Mining Time-delayed Gene Regulation Patterns from Gene Expression Data

Discovered gene regulation networks are very helpful to predict unknown gene functions. The activating and deactivating relations between genes and genes are mined from microarray gene expression data. There are evidences showing that multiple time units delay exist in a gene regulation process. Association rule mining technique is very suitable for finding regulation relations among genes. However, current association rule mining techniques cannot handle temporally ordered transactions. We propose a modified association rule mining technique for efficiently discovering time-delayed regulation relationships among genes.By analyzing gene expression data, we can discover gene relations. Thus, we use modified association rule to mine gene regulation patterns. Our proposed method, BC3, is designed to mine time-delayed gene regulation patterns with length 3 from time series gene expression data. However, the front two items are regulators, and the last item is their affecting target. First we use Apriori to find frequent 2-itemset in order to figure backward to BL1. The Apriori mined the frequent 2-itemset in the same time point, so we make the L2 split to length one for having relation in the same time point. Then we combine BL1 with L1 to a new ordered-set BC2 with time-delayed relations. After pruning BC2 with the threshold, BL2 is derived. The results are worked out by BL2 joining itself to BC3, and sifting BL3 from BC3. We use yeast gene expression data to evaluate our method and analyze the results to show our work is efficient

XRCC1, but not APE1 and hOGG1 gene polymorphisms is a risk factor for pterygium.

PurposeEpidemiological evidence suggests that UV irradiation plays an important role in pterygium pathogenesis. UV irradiation can produce a wide range of DNA damage. The base excision repair (BER) pathway is considered the most important pathway involved in the repair of radiation-induced DNA damage. Based on previous studies, single-nucleotide polymorphisms (SNPs) in 8-oxoguanine glycosylase-1 (OGG1), X-ray repair cross-complementing-1 (XRCC1), and AP-endonuclease-1 (APE1) genes in the BER pathway have been found to affect the individual sensitivity to radiation exposure and induction of DNA damage. Therefore, we hypothesize that the genetic polymorphisms of these repair genes increase the risk of pterygium.MethodsXRCC1, APE1, and hOGG1 polymorphisms were studied using fluorescence-labeled Taq Man probes on 83 pterygial specimens and 206 normal controls.ResultsThere was a significant difference between the case and control groups in the XRCC1 genotype (p=0.038) but not in hOGG1 (p=0.383) and APE1 (p=0.898). The odds ratio of the XRCC1 A/G polymorphism was 2.592 (95% CI=1.225-5.484, p=0.013) and the G/G polymorphism was 1.212 (95% CI=0.914-1.607), compared to the A/A wild-type genotype. Moreover, individuals who carried at least one C-allele (A/G and G/G) had a 1.710 fold increased risk of developing pterygium compared to those who carried the A/A wild type genotype (OR=1.710; 95% CI: 1.015-2.882, p=0.044). The hOGG1 and APE1 polymorphisms did not have an increased odds ratio compared with the wild type.ConclusionsXRCC1 (Arg399 Glu) is correlated with pterygium and might become a potential marker for the prediction of pterygium susceptibility

Planning and Implantation of NetFPGA Platform on Network Emulation Testbed

The concepts of cloud computing and Internet applications have expanded gradually and have become more and more important. Researchers need a new, high-speed network to build experimental environments for testing new network protocolswithout affecting existing traffic. In this paper, we describe a way to integrate NetFPGA platform, OpenFlow concept and NetFPGA reference designs into anetwork testbed to improve the packet processing speed and the dynamic adjustability for network emulation experiments. Furthermore, combined with Tunneling and VPLS, the proposed network testbed can be connected to distributed network, thus providing researchers a traffic-controllable and NIC-programmable experimental networking testbed in intra-communicating part

Kappa-Opioid Receptors in the Caudal Nucleus Tractus Solitarius Mediate 100 Hz Electroacupuncture-Induced Sleep Activities in Rats

