Search results for: multi-time delay gene network.

Authors: Ankit Agrawal, Ankush Mittal

Abstract:

A gene network gives the knowledge of the regulatory relationships among the genes. Each gene has its activators and inhibitors that regulate its expression positively and negatively respectively. Genes themselves are believed to act as activators and inhibitors of other genes. They can even activate one set of genes and inhibit another set. Identifying gene networks is one of the most crucial and challenging problems in Bioinformatics. Most work done so far either assumes that there is no time delay in gene regulation or there is a constant time delay. We here propose a Dynamic Time- Lagged Correlation Based Method (DTCBM) to learn the gene networks, which uses time-lagged correlation to find the potential gene interactions, and then uses a post-processing stage to remove false gene interactions to common parents, and finally uses dynamic correlation thresholds for each gene to construct the gene network. DTCBM finds correlation between gene expression signals shifted in time, and therefore takes into consideration the multi time delay relationships among the genes. The implementation of our method is done in MATLAB and experimental results on Saccharomyces cerevisiae gene expression data and comparison with other methods indicate that it has a better performance.

Keywords: Activators, correlation, dynamic time-lagged correlation based method, inhibitors, multi-time delay gene network.

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Authors: Hiba Hasan, Khalid Raza

Abstract:

Reverse engineering of genetic regulatory network involves the modeling of the given gene expression data into a form of the network. Computationally it is possible to have the relationships between genes, so called gene regulatory networks (GRNs), that can help to find the genomics and proteomics based diagnostic approach for any disease. In this paper, clustering based method has been used to reconstruct genetic regulatory network from time series gene expression data. Supercoiled data set from Escherichia coli has been taken to demonstrate the proposed method.

Keywords: Gene expression, gene regulatory networks (GRNs), clustering, data preprocessing, network visualization.

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Authors: P. O. Umenne, Odhiambo Marcel O.

Abstract:

A simple network model is developed in OPNET to study the performance of the Wi-Fi protocol. The model is simulated in OPNET and performance factors such as load, throughput and delay are analysed from the model. Four applications such as oracle, http, ftp and voice are applied over the Wireless LAN network to determine the throughput. The voice application utilises a considerable amount of bandwidth of up to 5Mbps, as a result the 802.11g standard of the Wi-Fi protocol was chosen which can support a data rate of up to 54Mbps. Results indicate that when the load in the Wi-Fi network is increased the queuing delay on the point-to-point links in the Wi-Fi network significantly reduces until it is comparable to that of WiMAX. In conclusion, the queuing delay of the Wi-Fi protocol for the network model simulated was about 0.00001secs comparable to WiMAX network values.

Keywords: WLAN-Wireless Local Area Network, MIMO-Multiple Input Multiple Output, Queuing delay, Throughput, AP-Access Point, IP-Internet protocol, TOS-Type of Service.

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Authors: Manoj Kumar, A.K. Verma, A. Srividya

Abstract:

Time varying network induced delays in networked control systems (NCS) are known for degrading control system-s quality of performance (QoP) and causing stability problems. In literature, a control method employing modeling of communication delays as probability distribution, proves to be a better method. This paper focuses on modeling of network induced delays as probability distribution. CAN and MIL-STD-1553B are extensively used to carry periodic control and monitoring data in networked control systems. In literature, methods to estimate only the worst-case delays for these networks are available. In this paper probabilistic network delay model for CAN and MIL-STD-1553B networks are given. A systematic method to estimate values to model parameters from network parameters is given. A method to predict network delay in next cycle based on the present network delay is presented. Effect of active network redundancy and redundancy at node level on network delay and system response-time is also analyzed.

Keywords: NCS (networked control system), delay analysis, response-time distribution, worst-case delay, CAN, MIL-STD-1553B, redundancy

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Authors: Kejun Zhuang, Zhaohui Wen

Abstract:

In this paper, a tri–neuron network model with time delay is investigated. By using the Bendixson-s criterion for high– dimensional ordinary differential equations and global Hopf bifurcation theory for functional differential equations, sufficient conditions for existence of periodic solutions when the time delay is sufficiently large are established.

Keywords: Delay, global Hopf bifurcation, neural network, periodicsolutions.

