Browsing by Author "De Silva, D."

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Degree of ICT Integration on SMEs in Health Services: A Study of Mahara Divisional Secretariat, Sri Lanka
(International Postgraduate Research Conference 2019, Faculty of Graduate Studies, University of Kelaniya, Sri Lanka, 2019) Dileep, A.H.; Sivalogathasan, V.; De Silva, D.
Integration of Information and Communication Technology(ICT) is very widespread in businesses of all sizes. As is the case with all technologies, small businesses are slower than large ones to adopt new ICT. Known fundamental reasons for non-adoption are lack of applicability and little incentive to change business models when returns are unclear. Also trust and transaction security, and challenges in areas of management skills, technological capabilities are significant barriers to adaptation of ICT in to SMEs. This research focuses on the degree of ICT integration on SMEs in health services at the Mahara Divisional Secretariat - Sri Lanka. The degree of ICT applications in SMEs observed according to the use of ICT at each level in the business (inbound logistics, operation, outbound logistics, marketing and sales, services), include: readiness for ICT, infrastructure facilities for ICT, available ICT. Response data of a sample of 50 SMEs in health services have been gathered through interviews with the help of structured questionnaires. There is a high usage of ICT in their background infrastructure for support inbound logistics, operation, outbound logistics, marketing and sales, services (Telephone -100%, Fax-90%, VOIP – 0%, Dial up connection - 22%, ADSL – 0%, Leased line - 0%, Fiber – 96%, Laptop or Desktop PC – 100%). Also there is a favorable usage of ICT applications in marketing and sales, services (Office package – 100%, E-mail / social media – 100%, Own Website / systems – 0 %, POS – 62%, Online payment – 0%). In conclusion, more than 50% of SMEs in health services use ICT facilities in their business processes. They have accumulated strong customer relationships through ICT and have reduced non value adding activities and wastages.
Deletion analysis of the RB1 gene in retinoblastoma patients in Sri Lanka
(Faculty of Science, University of Kelaniya, Sri Lanka, 2020) Panchananthan, N.; De Silva, D.; Abeysekera, H.; Nanayakara, D.P.S.; Tirimanne, T.L.S.; Chandrasekharan, N.V.
Retinoblastoma (RB), a tumour, affecting children aged less than 5 years has a prevalence of 1 in 20,000 with twenty cases/ year predicted in Sri Lanka. Unilateral RB (60%) presents on average at 24 months and bilateral RB (40%) presents around 15 months. A family history is reported in 10%. Many cases, diagnosed late, require enucleation. Genetic testing has not been available locally, but may enable better targeting of screening for patients and their siblings and reduce the need for enucleation in affected cases. Mutations of RB1 gene lead to inactivation of pRB (retinoblastoma protein) and loss of its function. Different mutations of RB1 gene include nonsense (37%), frameshift (20%), splice site (21%), missense (5%), deletions/ duplications of one or several exons or even the entire gene (15%) and mutations in the promoter region (1%). Hypermethylation of the promoter region is also found in the tumours of some retinoblastoma cases. About 5-15% of retinoblastoma patients have microscopic or submicroscopic deletions, which includes the entire or substantial parts (one or several exons) of the RB1 gene. The objective of this study was to identify the presence of germline copy number variations of the RB1 gene or any of its exons in retinoblastoma patients. Primers were designed for the 27 exons and promoter region of the target gene (RB1) and a control gene (Cystic fibrosis transmembrane conductance regulator - CFTR) to compare the copy number of both genes using gene ratio analysis copy enumeration PCR (GRACE-PCR). The peak height of the melting curve was analysed for calculation of the ratio. The ratio of the peak height of the melting curve of the target (RB1) to the control gene (CFTR) was calculated for patients and normal individuals separately. A ratio of patient to normal of 1 indicates the patient is deletion negative. A ratio of 0.5 indicates a deletion and a ratio of 1.5 indicates a duplication. Seven exons (exons 3, 4, 5, 6, 8, 9 and 10) of 32 patients and 3 more exons (exons 11, 12 and 16) of 16 patients who have no germline mutation identified from targeted amplicon sequencing, were tested. One case had a deletion for all 10 exons, while one case each had deletions of exon 11 and exon 12. In conclusion, three RB cases out of 32 patients (9%) have a deletion of one or several exons which is similar to world wide data and further testing is ongoing. Genetic testing helps to determine the recurrence risk and to target intensive screening to at risk family members. This can contribute to balance the resource limited healthcare services of developing countries.
