Showing papers by "Masayuki Murata published in 2013"

PPARγ-induced PARylation promotes local DNA demethylation by production of 5-hydroxymethylcytosine

Abstract: Recent studies have shown that DNA demethylation goes through the conversion of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC) by Tet proteins. However, it is still unclear how the target regions for demethylation are distinguished within their genomic context. Here we show that the nuclear receptor peroxisome proliferator-activated receptor-γ (PPARγ) has the ability to direct local demethylation around its binding sites, the PPAR response elements (PPREs), during adipocyte differentiation. PPARγ is a key regulator of the differentiation process that forms a PPARγ co-activator complex on PPREs and activates the expression of adipocyte-specific genes. The complex is poly(ADP-ribosyl)ated (PARylated) on PPREs, and Tet proteins catalyse the conversion of 5mC to 5hmC locally by their ability to bind to the PAR polymer, thereby inducing region-specific demethylation. Our study demonstrates that a sequence-dependent transcription factor complex can, through its post-translational modification, serve for Tet proteins as a landmark to identify sites of DNA demethylation.

Controlled and self-organized routing for large-scale wireless sensor networks

Abstract: Improving the scalability and robustness of wireless sensor networks is an important task, and much research on self-organization has been conducted toward this end. However, desired behavior is not yet guaranteed in much larger networks based on pure self-organization. In this article, we propose a controlled potential-based routing protocol implementing a novel controlled self-organization scheme that also allows for external control. The scheme obtains close-to-optimal network behavior by this external control which controls a part of nodes in the network. We show that global traffic flow can be controlled through simulation experiments with a multi-sink sensor network. For example, traffic loads can be equalized among heterogeneously distributed sink nodes, and load balancing among the relay nodes based on remaining energy can bring an approximate four times extension of network lifetime. The proposed method is furthermore robust to message loss and resilient to failure of the sink node.

Pre-treatment role of inosine triphosphate pyrophosphatase polymorphism for predicting anemia in Egyptian hepatitis C virus patients

Abstract: AIM: To investigate and clarify, for the first time, the role of inosine triphosphate pyrophosphatase (ITPA) polymorphism in Egyptian chronic hepatitis C virus (HCV) patients. METHODS:The human genomic DNA of all patients was extracted from peripheral blood cells in order to determine the single nucleotide polymorphism (SNP) of ITPA (rs1127354). SNP genotyping was performed by real time polymerase chain reaction (PCR, ABI TaqMan allelic discrimination kit) for 102 treatment-naive Egyptian patients with chronic HCV. All patients had no evidence of cardiovascular or renal diseases. They received a combination treatment of pegylated interferon α (PEG-IFNα) as a weekly subcutaneous dose plus an oral weight-adjusted dose of ribavirin (RBV). The majority received PEG-IFNα2a (70.6%) while 29.4% received PEG-IFNα2b. The planned duration of treatment was 24-48 wk according to the viral kinetics throughout the course of treatment. Pre-treatment liver biopsy was done for each patient for evaluation of fibrosis stage and liver disease activity. The basal viral load level was detected quantitatively by real time PCR while viral load throughout the treatment course was performed qualitatively by COBAS TaqMan assay. RESULTS: Ninety-three patients (91.2%) had ITPA SNP CC genotype and 9 (8.8%) had non-CC genotype (CA and AA). The percentage of hemoglobin (Hb) decline was higher for CC patients than for non-CC patients, particularly at weeks 4 and 8 (P = 0.047 and 0.034, respectively). During the first 12 wk of treatment, CC patients had significantly more Hb decline > 3 g/dL than non-CC patients: 64.5% vs 22.2% at weeks 8 and 12, respectively, (P = 0.024 and 0.038). Reduction of the amount of the planned RBV dose was significantly higher for CC patients than non-CC patients during the first 12 wk (18% ± 12.1% vs 8.5% ± 10.2%, P = 0.021). The percentage of CC patients with RBV dose reduction was significantly greater than that of non-CC patients (77.4% vs 44.4%, P = 0.044). Multivariate analysis identified only the percentage of RBV dose as a predictor for Hb decline. Platelet decline was significantly higher in non-CC patients than CC patients at weeks 12, 24 and 48 (P = 0.018, 0.009 and 0.026, respectively). CONCLUSION: Rs1127354 ITPA polymorphism plays a decisive role in protecting against treatment-induced anemia and the need for RBV dose reduction in Egyptian HCV patients.

