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Sample records for 3g cellular network

  1. Key technologies and concepts for beyond-3G networks

    NASA Astrophysics Data System (ADS)

    Pehkonen, Kari; Uskela, Sami; Kalliojarvi, Kari; Oksanen, Lauri; Rikkinen, Kari

    2001-10-01

    Standardization of 3rd Generation (3G) mobile communication systems has produced the first specification releases and the commercial deployment of the 3G systems has started. Whereas 1G and 2G focused on efficiently providing voice services, in 3G a lot of attention has been devoted to solutions that support both Circuit Switched (CS) and Packet Switched (PS) communication. That has called for very flexible air interface and network solutions. 3G will continue to evolve and there are already on-going standardization activities that will, for example, boost the peak data rates up to 5-10 Mbps and improve spectral efficiency by 2-4 times. In the future, 3G evolution will be going towards 10/100 Mbps peak data rates in wide/local are coverage, respectively. This will take place partly because of technical improvements of 3G radio interface solutions, but also due to network evolution which will allow the integration other radio access methods like radio LANs into the 3G system. In longer term the 3G network evolution will be going towards ALL-IP networks. As 3G evolution seems to be going towards 10 Mbps/100 Mbps peak data rates and ALL-IP networks any beyond 3G air interface or network solution should be clearly better in order to justify its technical and commercial feasibility. Given the long evolution time of 3G and integration of other radio access schemes with 3G radio we may not even see a new, complete beyond 3G system being developed. Maybe we will just witness the emergence of a new, more advanced radio access solution which will then be connected to the evolving 3G network. As 3G evolution will continue for several years to come the research targets for any beyond 3G solutions must be set very high. When it comes to air interface, we should aim at 100 Mbps peak data rates for wide area access with high mobility, and at 1 Gbps for local area access with low mobility. Regarding possible commercial launches of any beyond 3G systems or solutions they could then

  2. MSAT and cellular hybrid networking

    NASA Technical Reports Server (NTRS)

    Baranowsky, Patrick W., II

    1993-01-01

    Westinghouse Electric Corporation is developing both the Communications Ground Segment and the Series 1000 Mobile Phone for American Mobile Satellite Corporation's (AMSC's) Mobile Satellite (MSAT) system. The success of the voice services portion of this system depends, to some extent, upon the interoperability of the cellular network and the satellite communication circuit switched communication channels. This paper will describe the set of user-selectable cellular interoperable modes (cellular first/satellite second, etc.) provided by the Mobile Phone and described how they are implemented with the ground segment. Topics including roaming registration and cellular-to-satellite 'seamless' call handoff will be discussed, along with the relevant Interim Standard IS-41 Revision B Cellular Radiotelecommunications Intersystem Operations and IOS-553 Mobile Station - Land Station Compatibility Specification.

  3. Predicting and Analyzing Cellular Networks

    NASA Astrophysics Data System (ADS)

    Singh, Mona

    High-throughput experimental technologies, along with computational predictions, have resulted in large-scale biological networks for numerous organisms. Global analyses of biological networks provide new opportunities for revealing protein functions and pathways, and for uncovering cellular organization principles. In my talk, I will discuss a number of approaches we have developed over the years for the complementary problems of predicting interactions and analyzing interaction networks. First, I will describe a genomic approach for uncovering high-confidence regulatory interactions, and show how it can be effectively combined with a framework for predicting regulatory interactions for proteins with known structural domains but unknown binding specificity. Next, I will describe algorithms for analyzing protein interaction networks in order to uncover protein function and functional modules, and demonstrate the importance of considering the topological structure of interaction networks in order to make high quality predictions. Finally, I will present a framework for explicitly incorporating known attributes of individual proteins into the analysis of biological networks, and utilize it to discover recurring network patterns underlying a range of biological processes.

  4. Comparison of average global exposure of population induced by a macro 3G network in different geographical areas in France and Serbia.

    PubMed

    Huang, Yuanyuan; Varsier, Nadège; Niksic, Stevan; Kocan, Enis; Pejanovic-Djurisic, Milica; Popovic, Milica; Koprivica, Mladen; Neskovic, Aleksandar; Milinkovic, Jelena; Gati, Azeddine; Person, Christian; Wiart, Joe

    2016-09-01

    This article is the first thorough study of average population exposure to third generation network (3G)-induced electromagnetic fields (EMFs), from both uplink and downlink radio emissions in different countries, geographical areas, and for different wireless device usages. Indeed, previous publications in the framework of exposure to EMFs generally focused on individual exposure coming from either personal devices or base stations. Results, derived from device usage statistics collected in France and Serbia, show a strong heterogeneity of exposure, both in time, that is, the traffic distribution over 24 h was found highly variable, and space, that is, the exposure to 3G networks in France was found to be roughly two times higher than in Serbia. Such heterogeneity is further explained based on real data and network architecture. Among those results, authors show that, contrary to popular belief, exposure to 3G EMFs is dominated by uplink radio emissions, resulting from voice and data traffic, and average population EMF exposure differs from one geographical area to another, as well as from one country to another, due to the different cellular network architectures and variability of mobile usage. Bioelectromagnetics. 37:382-390, 2016. © 2016 Wiley Periodicals, Inc. PMID:27385053

  5. Micromechanics of cellularized biopolymer networks

    PubMed Central

    Jones, Christopher A. R.; Cibula, Matthew; Feng, Jingchen; Krnacik, Emma A.; McIntyre, David H.; Levine, Herbert; Sun, Bo

    2015-01-01

    Collagen gels are widely used in experiments on cell mechanics because they mimic the extracellular matrix in physiological conditions. Collagen gels are often characterized by their bulk rheology; however, variations in the collagen fiber microstructure and cell adhesion forces cause the mechanical properties to be inhomogeneous at the cellular scale. We study the mechanics of type I collagen on the scale of tens to hundreds of microns by using holographic optical tweezers to apply pN forces to microparticles embedded in the collagen fiber network. We find that in response to optical forces, particle displacements are inhomogeneous, anisotropic, and asymmetric. Gels prepared at 21 °C and 37 °C show qualitative difference in their micromechanical characteristics. We also demonstrate that contracting cells remodel the micromechanics of their surrounding extracellular matrix in a strain- and distance-dependent manner. To further understand the micromechanics of cellularized extracellular matrix, we have constructed a computational model which reproduces the main experiment findings. PMID:26324923

  6. Influence of the Packet Size on the One-Way Delay in 3G Networks

    NASA Astrophysics Data System (ADS)

    Arlos, Patrik; Fiedler, Markus

    We currently observe a rising interest in mobile broadband, which users expect to perform in a similar way as its fixed counterpart. On the other hand, the capacity allocation process on mobile access links is far less transparent to the user; still, its properties need to be known in order to minimize the impact of the network on application performance. This paper investigates the impact of the packet size on the minimal one-way delay for the uplink in third-generation mobile networks. For interactive and real-time applications such as VoIP, one-way delays are of major importance for user perception; however, they are challenging to measure due to their sensitivity to clock synchronisation. Therefore, the paper applies a robust and innovative method to assure the quality of these measurements. Results from measurements from several Swedish mobile operators show that applications can gain significantly in terms of one-way delay from choosing optimal packet sizes. We show that, in certain cases, an increased packet size can improve the one-way delay performance at best by several hundred milliseconds.

  7. Aging cellular networks: chaperones as major participants.

    PubMed

    Soti, C; Csermely, P

    2007-01-01

    We increasingly rely on the network approach to understand the complexity of cellular functions. Chaperones (heat shock proteins) are key "networkers", which sequester and repair damaged proteins. In order to link the network approach and chaperones with the aging process, we first summarize the properties of aging networks suggesting a "weak link theory of aging". This theory suggests that age-related random damage primarily affects the overwhelming majority of the low affinity, transient interactions (weak links) in cellular networks leading to increased noise, destabilization and diversity. These processes may be further amplified by age-specific network remodelling and by the sequestration of weakly linked cellular proteins to protein aggregates of aging cells. Chaperones are weakly linked hubs (i.e., network elements with a large number of connections) and inter-modular bridge elements of protein-protein interaction, signalling and mitochondrial networks. As aging proceeds, the increased overload of damaged proteins is an especially important element contributing to cellular disintegration and destabilization. Additionally, chaperone overload may contribute to the increase of "noise" in aging cells, which leads to an increased stochastic resonance resulting in a deficient discrimination between signals and noise. Chaperone- and other multi-target therapies, which restore the missing weak links in aging cellular networks, may emerge as important anti-aging interventions. PMID:16814508

  8. Stability of Stochastic Neutral Cellular Neural Networks

    NASA Astrophysics Data System (ADS)

    Chen, Ling; Zhao, Hongyong

    In this paper, we study a class of stochastic neutral cellular neural networks. By constructing a suitable Lyapunov functional and employing the nonnegative semi-martingale convergence theorem we give some sufficient conditions ensuring the almost sure exponential stability of the networks. The results obtained are helpful to design stability of networks when stochastic noise is taken into consideration. Finally, two examples are provided to show the correctness of our analysis.

  9. Inferring cellular networks – a review

    PubMed Central

    Markowetz, Florian; Spang, Rainer

    2007-01-01

    In this review we give an overview of computational and statistical methods to reconstruct cellular networks. Although this area of research is vast and fast developing, we show that most currently used methods can be organized by a few key concepts. The first part of the review deals with conditional independence models including Gaussian graphical models and Bayesian networks. The second part discusses probabilistic and graph-based methods for data from experimental interventions and perturbations. PMID:17903286

  10. Analysis of Blocking Rate and Bandwidth Usage of Mobile IPTV Services in Wireless Cellular Networks

    PubMed Central

    Li, Mingfu

    2014-01-01

    Mobile IPTV services over wireless cellular networks become more and more popular, owing to the significant growth in access bandwidth of wireless cellular networks such as 3G/4G and WiMAX. However, the spectrum resources of wireless cellular networks is rare. How to enhance the spectral efficiency of mobile networks becomes an important issue. Unicast, broadcast, and multicast are the most important transport schemes for offering mobile IPTV services over wireless cellular networks. Therefore, bandwidth usages and blocking rates of unicast, broadcast, and multicast IPTV services were analyzed and compared in this paper. Simulations were also conducted to validate the analytical results. Numerical results demonstrate that the presented analysis is correct, and multicast scheme achieves the best bandwidth usage and blocking rate performance, relative to the other two schemes. PMID:25379521

  11. Analysis of blocking rate and bandwidth usage of mobile IPTV services in wireless cellular networks.

    PubMed

    Li, Mingfu

    2014-01-01

    Mobile IPTV services over wireless cellular networks become more and more popular, owing to the significant growth in access bandwidth of wireless cellular networks such as 3G/4G and WiMAX. However, the spectrum resources of wireless cellular networks is rare. How to enhance the spectral efficiency of mobile networks becomes an important issue. Unicast, broadcast, and multicast are the most important transport schemes for offering mobile IPTV services over wireless cellular networks. Therefore, bandwidth usages and blocking rates of unicast, broadcast, and multicast IPTV services were analyzed and compared in this paper. Simulations were also conducted to validate the analytical results. Numerical results demonstrate that the presented analysis is correct, and multicast scheme achieves the best bandwidth usage and blocking rate performance, relative to the other two schemes. PMID:25379521

  12. Heterogeneous Force Chains in Cellularized Biopolymer Network

    NASA Astrophysics Data System (ADS)

    Liang, Long; Jones, Christopher Allen Rucksack; Sun, Bo; Jiao, Yang

    Biopolymer Networks play an important role in coordinating and regulating collective cellular dynamics via a number of signaling pathways. Here, we investigate the mechanical response of a model biopolymer network due to the active contraction of embedded cells. Specifically, a graph (bond-node) model derived from confocal microscopy data is used to represent the network microstructure, and cell contraction is modeled by applying correlated displacements at specific nodes, representing the focal adhesion sites. A force-based stochastic relaxation method is employed to obtain force-balanced network under cell contraction. We find that the majority of the forces are carried by a small number of heterogeneous force chains emerged from the contracting cells. The force chains consist of fiber segments that either possess a high degree of alignment before cell contraction or are aligned due to the reorientation induced by cell contraction. Large fluctuations of the forces along different force chains are observed. Importantly, the decay of the forces along the force chains is significantly slower than the decay of radially averaged forces in the system, suggesting that the fibreous nature of biopolymer network structure could support long-range mechanical signaling between cells.

  13. Cellular automata modelling of biomolecular networks dynamics.

    PubMed

    Bonchev, D; Thomas, S; Apte, A; Kier, L B

    2010-01-01

    The modelling of biological systems dynamics is traditionally performed by ordinary differential equations (ODEs). When dealing with intracellular networks of genes, proteins and metabolites, however, this approach is hindered by network complexity and the lack of experimental kinetic parameters. This opened the field for other modelling techniques, such as cellular automata (CA) and agent-based modelling (ABM). This article reviews this emerging field of studies on network dynamics in molecular biology. The basics of the CA technique are discussed along with an extensive list of related software and websites. The application of CA to networks of biochemical reactions is exemplified in detail by the case studies of the mitogen-activated protein kinase (MAPK) signalling pathway, the FAS-ligand (FASL)-induced and Bcl-2-related apoptosis. The potential of the CA method to model basic pathways patterns, to identify ways to control pathway dynamics and to help in generating strategies to fight with cancer is demonstrated. The different line of CA applications presented includes the search for the best-performing network motifs, an analysis of importance for effective intracellular signalling and pathway cross-talk. PMID:20373215

  14. Optimal flux patterns in cellular metabolic networks

    SciTech Connect

    Almaas, E

    2007-01-20

    The availability of whole-cell level metabolic networks of high quality has made it possible to develop a predictive understanding of bacterial metabolism. Using the optimization framework of flux balance analysis, I investigate metabolic response and activity patterns to variations in the availability of nutrient and chemical factors such as oxygen and ammonia by simulating 30,000 random cellular environments. The distribution of reaction fluxes is heavy-tailed for the bacteria H. pylori and E. coli, and the eukaryote S. cerevisiae. While the majority of flux balance investigations have relied on implementations of the simplex method, it is necessary to use interior-point optimization algorithms to adequately characterize the full range of activity patterns on metabolic networks. The interior-point activity pattern is bimodal for E. coli and S. cerevisiae, suggesting that most metabolic reaction are either in frequent use or are rarely active. The trimodal activity pattern of H. pylori indicates that a group of its metabolic reactions (20%) are active in approximately half of the simulated environments. Constructing the high-flux backbone of the network for every environment, there is a clear trend that the more frequently a reaction is active, the more likely it is a part of the backbone. Finally, I briefly discuss the predicted activity patterns of the central-carbon metabolic pathways for the sample of random environments.

  15. Optimal flux patterns in cellular metabolic networks

    NASA Astrophysics Data System (ADS)

    Almaas, Eivind

    2007-06-01

    The availability of whole-cell-level metabolic networks of high quality has made it possible to develop a predictive understanding of bacterial metabolism. Using the optimization framework of flux balance analysis, I investigate the metabolic response and activity patterns to variations in the availability of nutrient and chemical factors such as oxygen and ammonia by simulating 30 000 random cellular environments. The distribution of reaction fluxes is heavy tailed for the bacteria H. pylori and E. coli, and the eukaryote S. cerevisiae. While the majority of flux balance investigations has relied on implementations of the simplex method, it is necessary to use interior-point optimization algorithms to adequately characterize the full range of activity patterns on metabolic networks. The interior-point activity pattern is bimodal for E. coli and S. cerevisiae, suggesting that most metabolic reactions are either in frequent use or are rarely active. The trimodal activity pattern of H. pylori indicates that a group of its metabolic reactions (20%) are active in approximately half of the simulated environments. Constructing the high-flux backbone of the network for every environment, there is a clear trend that the more frequently a reaction is active, the more likely it is a part of the backbone. Finally, I briefly discuss the predicted activity patterns of the central carbon metabolic pathways for the sample of random environments.

  16. A Wireless Communications Laboratory on Cellular Network Planning

    ERIC Educational Resources Information Center

    Dawy, Z.; Husseini, A.; Yaacoub, E.; Al-Kanj, L.

    2010-01-01

    The field of radio network planning and optimization (RNPO) is central for wireless cellular network design, deployment, and enhancement. Wireless cellular operators invest huge sums of capital on deploying, launching, and maintaining their networks in order to ensure competitive performance and high user satisfaction. This work presents a lab…

  17. Internet roaming: a WLAN/3G integration system for enterprises

    NASA Astrophysics Data System (ADS)

    Luo, Hui; Jiang, Zhimei; Kim, Byoung J.; Shankar, Narendra K.; Henry, Paul

    2002-08-01

    This paper proposes an enterprise-oriented WLAN/3G network integration solution, called the Internet Roaming system. Differing from other operator-oriented WLAN/3G network integration solutions, the Internet Roaming system is a practical IP-based corporate network architecture that provides seamless internetworking across office WLAN, home WLAN, public WLAN, and 2.5G/3G cellular network for corporate wireless data users. An Internet Roaming system may have four building blocks. They are IRC (Internet Roaming Client), SMG (secure mobility gateway), SIA (Secure IP Access) gateway, and VSA (virtual single account) server. The IRC is a special client tool (software or hardware) installed on a wireless data device. It provides a secure mobile IP connection from the wireless data device to the corporate network transparent to the operating system of the wireless data devices. The SMG is a mobile IPsec gateway installed on the corporate core network facing the Internet. It works with the IRC to maintain a secure mobile IP connection when the wireless data device is connected on the Internet through a home WLAN, a public WLAN, or a cellular network. The SIA server is a special IPsec gateway installed on the corporate intranet where office WLAN is installed. It works with the IRC to assure the security of office WLAN while improving the routing efficiency for users computers. The VSA server manages the IRC, SMG, and SIA servers.

  18. Optimizing Cellular Networks Enabled with Renewal Energy via Strategic Learning.

    PubMed

    Sohn, Insoo; Liu, Huaping; Ansari, Nirwan

    2015-01-01

    An important issue in the cellular industry is the rising energy cost and carbon footprint due to the rapid expansion of the cellular infrastructure. Greening cellular networks has thus attracted attention. Among the promising green cellular network techniques, the renewable energy-powered cellular network has drawn increasing attention as a critical element towards reducing carbon emissions due to massive energy consumption in the base stations deployed in cellular networks. Game theory is a branch of mathematics that is used to evaluate and optimize systems with multiple players with conflicting objectives and has been successfully used to solve various problems in cellular networks. In this paper, we model the green energy utilization and power consumption optimization problem of a green cellular network as a pilot power selection strategic game and propose a novel distributed algorithm based on a strategic learning method. The simulation results indicate that the proposed algorithm achieves correlated equilibrium of the pilot power selection game, resulting in optimum green energy utilization and power consumption reduction. PMID:26167934

  19. Optimizing Cellular Networks Enabled with Renewal Energy via Strategic Learning

    PubMed Central

    Sohn, Insoo; Liu, Huaping; Ansari, Nirwan

    2015-01-01

    An important issue in the cellular industry is the rising energy cost and carbon footprint due to the rapid expansion of the cellular infrastructure. Greening cellular networks has thus attracted attention. Among the promising green cellular network techniques, the renewable energy-powered cellular network has drawn increasing attention as a critical element towards reducing carbon emissions due to massive energy consumption in the base stations deployed in cellular networks. Game theory is a branch of mathematics that is used to evaluate and optimize systems with multiple players with conflicting objectives and has been successfully used to solve various problems in cellular networks. In this paper, we model the green energy utilization and power consumption optimization problem of a green cellular network as a pilot power selection strategic game and propose a novel distributed algorithm based on a strategic learning method. The simulation results indicate that the proposed algorithm achieves correlated equilibrium of the pilot power selection game, resulting in optimum green energy utilization and power consumption reduction. PMID:26167934

  20. Extracting insight from noisy cellular networks.

    PubMed

    Landry, Christian R; Levy, Emmanuel D; Abd Rabbo, Diala; Tarassov, Kirill; Michnick, Stephen W

    2013-11-21

    Network biologists attempt to extract meaningful relationships among genes or their products from very noisy data. We argue that what we categorize as noisy data may sometimes reflect noisy biology and therefore may shield a hidden meaning about how networks evolve and how matter is organized in the cell. We present practical solutions, based on existing evolutionary and biophysical concepts, through which our understanding of cell biology can be enormously enriched. PMID:24267884

  1. Energy efficiency analysis of relay-assisted cellular networks

    NASA Astrophysics Data System (ADS)

    Yu, Huan; Li, Yunzhou; Kountouris, Marios; Xu, Xibin; Wang, Jing

    2014-12-01

    To meet the demand for higher throughput, improved coverage and enhanced reliability, future wireless cellular networks face significant technical challenges. One promising solution is to place relay stations between transmitters and receivers in the cellular network. Meanwhile, as energy consumption reduction has been an important concern for the wireless industry, energy-efficient communications is of prime interest for future networks. In this paper, we study whether and how relays can improve the energy efficiency of cellular networks. Specifically, the energy efficiency of relay-assisted cellular networks is analyzed using tools of stochastic geometry. We first derive the coverage probability for the macro base station (MBS) to user (UE), the MBS to relay station (RS), and the RS to UE links, and then we model the power consumption at the MBS and RS. Based on the analytical model and expressions, the energy efficiency of relay-assisted cellular networks is then evaluated and is shown to be strictly quasi-concave on the transmit power for MBS to UE link or the RS to UE link. Numerical results show that the energy efficiency first improves while it hits a ceiling as the MBS density increases.

  2. A new small-world network created by Cellular Automata

    NASA Astrophysics Data System (ADS)

    Ruan, Yuhong; Li, Anwei

    2016-08-01

    In this paper, we generate small-world networks by the Cellular Automaton based on starting with one-dimensional regular networks. Besides the common properties of small-world networks with small average shortest path length and large clustering coefficient, the small-world networks generated in this way have other properties: (i) The edges which are cut in the regular network can be controlled that whether the edges are reconnected or not, and (ii) the number of the edges of the small-world network model equals the number of the edges of the original regular network. In other words, the average degree of the small-world network model equals to the average degree of the original regular network.

  3. Optimal Prediction by Cellular Signaling Networks

    NASA Astrophysics Data System (ADS)

    Becker, Nils B.; Mugler, Andrew; ten Wolde, Pieter Rein

    2015-12-01

    Living cells can enhance their fitness by anticipating environmental change. We study how accurately linear signaling networks in cells can predict future signals. We find that maximal predictive power results from a combination of input-noise suppression, linear extrapolation, and selective readout of correlated past signal values. Single-layer networks generate exponential response kernels, which suffice to predict Markovian signals optimally. Multilayer networks allow oscillatory kernels that can optimally predict non-Markovian signals. At low noise, these kernels exploit the signal derivative for extrapolation, while at high noise, they capitalize on signal values in the past that are strongly correlated with the future signal. We show how the common motifs of negative feedback and incoherent feed-forward can implement these optimal response functions. Simulations reveal that E. coli can reliably predict concentration changes for chemotaxis, and that the integration time of its response kernel arises from a trade-off between rapid response and noise suppression.

  4. Stochastic cellular automata model of neural networks.

    PubMed

    Goltsev, A V; de Abreu, F V; Dorogovtsev, S N; Mendes, J F F

    2010-06-01

    We propose a stochastic dynamical model of noisy neural networks with complex architectures and discuss activation of neural networks by a stimulus, pacemakers, and spontaneous activity. This model has a complex phase diagram with self-organized active neural states, hybrid phase transitions, and a rich array of behaviors. We show that if spontaneous activity (noise) reaches a threshold level then global neural oscillations emerge. Stochastic resonance is a precursor of this dynamical phase transition. These oscillations are an intrinsic property of even small groups of 50 neurons. PMID:20866454

  5. Personal communication in traditional cellular networks

    NASA Astrophysics Data System (ADS)

    Neuer, Ellwood I.

    1996-01-01

    The purpose of this paper is to describe the flow of calls through the mobile network as it applies to the operation of Basic and Enhanced Services. Included in the discussion is the overall network layout, the physical connections between the network entities, and the signaling protocols which allow the entities to be integrated. The specific functionality of the applications and services are not detailed as the specific implementation varies from vendor to vendor and from service provider to service provider. The Enhanced Services Platform is installed in a service providers network in order to offer mobile subscribers services and applications which would otherwise not be available. The service providers' objective is to increase revenue/subscriber, increase subscriber loyalty/decrease churn, and build competitive advantages through differentiation. The services provided on the Enhanced Services platform can be viewed as either Basic or Enhanced. For the purpose of this paper, Basic Services refers to Numeric Paging, Call Answering, and Voice Messaging while Enhanced Services refers to FAX Messaging, One Number Service, Voice Dialing and other Voice Recognition applications, Information Services including FAX on Demand, and Automated Call Routing.

  6. Increasing cellular coverage within integrated terrestrial/satellite mobile networks

    NASA Technical Reports Server (NTRS)

    Castro, Jonathan P.

    1995-01-01

    When applying the hierarchical cellular concept, the satellite acts as giant umbrella cell covering a region with some terrestrial cells. If a mobile terminal traversing the region arrives to the border-line or limits of a regular cellular ground service, network transition occurs and the satellite system continues the mobile coverage. To adequately assess the boundaries of service of a mobile satellite system an a cellular network within an integrated environment, this paper provides an optimized scheme to predict when a network transition may be necessary. Under the assumption of a classified propagation phenomenon and Lognormal shadowing, the study applies an analytical approach to estimate the location of a mobile terminal based on a reception of the signal strength emitted by a base station.

