bluuebunny/crossref_metadata_2025 huggingface dataset:
NS2 Extension for Multi-Channel MAC Simulation Model
Authors: Geng-Yu Wei , Hua Wang , Xiao-Xiao Li , Liu-Tong Xu
Published: January 2009

In order to improve network performance of delay and throughput, an increasing number of networks begin to support multi-channel communications. Although Network Simulator 2 (NS2) has been the dominant network simulation tool, it does not provide native support for multi-channel simulation. Existing works on extending NS2, such as Hyacinth's and Ramon's contributions, show apparent limitations for usage. This paper proposes a novel extension of NS2, named Multi-channel MAC Simulation Model (MMSM), which defines the facilities for multi-channel MAC protocol simulation.

This paper describes the initiative, simulation model architecture of MMSM. Based on extensions of NS2 MobileNode architecture, MMSM has features of flexibility of configuration and transparency to the upper layer. MMSM defines one MAC entity associated with a number of NetIF (Network Interface) entities and each NetIF adhered to one channel. So the mobile node has the ability to send and receive packets simultaneously through multiple channels to or from different adjoining nodes. Thus MMSM provides strong support for simulating newly designed multi-channel MAC protocols such as MAC over Multiple Input Multiple Output (MIMO) or MIMO-like mechanisms. MMSM not only makes the specific simulation available, but also keeps the upper layer facilities unchanged as usual when implementing multi-channel simulation.

The paper also describes the implementation of MMSM in NS2 (version 2.29). Modifications are carried out both on TCL and on C++ codes. In TCL level ns-mobilenode.tcl and ns-lib.tcl are modified to assemble the multi-channel components and to make TCL scripts to support multi-channel configuration. In C++ level mac.{h,cc}, mobilenode.{h,cc} and channel.{h,cc} are modified to add the channel selection algorithm and to manage the multi-channel node lists. Based on modifications of NS2 described above, researchers can implement their multi-channel MAC protocols conveniently.

To validate the implementation of MMSM, two existing MAC protocols in NS-2.29, the Mac802_11 and Tdma, are extended to have the capability of multi-channel processing. Two typical scenarios are chosen to run the simulation on both the multi-channel and the single channel. Simulation results show that the network throughput of multi-channel MAC is enhanced over the single channel MAC, and therefore it proves the multi-channel capability of MMSM.
ePet: A Physical Game Based on Wireless Sensor Networks
Authors: Tan Wei-Hua , Li Wen-Jun , Zheng Yao-Zhan , Zhou Xiao-Cong
Published: January 2009

This paper describes ePet, a novel multi-player physical game based on the WSN (Wireless Sensor Network). ePet shifts the traditional virtual pet games to the real world, featuring with the popular RPG (Role-Playing Game) elements. The game, capitalizing on the wireless communication, mobile computing, and sensing ability, can be played both indoors and outdoors, and thus gives players a new exciting gaming experience that profits by the blend of real and virtual game elements.

The physical game acquires physical interactions among players, which can bring exciting and novel features to the game and more importantly, avoids some problems caused by traditional computer games such as health problems. The WSN is a promising technology for developing physical games. Although there is already some research and applications of WSN based physical games, the major advantages of the WSN (e.g. wireless communication, mobile computing, and sensing ability) are not fully cultivated in these gaming applications.

ePet, which takes good advantages of both the WSN and traditional computer games, simulates a pet both indoors and outdoors. The pet has two life modes: Peaceful Life Mode (PLM) and Aggressive Life Mode (ALM). In the PLM, ePet simulates the physiological activities of a real pet such as hunger and easily getting flu when it is cold in the real world. Moreover, the pet can date with other pets to increase its physiological values. In the ALM, the pet is a character of an RPG controlled by the player and the pet can have a fight with other pets, from which the pet gains experience for level up. This ALM is similar to the computer RPG games but relatively novel in WSN based games. All of the above features are enabled by the WSN technology. For the two life modes, a friend-making protocol and an RPG battle protocol are designed respectively. The architecture design and implementation of ePet are described in detailed. Unlike traditional WSN based games, ePet does not need a centralized base station to organize the network. To implement a self-adaptive wireless sensor network in which each node has a similar functionality, and solve the network conflict problems in the WSN communications, a multi-hop communication routing protocol is designed for ePet. Furthermore, a PC application was developed as the game interface, from which players can check out the ePet's properties and interact with ePet. It makes ePet more attractive than traditional WSN based games without losing WSN's advantages.
An Efficient Semantic-Based Search Schema in Unstructured P2P Network
Authors: Sun Xin , Chao Zhao , Liu Yushu , Zhang Lei
Published: January 2009

How to efficiently organize and manage distributed resources is a critical issue of P2P systems. In this paper, we focus on both the P2P search mechanism and the topology structure of overlay network which are the key factors to dominate the performance of resource search and discovery.

We mostly concern these issues as follows: Heterogeneity of nodes in P2P networks. Topology match between the P2P overlay network and the underlying physical network. In general, most peers that hold similar shared resources have similar requirements.