Development and evaluation of a cost effective method for the molecular diagnosis of Prader-Willi syndrome (PWS) and Angelman syndrome (AS) in Sri Lanka.
(International Research Symposium on Pure and Applied Sciences, 2017 Faculty of Science, University of Kelaniya, Sri Lanka., 2017) Panchananthan, V.; De Silva, D.; Rathnayake, P.; Atapattu, N.; Chandrasekharan, N.V.
Prader-Willi syndrome (PWS) and Angelman syndrome (AS) are genetic disorders caused by imprinting defects on chromosome 15q11-q13. Prader –Willi syndrome is caused by loss of expression of some paternal genes and Angelman syndrome is caused by loss of expression of some maternal genes on chromosome 15q due to a deletion or uniparental disomy (UPD) of chromosome 15q or methylation centre defects in this region. The methylation specific PCR assay can detect ~99% of cases of PWS caused by deletion or UPD but can miss the 1% of cases caused by imprinting centre defects. The methylation specific PCR can detect around 90% of cases of AS caused by a deletion or UPD but can miss the 10% of cases caused by UBE3A mutation and imprinting centre defects. Objectives of this study were to establish diagnostic testing for PWS and AS among Sri Lankan patients using methylation specific PCR and to develop an in house DNA modification method for use in the methylation specific PCR assay. Forty three patients (suspected PWS = 24, AS =19) were recruited after ethical clearance and informed consent from parents. DNA was extracted from blood and methylation specific PCR (MS-PCR) performed using control primers (SNRPNF and SNRPNR), maternal (MF1 and MR1) and paternal (PF2 and PR2) primers after the modification of DNA using a sodium bisulfite modification kit while some of the samples were modified using a modified protocol established in our laboratory. Eleven out of twenty four suspected PWS cases and none of the nineteen suspected AS cases were positive on testing. The kit based modification generated consistent reliable results while the in house method requires further optimization. In conclusion, the methylation specific PCR was successful in detecting methylation abnormalities associated with PWS and AS and is a potentially useful test to confirm or refute the diagnosis of suspected cases. The MS-PCR negative, suspected AS cases merit clinical review to determine the need for mutation testing prior to exclusion of AS.
Evaluation of an In-House genetic testing method for confirming Prader-Willi and Angelman Syndromes in Sri Lanka
(Clinical Laboratory Publications, 2024) Kugalingam, N.; De Silva, D.; Rathnayake, P.; Atapattu, N.; Ranaweera, D.M.; Chandrasekharan, N.V.
BACKGROUND Prader-Willi syndrome (PWS, MIM 176,270) and Angelman syndrome (AS, MIM 105,830) are caused by imprinting defects of chromosome 15q11-13, with loss of maternal gene expression causing AS and paternal gene expression causing PWS. The diagnosis, once established in most cases by using a methylation-specific PCR test, enables appropriate therapeutic interventions and avoids the need for further investigations. Genetic testing for PWS/AS is limited in Sri Lanka (and in other low- and middle-income countries), mainly because parents are unable to pay for testing as these are not funded by the health service.METHODS Ninety cases (46 female) with clinical features suggesting PWS (n = 37) and AS (n = 53), referred by a pediatric endocrinologist and a pediatric neurologist, were recruited. Clinical information and blood samples were obtained following informed consent. DNA was extracted and methylation-specific PCR (MS-PCR) was performed following bisulfite modification of DNA by using an in-house method and a kit. Results were validated using known positive controls. Parent-child trio DNA samples were used in cases with confirmed PWS and AS to determine if the disease was due to a deletion or uniparental disomy. The cost of the MS-PCR testing of the two modification methods and the microsatellite analysis was determined.RESULTS Among the suspected PWS cases, 19/37 were positive, while 5/53 of the suspected AS cases were positive. The lower identification rate of AS is probably related to the overlap of clinical features of this condition with other disorders. The kit-based modification method was more reliable, less time-consuming, and cost-effective in our laboratory.CONCLUSIONS The kit-based modification followed by MS-PCR described in this study enables more affordable genetic testing of suspected PWS/AS cases, and this is likely to improve patient care by targeting appropriate therapy for the affected cases. Parental genetic counselling is made possible regarding the low recurrence risk, especially where a deletion or uniparental disomy is confirmed. In MS-PCR, negative cases with a strong clinical suspicion of AS, UBE3A mutation testing is required. In addition, imprinting center mutation/deletion testing may also be needed in strongly clinically suspected, MS-PCR negative PWS and AS cases.