  7. Optimising base station location for UMTS cellular networks

    NASA Astrophysics Data System (ADS)

    Kalata, G.; Pozniak-Koszalka, I.; Koszalka, L.; Kasprzak, A.

    2014-12-01

    Rapid development of universal mobile telecommunication systems put demands on tools for assisting planning of cellular network infrastructure. The tools need to focus on critical issues in modern cellular networks and techniques used for previous generation system no longer serve useful. In this paper, an algorithm based on Branch & Bound approach is proposed for solving base station location problem, covering interference levels, traffic demands and power control mechanism. The efficiency of the algorithm is evaluated with respect to existing approaches for solving this problem - using the designed and implemented experimentation system.

  8. Millimeter-Wave Evolution for 5G Cellular Networks

    NASA Astrophysics Data System (ADS)

    Sakaguchi, Kei; Tran, Gia Khanh; Shimodaira, Hidekazu; Nanba, Shinobu; Sakurai, Toshiaki; Takinami, Koji; Siaud, Isabelle; Strinati, Emilio Calvanese; Capone, Antonio; Karls, Ingolf; Arefi, Reza; Haustein, Thomas

    Triggered by the explosion of mobile traffic, 5G (5th Generation) cellular network requires evolution to increase the system rate 1000 times higher than the current systems in 10 years. Motivated by this common problem, there are several studies to integrate mm-wave access into current cellular networks as multi-band heterogeneous networks to exploit the ultra-wideband aspect of the mm-wave band. The authors of this paper have proposed comprehensive architecture of cellular networks with mm-wave access, where mm-wave small cell basestations and a conventional macro basestation are connected to Centralized-RAN (C-RAN) to effectively operate the system by enabling power efficient seamless handover as well as centralized resource control including dynamic cell structuring to match the limited coverage of mm-wave access with high traffic user locations via user-plane/control-plane splitting. In this paper, to prove the effectiveness of the proposed 5G cellular networks with mm-wave access, system level simulation is conducted by introducing an expected future traffic model, a measurement based mm-wave propagation model, and a centralized cell association algorithm by exploiting the C-RAN architecture. The numerical results show the effectiveness of the proposed network to realize 1000 times higher system rate than the current network in 10 years which is not achieved by the small cells using commonly considered 3.5 GHz band. Furthermore, the paper also gives latest status of mm-wave devices and regulations to show the feasibility of using mm-wave in the 5G systems.

  9. Cellular neural networks for welding arc thermograms segmentation

    NASA Astrophysics Data System (ADS)

    Jamrozik, Wojciech

    2014-09-01

    Machine vision systems are used in many areas for monitoring of technological processes. Among this processes welding takes important place, where often infrared cameras are used. Besides reliable hardware, successful application of vision systems requires suitable software based on proper algorithms. One of most important group of image processing algorithms is connected to image segmentation. Obtainment of exact boundary of an object that changes shape in time, such as the welding arc, represented on a thermogram is not a trivial task. In the paper a segmentation method using supervised approach based on a cellular neural networks is presented. Simulated annealing and genetic algorithm were used for training of the network (template optimization). Comparison of proposed method to a well elaborated segmentation method based on region growing approach was made. Obtained results prove that the cellular neural network can be a valuable tool for infrared welding pool images segmentation.

  10. The role of actin networks in cellular mechanosensing

    NASA Astrophysics Data System (ADS)

    Azatov, Mikheil

    Physical processes play an important role in many biological phenomena, such as wound healing, organ development, and tumor metastasis. During these processes, cells constantly interact with and adapt to their environment by exerting forces to mechanically probe the features of their surroundings and generating appropriate biochemical responses. The mechanisms underlying how cells sense the physical properties of their environment are not well understood. In this thesis, I present my studies to investigate cellular responses to the stiffness and topography of the environment. In order to sense the physical properties of their environment, cells dynamically reorganize the structure of their actin cytoskeleton, a dynamic network of biopolymers, altering the shape and spatial distribution of protein assemblies. Several observations suggest that proteins that crosslink actin filaments may play an important role in cellular mechanosensitivity. Palladin is an actin-crosslinking protein that is found in the lamellar actin network, stress fibers and focal adhesions, cellular structures that are critical for mechanosensing of the physical environment. By virtue of its close interactions with these structures in the cell, palladin may play an important role in cell mechanics. However, the role of actin crosslinkers in general, and palladin in particular, in cellular force generation and mechanosensing is not well known. I have investigated the role of palladin in regulating the plasticity of the actin cytoskeleton and cellular force generation in response to alterations in substrate stiffness. I have shown that the expression levels of palladin modulate the forces exerted by cells and their ability to sense substrate stiffness. Perturbation experiments also suggest that palladin levels in cells altered myosin motor activity. These results suggest that the actin crosslinkers, such as palladin, and myosin motors coordinate for optimal cell function and to prevent aberrant

  11. Interference from the Deep Space Network's 70-m High Power Transmitter in Goldstone, CA to 3G Mobile Users Operating in the Surrounding Area

    NASA Technical Reports Server (NTRS)

    Ho, Christian

    2004-01-01

    The International Telecommunications Union (ITU) has allocated 2110-2200 MHz for the third generation (3G) mobile services. Part of the spectrum (2110-2120 MHz) is allocated for space research service and has been used by the DSN for years for sending command uplinks to deep space missions. Due to the extremely high power transmitted, potential interference to 3G users in areas surrounding DSN Goldstone exists. To address this issue, a preliminary analytical study has been performed and computer models have been developed. The goal is to provide theoretical foundation and tools to estimate the strength of interference as a function of distance from the transmitter for various interference mechanisms, (or propagation modes), and then determine the size of the area in which 3G users are susceptible to interference from the 400-kW transmitter in Goldstone. The focus is non-line-of-sight interference, taking into account of terrain shielding, anomalous propagation mechanisms, and technical and operational characteristics of the DSN and the 3G services.

  12. Using Cellular Communication Networks To Detect Air Pollution.

    PubMed

    David, Noam; Gao, H Oliver

    2016-09-01

    Accurate real time monitoring of atmospheric conditions at ground level is vital for hazard warning, meteorological forecasting, and various environmental applications required for public health and safety. However, conventional monitoring facilities are costly and often insufficient, for example, since they are not representative of the larger space and are not deployed densely enough in the field. There have been numerous scientific works showing the ability of commercial microwave links that comprise the data transmission infrastructure in cellular communication networks to monitor hydrometeors as a potential complementary solution. However, despite the large volume of research carried out in this emerging field during the past decade, no study has shown the ability of the system to provide critical information regarding air quality. Here we reveal the potential for identifying atmospheric conditions prone to air pollution by detecting temperature inversions that trap pollutants at ground level. The technique is based on utilizing standard signal measurements from an existing cellular network during routine operation. PMID:27490182

  13. Analysing Dynamical Behavior of Cellular Networks via Stochastic Bifurcations

    PubMed Central

    Zakharova, Anna; Kurths, Jürgen; Vadivasova, Tatyana; Koseska, Aneta

    2011-01-01

    The dynamical structure of genetic networks determines the occurrence of various biological mechanisms, such as cellular differentiation. However, the question of how cellular diversity evolves in relation to the inherent stochasticity and intercellular communication remains still to be understood. Here, we define a concept of stochastic bifurcations suitable to investigate the dynamical structure of genetic networks, and show that under stochastic influence, the expression of given proteins of interest is defined via the probability distribution of the phase variable, representing one of the genes constituting the system. Moreover, we show that under changing stochastic conditions, the probabilities of expressing certain concentration values are different, leading to different functionality of the cells, and thus to differentiation of the cells in the various types. PMID:21647432

  14. Performance evaluation of cellular phone network based portable ECG device.

    PubMed

    Hong, Joo-Hyun; Cha, Eun-Jong; Lee, Tae-Soo

    2008-01-01

    In this study, cellular phone network based portable ECG device was developed and three experiments were performed to evaluate the accuracy, reliability and operability, applicability during daily life of the developed device. First, ECG signals were measured using the developed device and Biopac device (reference device) during sitting and marking time and compared to verify the accuracy of R-R intervals. Second, the reliable data transmission to remote server was verified on two types of simulated emergency event using patient simulator. Third, during daily life with five types of motion, accuracy of data transmission to remote server was verified on two types of event occurring. By acquiring and comparing subject's biomedical signal and motion signal, the accuracy, reliability and operability, applicability during daily life of the developed device were verified. Therefore, cellular phone network based portable ECG device can monitor patient with inobtrusive manner. PMID:19162767

  15. Cellular Automata with network incubation in information technology diffusion

    NASA Astrophysics Data System (ADS)

    Guseo, Renato; Guidolin, Mariangela

    2010-06-01

    Innovation diffusion of network goods determines direct network externalities that depress sales for long periods and delay full benefits. We model this effect through a multiplicative dynamic market potential driven by a latent individual threshold embedded in a special Cellular Automata representation. The corresponding mean field approximation of its aggregate version is a Riccati equation with a closed form solution. This allows the detection of a change-point time separating an incubation period from a subsequent take-off due to a collective threshold (critical mass). Weighted nonlinear least squares are the main inferential methodology. An application is analysed with reference to USA fax machine diffusion.

  16. Ion beam analysis based on cellular nonlinear networks

    NASA Astrophysics Data System (ADS)

    Senger, V.; Tetzlaff, R.; Reichau, H.; Ratzinger, U.

    2011-07-01

    The development of a non- destructive measurement method for ion beam parameters has been treated in various projects. Although results are promising, the high complexity of beam dynamics has made it impossible to implement a real time process control up to now. In this paper we will propose analysing methods based on the dynamics of Cellular Nonlinear Networks (CNN) that can be implemented on pixel parallel CNN based architectures and yield satisfying results even at low resolutions.

  17. Network Medicine: From Cellular Networks to the Human Diseasome

    NASA Astrophysics Data System (ADS)

    Barabasi, Albert-Laszlo

    2014-03-01

    Given the functional interdependencies between the molecular components in a human cell, a disease is rarely a consequence of an abnormality in a single gene, but reflects the perturbations of the complex intracellular network. The tools of network science offer a platform to explore systematically not only the molecular complexity of a particular disease, leading to the identification of disease modules and pathways, but also the molecular relationships between apparently distinct (patho)phenotypes. Advances in this direction not only enrich our understanding of complex systems, but are also essential to identify new disease genes, to uncover the biological significance of disease-associated mutations identified by genome-wide association studies and full genome sequencing, and to identify drug targets and biomarkers for complex diseases.

  18. Tensegrity II. How structural networks influence cellular information processing networks

    NASA Technical Reports Server (NTRS)

    Ingber, Donald E.

    2003-01-01

    The major challenge in biology today is biocomplexity: the need to explain how cell and tissue behaviors emerge from collective interactions within complex molecular networks. Part I of this two-part article, described a mechanical model of cell structure based on tensegrity architecture that explains how the mechanical behavior of the cell emerges from physical interactions among the different molecular filament systems that form the cytoskeleton. Recent work shows that the cytoskeleton also orients much of the cell's metabolic and signal transduction machinery and that mechanical distortion of cells and the cytoskeleton through cell surface integrin receptors can profoundly affect cell behavior. In particular, gradual variations in this single physical control parameter (cell shape distortion) can switch cells between distinct gene programs (e.g. growth, differentiation and apoptosis), and this process can be viewed as a biological phase transition. Part II of this article covers how combined use of tensegrity and solid-state mechanochemistry by cells may mediate mechanotransduction and facilitate integration of chemical and physical signals that are responsible for control of cell behavior. In addition, it examines how cell structural networks affect gene and protein signaling networks to produce characteristic phenotypes and cell fate transitions during tissue development.

  19. Hybrid Spectral Efficient Cellular Network Deployment to Reduce RF Pollution

    NASA Astrophysics Data System (ADS)

    Katiyar, Sumit; K. Jain, R.; K. Agrawal, N.

    2012-09-01

    As the mobile telecommunication systems are growing tremendously all over the world, the numbers of handheld and base stations are also rapidly growing and it became very popular to see these base stations distributed everywhere in the neighborhood and on roof tops which has caused a considerable amount of panic to the public in Palestine concerning wither the radiated electromagnetic fields from these base stations may cause any health effect or hazard. Recently UP High Court in India ordered for removal of BTS towers from residential area, it has created panic among cellular communication network designers too. Green cellular networks could be a solution for the above problem. This paper deals with green cellular networks with the help of multi-layer overlaid hierarchical structure (macro / micro / pico / femto cells). Macrocell for area coverage, micro for pedestrian and a slow moving traffic while pico for indoor use and femto for individual high capacity users. This could be the answer of the problem of energy conservation and enhancement of spectral density also.

  20. ATR inhibition rewires cellular signaling networks induced by replication stress.

    PubMed

    Wagner, Sebastian A; Oehler, Hannah; Voigt, Andrea; Dalic, Denis; Freiwald, Anja; Serve, Hubert; Beli, Petra

    2016-02-01

    The slowing down or stalling of replication forks is commonly known as replication stress and arises from multiple causes such as DNA lesions, nucleotide depletion, RNA-DNA hybrids, and oncogene activation. The ataxia telangiectasia and Rad3-related kinase (ATR) plays an essential role in the cellular response to replication stress and inhibition of ATR has emerged as therapeutic strategy for the treatment of cancers that exhibit high levels of replication stress. However, the cellular signaling induced by replication stress and the substrate spectrum of ATR has not been systematically investigated. In this study, we employed quantitative MS-based proteomics to define the cellular signaling after nucleotide depletion-induced replication stress and replication fork collapse following ATR inhibition. We demonstrate that replication stress results in increased phosphorylation of a subset of proteins, many of which are involved in RNA splicing and transcription and have previously not been associated with the cellular replication stress response. Furthermore, our data reveal the ATR-dependent phosphorylation following replication stress and discover novel putative ATR target sites on MCM6, TOPBP1, RAD51AP1, and PSMD4. We establish that ATR inhibition rewires cellular signaling networks induced by replication stress and leads to the activation of the ATM-driven double-strand break repair signaling. PMID:26572502

  1. Distinctive Behaviors of Druggable Proteins in Cellular Networks

    PubMed Central

    Workman, Paul; Al-Lazikani, Bissan

    2015-01-01

    The interaction environment of a protein in a cellular network is important in defining the role that the protein plays in the system as a whole, and thus its potential suitability as a drug target. Despite the importance of the network environment, it is neglected during target selection for drug discovery. Here, we present the first systematic, comprehensive computational analysis of topological, community and graphical network parameters of the human interactome and identify discriminatory network patterns that strongly distinguish drug targets from the interactome as a whole. Importantly, we identify striking differences in the network behavior of targets of cancer drugs versus targets from other therapeutic areas and explore how they may relate to successful drug combinations to overcome acquired resistance to cancer drugs. We develop, computationally validate and provide the first public domain predictive algorithm for identifying druggable neighborhoods based on network parameters. We also make available full predictions for 13,345 proteins to aid target selection for drug discovery. All target predictions are available through canSAR.icr.ac.uk. Underlying data and tools are available at https://cansar.icr.ac.uk/cansar/publications/druggable_network_neighbourhoods/. PMID:26699810

  2. Network Coordinated Opportunistic Beamforming in Downlink Cellular Networks

    NASA Astrophysics Data System (ADS)

    Shin, Won-Yong; Jung, Bang Chul

    We propose a network coordinated opportunistic beamforming (NC-OBF) protocol for downlink K-cell networks with M-antenna base stations (BSs). In the NC-OBF scheme, based on pseudo-randomly generated BF vectors, a user scheduling strategy is introduced, where each BS opportunistically selects a set of mobile stations (MSs) whose desired signals generate the minimum interference to the other MSs. Its performance is then analyzed in terms of degrees-of-freedom (DoFs). As our achievability result, it is shown that KM DoFs are achievable if the number N of MSs in a cell scales at least as SNRKM-1, where SNR denotes the received signal-to-noise ratio. Furthermore, by deriving the corresponding upper bound on the DoFs, it is shown that the NC-OBF scheme is DoF-optimal. Note that the proposed scheme does not require the global channel state information and dimension expansion, thereby resulting in easier implementation.

  3. Mechanics of composite actin networks: in vitro and cellular perspectives

    NASA Astrophysics Data System (ADS)

    Upadhyaya, Arpita

    2014-03-01

    Actin filaments and associated actin binding proteins play an essential role in governing the mechanical properties of eukaryotic cells. Even though cells have multiple actin binding proteins (ABPs) that exist simultaneously to maintain the structural and mechanical integrity of the cellular cytoskeleton, how these proteins work together to determine the properties of actin networks is not well understood. The ABP, palladin, is essential for the integrity of cell morphology and movement during development. Palladin coexists with alpha-actinin in stress fibers and focal adhesions and binds to both actin and alpha-actinin. To obtain insight into how mutually interacting actin crosslinking proteins modulate the properties of actin networks, we have characterized the micro-structure and mechanics of actin networks crosslinked with palladin and alpha-actinin. Our studies on composite networks of alpha-actinin/palladin/actin show that palladin and alpha-actinin synergistically determine network viscoelasticity. We have further examined the role of palladin in cellular force generation and mechanosensing. Traction force microscopy revealed that TAFs are sensitive to substrate stiffness as they generate larger forces on substrates of increased stiffness. Contrary to expectations, knocking down palladin increased the forces generated by cells, and also inhibited the ability to sense substrate stiffness for very stiff gels. This was accompanied by significant differences in the actin organization and adhesion dynamics of palladin knock down cells. Perturbation experiments also suggest altered myosin activity in palladin KD cells. Our results suggest that the actin crosslinkers such as palladin and myosin motors coordinate for optimal cell function and to prevent aberrant behavior as in cancer metastasis.

  4. Study and Simulation of Traffic Behavior in Cellular Network

    NASA Astrophysics Data System (ADS)

    Madhup, D. K.; Shrestha, C. L.; Sharma, R. K.

    2007-07-01

    Cellular radio systems accommodate a large number of users with a limited radio spectrum. The concept of trunking allows a large number of users to share the relatively small number of channels in a cell by providing access to each user, on demand, from a pool of available channels. Traffic engineering deals with provisioning of communication circuits in a given area for a number of subscribers with a required grade of service. Traffic in any cell depends upon the number of users, the average request rate and average call duration. Certain number of channels is required for the required GOS. To design an optimum capacity cellular system, traffic behavior on that system is important. The number of channel required can be estimated by using Erlang formula and Erlang table. Erlang table is not always useful to calculate the probability of blocking in various complex scenarios such as channel borrowing strategies. When the total number of channel available in a given cell are divided to serve partly for newly generated calls and partly for handover calls, and if they use dynamic channel assignment strategies like channel borrowing, then the probability of blocking can't be calculated from Erlang table. Simulation model of the behavior help us to determine the blocking and the channel utilization while using various channel assignment strategies. The title "Study and Simulation of Traffic Behavior in Cellular Network" entail the study of the blocking probability of traffic in cellular network for static channel assignment strategies and dynamic channel borrowing strategies through MATLAB programming language and graphic user interface (GUI). The result shows that the dynamic scheme can perform better than static maximizing the overall utilization of the circuits and minimizing the overall blocking.

  5. Cutting the Wires: Modularization of Cellular Networks for Experimental Design

    PubMed Central

    Lang, Moritz; Summers, Sean; Stelling, Jörg

    2014-01-01

    Understanding naturally evolved cellular networks requires the consecutive identification and revision of the interactions between relevant molecular species. In this process, initially often simplified and incomplete networks are extended by integrating new reactions or whole subnetworks to increase consistency between model predictions and new measurement data. However, increased consistency with experimental data alone is not sufficient to show the existence of biomolecular interactions, because the interplay of different potential extensions might lead to overall similar dynamics. Here, we present a graph-based modularization approach to facilitate the design of experiments targeted at independently validating the existence of several potential network extensions. Our method is based on selecting the outputs to measure during an experiment, such that each potential network extension becomes virtually insulated from all others during data analysis. Each output defines a module that only depends on one hypothetical network extension, and all other outputs act as virtual inputs to achieve insulation. Given appropriate experimental time-series measurements of the outputs, our modules can be analyzed, simulated, and compared to the experimental data separately. Our approach exemplifies the close relationship between structural systems identification and modularization, an interplay that promises development of related approaches in the future. PMID:24411264

  6. Country-wide rainfall maps from cellular communication networks

    PubMed Central

    Overeem, Aart; Leijnse, Hidde; Uijlenhoet, Remko

    2013-01-01

    Accurate and timely surface precipitation measurements are crucial for water resources management, agriculture, weather prediction, climate research, as well as ground validation of satellite-based precipitation estimates. However, the majority of the land surface of the earth lacks such data, and in many parts of the world the density of surface precipitation gauging networks is even rapidly declining. This development can potentially be counteracted by using received signal level data from the enormous number of microwave links used worldwide in commercial cellular communication networks. Along such links, radio signals propagate from a transmitting antenna at one base station to a receiving antenna at another base station. Rain-induced attenuation and, subsequently, path-averaged rainfall intensity can be retrieved from the signal’s attenuation between transmitter and receiver. Here, we show how one such a network can be used to retrieve the space–time dynamics of rainfall for an entire country (The Netherlands, ∼35,500 km2), based on an unprecedented number of links (∼2,400) and a rainfall retrieval algorithm that can be applied in real time. This demonstrates the potential of such networks for real-time rainfall monitoring, in particular in those parts of the world where networks of dedicated ground-based rainfall sensors are often virtually absent. PMID:23382210

  7. Country-wide rainfall maps from cellular communication networks.

    PubMed

    Overeem, Aart; Leijnse, Hidde; Uijlenhoet, Remko

    2013-02-19

    Accurate and timely surface precipitation measurements are crucial for water resources management, agriculture, weather prediction, climate research, as well as ground validation of satellite-based precipitation estimates. However, the majority of the land surface of the earth lacks such data, and in many parts of the world the density of surface precipitation gauging networks is even rapidly declining. This development can potentially be counteracted by using received signal level data from the enormous number of microwave links used worldwide in commercial cellular communication networks. Along such links, radio signals propagate from a transmitting antenna at one base station to a receiving antenna at another base station. Rain-induced attenuation and, subsequently, path-averaged rainfall intensity can be retrieved from the signal's attenuation between transmitter and receiver. Here, we show how one such a network can be used to retrieve the space-time dynamics of rainfall for an entire country (The Netherlands, ∼35,500 km(2)), based on an unprecedented number of links (∼2,400) and a rainfall retrieval algorithm that can be applied in real time. This demonstrates the potential of such networks for real-time rainfall monitoring, in particular in those parts of the world where networks of dedicated ground-based rainfall sensors are often virtually absent. PMID:23382210

  8. Application-Aware Dynamic Retransmission Control in Mobile Cellular Networks

    NASA Astrophysics Data System (ADS)

    Halima, Nadhir Ben; Kliazovich, Dzmitry; Granelli, Fabrizio

    This paper proposes an application-aware cross-layer approach between application/transport layers on the mobile terminal and link layer at the wireless base station to enable dynamic control on the strength of per-packet error protection for multimedia and data transfers. Specifically, in the context of cellular networks, the proposed scheme allows to control the desired level of Hybrid ARQ (HARQ) protection by using an in-band control feedback channel. Such protection is dynamically adapted on a per-packet basis and depends on the perceptual importance of different packets as well as on the reception history of the flow.

  9. Emulating fire propagation by using cellular nonlinear networks

    NASA Astrophysics Data System (ADS)

    Buscarino, A.; Fortuna, L.; Frasca, M.; Xibilia, M. G.

    2012-09-01

    In this paper a new approach based on Cellular Nonlinear Networks (CNNs) for modeling the diffusion of forest fires is presented. Based on a model relying on an hyperbolic reaction-diffusion equation, the proposed approach exploits the peculiarity of CNNs allowing the investigation of different types of forest fires, also considering specific morphological characteristics of the terrain and the presence of external perturbations like wind flows. Results show the emergence of particular phenomena really observed in wildfires, allowing to assess the validity of the approach.

  10. GPM ground validation via commercial cellular networks: an exploratory approach

    NASA Astrophysics Data System (ADS)

    Rios Gaona, Manuel Felipe; Overeem, Aart; Leijnse, Hidde; Brasjen, Noud; Uijlenhoet, Remko

    2016-04-01

    The suitability of commercial microwave link networks for ground validation of GPM (Global Precipitation Measurement) data is evaluated here. Two state-of-the-art rainfall products are compared over the land surface of the Netherlands for a period of 7 months, i.e., rainfall maps from commercial cellular communication networks and Integrated Multi-satellite Retrievals for GPM (IMERG). Commercial microwave link networks are nowadays the core component in telecommunications worldwide. Rainfall rates can be retrieved from measurements of attenuation between transmitting and receiving antennas. If adequately set up, these networks enable rainfall monitoring tens of meters above the ground at high spatiotemporal resolutions (temporal sampling of seconds to tens of minutes, and spatial sampling of hundreds of meters to tens of kilometers). The GPM mission is the successor of TRMM (Tropical Rainfall Measurement Mission). For two years now, IMERG offers rainfall estimates across the globe (180°W - 180°E and 60°N - 60°S) at spatiotemporal resolutions of 0.1° x 0.1° every 30 min. These two data sets are compared against a Dutch gauge-adjusted radar data set, considered to be the ground truth given its accuracy, spatiotemporal resolution and availability. The suitability of microwave link networks in satellite rainfall evaluation is of special interest, given the independent character of this technique, its high spatiotemporal resolutions and availability. These are valuable assets for water management and modeling of floods, landslides, and weather extremes; especially in places where rain gauge networks are scarce or poorly maintained, or where weather radar networks are too expensive to acquire and/or maintain.