OpenFlow-based content-centric networking architecture and router implementation

Abstract: Content-Centric Networking (CCN) is a novel architecture that has been proposed as a solution for dealing with various problems facing the Internet, such as the excessive bandwidth costs that result from peer-to-peer (P2P) traffic and content delivery networks (CDN). In order to deal with the difference between the principles of the Internet and the purposes for which it is actually used, CCN entails a change from a host-centric to content-centric architecture. However, there are deployment issues that will require a gradual approach in order to realize migration from the Internet to CCN. Additionally, the shortage of testbed environments needs to be addressed as quickly as possible. We focus on OpenFlow, which is a promising candidate to provide a programmable environment without disrupting existing networks. Specific implementations of CCN using OpenFlow have not been examined in sufficient detail, although there have been investigations into the conceptual design. This paper presents the detailed design and implementation of an OpenFlow-based CCN with the primary aim to achieve forwarding and end-to-end communication. Our approach can solve the issues in existing designs by using a map from content names to hierarchically structured hash values and the longest prefix match. We also discuss the advantage of retaining significant attributes of CCN and OpenFlow such as high-speed forwarding and network slicing which promotes deployment of CCN and research for routing, caching, and security strategies.

Crucial Roles of MicA and RybB as Vital Factors for σE-Dependent Cell Lysis in Escherichia coli Long-Term Stationary Phase

Abstract: σE-dependent cell lysis has been proposed to eliminate damaged cells in the stationary phase in Escherichia coli . In order to explore the relationship of this process to

The serum undercarboxylated osteocalcin level and the diet of a Japanese population: Results from the Kyushu and Okinawa Population Study (KOPS)

Abstract: The elevated serum undercarboxylated osteocalcin (ucOC) level is related to osteoporosis. In Japan, vitamin K intake is lower, and the incidence of hip fractures noticeably higher in northern Kyushu than in other areas. The study was done to determine the serum ucOC levels in a Japanese population and its association with diet and glucose metabolism. The data of 3,658 healthy adults aged 40-69 (1,373 men and 2,285 women) who lived in northern Kyushu area were analyzed. The data included anthropometric measurements and a self-reported personal interview on daily intake of foods. The serum ucOC level of each participant was measured by electrochemiluminescence immunoassay. Glycohemoglobin A1c (HbA1c), fasting plasma glucose, and serum insulin concentrations were measured. The median serum ucOC level of the women (4.65 ng/mL) was significantly higher than that of the men (3.04 ng/mL) (P = 0.0021). The age-specific ucOC levels of the men decreased significantly with age. In contrast, the ucOC levels of the women aged ≥50 were elevated, but the levels varied markedly within the other age groups. For both men and women, multivariate analysis identified a daily diet rich in vitamin K and HbA1c level as independently having a significant, negative relationship to serum ucOC level. Our study indicates that the serum ucOC decreases with age in men, increases postmenopausally in women, and correlates inversely with dietary consumption of certain foods and with fasting glucose and HbA1c level.

A population-based epidemiological survey of human parvovirus B19 infection: A project of the Kyushu and Okinawa Population Study (KOPS)

Abstract: Human parvovirus B19 infection occurs by droplet nuclei through the respiratory tract and causes a wide range of diseases. It can be transmitted through blood transfusion from asymptomatic blood donors. This study was done to investigate the parvovirus B19 infection rate of a group of healthy Japanese residents. Of 2,081 blood samples tested, 15 (0.72 %) were positive for parvovirus B19 IgM, 1,412 (67.9 %) for B19 virus IgG, and 4 (0.2 %) for parvovirus B19 DNA. About half of all women of childbearing age were susceptible to parvovirus B19 infection. No relationship was found between the frequency of symptoms and the prevalence of parvovirus B19 IgG and IgM, suggesting that there are asymptomatic carriers in the healthy Japanese population. There is a risk of parvovirus B19 infection by blood transfusion from asymptomatic donors and that pregnant women are at high risk for parvovirus B19 infection.

