Showing papers by "Masayuki Murata published in 2004"

Activation of mammalian unfolded protein response is compatible with the quality control system operating in the endoplasmic reticulum

Abstract: Newly synthesized secretory and transmembrane proteins are folded and assembled in the endoplasmic reticulum (ER) where an efficient quality control system operates so that only correctly folded molecules are allowed to move along the secretory pathway. The productive folding process in the ER has been thought to be supported by the unfolded protein response (UPR), which is activated by the accumulation of unfolded proteins in the ER. However, a dilemma has emerged; activation of ATF6, a key regulator of mammalian UPR, requires intracellular transport from the ER to the Golgi apparatus. This suggests that unfolded proteins might be leaked from the ER together with ATF6 in response to ER stress, exhibiting proteotoxicity in the secretory pathway. We show here that ATF6 and correctly folded proteins are transported to the Golgi apparatus via the same route and by the same mechanism under conditions of ER stress, whereas unfolded proteins are retained in the ER. Thus, activation of the UPR is compatible with the quality control in the ER and the ER possesses a remarkable ability to select proteins to be transported in mammalian cells in marked contrast to yeast cells, which actively utilize intracellular traffic to deal with unfolded proteins accumulated in the ER.

Selective CD27+ (memory) B cell reduction and characteristic B cell alteration in drug-naive and HAART-treated HIV type 1-infected patients.

Abstract: To investigate HIV-1-related B cell disorders, the quantity of CD27 positive (CD27+) B cells and their CD38, CD95, and bcl-2 intensities were examined by flow cytometry analysis in 16 drug-naive patients, 27 highly active antiretroviral therapy (HAART)-treated patients, and 20 uninfected controls. CD27+ B cells have been recognized as memory B cells. The mean percentage of CD27+ B cells was significantly lower in drug-naive patients (11.9%) and in HAART-treated patients (16.1%) than in controls (31.4%) (p < 0.01). The intensities of CD38 and CD95 on CD27+ B cells were higher in drug-naive patients than in controls (p < 0.01 in CD95). The intensity of CD95 on CD27+ B cells in HAART-treated patients was lower than that of drug-naive patients, but significantly higher than that of controls (p < 0.01). The intensity of bcl-2 on CD27+ B cells was equivalent among the three groups. These findings suggest that disturbance of peripheral B cell composition, exemplified by CD27+ B cell reduction, exists in both drug-naive and HAART-treated HIV-1-infected patients. In addition, the augmented apoptotic state of CD27+ B cells found in HAART-treated patients with undetectable viral loads, indicated by CD95 elevation, suggests that some HIV-1-related B cell disorders last for years after effective antiviral therapy.

Cdc2 kinase-dependent disassembly of endoplasmic reticulum (ER) exit sites inhibits ER-to-Golgi vesicular transport during mitosis

Abstract: We observed the disassembly of endoplasmic reticulum (ER) exit sites (ERES) by confocal microscopy during mitosis in Chinese hamster ovary (CHO) cells by using Yip1A fused to green fluorescence pro...

Detecting distributed denial-of-service attacks by analyzing TCP SYN packets statistically

Abstract: Distributed denial-of-service attacks on public servers have recently become more serious. More are SYN flood attacks, since the malicious attackers can easily exploit the TCP specification to generate traffic making public servers unavailable. To assure that network services will not be interrupted, we need faster and more accurate defense mechanisms against malicious traffic, especially SYN floods. One of the problems in detecting SYN flood traffic is that server nodes or firewalls cannot distinguish the SYN packets of normal TCP connections from those of SYN flood attack. Moreover, since the rate of normal network traffic may vary, we cannot use an explicit threshold of SYN arrival rates to detect SYN flood traffic. In this paper we introduce a mechanism for detecting SYN flood traffic more accurately by taking into consideration the the time variation of arrival traffic. We first investigate the statistics of the arrival rates of both normal TCP SYN packets and SYN flood attack packets. We then describe our new detection mechanism based on the statistics of SYN arrival rates. Our analytical results show that the arrival rate of normal TCP SYN packets can be modeled by a normal distribution and that our proposed mechanism can detect SYN flood traffic quickly and accurately regardless of time variance of the traffic.