  11. Sources of Uncertainty in Rainfall Maps from Cellular Communication Networks

    NASA Astrophysics Data System (ADS)

    Rios Gaona, Manuel Felipe; Overeem, Aart; Leijnse, Hidde; Uijlenhoet, Remko

    2015-04-01

    and quantify the sources of uncertainty in such rainfall maps, but also to test the actual and optimal performance of one commercial microwave network from one of the cellular providers in The Netherlands.

  12. Cellular telephone-based wide-area radiation detection network

    DOEpatents

    Craig, William W.; Labov, Simon E.

    2009-06-09

    A network of radiation detection instruments, each having a small solid state radiation sensor module integrated into a cellular phone for providing radiation detection data and analysis directly to a user. The sensor module includes a solid-state crystal bonded to an ASIC readout providing a low cost, low power, light weight compact instrument to detect and measure radiation energies in the local ambient radiation field. In particular, the photon energy, time of event, and location of the detection instrument at the time of detection is recorded for real time transmission to a central data collection/analysis system. The collected data from the entire network of radiation detection instruments are combined by intelligent correlation/analysis algorithms which map the background radiation and detect, identify and track radiation anomalies in the region.

  13. Assessing the weather monitoring capabilities of cellular microwave link networks

    NASA Astrophysics Data System (ADS)

    Fencl, Martin; Vrzba, Miroslav; Rieckermann, Jörg; Bareš, Vojtěch

    2016-04-01

    Using of microwave links for rainfall monitoring was suggested already by (Atlas and Ulbrich, 1977). However, this technique attracted broader attention of scientific community only in the recent decade, with the extensive growth of cellular microwave link (CML) networks, which form the backbone of today's cellular telecommunication infrastructure. Several studies have already shown that CMLs can be conveniently used as weather sensors and have potential to provide near-ground path-integrated observations of rainfall but also humidity or fog. However, although research is still focusing on algorithms to improve the weather sensing capabilities (Fencl et al., 2015), it is not clear how to convince cellular operators to provide the power levels of their network. One step in this direction is to show in which regions or municipalities the networks are sufficiently dense to provide/develop good services. In this contribution we suggest a standardized approach to evaluate CML networks in terms of rainfall observation and to identify suitable regions for CML rainfall monitoring. We estimate precision of single CML based on its sensitivity to rainfall, i.e. as a function of frequency, polarization and path length. Capability of a network to capture rainfall spatial patterns is estimated from the CML coverage and path lengths considering that single CML provides path-integrated rain rates. We also search for suitable predictors for regions where no network topologies are available. We test our approach on several European networks and discuss the results. Our results show that CMLs are very dense in urban areas (> 1 CML/km2), but less in rural areas (< 0.02 CML/km2). We found a strong correlation between a population and CML network density (e.g. R2 = 0.97 in Czech Republic), thus population could be a simple proxy to identify suitable regions for CML weather monitoring. To enable a simple and efficient assessment of the CML monitoring potential for any region worldwide

  14. Sigma-delta cellular neural network for 2D modulation.

    PubMed

    Aomori, Hisashi; Otake, Tsuyoshi; Takahashi, Nobuaki; Tanaka, Mamoru

    2008-01-01

    Although sigma-delta modulation is widely used for analog-to-digital (A/D) converters, sigma-delta concepts are only for 1D signals. Signal processing in the digital domain is extremely useful for 2D signals such as used in image processing, medical imaging, ultrasound imaging, and so on. The intricate task that provides true 2D sigma-delta modulation is feasible in the spatial domain sigma-delta modulation using the discrete-time cellular neural network (DT-CNN) with a C-template. In the proposed architecture, the A-template is used for a digital-to-analog converter (DAC), the C-template works as an integrator, and the nonlinear output function is used for the bilevel output. In addition, due to the cellular neural network (CNN) characteristics, each pixel of an image corresponds to a cell of a CNN, and each cell is connected spatially by the A-template. Therefore, the proposed system can be thought of as a very large-scale and super-parallel sigma-delta modulator. Moreover, the spatio-temporal dynamics is designed to obtain an optimal reconstruction signal. The experimental results show the excellent reconstruction performance and capabilities of the CNN as a sigma-delta modulator. PMID:18215502

  15. Mesoscale assembly of chemically modified graphene into complex cellular networks

    NASA Astrophysics Data System (ADS)

    Barg, Suelen; Perez, Felipe Macul; Ni, Na; Do Vale Pereira, Paula; Maher, Robert C.; Garcia-Tuñon, Esther; Eslava, Salvador; Agnoli, Stefano; Mattevi, Cecilia; Saiz, Eduardo

    2014-07-01

    The widespread technological introduction of graphene beyond electronics rests on our ability to assemble this two-dimensional building block into three-dimensional structures for practical devices. To achieve this goal we need fabrication approaches that are able to provide an accurate control of chemistry and architecture from nano to macroscopic levels. Here, we describe a versatile technique to build ultralight (density ≥1 mg cm-3) cellular networks based on the use of soft templates and the controlled segregation of chemically modified graphene to liquid interfaces. These novel structures can be tuned for excellent conductivity; versatile mechanical response (elastic-brittle to elastomeric, reversible deformation, high energy absorption) and organic absorption capabilities (above 600 g per gram of material). The approach can be used to uncover the basic principles that will guide the design of practical devices that by combining unique mechanical and functional performance will generate new technological opportunities.

  16. Mesoscale assembly of chemically modified graphene into complex cellular networks

    PubMed Central

    Barg, Suelen; Perez, Felipe Macul; Ni, Na; do Vale Pereira, Paula; Maher, Robert C.; Garcia-Tuñon, Esther; Eslava, Salvador; Agnoli, Stefano; Mattevi, Cecilia; Saiz, Eduardo

    2014-01-01

    The widespread technological introduction of graphene beyond electronics rests on our ability to assemble this two-dimensional building block into three-dimensional structures for practical devices. To achieve this goal we need fabrication approaches that are able to provide an accurate control of chemistry and architecture from nano to macroscopic levels. Here, we describe a versatile technique to build ultralight (density ≥1 mg cm−3) cellular networks based on the use of soft templates and the controlled segregation of chemically modified graphene to liquid interfaces. These novel structures can be tuned for excellent conductivity; versatile mechanical response (elastic-brittle to elastomeric, reversible deformation, high energy absorption) and organic absorption capabilities (above 600 g per gram of material). The approach can be used to uncover the basic principles that will guide the design of practical devices that by combining unique mechanical and functional performance will generate new technological opportunities. PMID:24999766

  17. A 'bioproduction breadboard': programming, assembling, and actuating cellular networks.

    PubMed

    Zargar, Amin; Payne, Gregory F; Bentley, William E

    2015-12-01

    With advances in synthetic biology and biofabrication, cellular networks can be functionalized and connected with unprecedented sophistication. We describe a platform for the creation of a 'bioproduction breadboard'. This would consist of physically isolated product-producing cell populations, product capture devices, and other unit operations that function as programmed in place, using unique, orthogonal inputs. For product synthesis, customized cell populations would be connected through standardized, generic inputs allowing 'plug and play' functionality and primary, user-mediated regulation. In addition, through autonomous pathway redirection and balancing, the cells themselves would provide secondary, self-directed regulation to optimize bioproduction. By leveraging specialization and division of labor, we envision diverse cell populations linked to create new pathway designs. PMID:26342587

  18. Automatic generation of multipath algorithms in the cellular nonlinear network

    NASA Astrophysics Data System (ADS)

    Preciado, Victor M.; Guinea, Domingo; Montufar-Chaveznava, Rodrigo

    2001-04-01

    The objective of this work is to generate a learning machine capable of find solutions for complex image processing task by Cellular Neural Network (CNN's). First a general machine for automatic analog algorithm design independent of the problem to solve is created, this is accomplished through an evolutionary strategy that is an extension of genetic programming. Second, this work introduces a suite of sub- mechanisms that increase the power of genetic programming and contribute to reduce the enormous space search for producing a plentiful search. Some concepts in this section are related with AI theory, in such a way that in this work we are in the intersection field of AI and Image Processing by CNN.

  19. Edge detection of noisy images based on cellular neural networks

    NASA Astrophysics Data System (ADS)

    Li, Huaqing; Liao, Xiaofeng; Li, Chuandong; Huang, Hongyu; Li, Chaojie

    2011-09-01

    This paper studies a technique employing both cellular neural networks (CNNs) and linear matrix inequality (LMI) for edge detection of noisy images. Our main work focuses on training templates of noise reduction and edge detection CNNs. Based on the Lyapunov stability theorem, we derive a criterion for global asymptotical stability of a unique equilibrium of the noise reduction CNN. Then we design an approach to train edge detection templates, and this approach can detect the edge precisely and efficiently, i.e., by only one iteration. Finally, we illustrate performance of the proposed methodology from the aspect of peak signal to noise ratio (PSNR) through computer simulations. Moreover, some comparisons are also given to prove that our method outperforms classical operators in gray image edge detection.

  20. Country-wide rainfall maps from cellular communication networks

    NASA Astrophysics Data System (ADS)

    Leijnse, Hidde; Overeem, Aart; Uijlenhoet, Remko

    2013-04-01

    Accurate rainfall observations with high spatial and temporal resolutions are needed for hydrological applications, agriculture, meteorology, and climate monitoring. However, the majority of the land surface of the earth lacks accurate rainfall information and the number of rain gauges is even severely declining in Europe, South-America, and Africa. This calls for alternative sources of rainfall information. Various studies have shown that microwave links from operational cellular telecommunication networks may be employed for rainfall monitoring. Such networks cover 20% of the land surface of the earth and have a high density, especially in urban areas. The basic principle of rainfall monitoring using microwave links is as follows. Rainfall attenuates the electromagnetic signals transmitted from one telephone tower to another. By measuring the received power at one end of a microwave link as a function of time, the path-integrated attenuation due to rainfall can be calculated. Previous studies have shown that average rainfall intensities over the length of a link can be derived from the path-integrated attenuation. Here we show how one cellular telecommunication network can be used to retrieve the space-time dynamics of rainfall for an entire country. A dataset from a commercial microwave link network over the Netherlands is analyzed, containing data from an unprecedented number of links (2400) covering the land surface of the Netherlands (35500 km2). This dataset consists of 24 days with substantial rainfall in June - September 2011. A rainfall retrieval algorithm is presented to derive rainfall intensities from the microwave link data, which have a temporal resolution of 15 min. Rainfall maps (1 km spatial resolution) are generated from these rainfall intensities using Kriging. This algorithm is suited for real-time application, and is calibrated on a subset (12 days) of the dataset. The other 12 days in the dataset are used to validate the algorithm. Both

  1. Simulating Quantitative Cellular Responses Using Asynchronous Threshold Boolean Network Ensembles

    PubMed Central

    2011-01-01

    Background With increasing knowledge about the potential mechanisms underlying cellular functions, it is becoming feasible to predict the response of biological systems to genetic and environmental perturbations. Due to the lack of homogeneity in living tissues it is difficult to estimate the physiological effect of chemicals, including potential toxicity. Here we investigate a biologically motivated model for estimating tissue level responses by aggregating the behavior of a cell population. We assume that the molecular state of individual cells is independently governed by discrete non-deterministic signaling mechanisms. This results in noisy but highly reproducible aggregate level responses that are consistent with experimental data. Results We developed an asynchronous threshold Boolean network simulation algorithm to model signal transduction in a single cell, and then used an ensemble of these models to estimate the aggregate response across a cell population. Using published data, we derived a putative crosstalk network involving growth factors and cytokines - i.e., Epidermal Growth Factor, Insulin, Insulin like Growth Factor Type 1, and Tumor Necrosis Factor α - to describe early signaling events in cell proliferation signal transduction. Reproducibility of the modeling technique across ensembles of Boolean networks representing cell populations is investigated. Furthermore, we compare our simulation results to experimental observations of hepatocytes reported in the literature. Conclusion A systematic analysis of the results following differential stimulation of this model by growth factors and cytokines suggests that: (a) using Boolean network ensembles with asynchronous updating provides biologically plausible noisy individual cellular responses with reproducible mean behavior for large cell populations, and (b) with sufficient data our model can estimate the response to different concentrations of extracellular ligands. Our results suggest that this

  2. Cellular computational networks--a scalable architecture for learning the dynamics of large networked systems.

    PubMed

    Luitel, Bipul; Venayagamoorthy, Ganesh Kumar

    2014-02-01

    Neural networks for implementing large networked systems such as smart electric power grids consist of multiple inputs and outputs. Many outputs lead to a greater number of parameters to be adapted. Each additional variable increases the dimensionality of the problem and hence learning becomes a challenge. Cellular computational networks (CCNs) are a class of sparsely connected dynamic recurrent networks (DRNs). By proper selection of a set of input elements for each output variable in a given application, a DRN can be modified into a CCN which significantly reduces the complexity of the neural network and allows use of simple training methods for independent learning in each cell thus making it scalable. This article demonstrates this concept of developing a CCN using dimensionality reduction in a DRN for scalability and better performance. The concept has been analytically explained and empirically verified through application. PMID:24300549

  3. Sources of uncertainty in rainfall maps from cellular communication networks

    NASA Astrophysics Data System (ADS)

    Rios Gaona, M. F.; Overeem, A.; Leijnse, H.; Uijlenhoet, R.

    2015-03-01

    ground truth). Thus, we were able to not only identify and quantify the sources of uncertainty in such rainfall maps, but also to test the actual and optimal performance of one commercial microwave network from one of the cellular providers in the Netherlands.

  4. Coexistence of 3G Repeaters with LTE Base Stations

    PubMed Central

    Yeo, Woon-Young

    2013-01-01

    Repeaters have been an attractive solution for mobile operators to upgrade their wireless networks at low cost and to extend network coverage effectively. Since the first LTE commercial deployment in 2009, many mobile operators have launched LTE networks by upgrading their 3G and legacy networks. Because all 3G frequency bands are shared with the frequency bands for LTE deployment and 3G mobile operators have an enormous number of repeaters, reusing 3G repeaters in LTE networks is definitely a practical and cost-efficient solution. However, 3G repeaters usually do not support spatial multiplexing with multiple antennas, and thus it is difficult to reuse them directly in LTE networks. In order to support spatial multiplexing of LTE, the role of 3G repeaters should be replaced with small LTE base stations or MIMO-capable repeaters. In this paper, a repeater network is proposed to reuse 3G repeaters in LTE deployment while still supporting multilayer transmission of LTE. Interestingly, the proposed network has a higher cluster throughput than an LTE network with MIMO-capable repeaters. PMID:24459420

  5. Environmental Monitoring using Measurements from Cellular Network Infrastructure

    NASA Astrophysics Data System (ADS)

    David, N.; Gao, O. H.

    2015-12-01

    atmospheric phenomena using current and future planned frequencies of cellular network infrastructure will be introduced.

  6. Cellular and network mechanisms of genetically-determined absence seizures.

    PubMed

    Pinault, Didier; O'Brien, Terence J

    2005-01-01

    The absence epilepsies are characterized by recurrent episodes of loss of consciousness associated with generalized spike-and-wave discharges, with an abrupt onset and offset, in the thalamocortical system. In the absence of detailed neurophysiological studies in humans, many of the concepts regarding the pathophysiological basis of absence seizures are based on studies in animal models. Each of these models has its particular strengths and limitations, and the validity of findings from these models for the human condition cannot be assumed. Consequently, studies in different models have produced some conflicting findings and conclusions. A long-standing concept, based primarily from studies in vivo in cats and in vitro brain slices, is that these paroxysmal electrical events develop suddenly from sleep-related spindle oscillations. More specifically, it is proposed that the initial mechanisms that underlie absence-related spike-and-wave discharges are located in the thalamus, involving especially the thalamic reticular nucleus. By contrast, more recent studies in well-established, genetic models of absence epilepsy in rats demonstrate that spike-and-wave discharges originate in a cortical focus and develop from a wake-related natural corticothalamic sensorimotor rhythm. In this review we integrate recent findings showing that, in both the thalamus and the neocortex, genetically-determined, absence-related spike-and-wave discharges are the manifestation of hypersynchronized, cellular, rhythmic excitations and inhibitions that result from a combination of complex, intrinsic, synaptic mechanisms. Arguments are put forward supporting the hypothesis that layer VI corticothalamic neurons act as 'drivers' in the generation of spike-and-wave discharges in the somatosensory thalamocortical system that result in corticothalamic resonances particularly initially involving the thalamic reticular nucleus. However an important unresolved question is: what are the cellular and

  7. Radio Resource Allocation on Complex 4G Wireless Cellular Networks

    NASA Astrophysics Data System (ADS)

    Psannis, Kostas E.

    2015-09-01

    In this article we consider the heuristic algorithm which improves step by step wireless data delivery over LTE cellular networks by using the total transmit power with the constraint on users’ data rates, and the total throughput with the constraints on the total transmit power as well as users’ data rates, which are jointly integrated into a hybrid-layer design framework to perform radio resource allocation for multiple users, and to effectively decide the optimal system parameter such as modulation and coding scheme (MCS) in order to adapt to the varying channel quality. We propose new heuristic algorithm which balances the accessible data rate, the initial data rates of each user allocated by LTE scheduler, the priority indicator which signals delay- throughput- packet loss awareness of the user, and the buffer fullness by achieving maximization of radio resource allocation for multiple users. It is noted that the overall performance is improved with the increase in the number of users, due to multiuser diversity. Experimental results illustrate and validate the accuracy of the proposed methodology.

  8. Cellular nonlinear networks for strike-point localization at JET

    NASA Astrophysics Data System (ADS)

    Arena, P.; Fortuna, L.; Bruno, M.; Vagliasindi, G.; Murari, A.; Andrew, P.; Mazzitelli, G.

    2005-11-01

    At JET, the potential of fast image processing for real-time purposes is thoroughly investigated. Particular attention is devoted to smart sensors based on system on chip technology. The data of the infrared cameras were processed with a chip implementing a cellular nonlinear network (CNN) structure so as to support and complement the magnetic diagnostics in the real-time localization of the strike-point position in the divertor. The circuit consists of two layers of complementary metal-oxide semiconductor components, the first being the sensor and the second implementing the actual CNN. This innovative hardware has made it possible to determine the position of the maximum thermal load with a time resolution of the order of 30 ms. Good congruency has been found with the measurement from the thermocouples in the divertor, proving the potential of the infrared data in locating the region of the maximum thermal load. The results are also confirmed by JET magnetic codes, both those used for the equilibrium reconstructions and those devoted to the identification of the plasma boundary.

  9. Network signatures of cellular immortalization in human lymphoblastoid cell lines

    SciTech Connect

    Shim, Sung-Mi; Jung, So-Young; Nam, Hye-Young; Kim, Hye-Ryun; Lee, Mee-Hee; Kim, Jun-Woo; Han, Bok-Ghee; Jeon, Jae-Pil

    2013-11-15

    Highlights: •We identified network signatures of LCL immortalization from transcriptomic profiles. •More than 41% of DEGs are possibly regulated by miRNAs in LCLs. •MicroRNA target genes in LCLs are involved in apoptosis and immune-related functions. •This approach is useful to find functional miRNA targets in specific cell conditions. -- Abstract: Human lymphoblastoid cell line (LCL) has been used as an in vitro cell model in genetic and pharmacogenomic studies, as well as a good model for studying gene expression regulatory machinery using integrated genomic analyses. In this study, we aimed to identify biological networks of LCL immortalization from transcriptomic profiles of microRNAs and their target genes in LCLs. We first selected differentially expressed genes (DEGs) and microRNAs (DEmiRs) between early passage LCLs (eLCLs) and terminally differentiated late passage LCLs (tLCLs). The in silico and correlation analysis of these DEGs and DEmiRs revealed that 1098 DEG–DEmiR pairs were found to be positively (n = 591 pairs) or negatively (n = 507 pairs) correlated with each other. More than 41% of DEGs are possibly regulated by miRNAs in LCL immortalizations. The target DEGs of DEmiRs were enriched for cellular functions associated with apoptosis, immune response, cell death, JAK–STAT cascade and lymphocyte activation while non-miRNA target DEGs were over-represented for basic cell metabolisms. The target DEGs correlated negatively with miR-548a-3p and miR-219-5p were significantly associated with protein kinase cascade, and the lymphocyte proliferation and apoptosis, respectively. In addition, the miR-106a and miR-424 clusters located in the X chromosome were enriched in DEmiR–mRNA pairs for LCL immortalization. In this study, the integrated transcriptomic analysis of LCLs could identify functional networks of biologically active microRNAs and their target genes involved in LCL immortalization.

  10. When are two multi-layer cellular neural networks the same?

    PubMed

    Ban, Jung-Chao; Chang, Chih-Hung

    2016-07-01

    This paper aims to characterize whether a multi-layer cellular neural network is of deep architecture; namely, when can an n-layer cellular neural network be replaced by an m-layer cellular neural network for mnetwork is revealed. PMID:27085113

  11. Predict drug-protein interaction in cellular networking.

    PubMed

    Xiao, Xuan; Min, Jian-Liang; Wang, Pu; Chou, Kuo-Chen

    2013-01-01

    Involved with many diseases such as cancer, diabetes, neurodegenerative, inflammatory and respiratory disorders, GPCRs (G-protein-coupled receptors) are the most frequent targets for drug development: over 50% of all prescription drugs currently on the market are actually acting by targeting GPCRs directly or indirectly. Found in every living thing and nearly all cells, ion channels play crucial roles for many vital functions in life, such as heartbeat, sensory transduction, and central nervous system response. Their dysfunction may have significant impact to human health, and hence ion channels are deemed as "the next GPCRs". To develop GPCR-targeting or ion-channel-targeting drugs, the first important step is to identify the interactions between potential drug compounds with the two kinds of protein receptors in the cellular networking. In this minireview, we are to introduce two predictors. One is called iGPCR-Drug accessible at http://www.jci-bioinfo.cn/iGPCR-Drug/; the other called iCDI-PseFpt at http://www.jci-bioinfo.cn/iCDI-PseFpt. The former is for identifying the interactions of drug compounds with GPCRs; while the latter for that with ion channels. In both predictors, the drug compound was formulated by the two-dimensional molecular fingerprint, and the protein receptor by the pseudo amino acid composition generated with the grey model theory, while the operation engine was the fuzzy K-nearest neighbor algorithm. For the convenience of most experimental pharmaceutical and medical scientists, a step-bystep guide is provided on how to use each of the two web-servers to get the desired results without the need to follow the complicated mathematics involved originally for their establishment. PMID:23889048

  12. Design mobile satellite system architecture as an integral part of the cellular access digital network

    NASA Technical Reports Server (NTRS)

    Chien, E. S. K.; Marinho, J. A.; Russell, J. E., Sr.

    1988-01-01

    The Cellular Access Digital Network (CADN) is the access vehicle through which cellular technology is brought into the mainstream of the evolving integrated telecommunications network. Beyond the integrated end-to-end digital access and per call network services provisioning of the Integrated Services Digital Network (ISDN), the CADN engenders the added capability of mobility freedom via wireless access. One key element of the CADN network architecture is the standard user to network interface that is independent of RF transmission technology. Since the Mobile Satellite System (MSS) is envisioned to not only complement but also enhance the capabilities of the terrestrial cellular telecommunications network, compatibility and interoperability between terrestrial cellular and mobile satellite systems are vitally important to provide an integrated moving telecommunications network of the future. From a network standpoint, there exist very strong commonalities between the terrestrial cellular system and the mobile satellite system. Therefore, the MSS architecture should be designed as an integral part of the CADN. This paper describes the concept of the CADN, the functional architecture of the MSS, and the user-network interface signaling protocols.