We consider all the factors mentioned above, and propose a semantic-based and locality-aware hybrid P2P architecture (SLHP) including the method of model construction and maintenance and the multi-root mechanism to avoid the single point failure. SLHP considers the physical locality and the semantic similarity of the shared resource at the same time, in which nodes are clustered into domains according to the physical distance, and the nodes in a domain are clustered into groups according to the similar shared resource. The physical distance is measured by the RTT value of two peers. The calculation method of semantic similarity is also given.

And then a semantic-based search schema is proposed. When the search occurs, the query is forwarded to super peers, and among super peers the query is forwarded to the neighbors who have the most similar shared resource with the query keyword. We also give a proof that according to the algorithm of construction and maintenance of SLHP, it is ensured that the existed resource must be found in theory. The semantic-based search can reduce the number of the transferred messages comparing with the standard flooding scheme, since it only produces k messages each hop, and forward to the most expected peers. Along with the routing indices being optimized continuously, which represents the knowledge of nodes about the entire overlay network, the hit ratio can be improved.

Finally, in order to evaluate the performance of semantic-based search schema, three sets of simulations are set up to evaluate the key features of the network topology and semantic-based search algorithm. Experimental results show that the semantic-based search schema can reduce the search space, and get a good tradeoff between the performance and the overhead.
Improving Cluster-Based Peer-to-Peer Systems
Authors: Gong Yadong , Lin Xiaola
Published: January 2009

To make P2P (Peer-to-Peer) logical overlay network match the physical topology, cluster-based P2P systems have been proposed. In such systems, nodes maintain two types of links: local link and remote link. Node uses local links to cluster nodes with short network distance and the remote link to build connections with some remote nodes according to certain rules. When a query is generated, it is first processed in local cluster (intra-cluster query) based on local links, and if it fails, it will be selectively relayed to other clusters (inter-cluster query) based on remote links. Because the number of nodes and the distance between nodes in local clusters are small compared to the entire P2P network, intra-cluster query processes can get high efficiency just using some simple search methods such as Flooding or Random Walk. Nevertheless, the dynamic character of nodes and decentralized distribution of resources in the systems make the nodes in one cluster difficult to maintain up-to-date resource distribution information in other clusters. Thus, the efficiency of inter-cluster query is limited.

In P2P systems, stable nodes have much longer online time, so they have a longer time to let other nodes download resources from them. Also, maintaining resource distribution of stable nodes can cause much less traffic, incurred by the dynamic nature of nodes, than dynamic nodes. Based on the above analysis, we propose the Differentiated Publishing (DiffPublishing) architecture by letting resources of stable nodes serve queries in large areas and having resources of dynamic nodes answer queries in local clusters. In the proposed system, the resources of the stable nodes are indexed by a decentralized topology: service provider overlay. When a query is generated, it is first processed in the local cluster, and if it fails, it will be forwarded to the service provider overlay.

Because most resources in P2P systems are provided by a small portion of super nodes that tend to be stable, a high query success rate can be achieved in the service provider overlay. Also, maintaining resource indices of stable nodes can save much traffic caused by the dynamic nature of nodes, so the maintenance cost in service provider overlay is not expensive. Search traffic in the proposed system is dramatically reduced due to the shrunken search scope. More importantly, the proposed DiffPublishing architecture can be easily deployed in existing cluster-based P2P systems to improve their inter-cluster query processes.
Dynamic Coverage Based on Neural Gas Learning Algorithm for Wireless Sensor Network
Authors: Sun Yanjing , Qian Jiansheng , Li Li
Published: January 2009

With the rapid development of microelectro mechanical systems (MEMS), wireless communications, and information networking and integrated circuits technologies, wireless sensor network technology came into being. For the monitoring of large areas or dangerous region or enemy region, commonly used, such as randomly dropping the sensor nodes, and coverage is one of the main problems to solve for the WSN. Control of the coverage for WSN, can be seen as when the energy of sensor network nodes, wireless communications network bandwidth, network computing ability are limited, through placing the sensor nodes and choosing routing at the network and other means to optimize the allocation of resources of WSN, avoid blind spots in the coverage area, or get in a local minimum value.

Covering algorithm needs to consider network connectivity, energy efficiency, dynamics of the network, and other issues. According to the configuration of wireless sensor nodes, coverage is divided into certainty coverage and random coverage. In the actual environment, network topology is unpredictable, and network topology changes complexly, so it seems particularly important to achieve a dynamic coverage. It is a NP problem to achieve optimal coverage for monitoring the area of unfixed and intensive signals, so we made an effective distributed approximation algorithm to ensure that the sensor nodes change rapidly to achieve optimal coverage. Assuming each sensor node can directly communicate with other nearby sensors, have the same sensing range, and have data-processing functions, and move free according to the “order” of the nodes surrounding. Assume that each sensor can know its position, and the positioning algorithm has been adopted.