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Authors: B. S. Yew , B. L. Ong , R. B. Ahmad

Abstract:

This paper describes the performance of TCP Vegas over the wireless IPv6 network. The performance of TCP Vegas is evaluated using network simulator (ns-2). The simulation experiment investigates how packet spacing affects the network delay, network throughput and network efficiency of TCP Vegas. Moreover, we investigate how the variable FTP packet sizes affect the network performance. The result of the simulation experiment shows that as the packet spacing is implements, the network delay is reduces, network throughput and network efficiency is optimizes. As the FTP packet sizes increase, the ratio of delay per throughput decreases. From the result of experiment, we propose the appropriate packet size in transmitting file transfer protocol application using TCP Vegas with packet spacing enhancement over wireless IPv6 environment in ns-2. Additionally, we suggest the appropriate ratio in determining the appropriate RTT and buffer size in a network.

Keywords: TCP Vegas, Packet Spacing, Packet Size, Wireless IPv6, ns-2

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Authors: Mona Heydari, Ehsan Motamedian, Seyed Abbas Shojaosadati

Abstract:

Prediction of perturbations after genetic manipulation (especially gene knockout) is one of the important challenges in systems biology. In this paper, a new algorithm is introduced that integrates microarray data into the metabolic model. The algorithm was used to study the change in the cell phenotype after knockout of Gss gene in Escherichia coli BW25113. Algorithm implementation indicated that gene deletion resulted in more activation of the metabolic network. Growth yield was more and less regulating gene were identified for mutant in comparison with the wild-type strain.

Keywords: Metabolic network, gene knockout, flux balance analysis, microarray data, integration.

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Authors: Nyan Phyo Aung, Zaw Min Naing, Hla Myo Tun

Abstract:

The paper presents a PD controller for the Networked Control Systems (NCS) with delay. The major challenges in this networked control system (NCS) are the delay of the data transmission throughout the communication network. The comparative performance analysis is carried out for different delays network medium. In this paper, simulation is carried out on Ac servo motor control system using CAN Bus as communication network medium. The True Time toolbox of MATLAB is used for simulation to analyze the effect of different delays.

Keywords: NCS, Time delay, CAN Bus, True time, MATLAB.

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Authors: El Miloud Ar Reyouchi, Kamal Ghoumid, Koutaiba Ameziane, Otman El Mrabet, Slimane Mekaoui

Abstract:

In this paper we focus on the Round Trip Delay (RTD) time measurement technique which is an easy way to obtain the operating condition information in wireless network (WN). RTD measurement is affected by various parameters of wireless network. We illustrate how these RTD parameters vary (in a telemanagement application) versus distance, baud rates, number of hops, between nodes, using radio modem & router unit as a means of transmission and wireless routing.

Keywords: Wireless Network, Round Trip Delay, Radio modem, Router.

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Authors: P.S.Prakash, S.Selvan

Abstract:

Packet switched data network like Internet, which has traditionally supported throughput sensitive applications such as email and file transfer, is increasingly supporting delay-sensitive multimedia applications such as interactive video. These delaysensitive applications would often rather sacrifice some throughput for better delay. Unfortunately, the current packet switched network does not offer choices, but instead provides monolithic best-effort service to all applications. This paper evaluates Class Based Queuing (CBQ), Coordinated Earliest Deadline First (CEDF), Weighted Switch Deficit Round Robin (WSDRR) and RED-Boston scheduling schemes that is sensitive to delay bound expectations for variety of real time applications and an enhancement of WSDRR is proposed.

Keywords: QoS, Delay-sensitive, Queuing delay, Scheduling

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Authors: U. Kairov, T. Karpenyuk, E. Ramanculov, A. Zinovyev

Abstract:

The most common result of analysis of highthroughput data in molecular biology represents a global list of genes, ranked accordingly to a certain score. The score can be a measure of differential expression. Recent work proposed a new method for selecting a number of genes in a ranked gene list from microarray gene expression data such that this set forms the Optimally Functionally Enriched Network (OFTEN), formed by known physical interactions between genes or their products. Here we present calculation results of relative connectivity of genes from META-OFTEN network and tentative biological interpretation of the most reproducible signal. The relative connectivity and inbetweenness values of genes from META-OFTEN network were estimated.

Keywords: Microarray, META-OFTEN, gene network.