  13. Traffic Driven Analysis of Cellular and WiFi Networks

    ERIC Educational Resources Information Center

    Paul, Utpal Kumar

    2012-01-01

    Since the days Internet traffic proliferated, measurement, monitoring and analysis of network traffic have been critical to not only the basic understanding of large networks, but also to seek improvements in resource management, traffic engineering and security. At the current times traffic in wireless local and wide area networks are facing…

  14. Glycoengineered Monoclonal Antibodies with Homogeneous Glycan (M3, G0, G2, and A2) Using a Chemoenzymatic Approach Have Different Affinities for FcγRIIIa and Variable Antibody-Dependent Cellular Cytotoxicity Activities

    PubMed Central

    Kurogochi, Masaki; Mori, Masako; Osumi, Kenji; Tojino, Mami; Sugawara, Shu-ichi; Takashima, Shou; Hirose, Yuriko; Tsukimura, Wataru; Mizuno, Mamoru; Amano, Junko; Matsuda, Akio; Tomita, Masahiro; Takayanagi, Atsushi; Shoda, Shin-Ichiro; Shirai, Takashi

    2015-01-01

    Many therapeutic antibodies have been developed, and IgG antibodies have been extensively generated in various cell expression systems. IgG antibodies contain N-glycans at the constant region of the heavy chain (Fc domain), and their N-glycosylation patterns differ during various processes or among cell expression systems. The Fc N-glycan can modulate the effector functions of IgG antibodies, such as antibody-dependent cellular cytotoxicity (ADCC) and complement dependent cytotoxicity (CDC). To control Fc N-glycans, we performed a rearrangement of Fc N-glycans from a heterogeneous N-glycosylation pattern to homogeneous N-glycans using chemoenzymatic approaches with two types of endo-β-N-acetyl glucosaminidases (ENG’ases), one that works as a hydrolase to cleave all heterogeneous N-glycans, another that is used as a glycosynthase to generate homogeneous N-glycans. As starting materials, we used an anti-Her2 antibody produced in transgenic silkworm cocoon, which consists of non-fucosylated pauci-mannose type (Man2-3GlcNAc2), high-mannose type (Man4-9GlcNAc2), and complex type (Man3GlcNAc3-4) N-glycans. As a result of the cleavage of several ENG’ases (endoS, endoM, endoD, endoH, and endoLL), the heterogeneous glycans on antibodies were fully transformed into homogeneous-GlcNAc by a combination of endoS, endoD, and endoLL. Next, the desired N-glycans (M3; Man3GlcNAc1, G0; GlcNAc2Man3GlcNAc1, G2; Gal2GlcNAc2Man3GlcNAc1, A2; NeuAc2Gal2GlcNAc2Man3GlcNAc1) were transferred from the corresponding oxazolines to the GlcNAc residue on the intact anti-Her2 antibody with an ENG’ase mutant (endoS-D233Q), and the glycoengineered anti-Her2 antibody was obtained. The binding assay of anti-Her2 antibody with homogenous N-glycans with FcγRIIIa-V158 showed that the glycoform influenced the affinity for FcγRIIIa-V158. In addition, the ADCC assay for the glycoengineered anti-Her2 antibody (mAb-M3, mAb-G0, mAb-G2, and mAb-A2) was performed using SKBR-3 and BT-474 as target cells

  15. Methods for the Analysis of Protein Phosphorylation-Mediated Cellular Signaling Networks.

    PubMed

    White, Forest M; Wolf-Yadlin, Alejandro

    2016-06-12

    Protein phosphorylation-mediated cellular signaling networks regulate almost all aspects of cell biology, including the responses to cellular stimulation and environmental alterations. These networks are highly complex and comprise hundreds of proteins and potentially thousands of phosphorylation sites. Multiple analytical methods have been developed over the past several decades to identify proteins and protein phosphorylation sites regulating cellular signaling, and to quantify the dynamic response of these sites to different cellular stimulation. Here we provide an overview of these methods, including the fundamental principles governing each method, their relative strengths and weaknesses, and some examples of how each method has been applied to the analysis of complex signaling networks. When applied correctly, each of these techniques can provide insight into the topology, dynamics, and regulation of protein phosphorylation signaling networks. PMID:27049636

  16. Methods for the Analysis of Protein Phosphorylation–Mediated Cellular Signaling Networks

    NASA Astrophysics Data System (ADS)

    White, Forest M.; Wolf-Yadlin, Alejandro

    2016-06-01

    Protein phosphorylation–mediated cellular signaling networks regulate almost all aspects of cell biology, including the responses to cellular stimulation and environmental alterations. These networks are highly complex and comprise hundreds of proteins and potentially thousands of phosphorylation sites. Multiple analytical methods have been developed over the past several decades to identify proteins and protein phosphorylation sites regulating cellular signaling, and to quantify the dynamic response of these sites to different cellular stimulation. Here we provide an overview of these methods, including the fundamental principles governing each method, their relative strengths and weaknesses, and some examples of how each method has been applied to the analysis of complex signaling networks. When applied correctly, each of these techniques can provide insight into the topology, dynamics, and regulation of protein phosphorylation signaling networks.

  17. Effects of cellular homeostatic intrinsic plasticity on dynamical and computational properties of biological recurrent neural networks.

    PubMed

    Naudé, Jérémie; Cessac, Bruno; Berry, Hugues; Delord, Bruno

    2013-09-18

    Homeostatic intrinsic plasticity (HIP) is a ubiquitous cellular mechanism regulating neuronal activity, cardinal for the proper functioning of nervous systems. In invertebrates, HIP is critical for orchestrating stereotyped activity patterns. The functional impact of HIP remains more obscure in vertebrate networks, where higher order cognitive processes rely on complex neural dynamics. The hypothesis has emerged that HIP might control the complexity of activity dynamics in recurrent networks, with important computational consequences. However, conflicting results about the causal relationships between cellular HIP, network dynamics, and computational performance have arisen from machine-learning studies. Here, we assess how cellular HIP effects translate into collective dynamics and computational properties in biological recurrent networks. We develop a realistic multiscale model including a generic HIP rule regulating the neuronal threshold with actual molecular signaling pathways kinetics, Dale's principle, sparse connectivity, synaptic balance, and Hebbian synaptic plasticity (SP). Dynamic mean-field analysis and simulations unravel that HIP sets a working point at which inputs are transduced by large derivative ranges of the transfer function. This cellular mechanism ensures increased network dynamics complexity, robust balance with SP at the edge of chaos, and improved input separability. Although critically dependent upon balanced excitatory and inhibitory drives, these effects display striking robustness to changes in network architecture, learning rates, and input features. Thus, the mechanism we unveil might represent a ubiquitous cellular basis for complex dynamics in neural networks. Understanding this robustness is an important challenge to unraveling principles underlying self-organization around criticality in biological recurrent neural networks. PMID:24048833

  18. Cues for cellular assembly of vascular elastin networks

    NASA Astrophysics Data System (ADS)

    Kothapalli, Chandrasekhar R.

    Elastin, a structural protein distributed in the extracellular matrix of vascular tissues is critical to the maintenance of vascular mechanics, besides regulation of cell-signaling pathways involved in injury response and morphogenesis. Thus, congenital absence or disease-mediated degradation of vascular elastin and its malformation within native vessels due to innately poor elastin synthesis by adult vascular cells compromise vascular homeostasis. Current elastin regenerative strategies using tissue engineering principles are limited by the progressive destabilization of tropoelastin mRNA expression in adult vascular cells and the unavailability of scaffolds that can provide cellular cues necessary to up-regulate elastin synthesis and regenerate faithful mimics of native elastin. Since our earlier studies demonstrated the elastogenic utility of hyaluronan (HA)-based cues, we have currently sought to identify a unique set of culture conditions based on HA fragments (0.756-2000 kDa), growth factors (TGF-beta1, IGF-1) and other biomolecules (Cu2+ ions, LOX), which will together enhance synthesis, crosslinking, maturation and fibrous elastin matrix formation by adult SMCs, under both healthy and inflammatory conditions. It was observed that TGF-beta1 (1 ng/mL) together with HA oligomers (0.2 microg/mL) synergistically suppressed SMC proliferation, enhanced tropoelastin (8-fold) and matrix elastin synthesis (5.5-fold), besides improving matrix yield (4.5-fold), possibly by increasing production and activity of lysyl oxidase (LOX). Though addition of IGF-1 alone did not offer any advantage, HA fragments (20-200 kDa) in the presence of IGF-1 stimulated tropoelastin and soluble elastin synthesis more than 2.2-fold, with HMW HA contributing for ˜5-fold increase in crosslinked matrix elastin synthesis. Similarly, 0.1 M of Cu2+ ions, alone or together with HA fragments stimulated synthesis of tropoelastin (4-fold) and crosslinked matrix elastin (4.5-fold), via increases in

  19. Participatory sensing as an enabler for self-organisation in future cellular networks

    NASA Astrophysics Data System (ADS)

    Imran, Muhammad Ali; Imran, Ali; Onireti, Oluwakayode

    2013-12-01

    In this short review paper we summarise the emerging challenges in the field of participatory sensing for the self-organisation of the next generation of wireless cellular networks. We identify the potential of participatory sensing in enabling the self-organisation, deployment optimisation and radio resource management of wireless cellular networks. We also highlight how this approach can meet the future goals for the next generation of cellular system in terms of infrastructure sharing, management of multiple radio access techniques, flexible usage of spectrum and efficient management of very small data cells.

  20. Performance evaluation of power control algorithms in wireless cellular networks

    NASA Astrophysics Data System (ADS)

    Temaneh-Nyah, C.; Iita, V.

    2014-10-01

    Power control in a mobile communication network intents to control the transmission power levels in such a way that the required quality of service (QoS) for the users is guaranteed with lowest possible transmission powers. Most of the studies of power control algorithms in the literature are based on some kind of simplified assumptions which leads to compromise in the validity of the results when applied in a real environment. In this paper, a CDMA network was simulated. The real environment was accounted for by defining the analysis area and the network base stations and mobile stations are defined by their geographical coordinates, the mobility of the mobile stations is accounted for. The simulation also allowed for a number of network parameters including the network traffic, and the wireless channel models to be modified. Finally, we present the simulation results of a convergence speed based comparative analysis of three uplink power control algorithms.

  1. Simulating Quantitative Cellular Responses Using Asynchronous Threshold Boolean Network Ensembles

    EPA Science Inventory

    With increasing knowledge about the potential mechanisms underlying cellular functions, it is becoming feasible to predict the response of biological systems to genetic and environmental perturbations. Due to the lack of homogeneity in living tissues it is difficult to estimate t...

  2. Tools and Models for Integrating Multiple Cellular Networks

    SciTech Connect

    Gerstein, Mark

    2015-11-06

    In this grant, we have systematically investigated the integrated networks, which are responsible for the coordination of activity between metabolic pathways in prokaryotes. We have developed several computational tools to analyze the topology of the integrated networks consisting of metabolic, regulatory, and physical interaction networks. The tools are all open-source, and they are available to download from Github, and can be incorporated in the Knowledgebase. Here, we summarize our work as follow. Understanding the topology of the integrated networks is the first step toward understanding its dynamics and evolution. For Aim 1 of this grant, we have developed a novel algorithm to determine and measure the hierarchical structure of transcriptional regulatory networks [1]. The hierarchy captures the direction of information flow in the network. The algorithm is generally applicable to regulatory networks in prokaryotes, yeast and higher organisms. Integrated datasets are extremely beneficial in understanding the biology of a system in a compact manner due to the conflation of multiple layers of information. Therefore for Aim 2 of this grant, we have developed several tools and carried out analysis for integrating system-wide genomic information. To make use of the structural data, we have developed DynaSIN for protein-protein interactions networks with various dynamical interfaces [2]. We then examined the association between network topology with phenotypic effects such as gene essentiality. In particular, we have organized E. coli and S. cerevisiae transcriptional regulatory networks into hierarchies. We then correlated gene phenotypic effects by tinkering with different layers to elucidate which layers were more tolerant to perturbations [3]. In the context of evolution, we also developed a workflow to guide the comparison between different types of biological networks across various species using the concept of rewiring [4], and Furthermore, we have developed

  3. C. elegans Metabolic Gene Regulatory Networks Govern the Cellular Economy

    PubMed Central

    Watson, Emma; Walhout, Albertha J.M.

    2014-01-01

    Diet greatly impacts metabolism in health and disease. In response to the presence or absence of specific nutrients, metabolic gene regulatory networks sense the metabolic state of the cell and regulate metabolic flux accordingly, for instance by the transcriptional control of metabolic enzymes. Here we discuss recent insights regarding metazoan metabolic regulatory networks using the nematode Caenorhabditis elegans as a model, including the modular organization of metabolic gene regulatory networks, the prominent impact of diet on the transcriptome and metabolome, specialized roles of nuclear hormone receptors in responding to dietary conditions, regulation of metabolic genes and metabolic regulators by microRNAs, and feedback between metabolic genes and their regulators. PMID:24731597

  4. Detection of silent cells, synchronization and modulatory activity in developing cellular networks.

    PubMed

    Hjorth, Johannes J J; Dawitz, Julia; Kroon, Tim; Pires, Johny; Dassen, Valerie J; Berkhout, Janna A; Emperador Melero, Javier; Nadadhur, Aish G; Alevra, Mihai; Toonen, Ruud F; Heine, Vivi M; Mansvelder, Huibert D; Meredith, Rhiannon M

    2016-04-01

    Developing networks in the immature nervous system and in cellular cultures are characterized by waves of synchronous activity in restricted clusters of cells. Synchronized activity in immature networks is proposed to regulate many different developmental processes, from neuron growth and cell migration, to the refinement of synapses, topographic maps, and the mature composition of ion channels. These emergent activity patterns are not present in all cells simultaneously within the network and more immature "silent" cells, potentially correlated with the presence of silent synapses, are prominent in different networks during early developmental periods. Many current network analyses for detection of synchronous cellular activity utilize activity-based pixel correlations to identify cellular-based regions of interest (ROIs) and coincident cell activity. However, using activity-based correlations, these methods first underestimate or ignore the inactive silent cells within the developing network and second, are difficult to apply within cell-dense regions commonly found in developing brain networks. In addition, previous methods may ignore ROIs within a network that shows transient activity patterns comprising both inactive and active periods. We developed analysis software to semi-automatically detect cells within developing neuronal networks that were imaged using calcium-sensitive reporter dyes. Using an iterative threshold, modulation of activity was tracked within individual cells across the network. The distribution pattern of both inactive and active, including synchronous cells, could be determined based on distance measures to neighboring cells and according to different anatomical layers. PMID:26097169

  5. Retrieval algorithm for rainfall mapping from microwave links in a cellular communication network

    NASA Astrophysics Data System (ADS)

    Overeem, Aart; Uijlenhoet, Remko; Leijnse, Hidde

    2016-04-01

    Microwave links in commercial cellular communication networks hold a promise for areal rainfall monitoring and could complement rainfall estimates from ground-based weather radars, rain gauges, and satellites. It has been shown that country-wide rainfall maps can be derived from the signal attenuations of microwave links in such a network. We present a rainfall retrieval algorithm, which is employed to obtain rainfall maps from microwave links in a cellular communication network. We compare these rainfall maps to gauge-adjusted radar rainfall maps. The microwave link data set, as well as the developed code, a package in the open source scripting language "R", are freely available at GitHub (https://github.com/overeem11/RAINLINK). The purpose of this presentation is to promote rainfall mapping utilizing microwave links from cellular communication networks as an alternative or complementary means for continental-scale rainfall monitoring.

  6. Quantifying Uncertainties in Rainfall Maps from Cellular Communication Networks

    NASA Astrophysics Data System (ADS)

    Uijlenhoet, R.; Rios Gaona, M. F.; Overeem, A.; Leijnse, H.

    2014-12-01

    The core idea behind rainfall retrievals from commercial microwave link networks is to measure the decrease in power due to attenuation of the electromagnetic signal by raindrops along the link path. Accurate rainfall measurements are of vital importance in hydrological applications, for instance, flash-flood early-warning systems, agriculture, and climate modeling. Hence, such an alternative technique fulfills the need for measurements with higher resolution in time and space, especially in places where standard rain gauge-networks are scarce or poorly maintained. Rainfall estimation via commercial microwave link networks, at country-wide scales, has recently been demonstrated. Despite their potential applicability in rainfall estimation at higher spatiotemporal resolutions, the uncertainties present in link-based rainfall maps are not yet fully comprehended. Now we attempt to quantify the inherent sources of uncertainty present in interpolated maps computed from commercial microwave link rainfall retrievals. In order to disentangle these sources of uncertainty we identified four main sources of error: 1) microwave link measurements, 2) availability of microwave link measurements, 3) spatial distribution of the network, and 4) interpolation methodology. We computed more than 1000 rainfall fields, for The Netherlands, from real and simulated microwave link data. These rainfall fields were compared to quality-controlled gauge-adjusted radar rainfall maps considered as ground-truth. Thus we were able to quantify the contribution of errors in microwave link measurements to the overall uncertainty. The actual performance of the commercial microwave link network is affected by the intermittent availability of the links, not only in time but also in space. We simulated a fully-operational network in time and space, and thus we quantified the role of the availability of microwave link measurements to the overall uncertainty. This research showed that the largest source of

  7. Resource Management in QoS-Aware Wireless Cellular Networks

    ERIC Educational Resources Information Center

    Zhang, Zhi

    2011-01-01

    Emerging broadband wireless networks that support high speed packet data with heterogeneous quality of service (QoS) requirements demand more flexible and efficient use of the scarce spectral resource. Opportunistic scheduling exploits the time-varying, location-dependent channel conditions to achieve multiuser diversity. In this work, we study…

  8. Reverse engineering cellular decisions for hybrid reconfigurable network modeling

    NASA Astrophysics Data System (ADS)

    Blair, Howard A.; Saranak, Jureepan; Foster, Kenneth W.

    2011-06-01

    Cells as microorganisms and within multicellular organisms make robust decisions. Knowing how these complex cells make decisions is essential to explain, predict or mimic their behavior. The discovery of multi-layer multiple feedback loops in the signaling pathways of these modular hybrid systems suggests their decision making is sophisticated. Hybrid systems coordinate and integrate signals of various kinds: discrete on/off signals, continuous sensory signals, and stochastic and continuous fluctuations to regulate chemical concentrations. Such signaling networks can form reconfigurable networks of attractors and repellors giving them an extra level of organization that has resilient decision making built in. Work on generic attractor and repellor networks and on the already identified feedback networks and dynamic reconfigurable regulatory topologies in biological cells suggests that biological systems probably exploit such dynamic capabilities. We present a simple behavior of the swimming unicellular alga Chlamydomonas that involves interdependent discrete and continuous signals in feedback loops. We show how to rigorously verify a hybrid dynamical model of a biological system with respect to a declarative description of a cell's behavior. The hybrid dynamical systems we use are based on a unification of discrete structures and continuous topologies developed in prior work on convergence spaces. They involve variables of discrete and continuous types, in the sense of type theory in mathematical logic. A unification such as afforded by convergence spaces is necessary if one wants to take account of the affect of the structural relationships within each type on the dynamics of the system.

  9. Application of Cellular Automata to Detection of Malicious Network Packets

    ERIC Educational Resources Information Center

    Brown, Robert L.

    2014-01-01

    A problem in computer security is identification of attack signatures in network packets. An attack signature is a pattern of bits that characterizes a particular attack. Because there are many kinds of attacks, there are potentially many attack signatures. Furthermore, attackers may seek to avoid detection by altering the attack mechanism so that…

  10. Frequency-dependent micromechanics of cellularized biopolymer networks

    NASA Astrophysics Data System (ADS)

    Jones, Chris; Kim, Jihan; McIntyre, David; Sun, Bo

    Mechanical interactions between cells and the extracellular matrix (ECM) influence many cellular behaviors such as growth, differentiation, and migration. These are dynamic processes in which the cells actively remodel the ECM. Reconstituted collagen gel is a common model ECM for studying cell-ECM interactions in vitro because collagen is the most abundant component of mammalian ECM and gives the ECM its material stiffness. We embed micron-sized particles in collagen and use holographic optical tweezers to apply forces to the particles in multiple directions and over a range of frequencies up to 10 Hz. We calculate the local compliance and show that it is dependent on both the direction and frequency of the applied force. Performing the same measurement on many particles allows us to characterize the spatial inhomogeneity of the mechanical properties and shows that the compliance decreases at higher frequencies. Performing these measurements on cell-populated collagen gels shows that cellular remodeling of the ECM changes the mechanical properties of the collagen and we investigate whether this change is dependent on the local strain and distance from nearby cells.

  11. Cellular network entropy as the energy potential in Waddington's differentiation landscape

    NASA Astrophysics Data System (ADS)

    Banerji, Christopher R. S.; Miranda-Saavedra, Diego; Severini, Simone; Widschwendter, Martin; Enver, Tariq; Zhou, Joseph X.; Teschendorff, Andrew E.

    2013-10-01

    Differentiation is a key cellular process in normal tissue development that is significantly altered in cancer. Although molecular signatures characterising pluripotency and multipotency exist, there is, as yet, no single quantitative mark of a cellular sample's position in the global differentiation hierarchy. Here we adopt a systems view and consider the sample's network entropy, a measure of signaling pathway promiscuity, computable from a sample's genome-wide expression profile. We demonstrate that network entropy provides a quantitative, in-silico, readout of the average undifferentiated state of the profiled cells, recapitulating the known hierarchy of pluripotent, multipotent and differentiated cell types. Network entropy further exhibits dynamic changes in time course differentiation data, and in line with a sample's differentiation stage. In disease, network entropy predicts a higher level of cellular plasticity in cancer stem cell populations compared to ordinary cancer cells. Importantly, network entropy also allows identification of key differentiation pathways. Our results are consistent with the view that pluripotency is a statistical property defined at the cellular population level, correlating with intra-sample heterogeneity, and driven by the degree of signaling promiscuity in cells. In summary, network entropy provides a quantitative measure of a cell's undifferentiated state, defining its elevation in Waddington's landscape.

  12. Logical Modeling and Dynamical Analysis of Cellular Networks

    PubMed Central

    Abou-Jaoudé, Wassim; Traynard, Pauline; Monteiro, Pedro T.; Saez-Rodriguez, Julio; Helikar, Tomáš; Thieffry, Denis; Chaouiya, Claudine

    2016-01-01

    The logical (or logic) formalism is increasingly used to model regulatory and signaling networks. Complementing these applications, several groups contributed various methods and tools to support the definition and analysis of logical models. After an introduction to the logical modeling framework and to several of its variants, we review here a number of recent methodological advances to ease the analysis of large and intricate networks. In particular, we survey approaches to determine model attractors and their reachability properties, to assess the dynamical impact of variations of external signals, and to consistently reduce large models. To illustrate these developments, we further consider several published logical models for two important biological processes, namely the differentiation of T helper cells and the control of mammalian cell cycle. PMID:27303434

  13. Dynamical modeling and analysis of large cellular regulatory networks

    NASA Astrophysics Data System (ADS)

    Bérenguier, D.; Chaouiya, C.; Monteiro, P. T.; Naldi, A.; Remy, E.; Thieffry, D.; Tichit, L.

    2013-06-01

    The dynamical analysis of large biological regulatory networks requires the development of scalable methods for mathematical modeling. Following the approach initially introduced by Thomas, we formalize the interactions between the components of a network in terms of discrete variables, functions, and parameters. Model simulations result in directed graphs, called state transition graphs. We are particularly interested in reachability properties and asymptotic behaviors, which correspond to terminal strongly connected components (or "attractors") in the state transition graph. A well-known problem is the exponential increase of the size of state transition graphs with the number of network components, in particular when using the biologically realistic asynchronous updating assumption. To address this problem, we have developed several complementary methods enabling the analysis of the behavior of large and complex logical models: (i) the definition of transition priority classes to simplify the dynamics; (ii) a model reduction method preserving essential dynamical properties, (iii) a novel algorithm to compact state transition graphs and directly generate compressed representations, emphasizing relevant transient and asymptotic dynamical properties. The power of an approach combining these different methods is demonstrated by applying them to a recent multilevel logical model for the network controlling CD4+ T helper cell response to antigen presentation and to a dozen cytokines. This model accounts for the differentiation of canonical Th1 and Th2 lymphocytes, as well as of inflammatory Th17 and regulatory T cells, along with many hybrid subtypes. All these methods have been implemented into the software GINsim, which enables the definition, the analysis, and the simulation of logical regulatory graphs.

  14. Cellular Metabolic Network Analysis: Discovering Important Reactions in Treponema pallidum

    PubMed Central

    Chen, Xueying; Zhao, Min; Qu, Hong

    2015-01-01

    T. pallidum, the syphilis-causing pathogen, performs very differently in metabolism compared with other bacterial pathogens. The desire for safe and effective vaccine of syphilis requests identification of important steps in T. pallidum's metabolism. Here, we apply Flux Balance Analysis to represent the reactions quantitatively. Thus, it is possible to cluster all reactions in T. pallidum. By calculating minimal cut sets and analyzing topological structure for the metabolic network of T. pallidum, critical reactions are identified. As a comparison, we also apply the analytical approaches to the metabolic network of H. pylori to find coregulated drug targets and unique drug targets for different microorganisms. Based on the clustering results, all reactions are further classified into various roles. Therefore, the general picture of their metabolic network is obtained and two types of reactions, both of which are involved in nucleic acid metabolism, are found to be essential for T. pallidum. It is also discovered that both hubs of reactions and the isolated reactions in purine and pyrimidine metabolisms play important roles in T. pallidum. These reactions could be potential drug targets for treating syphilis. PMID:26495292

  15. Cellular metabolic network analysis: discovering important reactions in Treponema pallidum.

    PubMed

    Chen, Xueying; Zhao, Min; Qu, Hong

    2015-01-01

    T. pallidum, the syphilis-causing pathogen, performs very differently in metabolism compared with other bacterial pathogens. The desire for safe and effective vaccine of syphilis requests identification of important steps in T. pallidum's metabolism. Here, we apply Flux Balance Analysis to represent the reactions quantitatively. Thus, it is possible to cluster all reactions in T. pallidum. By calculating minimal cut sets and analyzing topological structure for the metabolic network of T. pallidum, critical reactions are identified. As a comparison, we also apply the analytical approaches to the metabolic network of H. pylori to find coregulated drug targets and unique drug targets for different microorganisms. Based on the clustering results, all reactions are further classified into various roles. Therefore, the general picture of their metabolic network is obtained and two types of reactions, both of which are involved in nucleic acid metabolism, are found to be essential for T. pallidum. It is also discovered that both hubs of reactions and the isolated reactions in purine and pyrimidine metabolisms play important roles in T. pallidum. These reactions could be potential drug targets for treating syphilis. PMID:26495292

  16. Multiperiod cellular network design via price-influenced simulated annealing (PISA).

    PubMed

    Menon, Syam; Amiri, Ali

    2006-06-01

    Cellular telecommunications systems tend to be more flexible than traditional ones. As a result, traditional approaches to telecommunications network design are often inappropriate for the design of cellular networks, and approaches that explicitly incorporate the increased flexibility into the design process need to be developed. This paper presents one such multiperiod cellular network design problem and solves it via a hybrid heuristic that incorporates ideas from linear programming (LP) and simulated annealing (SA). Extensive computational results comparing the performance of the heuristic with the lower bound obtained from the LP relaxation are presented. These results indicate that this price-influenced simulated annealing (PISA) procedure is extremely efficient, consistently providing solutions with average gaps of 0.30% or less in fewer than 30 s. PMID:16761813

  17. Protease-associated cellular networks in malaria parasite Plasmodium falciparum

    PubMed Central

    2011-01-01

    Background Malaria continues to be one of the most severe global infectious diseases, responsible for 1-2 million deaths yearly. The rapid evolution and spread of drug resistance in parasites has led to an urgent need for the development of novel antimalarial targets. Proteases are a group of enzymes that play essential roles in parasite growth and invasion. The possibility of designing specific inhibitors for proteases makes them promising drug targets. Previously, combining a comparative genomics approach and a machine learning approach, we identified the complement of proteases (degradome) in the malaria parasite Plasmodium falciparum and its sibling species [1-3], providing a catalog of targets for functional characterization and rational inhibitor design. Network analysis represents another route to revealing the role of proteins in the biology of parasites and we use this approach here to expand our understanding of the systems involving the proteases of P. falciparum. Results We investigated the roles of proteases in the parasite life cycle by constructing a network using protein-protein association data from the STRING database [4], and analyzing these data, in conjunction with the data from protein-protein interaction assays using the yeast 2-hybrid (Y2H) system [5], blood stage microarray experiments [6-8], proteomics [9-12], literature text mining, and sequence homology analysis. Seventy-seven (77) out of 124 predicted proteases were associated with at least one other protein, constituting 2,431 protein-protein interactions (PPIs). These proteases appear to play diverse roles in metabolism, cell cycle regulation, invasion and infection. Their degrees of connectivity (i.e., connections to other proteins), range from one to 143. The largest protease-associated sub-network is the ubiquitin-proteasome system which is crucial for protein recycling and stress response. Proteases are also implicated in heat shock response, signal peptide processing, cell cycle

  18. [Construction and structural analysis of integrated cellular network of Corynebacterium glutamicum].

