Enabling Genomics Pipelines in Commodity Personal Computers With Flash Storage.

Analysis of a patient's genomics data is the first step toward precision medicine. Such analyses are performed on expensive enterprise-class server machines because input data sets are large, and the intermediate data structures are even larger (TB-size) and require random accesses. We present a general method to perform a specific genomics problem, mutation detection, on a cheap commodity personal computer (PC) with a small amount of DRAM. We construct and access large histograms of k-mers efficiently on external storage (SSDs) and apply our technique to a state-of-the-art reference-free genomics algorithm, SMUFIN, to create SMUFIN-F. We show that on two PCs, SMUFIN-F can achieve the same throughput at only one third (36%) the hardware cost and half (45%) the energy compared to SMUFIN on an enterprise-class server. To the best of our knowledge, SMUFIN-F is the first reference-free system that can detect somatic mutations on commodity PCs for whole human genomes. We believe our technique should apply to other k-mer or n-gram-based algorithms.

High-Frequency Repetitive Magnetic Stimulation Enhances the Expression of Brain-Derived Neurotrophic Factor Through Activation of Ca2+-Calmodulin-Dependent Protein Kinase II-cAMP-Response Element-Binding Protein Pathway.

Repetitive transcranial magnetic stimulation (rTMS) can be used in various neurological disorders. However, neurobiological mechanism of rTMS is not well known. Therefore, in this study, we examined the global gene expression patterns depending on different frequencies of repetitive magnetic stimulation (rMS) in both undifferentiated and differentiated Neuro-2a cells to generate a comprehensive view of the biological mechanisms. The Neuro-2a cells were randomly divided into three groups-the sham (no active stimulation) group, the low-frequency (0.5 Hz stimulation) group, and high-frequency (10 Hz stimulation) group-and were stimulated 10 min for 3 days. The low- and high-frequency groups of rMS on Neuro-2a cells were characterized by transcriptome array. Differentially expressed genes were analyzed using the Database of Annotation Visualization and Integrated Discovery program, which yielded a Kyoto Encyclopedia of Genes and Genomes pathway. Amphetamine addiction pathway, circadian entrainment pathway, long-term potentiation (LTP) pathway, neurotrophin signaling pathway, prolactin signaling pathway, and cholinergic synapse pathway were significantly enriched in high-frequency group compared with low-frequency group. Among these pathways, LTP pathway is relevant to rMS, thus the genes that were involved in LTP pathway were validated by quantitative real-time polymerase chain reaction and western blotting. The expression of glutamate ionotropic receptor N-methyl d-aspartate 1, calmodulin-dependent protein kinase II (CaMKII) δ, and CaMKIIα was increased, and the expression of CaMKIIγ was decreased in high-frequency group. These genes can activate the calcium (Ca2+)-CaMKII-cAMP-response element-binding protein (CREB) pathway. Furthermore, high-frequency rMS induced phosphorylation of CREB, brain-derived neurotrophic factor (BDNF) transcription via activation of Ca2+-CaMKII-CREB pathway. In conclusion, high-frequency rMS enhances the expression of BDNF by activating Ca2+-CaMKII-CREB pathway in the Neuro-2a cells. These findings may help clarify further therapeutic mechanisms of rTMS.

Brief report: Preliminary study on evaluation of spasticity in patients with brain lesions using mechanomyography.

BACKGROUND: Electromyography and the modified Ashworth scale (MAS) are among the most effective methods for evaluating spasticity; however, these are often inappropriate for clinical use, owing to the complicated procedure and subjective evaluation outcomes. METHODS: A passive stretch reflex test was performed on 10 subjects with brain lesions. Furthermore, mechanomyography and electromyography were conducted on the vastus lateralis muscle (agonist) and semitendinosus muscle (antagonist) of the subjects with brain lesions. A new equation to define the normalized hull area; that is, the mechanomyography (MMG) ratio, was applied to quantify the triaxial motion of the agonist muscle versus antagonist muscles, reflecting the electromyographic firing point of the spastic muscle. FINDINGS: The MMG ratio was proposed, which statistically distinguishes the spastic and normal muscles (p = 0.01) and exhibits a concordance with the conventional mean MAS (r = 0.69, p = 0.01). INTERPRETATION: Patients suspected to have spasticity of 0 to 1+ grade can be quantitatively evaluated using the normalized hull area ratio, which can be used as an additional clinical indicator for spasticity evaluation. REGISTRATION OF CLINICAL TRIALS: The study was conducted in conformity with the Helsinki declaration principles and performed in the Korea Centers for Disease Control and Prevention, Ministry of Health and Welfare (Republic of Korea); 2010; KCT0002385; A new approach of spasticity measurement using mechanomyography in patients with brain lesions: A randomized pilot study for a parallel randomized controlled trial; October 8, 2015 [Cited on July 21, 2017]; [1 screen]. Available from: https://cris.nih.go.kr/cris/search/search_result_st01_en.jsp?seq=7805<ype=&rtype=.