IPv6 anycast for simple and effective service-oriented communications

Abstract: Although anycast communication supports service-oriented addresses, many of its current definitions in IPv6 are unclear Furthermore, since there are no protocol standards or even a consensus on controlling routing, intersegment anycast communications are not yet available In this article we first review IPv6-based anycast communication At present, there are several possible applications that are suited to this We then raise several problems and provide possible solutions to these Based on this background, we present the Anycast Address Resolving Protocol (AARP) to establish TCP connections with a specific anycast address, and then propose a routing protocol for intersegment anycasts Our proposed architecture makes anycast addressesmore useful without (or with at most minimal) need for modifications/extensions to existing applications and/or upper-layer protocols

Increased frequency of CD27- (naive) B cells and their phenotypic alteration in HIV type 1-infected patients.

Abstract: To investigate HIV-1-related B cell disorders, the quantity of peripheral CD27 negative (CD27-) B cells, their CD38, CD95, and bcl-2 intensities, and their apoptosis susceptibility were examined by flow cytometry analysis in 16 drug-naive patients, 27 HAART-treated patients, and 20 uninfected controls. CD27- B cells have been recognized as naive B cells. The mean percentage of CD27- B cells was significantly higher in drugnaive patients (88.1%) and in HAART-treated patients (83.9%) than in controls (68.6%) (p < 0.01). The intensities of CD38 and CD95 on CD27- B cells were significantly higher in drug-naive patients than in controls (p < 0.01). The intensity of CD95 on CD27- B cells in HAART-treated patients was lower than that of drug-naive patients, but significantly higher than that of controls (p < 0.01). The intensity of bcl-2 on CD27- B cells in drug-naive patients was lower than that of controls. In drug-naive patients, CD27-B cells with high CD38 expression represented low bcl-2 expression. The CD2...

Implementation and evaluation of cooperative proxy caching mechanisms for video streaming services

Abstract: The proxy mechanism widely used in WWW systems offers low-delay and scalable delivery of data by means of a "proxy server" By applying proxy mechanism to video streaming systems, high-quality and low-delay video distribution can be accomplished without imposing extra load on the system We have proposed proxy caching mechanisms to accomplish the high-quality and highly-interactive video streaming services In our proposed mechanisms, proxies communicate with each other, retrieve a missing video data from an appropriate server by taking into account transfer delay and offerable quality In addition, the quality of cached video data can be adapted appropriately in the proxy to cope with the client-to-client heterogeneity, in terms of the available bandwidth, end-system performance, and user preferences on the perceived video quality In this paper, to verify the practicality of our mechanisms, we implemented them on a real system for MPEG-4 video streaming services, and conducted experiments Through evaluations, it was shown that our proxy caching system can provide users with a continuous and high-quality video distribution in accordance with network condition

Scalable ant-based routing algorithm for ad-hoc networks.

Abstract: Ants-based routing algorithms have attracted the attention of researchers because they are more robust, reliable, and scalable than other conventional routing algorithms. Since they do not involve extra message exchanges to maintain paths when network topology changes, they are suitable for mobile ad-hoc networks where nodes move dynamically and topology changes frequently. As the number of nodes increases, however, the number of ants (i.e., mobile agents or control messages) also increases and it reduces the scalability of algorithms. In this paper, we propose a scalable ant-based routing algorithm that makes the overhead low while keeping paths short. Our algorithm uses a multistep TTL (Time To Live) scheme, an effective message migration scheme, and an efficient scheme for updating the probability of packet forwarding. Simulation experiments have confirmed that our proposed algorithm can establish shorter paths than the conventional ant-based algorithm with the same signaling overhead.