    PubMed

    Jiang, Jinguo; Song, Lifu; Zheng, Ping; Jia, Shiru; Sun, Jibin

    2012-05-01

    Corynebacterium glutamicum is one of the most important traditional industrial microorganisms and receiving more and more attention towards a novel cellular factory due to the recently rapid development in genomics and genetic operation toolboxes for Corynebacterium. However, compared to other model organisms such as Escherichia coli, there were few studies on its metabolic regulation, especially a genome-scale integrated cellular network model currently missing for Corynebacterium, which hindered the systematic study of Corynebacterium glutamicum and large-scale rational design and optimization for strains. Here, by gathering relevant information from a number of public databases, we successfully constructed an integrated cellular network, which was composed of 1384 reactions, 1276 metabolites, 88 transcriptional factors and 999 pairs of transcriptional regulatory relationships. The transcriptional regulatory sub-network could be arranged into five layers and the metabolic sub-network presented a clear bow-tie structure. We proposed a new method to extract complex metabolic and regulatory sub-network for product-orientated study taking lysine biosynthesis as an example. The metabolic and regulatory sub-network extracted by our method was more close to the real functional network than the simplex biochemical pathways. The results would be greatly helpful for understanding the high-yielding biomechanism for amino acids and the re-design of the industrial strains. PMID:22916496

  19. A malignant cellular network in gliomas: potential clinical implications.

    PubMed

    Osswald, Matthias; Solecki, Gergely; Wick, Wolfgang; Winkler, Frank

    2016-04-01

    The recent discovery of distinct, ultra-long, and highly functional membrane protrusions in gliomas, particularly in astrocytomas, extends our understanding of how these tumors progress in the brain and how they resist therapies. In this article, we will focus on ideas on how to target these membrane protrusions, for which we have suggested the term "tumor microtubes" (TMs), and the malignant multicellular network they form. First, we discuss TM-specific features and their differential biological functions known so far. Second, the connection between 1p/19q codeletion and the inability to form functional TMs via certain neurodevelopmental pathways is presented; this could provide an explanation for the distinct clinical features of oligodendrogliomas. Third, the role of TMs for primary and potentially also adaptive resistance to cytotoxic therapies is highlighted. Fourth, avenues for therapeutic approaches to inhibit TM formation and/or function are discussed, with a focus on disruption (or exploitation) of network functionality. Finally, we propose ideas on how to use TMs as a biomarker in glioma patients. An increasing understanding of TMs in clinical and preclinical settings will show us whether they really are a long-sought-after Achilles' heel of treatment-resistant gliomas. PMID:26995789

  20. Cellular Origins of Type IV Collagen Networks in Developing Glomeruli

    PubMed Central

    Abrahamson, Dale R.; Hudson, Billy G.; Stroganova, Larysa; Borza, Dorin-Bogdan; St. John, Patricia L.

    2009-01-01

    Laminin and type IV collagen composition of the glomerular basement membrane changes during glomerular development and maturation. Although it is known that both glomerular endothelial cells and podocytes produce different laminin isoforms at the appropriate stages of development, the cellular origins for the different type IV collagen heterotrimers that appear during development are unknown. Here, immunoelectron microscopy demonstrated that endothelial cells, mesangial cells, and podocytes of immature glomeruli synthesize collagen α1α2α1(IV). However, intracellular labeling revealed that podocytes, but not endothelial or mesangial cells, contain collagen α3α4α5(IV). To evaluate the origins of collagen IV further, we transplanted embryonic kidneys from Col4a3-null mutants (Alport mice) into kidneys of newborn, wildtype mice. Hybrid glomeruli within grafts containing numerous host-derived, wildtype endothelial cells never expressed collagen α3α4α5(IV). Finally, confocal microscopy of glomeruli from infant Alport mice that had been dually labeled with anti-collagen α5(IV) and the podocyte marker anti-GLEPP1 showed immunolabeling exclusively within podocytes. Together, these results indicate that collagen α3α4α5(IV) originates solely from podocytes; therefore, glomerular Alport disease is a genetic defect that manifests specifically within this cell type. PMID:19423686

  1. Cellular origins of type IV collagen networks in developing glomeruli.

    PubMed

    Abrahamson, Dale R; Hudson, Billy G; Stroganova, Larysa; Borza, Dorin-Bogdan; St John, Patricia L

    2009-07-01

    Laminin and type IV collagen composition of the glomerular basement membrane changes during glomerular development and maturation. Although it is known that both glomerular endothelial cells and podocytes produce different laminin isoforms at the appropriate stages of development, the cellular origins for the different type IV collagen heterotrimers that appear during development are unknown. Here, immunoelectron microscopy demonstrated that endothelial cells, mesangial cells, and podocytes of immature glomeruli synthesize collagen alpha 1 alpha 2 alpha1(IV). However, intracellular labeling revealed that podocytes, but not endothelial or mesangial cells, contain collagen alpha 3 alpha 4 alpha 5(IV). To evaluate the origins of collagen IV further, we transplanted embryonic kidneys from Col4a3-null mutants (Alport mice) into kidneys of newborn, wildtype mice. Hybrid glomeruli within grafts containing numerous host-derived, wildtype endothelial cells never expressed collagen alpha 3 alpha 4 alpha 5(IV). Finally, confocal microscopy of glomeruli from infant Alport mice that had been dually labeled with anti-collagen alpha 5(IV) and the podocyte marker anti-GLEPP1 showed immunolabeling exclusively within podocytes. Together, these results indicate that collagen alpha 3 alpha 4 alpha 5(IV) originates solely from podocytes; therefore, glomerular Alport disease is a genetic defect that manifests specifically within this cell type. PMID:19423686

  2. The role of topological features of intercellular communication networks by the synchronization of cellular oscillators

    NASA Astrophysics Data System (ADS)

    Markovič, R.; Gosak, M.; Marhl, M.

    2012-08-01

    Because of the complexity of processes that govern the regulatory mechanisms which control the cellular functions and dynamic behavior, mathematical models and numerical simulations are needed to fully grasp the mechanisms and functions of biological rhythms. In the last decade the theory of complex networks is frequently applied to address those issues. In the present paper we investigate theoretically the role of the intercellular communication network structure by synchronization of cellular oscillators. Motivated by the fact that in biological systems the interplay between the network structure and the dynamics taking place on it is closely interrelated, we develop a spatial network representation of an ensemble of cells in which we can tune the network organization between a scale-free network with dominating long-range connections and a homogeneous network with mostly adjacent neurons connected. Our results reveal that for noise-induced oscillations in excitable cells and for chaotic bursting oscillations the most synchronized response is obtained for the intermediate regime where long-as well as short-range connections constitute the intercellular network. On the other hand, for periodic oscillations it is found than the scale-free network topology ensures the greatest collective response. We argue that those findings are related to flexibility properties of individual cells.

  3. A Mathematical Model to study the Dynamics of Epithelial Cellular Networks

    PubMed Central

    Abate, Alessandro; Vincent, Stéphane; Dobbe, Roel; Silletti, Alberto; Master, Neal; Axelrod, Jeffrey D.; Tomlin, Claire J.

    2013-01-01

    Epithelia are sheets of connected cells that are essential across the animal kingdom. Experimental observations suggest that the dynamical behavior of many single-layered epithelial tissues has strong analogies with that of specific mechanical systems, namely large networks consisting of point masses connected through spring-damper elements and undergoing the influence of active and dissipating forces. Based on this analogy, this work develops a modeling framework to enable the study of the mechanical properties and of the dynamic behavior of large epithelial cellular networks. The model is built first by creating a network topology that is extracted from the actual cellular geometry as obtained from experiments, then by associating a mechanical structure and dynamics to the network via spring-damper elements. This scalable approach enables running simulations of large network dynamics: the derived modeling framework in particular is predisposed to be tailored to study general dynamics (for example, morphogenesis) of various classes of single-layered epithelial cellular networks. In this contribution we test the model on a case study of the dorsal epithelium of the Drosophila melanogaster embryo during early dorsal closure (and, less conspicuously, germband retraction). PMID:23221083

  4. Identification of driving network of cellular differentiation from single sample time course gene expression data

    NASA Astrophysics Data System (ADS)

    Chen, Ye; Wolanyk, Nathaniel; Ilker, Tunc; Gao, Shouguo; Wang, Xujing

    Methods developed based on bifurcation theory have demonstrated their potential in driving network identification for complex human diseases, including the work by Chen, et al. Recently bifurcation theory has been successfully applied to model cellular differentiation. However, there one often faces a technical challenge in driving network prediction: time course cellular differentiation study often only contains one sample at each time point, while driving network prediction typically require multiple samples at each time point to infer the variation and interaction structures of candidate genes for the driving network. In this study, we investigate several methods to identify both the critical time point and the driving network through examination of how each time point affects the autocorrelation and phase locking. We apply these methods to a high-throughput sequencing (RNA-Seq) dataset of 42 subsets of thymocytes and mature peripheral T cells at multiple time points during their differentiation (GSE48138 from GEO). We compare the predicted driving genes with known transcription regulators of cellular differentiation. We will discuss the advantages and limitations of our proposed methods, as well as potential further improvements of our methods.

  5. Retrieval algorithm for rainfall mapping from microwave links in a cellular communication network

    NASA Astrophysics Data System (ADS)

    Overeem, A.; Leijnse, H.; Uijlenhoet, R.

    2015-08-01

    Microwave links in commercial cellular communication networks hold a promise for areal rainfall monitoring and could complement rainfall estimates from ground-based weather radars, rain gauges, and satellites. It has been shown that country-wide rainfall maps can be derived from the signal attenuations of microwave links in such a network. Here we give a detailed description of the employed rainfall retrieval algorithm and provide the corresponding code. Moreover, the code (in the scripting language "R") is made available including a data set of commercial microwave links. The purpose of this paper is to promote rainfall monitoring utilizing microwave links from cellular communication networks as an alternative or complementary means for global, continental-scale rainfall monitoring.

  6. Retrieval algorithm for rainfall mapping from microwave links in a cellular communication network

    NASA Astrophysics Data System (ADS)

    Overeem, Aart; Leijnse, Hidde; Uijlenhoet, Remko

    2016-06-01

    Microwave links in commercial cellular communication networks hold a promise for areal rainfall monitoring and could complement rainfall estimates from ground-based weather radars, rain gauges, and satellites. It has been shown that country-wide (≈ 35 500 km2) 15 min rainfall maps can be derived from the signal attenuations of approximately 2400 microwave links in such a network. Here we give a detailed description of the employed rainfall retrieval algorithm. Moreover, the documented, modular, and user-friendly code (a package in the scripting language "R") is made available, including a 2-day data set of approximately 2600 commercial microwave links from the Netherlands. The purpose of this paper is to promote rainfall mapping utilising microwave links from cellular communication networks as an alternative or complementary means for continental-scale rainfall monitoring.

  7. A self-learning call admission control scheme for CDMA cellular networks.

    PubMed

    Liu, Derong; Zhang, Yi; Zhang, Huaguang

    2005-09-01

    In the present paper, a call admission control scheme that can learn from the network environment and user behavior is developed for code division multiple access (CDMA) cellular networks that handle both voice and data services. The idea is built upon a novel learning control architecture with only a single module instead of two or three modules in adaptive critic designs (ACDs). The use of adaptive critic approach for call admission control in wireless cellular networks is new. The call admission controller can perform learning in real-time as well as in offline environments and the controller improves its performance as it gains more experience. Another important contribution in the present work is the choice of utility function for the present self-learning control approach which makes the present learning process much more efficient than existing learning control methods. The performance of our algorithm will be shown through computer simulation and compared with existing algorithms. PMID:16252828

  8. The Electrophysiological MEMS Device with Micro Channel Array for Cellular Network Analysis

    NASA Astrophysics Data System (ADS)

    Tonomura, Wataru; Kurashima, Toshiaki; Takayama, Yuzo; Moriguchi, Hiroyuki; Jimbo, Yasuhiko; Konishi, Satoshi

    This paper describes a new type of MCA (Micro Channel Array) for simultaneous multipoint measurement of cellular network. Presented MCA employing the measurement principles of the patch-clamp technique is designed for advanced neural network analysis which has been studied by co-authors using 64ch MEA (Micro Electrode Arrays) system. First of all, sucking and clamping of cells through channels of developed MCA is expected to improve electrophysiological signal detections. Electrophysiological sensing electrodes integrated around individual channels of MCA by using MEMS (Micro Electro Mechanical System) technologies are electrically isolated for simultaneous multipoint measurement. In this study, we tested the developed MCA using the non-cultured rat's cerebral cortical slice and the hippocampal neurons. We could measure the spontaneous action potential of the slice simultaneously at multiple points and culture the neurons on developed MCA. Herein, we describe the experimental results together with the design and fabrication of the electrophysiological MEMS device with MCA for cellular network analysis.

  9. Cellular automata with object-oriented features for parallel molecular network modeling.

    PubMed

    Zhu, Hao; Wu, Yinghui; Huang, Sui; Sun, Yan; Dhar, Pawan

    2005-06-01

    Cellular automata are an important modeling paradigm for studying the dynamics of large, parallel systems composed of multiple, interacting components. However, to model biological systems, cellular automata need to be extended beyond the large-scale parallelism and intensive communication in order to capture two fundamental properties characteristic of complex biological systems: hierarchy and heterogeneity. This paper proposes extensions to a cellular automata language, Cellang, to meet this purpose. The extended language, with object-oriented features, can be used to describe the structure and activity of parallel molecular networks within cells. Capabilities of this new programming language include object structure to define molecular programs within a cell, floating-point data type and mathematical functions to perform quantitative computation, message passing capability to describe molecular interactions, as well as new operators, statements, and built-in functions. We discuss relevant programming issues of these features, including the object-oriented description of molecular interactions with molecule encapsulation, message passing, and the description of heterogeneity and anisotropy at the cell and molecule levels. By enabling the integration of modeling at the molecular level with system behavior at cell, tissue, organ, or even organism levels, the program will help improve our understanding of how complex and dynamic biological activities are generated and controlled by parallel functioning of molecular networks. Index Terms-Cellular automata, modeling, molecular network, object-oriented. PMID:16117022

  10. Interference Avoiding Radio Resource Allocation Scheme for Multi-hop OFDMA Cellular Networks with Random Topology

    NASA Astrophysics Data System (ADS)

    Lim, Sunggook; Lee, Jaiyong

    Relaying technology is the one of the solutions to expand the coverage and enhance the throughput of a cellular network with low cost, therefore numerous smart relay stations (RSs) which are able to schedule its own transmission frame and manage radio resources allocated by its serving base station (BS) will be deployed within the cellular network. while more RSs are deployed, the network topology is turning to the random topology. In the random topology, however, conventional frequency reuse schemes based on the uniformly distributed RSs are not adoptable because of the randomness for locations of RSs. Another problem is severe increase of interference during the transmission period for an access link because more transmitters including BSs and RSs are existed within a cell. We suggest the random-topology frequency reuse (RFR) scheme supporting the frequency reuse in the cellular multi-hop network with random topology to reduce intra-cell interference. The simulation results show RFR is reducing the overall intra-cell interference compared to the full allocation scheme whose reuse factor is one. The throughput and average signal to interference plus noise ratio (SINR) is still greater than the full allocation scheme although the spectral efficiency is lower than the compared scheme.

  11. Relating the sequential dynamics of excitatory neural networks to synaptic cellular automata.

    PubMed

    Nekorkin, V I; Dmitrichev, A S; Kasatkin, D V; Afraimovich, V S

    2011-12-01

    We have developed a new approach for the description of sequential dynamics of excitatory neural networks. Our approach is based on the dynamics of synapses possessing the short-term plasticity property. We suggest a model of such synapses in the form of a second-order system of nonlinear ODEs. In the framework of the model two types of responses are realized-the fast and the slow ones. Under some relations between their timescales a cellular automaton (CA) on the graph of connections is constructed. Such a CA has only a finite number of attractors and all of them are periodic orbits. The attractors of the CA determine the regimes of sequential dynamics of the original neural network, i.e., itineraries along the network and the times of successive firing of neurons in the form of bunches of spikes. We illustrate our approach on the example of a Morris-Lecar neural network. PMID:22225361

  12. Two programmed replicative lifespans of Saccharomyces cerevisiae formed by the endogenous molecular-cellular network.

    PubMed

    Hu, Jie; Zhu, Xiaomei; Wang, Xinan; Yuan, Ruoshi; Zheng, Wei; Xu, Minjuan; Ao, Ping

    2014-12-01

    Cellular replicative capacity is a therapeutic target for regenerative medicine as well as cancer treatment. The mechanism of replicative senescence and cell immortality is still unclear. We investigated the diauxic growth of Saccharomyces cerevisiae and demonstrate that the replicative capacity revealed by the yeast growth curve can be understood by using the dynamical property of the molecular-cellular network regulating S. cerevisiae. The endogenous network we proposed has a limit cycle when pheromone signaling is disabled, consistent with the exponential growth phase with an infinite replicative capacity. In the post-diauxic phase, the cooperative effect of the pheromone activated mitogen-activated protein kinase (MAPK) signaling pathway with the cell cycle leads to a fixed point attractor instead of the limit cycle. The cells stop dividing after several generations counting from the beginning of the post-diauxic growth. By tuning the MAPK pathway, S. cerevisiae therefore programs the number of offsprings it replicates. PMID:24447585

  13. A new cellular nonlinear network emulation on FPGA for EEG signal processing in epilepsy

    NASA Astrophysics Data System (ADS)

    Müller, Jens; Müller, Jan; Tetzlaff, Ronald

    2011-05-01

    For processing of EEG signals, we propose a new architecture for the hardware emulation of discrete-time Cellular Nonlinear Networks (DT-CNN). Our results show the importance of a high computational accuracy in EEG signal prediction that cannot be achieved with existing analogue VLSI circuits. The refined architecture of the processing elements and its resource schedule, the cellular network structure with local couplings, the FPGA-based embedded system containing the DT-CNN, and the data flow in the entire system will be discussed in detail. The proposed DT-CNN design has been implemented and tested on an Xilinx FPGA development platform. The embedded co-processor with a multi-threading kernel is utilised for control and pre-processing tasks and data exchange to the host via Ethernet. The performance of the implemented DT-CNN has been determined for a popular example and compared to that of a conventional computer.

  14. Application of GA in optimization of pore network models generated by multi-cellular growth algorithms

    NASA Astrophysics Data System (ADS)

    Jamshidi, Saeid; Boozarjomehry, Ramin Bozorgmehry; Pishvaie, Mahmoud Reza

    2009-10-01

    In pore network modeling, the void space of a rock sample is represented at the microscopic scale by a network of pores connected by throats. Construction of a reasonable representation of the geometry and topology of the pore space will lead to a reliable prediction of the properties of porous media. Recently, the theory of multi-cellular growth (or L-systems) has been used as a flexible tool for generation of pore network models which do not require any special information such as 2D SEM or 3D pore space images. In general, the networks generated by this method are irregular pore network models which are inherently closer to the complicated nature of the porous media rather than regular lattice networks. In this approach, the construction process is controlled only by the production rules that govern the development process of the network. In this study, genetic algorithm has been used to obtain the optimum values of the uncertain parameters of these production rules to build an appropriate irregular lattice network capable of the prediction of both static and hydraulic information of the target porous medium.

  15. Application of neural networks to channel assignment for cellular CDMA networks with multiple services and mobile base stations

    NASA Astrophysics Data System (ADS)

    Hortos, William S.

    1996-03-01

    The use of artificial neural networks to the channel assignment problem for cellular code- division multiple access (CDMA) telecommunications systems is considered. CDMA takes advantage of voice activity and spatial isolation because its capacity is only interference limited, unlike time-division multiple access (TDMA) and frequency-division multiple access (FDMA) where capacities are bandwidth limited. Any reduction in interference in CDMA translates linearly into increased capacity. FDMA and TDMA use a frequency reuse pattern as a method to increase capacity, while CDMA reuses the same frequency for all cells and gains a reuse efficiency by means of orthogonal codes. The latter method can improve system capacity by factors of four to six over digital TDMA or FDMA. Cellular carriers are planning to provide multiple communication services using CDMA in the next generation cellular system infrastructure. The approach of this study is the use of neural network methods for automatic and local network control, based on traffic behavior in specific cell cites and demand history. The goal is to address certain problems associated with the management of mobile and personal communication services in a cellular radio communications environment. In planning a cellular radio network, the operator assigns channels to the radio cells so that the probability of the processed carrier-to-interference ratio, CII, exceeding a predefined value is sufficiently low. The RF propagation, determined from the topography and infrastructure in the operating area, is used in conjunction with the densities of expected communications traffic to formulate interference constraints. These constraints state which radio cells may use the same code (channel) or adjacent channels at a time. The traffic loading and the number of service grades can also be used to calculate the number of required channels (codes) for each cell. The general assignment problem is the task of assigning the required number

  16. Cellular Neural Network Models of Growth and Immune of Effector Cells Response to Cancer

    NASA Astrophysics Data System (ADS)

    Su, Yongmei; Min, Lequan

    Four reaction-diffusion cellular neural network (R-D CNN) models are set up based on the differential equation models for the growths of effector cells and cancer cells, and the model of the immune response to cancer proposed by Allison et al. The CNN models have different reaction-diffusion coefficients and coupling parameters. The R-D CNN models may provide possible quantitative interpretations, and are good in agreement with the in vitro experiment data reported by Allison et al.

  17. Measuring information flow in cellular networks by the systems biology method through microarray data

    PubMed Central

    Chen, Bor-Sen; Li, Cheng-Wei

    2015-01-01

    In general, it is very difficult to measure the information flow in a cellular network directly. In this study, based on an information flow model and microarray data, we measured the information flow in cellular networks indirectly by using a systems biology method. First, we used a recursive least square parameter estimation algorithm to identify the system parameters of coupling signal transduction pathways and the cellular gene regulatory network (GRN). Then, based on the identified parameters and systems theory, we estimated the signal transductivities of the coupling signal transduction pathways from the extracellular signals to each downstream protein and the information transductivities of the GRN between transcription factors in response to environmental events. According to the proposed method, the information flow, which is characterized by signal transductivity in coupling signaling pathways and information transductivity in the GRN, can be estimated by microarray temporal data or microarray sample data. It can also be estimated by other high-throughput data such as next-generation sequencing or proteomic data. Finally, the information flows of the signal transduction pathways and the GRN in leukemia cancer cells and non-leukemia normal cells were also measured to analyze the systematic dysfunction in this cancer from microarray sample data. The results show that the signal transductivities of signal transduction pathways change substantially from normal cells to leukemia cancer cells. PMID:26082788

  18. A New Cellular Architecture for Information Retrieval from Sensor Networks through Embedded Service and Security Protocols.