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Authors: R. Asokan, A. M. Natarajan

Abstract:

Mobile adhoc network (MANET) is a collection of mobile devices which form a communication network with no preexisting wiring or infrastructure. Multiple routing protocols have been developed for MANETs. As MANETs gain popularity, their need to support real time applications is growing as well. Such applications have stringent quality of service (QoS) requirements such as throughput, end-to-end delay, and energy. Due to dynamic topology and bandwidth constraint supporting QoS is a challenging task. QoS aware routing is an important building block for QoS support. The primary goal of the QoS aware protocol is to determine the path from source to destination that satisfies the QoS requirements. This paper proposes a new energy and delay aware protocol called energy and delay aware TORA (EDTORA) based on extension of Temporally Ordered Routing Protocol (TORA).Energy and delay verifications of query packet have been done in each node. Simulation results show that the proposed protocol has a higher performance than TORA in terms of network lifetime, packet delivery ratio and end-to-end delay.

Keywords: EDTORA, Mobile Adhoc Networks, QoS, Routing, TORA

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Authors: Micheal Olaolu Arowolo, Muhammad Azam, Fei He, Mihail Popescu, Dong Xu

Abstract:

As the quantity of biological articles rises, so does the number of biological route figures. Each route figure shows gene names and relationships. Manually annotating pathway diagrams is time-consuming. Advanced image understanding models could speed up curation, but they must be more precise. There is rich information in biological pathway figures. The first step to performing image understanding of these figures is to recognize gene names automatically. Classical optical character recognition methods have been employed for gene name recognition, but they are not optimized for literature mining data. This study devised a method to recognize an image bounding box of gene name as a photo using deep Siamese neural network models to outperform the existing methods using ResNet, DenseNet and Inception architectures, the results obtained about 84% accuracy.

Keywords: Biological pathway, gene identification, object detection, Siamese network, ResNet.

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Authors: T. T. Manikandan, Rajeev Sukumaran

Abstract:

Coral Reefs are very important for the majority of marine ecosystems. But, such vital species are under major threat due to the factors such as ocean acidification, overfishing, and coral bleaching. To conserve the coral reefs, reef restoration activities are carried out across the world. After reef restoration, various parameters have to be monitored in order to ensure the overall effectiveness of the reef restoration. Underwater Wireless Sensor Network (UWSN) based  monitoring is widely adopted for such long monitoring activities. Since monitoring of coral reef restoration activities is time sensitive, the QoS guarantee offered by the network with respect to delay is vital. So this research focuses on the analytical modeling of network layer delay using Stochastic Network Calculus (SNC). The core focus of the proposed model will be on the analysis of stochastic dependencies between the network flow and deriving the stochastic delay bounds for the flows that traverse in tandem in UWSNs. The derived analytical bounds are evaluated for their effectiveness using discrete event simulations.

Keywords: Coral Reef Restoration, SNC, SFA, PMOO, Tandem of Queues, Delay Bound.

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Authors: M. Kollar, A. Zieba

Abstract:

In this paper, we present a method for a time synchronization between the two eNodeBs (eNBs) in E-UTRAN (Evolved Universal Terrestrial Radio Access) network. The two eNBs are cooperating in so-called inter eNB CA (Carrier Aggregation) case and connected via asymmetrical IP network. We solve the problem by using broadcasting signals generated in E-UTRAN as synchronization signals. The results show that the time synchronization with the proposed method is possible with the error significantly less than 1 ms which is sufficient considering the time transmission interval is 1 ms in E-UTRAN. This makes this method (with low complexity) more suitable than Network Time Protocol (NTP) in the mobile applications with generated broadcasting signals where time synchronization in asymmetrical network is required.

Keywords: E-UTRAN, IP scheduled throughput, initial burst delay, synchronization, NTP, delay, asymmetric network.

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Authors: H. El-Madbouly

Abstract:

In this paper, genetic algorithm (GA) is proposed for the design of an optimization algorithm to achieve the bandwidth allocation of ATM network. In Broadband ISDN, the ATM is a highbandwidth; fast packet switching and multiplexing technique. Using ATM it can be flexibly reconfigure the network and reassign the bandwidth to meet the requirements of all types of services. By dynamically routing the traffic and adjusting the bandwidth assignment, the average packet delay of the whole network can be reduced to a minimum. M/M/1 model can be used to analyze the performance.