Energy efficient data caching for content dissemination networks

Abstract: As various multimedia services are being provided on networks, broadband traffic is growing as well Reducing traffic is important because power consumption in networks has been increasing year by year Meanwhile, in-network caching for CCN Content-Centric Networking is expected to achieve an adaptive content delivery in the network and to reduce traffic by storing content data on each router Therefore, in-network caching is beneficial in view of energy efficiency However, in order to improve energy efficiency of the network, it is necessary to cache content appropriately in consideration of both power consumption of content caching and transmission of traffic In this paper, we propose a design method which derives the most energy efficient cache locations of content and a distributed cache mechanism for CCN to search for energy efficient cache locations Furthermore, we demonstrate the effectiveness of the proposed method

Traffic prediction for dynamic traffic engineering considering traffic variation

Abstract: Traffic engineering with traffic prediction is one approach to accommodate time-varying traffic without frequent route changes. In this approach, the routes are calculated so as to avoid congestion based on the predicted traffic. The accuracy of the traffic prediction however has large impacts on this approach. Especially, if the predicted traffic amount is significantly less than the actual traffic, the congestion may occur. In this paper, we propose the traffic prediction methods suitable to the traffic engineering. In our method, we perform preprocessing before the prediction in order to predict the periodical variation accurately. Moreover, we consider the confidence interval for the prediction error and the variation excluded by the preprocessing to avoid the congestion caused by the temporal traffic variation. In this paper, we discuss three preprocessing approaches; the trend component, the lowpass filter, and the envelope. Through simulation, we clarify that the preprocessing by the trend component or the lowpass filter increases the accuracy of the prediction. In addition, considering the confidence interval achieves the lower link utilization within a fixed control period.

Energy-Aware Cache Management for Content-Centric Networking

Abstract: In-network caching for CCN (Content-Centric Networking)is expected to achieve an adaptive content delivery in the network and to reduce traffic by storing content data on each router. Reducing traffic is also important because power consumption in networks has been increasing yearly year. Therefore, in-network caching is beneficial in view of energy-efficiency. However, in order to improve energy efficiency of the network, it is necessary to cache content appropriately in consideration of both power consumption of content caching and transmission of traffic. Moreover for a distributed cache framework such as CCN, content caching should be autonomously controlled by distributed cache nodes. In this paper, we propose a distributed cache management mechanism to control energy-efficient cache locations of content. Furthermore, we demonstrate the effectiveness of the proposed mechanism by simulations.

Experimental demonstration of adaptive virtual network topology control mechanism based on SDTN architecture

Abstract: We designed and developed the first proto-type system of adaptive virtual network topology control based on an SDTN architecture for robust network virtualization. Dynamic resource optimization among multiple virtual networks based on measured traffic was successfully demonstrated on testbed network.

Towards early deployable Content-Centric Networking enhanced by using IPv6

Abstract: Content-Centric Networking (CCN) is promising as a future communication paradigm to exchange contents without specifying address of nodes. However, deployment of CCN from clean-slate would take a long time since all routing facilities are needed to be replaced. For early deployment of CCN it is feasible to use the current Internet infrastructure as much as possible, and achieve minimum modifications of applications and/or end nodes. Based on such background we propose a novel approach which enables to deploy CCN rapidly with extremely small modifications compared to other approaches. Our solution is based on the use of IPv6 network as a lower layer routing scheme. To realize we design some important components such as Name Mapper and Address Mapper. We also discuss about a deployment scenario for early adaptation of CCN in IPv6 networks.