    PubMed

    Shahzad, Aamir; Landry, René; Lee, Malrey; Xiong, Naixue; Lee, Jongho; Lee, Changhoon

    2016-01-01

    Substantial changes have occurred in the Information Technology (IT) sectors and with these changes, the demand for remote access to field sensor information has increased. This allows visualization, monitoring, and control through various electronic devices, such as laptops, tablets, i-Pads, PCs, and cellular phones. The smart phone is considered as a more reliable, faster and efficient device to access and monitor industrial systems and their corresponding information interfaces anywhere and anytime. This study describes the deployment of a protocol whereby industrial system information can be securely accessed by cellular phones via a Supervisory Control And Data Acquisition (SCADA) server. To achieve the study goals, proprietary protocol interconnectivity with non-proprietary protocols and the usage of interconnectivity services are considered in detail. They support the visualization of the SCADA system information, and the related operations through smart phones. The intelligent sensors are configured and designated to process real information via cellular phones by employing information exchange services between the proprietary protocol and non-proprietary protocols. SCADA cellular access raises the issue of security flaws. For these challenges, a cryptography-based security method is considered and deployed, and it could be considered as a part of a proprietary protocol. Subsequently, transmission flows from the smart phones through a cellular network. PMID:27314351

  19. A New Cellular Architecture for Information Retrieval from Sensor Networks through Embedded Service and Security Protocols

    PubMed Central

    Shahzad, Aamir; Landry, René; Lee, Malrey; Xiong, Naixue; Lee, Jongho; Lee, Changhoon

    2016-01-01

    Substantial changes have occurred in the Information Technology (IT) sectors and with these changes, the demand for remote access to field sensor information has increased. This allows visualization, monitoring, and control through various electronic devices, such as laptops, tablets, i-Pads, PCs, and cellular phones. The smart phone is considered as a more reliable, faster and efficient device to access and monitor industrial systems and their corresponding information interfaces anywhere and anytime. This study describes the deployment of a protocol whereby industrial system information can be securely accessed by cellular phones via a Supervisory Control And Data Acquisition (SCADA) server. To achieve the study goals, proprietary protocol interconnectivity with non-proprietary protocols and the usage of interconnectivity services are considered in detail. They support the visualization of the SCADA system information, and the related operations through smart phones. The intelligent sensors are configured and designated to process real information via cellular phones by employing information exchange services between the proprietary protocol and non-proprietary protocols. SCADA cellular access raises the issue of security flaws. For these challenges, a cryptography-based security method is considered and deployed, and it could be considered as a part of a proprietary protocol. Subsequently, transmission flows from the smart phones through a cellular network. PMID:27314351

  20. An Asynchronous Recurrent Network of Cellular Automaton-Based Neurons and Its Reproduction of Spiking Neural Network Activities.

    PubMed

    Matsubara, Takashi; Torikai, Hiroyuki

    2016-04-01

    Modeling and implementation approaches for the reproduction of input-output relationships in biological nervous tissues contribute to the development of engineering and clinical applications. However, because of high nonlinearity, the traditional modeling and implementation approaches encounter difficulties in terms of generalization ability (i.e., performance when reproducing an unknown data set) and computational resources (i.e., computation time and circuit elements). To overcome these difficulties, asynchronous cellular automaton-based neuron (ACAN) models, which are described as special kinds of cellular automata that can be implemented as small asynchronous sequential logic circuits have been proposed. This paper presents a novel type of such ACAN and a theoretical analysis of its excitability. This paper also presents a novel network of such neurons, which can mimic input-output relationships of biological and nonlinear ordinary differential equation model neural networks. Numerical analyses confirm that the presented network has a higher generalization ability than other major modeling and implementation approaches. In addition, Field-Programmable Gate Array-implementations confirm that the presented network requires lower computational resources. PMID:25974951

  1. Motion Adaptive Vertical Handoff in Cellular/WLAN Heterogeneous Wireless Network

    PubMed Central

    Ma, Lin; Xu, Yubin; Fu, Yunhai

    2014-01-01

    In heterogeneous wireless network, vertical handoff plays an important role for guaranteeing quality of service and overall performance of network. Conventional vertical handoff trigger schemes are mostly developed from horizontal handoff in homogeneous cellular network. Basically, they can be summarized as hysteresis-based and dwelling-timer-based algorithms, which are reliable on avoiding unnecessary handoff caused by the terminals dwelling at the edge of WLAN coverage. However, the coverage of WLAN is much smaller compared with cellular network, while the motion types of terminals can be various in a typical outdoor scenario. As a result, traditional algorithms are less effective in avoiding unnecessary handoff triggered by vehicle-borne terminals with various speeds. Besides that, hysteresis and dwelling-timer thresholds usually need to be modified to satisfy different channel environments. For solving this problem, a vertical handoff algorithm based on Q-learning is proposed in this paper. Q-learning can provide the decider with self-adaptive ability for handling the terminals' handoff requests with different motion types and channel conditions. Meanwhile, Neural Fuzzy Inference System (NFIS) is embedded to retain a continuous perception of the state space. Simulation results verify that the proposed algorithm can achieve lower unnecessary handoff probability compared with the other two conventional algorithms. PMID:24741347

  2. Motion adaptive vertical handoff in cellular/WLAN heterogeneous wireless network.

    PubMed

    Li, Limin; Ma, Lin; Xu, Yubin; Fu, Yunhai

    2014-01-01

    In heterogeneous wireless network, vertical handoff plays an important role for guaranteeing quality of service and overall performance of network. Conventional vertical handoff trigger schemes are mostly developed from horizontal handoff in homogeneous cellular network. Basically, they can be summarized as hysteresis-based and dwelling-timer-based algorithms, which are reliable on avoiding unnecessary handoff caused by the terminals dwelling at the edge of WLAN coverage. However, the coverage of WLAN is much smaller compared with cellular network, while the motion types of terminals can be various in a typical outdoor scenario. As a result, traditional algorithms are less effective in avoiding unnecessary handoff triggered by vehicle-borne terminals with various speeds. Besides that, hysteresis and dwelling-timer thresholds usually need to be modified to satisfy different channel environments. For solving this problem, a vertical handoff algorithm based on Q-learning is proposed in this paper. Q-learning can provide the decider with self-adaptive ability for handling the terminals' handoff requests with different motion types and channel conditions. Meanwhile, Neural Fuzzy Inference System (NFIS) is embedded to retain a continuous perception of the state space. Simulation results verify that the proposed algorithm can achieve lower unnecessary handoff probability compared with the other two conventional algorithms. PMID:24741347

  3. Phase transitions in pancreatic islet cellular networks and implications for type-1 diabetes

    NASA Astrophysics Data System (ADS)

    Stamper, I. J.; Jackson, Elais; Wang, Xujing

    2014-01-01

    In many aspects the onset of a chronic disease resembles a phase transition in a complex dynamic system: Quantitative changes accumulate largely unnoticed until a critical threshold is reached, which causes abrupt qualitative changes of the system. In this study we examine a special case, the onset of type-1 diabetes (T1D), a disease that results from loss of the insulin-producing pancreatic islet β cells. Within each islet, the β cells are electrically coupled to each other via gap-junctional channels. This intercellular coupling enables the β cells to synchronize their insulin release, thereby generating the multiscale temporal rhythms in blood insulin that are critical to maintaining blood glucose homeostasis. Using percolation theory we show how normal islet function is intrinsically linked to network connectivity. In particular, the critical amount of β-cell death at which the islet cellular network loses site percolation is consistent with laboratory and clinical observations of the threshold loss of β cells that causes islet functional failure. In addition, numerical simulations confirm that the islet cellular network needs to be percolated for β cells to synchronize. Furthermore, the interplay between site percolation and bond strength predicts the existence of a transient phase of islet functional recovery after onset of T1D and introduction of treatment, potentially explaining the honeymoon phenomenon. Based on these results, we hypothesize that the onset of T1D may be the result of a phase transition of the islet β-cell network.

  4. A computable cellular stress network model for non-diseased pulmonary and cardiovascular tissue

    PubMed Central

    2011-01-01

    Background Humans and other organisms are equipped with a set of responses that can prevent damage from exposure to a multitude of endogenous and environmental stressors. If these stress responses are overwhelmed, this can result in pathogenesis of diseases, which is reflected by an increased development of, e.g., pulmonary and cardiac diseases in humans exposed to chronic levels of environmental stress, including inhaled cigarette smoke (CS). Systems biology data sets (e.g., transcriptomics, phosphoproteomics, metabolomics) could enable comprehensive investigation of the biological impact of these stressors. However, detailed mechanistic networks are needed to determine which specific pathways are activated in response to different stressors and to drive the qualitative and eventually quantitative assessment of these data. A current limiting step in this process is the availability of detailed mechanistic networks that can be used as an analytical substrate. Results We have built a detailed network model that captures the biology underlying the physiological cellular response to endogenous and exogenous stressors in non-diseased mammalian pulmonary and cardiovascular cells. The contents of the network model reflect several diverse areas of signaling, including oxidative stress, hypoxia, shear stress, endoplasmic reticulum stress, and xenobiotic stress, that are elicited in response to common pulmonary and cardiovascular stressors. We then tested the ability of the network model to identify the mechanisms that are activated in response to CS, a broad inducer of cellular stress. Using transcriptomic data from the lungs of mice exposed to CS, the network model identified a robust increase in the oxidative stress response, largely mediated by the anti-oxidant NRF2 pathways, consistent with previous reports on the impact of CS exposure in the mammalian lung. Conclusions The results presented here describe the construction of a cellular stress network model and its

  5. Increasing the coverage area through relay node deployment in long term evolution advanced cellular networks

    NASA Astrophysics Data System (ADS)

    Aldhaibani, Jaafar A.; Ahmad, R. B.; Yahya, A.; Azeez, Suzan A.

    2015-05-01

    Wireless multi-hop relay networks have become very important technologies in mobile communications. These networks ensure high throughput and coverage extension with a low cost. The poor capacity at cell edges is not enough to meet with growing demand of high capacity and throughput irrespective of user's placement in the cellular network. In this paper we propose optimal placement of relay node that provides maximum achievable rate at users and enhances the throughput and coverage at cell edge region. The proposed scheme is based on the outage probability at users and taken on account the interference between nodes. Numerical analyses along with simulation results indicated there are an improvement in capacity for users at the cell edge is 40% increment from all cell capacity.

  6. Optimal design of sewer networks using cellular automata-based hybrid methods: Discrete and continuous approaches

    NASA Astrophysics Data System (ADS)

    Afshar, M. H.; Rohani, M.

    2012-01-01

    In this article, cellular automata based hybrid methods are proposed for the optimal design of sewer networks and their performance is compared with some of the common heuristic search methods. The problem of optimal design of sewer networks is first decomposed into two sub-optimization problems which are solved iteratively in a two stage manner. In the first stage, the pipe diameters of the network are assumed fixed and the nodal cover depths of the network are determined by solving a nonlinear sub-optimization problem. A cellular automata (CA) method is used for the solution of the optimization problem with the network nodes considered as the cells and their cover depths as the cell states. In the second stage, the nodal cover depths calculated from the first stage are fixed and the pipe diameters are calculated by solving a second nonlinear sub-optimization problem. Once again a CA method is used to solve the optimization problem of the second stage with the pipes considered as the CA cells and their corresponding diameters as the cell states. Two different updating rules are derived and used for the CA of the second stage depending on the treatment of the pipe diameters. In the continuous approach, the pipe diameters are considered as continuous variables and the corresponding updating rule is derived mathematically from the original objective function of the problem. In the discrete approach, however, an adhoc updating rule is derived and used taking into account the discrete nature of the pipe diameters. The proposed methods are used to optimally solve two sewer network problems and the results are presented and compared with those obtained by other methods. The results show that the proposed CA based hybrid methods are more efficient and effective than the most powerful search methods considered in this work.

  7. Cellular neural network-based hybrid approach toward automatic image registration

    NASA Astrophysics Data System (ADS)

    Arun, Pattathal VijayaKumar; Katiyar, Sunil Kumar

    2013-01-01

    Image registration is a key component of various image processing operations that involve the analysis of different image data sets. Automatic image registration domains have witnessed the application of many intelligent methodologies over the past decade; however, inability to properly model object shape as well as contextual information has limited the attainable accuracy. A framework for accurate feature shape modeling and adaptive resampling using advanced techniques such as vector machines, cellular neural network (CNN), scale invariant feature transform (SIFT), coreset, and cellular automata is proposed. CNN has been found to be effective in improving feature matching as well as resampling stages of registration and complexity of the approach has been considerably reduced using coreset optimization. The salient features of this work are cellular neural network approach-based SIFT feature point optimization, adaptive resampling, and intelligent object modelling. Developed methodology has been compared with contemporary methods using different statistical measures. Investigations over various satellite images revealed that considerable success was achieved with the approach. This system has dynamically used spectral and spatial information for representing contextual knowledge using CNN-prolog approach. This methodology is also illustrated to be effective in providing intelligent interpretation and adaptive resampling.

  8. A multimedia session-aware QoS provisioning scheme for cellular networks

    NASA Astrophysics Data System (ADS)

    Rizvi, Mona E.; Olariu, Stephan

    2005-03-01

    Multimedia applications often involve a set of cooperating streams that together form a multimedia session. We propose a novel local QoS provisioning scheme for cellular networks that is aware of the relationships between the streams that compose a session. As a rule, existing schemes either allow composite streams to compete with one another for resources or else provide QoS to the session as an atomic entity, leaving to the application the task of managing QoS for the individual streams. Our new MUltimedia SessIon-aware Cellular (MUSIC) QoS provisioning scheme manages the QoS of the individual streams in a session, and with the knowledge of their relationships, it prevents competition between the streams. Further, by allowing an application-specified prioritization between streams in a session, MUSIC scheme features a significant improvement in performance over session-unaware schemes.

  9. Segmentation algorithm via Cellular Neural/Nonlinear Network: implementation on Bio-inspired hardware platform

    NASA Astrophysics Data System (ADS)

    Karabiber, Fethullah; Vecchio, Pietro; Grassi, Giuseppe

    2011-12-01

    The Bio-inspired (Bi-i) Cellular Vision System is a computing platform consisting of sensing, array sensing-processing, and digital signal processing. The platform is based on the Cellular Neural/Nonlinear Network (CNN) paradigm. This article presents the implementation of a novel CNN-based segmentation algorithm onto the Bi-i system. Each part of the algorithm, along with the corresponding implementation on the hardware platform, is carefully described through the article. The experimental results, carried out for Foreman and Car-phone video sequences, highlight the feasibility of the approach, which provides a frame rate of about 26 frames/s. Comparisons with existing CNN-based methods show that the conceived approach is more accurate, thus representing a good trade-off between real-time requirements and accuracy.

  10. Cellular Signaling Networks Function as Generalized Wiener-Kolmogorov Filters to Suppress Noise

    NASA Astrophysics Data System (ADS)

    Hinczewski, Michael; Thirumalai, D.

    2014-10-01

    Cellular signaling involves the transmission of environmental information through cascades of stochastic biochemical reactions, inevitably introducing noise that compromises signal fidelity. Each stage of the cascade often takes the form of a kinase-phosphatase push-pull network, a basic unit of signaling pathways whose malfunction is linked with a host of cancers. We show that this ubiquitous enzymatic network motif effectively behaves as a Wiener-Kolmogorov optimal noise filter. Using concepts from umbral calculus, we generalize the linear Wiener-Kolmogorov theory, originally introduced in the context of communication and control engineering, to take nonlinear signal transduction and discrete molecule populations into account. This allows us to derive rigorous constraints for efficient noise reduction in this biochemical system. Our mathematical formalism yields bounds on filter performance in cases important to cellular function—such as ultrasensitive response to stimuli. We highlight features of the system relevant for optimizing filter efficiency, encoded in a single, measurable, dimensionless parameter. Our theory, which describes noise control in a large class of signal transduction networks, is also useful both for the design of synthetic biochemical signaling pathways and the manipulation of pathways through experimental probes such as oscillatory input.

  11. Cellular network formation of hydrophobic alkanethiol capped gold nanoparticles on mica surface mediated by water islands.

    PubMed

    John, Neena S; Raina, Gargi; Sharma, Ashutosh; Kulkarni, Giridhar U

    2010-09-01

    Dendritic and cellular networks of nanoparticles are known to form commonly either by random diffusion-limited aggregation or by solvent evaporation dynamics. Using alkanethiol capped gold nanoparticles deposited on mica imaged under ambient and controlled water vapor conditions by atomic force microscope and in situ scanning electron microscope, respectively, we show a third mechanism in action. The cellular network consisting of open and closed polygons is formed by the nucleation and lateral growth of adsorbed water islands, the contact lines of which push the randomly distributed hydrophobic nanoparticles along the growth directions, eventually leading to the polygonal structure formation as the boundaries of the growing islands meet. Such nanoparticle displacement has been possible due to the weakly adhering nature of the hydrophilic substrate, mica. These results demonstrate an important but hitherto neglected effect of adsorbed water in the structure formation on hydrophilic substrates and provide a facile tool for the fabrication of nanoparticle networks without specific particle or substrate modifications and without a tight control on particle deposition conditions during the solvent evaporation. PMID:20831330

  12. Alzheimer's as a Systems-Level Disease Involving the Interplay of Multiple Cellular Networks.

    PubMed

    Castrillo, Juan I; Oliver, Stephen G

    2016-01-01

    Alzheimer's disease (AD), and many neurodegenerative disorders, are multifactorial in nature. They involve a combination of genomic, epigenomic, interactomic and environmental factors. Progress is being made, and these complex diseases are beginning to be understood as having their origin in altered states of biological networks at the cellular level. In the case of AD, genomic susceptibility and mechanisms leading to (or accompanying) the impairment of the central Amyloid Precursor Protein (APP) processing and tau networks are widely accepted as major contributors to the diseased state. The derangement of these networks may result in both the gain and loss of functions, increased generation of toxic species (e.g., toxic soluble oligomers and aggregates) and imbalances, whose effects can propagate to supra-cellular levels. Although well sustained by empirical data and widely accepted, this global perspective often overlooks the essential roles played by the main counteracting homeostatic networks (e.g., protein quality control/proteostasis, unfolded protein response, protein folding chaperone networks, disaggregases, ER-associated degradation/ubiquitin proteasome system, endolysosomal network, autophagy, and other stress-protective and clearance networks), whose relevance to AD is just beginning to be fully realized. In this chapter, an integrative perspective is presented. Alzheimer's disease is characterized to be a result of: (a) intrinsic genomic/epigenomic susceptibility and, (b) a continued dynamic interplay between the deranged networks and the central homeostatic networks of nerve cells. This interplay of networks will underlie both the onset and rate of progression of the disease in each individual. Integrative Systems Biology approaches are required to effect its elucidation. Comprehensive Systems Biology experiments at different 'omics levels in simple model organisms, engineered to recapitulate the basic features of AD may illuminate the onset and

  13. Robust tracking by cellular automata and neural networks with nonlocal weights

    NASA Astrophysics Data System (ADS)

    Ososkov, Gennadii A.

    1995-04-01

    A modified rotor model of the Hopfield neural networks (HNN) is proposed for finding tracks in multiwire proportional chambers. That requires us to apply both raw data prefiltering by cellular automaton and HNN weights furnishing by a special robust multiplier. Then this model is developed to be applicable for a more general type of data and detectors. As an example, data processing of ionospheric measurements are considered. For handling tracks detected by high pressure drift chambers with their up-down ambiguity a modification of deformable templates method is proposed. A new concept of controlled HNN is proposed for solving the so-called track-match problem.

  14. Functional recognition imaging using artificial neural networks: applications to rapid cellular identification via broadband electromechanical response

    NASA Astrophysics Data System (ADS)

    Nikiforov, M. P.; Reukov, V. V.; Thompson, G. L.; Vertegel, A. A.; Guo, S.; Kalinin, S. V.; Jesse, S.

    2009-10-01

    Functional recognition imaging in scanning probe microscopy (SPM) using artificial neural network identification is demonstrated. This approach utilizes statistical analysis of complex SPM responses at a single spatial location to identify the target behavior, which is reminiscent of associative thinking in the human brain, obviating the need for analytical models. We demonstrate, as an example of recognition imaging, rapid identification of cellular organisms using the difference in electromechanical activity over a broad frequency range. Single-pixel identification of model Micrococcus lysodeikticus and Pseudomonas fluorescens bacteria is achieved, demonstrating the viability of the method.

  15. Existence and stability of traveling wave solutions for multilayer cellular neural networks

    NASA Astrophysics Data System (ADS)

    Hsu, Cheng-Hsiung; Lin, Jian-Jhong; Yang, Tzi-Sheng

    2015-08-01

    The purpose of this article is to investigate the existence and stability of traveling wave solutions for one-dimensional multilayer cellular neural networks. We first establish the existence of traveling wave solutions using the truncated technique. Then we study the asymptotic behaviors of solutions for the Cauchy problem of the neural model. Applying two kinds of comparison principles and the weighed energy method, we show that all solutions of the Cauchy problem converge exponentially to the traveling wave solutions provided that the initial data belong to a suitable weighted space.

  16. A new design for reconfigurable XOR function based on cellular neural networks

    NASA Astrophysics Data System (ADS)

    Liu, Yanyi; Liu, Wenbo

    2014-10-01

    We have described a new method to construct the reconfigurable XOR logic circuit by using the modification of the standard uncoupled cellular neural network (CNN) cells. The modification of the cell is easier to implement in engineering applications. The scheme proposed in this paper, using the modification of standard uncoupled CNN cells, allows less hardware consumption in comparison to the utilisation of chaos computing system or harnessing piecewise-linear systems. The template parameters of the modified cell have been discussed, and the physical circuit implementing the reconfigurable two-input and three-input XOR function has also been presented.

  17. Anisotropic optical flow algorithm based on self-adaptive cellular neural network

    NASA Astrophysics Data System (ADS)

    Zhang, Congxuan; Chen, Zhen; Li, Ming; Sun, Kaiqiong

    2013-01-01

    An anisotropic optical flow estimation method based on self-adaptive cellular neural networks (CNN) is proposed. First, a novel optical flow energy function which contains a robust data term and an anisotropic smoothing term is projected. Next, the CNN model which has the self-adaptive feedback operator and threshold is presented according to the Euler-Lagrange partial differential equations of the proposed optical flow energy function. Finally, the elaborate evaluation experiments indicate the significant effects of the various proposed strategies for optical flow estimation, and the comparison results with the other methods show that the proposed algorithm has better performance in computing accuracy and efficiency.

  18. Evolving Transport Networks With Cellular Automata Models Inspired by Slime Mould.

    PubMed

    Tsompanas, Michail-Antisthenis I; Sirakoulis, Georgios Ch; Adamatzky, Andrew I

    2015-09-01

    Man-made transport networks and their design are closely related to the shortest path problem and considered amongst the most debated problems of computational intelligence. Apart from using conventional or bio-inspired computer algorithms, many researchers tried to solve this kind of problem using biological computing substrates, gas-discharge solvers, prototypes of a mobile droplet, and hot ice computers. In this aspect, another example of biological computer is the plasmodium of acellular slime mould Physarum polycephalum (P. polycephalum), which is a large single cell visible by an unaided eye and has been proven as a reliable living substrate for implementing biological computing devices for computational geometry, graph-theoretical problems, and optimization and imitation of transport networks. Although P. polycephalum is easy to experiment with, computing devices built with the living slime mould are extremely slow; it takes slime mould days to execute a computation. Consequently, mapping key computing mechanisms of the slime mould onto silicon would allow us to produce efficient bio-inspired computing devices to tackle with hard to solve computational intelligence problems like the aforementioned. Toward this direction, a cellular automaton (CA)-based, Physarum-inspired, network designing model is proposed. This novel CA-based model is inspired by the propagating strategy, the formation of tubular networks, and the computing abilities of the plasmodium of P. polycephalum. The results delivered by the CA model demonstrate a good match with several previously published results of experimental laboratory studies on imitation of man-made transport networks with P. polycephalum. Consequently, the proposed CA model can be used as a virtual, easy-to-access, and biomimicking laboratory emulator that will economize large time periods needed for biological experiments while producing networks almost identical to the tubular networks of the real-slime mould. PMID

  19. Cellular telephone-based radiation sensor and wide-area detection network

    DOEpatents

    Craig, William W.; Labov, Simon E.

    2006-12-12

    A network of radiation detection instruments, each having a small solid state radiation sensor module integrated into a cellular phone for providing radiation detection data and analysis directly to a user. The sensor module includes a solid-state crystal bonded to an ASIC readout providing a low cost, low power, light weight compact instrument to detect and measure radiation energies in the local ambient radiation field. In particular, the photon energy, time of event, and location of the detection instrument at the time of detection is recorded for real time transmission to a central data collection/analysis system. The collected data from the entire network of radiation detection instruments are combined by intelligent correlation/analysis algorithms which map the background radiation and detect, identify and track radiation anomalies in the region.

  20. Multilayer cellular neural network and fuzzy C-mean classifiers: comparison and performance analysis

    NASA Astrophysics Data System (ADS)

    Trujillo San-Martin, Maite; Hlebarov, Vejen; Sadki, Mustapha

    2004-11-01

    Neural Networks and Fuzzy systems are considered two of the most important artificial intelligent algorithms which provide classification capabilities obtained through different learning schemas which capture knowledge and process it according to particular rule-based algorithms. These methods are especially suited to exploit the tolerance for uncertainty and vagueness in cognitive reasoning. By applying these methods with some relevant knowledge-based rules extracted using different data analysis tools, it is possible to obtain a robust classification performance for a wide range of applications. This paper will focus on non-destructive testing quality control systems, in particular, the study of metallic structures classification according to the corrosion time using a novel cellular neural network architecture, which will be explained in detail. Additionally, we will compare these results with the ones obtained using the Fuzzy C-means clustering algorithm and analyse both classifiers according to its classification capabilities.

