Performance Evaluation of WAP and Internet Protocols over W-CDMA Networks

This paper compares the performance of WAP 1.x to that of Internet protocols. We implement a WAP client and a WAP gateway based on the WAP version 1.1 and assess the overall response time to compare it to those of HTTP and TCP. We use a W-CDMA emulator to evaluate WAP 1.x performance in high-speed wireless networks such as 3G. The results show that all protocols have comparable performance (i.e., response time) except when transmitting large content sets (e.g., multimedia data files), in which case HTTP/TCP offers better performance than WAP 1.x. We also evaluate WAP specific functions such as the binary encoding of WAP headers and WML contents. While binary encoding is effective for small content sets, its effectiveness and performance are questionable for large content sets. Based on the results of our evaluation, we conclude that standard Internet protocols (i.e., HTTP/TCP) are suitable for high-speed wireless networks such as 3G.     

Fast VMM-based overlay networking for bridging the cloud and high performance computing

A collection of virtual machines (VMs) interconnected with an overlay network with a layer 2 abstraction has proven to be a powerful, unifying abstraction for adaptive distributed and parallel computing on loosely-coupled environments. It is now feasible to allow VMs hosting high performance computing (HPC) applications to seamlessly bridge distributed cloud resources and tightly-coupled supercomputing and cluster resources. However, to achieve the application performance that the tightly-coupled resources are capable of, it is important that the overlay network not introduce significant overhead relative to the native hardware, which is not the case for current user-level tools, including our own existing VNET/U system. In response, we describe the design, implementation, and evaluation of a virtual networking system that has negligible latency and bandwidth overheads in 1–10 Gbps networks. Our system, VNET/P, is directly embedded into our publicly available Palacios virtual machine monitor (VMM). VNET/P achieves native performance on 1 Gbps Ethernet networks and very high performance on 10 Gbps Ethernet networks. The NAS benchmarks generally achieve over 95 % of their native performance on both 1 and 10 Gbps. We have further demonstrated that VNET/P can operate successfully over more specialized tightly-coupled networks, such as Infiniband and Cray Gemini. Our results suggest it is feasible to extend a software-based overlay network designed for computing at wide-area scales into tightly-coupled environments.     

Protection and attachment of Vibrio cholerae mediated by the toxin-coregulated pilus in the infant mouse model

Colonization of the human small intestine by Vibrio cholerae is an essential step in pathogenesis that requires the type IV toxin-coregulated pilus (TCP). To date, three functions of TCP have been characterized: it serves as the CTXΦ receptor, secretes the colonization factor TcpF, and functions in microcolony formation by mediating bacterium-bacterium interactions. Although type IV pili in other pathogenic bacteria have been characterized as playing a major role in attachment to epithelial cells, there are very few studies to suggest that TCP acts as an attachment factor. Taking this into consideration, we investigated the function of TCP in attachment to Caco-2 cells and found that mutants lacking TCP were defective in attachment compared to the wild type. Overexpression of ToxT, the activator of TCP, significantly increased attachment of wild-type V. cholerae to Caco-2 cells. Using field-emission scanning electron microscopy (FESEM), we also observed TCP-mediated attachment to the small intestines of infected infant mice by using antibodies specific to TCP and V. cholerae. Remarkably, we also visualized matrices comprised of TCP appearing to engulf V. cholerae during infection, and we demonstrated that these matrices protected the bacteria from a component of bile, disclosing a possible new role of this pilus in protection of the bacterial cells from antimicrobial agents. This study provides new insights into TCP's function in V. cholerae colonization of the small intestine, describing additional roles in mediating attachment and protection of V. cholerae bacterial cells.     

Using ant-based agents for congestion control in ad-hoc wireless sensor networks

Ad-hoc wireless sensor networks suffer from problems of congestion, which lead to packet loss and excessive energy consumption. In this paper, we address the issue of congestion in these networks. We propose a new routing protocol for wireless sensor networks namely Ant-based Routing with Congestion Control (ARCC), which takes into account the congestion of the network at a given instant and proposes to reduce it and then finds the optimum paths between the source and the sink nodes. Simulation results show that ARCC performs better with respect to the throughput, the number of packets lost and the priority performance.     

