University of Peradeniya

About: University of Peradeniya is a education organization based out in Kandy, Sri Lanka. It is known for research contribution in the topics: Population & Poison control. The organization has 5970 authors who have published 7388 publications receiving 197002 citations.

GPU accelerated adaptive banded event alignment for rapid comparative nanopore signal analysis

Abstract: Nanopore sequencing enables portable, real-time sequencing applications, including point-of-care diagnostics and in-the-field genotyping. Achieving these outcomes requires efficient bioinformatic algorithms for the analysis of raw nanopore signal data. However, comparing raw nanopore signals to a biological reference sequence is a computationally complex task. The dynamic programming algorithm called Adaptive Banded Event Alignment (ABEA) is a crucial step in polishing sequencing data and identifying non-standard nucleotides, such as measuring DNA methylation. Here, we parallelise and optimise an implementation of the ABEA algorithm (termed f5c) to efficiently run on heterogeneous CPU-GPU architectures. By optimising memory, computations and load balancing between CPU and GPU, we demonstrate how f5c can perform ∼3-5 × faster than an optimised version of the original CPU-only implementation of ABEA in the Nanopolish software package. We also show that f5c enables DNA methylation detection on-the-fly using an embedded System on Chip (SoC) equipped with GPUs. Our work not only demonstrates that complex genomics analyses can be performed on lightweight computing systems, but also benefits High-Performance Computing (HPC). The associated source code for f5c along with GPU optimised ABEA is available at https://github.com/hasindu2008/f5c .

Epidemiology, Clinical Manifestations, and Long-Term Outcomes of a Major Outbreak of Chikungunya in a Hamlet in Sri Lanka, in 2007: A Longitudinal Cohort Study

Abstract: Chikungunya outbreaks occurred in the central province, Sri Lanka in 2006. This community-based study reports the epidemiology and the natural history of the infection from an affected village. Of the 199 families and 1001 individuals in the village, 159 (80%) and 513 (51%) were affected, respectively, comprising 237 (46%) males with peak incidence at 40–50 years. The acute illness caused polyarthritis in 233 (46%), and of them 230 (98%) progressed to chronic arthritic disability (CAD). Of the CAD patients, 102 (44%) had recovered in 141 days (range 30–210 days) from the disability state whilst 128 (56%) had persisting disability which lasted 12, 24, and 36 months in 41 (17.8%), 22 (9.5%), and 14 (6.1%) individuals, respectively. Carpal tunnel syndrome (CTS) manifested in 110 (21%). Females showed preponderance for complications over males: acute arthritis 147 versus 86, P = 0.001; CAD 136 versus 84, P = 0.029; CTS 88 versus 22, P = 0.001; relapses 105 versus 68, P = 0.001. Chikungunya was highly communicable and caused lasting crippling complications.

Preparation and characterization of fully oxidized form of polyaniline

Abstract: The oxidation state of polyaniline (PANI) can be varied from the fully reduced leucoemeraldine base (LEB) to the half oxidized emeraldine base (EB) and to the fully oxidized form pernigraniline base (PNB). In this work, the synthesis and properties of the highest oxidation state of polyaniline, pernigraniline, in the base as well as the corresponding salt form are discussed.