Keywords: Bandwidth allocation, Genetic algorithm, ATMNetwork, packet delay.

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Authors: Muhammad Azam, Micheal Olaolu Arowolo, Fei He, Mihail Popescu, Dong Xu

Abstract:

The number of biological papers is growing quickly, which means that the number of biological pathway figures in those papers is also increasing quickly. Each pathway figure shows extensive biological information, like the names of genes and how the genes are related. However, manually annotating pathway figures takes a lot of time and work. Even though using advanced image understanding models could speed up the process of curation, these models still need to be made more accurate. To improve gene name recognition from pathway figures, we applied a Siamese network to map image segments to a library of pictures containing known genes in a similar way to person recognition from photos in many photo applications. We used a triple loss function and a triplet spatial pyramid pooling network by combining the triplet convolution neural network and the spatial pyramid pooling (TSPP-Net). We compared VGG19 and VGG16 as the Siamese network model. VGG16 achieved better performance with an accuracy of 93%, which is much higher than Optical Character Recognition (OCR) results.

Keywords: Biological pathway, image understanding, gene name recognition, object detection, Siamese network, Visual Geometry Group.

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Authors: Frank Emmert Streib, Matthias Dehmer, Jing Liu, Max Mühlhauser

Abstract:

In this paper we present a method for gene ranking from DNA microarray data. More precisely, we calculate the correlation networks, which are unweighted and undirected graphs, from microarray data of cervical cancer whereas each network represents a tissue of a certain tumor stage and each node in the network represents a gene. From these networks we extract one tree for each gene by a local decomposition of the correlation network. The interpretation of a tree is that it represents the n-nearest neighbor genes on the n-th level of a tree, measured by the Dijkstra distance, and, hence, gives the local embedding of a gene within the correlation network. For the obtained trees we measure the pairwise similarity between trees rooted by the same gene from normal to cancerous tissues. This evaluates the modification of the tree topology due to progression of the tumor. Finally, we rank the obtained similarity values from all tissue comparisons and select the top ranked genes. For these genes the local neighborhood in the correlation networks changes most between normal and cancerous tissues. As a result we find that the top ranked genes are candidates suspected to be involved in tumor growth and, hence, indicates that our method captures essential information from the underlying DNA microarray data of cervical cancer.

Keywords: Graph similarity, DNA microarray data, cancer.

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Authors: T. N. Janakiraman, J. Janet Lourds Rani

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In practice, wireless networks has the property that the signal strength attenuates with respect to the distance from the base station, it could be better if the nodes at two hop away are considered for better quality of service. In this paper, we propose a procedure to identify delay preserving substructures for a given wireless ad-hoc network using a new graph operation G 2 – E (G) = G* (Edge difference of square graph of a given graph and the original graph). This operation helps to analyze some induced substructures, which preserve delay in communication among them. This operation G* on a given graph will induce a graph, in which 1- hop neighbors of any node are at 2-hop distance in the original network. In this paper, we also identify some delay preserving substructures in G*, which are (i) set of all nodes, which are mutually at 2-hop distance in G that will form a clique in G*, (ii) set of nodes which forms an odd cycle C2k+1 in G, will form an odd cycle in G* and the set of nodes which form a even cycle C2k in G that will form two disjoint companion cycles ( of same parity odd/even) of length k in G*, (iii) every path of length 2k+1 or 2k in G will induce two disjoint paths of length k in G*, and (iv) set of nodes in G*, which induces a maximal connected sub graph with radius 1 (which identifies a substructure with radius equal 2 and diameter at most 4 in G). The above delay preserving sub structures will behave as good clusters in the original network.

Keywords: Clique, cycles, delay preserving substructures, maximal connected sub graph.

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Authors: Jirawat Thaenthong, Steven Gordon

Abstract:

MANEMO is the integration of Network Mobility (NEMO) and Mobile Ad Hoc Network (MANET). A MANEMO node has an interface to both a MANET and NEMO network, and therefore should choose the optimal interface for packet delivery, however such a handover between interfaces will introduce packet loss. We define the steps necessary for a MANEMO handover, using Mobile IP and NEMO to signal the new binding to the relevant Home Agent(s). The handover steps aim to minimize the packet loss by avoiding waiting for Duplicate Address Detection and Neighbour Unreachability Detection. We present expressions for handover delay and packet loss, and then use numerical examples to evaluate a MANEMO handover. The analysis shows how the packet loss depends on level of nesting within NEMO, the delay between Home Agents and the load on the MANET, and hence can be used to developing optimal MANEMO handover algorithms.