Association between chronic hepatitis C virus infection and high levels of circulating N-terminal pro-brain natriuretic peptide

Abstract: The association between HCV infection and myocardial disorders remains unclear. This study aimed to assess whether or not HCV infection influences myocardial dysfunction by the use of NT-proBNP, a sensitive marker of myocardial dysfunction. A total of 198 participants [99 patients with chronic HCV infection (aged 46-68 years) and 99 anti-HCV-negative sex and age matched controls] were examined. Serum HCV-RNA level and HCV genotype were tested and liver biopsy was done only for the patient group. The NT-proBNP concentration of the HCV patients (mean 71.6 ± 79.1 pg/ml; median 46.0 pg/ml, range 5.0-400.0) was significantly higher than that of the controls (mean 39.8 ± 24.4 pg/ml; median 35.8 pg/ml, range 7.0-108.0) (P < 0.05). 20.0 % of the HCV patients and 0.6 % of the controls had high NT-proBNP (higher than 125 pg/ml; the single cut off point for patients under 75 years of age) (P < 0.05). Stepwise multiple regression analysis revealed that chronic HCV infection was independently correlated with NT-proBNP level after adjustment for parameters that might influence NT-proBNP (P = 0.005). Our data suggest that chronic HCV infection is associated with increased NT-proBNP, indicating that chronic HCV infection might induce myocardial dysfunction.

Maximum entropy based randomized routing in data-centric networks

Abstract: Recently, there are increasing efforts to define new protocols and architectures for data-centric networking that do not rely on the addresses of the individual network nodes. In that case, queries are usually disseminated by flooding throughout the network until the node with the requested content is found. However, flooding always imposes an additional burden on the network since many unnecessary requests are circulated, particularly in the case of energy-constrained systems. In this paper, we examine the feasibility of a more lightweight search method by using a random walk in the network and investigate the possibility of a better load balancing through a maximum entropy random walk. We perform simulation studies and analyze the performance compared to the general random walk and flooding mechanisms in terms of search time and energy per query. We conclude that under suitable topologies the maximum entropy random walk is a viable alternative to flooding.

A Low-Cost, Distributed and Conflict-Aware Measurement Method for Overlay Network Services Utilizing Local Information Exchange

Abstract: Measuring network resource information, including available bandwidth, propagation delay, and packet loss ratio, is an important task for efficient operation of overlay network services. Although measurement accuracy can be enhanced by frequent measurements, performing measurements with high frequency can cause measurement conflict problem that increases the network load and degrades measurement accuracy. In this paper, we propose a low-cost, distributed and conflict-aware measurement method that reduces measurement conflicts while maintaining high measurement accuracy. The main idea is that the overlay node exchanges the route information and the measurement results with its neighboring overlay nodes while decreasing the measurement frequency. This means our method trades the overhead of conducting measurements for the overhead of information exchange to enhance measurement accuracy. Simulation results show that the relative error in the measurement results of our method can be decreased by half compared with the existing method when the total measurement overheads of both methods are equal. We also confirm that exchanging measurement results contributes more to the enhancement of measurement accuracy than performing measurements. key words: overlay networks, network measurement, measurement conflict, distributed measurement method, information exchange

Potential-based routing for supporting robust any-to-any communication in wireless sensor networks

Abstract: In most applications, wireless sensor networks are supposed to operate in an unattended manner for a long period after sensor nodes’ deployment. However, in such networks, sensor nodes frequently become faulty and unreliable because of the harsh environment of the observed area. Therefore, protocols used in wireless sensor networks must be designed to be robust. Moreover, because the battery capacity of a node is limited, energy savings are crucial in wireless sensor networks. To meet the requirements of future diverse wireless sensor networks, a sophisticated any-to-any routing protocol is thus required. As well as meeting the typical demands of wireless sensor networks, an any-to-any routing protocol needs to achieve low energy consumption, high scalability, robustness, and reliability. In this paper, we realize a potential-based any-to-any routing protocol (PBAR) by merging potential-based upstream and downstream routing. In PBAR, sensor nodes can send data to a certain sensor node by routing the data via a sink node. In simulation experiments, we show that, given a suitable node density, PBAR attains a data delivery ratio greater than 99.7%. We also show that the data delivery ratio recovers immediately after failure of 30% of sensor nodes or failure of a sink node.

