FPGA acceleration of reference-based compression for genomic data

One of the key challenges facing genomics today is efficiently storing the massive amounts of data generated by next-generation sequencing platforms. Reference-based compression is a popular strategy for reducing the size of genomic data, whereby sequence information is encoded as a mapping to a known reference sequence. Determining the mapping is a computationally intensive problem, and is the bottleneck of most reference-based compression tools currently available. This paper presents the first FPGA acceleration of reference-based compression for genomic data. We develop a new mapping algorithm based on the FM-index search operation which includes optimisations targeting the compression ratio and speed. Our hardware design is implemented on a Maxeler MPC-X2000 node comprising 8 Altera Stratix V FPGAs. When evaluated against compression tools currently available, our tool achieves a superior compression ratio, compression time, and energy consumption for both FASTA and FASTQ formats. For example, our tool achieves a 30% higher compression ratio and is 71.9 times faster than the fastqz tool

Microparticles mediate the intercellular regulation of microRNA-503 and proline-rich tyrosine kinase 2 to alter the migration and invasion capacity of breast cancer cells

The successful treatment of cancer is hampered by drug resistance and metastasis. While these two obstacles were once considered separately, recent evidence associates resistance with an enhanced metastatic capacity. However, the underlying mechanisms remain undefined. We previously described the intercellular transfer of drug resistance via submicron vesicles called microparticles (MPs). We now propose that MPs derived from drug-resistant cells are also involved in the intercellular transfer of components to enhance the migration and invasion capacity of cells. Thus, MPs may be a conduit between resistance and metastasis. We used microarray analysis to identify regulatory microRNAs (miRNAs), which contribute to the dissemination of metastatic traits. miR-503 was downregulated in recipient cells following co-culture with MPs isolated from drug-resistant cells. miR-503 was inversely associated with metastasis, as demonstrated using wound healing/scratch migration assays and Matrigel®-coated transwell invasion assays. Proline-rich tyrosine kinase 2 (PYK2) was upregulated in recipient cells and associated with increased migration and invasion, with these phenotypes being reversed using a pharmacological inhibitor of PYK2 phosphorylation, tyrphostin A9. However, the MP-mediated promotion of metastatic traits was not due to the presence of these effectors in the MP cargo but rather due to down stream effector molecules in these pathways. This is the first demonstration that the role of MPs in trait acquisition extends beyond the direct transfer of vesicle components and also includes transfer of intermediary regulators that induce down stream mediators following transfer to recipient cells. This implicates an expanding role of MPs in cancer pathogenesis. © 2014 Gong, Luk, Jaiswal and Bebawy

Kaluza-Klein towers for real vector fields in flat space

We consider a free real vector field propagating in a five dimensional flat space with its fifth dimension compactified either on a strip or on a circle and perform a Kalaza Klein reduction which breaks SO(4,1) invariance while reserving SO(3,1) invariance. Taking into account the Lorenz gauge condition, we obtain from the most general hermiticity conditions for the relevant operators all the allowed boundary conditions which have to be imposed on the fields in the extra-dimension. The physical Kaluza-Klein mass towers, which result in a four-dimensional brane, are determined in the different distinct allowed cases. They depend on the bulk mass, on the parameters of the boundary conditions and on the extra parameter present in the Lagrangian. In general, they involve vector states together with accompanying scalar states.Comment: 28 pages, 4 independent table

Microparticles in cancer: A review of recent developments and the potential for clinical application

© 2015 . Once thought of as inert remnants of cellular processes, the significance of membrane vesicles is now expanding as their capacity to package and transfer bioactive molecules during intercellular communication is established. This ability to serve as vectors in the trafficking of cellular cargo is of mounting interest in the context of cancer, particularly in the dissemination of deleterious cancer traits from donor cells to recipient cells. Although microparticles (MPs) contribute to the pathogenesis of cancer, their unique characteristics can also be exploited in the context of cancer management. The detection of MPs in body fluids has the potential to provide an effective means for the diagnosis, prognosis and surveillance of cancer patients. The use of these readily accessible systemic biomarkers has the potential to circumvent the need for invasive biopsy procedures. In addition, the autologous nature of MPs may allow them to be used as novel drug delivery carriers. Consequently, the modulation of MP vesiculation to treat disease, the detection of MPs in disease monitoring, and the application of MPs as therapeutic delivery vehicles present prospective clinical interventions in the treatment of cancer

The Radon Monitoring System in Daya Bay Reactor Neutrino Experiment

We developed a highly sensitive, reliable and portable automatic system (H$^{3}$) to monitor the radon concentration of the underground experimental halls of the Daya Bay Reactor Neutrino Experiment. H$^{3}$ is able to measure radon concentration with a statistical error less than 10\% in a 1-hour measurement of dehumidified air (R.H. 5\% at 25$^{\circ}$C) with radon concentration as low as 50 Bq/m$^{3}$. This is achieved by using a large radon progeny collection chamber, semiconductor $\alpha$-particle detector with high energy resolution, improved electronics and software. The integrated radon monitoring system is highly customizable to operate in different run modes at scheduled times and can be controlled remotely to sample radon in ambient air or in water from the water pools where the antineutrino detectors are being housed. The radon monitoring system has been running in the three experimental halls of the Daya Bay Reactor Neutrino Experiment since November 2013

Congenital Midline Nodules on the Chin and Sternum

History: A 5-day old black male full-term neonate born via vacuum-assisted delivery for non-reassuring fetal heart rate presented with congenital presentation of two asymptomatic midline lesions which appeared asymptomatic. There was no history of seizures, ophthalmologic findings, abnormalities in head circumference, height, weight or limb size. Newborn screening examination was unremarkable. Examination: On the midline submental chin there was a soft, brown dome-shaped plaque measuring 0.8-centimeters with a circumferential ring of light brown pigmentation; on the midline upper chest there was a light brown 2-millimeter dome-shaped papule. Course and Therapy: Ultrasound of the submental chin lesion revealed a 0.5 x 0.8 x 0.4-centimeter heterogeneously hypoechoic structure with a peripheral soft tissue rind. Punch biopsies of the submental chin and the midline upper chest revealed haphazardly arranged striated muscle fibers in the dermis, some of which inserted directly into the epidermis. The muscle fibers were highlighted by Masson’s trichrome and myogenin. Alcian blue revealed increased dermal mucin. Discussion: Striated muscle hamartomas (SMH) are rare, benign congenital skin tumors characterized by haphazard arrangement of mature striated skeletal muscle, collagen, nerve bundles, and adipose tissue in the dermal and subcutaneous tissue. Although a rare entity, it is important to recognize this benign hamartoma as a congenital midline defect. Conservative management with clinical monitoring is recommended if cosmetically acceptable, as spontaneous regression over a period of years has been reported. Surgical excision may be pursued; however, the hamartoma may recur.https://scholarlycommons.henryford.com/merf2020caserpt/1133/thumbnail.jp