Conformal Pad-Printing Electrically Conductive Composites onto Thermoplastic Hemispheres: Toward Sustainable Fabrication of 3-Cents Volumetric Electrically Small Antennas

Electrically small antennas (ESAs) are becoming one of the key components in the compact wireless devices for telecommunications, defence, and aerospace systems, especially for the spherical one whose geometric layout is more closely approaching Chu’s limit, thus yielding significant bandwidth improvements relative to the linear and planar counterparts. Yet broad applications of the volumetric ESAs are still hindered since the low cost fabrication has remained a tremendous challenge. Here we report a state-of-the-art technology to transfer electrically conductive composites (ECCs) from a planar mould to a volumetric thermoplastic substrate by using pad-printing technology without pattern distortion, benefit from the excellent properties of the ECCs as well as the printing-calibration method that we developed. The antenna samples prepared in this way meet the stringent requirement of an ESA (ka is as low as 0.32 and the antenna efficiency is as high as 57%), suggesting that volumetric electronic components i.e. the antennas can be produced in such a simple, green, and cost-effective way. This work can be of interest for the development of studies on green and high performance wireless communication devices.     

A simple and efficient approach for reducing TCP timeouts due to lack of duplicate acknowledgments in data center networks

The problem of TCP incast in data centers attracts a lot of attention in our research community. TCP incast is a catastrophic throughput collapse that occurs when multiple senders transmitting TCP data simultaneously to a single aggregator. Based on several experiments, researchers found that TCP timeouts are the primary cause of incast problem. Particularly, timeouts due to insufficient duplicate acknowledgments is unavoidable when at least one of the last three segments is lost from the tail of a window. As a result, this type of timeouts should be avoided to improve the goodput of TCP in data center networks. A few attempts have been made to reduce timeouts, but still the problem is not completely solved especially in the case of timeouts due to insufficient duplicate acknowledgments. In this paper, we present an efficient TCP fast retransmission approach, called TCP-EFR, which is capable to reduce TCP timeouts due to lack of duplicate acknowledgments which is caused by the loss of packets from the tail of a window in data center networks. TCP-EFR makes changes in the fast retransmission and recovery algorithm of TCP by using the congestion signal mechanism of DCTCP based on instantaneous queue length. In addition, TCP-EFR controls the sending rate for avoiding the overflow of switch buffer in order to reduce the loss of packets. The results of a series of simulations in single as well as multiple bottleneck topologies using qualnet 4.5 demonstrates that TCP-EFR can significantly reduce the timeouts due to inadequate duplicate acknowledgments and noticeably improves the performance compared to DCTCP, ICTCP and TCP in terms of goodput, accuracy and stability under various network conditions.     

Comparing the Fundamental Physics and Device Performance of Transparent,Conductive Nanostructured Networks with Conventional Transparent Conducting Oxides

Networks made of single‐walled carbon nanotubes (SWNTs) and metallic nanowire networks, graphene, and ultra‐thin metal films have all been proposed as replacements for transparent conducting oxides (TCOs) in photovoltaic and other applications. However, only limited comparisons of nanostructured networks and TCOs are available. Several common figures of merit that are often used to compare the electrical and optical performance of the transparent contacts are evaluated here, and the merits of each method of comparison are discussed. Calculating the current loss due to absorption in the TCO is the most useful metric for evaluating new materials for use in solar cells with well‐defined sheet resistance requirements and known quantum efficiencies. The ‘Haacke’ figure of merit, Φ_H, correlates fairly well with current loss and is a good metric for evaluating electro‐optical performance for more general applications. The analyses presented here demonstrate that silver nanowire networks are much closer to achieving optimal electrical and optical properties than carbon‐based networks.     