Previous results demonstrated that 10 Hz electroacupuncture (EA) of Anmian acupoints in rats during the dark period enhances slow wave sleep (SWS), which involves the induction of cholinergic activity in the caudal nucleus tractus solitarius (NTS) and subsequent activation of opioidergic neurons and μ-receptors. Studies have shown that different kinds of endogenous opiate peptides and receptors may mediate the consequences of EA with different frequencies. Herein, we further elucidated that high-frequency (100 Hz)-EA of Anmian enhanced SWS during the dark period but exhibited no direct effect on rapid eye movement (REM) sleep. High-frequency EA-induced SWS enhancement was dose-dependently blocked by microinjection of naloxone or κ-receptor antagonist (nor-binaltorphimine) into the caudal NTS, but was affected neither by μ- (naloxonazine) nor δ-receptor antagonists (natatrindole), suggesting the role of NTS κ-receptors in the high-frequency EA-induced SWS enhancement. Current and previous results depict the opioid mechanisms of EA-induced sleep

Toward Inter-Connection on OpenFlow Research Networks

With the advance of Future Internet technologies, many research issues andideas are growing fast in recent years. In the field of network virtualization, softwaredefined network becomes a common topic on network research. In Taiwan, manyinstitutes and laboratories of universities already built their bench-scale testbed forresearch and educational use with OpenFlow protocol. As time goes by, stitchingexperimental networks is a growing trend to fulfill requirements for large scaleemulation. Hence, this paper revealed a progressing deployment which connectsdifferent experimental networks with centralized control policy. The objective is tobuild an integrated research network with a proposed solution which utilizesOpenFlow protocol to deal with the inter-connections. With a centralized controllerand implemented architecture, the deployment not only solves the limitation of VLANtag number in network but also improves the flexibility of configuration. This designcould be a solution for the realistic constraints of network environment in Taiwan, andit also supports the possibility of stitching regional experimental networks fornetworking research

Glycogen synthase kinase 3α and 3β have distinct functions during cardiogenesis of zebrafish embryo

<p>Abstract</p> <p>Background</p> <p>Glycogen synthase kinase 3 (GSK3) encodes a serine/threonine protein kinase, is known to play roles in many biological processes. Two closely related GSK3 isoforms encoded by distinct genes: GSK3α (51 kDa) and GSK3β (47 kDa). In previously studies, most GSK3 inhibitors are not only inhibiting GSK3, but are also affecting many other kinases. In addition, because of highly similarity in amino acid sequence between GSK3α and GSK3β, making it difficult to identify an inhibitor that can be selective against GSK3α or GSK3β. Thus, it is relatively difficult to address the functions of GSK3 isoforms during embryogenesis. At this study, we attempt to specifically inhibit either GSK3α or GSK3β and uncover the isoform-specific roles that GSK3 plays during cardiogenesis.</p> <p>Results</p> <p>We blocked <it>gsk3α </it>and <it>gsk3β </it>translations by injection of morpholino antisense oligonucleotides (MO). Both <it>gsk3α</it>- and <it>gsk3β</it>-MO-injected embryos displayed similar morphological defects, with a thin, string-like shaped heart and pericardial edema at 72 hours post-fertilization. However, when detailed analysis of the <it>gsk3α</it>- and <it>gsk3β</it>-MO-induced heart defects, we found that the reduced number of cardiomyocytes in <it>gsk3α </it>morphants during the heart-ring stage was due to apoptosis. On the contrary, <it>gsk3β </it>morphants did not exhibit significant apoptosis in the cardiomyocytes, and the heart developed normally during the heart-ring stage. Later, however, the heart positioning was severely disrupted in <it>gsk3β </it>morphants. <it>bmp4 </it>expression in <it>gsk3β </it>morphants was up-regulated and disrupted the asymmetry pattern in the heart. The cardiac valve defects in <it>gsk3β </it>morphants were similar to those observed in <it>axin1 </it>and <it>apc</it>^{<it>mcr </it>}mutants, suggesting that GSK3β might play a role in cardiac valve development through the Wnt/β-catenin pathway. Finally, the phenotypes of <it>gsk3α </it>mutant embryos cannot be rescued by <it>gsk3β </it>mRNA, and vice versa, demonstrating that GSK3α and GSK3β are not functionally redundant.</p> <p>Conclusion</p> <p>We conclude that (1) GSK3α, but not GSK3β, is necessary in cardiomyocyte survival; (2) the GSK3β plays important roles in modulating the left-right asymmetry and affecting heart positioning; and (3) GSK3α and GSK3β play distinct roles during zebrafish cardiogenesis.</p