  1. Evaluating a Novel Cellular Automata-Based Distributed Power Management Approach for Mobile Wireless Sensor Networks

    NASA Astrophysics Data System (ADS)

    Adabi, Sepideh; Adabi, Sahar; Rezaee, Ali

    According to the traditional definition of Wireless Sensor Networks (WSNs), static sensors have limited the feasibility of WSNs in some kind of approaches, so the mobility was introduced in WSN. Mobile nodes in a WSN come equipped with battery and from the point of deployment, this battery reserve becomes a valuable resource since it cannot be replenished. Hence, maximizing the network lifetime by minimizing the energy is an important challenge in Mobile WSN. Energy conservation can be accomplished by different approaches. In this paper, we presented an energy conservation solution based on Cellular Automata. The main objective of this solution is based on dynamically adjusting the transmission range and switching between operational states of the sensor nodes.

  2. Using prior knowledge from cellular pathways and molecular networks for diagnostic specimen classification

    PubMed Central

    2016-01-01

    For many complex diseases, an earlier and more reliable diagnosis is considered a key prerequisite for developing more effective therapies to prevent or delay disease progression. Classical statistical learning approaches for specimen classification using omics data, however, often cannot provide diagnostic models with sufficient accuracy and robustness for heterogeneous diseases like cancers or neurodegenerative disorders. In recent years, new approaches for building multivariate biomarker models on omics data have been proposed, which exploit prior biological knowledge from molecular networks and cellular pathways to address these limitations. This survey provides an overview of these recent developments and compares pathway- and network-based specimen classification approaches in terms of their utility for improving model robustness, accuracy and biological interpretability. Different routes to translate omics-based multifactorial biomarker models into clinical diagnostic tests are discussed, and a previous study is presented as example. PMID:26141830

  3. Effect of crystals and fibrous network polymer additives on cellular morphology of microcellular foams

    NASA Astrophysics Data System (ADS)

    Miyamoto, Ryoma; Utano, Tatsumi; Yasuhara, Shunya; Ishihara, Shota; Ohshima, Masahiro

    2015-05-01

    In this study, the core-back foam injection molding was used for preparing microcelluar polypropylene (PP) foam with either a 1,3:2,4 bis-O-(4-methylbenzylidene)-D-sorbitol gelling agent (Gel-all MD) or a fibros network polymer additive (Metablen 3000). Both agent and addiive could effectively control the celluar morphology in foams but somehow different ways. In course of cooling the polymer with Gel-all MD in the mold caity, the agent enhanced the crystal nucleation and resulted in the large number of small crystals. The crystals acted as effective bubble nucleation agent in foaming process. Thus, the agent reduced the cell size and increased the cell density, drastically. Furthermore, the small crystals provided an inhomogenuity to the expanding cell wall and produced the high open cell content with nano-scale fibril structure. Gell-all as well as Metablene 3000 formed a gel-like fibrous network in melt. The network increased the elongational viscosity and tended to prevent the cell wall from breaking up. The foaming temperature window was widened by the presence of the network. Especially, the temperature window where the macro-fibrous structure was formed was expanded to the higher temperature. The effects of crystal nucleating agent and PTFE on crystals' size and number, viscoelsticity, rheological propreties of PP and cellular morphology were compared and thorougly investigated.

  4. ComPPI: a cellular compartment-specific database for protein–protein interaction network analysis

    PubMed Central

    Veres, Daniel V.; Gyurkó, Dávid M.; Thaler, Benedek; Szalay, Kristóf Z.; Fazekas, Dávid; Korcsmáros, Tamás; Csermely, Peter

    2015-01-01

    Here we present ComPPI, a cellular compartment-specific database of proteins and their interactions enabling an extensive, compartmentalized protein–protein interaction network analysis (URL: http://ComPPI.LinkGroup.hu). ComPPI enables the user to filter biologically unlikely interactions, where the two interacting proteins have no common subcellular localizations and to predict novel properties, such as compartment-specific biological functions. ComPPI is an integrated database covering four species (S. cerevisiae, C. elegans, D. melanogaster and H. sapiens). The compilation of nine protein–protein interaction and eight subcellular localization data sets had four curation steps including a manually built, comprehensive hierarchical structure of >1600 subcellular localizations. ComPPI provides confidence scores for protein subcellular localizations and protein–protein interactions. ComPPI has user-friendly search options for individual proteins giving their subcellular localization, their interactions and the likelihood of their interactions considering the subcellular localization of their interacting partners. Download options of search results, whole-proteomes, organelle-specific interactomes and subcellular localization data are available on its website. Due to its novel features, ComPPI is useful for the analysis of experimental results in biochemistry and molecular biology, as well as for proteome-wide studies in bioinformatics and network science helping cellular biology, medicine and drug design. PMID:25348397

  5. Uniqueness and stability of traveling waves for cellular neural networks with multiple delays

    NASA Astrophysics Data System (ADS)

    Yu, Zhi-Xian; Mei, Ming

    2016-01-01

    In this paper, we investigate the properties of traveling waves to a class of lattice differential equations for cellular neural networks with multiple delays. Following the previous study [38] on the existence of the traveling waves, here we focus on the uniqueness and the stability of these traveling waves. First of all, by establishing the a priori asymptotic behavior of traveling waves and applying Ikehara's theorem, we prove the uniqueness (up to translation) of traveling waves ϕ (n - ct) with c ≤c* for the cellular neural networks with multiple delays, where c* < 0 is the critical wave speed. Then, by the weighted energy method together with the squeezing technique, we further show the global stability of all non-critical traveling waves for this model, that is, for all monotone waves with the speed c

  6. APOBEC3G enhances lymphoma cell radioresistance by promoting cytidine deaminase-dependent DNA repair.

    PubMed

    Nowarski, Roni; Wilner, Ofer I; Cheshin, Ori; Shahar, Or D; Kenig, Edan; Baraz, Leah; Britan-Rosich, Elena; Nagler, Arnon; Harris, Reuben S; Goldberg, Michal; Willner, Itamar; Kotler, Moshe

    2012-07-12

    APOBEC3 proteins catalyze deamination of cytidines in single-stranded DNA (ssDNA), providing innate protection against retroviral replication by inducing deleterious dC > dU hypermutation of replication intermediates. APOBEC3G expression is induced in mitogen-activated lymphocytes; however, no physiologic role related to lymphoid cell proliferation has yet to be determined. Moreover, whether APOBEC3G cytidine deaminase activity transcends to processing cellular genomic DNA is unknown. Here we show that lymphoma cells expressing high APOBEC3G levels display efficient repair of genomic DNA double-strand breaks (DSBs) induced by ionizing radiation and enhanced survival of irradiated cells. APOBEC3G transiently accumulated in the nucleus in response to ionizing radiation and was recruited to DSB repair foci. Consistent with a direct role in DSB repair, inhibition of APOBEC3G expression or deaminase activity resulted in deficient DSB repair, whereas reconstitution of APOBEC3G expression in leukemia cells enhanced DSB repair. APOBEC3G activity involved processing of DNA flanking a DSB in an integrated reporter cassette. Atomic force microscopy indicated that APOBEC3G multimers associate with ssDNA termini, triggering multimer disassembly to multiple catalytic units. These results identify APOBEC3G as a prosurvival factor in lymphoma cells, marking APOBEC3G as a potential target for sensitizing lymphoma to radiation therapy. PMID:22645179

  7. Network, cellular, and molecular mechanisms underlying long-term memory formation.

    PubMed

    Carasatorre, Mariana; Ramírez-Amaya, Víctor

    2013-01-01

    The neural network stores information through activity-dependent synaptic plasticity that occurs in populations of neurons. Persistent forms of synaptic plasticity may account for long-term memory storage, and the most salient forms are the changes in the structure of synapses. The theory proposes that encoding should use a sparse code and evidence suggests that this can be achieved through offline reactivation or by sparse initial recruitment of the network units. This idea implies that in some cases the neurons that underwent structural synaptic plasticity might be a subpopulation of those originally recruited; However, it is not yet clear whether all the neurons recruited during acquisition are the ones that underwent persistent forms of synaptic plasticity and responsible for memory retrieval. To determine which neural units underlie long-term memory storage, we need to characterize which are the persistent forms of synaptic plasticity occurring in these neural ensembles and the best hints so far are the molecular signals underlying structural modifications of the synapses. Structural synaptic plasticity can be achieved by the activity of various signal transduction pathways, including the NMDA-CaMKII and ACh-MAPK. These pathways converge with the Rho family of GTPases and the consequent ERK 1/2 activation, which regulates multiple cellular functions such as protein translation, protein trafficking, and gene transcription. The most detailed explanation may come from models that allow us to determine the contribution of each piece of this fascinating puzzle that is the neuron and the neural network. PMID:22976275

  8. A quantitative chaperone interaction network reveals the architecture of cellular protein homeostasis pathways.

    PubMed

    Taipale, Mikko; Tucker, George; Peng, Jian; Krykbaeva, Irina; Lin, Zhen-Yuan; Larsen, Brett; Choi, Hyungwon; Berger, Bonnie; Gingras, Anne-Claude; Lindquist, Susan

    2014-07-17

    Chaperones are abundant cellular proteins that promote the folding and function of their substrate proteins (clients). In vivo, chaperones also associate with a large and diverse set of cofactors (cochaperones) that regulate their specificity and function. However, how these cochaperones regulate protein folding and whether they have chaperone-independent biological functions is largely unknown. We combined mass spectrometry and quantitative high-throughput LUMIER assays to systematically characterize the chaperone-cochaperone-client interaction network in human cells. We uncover hundreds of chaperone clients, delineate their participation in specific cochaperone complexes, and establish a surprisingly distinct network of protein-protein interactions for cochaperones. As a salient example of the power of such analysis, we establish that NUDC family cochaperones specifically associate with structurally related but evolutionarily distinct β-propeller folds. We provide a framework for deciphering the proteostasis network and its regulation in development and disease and expand the use of chaperones as sensors for drug-target engagement. PMID:25036637

  9. Proof-of-Concept of a Millimeter-Wave Integrated Heterogeneous Network for 5G Cellular.

    PubMed

    Okasaka, Shozo; Weiler, Richard J; Keusgen, Wilhelm; Pudeyev, Andrey; Maltsev, Alexander; Karls, Ingolf; Sakaguchi, Kei

    2016-01-01

    The fifth-generation mobile networks (5G) will not only enhance mobile broadband services, but also enable connectivity for a massive number of Internet-of-Things devices, such as wireless sensors, meters or actuators. Thus, 5G is expected to achieve a 1000-fold or more increase in capacity over 4G. The use of the millimeter-wave (mmWave) spectrum is a key enabler to allowing 5G to achieve such enhancement in capacity. To fully utilize the mmWave spectrum, 5G is expected to adopt a heterogeneous network (HetNet) architecture, wherein mmWave small cells are overlaid onto a conventional macro-cellular network. In the mmWave-integrated HetNet, splitting of the control plane (CP) and user plane (UP) will allow continuous connectivity and increase the capacity of the mmWave small cells. mmWave communication can be used not only for access linking, but also for wireless backhaul linking, which will facilitate the installation of mmWave small cells. In this study, a proof-of-concept (PoC) was conducted to demonstrate the practicality of a prototype mmWave-integrated HetNet, using mmWave technologies for both backhaul and access. PMID:27571074

  10. Firing patterns in a random network cellular automata model of the brain

    NASA Astrophysics Data System (ADS)

    Acedo, L.; Lamprianidou, E.; Moraño, J.-A.; Villanueva-Oller, J.; Villanueva, R.-J.

    2015-10-01

    One of the main challenges in the simulation of even reduced areas of the brain is the presence of a large number of neurons and a large number of connections among them. Even from a theoretical point of view, the behaviour of dynamical models of complex networks with high connectivity is unknown, precisely because the cost of computation is still unaffordable and it will likely be in the near future. In this paper we discuss the simulation of a cellular automata network model of the brain including up to one million sites with a maximum average of three hundred connections per neuron. This level of connectivity was achieved thanks to a distributed computing environment based on the BOINC (Berkeley Open Infrastructure for Network Computing) platform. Moreover, in this work we consider the interplay among excitatory neurons (which induce the excitation of their neighbours) and inhibitory neurons (which prevent resting neurons from firing and induce firing neurons to pass to the refractory state). Our objective is to classify the normal (noisy but asymptotically constant patterns) and the abnormal (high oscillations with spindle-like behaviour) patterns of activity in the model brain and their stability and parameter ranges in order to determine the role of excitatory and inhibitory compensatory effects in healthy and diseased individuals.

  11. Viral Replication Protein Inhibits Cellular Cofilin Actin Depolymerization Factor to Regulate the Actin Network and Promote Viral Replicase Assembly

    PubMed Central

    Kovalev, Nikolay; de Castro Martín, Isabel Fernández; Barajas, Daniel; Risco, Cristina; Nagy, Peter D.

    2016-01-01

    RNA viruses exploit host cells by co-opting host factors and lipids and escaping host antiviral responses. Previous genome-wide screens with Tomato bushy stunt virus (TBSV) in the model host yeast have identified 18 cellular genes that are part of the actin network. In this paper, we show that the p33 viral replication factor interacts with the cellular cofilin (Cof1p), which is an actin depolymerization factor. Using temperature-sensitive (ts) Cof1p or actin (Act1p) mutants at a semi-permissive temperature, we find an increased level of TBSV RNA accumulation in yeast cells and elevated in vitro activity of the tombusvirus replicase. We show that the large p33 containing replication organelle-like structures are located in the close vicinity of actin patches in yeast cells or around actin cable hubs in infected plant cells. Therefore, the actin filaments could be involved in VRC assembly and the formation of large viral replication compartments containing many individual VRCs. Moreover, we show that the actin network affects the recruitment of viral and cellular components, including oxysterol binding proteins and VAP proteins to form membrane contact sites for efficient transfer of sterols to the sites of replication. Altogether, the emerging picture is that TBSV, via direct interaction between the p33 replication protein and Cof1p, controls cofilin activities to obstruct the dynamic actin network that leads to efficient subversion of cellular factors for pro-viral functions. In summary, the discovery that TBSV interacts with cellular cofilin and blocks the severing of existing filaments and the formation of new actin filaments in infected cells opens a new window to unravel the way by which viruses could subvert/co-opt cellular proteins and lipids. By regulating the functions of cofilin and the actin network, which are central nodes in cellular pathways, viruses could gain supremacy in subversion of cellular factors for pro-viral functions. PMID:26863541

  12. Smart-Pixel Array Processors Based on Optimal Cellular Neural Networks for Space Sensor Applications

    NASA Technical Reports Server (NTRS)

    Fang, Wai-Chi; Sheu, Bing J.; Venus, Holger; Sandau, Rainer

    1997-01-01

    A smart-pixel cellular neural network (CNN) with hardware annealing capability, digitally programmable synaptic weights, and multisensor parallel interface has been under development for advanced space sensor applications. The smart-pixel CNN architecture is a programmable multi-dimensional array of optoelectronic neurons which are locally connected with their local neurons and associated active-pixel sensors. Integration of the neuroprocessor in each processor node of a scalable multiprocessor system offers orders-of-magnitude computing performance enhancements for on-board real-time intelligent multisensor processing and control tasks of advanced small satellites. The smart-pixel CNN operation theory, architecture, design and implementation, and system applications are investigated in detail. The VLSI (Very Large Scale Integration) implementation feasibility was illustrated by a prototype smart-pixel 5x5 neuroprocessor array chip of active dimensions 1380 micron x 746 micron in a 2-micron CMOS technology.

  13. Multiscale Systems Analysis of Root Growth and Development: Modeling Beyond the Network and Cellular Scales

    PubMed Central

    Band, Leah R.; Fozard, John A.; Godin, Christophe; Jensen, Oliver E.; Pridmore, Tony; Bennett, Malcolm J.; King, John R.

    2012-01-01

    Over recent decades, we have gained detailed knowledge of many processes involved in root growth and development. However, with this knowledge come increasing complexity and an increasing need for mechanistic modeling to understand how those individual processes interact. One major challenge is in relating genotypes to phenotypes, requiring us to move beyond the network and cellular scales, to use multiscale modeling to predict emergent dynamics at the tissue and organ levels. In this review, we highlight recent developments in multiscale modeling, illustrating how these are generating new mechanistic insights into the regulation of root growth and development. We consider how these models are motivating new biological data analysis and explore directions for future research. This modeling progress will be crucial as we move from a qualitative to an increasingly quantitative understanding of root biology, generating predictive tools that accelerate the development of improved crop varieties. PMID:23110897

  14. Modeling of trophospheric ozone concentrations using genetically trained multi-level cellular neural networks

    NASA Astrophysics Data System (ADS)

    Ozcan, H. Kurtulus; Bilgili, Erdem; Sahin, Ulku; Ucan, O. Nuri; Bayat, Cuma

    2007-09-01

    Tropospheric ozone concentrations, which are an important air pollutant, are modeled by the use of an artificial intelligence structure. Data obtained from air pollution measurement stations in the city of Istanbul are utilized in constituting the model. A supervised algorithm for the evaluation of ozone concentration using a genetically trained multi-level cellular neural network (ML-CNN) is introduced, developed, and applied to real data. A genetic algorithm is used in the optimization of CNN templates. The model results and the actual measurement results are compared and statistically evaluated. It is observed that seasonal changes in ozone concentrations are reflected effectively by the concentrations estimated by the multilevel-CNN model structure, with a correlation value of 0.57 ascertained between actual and model results. It is shown that the multilevel-CNN modeling technique is as satisfactory as other modeling techniques in associating the data in a complex medium in air pollution applications.

  15. Convergence and attractivity of memristor-based cellular neural networks with time delays.

    PubMed

    Qin, Sitian; Wang, Jun; Xue, Xiaoping

    2015-03-01

    This paper presents theoretical results on the convergence and attractivity of memristor-based cellular neural networks (MCNNs) with time delays. Based on a realistic memristor model, an MCNN is modeled using a differential inclusion. The essential boundedness of its global solutions is proven. The state of MCNNs is further proven to be convergent to a critical-point set located in saturated region of the activation function, when the initial state locates in a saturated region. It is shown that the state convergence time period is finite and can be quantitatively estimated using given parameters. Furthermore, the positive invariance and attractivity of state in non-saturated regions are also proven. The simulation results of several numerical examples are provided to substantiate the results. PMID:25562569

  16. Parallelism on the Intel 860 Hypercube:. Ising Magnets, Hydrodynamical Cellular Automata and Neural Networks

    NASA Astrophysics Data System (ADS)

    Kohring, G. A.; Stauffer, D.

    Geometric parallelization was tested on the Intel Hypercube with 32 MIMD processors of 1860 type, each with 16 Mbytes of distributed memory. We applied it to Ising models in two and three dimensions as well as to neural networks and two-dimensional hydrodynamic cellular automata. For system sizes suited to this machine, up to 60960*60960 and 1410*1410*1408 Ising spins, we found nearly hundred percent parallel efficiency in spite of the needed inter-processor communications. For small systems, the observed deviations from full efficiency were compared with the scaling concepts of Heermann and Burkitt and of Jakobs and Gerling. For Ising models, we determined the Glauber kinetic exponent z≃2.18 in two dimensions and confirmed the stretched exponential relaxation of the magnetization towards the spontaneous magnetization below Tc. For three dimensions we found z≃2.09 and simple exponential relaxation.

  17. Global Detection of Live Virtual Machine Migration Based on Cellular Neural Networks

    PubMed Central

    Xie, Kang; Yang, Yixian; Zhang, Ling; Jing, Maohua; Xin, Yang; Li, Zhongxian

    2014-01-01

    In order to meet the demands of operation monitoring of large scale, autoscaling, and heterogeneous virtual resources in the existing cloud computing, a new method of live virtual machine (VM) migration detection algorithm based on the cellular neural networks (CNNs), is presented. Through analyzing the detection process, the parameter relationship of CNN is mapped as an optimization problem, in which improved particle swarm optimization algorithm based on bubble sort is used to solve the problem. Experimental results demonstrate that the proposed method can display the VM migration processing intuitively. Compared with the best fit heuristic algorithm, this approach reduces the processing time, and emerging evidence has indicated that this new approach is affordable to parallelism and analog very large scale integration (VLSI) implementation allowing the VM migration detection to be performed better. PMID:24959631

  18. Global detection of live virtual machine migration based on cellular neural networks.

    PubMed

    Xie, Kang; Yang, Yixian; Zhang, Ling; Jing, Maohua; Xin, Yang; Li, Zhongxian

    2014-01-01

    In order to meet the demands of operation monitoring of large scale, autoscaling, and heterogeneous virtual resources in the existing cloud computing, a new method of live virtual machine (VM) migration detection algorithm based on the cellular neural networks (CNNs), is presented. Through analyzing the detection process, the parameter relationship of CNN is mapped as an optimization problem, in which improved particle swarm optimization algorithm based on bubble sort is used to solve the problem. Experimental results demonstrate that the proposed method can display the VM migration processing intuitively. Compared with the best fit heuristic algorithm, this approach reduces the processing time, and emerging evidence has indicated that this new approach is affordable to parallelism and analog very large scale integration (VLSI) implementation allowing the VM migration detection to be performed better. PMID:24959631

  19. A novel method to assess human population exposure induced by a wireless cellular network.

    PubMed

    Varsier, Nadège; Plets, David; Corre, Yoann; Vermeeren, Günter; Joseph, Wout; Aerts, Sam; Martens, Luc; Wiart, Joe

    2015-09-01

    This paper presents a new metric to evaluate electromagnetic exposure induced by wireless cellular networks. This metric takes into account the exposure induced by base station antennas as well as exposure induced by wireless devices to evaluate average global exposure of the population in a specific geographical area. The paper first explains the concept and gives the formulation of the Exposure Index (EI). Then, the EI computation is illustrated through simple phone call scenarios (indoor office, in train) and a complete macro urban data long-term evolution scenario showing how, based on simulations, radio-planning predictions, realistic population statistics, user traffic data, and specific absorption rate calculations can be combined to assess the index. Bioelectromagnetics. 36:451-463, 2015. © 2015 Wiley Periodicals, Inc. PMID:26113174

  20. Co-evolutionary networks of genes and cellular processes across fungal species

    PubMed Central

    Tuller, Tamir; Kupiec, Martin; Ruppin, Eytan

    2009-01-01

    Background The introduction of measures such as evolutionary rate and propensity for gene loss have significantly advanced our knowledge of the evolutionary history and selection forces acting upon individual genes and cellular processes. Results We present two new measures, the 'relative evolutionary rate pattern' (rERP), which records the relative evolutionary rates of conserved genes across the different branches of a species' phylogenetic tree, and the 'copy number pattern' (CNP), which quantifies the rate of gene loss of less conserved genes. Together, these measures yield a high-resolution study of the co-evolution of genes in 9 fungal species, spanning 3,540 sets of orthologs. We find that the evolutionary tempo of conserved genes varies in different evolutionary periods. The co-evolution of genes' Gene Ontology categories exhibits a significant correlation with their functional distance in the Gene Ontology hierarchy, but not with their location on chromosomes, showing that cellular functions are a more important driving force in gene co-evolution than their chromosomal proximity. Two fundamental patterns of co-evolution of conserved genes, cooperative and reciprocal, are identified; only genes co-evolving cooperatively functionally back each other up. The co-evolution of conserved and less conserved genes exhibits both commonalities and differences; DNA metabolism is positively correlated with nuclear traffic, transcription processes and vacuolar biology in both analyses. Conclusions Overall, this study charts the first global network view of gene co-evolution in fungi. The future application of the approach presented here to other phylogenetic trees holds much promise in characterizing the forces that shape cellular co-evolution. PMID:19416514

  1. BioJazz: in silico evolution of cellular networks with unbounded complexity using rule-based modeling

    PubMed Central

    Feng, Song; Ollivier, Julien F.; Swain, Peter S.; Soyer, Orkun S.

    2015-01-01

    Systems biologists aim to decipher the structure and dynamics of signaling and regulatory networks underpinning cellular responses; synthetic biologists can use this insight to alter existing networks or engineer de novo ones. Both tasks will benefit from an understanding of which structural and dynamic features of networks can emerge from evolutionary processes, through which intermediary steps these arise, and whether they embody general design principles. As natural evolution at the level of network dynamics is difficult to study, in silico evolution of network models can provide important insights. However, current tools used for in silico evolution of network dynamics are limited to ad hoc computer simulations and models. Here we introduce BioJazz, an extendable, user-friendly tool for simulating the evolution of dynamic biochemical networks. Unlike previous tools for in silico evolution, BioJazz allows for the evolution of cellular networks with unbounded complexity by combining rule-based modeling with an encoding of networks that is akin to a genome. We show that BioJazz can be used to implement biologically realistic selective pressures and allows exploration of the space of network architectures and dynamics that implement prescribed physiological functions. BioJazz is provided as an open-source tool to facilitate its further development and use. Source code and user manuals are available at: http://oss-lab.github.io/biojazz and http://osslab.lifesci.warwick.ac.uk/BioJazz.aspx. PMID:26101250

  2. Intragranular cellular segregation network structure strengthening 316L stainless steel prepared by selective laser melting

    NASA Astrophysics Data System (ADS)

    Zhong, Yuan; Liu, Leifeng; Wikman, Stefan; Cui, Daqing; Shen, Zhijian

    2016-03-01

    A feasibility study was performed to fabricate ITER In-Vessel components by Selective Laser Melting (SLM) supported by Fusion for Energy (F4E). Almost fully dense 316L stainless steel (SS316L) components were prepared from gas-atomized powder and with optimized SLM processing parameters. Tensile tests and Charpy-V tests were carried out at 22 °C and 250 °C and the results showed that SLM SS316L fulfill the RCC-MR code. Microstructure characterization reveals the presence of hierarchical macro-, micro- and nano-structures in as-built samples that were very different from SS316L microstructures prepared by other established methods. The formation of a characteristic intragranular cellular segregation network microstructure appears to contribute to the increase of yield strength without losing ductility. Silicon oxide nano-inclusions were formed during the SLM process that generated a micro-hardness fluctuation in the building direction. The combined influence of a cellular microstructure and the nano-inclusions constraints the size of ductile dimples to nano-scale. The crack propagation is hindered by a pinning effect that improves the defect-tolerance of the SLM SS316L. This work proves that it was possible to manufacture SS316L with properties suitable for ITER First Wall panels. Further studies on irradiation properties of SLM SS316L and manufacturing of larger real-size components are needed.