SCTP Tunneling: Flow Aggregation and Burst Transmission to Save Energy for Multiple TCP Flows over a WLAN

Abstract: SUMMARY To raise the energy efficiency of wireless clients, it is important to sleep in idle periods. When multiple network applications are running concurrently on a single wireless client, packets of each application are sent and received independently, but multiplexed at MAC-level. This uncoordinated behavior makes it difficult to control of sleep timing. In addition, frequent state transitions between active and sleep modes consume non-negligible energy. In this paper, we propose a transport-layer approach that resolves this problem and so reduces energy consumed by multiple TCP flows on a wireless LAN (WLAN) client. The proposed method, called SCTP tunneling, has two key features: flow aggregation and burst transmission. It aggregates multiple TCP flows into a single SCTP association between a wireless client and an access point to control packet transmission and reception timing. Furthermore, to improve the sleep efficiency, SCTP tunneling reduces the number of state transitions by handling multiple packets in a bursty fashion. In this study, we construct a mathematical model of the energy consumed by SCTP tunneling to assess its energy efficiency. Through numerical examples, we show that the proposed method can reduce energy consumption by up to 69%.

Virtual topology control with multistate neural associative memories

Abstract: Previously, a highly adaptive virtual network topology (VNT) reconfiguration method called Attractor Selection Based (ASB) topology control was presented. ASB has an important drawback: it can only work with binary path tables. We propose a novel VNT controller by adding multistate path capabilities into ASB. However, adding multistate path capabilities reduces topology exploration space. We solve this problem by changing the system dynamics of ASB. With the modification of the system dynamics and the extension from binary to multistate paths, we observed a 60% performance improvement over ASB, and a 21% reduction in processing time in the simulations.

Proactive recovery from multiple failures utilizing overlay networking technique

Abstract: In this paper, we propose a proactive recovery method against multiple network failures for large-scale packet switching networks. The proposed method exploits the overlay networking technique. Specifically, it constructs multiple logical network topologies from the original overlay network topology by assuming various failure patterns. When a failure is detected, our method selects one topology. Consequently, it can immediately recover from the failure by utilizing the selected topology without waiting for routing convergence in the network. When constructing multiple logical topologies, we take into account the correlation among overlay links in terms of the underlay links. Through the numerical evaluation results of the network reachability and average path length, we show that our method improves network reachability from 51% to 95% while keeping the path length short, when 25% underlay links are simultaneously down.

Noise-assisted concurrent multipath traffic distribution in ad hoc networks.

Abstract: The concept of biologically inspired networking has been introduced to tackle unpredictable and unstable situations in computer networks, especially in wireless ad hoc networks where network conditions are continuously changing, resulting in the need of robustness and adaptability of control methods. Unfortunately, existing methods often rely heavily on the detailed knowledge of each network component and the preconfigured, that is, fine-tuned, parameters. In this paper, we utilize a new concept, called attractor perturbation (AP), which enables controlling the network performance using only end-to-end information. Based on AP, we propose a concurrent multipath traffic distribution method, which aims at lowering the average end-to-end delay by only adjusting the transmission rate on each path. We demonstrate through simulations that, by utilizing the attractor perturbation relationship, the proposed method achieves a lower average end-to-end delay compared to other methods which do not take fluctuations into account.

Valuable antiviral therapeutic options for the treatment of chronic hepatitis C patients with thrombocytopenia.