Using a neural network algorithm can solve the nodal redistribution problem of WSN according to the detected region changes. In the artificial neural network, the learning algorithm can be divided into erection and growth structure learning algorithm. Growth learning algorithm starts training from a small network structure, then gradually increases until it achieves the final request. We choose the GNG algorithm, and the improved GNG-U algorithm which is improved on the basis of the GNG algorithm. To the nonstationary input signal, if the distribution suddenly changes, using the algorithm can quickly delete unused nodes, effect nodes will unite together fast, and redistribution, reduce redundant nodes finally reach optimal coverage rapidly.

Combine the improved GNG-U algorithm with wireless sensor network, the network can rapidly re-coverage the target region especially for special environments. The simulation results show that, compared with the growing neural gas algorithm, the GNG-U and improve GNG-U algorithm can reduce redundant nodes, improve mobility of the network, accelerate the rate of convergence, and arrive at the optimal re-coverage dynamically.
A Markov Prediction Model Based on Page Hierarchical Clustering
Authors: Yao Yao , Shi Lei , Wang Zhanhong
Published: January 2009

The Markov prediction model is the basis of Web prefetching and personalized recommendation. It can be used to extract connotative Web link hierarchy. The visualized site structure can not only help users understand the relationships between the pages they have visited, but also suggest where they can go next. But the existence of a large amount of Web objects results in data redundancy and model hugeness. Therefore, how to mine and improve the link structure of a website has become a chief problem and it has positive meanings for prefetching.

This paper presents an improved method that simplifies the topology structure of a website and extracted the conceptual link hierarchy which can make the organization clearly and legibly. First, the Markov Tree is constructed for the reason that a more capable mechanism for representing past activity in a form usable for prediction is a Markov Tree. In this case the Markov chain model can be defined as a three-tuple (A, S, P), where A is the collection of operation, S is the state space consisting of all the states in a link structure, and P is the one-step transition probability matrix. The transition probability matrix is calculated based on the Markov tree. Second, an algorithm is given to extract the hierarchical tree from the above matrix. The website link hierarchy (WLH) is obtained accordingly. A WLH only contains a trunk link which is a hyperlink from a page on a higher conceptual level to a page on its adjacent lower conceptual level. With the levels increment, there must be more and more pages in each level. It may blur the structure of the website. In order to tackle the problem, a clustering algorithm is proposed to cluster conceptually-related pages on same levels based on their in-link and out-link similarities, which are measured by the concept of weighted Euclidean distance. After the pages in WLH have been clustered, WLC can be constructed. Finally, the simplified model will be used for Web page prediction. Three parameters, i.e. precision, recall, and PRS have been employed to measure the performance in the experiments. Experiments based on two real Web log data demonstrate the efficiency of the proposed method, which can not only have good overall performance and clustering effect but also keep the relative higher prediction accuracy and recall.
Performance Analysis for Large-Scale Parallel Microscopic Traffic Simulation System
Authors: Fei Yin , Dongliang Zhang
Published: January 2009

PMTS (Parallel Microscopic Traffic Simulation) is a large-scale microscopic traffic network simulation system using a real traffic network of Shanghai, China. It describes traffic events in object oriented mode, uses MPI (Message Passing Interface) as communicate middleware, partitions the simulation traffic network into subnetworks, and runs simulations of subnetworks concurrently on a cluster of processors connected by high-speed Ethernet. To optimize the performance of PMTS, a number of challenges need to be solved, including traffic network partition, subnetworks communication and synchronization, and workload balance.

The parallelization of PMTS is domain decomposition, which means that the geographical region for simulation is decomposed into several domains of similar size and each processor of the PC cluster is responsible for a different geographical area. The partition method needs to fulfill two conditions to make it efficient: minimize the communication overhead and partition the subnetworks of the equal computation load. The goals of maximizing the parallelization and minimizing the communication overhead is conflict, and the tradeoff should be made.

PVTM simulates the vehicles activities on the traffic network, and the computation overhead for one vehicle is certain. The time overhead on one processor depends on the number of vehicles for simulation. The individual simulation of vehicle activity includes: vehicle generation, vehicle running, and the vehicle going through the boundary zone. The derivation of the predictive performance is demonstrated and the calculation of the time cost for one processor with a certain number of vehicles is provided.

In order to be efficient, the load on different processors should be as similar as possible. The load depends on the actual vehicle number on the respective processor that also varies as the simulation run. In each time step, the workload is collected for each processor. For the next iteration, the information will be fed back to the load-balancer, which will move the boundary of the grid to balance the vehicle numbers among the domains.