Group A Streptococcus Subcutaneous Infection-Induced Central Nervous System Inflammation Is Attenuated by Blocking Peripheral TNF

Group A streptococcus (GAS) infection causes a strong inflammatory response associated with cytokine storms, leading to multiorgan failure, which is characterized as streptococcal toxic shock syndrome. However, little is known about GAS subcutaneous infection-mediated brain inflammation. Therefore, we used a bioluminescent GAS strain and reporter mice carrying firefly luciferase under transcriptional control of the nuclear factor-kappa B (NF-κB) promoter to concurrently monitor the host immune response and bacterial burden in a single mouse. Notably, in addition to the subcutaneous inoculation locus at the back of mice, we detected strong luminescence signals from NF-κB activation and increased inflammatory cytokine production in the brain, implying the existence of central nervous system inflammation after GAS subcutaneous infection. The inflamed brain exhibited an increased expression of glial fibrillary acidic protein and nicotinamide adenine dinucleotide phosphate oxidase components and greater microglial activation and blood–brain barrier (BBB) disruption. Furthermore, Fluoro-Jade C positive cells increased in the brain, indicating that neurons underwent degeneration. Peripheral tumor necrosis factor (TNF), which contributes to pathology in brain injury, was elevated in the circulation, and the expression of its receptor was also increased in the inflamed brain. Blockage of peripheral TNF effectively reduced brain inflammation and injury, thereby preventing BBB disruption and improving survival. Our study provides new insights into GAS-induced central nervous system inflammation, such as encephalopathy, which can be attenuated by circulating TNF blockage

Usability Assessment of a Cable-Driven Exoskeletal Robot for Hand Rehabilitation

Study design: Case series.Background: Robot-assisted rehabilitation mediated by exoskeletal devices is a popular topic of research. The biggest difficulty in the development of rehabilitation robots is the consideration of the clinical needs. This study investigated the usability of a novel cable-driven exoskeletal robot specifically designed for hand rehabilitation.Methods: The study consists of three steps, including prototype development, spasticity observation, and usability evaluation. First, we developed the prototype robot DexoHand to manipulate the patient's fingers based on the clinical needs and the cable-driven concept established in our previous work. Second, we applied DexoHand to patients with different levels of spasticity. Finally, we obtained the system usability scale (SUS) and assessed its usability.Results: Two healthy subjects were recruited in the pre-test, and 18 patients with stroke and four healthy subjects were recruited in the formal test for usability. The total SUS score obtained from the patients and healthy subjects was 94.77 ± 2.98 (n = 22), indicating an excellent level of usability. The satisfaction score was 4.74 ± 0.29 (n = 22), revealing high satisfaction with DexoHand. The tension profile measured by the cables showed the instantaneous force used to manipulate fingers among different muscle tone groups.Conclusions:DexoHand meets the clinical needs with excellent usability, satisfaction, and reliable tension force monitoring, yielding a feasible platform for robot-assisted hand rehabilitation

Ocimum gratissimum Aqueous Extract Induces Apoptotic Signalling in Lung Adenocarcinoma Cell A549

Ocimum gratissimum (OG) is widely used as a traditional herb for its antibacterial activity in Taiwan. Recently, antitumor effect of OG on breast cancer cell is also reported; however, the effects of OG on human pulmonary adenocarcinoma cell A549 remain unclear. Therefore, we aimed to investigate whether aqueous OG extract (OGE) affects viability of A549 cells and the signals induced by OGE in A549 cells. Cell viability assays revealed that OGE significantly and dose-dependently decreased the viability of A549 cell but not that of BEAS-2B cell. Morphological examination and DAPI staining indicated that OGE induced cell shrinkage and DNA condensation for A549 cells. Further investigation showed that OGE enhanced activation of caspase-3, caspase-9 and caspase-8 and increased protein level of Apaf-1 and Bak, but diminished the level of Bcl-2. Additionally, OGE inhibited the phosphorylation of extracellular signal-regulated kinase (ERK) yet enhanced the phosphorylation of c-Jun N-terminal kinase (JNK) and p38 MAP kinase (p38). In conclusion, our findings indicate that OGE suppressed the cell viability of A549 cells, which may result from the activation of apoptotic signaling and the inhibition of anti-apoptotic signaling, suggesting that OGE might be beneficial to lung carcinoma treatment