Performance improvement of TCP over an ad hoc network

Abstract: FRN (flexible radio network) is an ad hoc network product that can realize a wide-area data collection network. This paper discusses a performance improvement method when TCP is applied to the transport layer in FRN. It is shown that even when the terminal is not moving as in FRN, the throughput can be improved in radio link failure due to noise or obstacles by combining ELFN (explicit link failure notification), which is proposed as a method for TCP performance improvement in ad hoc networks, with routing information. The proposed method is evaluated by simulation in this paper. A further objective is to reduce the performance degradation due to packet collision. The delayed ACK and the ACK retransmission with priority in the case of packet collisions are analyzed and the effectiveness of the method is demonstrated. © 2004 Wiley Periodicals, Inc. Electron Comm Jpn Pt 1, 87(11): 99–107, 2004; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/ecja.10134

Scalable and Robust Scheme for Data Gathering in Sensor Networks

Abstract: In wireless sensor networks, hundreds or thousands of microsensors are deployed in an uncontrolled way to monitor and gather information of environments. Sensor nodes have limited power, computational capacities, memory, and communication capability. In this paper, we propose a novel scheme for data gathering where sensor information periodically propagates without any centralized control from the edge of a sensor network to a base station as the propagation forms a concentric circle. By observing the radio signals emitted by sensor nodes in its vicinity, a sensor node independently determines the cycle and the timing at which it emits sensor information in synchrony. For this purpose, we adopt a pulse-coupled oscillator model based on biological mutual synchronization such as that used by flashing fireflies, chirping crickets, and pacemaker cells. Through simulation experiments, we confirmed that our scheme can gather sensor information in a fully-distributed, self-organizing, robust, adaptable, scalable, and energy-efficient manner.

Improvement of TCP Throughput by Combination of Data and ACK Packets in Ad Hoc Networks

Abstract: SUMMARY Since a radio channel is shared among terminals in an ad hoc network, packet collisions are frequent. In case of transmitting packets especially using TCP, data and ACK packets are transmitted in opposite directions on the same radio channel. Therefore, frequent collisions are unavoidable, and this seriously degrades TCP throughput. It is possible to transmit to two or more nodes which adjoin from a certain node simultaneously on the radio channel. To reduce the likelihood of packet collisions when an intermediate node transmits both data and ACK packets, these two types of packet can be combined and transmitted at the same time to increase the efficiency of radio channel utilization. In this paper, we propose a new technique to improve TCP performance by combining data and ACK packets. Our proposed technique is applicable to generic ad hoc networks easily. By means of a simulation using networks with various topologies, we have found that throughput can be improved by up to 60% by applying our proposed technique.

Downregulation of CXCR5 in CD27- B cells of HIV-1 infected patients.

Abstract: The CD27− (naive) B cells of HIV-1 infected patients have been shown to be increased in frequency and to be activated, as indicated by high CD38 expression on the cell surface. CXCR5, a B cell chemokine receptor, is expressed on circulating CD27− (naive) B cells and plays a pivotal role in peripheral B cell development. To investigate the effect of HIV-1 infection on the expression of this chemokine receptor on naive B cells, the expression level of CXCR5 on CD27− B cells was examined in 19 drug-naive HIV-1 infected patients, 27 HAART-treated patients, and 20 controls. CXCR5 expression on CD27− B cells was significantly lower in drug-naive patients than in HAART-treated patients and controls (P < 0.01). CD27− B cells with high CD38 expression exhibited low CXCR5 expression. The CXCR5 expression level on CD27− B cells recovered to within the normal range after effective antiretroviral therapy. These findings suggested that HIV-1 infection induces a remarkable phenotypic alteration of naive B cells and that the activated naive B cells found in HIV-1 infection downregulate CXCR5 on their surface. Impaired homing of naive B cells may contribute to HIV-1 induced immunological deficiencies. J. Med. Virol. 73:362–367, 2004. © 2004 Wiley-Liss, Inc.