The performance metrics of the simulation system mainly depend on the load balance, scalability, speedup, and efficiency. The performance optimization of PMTS has been proved to be effective when it is put into use and the experiment results are also provided which match the analysis.
A New Heuristic Metatask Scheduling Algorithm Based on Choosing QoS Policy Mechanism
Authors: Hou Yong , Wo Xur , Zhao Hong , Zhao Wei
Published: January 2009

More and more applications of grid have been achieved. How to support Quality of Service (QoS) to meet different users' demand has raised an outstanding challenge. Currently, several QoS policies of resource have been widely used in Grid. Thus, how to use them freely and efficiently is a serious problem. In this study, we illustrated three QoS policies of resources: best effort, real time, and competing, and explain their mechanisms. Following this, we proposed a new QoS policy, namely Free QoS policy, to help the user who is not very familiar with QoS polices. The first step is that we can get the matrix of QoS parameters of each resource from the Policy Pool in which all the information about QoS policies of resources in “virtual organizations” could be obtained. Second, we will calculate every resource's P adjugment value by a comparison algorithm. Finally, the QoS policy matching the maximum value of P adjugment value is the user's decision. After choosing a suitable resource with a clear QoS policy, the next question is how to achieve an optimum quality under the given policy, which is the problem of scheduling. Min_Min algorithm has been widely used as a higher efficiency and simple algorithm. However, it has a serious problem: load unbalance. In order to solve the problem, we propose a novel task scheduling algorithm, called the Heuristic task scheduling algorithm based on Min-Min and Max-Min (H-MM) in the best effort of the QoS policy, which is merged with the high efficiency of the traditional Min-Min scheduling algorithm and the load balance of the traditional Max-Min scheduling algorithm. Through plenty of experiments, we know that the performance of Max-Min is better than that of Min-Min in the condition that the values of ETC are not uniform, and the performance of Min-Min is a priority to Max-Min when there are many tasks in which the value of ETC are uniform. In this paper, we take the relative standard deviation value of ETC matrix's Min_Time as the criterion to judge whether the set of tasks is uniform or not. Finally, the scheduler selects the Max-Min or Min-Min to assign tasks. The experiments have shown that the H-MM algorithm overweighs traditional algorithms a lot in the makespan and the scalability of the scheduling algorithm.
Nodes Deployment Mechanism Based on Energy Efficiency in Wireless Sensor Networks
Authors: Zhang Rui-Hua , Jia Zhi-Ping , Xu Xin-Shun
Published: January 2009

In wireless sensor networks, devices are required to self-organize themselves into a network without previously established infrastructure. Because the device is battery-powered, one of the most important design criteria for this type of network is energy efficiency. Based on two linear traffic models and an extension of energy model of the radio, we consider different multi-hop scenarios to compute the energy and energy efficiency of the whole network. Through analyzing these results, we present two valid deployment mechanisms for sensor nodes.

The first deployment mechanism is that nodes are deployed with equidistant spacing. Under this topology, we compute energy per payload bit, energy efficiency, and the total energy consumed by individual nodes, and the whole network. Simulation results show that a single-hop strategy is more efficient than a multi-hop one, especially for low path loss exponents, when the total distance is less than the feasible range of the radio. The receive and startup energy overhead, in addition to the energy drain increase at nodes close to the sink, makes multi-hop an inefficient technique. If overheads can be reduced with new transceiver technologies, multi-hop becomes more attractive.

We derive the optimum value for one-hop spacing for the first mechanism, and present the formula to calculate the optimal value with the different application parameters. It is independent of the physical network topology, the number of transmission sources, and the total transmission distance. It only depends on the propagation environment and the device parameters. This mechanism can minimize the energy consumption of the whole network.

The first deployment mechanism can achieve minimized energy consumption for the multi-hop scenario where each node transmits a data frame to the sink. However, it brings up a question of energy consumption disproportion between nodes. It is because those nodes close to the sink will relay larger amounts of data packets and their energy consumption will be more. In my intuition, node spacing is chosen shorter to consume less energy for the node closer to the sink. This strategy can balance energy consumption between nodes. So another deployment mechanism is that nodes are deployed with optimal spacing. We present the formula to calculate the optimal spacing. This mechanism can balance every node's energy consumption, thus prolonging the whole network's lifetime. Simulation results show that two deployment mechanisms are good and useful with energy efficiency in wireless sensor networks.
Actin filament dynamics are dominated by rapid growth and severing activity in the Arabidopsis cortical array
Authors: Staiger Christopher J. , Sheahan Michael B. , Khurana Parul , Wang Xia , McCurdy David W. , Blanchoin Laurent
Published: January 2009

Metazoan cells harness the power of actin dynamics to create cytoskeletal arrays that stimulate protrusions and drive intracellular organelle movements. In plant cells, the actin cytoskeleton is understood to participate in cell elongation; however, a detailed description and molecular mechanism(s) underpinning filament nucleation, growth, and turnover are lacking. Here, we use variable-angle epifluorescence microscopy (VAEM) to examine the organization and dynamics of the cortical cytoskeleton in growing and nongrowing epidermal cells. One population of filaments in the cortical array, which most likely represent single actin filaments, is randomly oriented and highly dynamic. These filaments grow at rates of 1.7 µm/s, but are generally short-lived. Instead of depolymerization at their ends, actin filaments are disassembled by severing activity. Remodeling of the cortical actin array also features filament buckling and straightening events. These observations indicate a mechanism inconsistent with treadmilling. Instead, cortical actin filament dynamics resemble the stochastic dynamics of an in vitro biomimetic system for actin assembly.
Benchmarks for identification of ordinary differential equations from time series data
Authors: Gennemark Peter , Wedelin Dag
Published: January 2009

Motivation: In recent years, the biological literature has seen a significant increase of reported methods for identifying both structure and parameters of ordinary differential equations (ODEs) from time series data. A natural way to evaluate the performance of such methods is to try them on a sufficient number of realistic test cases. However, weak practices in specifying identification problems and lack of commonly accepted benchmark problems makes it difficult to evaluate and compare different methods.