Multi-Parametric Clustering for Sensor Node Coordination in Cognitive Wireless Sensor Networks

The deployment of wireless sensor networks for healthcare applications have been motivated and driven by the increasing demand for real-time monitoring of patients in hospital and large disaster response environments. A major challenge in developing such sensor networks is the need for coordinating a large number of randomly deployed sensor nodes. In this study, we propose a multi-parametric clustering scheme designed to aid in the coordination of sensor nodes within cognitive wireless sensor networks. In the proposed scheme, sensor nodes are clustered together based on similar network behaviour across multiple network parameters, such as channel availability, interference characteristics, and topological characteristics, followed by mechanisms for forming, joining and switching clusters. Extensive performance evaluation is conducted to study the impact on important factors such as clustering overhead, cluster joining estimation error, interference probability, as well as probability of reclustering. Results show that the proposed clustering scheme can be an excellent candidate for use in large scale cognitive wireless sensor network deployments with high dynamics.     

Algorithms for energy efficient mobile object tracking in wireless sensor networks

Wireless sensor networks have found more and more applications in a variety of pervasive computing environments, in their functions as data acquisition in pervasive applications. However, how to get better performance to support data acquisition of pervasive applications over WSNs remains to be a nontrivial and challenging task. The network lifetime and application requirement are two fundamental, yet conflicting, design objectives in wireless sensor networks for tracking mobile objects. The application requirement is often correlated to the delay time within which the application can send its sensing data back to the users in tracking networks. In this paper we study the network lifetime maximization problem and the delay time minimization problem together. To make both problems tractable, we have the assumption that each sensor node keeps working since it turns on. And we formulate the network lifetime maximization problem as maximizing the number of sensor nodes who don’t turn on, and the delay time minimization problem as minimizing the routing path length, after achieving the required tracking tasks. Since we prove the problems are NP-complete and APX-complete, we propose three heuristic algorithms to solve them. And we present several experiments to show the advantages and disadvantages referring to the network lifetime and the delay time among these three algorithms on three models, random graphs, grids and hypercubes. Furthermore, we implement the distributed version of these algorithms.     

Vibrio cholerae toxin-coregulated pilus structure analyzed by hydrogen/deuterium exchange mass spectrometry

The bacterial pathogen Vibrio cholerae uses toxin-coregulated pili (TCP) to colonize the human intestine, causing the severe diarrheal disease cholera. TCP are long, thin, flexible homopolymers of the TcpA subunit that self-associate to hold cells together in microcolonies and serve as the receptor for the cholera toxin phage. To better understand TCP's roles in pathogenesis, we characterized its structure using hydrogen/deuterium exchange mass spectrometry and computational modeling. We show that the pilin subunits are held together by tight packing of the N-terminal alpha helices, but loose packing of the C-terminal globular domains leaves substantial gaps on the filament surface. These gaps expose a glycine-rich, amphipathic segment of the N-terminal alpha-helix, contradicting the consensus view that this region is buried in the filament core. Our results explain extreme filament flexibility, suggest a molecular basis for pilus-pilus interactions, and reveal a previously unrecognized therapeutic target for V. cholerae and other enteric pathogens.     

Optimizing transport protocol parameters for large scale PC cluster and its evaluation with parallel data mining

Recently, PC clusters have come to be studied intensively for large scale parallel computers of the next generation. ATM technology is a strong candidate as a de facto standard of high speed communication networks. Therefore, an ATM-connected PC cluster is a promising platform from the cost/performance point of view, as a future high performance computing environment. Data intensive applications, such as data mining and ad hoc query processing in databases, are considered very important for massively parallel processors, as well as for conventional scientific calculations. Thus, investigating the feasibility of applications on an ATM-connected PC cluster is meaningful. In this paper, an ATM-connected PC cluster consisting of 100 PCs is reported, and characteristics of a transport layer protocol for the PC cluster are evaluated. Point-to-point communication performance is measured and discussed, when a TCP window size parameter is changed. Parallel data mining is implemented and evaluated on the cluster. Retransmission caused by cell loss at the ATM switch is analyzed, and parameters of retransmission mechanism suitable for parallel processing on the large scale PC cluster are clarified. Default TCP protocol cannot provide good performance, since a lot of collisions happen during all-to-all multicasting executed on the large scale PC cluster. Using TCP parameters with the proposed optimization, performance improvement is achieved for parallel data mining on 100 PCs. This revised version was published online in July 2006 with corrections to the Cover Date.     