Media Streaming on P2P Networks with Bio-inspired Cache Replacement Algorithm

Abstract: With the growth of computing power and the proliferation of broadband access to the Internet, the use of media streaming has become widely diffused. By using the P2P communication architecture, media streaming can be expected to smoothly react to changes in network conditions and user demands for media streams. To achieve continuous and scalable media streaming, we proposed scalable media search and retrieval methods in our previous work. However, through several simulation experiments, we have shown that an LRU (Least Recently Used) cache replacement algorithm cannot provide users with continuous media play-out for unpopular media streams. In this paper, inspired by biological systems, we propose a new algorithm that considers the balance between supply and demand for media streams. Through several simulation experiments, it has been shown that our proposed algorithm could improve the completeness of media play-out compared with LRU.

Effective methods for scalable and continuous media streaming on peer-to-peer networks

Abstract: With the growth of computing power and the proliferation of broadband access to the internet, the use of media streaming has become widely diffused. By using the peer-to-peer (P2P) communication architecture, media streaming can be expected to smoothly react to changes in network conditions and user demands for media streams. In this paper, to achieve continuous and scalable media streaming, we introduce our scalable media search and in-time retrieval methods. Through several simulation experiments, we show that our methods can accomplish continuous media play-out for popular media streams without introducing extra load on the system. However, we also show that an LRU cache replacement algorithm cannot provide users with continuous media play-out for unpopular media streams. To tackle this problem, we take inspiration from biological systems to propose a new cache replacement algorithm that considers the balance between supply and demand for media streams. We demonstrate that our proposed algorithm can improve the continuity of media play-out compared with LRU. Furthermore, we find that the proposed algorithm can adapt to changes in the popularity of various media. Copyright © 2004 AEI

Sheet with alignment film, optical anisotropic sheet, and polarizing plate

Abstract: PROBLEM TO BE SOLVED: To provide an optical anisotropic sheet such that the optical anisotropic sheet and a polarizing element can be laminated with good productivity while the slow phase axis of the optical anisotropic sheet and the axis of transmission of the polarizing element are arranged almost in parallel, and to provide a sheet with an alignment film for manufacturing it. SOLUTION: The alignment film 3 of the continuous sheet 1 with the alignment film is rubbed almost at right angles to a length direction Y-Y and liquid crystal is applied over the top surface of the sheet 1 with the alignment film, and dried and cured to form an optical function layer 5 which is aligned in the rubbing direction of the alignment film, thus manufacturing the optical anisotropic sheet 4. The slow phase axis of this optical anisotropic sheet 4 is in a direction B-B perpendicular to the length direction, so this is laminated on a continuous polarizing element merely along the lengths, so that they can be laminated having the slow phase axis and transmission axis arranged almost in parallel to each other. COPYRIGHT: (C)2006,JPO&NCIPI

Method and apparatus for rubbing

Abstract: PROBLEM TO BE SOLVED: To provide a method and apparatus for rubbing that can prevent foreign matter produced when a continuous substrate is bright into contact with a rubbing roll in rotation to perform rubbing processing from sticking on the continuous substrate and rubbing roll and also prevent the foreign matter from scattering or being deposited in the circumference. SOLUTION: The rubbing roll 6 which is brought into contact with the continuous substrate 2 which is traveling to perform the rubbing processing is covered with a dust collection box 11, which is always exhausted by an exhausting means 14. The foreign matter produced during the rubbing processing is discharged to the outside of the system without scattering out of the dust collection box to prevent the foreign matter from sticking on the continuous substrate or being deposited on peripheral devices. COPYRIGHT: (C)2005,JPO&NCIPI