Results: To enable better evaluation and comparisons between different methods, we propose how to specify identification problems as optimization problems with a model space of allowed reactions (e.g. reaction kinetics like Michaelis–Menten or S-systems), ranges for the parameters, time series data and an error function. We also define a file format for such problems.

We then present a collection of more than 40 benchmark problems for ODE model identification of cellular systems. The collection includes realistic problems of different levels of difficulty w.r.t. size and quality of data. We consider both problems with simulated data from known systems, and problems with real data. Finally, we present results based on our identification algorithm for all benchmark problems. In comparison with publications on which we have based some of the benchmark problems, our approach allows all problems to be solved without the use of supercomputing.

Availability: The benchmark problems are available at www.odeidentification.org

Contact:  peterg@chalmers.se

Supplementary information:  Supplementary data are available at Bioinformatics online.
The DICS repository: module-assisted analysis of disease-related gene lists
Authors: Dietmann Sabine , Georgii Elisabeth , Antonov Alexey , Tsuda Koji , Mewes Hans-Werner
Published: January 2009

Summary: The DICS database is a dynamic web repository of computationally predicted functional modules from the human protein–protein interaction network. It provides references to the CORUM, DrugBank, KEGG and Reactome pathway databases. DICS can be accessed for retrieving sets of overlapping modules and protein complexes that are significantly enriched in a gene list, thereby providing valuable information about the functional context.

Availability: Supplementary information on datasets and methods is available on the web server http://mips.gsf.de/proj/dics

Contact:  sabine.dietmann@googlemail.com
Growth Abnormalities Persist in Newly Diagnosed Children With Crohn Disease Despite Current Treatment Paradigms
Authors: Pfefferkorn Marian , Burke Georgine , Griffiths Anne , Markowitz James , Rosh Joel , Mack David , Otley Anthony , Kugathasan Subra , Evans Jonathan , Bousvaros Athos , Moyer M Susan , Wyllie Robert , Oliva‐Hemker Maria , Carvalho Ryan , Crandall Wallace , Keljo David , Walters TD , LeLeiko Neal , Hyams Jeffrey
Published: January 2009

Objectives:

We analyzed growth outcomes in children newly diagnosed with Crohn disease and determined whether growth abnormalities persist despite current therapies.

Patients and Methods:

Clinical and growth data were prospectively obtained on an inception cohort younger than 16 years old at diagnosis and Tanner I to III during the study.

Results:

In all, 176 children (mean age 10.1 years; 65% male) with mild (33%) or moderate/severe (67%) disease at diagnosis were studied. Disease activity at 1 year was inactive/mild (89%) or moderate/severe (11%). First‐year treatments included immunomodulators (60%), corticosteroids (77%), 5‐aminosalicylates (61%), infliximab (15%), and enteral nutrition (10%). By 2 years, 86% had received immunomodulators and 36% infliximab. Mean height z scores at diagnosis, 1 year, and 2 years were −0.49 ± 1.2 standard deviations (SDs), −0.50 ± 1.2, and −0.46 ± 1.1, respectively. Of the subjects, 10%, 8%, and 6.5% had height z scores less than −2 SD at diagnosis, 1 year, and 2 years. A height velocity z score less than −1SD was seen in 45% of subjects at 1 year and 38% at 2 years. The mean height velocity z score, however, increased between 1 and 2 years from −0.71 to 0.26 (P < 0.03). Corticosteroid use greater than 6 months in the first year was associated with abnormal height velocity at 1 year (adjusted odds ratio = 4.5; 95% confidence interval [CI] = 2.2–9.6). No statistically significant effect on height velocity z scores was noted when comparing those receiving or not receiving infliximab.

Conclusions:

Growth delay persists in many children with CD following diagnosis, despite improved disease activity and the frequent use of immunomodulators and biologics. Additional strategies to improve growth outcomes require development.
High‐Titer Antibody to Hepatitis B Surface Antigen Before Liver Transplantation Can Prevent De Novo Hepatitis B Infection
Authors: Su Wei‐Ju , Ho Ming‐Chih , Ni Yen‐Hsuan , Chen Huey‐Ling , Hu Rey‐Heng , Wu Yao‐Ming , Chang Mei‐Hwei , Lee Po‐Huang
Published: January 2009

Objective:

De novo hepatitis B virus (HBV) infection is defined as infection occurring in HBV surface antigen (HBsAg)–negative patients who become HbsAg positive after organ transplantation. We assessed the incidence and risk factors of de novo HBV infection in pediatric liver transplant recipients.