Keywords: IP mobility, handover, MANET, network mobility

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Authors: Jasmin Velagic

Abstract:

This paper addresses the design of predictive networked controller with adaptation of a communication delay. The networked control system contains random delays from sensor to controller and from controller to actuator. The proposed predictive controller includes an adaptation loop which decreases the influence of communication delay on the control performance. Also, the predictive controller contains a filter which improves the robustness of the control system. The performance of the proposed adaptive predictive controller is demonstrated by simulation results in comparison with PI controller and predictive controller with constant delay.

Keywords: Predictive control, adaptation, communication delay, communication network.

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Authors: Mohsen Maadani, Seyed Ahmad Motamedi

Abstract:

The use of wireless technology in industrial networks has gained vast attraction in recent years. In this paper, we have thoroughly analyzed the effect of contention window (CW) size on the performance of IEEE 802.11-based industrial wireless networks (IWN), from delay and reliability perspective. Results show that the default values of CWmin, CWmax, and retry limit (RL) are far from the optimum performance due to the industrial application characteristics, including short packet and noisy environment. In this paper, an adaptive CW algorithm (payload-dependent) has been proposed to minimize the average delay. Finally a simple, but effective CW and RL setting has been proposed for industrial applications which outperforms the minimum-average-delay solution from maximum delay and jitter perspective, at the cost of a little higher average delay. Simulation results show an improvement of up to 20%, 25%, and 30% in average delay, maximum delay and jitter respectively.

Keywords: Average Delay, Contention Window, Distributed Coordination Function (DCF), Jitter, Industrial Wireless Network (IWN), Maximum Delay, Reliability, Retry Limit.

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Authors: Pengdi Diao, Zhuo Wang, Zundong Zhang, Hua Cheng

Abstract:

In the urban traffic network, the intersections are the “bottleneck point" of road network capacity. And the arterials are the main body in road network and the key factor which guarantees the normal operation of the city-s social and economic activities. The rapid increase in vehicles leads to seriously traffic jam and cause the increment of vehicles- delay. Most cities of our country are traditional single control system, which cannot meet the need for the city traffic any longer. In this paper, Synchro6.0 as a platform to minimize the intersection delay, optimizesingle signal cycle and split for Zhonghua Street in Handan City. Meanwhile, linear control system uses to optimize the phase for the t arterial road in this system. Comparing before and after use the control, capacities and service levels of this road and the adjacent road have improved significantly.

Keywords: linear control system; delay mode; signal optimization; synchro6.0 simulation

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Authors: Frank Emmert-Streib, Matthias Dehmer

Abstract:

Inferring the network structure from time series data is a hard problem, especially if the time series is short and noisy. DNA microarray is a technology allowing to monitor the mRNA concentration of thousands of genes simultaneously that produces data of these characteristics. In this study we try to investigate the influence of the experimental design on the quality of the result. More precisely, we investigate the influence of two different types of random single gene perturbations on the inference of genetic networks from time series data. To obtain an objective quality measure for this influence we simulate gene expression values with a biologically plausible model of a known network structure. Within this framework we study the influence of single gene knock-outs in opposite to linearly controlled expression for single genes on the quality of the infered network structure.

Keywords: Dynamic Bayesian networks, microarray data, structure learning, Markov chain Monte Carlo.

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Authors: Lijiang Xiang, Shouming Zhong, Yucai Ding

Abstract:

The problems of globally exponential stability and dissipativity analysis for static neural networks (NNs) with time delay is investigated in this paper. Some delay-dependent stability criteria are established for static NNs with time delay using the delay partitioning technique. In terms of this criteria, the delay-dependent sufficient condition is given to guarantee the dissipativity of static NNs with time delay. All the given results in this paper are not only dependent upon the time delay but also upon the number of delay partitions. Two numerical examples are used to show the effectiveness of the proposed methods.

Keywords: Globally exponential stability, Dissipativity, Static neural networks, Time delay.