Facile, green approach for aqueous methylene blue dye adsorption: Coconut vinegar treated Trema orientalis wood biochar
(Environmental Engineering Research, 2022) Udawatta, M. M.; De Silva, R.; De Silva, D.
Biochar is widely utilized in low-cost water treatment. However, chemicals used in most of the recorded activation techniques are corrosive, may cause secondary pollution, and not accessible by rural communities, reducing their value of being cost-effective. In this study, Trema orientalis wood biochar (WB) was successfully activated with natural coconut vinegar employing a facile technique to produce a green adsorbent for efficient aqueous methylene blue (MB) removal. Batch studies showed a three-fold higher MB adsorption capacity of coconut vinegar treated wood biochar (CVWB) compared to WB. Percentage removal ranged between 98-79% at lower dye concentrations (50-100 mg/L) and 79-48% at higher dye concentrations (100-300 mg/L). Isotherm data best fitted to the Freundlich model. Kinetic data fitted to both pseudo second order and intraparticle diffusion models, suggesting that the adsorption was governed by a pore filling mechanism with predominant electrostatic attractions, and the reaction rate was diffusion controlled. FTIR, XPS, and water contact angle measurements confirmed increased surface oxygenated groups of CVWB. XPS showed a three-fold increase in O/C atomic ratio. BET and AFM studies gave evidence to the increased porosity. Therefore, the enhanced MB adsorption capacity of CVWB was attributed to both the increased surface oxygenated functional groups and porosity.
Molecular diagnosis of Williams syndrome using quantitative polymerase chain reaction (qPCR) in a cohort of Sri Lankan patients.
(International Research Symposium on Pure and Applied Sciences, 2017 Faculty of Science, University of Kelaniya, Sri Lanka., 2017) Ranaweera, D.M.; De Silva, D.; Panchananthan, N.; Samarasinghe, D.; Perera, S.; Morawakkorala, R.; Gunewardene, S.; Chandrasekharan, N.V.
Williams Beuren Syndrome (WBS) is a genetic cause of congenital heart defects associated with developmental delay, hypercalcaemia and characteristic facial features. Its cause is a 1.5 to 1.8 Mb hemizygous deletion of chromosome 7q11.23 involving the loss of around 23 genes including the elastin (ELN) gene. The deletion results in copy number alterations. The aim of this study was to identify whether a group of Sri Lankan children with a clinical diagnosis of WBS could have their diagnosis confirmed or refuted by the use of genetic testing using a validated low cost method. A quantitative PCR method was evaluated for use in deletion screening. Twenty four suspected WBS cases were recruited following ethical clearance and informed consent. DNA was extracted, spectrophotometrically quantified and qPCR performed. The target used for deletion screening was the ELN gene and TES was used as the reference gene for normalization. In all assays, a 10 fold dilution series of standards, a no template control (NTC) and a negative control (NC) were included. The fold copy number change (ΔKCt) was determined and the mean for normals (n=6) was -0.087 ± 0.11 representing no loss while the mean for previously clinically diagnosed WS patients and confirmed by either Fluorescent in situ hybridization (FISH) or microarray analysis (n=6) was -1.39 ± 0.086 representing the loss of one copy (deletion). Among twenty four suspected cases, 19 (79%) had an ELN gene deletion while 5 cases did not and the findings correlated strongly with the clinical suspicions. This qPCR method was able to distinguish ELN deleted cases from the non-deleted ones. The preliminary data supports this as a useful diagnostic test for WBS. Validation of this test using FISH has been performed for five patient’s samples and the microarray confirmed positive which correlated with the qPCR results.