Patients and Methods:

From 1996 to 2006, 71 Taiwanese children with non‐HBV‐related liver diseases underwent orthotopic liver transplantation (OLT) at the National Taiwan University Hospital. All of the surviving recipients were tested regularly for liver function, serum levels of immunosuppressant, HBsAg, titers of antibodies to hepatitis B surface antigen (anti‐HBs), antibodies to hepatitis B core antigen (anti‐HBc), and antibodies to hepatitis C virus (anti‐HCV). HBV vaccination histories and the anti‐HBs titers before OLT were recorded. No regular prophylaxis was given.

Results:

Fifty‐nine patients (33 girls and 26 boys) were followed up for a median of 4.4 years (range 1.0–10.0). Of those, 36 (61.0%) received allografts from anti‐HBc‐positive and HBsAg‐negative donors. De novo HBV infection was found in 9 (15.3%) patients after OLT, 8 of whom received allografts from HBsAg‐negative and anti‐HBc‐positive donors. Forty‐eight (81.4%) patients received 3 or more doses of HBV vaccine before OLT. Pre‐OLT anti‐HBs titers were available for 49 recipients. Of the 9 de novo HBV‐infected recipients, 8 had anti‐HBs titers <200 mIU/mL. No graft loss or fulminant hepatitis was noted.

Conclusions:

In the absence of adequate prophylaxis, the incidence of de novo HBV infection in pediatric OLT recipients is 15.3%. An anti‐HBs titer of >200 mIU/mL before OLT may be sufficient to prevent de novo HBV infection in HBsAg‐negative recipients.
Secondary Malnutrition and Overweight in a Pediatric Referral Hospital: Associated Factors
Authors: Macías‐Rosales Rocío , Vásquez‐Garibay Edgar M , Larrosa‐Haro Alfredo , Rojo‐Chávez Marina , Bernal‐Virgen Alicia , Romo‐Rubio Hugo
Published: January 2009

Objectives:

To establish the prevalence and identify the clinical and sociodemographic factors associated with malnutrition and overweight in a pediatric referral hospital.

Patients and Methods:

We studied a cross‐sectional, random sample from a pediatric hospital. Malnutrition was defined as acute when the z score of weight/height was less than −2.0 and as chronic if in addition the height/age z score was less than −2.0. Overweight risk was defined as a body mass index percentile between 85 and 94, and overweight as a body mass index percentile of 95 or higher.

Results:

The study included 641 patients, with mean age 7.1 ± 4.9 years (56% male). The overall prevalence of acute malnutrition was 8% and chronic malnutrition 17.0%. Overweight risk was present in 15.4% and overweight in 12.2%. Acute malnutrition was predicted by conditions on admission (hospitalization: odds ratio [OR] 2.3, confidence interval [CI] 1.3–4.3; nonsurgical subspecialty: OR 2.1, CI 1.0–4.3) and number of siblings (1 child, single mother: OR 2.6, CI 1.3–5.0). Chronic malnutrition was predicted by age (infants vs preschoolers: OR 2.0, CI 1.1–3.6; infants vs school children: OR 3.1, CI 1.8–5.5) and illness duration (>30 days: OR 2, CI 1.1–3.7). Overweight risk was associated with age (>36 months: OR 2.0, CI 1.6–3.4) and the father's educational level (college and university: OR 2.3, CI 1.3–4.3). Overweight was predicted by sex (boys: OR 2.0, CI 1.0–3.6) and age (>36 months: OR 1.7, CI 1.0–2.8).

Conclusions:

Overweight was as prevalent as malnutrition. Malnutrition was associated with clinical condition, age, family size, and illness duration, whereas overweight was related to age, sex, and father's education. Overweight appears as a novel finding in the nutritional profile of pediatric referral hospitals in Mexico.
Human papillomaviruses: a growing field: Figure 1.
Authors: Galloway Denise A.
Published: January 2009

A combination of functional studies on human papillomavirus (HPV) oncoproteins and epidemiological studies on persistence of HPV infection firmly established a role for HPV in the etiology of cervical cancers. Understanding the viral life cycle of HPVs has been more difficult. In this issue of Genes & Development, Wang et al. (pp. 181 – 194) describe an efficient method to propagate infectious HPV in differentiating epithelium, providing clear evidence for temporal separation of viral and cellular replication.
Temporal Global Expression Data Reveal Known and Novel Salicylate-Impacted Processes and Regulators Mediating Powdery Mildew Growth and Reproduction on Arabidopsis
Authors: Chandran Divya , Tai Yu Chuan , Hather Gregory , Dewdney Julia , Denoux Carine , Burgess Diane G. , Ausubel Frederick M. , Speed Terence P. , Wildermuth Mary C.
Published: January 2009