Performance analysis and improvement of HighSpeed TCP with TailDrop/RED routers

Abstract: The continuing and explosive growth of the Internet has shown that current TCP mechanisms cannot achieve efficient utilization of networks with large bandwidth-delay products. To address this problem, we propose an enhanced transport-layer protocol called gHSTCP, which is based on the HighSpeed TCP proposed by S. Floyd (see RFC 3649, 2003). By monitoring the changing trend of RTT (round trip time), gHSTCP adapts to the traffic load by switching between two congestion control modes, which is shown to provide significant performance improvement against traditional TCP Reno in terms of throughput and fairness. Furthermore, it is observed that the performance of gHSTCP is limited by both TailDrop and RED/ARED routers, thus we develop a modified adaptive RED called gARED to address the problem of simultaneous packet drops among multiple flows. By adapting to the trend in variation of the average queue length, gARED performs active queue management more effectively than ARED. Simulations show that combining gHSTCP with gARED leads to achieving utilization of network bandwidth and good fairness.

Performance analysis of signaling delay for wireless cellular networks

Abstract: In wireless cellular networks, signaling traffic such as location update, paging and handoff due to the user's mobility takes a considerable portion of the total traffic load. In addition, the maximum allowable delays may be different among the signaling packets. In this paper, we present an analytical model for evaluating a total processing delay of signaling packets of wireless cellular networks, which integrates the delays of the radio channel and the processing delay at the wired portion. Through numerical examples, we show that priority processing is effective for reducing the handoff processing delays. We also evaluate the delay difference among cells according to their position within the location area, and the influence of number of terminals upon the processing delays.

Evaluation of a New Ozone Apparatus, the BOX-O3, for the Bacteriological Disinfection of Medical Waste

Abstract: The BOX-O3 is a new, alternative apparatus that uses ozone for the disinfection of biomedical waste. This study evaluated the ability of the apparatus to disinfect contaminated medical and laboratory waste that included a variety of bacterial strains. Microbiological measurement was done on laboratory waste contaminated with a variety of bacterial strains, medical waste alone, and medical waste contaminated with Bacillus subtilis collected from the infectious disease ward of Kyushu-university hospital. The strains tested for were Bacillus subtilis, Pseudornonas aeruginosa , Staphylococcus aureus, Enterococcus faeciurn, and Candida albicans. A 100 mL (5 test tubes containing 20 mL each) bacterial suspension consisting of 108 to 109 colony forming units (CFU) /mL was added to waste in a container. The mean bacterial load of the waste was measured immediately after shredding and ozone treatment. Three samples were recovered from three different places at random in the bulk ground. The samples were diluted to 1 : 10 and 1 100, then cultured at 37•Ž for 48 hr in a blood agar medium. For the measurement of primary bacterial load, shredding alone was done without the boost additive (hydrogen peroxide and acetic acid) and ozone treatment. All assays were done in triplicate. In the laboratory waste contaminated with a variety of bacterial strains, all bacterial populations were decreased by at least 4 log10 immediately after ozone treatment. The primary mean bacterial load of the untreated medical waste alone was 3.8 log10 CFU/g, and only normal flora was observed. The primary mean bacterial load of the untreated medical waste contaminated with Bacillus subtilis was lower than that of the untreated laboratory waste contaminated with Bacillus subtilis. In the medical waste contaminated with or without Bacillus subtilis, no bacterial populations were detectable immediately after ozone treatment. The BOX-O3 safely and efficiently treated infectious medical waste collected from hospital ward, indicating that the BOX-O3 is an effective alternative technology for the treatment of infectious waste and for controlling hospital infection.

On the robustness of planning methods for traffic changes in WDM networks

Abstract: Many conventional WDM network planning and/or designing schemes assume that future traffic demand is known beforehand. However, it is difficult to predict future traffic demand accurately. We develop a scheme to design a WDM network that accommodates as much traffic as possible against a variety of traffic patterns, that is, a WDM network robust against traffic uncertainties. Our basic idea is to select a node pair that is expected to be a bottleneck in the future and then to deploy network equipment so that the volume of traffic accommodated by the node pair increases. Our simulation results show that the WDM network designed with our method can accommodate more traffic demand than those designed with the existing methods at the same cost.