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Authors: Kelvin Rozier, Vladimir E. Bondarenko

Abstract:

It is known that an analog Hopfield neural network with time delay can generate the outputs which are similar to the human electroencephalogram. To gain deeper insights into the mechanisms of rhythm generation by the Hopfield neural networks and to study the effects of noise on their activities, we investigated the behaviors of the networks with symmetric and asymmetric interneuron connections. The neural network under the study consists of 10 identical neurons. For symmetric (fully connected) networks all interneuron connections aij = +1; the interneuron connections for asymmetric networks form an upper triangular matrix with non-zero entries aij = +1. The behavior of the network is described by 10 differential equations, which are solved numerically. The results of simulations demonstrate some remarkable properties of a Hopfield neural network, such as linear growth of outputs, dependence of synchronization properties on the connection type, huge amplification of oscillation by the external uniform noise, and the capability of the neural network to transform one type of noise to another.

Keywords: Chaos, Hopfield neural network, noise, synchronization

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Authors: Laveen Sundararaj, Palanisamy Vellaiyan

Abstract:

Delay and Disruption Tolerant Networking is part of the Inter Planetary Internet with primary application being Deep Space Networks. Its Terrestrial form has interesting research applications such as Alagappa University Delay Tolerant Water Monitoring Network which doubles as test beds for improvising its routing scheme. DTNs depend on node mobility to deliver packets using a store-carry-and forward paradigm. Throwboxes are small and inexpensive stationary devices equipped with wireless interfaces and storage. We propose the use of Throwboxes to enhance the contact opportunities of the nodes and hence improve the Throughput. The enhancement is evaluated using Alunivdtnsim, a desktop simulator in C language and the results are graphically presented.

Keywords: Alunivdtnsim – Alagappa University Delay TolerantNetwork Simulator, AUDTWMN- Alagappa University DelayTolerant Water Monitoring Network, DTN - Delay and DisruptionTolerant Networking, LTP – Lick Lider Transmission Protocol.

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Authors: Rusliza Ahmad, Harun Budin

Abstract:

This paper studies the effect of time delay on stability of mutualism population model with limited resources for both species. First, the stability of the model without time delay is analyzed. The model is then improved by considering a time delay in the mechanism of the growth rate of the population. We analyze the effect of time delay on the stability of the stable equilibrium point. Result showed that the time delay can induce instability of the stable equilibrium point, bifurcation and stability switches.

Keywords: Bifurcation, Delay margin, Mutualism population model, Time delay

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Authors: Salem Belhaj, Moncef Tagina

Abstract:

This paper is aimed at describing a delay-based endto- end (e2e) congestion control algorithm, called Very FAST TCP (VFAST), which is an enhanced version of FAST TCP. The main idea behind this enhancement is to smoothly estimate the Round-Trip Time (RTT) based on a nonlinear filter, which eliminates throughput and queue oscillation when RTT fluctuates. In this context, an evaluation of the suggested scheme through simulation is introduced, by comparing our VFAST prototype with FAST in terms of throughput, queue behavior, fairness, stability, RTT and adaptivity to changes in network. The achieved simulation results indicate that the suggested protocol offer better performance than FAST TCP in terms of RTT estimation and throughput.

Keywords: Fast tcp, RTT, delay estimation, delay-based congestion control, high speed TCP, large bandwidth delay product.

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Authors: Vishwesh Kulkarni, Nikhil Bellarykar

Abstract:

Cellular complexity stems from the interactions among thousands of different molecular species. Thanks to the emerging fields of systems and synthetic biology, scientists are beginning to unravel these regulatory, signaling, and metabolic interactions and to understand their coordinated action. Reverse engineering of biological networks has has several benefits but a poor quality of data combined with the difficulty in reproducing it limits the applicability of these methods. A few years back, many of the commonly used predictive algorithms were tested on a network constructed in the yeast Saccharomyces cerevisiae (S. cerevisiae) to resolve this issue. The network was a synthetic network of five genes regulating each other for the so-called in vivo reverse-engineering and modeling assessment (IRMA). The network was constructed in S. cereviase since it is a simple and well characterized organism. The synthetic network included a variety of regulatory interactions, thus capturing the behaviour of larger eukaryotic gene networks on a smaller scale. We derive a new set of algorithms by solving a nonlinear optimization problem and show how these algorithms outperform other algorithms on these datasets.

Keywords: Synthetic gene network, network identification, nonlinear modeling, optimization.

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