University of Colombo e-Repository

UCER (University of Colombo Electronic Repository) is a collection of scientific research publications by researchers at the University of Colombo, Sri Lanka. This e-Repository serves to manage, preserve and make available the academic works of the faculty, postgraduate students, and research groups. The collection includes faculty publications, master's and doctoral theses abstracts. This repository is updated regularly, and new works are added to collections on a continuous basis

Guidelines

Authors are responsible for obtaining copyright permission from the publisher and submitting the signed declaration to ir@lib.cmb.ac.lk.

Recent Submissions

Identification of genetic variants associated with deep vein thrombosis (DVT) in a cohort of patients affected with DVT in Sri Lanka
(University of Colombo, 2020) Hasaranga, K.L.J.; Noordeen, N.; Wetthasinghe, T.K.; Dissanayake, V.H.W.
Introduction: Genetic thrombophilias are known to be inherited and led to an enhanced tendency of vascular blood-clot formation. Deep Vein Thrombosis (DVT) is a similar thromboembolic manifestation that occurs due to various genetic & non-genetic etiologies. The aim of this study was to design and implement an assay to identify genetic variants associated with DVT in a cohort of patients in Sri Lanka.Methods: A comprehensive literature review was conducted to identify genetic variants associated with Deep Vein Thrombosis. A Tetra-Amplification-Refractory-Mutation-System Allele Specific Polymerase Chain Reaction (T-ARMS-AS-PCR) was designed and optimized to genotype the extracted DNA samples of the study population who had given informed consent for such studies. The genotype results were validated by Sanger sequencing for the specificity. Results: Total of 110 individuals were genotyped using the designed assay. Out of which, 14 (12.7%) were normal (CC) for the variant, while 39 (35.5%) were heterozygotes (CA) and 57 (51.8%) were homozygotes (AA) for CYP4V2 c.775C>A (rs13146272) variant. The allele frequency for the variant allele at Hardy Weinberg’s equilibrium was 0.6955. Out of the 110 individuals, 37 (33.6%) were normal (AA) for F5 c.2573A>G (rs4524) variant with 73 (66.4%) heterozygotes (AG). No homozygotes (GG) were found for the F5 c.2573A>G variant. The allele frequencies were 0.6651 and 0.3349 for both ancestral allele and variant allele respectively. Conclusions: Allele frequencies of both CYP4V2 and F5 variants were consistent with South Asian population allele frequencies, suggesting the reliability of our finding. This is a simple genotypic assay which can be used as an efficient, sensitive and specific molecular diagnostic screening test for thrombophilic genetic variants in Patients affected with DVT in the Sri Lankan population.
The Importance of Media Literacy in the Dissemination and Acceptance of Disaster-Related Information on Digital Platforms: Specifically, to the Cyclonic Storm Ditwah Disaster in Sri Lanka in November 2025
(Social Science and Humanities Journal, 2025) Suraweera, S.A.N.P.
Sri Lanka has experienced recurrent natural disasters in recent years, including floods, landslides, cyclones, and extreme weather events. During such crises, digital platforms such as Facebook, WhatsApp, YouTube, and online news portals have become primary sources of information for the public. While these platforms enable rapid dissemination of disaster-related information, they also facilitate the spread of misinformation, rumors, and unverified content, often resulting in public confusion, fear, and inappropriate responses. Media literacy, defined as the ability to access, analyze, evaluate, and create media content critically, plays a crucial role in shaping how individuals interpret and respond to information in high-risk situations. Despite its growing importance, limited empirical research has examined the influence of media literacy on public acceptance and dissemination of disaster-related information in the Sri Lankan context. This study seeks to address this gap by examining the role of media literacy in shaping public responses to disaster-related information disseminated through digital platforms during recent natural disasters in Sri Lanka. This study adopts a mixed-methods research design, integrating both quantitative and qualitative approaches to provide a comprehensive analysis of the research problem, with quantitative data analyzed using SPSS (Statistical Package for the Social Sciences). The study population comprises adult residents of Gampaha, Kegalle, and Kandy districts who were directly or indirectly affected by Cyclone Ditwah. Data were collected through questionnaires, interviews, and case studies, and a structured questionnaire was administered to a randomly selected sample of 300 participants to obtain systematic and comparable quantitative data, while qualitative methods were used to capture in-depth insights into participants’ experiences and perceptions.
Inconspicuous vocal repertoire of endemic Sri Lanka Bush Warbler (Elaphrornis palliseri): A quantitative description of within-species variation in vocalization
(Sri Lanka Association for the Advancement of Science, 2020) Kalukapuge, K.T.; Weerakkody, S.; Seneviratne, S.