An evaluation of wavelength reservation protocol with delayed link state information

Abstract: Previous studies on routing and wavelength assignment algorithms assumed that the global link state information is obtained without delays. However, in distributed lightpath establishment, the probability of request blocking strongly depends on both the accuracy of the global link state information and the distributed protocol for wavelength reservation. In this paper, we evaluate how the frequency of link state information exchange affects the blocking probability in lightpath establishment. The evaluation is performed based on forward and backward reservation protocols in three network topologies. Simulation results show that while the forward reservation protocol is greatly affected by the frequency of link state information exchange and the amount of this information, the backward reservation protocol does not need as detailed information about the link state and as frequent link state exchange for routing as does the forward protocol.

ImTCP : TCP with an inline network measurement mechanism

Abstract: We introduce a new version of TCP (ImTCP: Inline Measurement TCP), which can make use of the data it transfers through a network path binding two end hosts to measure the bandwidth available in the path (inline measurement). ImTCP adjusts the transmission intervals of some data packets then utilize the arrival ACK packets to perform the measurement. ImTCP can be realized based RenoTCP by only changing the sender program. The simulation results show that the measurement mechanism does not degrade the performance of TCP’s data transmission, does not give extra effect on surrounding traffic while yielding measurement results in short intervals such as 1-4 RTTs.

PID congestion control in ATM with propagation delay

Abstract: Recently there have been many methods for rate control methods as applications of control theory. This paper considers congestion control in an ER system of ABR class in ATM as an example, and proposes a PID-type control rule under the existence of propagation delay. In the ATM switch, we predict the buffer level after time which equals the propagation delay elapsed. Based on the difference between the predicted and target values, a QoS value is calculated. It is stored in the ER field of an RM cell, and sent to each source. The connection sets the transfer rate corresponding to the extent of satisfaction and the QoS service class. We show conditions for the control parameters in order to stabilize the buffer level. © 2004 Wiley Periodicals, Inc. Electron Comm Jpn Pt 1, 87(12): 90–99, 2004; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/ecja.10071

Packet marking function of active queue management mechanism: should it be linear, concave, or convex?

Abstract: Recently, several gateway-based congestion control mechanisms have been proposed to support the end-to-end congestion control mechanism of TCP (Transmission Control Protocol). In this paper, we focus on RED (Random Early Detection), which is a promising gateway-based congestion control mechanism. RED randomly drops an arriving packet with a probability proportional to its average queue length (i.e., the number of packets in the buffer). However, it is still unclear whether the packet marking function of RED is optimal or not. In this paper, we investigate what type of packet marking function, which determines the packet marking probability from the average queue length, is suitable from the viewpoint of both steady state and transient state performances. Presenting several numerical examples, we investigate the advantages and disadvantages of three packet marking functions: linear, concave, and convex. We show that, although the average queue length in the steady state becomes larger, use of a concave function improves the transient behavior of RED and also realizes robustness against network status changes such as variation in the number of active TCP connections.

Virtual fully connected WDM network: architecture, scheduling and performance evaluation

Abstract: With the dramatic increase of bandwidth from WDM technology, packet switching has caused a bottleneck for multi-hop networks, where electronic switches cannot scale up to high capacity while optical packet switches are still immature due to lack of optical memory. This paper proposes virtual fully connected (VFC) architecture for WDM networks to provide high performance edge-to-edge all optical transportation capability. With moderate wavelength resources, VFC architecture emulates a fully connected network by transporting traffic between edge nodes without intermediate buffering, thus a single-hop network is realized and high speed packet switches are avoided, which facilitates performance guarantee and reduces network cost. A scheduling algorithm is developed for contention resolution and bandwidth allocation, which is proved to provide 100% throughput as well as bandwidth guarantee under arbitrary traffic. Simulations show that VFC network achieves good delay performance under both uniform and non-uniform load.