Abstract: Summary Thrombocytopenia in patients with chronic hepatitis C may represent an obstacle for the initiation of antiviral treatment. The aim of this study was to evaluate factors predictive of successful pegylated interferon (PEG-IFN) α2b and ribavirin (RBV) treatment for patients with thrombocytopenia with no history of splenectomy or partial splenic embolization. One hundred and fifty-one chronic hepatitis C patients (genotype 1: n = 110, genotype 2: n = 41) with TCP (<100 × 109/L) at baseline were enrolled. Pretreatment variables included interleukin 28B (IL28B) genotype (rs8099917) and homoeostasis model assessment of insulin resistance score (HOMA-IR). The kinetics of haemoglobin and platelets according to the inosine triphosphatase (ITPA) genotype (rs1127354) were investigated. Sustained virological response (SVR) was significantly more frequent in hepatitis C virus (HCV) genotype 2 (65.9%) than in genotype 1 (34.5%) patients (P < 0.0001). Multiple logistic regression analysis of HCV genotype 1 extracted IL28B TT genotype [odds ratio (OR) 5.97, P = 0.006] and HOMA-IR <2.5 (OR 7.14, P = 0.0016) as significant independent pretreatment predictors of SVR. The analyses of HCV genotype 2 showed that HOMA-IR was significantly related to SVR, but IL28B genotype was not. Patients with ITPA CC genotype showed a significant haemoglobin reduction and lower degree of platelets decrease than those with ITPA CA/AA genotypes. The most common reason for premature discontinuation of treatment was the development of hepatocellular carcinoma (n = 8, 5.3%). In conclusion, HOMA-IR is a useful predictor of SVR for patients with thrombocytopenia infected with HCV genotype 1 or 2 treated with PEG-IFNα2b and RBV. The inclusion of IL28B, ITPA genotypes and HOMA-IR adds valuable therapeutic information.

Staleness verification of caching data in ICN

Abstract: ICN can be considered as a largely distributed caching architecture which requires a mechanism to verify staleness of data objects at caching points. However, this staleness issue has rarely been addressed in ICN literature previously. This paper discusses this issue and proposes staleness verification algorithms for ICN, named ICN PER and ICN_CB which provide a strong consistency and coherence of caching data object. Intensive simulations were carried out to demonstrate the behaviors of the algorithms. The results demonstrate that ICN_CB improves cache hit probability around 20% higher than ICN_PER, which reduces user side delay and network resource usage. In addition, ICN CB is a superior choice when a network involves with high data communication cost such as wireless networks.

A case report of human immunodeficiency virus-associated anaplastic lymphoma kinase protein-negative anaplastic large cell lymphoma

Abstract: Human immunodeficiency virus (HIV)-associated anaplastic large cell lymphoma (ALCL) is not so common, and anaplastic lymphoma kinase protein (ALK)-negative ALCL is rare and has a low survival rate. We report a case of a 31-year-old Japanese man diagnosed with HIV-associated ALK-negative ALCL who presented with long-lasting fever of unknown origin. The diagnosis was based on a full work-up that included inguinal lymph-node biopsy. Eight-cycle chemotherapy that included cyclophosphamide, doxorubicin, vincristine, and prednisone in addition to antiretroviral therapy for HIV infection provided a complete remission of his ALCL and over 5-year survival for him.

Adaptability of virtual network topology control based on attractor selection against multiple node failures

Abstract: We propose a virtual network topology (VNT) control method that is adaptive to environmental changes in a network. It is based on attractor selection, which models the biological systems that behave adaptively against changes in their surrounding environments. The simulation results indicate that our VNT control method adaptively responds to changes in network environments caused by node failure and constructs operational VNTs in more than 95% of simulation trials when 20% of nodes in the physical network fail simultaneously.

Computing path blocking probability and delay in optical networks with retrial

Abstract: Hybrid optical architectures combining path and packet switching can be good candidates for future optical networks because they exploit the best of both worlds. However, the optimization of some parameters of the hybrid switch by some metrics is vital to maximize the benefit of the hybrid architecture. Blocking rate and reservation delay are two of the most important performance metrics in the path switching layer of the hybrid architecture. In this paper, we propose an analytical method with an improved backward blocking analysis to compute both blocking rates and reservation delays in path switching optical WDM networks with destination-initiated reservation allowing retrial of failed reservation attempts. On a mesh topology, we show that the results of our analytical method and simulations were close to each other, while the analytical method was several orders of magnitude faster than the simulation, which may allow much faster performance analysis, design, and optimization of hybrid networks.

Green, smart optical packet switching network with flow control for data centers

Abstract: Hybrid optoelectronic packet routers with 100Gbps (25Gbps × 4 wavelengths) links are introduced in an intra-DC network. A novel “Express path” enables the flow control to reduce the latency and the power consumption.