Many passerines possess extravagant vocalizations which often provide evolutionary advantages. Birds have evolved many variations in vocalization in order to withstand the associated costs. The current study focused on investigating intraspecific vocal variations in Sri Lanka Bush Warbler (Elaphrornis palliseri) which is a range restricted montane endemic to Sri Lanka. The vocal recordings were made in three locations in the central highlands; Galwaysland National Park, Horton Plains National Park and Hakgala Strict Nature Reserve using Telinga parabolic reflector containing a MKH 20-P48 omni directional RF condenser microphone and a PMD 661 MK solid state recorder. The sonogram analysis and statistical inferences were performed using Raven Pro 1.5.0 bioacoustics software program of the Cornell Lab of Ornithology, Friedman test and paired sample t-test, respectively. Key acoustic measurements reflecting temporal and frequency attributes in vocalization including the length of notes (in seconds), length of inter-note intervals (s) maximum frequency (Hz), minimum frequency (Hz) and Peak frequency (Hz) were analyzed. The vocal repertoire of Sri Lanka Bush Warbler consists of a single prominent call giving a metallic "chwrip...chwrip..." sound which is briefed but sharp and high pitched. The vocal episodes exhibited a less complex structural organization which contains several brief consecutive notes separated by distinct pauses of varying lengths. The mean highest frequency behaves within a range of 15,000 Hz-16,000 Hz while the range of mean lowest frequency is 1,900 Hz-2,300 Hz. The mean peak frequency of each successive note lies between 6,000 Hz and 8,000 Hz. The mean duration of each note lasts for 0.1 s-0.2 s and the mean durations of first two consecutive inter-note intervals are 3.4 s and 3.0 s, respectively. The peak frequency is significantly different (P = 0.04) among individuals while other frequency attributes including highest frequency (P = 0.529) and the lowest frequency (P = 0.266) are conserved. The temporal attributes including the length of notes (P = 0.139) and the lengths of the first two inter-note intervals (P = 0.478) also not varied among individuals. These results provide a deep descriptive analysis to describe inconspicuous vocalization of E. palliseri.
Implementation of a cloud-based bioinformatics pipeline for genetic variant discovery of next generation sequence data linked to hereditary cancer syndromes
(University of Colombo, 2020) Neththikumara, N.F.; Wetthasinghe, T.K.; Dissanayake, V.H.W.
Introduction: Next generation sequencing (NGS) has now become the norm for medical diagnostics worldwide. Sequencing data used for genetic variant discovery consists of millions of short sequences called reads. Depending on the platform used for sequencing, the reads have different properties like pairing, length and error-rate which can significantly impact the analysis and variant calling process. Thus, analysing NGS data using bioinformatics techniques has become a challenge in terms of complexity, efficiency and cost effectiveness. Methods: Index cases and at-risk family members of patients with hereditary cancer syndromes have been recruited for studies conducted in the Human Genetics Unit. These individuals have been sequenced by the Illumina Miseq NGS sequencer, with the Trusight Cancer library enrichment kit. An automated bioinformatics pipeline has been developed to analyse these data, which process mapping, filtering, realignment, recalibration, variant calling and annotation. Each module has been integrated together using python and bash scripts. A secondary variant analysis module was also implemented to systematically prioritize variants in genes associated with hereditary cancer syndromes. The pipeline has been deployed to a dedicated cloud server utilizing the Google cloud computing engine and cloud storage services. Results: This pipeline generates a fully annotated variant calling file (VCF) of single nucleotide polymorphisms (SNPs) and short insertions and deletions (Indels) with several data quality statistics reports. It also incorporates virtual gene panels to generate a variant list in a subset of genes associated with a specific hereditary cancer syndrome, with in-silico pathogenicity predictions for each variant. The amount of sample data that can be run at a given time is presumed to be unlimited, as the pipeline is fully scalable. Conclusion: The incorporation of custom bioinformatics pipelines into the sequencing workflow enables reliable, efficient and cost-effective data analysis for disease diagnosis.
Buerger’s angle and Pole test for chronic limb threatening ischaemia patients with diabetes
(University of Colombo, 2020) Godakandage, M. H. P.; Abeysekara, W. P. A. M.; Basnayake, B. M. O. D.; Gunawardena, R. M. T. M.; Abeywickrama, S. S.; Saseekaran. B.; Paviththiran, S.; Boulton, J. A.; Cassim, M. R. N.; Wijeyaratne, S. M.
Introduction: Quantification of chronic limb threatening ischaemia (CLTI) is widely done using ankle brachial pressure index (ABPI), toe pressure (TP) or transcutaneous oximetry (TcPO2). In diabetes, ankle level pressures are unreliable due to medial calcification of vessels. Ulcers and gangrene limit using TP and TcPO2. We explored the Buerger’s angle and the pole test; combined with continuous wave Doppler to identify CLTI. Methods: Consecutive 40 limbs in 28 diabetes patients assessed. ABPI was assessed following standard protocol. With the Doppler probe placed over ankle level anterior tibial and posterior tibial arteries sequentially, legs were slowly elevated until the signal was lost. The leg elevation angle (with femur greater trochanter as the pivot point) and the heights were documented, and the highest values analysed. Results: Majority were males [67.8% (19)]. Mean age was 64.14(39-83). Five (17.9%) had chronic kidney disease. Thirteen limbs (32.5%) were asymptomatic; 8(20%) had rest pain and 24(60%) had tissue loss. ABPI (0.38 – more than 1) was categorized as <0.4, 0.4-0.59, 0.6-0.79, 0.8 and more. The angle (12- 90 degrees) was categorized as < 30, 30-60 and 60-90. Height ranged 21-90cm. Linear regression reveal significant difference between ABPI, and Buerger’s angle (r= 0.467, p= 0.002) and the height (r = 0.440, p = 0.004). Angle categories are also significantly different(p=0.034). Conclusions: Leg elevation angle and pole test does not correlate with ABPI in this sample. These tests may be more accurate, and easier to perform than ABPI. However larger samples and follow up are necessary for its validation and implementation.