Dynamically forecasting network performance using the Network Weather Service

The Network Weather Service is a generalizable and extensible facility designed to provide dynamic resource performance forecasts in metacomputing environments. In this paper, we outline its design and detail the predictive performance of the forecasts it generates. While the forecasting methods are general, we focus on their ability to predict the TCP/IP end-to-end throughput and latency that is attainable by an application using systems located at different sites. Such network forecasts are needed both to support scheduling (Berman et al., 1996) and, by the metacomputing software infrastructure, to develop quality-of-service guarantees (DeFanti et al., to appear; Grimshaw et al., 1994). This revised version was published online in July 2006 with corrections to the Cover Date.     

Dynamic Max‐Min fairness in ring networks

Ring networks are enjoying renewed interest as Storage Area Networks (SANs), i.e., networks for interconnecting storage devices (e.g., disk, disk arrays and tape drives) and storage data clients. This paper addresses the problem of fairness in ring networks with spatial reuse operating under dynamic traffic scenarios. To this end, in the first part of the paper the Max-Min fairness definition is extended to dynamic traffic scenarios and an algorithm for computing Max-Min fair rates in a dynamic environment is introduced. In the second part of the paper the extended Max-Min fairness definition is used as a measure to compare the performance in dynamic conditions of three fairness algorithms proposed for ring-based SANs. These algorithms are characterized by different fairness cycle sizes (number of links involved in each instance of the fairness algorithm), i.e., different complexity. The results show that the performance increases as the fairness cycle size decreases. In particular, the Global-cycle algorithm (implemented in the Serial Storage Architecture - SSA), whose cycle size is equal to the number N of links in the ring, exhibits the lowest performance, while the One-cycle algorithm, so called because of its cycle size equal to 1, has the best performance. The Variable-cycle algorithm, whose cycle size changes between 1 and N links, performs in between and provides the best tradeoff between performance and complexity. This revised version was published online in July 2006 with corrections to the Cover Date.     

Ecoinformatics using wireless sensor networks: An overview

Wireless sensor networks have the potential to become significant subsystems of ecological experiment. Sensor networks consist of large number of tiny sensor nodes, all of which have sensing capabilities. These networks allow coordinated signal detection, monitoring, and tracking to enable sensor nodes to simultaneously capture geographically distinct measurements. Sensor nodes do not require predetermined positioning making such networks especially useful for applications in remote, inhospitable environments. In this paper we have tried to see the various ecological experimental scenarios, and how wireless sensor networks can be used in that field. One of the most challenging bottlenecks in the usage of wireless sensor networks in large scale experiments is the energy constraint. Various routing protocols which have tried to optimize the energy usage are also studied in the paper.     

Forwarding Group Multicast Protocol (FGMP) for multihop, mobile wireless networks

In this paper we propose a new multicast protocol for multihop mobile wireless networks. Instead of forming multicast trees, a group of nodes in charge of forwarding multicast packets is designated according to members' requests. Multicast is then carried out via “scoped” flooding over such a set of nodes. The forwarding group is periodically refreshed to handle topology/membership changes. Multicast using forwarding group takes advantage of wireless broadcast transmissions and reduces channel and storage overhead, thus improving the performance and scalability. The key innovation with respect to wired multicast schemes like DVMRP is the use of flags rather than upstream/downstream link state, making the protocol more robust to mobility. The dynamic reconfiguration capability makes this protocol particularly suitable for mobile networks. The performance of the proposed scheme is evaluated via simulation and is compared to that of DVMRP and global flooding. This revised version was published online in August 2006 with corrections to the Cover Date.     

Recent developments of genetically encoded optical sensors for cell biology

Optical sensors are powerful tools for live cell research as they permit to follow the location, concentration changes or activities of key cellular players such as lipids, ions and enzymes. Most of the current sensor probes are based on fluorescence which provides great spatial and temporal precision provided that high‐end microscopy is used and that the timescale of the event of interest fits the response time of the sensor. Many of the sensors developed in the past 20 years are genetically encoded. There is a diversity of designs leading to simple or sometimes complicated applications for the use in live cells. Genetically encoded sensors began to emerge after the discovery of fluorescent proteins, engineering of their improved optical properties and the manipulation of their structure through application of circular permutation. In this review, we will describe a variety of genetically encoded biosensor concepts, including those for intensiometric and ratiometric sensors based on single fluorescent proteins, Forster resonance energy transfer‐based sensors, sensors utilising bioluminescence, sensors using self‐labelling SNAP‐ and CLIP‐tags, and finally tetracysteine‐based sensors. We focus on the newer developments and discuss the current approaches and techniques for design and application. This will demonstrate the power of using optical sensors in cell biology and will help opening the field to more systematic applications in the future.     

