• Genomics & Informatics
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• v.20 no.4
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• pp.44.1-44.13
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• 2022

Brugada syndrome (BS) is an autosomal dominant inheritance cardiac arrhythmia disorder associated with sudden death in young adults. Thailand has the highest prevalence of BS worldwide, and over 60% of patients with BS still have unclear disease etiology. Here, we performed a new viral metagenome analysis pipeline called VIRIN and validated it with whole genome sequencing (WGS) data of HeLa cell lines and hepatocellular carcinoma. Then the VIRIN pipeline was applied to identify viral integration positions from unmapped WGS data of Thai males, including 100 BS patients (case) and 100 controls. Even though the sample preparation had no viral enrichment step, we can identify several virus genes from our analysis pipeline. The predominance of human endogenous retrovirus K (HERV-K) viruses was found in both cases and controls by blastn and blastx analysis. This study is the first report on the full-length HERV-K assembled genomes in the Thai population. Furthermore, the HERV-K integration breakpoint positions were validated and compared between the case and control datasets. Interestingly, Brugada cases contained HERV-K integration breakpoints at promoters five times more often than controls. Overall, the highlight of this study is the BS-specific HERV-K breakpoint positions that were found at the gene coding region "NBPF11" (n = 9), "NBPF12" (n = 8) and long non-coding RNA (lncRNA) "PCAT14" (n = 4) region. The genes and the lncRNA have been reported to be associated with congenital heart and arterial diseases. These findings provide another aspect of the BS etiology associated with viral genome integrations within the human genome.

• Journal of Biosystems Engineering
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• v.34 no.2
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• pp.95-105
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• 2009

A method was proposed which employed control of the drop location of fertilizer particles on a spinner disc to optimize the spread pattern uniformity. The system contained an optical sensor as a feedback mechanism, which measured discharge velocity and location, as well as particle diameters to predict a spread pattern of a single disc. Simulations showed that the feed gate adaptation algorithm produced high quality patterns for any given application rate in the dual disc spreader. The performance of the feed gate control method was assessed using data collected from a Sulky spinner disc spreader. The results showed that it was always possible to find a spread pattern with an acceptable CV lower than 15%, even though the spread pattern was obtained from a rudimentary flat disc with straight radial vanes. A mathematical optimization method was used to find the initial parameter settings for a specially designed experimental spreading arrangement, which included the feed gate control system, for a given flow rate and swath width. Several experiments were carried out to investigate the relationship between the gate opening and flow rate, disc speed and particle velocity, as well as disc speed and predicted landing location of fertilizer particles. All relationships found were highly linear ($r^2$ > 0.96), which showed that the time-of-flight sensor was well suited as a feedback sensor in the rate and uniformity controlled spreading system.