Salicylic acid (SA) is a critical mediator of plant innate immunity. It plays an important role in limiting the growth and reproduction of the virulent powdery mildew (PM) Golovinomyces orontii on Arabidopsis (Arabidopsis thaliana). To investigate this later phase of the PM interaction and the role played by SA, we performed replicated global expression profiling for wild-type and SA biosynthetic mutant isochorismate synthase1 (ics1) Arabidopsis from 0 to 7 d after infection. We found that ICS1-impacted genes constitute 3.8% of profiled genes, with known molecular markers of Arabidopsis defense ranked very highly by the multivariate empirical Bayes statistic (T  2 statistic). Functional analyses of T  2-selected genes identified statistically significant PM-impacted processes, including photosynthesis, cell wall modification, and alkaloid metabolism, that are ICS1 independent. ICS1-impacted processes include redox, vacuolar transport/secretion, and signaling. Our data also support a role for ICS1 (SA) in iron and calcium homeostasis and identify components of SA cross talk with other phytohormones. Through our analysis, 39 novel PM-impacted transcriptional regulators were identified. Insertion mutants in one of these regulators, PUX2 (for plant ubiquitin regulatory X domain-containing protein 2), results in significantly reduced reproduction of the PM in a cell death-independent manner. Although little is known about PUX2, PUX1 acts as a negative regulator of Arabidopsis CDC48, an essential AAA-ATPase chaperone that mediates diverse cellular activities, including homotypic fusion of endoplasmic reticulum and Golgi membranes, endoplasmic reticulum-associated protein degradation, cell cycle progression, and apoptosis. Future work will elucidate the functional role of the novel regulator PUX2 in PM resistance.
In vivo synthesis of meganuclease for generating transgenic zebrafish Danio rerio
Authors: Babaryka A. , Kühn E. , Köster R. W.
Published: January 2009

The authors show that co‐injection at the one‐cell stage of mRNA encoding a nuclear‐targeted meganuclease I‐SceI together with expression cassettes flanked by cognate restriction sites results in efficient stable transgenesis in zebrafish Danio rerio.
Population structure in a common Caribbean coral‐reef fish: implications for larval dispersal and early life‐history traits
Authors: Purcell J. F. H. , Cowen R. K. , Hughes C. R. , Williams D. A.
Published: January 2009

Genetic population structure throughout the Caribbean Basin for one of the most common and widespread reef fish species, the bicolour damselfishStegastes partituswas examined using microsatellite DNA markers. Spatial autocorrelation analysis showed a significant positive correlation between genetic and geographic distance (isolation by distance) over distances <1000 km, suggesting that populations are connected genetically but probably not demographically,i.e.over shorter time scales. A difference in spatial patterns of populations in the easternv.the western Caribbean also raises the probability of an important role for meso‐scale oceanographic features and landscape complexity within the same species. A comparison ofS. partituspopulation structure and life‐history traits with those of two other species of Caribbean reef fish studied earlier showed the findings to be concordant with a common hypothesis that shorter pelagic larval dispersal periods are associated with smaller larval dispersal scales.
A set of 37 microsatellite DNA markers for genetic diversity and structure analysis of Atlantic salmon Salmo salar populations
Authors: Nikolic N. , Fève K. , Chevalet C. , Høyheim B. , Riquet J.
Published: January 2009

Atlantic salmon Salmo salar microsatellite markers from a large database were analysed and selected with technical, economic and genetic criteria to provide an optimized set of polymorphic DNA markers for the analysis of the genetic diversity and the structure of anadromous Atlantic salmon populations. A set of 37 microsatellite markers was identified that are easy to use and provide a high level of differentiation power.
Genetic structure of Melanotaenia australis at local and regional scales in the east Kimberley, Western Australia
Authors: Phillips R. D. , Storey A. W. , Johnson M. S.
Published: January 2009

The Kimberley region of Western Australia possesses a poorly studied freshwater fish fauna with high endemism in an aquatic landscape subject to monsoonal floods and dry season isolation. In the first population genetic study of freshwater fish in this region, the authors tested the effects of geographic barriers on genetic structure at multiple spatial scales in east Kimberley populations of the western rainbowfish, Melanotaenia australis, the most widespread and abundant species in the region. Based on allozyme comparisons, hierarchical analysis of FST revealed increasing genetic subdivision with spatial scale. Minimal genetic structure within creeklines demonstrated that wet season dispersal, rather than dry season isolation, determines genetic structure at small scales. At the scale of sub‐catchments, a pattern of isolation by distance along creeklines was evident. Genetic subdivision between adjacent river systems was greater between rivers separated by a plateau than by lowlands. This implies greater connectivity of populations in lowland areas and may explain the greater similarity of the east Kimberly freshwater fish fauna with lowlands to the east than with the more rugged regions to the west. Similarly, greater connectivity between lowland populations may account for the on‐average larger distribution of lowland Melanotaeniids.
Expanding the frequency spectrum in marine CSEM applications
Authors: Dell’Aversana Paolo , Vivier Michel
Published: January 2009

In this paper we show how marine controlled source electromagnetic data interpretation can be improved if the data are acquired with an expanded frequency spectrum. Especially in the case of targets located at a wide range of depths, both high‐ and low‐frequency data can provide useful information for improving the risk analysis associated with different prospects with variable size and depth. We discuss an application to a real data set acquired in deep water offshore Nigeria using two values of fundamental frequency: 0.05 Hz and 0.25 Hz. Both frequencies, together with higher frequency harmonics, have been used for multi‐frequency and multi‐dimensional modelling and inversion with excellent results.

