concentrations was comparable to that of the control. No significant variations in these components between sexes were observed under either condition.

Squamous odontogenic tumor

Yaacob HB

J Nihon Univ Sch Dent, 1990 Sep;32(3):187-91.

PMID: 2230962

The twenty-fifth reported case of squamous odontogenic tumor is presented. The patient was a 39-year-old Chinese Malaysian male. The lesion was asymptomatic and did not recur after excision. It is important to distinguish this type of lesion from squamous odontogenic tumor-like proliferation. The rest of Malassez is thought to be responsible for the histogenesis of the lesion. Better understanding will only be achieved when more cases are reported and studied.

Fulltext Evaluation of a training programme for non-health professionals as oral health educators

Seman K, Yaacob H, Hamid AM, Ismail AR, Yusoff A

Malays J Med Sci, 2008 Apr;15(2):33-8.

PMID: 22589623

Involvement of oral health educators among non-health professionals in oral health promotion is important in the prevention of oral diseases. This study was carried out to compare the level of oral health knowledge among pre-school teachers before and after oral health seminar. Pre-test data was collected by distributing questionnaire to pre-school teachers in Pasir Mas, who attended the seminar on "Oral Health" (n=33) and they were required to fill anonymously before the seminar started. The questions consisted of information on general background, perceived oral health status, oral health knowledge and the environment where they work. After two weeks, post-test data was collected using the same structured questionnaire and identification code was used to match the pre and post data. SPSS 11.5 was use for statistical analysis. Two out of 33 eligible preschool teachers were considered non-respondents due to absenteeism during the post-test data collection. The response rate was 94.0% (n = 31). The study shows a significant improvement in oral health knowledge among pre-school teachers in Pasir Mas, after seminar (p < 0.001) as compared to controls. Thus, we can conclude that the oral health programme (seminar) appeared effective at influencing oral health educator's knowledge towards oral health.

Fulltext Rare case of primary leiomyosarcoma of sigmoid mesocolon

Ilias AS, Yaacob H, Wan Zain WZ, Zakaria AD

BMJ Case Rep, 2017 Sep 15;2017.

PMID: 28918402 DOI: 10.1136/bcr-2017-219826

We experienced a rare case of primary leiomyosarcoma of sigmoid mesentery. A 45-year-old woman was presented to us with left iliac fossa mass and discomfort for 4-month duration. CT scan of abdomen and pelvis revealed a huge mass 14 cm×14 cm×16 cm occupying left iliac fossa mimicked having a large left ovarian carcinoma. She was subsequently planned for elective total abdominal hysterectomy and bilateral salpingo-oophorectomy by gynaecology team. During laparotomy, a huge mass was revealed arising from sigmoid mesentery invaded to the left lower ureter. Curative resection was done and pathological findings show the tumour being leiomyosarcoma with immunohistochemistry tests on caldesmon, desmin, smooth muscle actin and CD34 reagent all positive. Clinicopathological and literature review of this rare primary leiomyosarcoma of mesocolon was discussed in our case presentation.

Prospective diagnostic study on the use of narrow-band imaging on suspicious lesions during colonoscopy examination

Yaacob H, Ikhwan SM, Hashim MN, Syed Abd Aziz SH, Wan Zain WZ, Tuan Sharif SE, et al.

Asian J Endosc Surg, 2018 Nov;11(4):318-324.

PMID: 29424061 DOI: 10.1111/ases.12463

INTRODUCTION: Colonoscopy is the gold standard to detect colorectal neoplasm. Narrow-band imaging (NBI) has a good diagnostic accuracy to differentiate between neoplastic and non-neoplastic colorectal lesions. This study explores the diagnostic validity of NBI colonoscopy as well as its associated factors related to neoplastic and non-neoplastic colorectal lesions.

METHODS: This study enrolled 100 patients in a single-center tertiary teaching hospital. Patients presented for screening colonoscopy, and those with suspicious colorectal lesions were included in this study. During colonoscopy, the most suspicious lesion in each patient was analyzed using the NBI system based on Sano's classification. Each lesion was biopsied for histopathological analysis, the gold standard. Endoscopic images were captured electronically. The sensitivity, specificity, and diagnostic accuracy of NBI colonoscopy were assessed. Other associated factors related to neoplastic and non-neoplastic lesions were analyzed accordingly.

RESULTS: The sensitivity and specificity of the NBI were 88.2% and 71.9%, respectively. The area under the receiver-operator curve was 0.801, indicating that NBI has a good ability to differentiate between disease and non-disease. There are significant associations between histopathological examination outcomes and both presenting symptoms, especially weight loss, and lesion site, even after other variables were controlled (P

A bibliometric analysis of rejuvenators in reclaimed asphalt pavement

Odubela CA, Yaacob H, Warid MNBM, Karim KJBA, Zakka WP

Environ Sci Pollut Res Int, 2023 Mar;30(11):28575-28596.

PMID: 36710309 DOI: 10.1007/s11356-023-25265-5

This study looked at the state-of-the-art present knowledge base and trends in the area of using rejuvenators in reclaimed asphalt pavement (RAP) by systemic analysis and visualisation using VOSviewer and Scopus analyser; a total of 1872 studies were mined from the Scopus database for the purpose of this study. This quantitative approach to the review of literature removes author bias. The study was able to identify keywords and their cluster groups making up of core research domains ((1) asphalt binder composition and properties, (2) reclaimed asphalt mixtures (recycling), (3) reclaimed asphalt performance characteristics, (4) reclaimed asphalt sustainability, (5) rejuvenating agents and their performance, and (6) area of application). The study was able to identify the top authors; their document counts and citations; the most influential journals, institutions, and countries leading the way in the research domain; and the link between these authors and keywords within the existing body of literature in the research area. This study will help policymakers in identifying the main research themes and possible area of investments for further research in RAP. This study will also be a valuable compendium to researchers who intend to broaden the scope of the research area.

Displaying publications 21 - 34 of 34 in total