Retinoblastoma patients treated in Sri Lanka from 2014 to 2020: epidemiology, clinical status and correlates of lag time in seeking tertiary care services
(BioMed Central, 2024) Kugalingam, N.; De Silva, D.; Abeysekera, H.; Nanayakkara, S.; Tirimanne, S.; Chandrasekharan, V.; Jayawardana, P.L.
BACKGROUND Retinoblastoma (RB) is a tumour of children < 5 years with a incidence of 1 in 20,000. Around 20 RB cases are diagnosed yearly in Sri Lanka, a lower middle-income country with high literacy levels and healthcare free at point of delivery. Incidence, local and systemic severity and mortality related to RB are reportedly high in low- and middle- income countries in comparison to higher income countries. Aims of this study were to describe demographic, socioeconomic, and clinical characteristics of Sri Lankan RB patients attending the designated RB unit at the Lady Ridgeway Hospital (LRH), Colombo between January 2014 to December 2020, and determine correlates of lag time (LT) for first tertiary care visit after detecting the first symptom/sign.METHODS Two descriptive cross-sectional studies (DCSS) were conducted, one on 171 RB patients with demographic and clinical data collected between 2017 and 2020. In 2021, the second DCSS took place where socioeconomic and further demographic data were collected using telephone interviews, recruiting a subgroup of 90 (53%), consenting and contactable RB patient/ parent pairs. Bivariate and multivariable analyses were applied to determine correlates of LT of > 4 weeks for first tertiary care visit. Results were expressed as odds ratios and 95% confidence intervals.RESULTS LRH survey (N = 171): Median age at diagnosis was 15 months (range 1-94 months; IQR: 8-27); 89 (52%) were females. Groups D and E tumours were 25.7% (n = 44) and 62.6% (n = 107) respectively with 121 (71%) enucleations. The number of deaths were 2 (1.2%). Telephone survey (N = 90): Proportion with LT of > 4 weeks for first tertiary care visit was 58% (n = 52). None of the putative risk factors (ethnicity, parental educational level, socioeconomic status, distance from residence to tertiary care unit and receiving financial assistance) were associated with LT in both analyses.CONCLUSION Despite a high proportion with groups D and E tumours and enucleations, mortality rate was low, most likely due to availability of designated tertiary care. No correlates for LT of > 4 weeks for tertiary care presentation were identified. Early RB detection needs rigorous implementation of screening strategies and increased awareness among primary care health workers and parents.
Surface modification of Trema orientalis wood biochar using natural coconut vinegar and its potential to remove aqueous calcium ions: column and batch studies
(Environmental Engineering Research, 2021) Udawatta, M.; De Silva, R.; De Silva, D.
Recent investigations have revealed the harmful health effects of elevated calcium levels in drinking water. Chemically activated biochar is the most popular option for low-cost cation adsorption. However, most of these chemicals are hardly available for rural communities, corrosive, and difficult to handle by unskilled personnel. This study aimed to determine the ability of natural coconut vinegar, a common mild acid, to activate Trema orientalis wood biochar pyrolyzed at 300˚C (BC) as a facile, safe, and low-cost approach for aqueous calcium ion (Ca2+) removal. Column tests showed a two-fold increase of Ca2+ adsorption capacity and a ten-fold increase of Ca2+ retaining capacity of BC after activation with vinegar. The isotherm results were well correlated with the Langmuir model. The maximum Langmuir adsorption of the activated biochar (BC-A) was 9.96 mg/g. Ca2+ amount was determined using flame photometry. EDX analysis showed that the O/C ratio of BC increased from 0.07 to 0.13 after activation. FTIR and wettability studies showed increased oxygenated functional groups on the BC-A surface. The authors suggest a possible acid-catalyzed hydration of the C-O-C bridges of the biochar, introducing new hydroxyl/carbonyl/ester/carboxylic/lactone groups to the biochar surface due to the vinegar activation, enhancing Ca2+ adsorption through chemisorption.