NeuroPXI: A real-time multi-electrode array system for recording,processing and stimulation of neural networks and the control of high-resolution neural implants for rehabilitation

The increasing number of channels offered by new Microelectrode Array (MEA) systems raises the problem of data handling and analysis in real time. The goal of the RETINE project is to develop a new MEA system, called NeuroPXI, offering 256 channels with online features for MEA data recording, processing and stimulation. This system is a complete redesign of the ASIC-based BioMEA system developed previously. NeuroPXI is based on a front-end device featuring integrated electronics handling signal amplification and current-mode stimulation, and a back-end device handling real-time data processing and 2D spatiotemporal stimulus generation. Initial tests of this system have been performed on mouse spinal cord networks in which waves of activity were successfully recorded. Further tests of NeuroPXI, performed on rats, will consist first, in recording activity waves in the newborn retina and second, in patterned retinal stimulation combined with optical cortical recordings of the primary visual cortex. Such experiments have recently been conducted using the BioMEA system with standard pulse stimuli, and will be repeated with the NeuroPXI system to include more complex 2D-pattern stimuli.     

Biodiversity as insurance: from concept to measurement and application

Biological insurance theory predicts that, in a variable environment, aggregate ecosystem properties will vary less in more diverse communities because declines in the performance or abundance of some species or phenotypes will be offset, at least partly, by smoother declines or increases in others. During the past two decades, ecology has accumulated strong evidence for the stabilising effect of biodiversity on ecosystem functioning. As biological insurance is reaching the stage of a mature theory, it is critical to revisit and clarify its conceptual foundations to guide future developments, applications and measurements. In this review, we first clarify the connections between the insurance and portfolio concepts that have been used in ecology and the economic concepts that inspired them. Doing so points to gaps and mismatches between ecology and economics that could be filled profitably by new theoretical developments and new management applications. Second, we discuss some fundamental issues in biological insurance theory that have remained unnoticed so far and that emerge from some of its recent applications. In particular, we draw a clear distinction between the two effects embedded in biological insurance theory, i.e. the effects of biodiversity on the mean and variability of ecosystem properties. This distinction allows explicit consideration of trade-offs between the mean and stability of ecosystem processes and services. We also review applications of biological insurance theory in ecosystem management. Finally, we provide a synthetic conceptual framework that unifies the various approaches across disciplines, and we suggest new ways in which biological insurance theory could be extended to address new issues in ecology and ecosystem management. Exciting future challenges include linking the effects of biodiversity on ecosystem functioning and stability, incorporating multiple functions and feedbacks, developing new approaches to partition biodiversity effects across scales, extending biological insurance theory to complex interaction networks, and developing new applications to biodiversity and ecosystem management.     

Ion channels and transporters regulate nutrient absorption in health and disease

Ion channels and transporters are ubiquitously expressed on cell membrane, which involve in a plethora of physiological process such as contraction, neurotransmission, secretion and so on. Ion channels and transporters is of great importance to maintaining membrane potential homeostasis, which is essential to absorption of nutrients in gastrointestinal tract. Most of nutrients are electrogenic and require ion channels and transporters to absorb. This review summarizes the latest research on the role of ion channels and transporters in regulating nutrient uptake such as K+ channels, Ca2+ channels and ion exchangers. Revealing the mechanism of ion channels and transporters associated with nutrient uptake will be helpful to provide new methods to diagnosis and find potential targets for diseases like diabetes, inflammatory bowel diseases, etc. Even though some of study still remain ambiguous and in early stage, we believe that ion channels and transporters will be novel therapeutic targets in the future.