At the end of the interpretation work, areas with different electric and magnetic anomalies were mapped and quantitatively interpreted in terms of resistivity distribution in the 3D space. Relatively high‐frequency data (0.25 Hz and the first two harmonics) were useful for constraining the shallowest part of the resistivity models, including the presence of thin resistive layers, such as the gas sand recognized in correspondence of the well previously drilled in the NW portion of the block.

Low‐frequency data (0.05 Hz) were useful for constraining the deepest portion of the models (from 2 km to 4 km below sea floor) and for characterizing the resistivity of the background.

From an exploration point of view, the whole workflow based on multi‐frequency data analysis of this electromagnetic data set was very useful for further de‐risking the different prospects previously individuated in the area using seismic information.
Decreased expression of the active subunit of the cystine/glutamate antiporter xCT is associated with loss of heterozygosity of 1p in oligodendroglial tumours WHO grade II
Authors: Stockhammer Florian , Von Deimling Andreas , Van Landeghem Frank K H
Published: January 2009

Aims:  Oligodendroglial tumours with loss of heterozygosity on 1p (LOH1p) respond better to treatment than oligodendrogliomas without LOH. Previous reports have assigned a crucial role of glutamate metabolism to glioma growth and invasion. The aim was to study the protein expression of different glutamate transporters in relation to LOH1p in low‐grade oligodendroglial tumours.

Methods and results:  Seventeen oligodendrogliomas World Health Organization (WHO) grade II, 16 oligoastrocytomas WHO grade II and seven astrocytomas WHO grade II were examined. Eleven oligodendrogliomas and five oligoastrocytomas exhibited LOH1p. Immunoreactivity scores (IRS) for glutamate transporters excitatory amino acid transporter (EAAT)‐1, ‐2 and ‐3 as well as the active cystine/glutamate antiporter subunit xCT were semiquantitatively rated by percentage of positive cells and intensity of immunoreactivity. Reactivity for xCT was lower in tumours with LOH1p than in those without (P = 0.03, Mann–Whitney U‐test). No association was found between LOH status and IRS for EAAT‐1, ‐2 or ‐3. High xCT immunoreactivity was associated with high expression of EAAT‐1, ‐2 or ‐3.

Conclusions:  Expression of xCT is significantly reduced in low‐grade oligodendroglial tumours harbouring LOH1p. Further studies should investigate a potential beneficial effect by inhibiting xCT in low‐grade gliomas.
The History of British Gynaecological Pathology
Authors: Young Robert H
Published: January 2009

The venerable tradition of British gynaecological pathology is honoured by brief comments on those who have pioneered work in this arena, using as the starting point the remarkable Scottish physician Dr Matthew Baillie who, with his uncles, the legendary William and John Hunter, can arguably be considered the founders of medicine in Great Britain. The impact of Baillie’s great work ‘The Morbid Anatomy of Some of the Most Important Parts of the Human Body’ is noted. Because of the fame they achieved in working in other areas, the contributions to gynaecological pathology of Thomas Hodgkin and Richard Bright, particularly the former, are often overlooked and are noted herein as is a remarkable book on the ovary by Charles G. Ritchie, published in 1865. The middle years of the 19th century were notable because of the activities of pioneering surgeons such as Sir Spencer Wells and Lawson Tait which gradually led to a greater emphasis on pathologic examination of specimens removed at operation, as opposed to autopsy evaluation. The closing years of the 19th century and early years of the 20th century were dominated by five individuals, Alban Doran, John Bland‐Sutton, Cuthbert Lockyer, Elizabeth Hurdon and John Hammond Teacher. Doran wrote an early study of tubal carcinoma and a book on that organ and the ovary. Bland‐Sutton was a remarkably influential surgeon with a significant interest in pathology and also contributed a book on the ovary and fallopian tube as well as one of the early good papers on metastatic tumours to the ovary. Lockyer wrote an outstanding book on uterine fibroids and established, and funded, a museum at Charing Cross Hospital. Hurdon can be considered the first female gynaecological pathologist. She spent much of her active career in the United States working at Johns Hopkins Hospital. She co‐authored a monumental book on the appendix, likely never to be equalled. Teacher worked in Glasgow for many years and was almost single‐handedly responsible for the acceptance in Britain of the concepts of trophoblastic disease espoused by the German investigator Felix Marchand. Wallace Park of Dundee also contributed significantly on trophoblastic disease in later years. The years following the death of Dr Teacher were largely dominated by three individuals, Magnus Haines working in London, Claud Taylor in Birmingham, and Frederick Langley in Manchester. The first two individuals wrote an excellent textbook and Langley brought great fame to the Manchester School, ably assisted by Harold Fox, the latter being the doyen of British gynaecologic pathologists throughout the latter decades of the 20th century. With Langley he wrote an important book on ovarian tumours, an equally influential book on the placenta, and with Dr Hilary Buckley he authored a book on endometrial biopsy interpretation. Additionally, his countless entertaining and instructive lectures throughout the world represented a remarkable educational experience.