  3. Computerized detection of pulmonary nodules using cellular neural networks in CT images

    NASA Astrophysics Data System (ADS)

    Zhang, Xiangwei; McLennan, Geoffrey; Hoffman, Eric A.; Sonka, Milan

    2004-05-01

    The purpose of this study is to develop a computer-aided diagnosis (CAD) system to detect small-sized (from 2mm to 10mm) non-pleural pulmonary nodules in high resolution helical CT scans. A new 3D automated scheme using cellular neural networks is presented. Different from most previous methods, this scheme employed the local shape property to perform voxel classification. The shape index feature successfully captured the local shape difference between nodules and non-nodules, especially vessels. A 3D discrete-time cellular neural network (DTCNN) was constructed to give a reliable voxel classification by collecting information in a neighborhood. To tailor it for lung nodule detection, this DTCNN was trained using genetic algorithms (GAs) to derive the shape index variation pattern of nodules. 19 clinical thoracic CT cases involving a total of 4838 sectional images were used in this work, with 2 scans forming the training set, and the remaining 17 cases being the testing set. The evaluation was composed of two stages. During the first stage, a pulmonologist and our CAD system independently detected nodules in the testing set. Then, the suspected nodule areas located by the computer were reviewed by the pulmonologist to confirm nodules missed by the human in the first review. There were 32 true nodules detected by the computer but missed by the pulmonologist in the first review, in which 30 non-juxtapleural nodules were found. Considering the nodules detected by the pulmonologist during the first and second reviews as the truth, 52 of 62 non-pleural nodules were detected by the CAD system (sensitivity being 83.9%), with the number of false positives being 3.47 per case.

  4. Inhibition of APOBEC3G activity impedes double-stranded DNA repair.

    PubMed

    Prabhu, Ponnandy; Shandilya, Shivender M D; Britan-Rosich, Elena; Nagler, Adi; Schiffer, Celia A; Kotler, Moshe

    2016-01-01

    The cellular cytidine deaminase APOBEC3G (A3G) was first described as an anti-HIV-1 restriction factor, acting by directly deaminating reverse transcripts of the viral genome. HIV-1 Vif neutralizes the activity of A3G, primarily by mediating degradation of A3G to establish effective infection in host target cells. Lymphoma cells, which express high amounts of A3G, can restrict Vif-deficient HIV-1. Interestingly, these cells are more stable in the face of treatments that result in double-stranded DNA damage, such as ionizing radiation and chemotherapies. Previously, we showed that the Vif-derived peptide (Vif25-39) efficiently inhibits A3G deamination, and increases the sensitivity of lymphoma cells to ionizing radiation. In the current study, we show that additional peptides derived from Vif, A3G, and APOBEC3F, which contain the LYYF motif, inhibit deamination activity. Each residue in the Vif25-39 sequence moderately contributes to the inhibitory effect, whereas replacing a single residue in the LYYF motif completely abrogates inhibition of deamination. Treatment of A3G-expressing lymphoma cells exposed to ionizing radiation with the new inhibitory peptides reduces double-strand break repair after irradiation. Incubation of cultured irradiated lymphoma cells with peptides that inhibit double-strand break repair halts their propagation. These results suggest that A3G may be a potential therapeutic target that is amenable to peptide and peptidomimetic inhibition. PMID:26460502

  5. Cellular Nonlinear Networks for the emergence of perceptual states: application to robot navigation control.

    PubMed

    Arena, Paolo; De Fiore, Sebastiano; Patané, Luca

    2009-01-01

    In this paper a new general purpose perceptual control architecture, based on nonlinear neural lattices, is presented and applied to solve robot navigation tasks. Insects show the ability to react to certain stimuli with simple reflexes, using direct sensory-motor pathways, which can be considered as basic behaviors, inherited and pre-wired. Relevant brain centres, known as Mushroom Bodies (MB) and Central Complex (CX) were recently identified in insects: though their functional details are not yet fully understood, it is known that they provide secondary pathways allowing the emergence of cognitive behaviors. These are gained through the coordination of the basic abilities to satisfy the insect's needs. Taking inspiration from this evidence, our architecture modulates, through a reinforcement learning, a set of competitive and concurrent basic behaviors in order to accomplish the task assigned through a reward function. The core of the architecture is constituted by the so-called Representation layer, used to create a concise picture of the current environment situation, fusing together different stimuli for the emergence of perceptual states. These perceptual states are steady state solutions of lattices of Reaction-Diffusion Cellular Nonlinear Networks (RD-CNN), designed to show Turing patterns. The exploitation of the dynamics of the multiple equilibria of the network is emphasized through the adaptive shaping of the basins of attraction for each emerged pattern. New experimental campaigns on standard robotic platforms are reported to demonstrate the potentiality and the effectiveness of the approach. PMID:19596552

  6. Energy-Efficient Crowdsensing of Human Mobility and Signal Levels in Cellular Networks

    PubMed Central

    Foremski, Paweł; Gorawski, Michał; Grochla, Krzysztof; Polys, Konrad

    2015-01-01

    The paper presents a practical application of the crowdsensing idea to measure human mobility and signal coverage in cellular networks. Currently, virtually everyone is carrying a mobile phone, which may be used as a sensor to gather research data by measuring, e.g., human mobility and radio signal levels. However, many users are unwilling to participate in crowdsensing experiments. This work begins with the analysis of the barriers for engaging people in crowdsensing. A survey showed that people who agree to participate in crowdsensing expect a minimum impact on their battery lifetime and phone usage habits. To address these requirements, this paper proposes an application for measuring the location and signal strength data based on energy-efficient GPS tracking, which allows one to perform the measurements of human mobility and radio signal levels with minimum energy utilization and without any engagement of the user. The method described combines measurements from the accelerometer with effective management of the GPS to monitor the user mobility with the decrease in battery lifetime by approximately 20%. To show the applicability of the proposed platform, the sample results of signal level distribution and coverage maps gathered for an LTE network and representing human mobility are shown. PMID:26340633

  7. Measurement and interpolation uncertainties in rainfall maps from cellular communication networks

    NASA Astrophysics Data System (ADS)

    Rios Gaona, M. F.; Overeem, A.; Leijnse, H.; Uijlenhoet, R.

    2015-08-01

    compared against quality-controlled gauge-adjusted radar rainfall fields (assumed to be the ground truth). Thus, we were able to not only identify and quantify the sources of uncertainty in such rainfall maps, but also test the actual and optimal performance of one commercial microwave network from one of the cellular providers in the Netherlands. Errors in microwave link measurements were found to be the source that contributes most to the overall uncertainty.

  8. Protein-protein interaction networks identify targets which rescue the MPP+ cellular model of Parkinson’s disease

    PubMed Central

    Keane, Harriet; Ryan, Brent J.; Jackson, Brendan; Whitmore, Alan; Wade-Martins, Richard

    2015-01-01

    Neurodegenerative diseases are complex multifactorial disorders characterised by the interplay of many dysregulated physiological processes. As an exemplar, Parkinson’s disease (PD) involves multiple perturbed cellular functions, including mitochondrial dysfunction and autophagic dysregulation in preferentially-sensitive dopamine neurons, a selective pathophysiology recapitulated in vitro using the neurotoxin MPP+. Here we explore a network science approach for the selection of therapeutic protein targets in the cellular MPP+ model. We hypothesised that analysis of protein-protein interaction networks modelling MPP+ toxicity could identify proteins critical for mediating MPP+ toxicity. Analysis of protein-protein interaction networks constructed to model the interplay of mitochondrial dysfunction and autophagic dysregulation (key aspects of MPP+ toxicity) enabled us to identify four proteins predicted to be key for MPP+ toxicity (P62, GABARAP, GBRL1 and GBRL2). Combined, but not individual, knockdown of these proteins increased cellular susceptibility to MPP+ toxicity. Conversely, combined, but not individual, over-expression of the network targets provided rescue of MPP+ toxicity associated with the formation of autophagosome-like structures. We also found that modulation of two distinct proteins in the protein-protein interaction network was necessary and sufficient to mitigate neurotoxicity. Together, these findings validate our network science approach to multi-target identification in complex neurological diseases. PMID:26608097

  9. Protein-protein interaction networks identify targets which rescue the MPP+ cellular model of Parkinson’s disease

    NASA Astrophysics Data System (ADS)

    Keane, Harriet; Ryan, Brent J.; Jackson, Brendan; Whitmore, Alan; Wade-Martins, Richard

    2015-11-01

    Neurodegenerative diseases are complex multifactorial disorders characterised by the interplay of many dysregulated physiological processes. As an exemplar, Parkinson’s disease (PD) involves multiple perturbed cellular functions, including mitochondrial dysfunction and autophagic dysregulation in preferentially-sensitive dopamine neurons, a selective pathophysiology recapitulated in vitro using the neurotoxin MPP+. Here we explore a network science approach for the selection of therapeutic protein targets in the cellular MPP+ model. We hypothesised that analysis of protein-protein interaction networks modelling MPP+ toxicity could identify proteins critical for mediating MPP+ toxicity. Analysis of protein-protein interaction networks constructed to model the interplay of mitochondrial dysfunction and autophagic dysregulation (key aspects of MPP+ toxicity) enabled us to identify four proteins predicted to be key for MPP+ toxicity (P62, GABARAP, GBRL1 and GBRL2). Combined, but not individual, knockdown of these proteins increased cellular susceptibility to MPP+ toxicity. Conversely, combined, but not individual, over-expression of the network targets provided rescue of MPP+ toxicity associated with the formation of autophagosome-like structures. We also found that modulation of two distinct proteins in the protein-protein interaction network was necessary and sufficient to mitigate neurotoxicity. Together, these findings validate our network science approach to multi-target identification in complex neurological diseases.

  10. APOBEC3G restricts early HIV-1 replication in the cytoplasm of target cells

    SciTech Connect

    Anderson, Jenny L.; Hope, Thomas J.

    2008-05-25

    Cellular APOBEC3G (A3G) protein is packaged into human immunodeficiency virus type 1 (HIV-1) virions in producer cells yet restricts viral replication in target cells. To characterize this restriction in target cells, the effect of A3G on generating various HIV-1 cDNA products was measured by quantitative real-time PCR. A3G decreased cDNA products from Vif-deficient HIV-1, with minor effects on early reverse transcripts and larger declines in late reverse transcripts. However, the greatest decline was typically observed in nuclear 2-LTR circles. Moreover, the magnitude of these declines varied with A3G dose. Adding integration inhibitor did not stop the A3G-mediated loss in 2-LTR circles. Moreover, obstructing HIV-1 nuclear entry using vesicular stomatitis virus matrix protein did not stop the A3G-mediated decline in late reverse transcripts. Collectively, these data suggest that A3G has important restriction activity in the cytoplasm and progressively diminishes viral cytoplasmic and nuclear cDNA forms with increasing magnitude during restriction.

  11. Noise-robust realization of Turing-complete cellular automata by using neural networks with pattern representation

    NASA Astrophysics Data System (ADS)

    Oku, Makito; Aihara, Kazuyuki

    2010-11-01

    A modularly-structured neural network model is considered. Each module, which we call a ‘cell’, consists of two parts: a Hopfield neural network model and a multilayered perceptron. An array of such cells is used to simulate the Rule 110 cellular automaton with high accuracy even when all the units of neural networks are replaced by stochastic binary ones. We also find that noise not only degrades but also facilitates computation if the outputs of multilayered perceptrons are below the threshold required to update the states of the cells, which is a stochastic resonance in computation.

  12. Astrocytic gap junctional networks suppress cellular damage in an in vitro model of ischemia

    SciTech Connect

    Shinotsuka, Takanori; Yasui, Masato; Nuriya, Mutsuo

    2014-02-07

    Highlights: • Astrocytes exhibit characteristic changes in [Ca{sup 2+}]{sub i} under OGD. • Astrocytic [Ca{sup 2+}]{sub i} increase is synchronized with a neuronal anoxic depolarization. • Gap junctional couplings protect neurons as well as astrocytes during OGD. - Abstract: Astrocytes play pivotal roles in both the physiology and the pathophysiology of the brain. They communicate with each other via extracellular messengers as well as through gap junctions, which may exacerbate or protect against pathological processes in the brain. However, their roles during the acute phase of ischemia and the underlying cellular mechanisms remain largely unknown. To address this issue, we imaged changes in the intracellular calcium concentration ([Ca{sup 2+}]{sub i}) in astrocytes in mouse cortical slices under oxygen/glucose deprivation (OGD) condition using two-photon microscopy. Under OGD, astrocytes showed [Ca{sup 2+}]{sub i} oscillations followed by larger and sustained [Ca{sup 2+}]{sub i} increases. While the pharmacological blockades of astrocytic receptors for glutamate and ATP had no effect, the inhibitions of gap junctional intercellular coupling between astrocytes significantly advanced the onset of the sustained [Ca{sup 2+}]{sub i} increase after OGD exposure. Interestingly, the simultaneous recording of the neuronal membrane potential revealed that the onset of the sustained [Ca{sup 2+}]{sub i} increase in astrocytes was synchronized with the appearance of neuronal anoxic depolarization. Furthermore, the blockade of gap junctional coupling resulted in a concurrent faster appearance of neuronal depolarizations, which remain synchronized with the sustained [Ca{sup 2+}]{sub i} increase in astrocytes. These results indicate that astrocytes delay the appearance of the pathological responses of astrocytes and neurons through their gap junction-mediated intercellular network under OGD. Thus, astrocytic gap junctional networks provide protection against tissue damage

  13. Numerically evaluated functional equivalence between chaotic dynamics in neural networks and cellular automata under totalistic rules.

    PubMed

    Takada, Ryu; Munetaka, Daigo; Kobayashi, Shoji; Suemitsu, Yoshikazu; Nara, Shigetoshi

    2007-09-01

    Chaotic dynamics in a recurrent neural network model and in two-dimensional cellular automata, where both have finite but large degrees of freedom, are investigated from the viewpoint of harnessing chaos and are applied to motion control to indicate that both have potential capabilities for complex function control by simple rule(s). An important point is that chaotic dynamics generated in these two systems give us autonomous complex pattern dynamics itinerating through intermediate state points between embedded patterns (attractors) in high-dimensional state space. An application of these chaotic dynamics to complex controlling is proposed based on an idea that with the use of simple adaptive switching between a weakly chaotic regime and a strongly chaotic regime, complex problems can be solved. As an actual example, a two-dimensional maze, where it should be noted that the spatial structure of the maze is one of typical ill-posed problems, is solved with the use of chaos in both systems. Our computer simulations show that the success rate over 300 trials is much better, at least, than that of a random number generator. Our functional simulations indicate that both systems are almost equivalent from the viewpoint of functional aspects based on our idea, harnessing of chaos. PMID:19003512

  14. Synchronization schemes for coupled identical Yang-Yang type fuzzy cellular neural networks

    NASA Astrophysics Data System (ADS)

    Xia, Yonghui; Yang, Zijiang; Han, Maoan

    2009-09-01

    This paper proposes an adaptive procedure to the problem of synchronization for a class of coupled identical Yang-Yang type fuzzy cellular neural networks (YYFCNN) with time-varying delays. Based on the simple adaptive controller, a set of sufficient conditions are developed to guarantee the synchronization of the coupled YYFCNN with time-varying delays. The results are much different from previous ones. It is proved that two coupled identical YYFCNN with time-varying delays can achieve synchronization by enhancing the coupled strength dynamically. In addition, this kind of controller is simple to be implemented and it is fairly robust against the effect of weak noise in the given time series. The approaches are based on using the invariance principle of functional differential equations, constructing a general Lyapunov-Krasovskii functional and employing a linear matrix inequality (LMI). An illustrative example and its simulations show the feasibility of our results. Finally, an application is given to show how to apply the presented synchronization scheme of YYFCNN to secure communication.

  15. Data fusion and classification using a hybrid intrinsic cellular inference network

    NASA Astrophysics Data System (ADS)

    Woodley, Robert; Walenz, Brett; Seiffertt, John; Robinette, Paul; Wunsch, Donald

    2010-04-01

    Hybrid Intrinsic Cellular Inference Network (HICIN) is designed for battlespace decision support applications. We developed an automatic method of generating hypotheses for an entity-attribute classifier. The capability and effectiveness of a domain specific ontology was used to generate automatic categories for data classification. Heterogeneous data is clustered using an Adaptive Resonance Theory (ART) inference engine on a sample (unclassified) data set. The data set is the Lahman baseball database. The actual data is immaterial to the architecture, however, parallels in the data can be easily drawn (i.e., "Team" maps to organization, "Runs scored/allowed" to Measure of organization performance (positive/negative), "Payroll" to organization resources, etc.). Results show that HICIN classifiers create known inferences from the heterogonous data. These inferences are not explicitly stated in the ontological description of the domain and are strictly data driven. HICIN uses data uncertainty handling to reduce errors in the classification. The uncertainty handling is based on subjective logic. The belief mass allows evidence from multiple sources to be mathematically combined to increase or discount an assertion. In military operations the ability to reduce uncertainty will be vital in the data fusion operation.

  16. Memristor-based cellular nonlinear/neural network: design, analysis, and applications.

    PubMed

    Duan, Shukai; Hu, Xiaofang; Dong, Zhekang; Wang, Lidan; Mazumder, Pinaki

    2015-06-01

    Cellular nonlinear/neural network (CNN) has been recognized as a powerful massively parallel architecture capable of solving complex engineering problems by performing trillions of analog operations per second. The memristor was theoretically predicted in the late seventies, but it garnered nascent research interest due to the recent much-acclaimed discovery of nanocrossbar memories by engineers at the Hewlett-Packard Laboratory. The memristor is expected to be co-integrated with nanoscale CMOS technology to revolutionize conventional von Neumann as well as neuromorphic computing. In this paper, a compact CNN model based on memristors is presented along with its performance analysis and applications. In the new CNN design, the memristor bridge circuit acts as the synaptic circuit element and substitutes the complex multiplication circuit used in traditional CNN architectures. In addition, the negative differential resistance and nonlinear current-voltage characteristics of the memristor have been leveraged to replace the linear resistor in conventional CNNs. The proposed CNN design has several merits, for example, high density, nonvolatility, and programmability of synaptic weights. The proposed memristor-based CNN design operations for implementing several image processing functions are illustrated through simulation and contrasted with conventional CNNs. Monte-Carlo simulation has been used to demonstrate the behavior of the proposed CNN due to the variations in memristor synaptic weights. PMID:25069124

  17. Adiponectin fine-tuning of liver regeneration dynamics revealed through cellular network modelling.

    PubMed

    Correnti, Jason M; Cook, Daniel; Aksamitiene, Edita; Swarup, Aditi; Ogunnaike, Babatunde; Vadigepalli, Rajanikanth; Hoek, Jan B

    2015-01-15

    Following partial hepatectomy, the liver initiates a regenerative programme involving hepatocyte priming and replication driven by the coordinated actions of cytokine and growth factors. We investigated the mechanisms underlying adiponectin's (Adn) regulation of liver regeneration through modulation of these mediators. Adn(-/-) mice showed delayed onset of hepatocyte replication, but accelerated cell cycle progression relative to wild-type mice, suggesting Adn has multiple effects fine-tuning the kinetics of liver regeneration. We developed a computational model describing the molecular and physiological kinetics of liver regeneration in Adn(-/-) mice. We employed this computational model to evaluate the underlying regulatory mechanisms. Our analysis predicted that Adn is required for an efficient early cytokine response to partial hepatectomy, but is inhibitory to later growth factor actions. Consistent with this prediction, Adn knockout reduced hepatocyte responses to interleukin-6 during the priming phase, but enhanced growth factor levels through peak hepatocyte replication. By contrast, supraphysiological concentrations of Adn resulting from rosiglitazone treatment suppressed regeneration by reducing growth factor levels during S phase, consistent with computational predictions. Together, these results revealed that Adn fine-tunes the progression of liver regeneration through dynamically modulating molecular mediator networks and cellular interactions within the liver. PMID:25630259

  18. Adiponectin fine-tuning of liver regeneration dynamics revealed through cellular network modelling

    PubMed Central

    Correnti, Jason M; Cook, Daniel; Aksamitiene, Edita; Swarup, Aditi; Ogunnaike, Babatunde; Vadigepalli, Rajanikanth; Hoek, Jan B

    2015-01-01

    Following partial hepatectomy, the liver initiates a regenerative programme involving hepatocyte priming and replication driven by the coordinated actions of cytokine and growth factors. We investigated the mechanisms underlying adiponectin's (Adn) regulation of liver regeneration through modulation of these mediators. Adn–/– mice showed delayed onset of hepatocyte replication, but accelerated cell cycle progression relative to wild-type mice, suggesting Adn has multiple effects fine-tuning the kinetics of liver regeneration. We developed a computational model describing the molecular and physiological kinetics of liver regeneration in Adn–/– mice. We employed this computational model to evaluate the underlying regulatory mechanisms. Our analysis predicted that Adn is required for an efficient early cytokine response to partial hepatectomy, but is inhibitory to later growth factor actions. Consistent with this prediction, Adn knockout reduced hepatocyte responses to interleukin-6 during the priming phase, but enhanced growth factor levels through peak hepatocyte replication. By contrast, supraphysiological concentrations of Adn resulting from rosiglitazone treatment suppressed regeneration by reducing growth factor levels during S phase, consistent with computational predictions. Together, these results revealed that Adn fine-tunes the progression of liver regeneration through dynamically modulating molecular mediator networks and cellular interactions within the liver. PMID:25630259

  19. The potential of cellular network infrastructures for sudden rainfall monitoring in dry climate regions

    NASA Astrophysics Data System (ADS)

    David, N.; Alpert, P.; Messer, H.

    2013-09-01

    Monitoring of precipitation and in particular sudden rain, in rural dry climate regions, is a subject of great significance in several weather related processes such as soil erosion, flash flooding, triggering epidemics and more. The rainfall monitoring facilities in these regions and as a result precipitation data are, however, commonly, severely lacking. As was recently shown, cellular networks infrastructures supply high resolution precipitation measurements at ground level while often being situated in dry areas, covering large parts of these climatic zones. The potential found in these systems to provide early monitoring and essential precipitation information, directly from arid regions, based on standard measurements of commercial microwave links, is exemplified here over the Negev and the Southern Judean desert, South Israel. We present the results of two different rainfall events occurred in these regions. It is shown that the microwave system measured precipitation between at least 50 min (in case 1) and at least 1 h and 40 min (in case 2) before each of the sparse rain gauges. During each case, the radar system, located relatively far from the arid sites, provided measurements from heights of at least 1500 m and 2000 m above surface, respectively. A third case study demonstrates a relative advantage of microwave links to measure precipitation intensity with respect to the radar system, over an area of complex topography located in northeastern Israel, which is relatively far (~ 150 km) from the radar.

  20. On-chip training for cellular neural networks using iterative annealing

    NASA Astrophysics Data System (ADS)

    Feiden, Dirk; Tetzlaff, Ronald

    2003-04-01

    Cellular Neural Network-Universal Machines (CNN-UM) are analog devices, which are excellently suited for image processing. A big challenge thereby is the determination of CNN templates for special image processing tasks. In many cases appropriate templates can only be found by a parameter optimization. The determination of templates for complex applications in the area of CNN is usually performed by using a CNN software simulator. Unfortunately, in many cases the determined templates cannot be used in hardware realizations of CNN caused by realization effects. In order to find robust templates, which are not only working on CNN simulators, but also on hardware implementations, we present in this contribution a new kind of on-chip-multi-template-training. Furthermore, as a possible application, we will also present a CNN-based solution of the problem of Pattern Matching, which is a processing step in many areas of image processing, like e.g. in Motion Estimation, Image- and Video-Compression.

  1. Residual Separation of Magnetic Fields Using a Cellular Neural Network Approach

    NASA Astrophysics Data System (ADS)

    Albora, A. M.; Özmen, A.; Uçan, O. N.

    - In this paper, a Cellular Neural Network (CNN) has been applied to a magnetic regional/residual anomaly separation problem. CNN is an analog parallel computing paradigm defined in space and characterized by the locality of connections between processing neurons. The behavior of the CNN is defined by the template matrices A, B and the template vector I. We have optimized weight coefficients of these templates using Recurrent Perceptron Learning Algorithm (RPLA). The advantages of CNN as a real-time stochastic method are that it introduces little distortion to the shape of the original image and that it is not effected significantly by factors such as the overlap of power spectra of residual fields. The proposed method is tested using synthetic examples and the average depth of the buried objects has been estimated by power spectrum analysis. Next the CNN approach is applied to magnetic data over the Golalan chromite mine in Elazig which lies East of Turkey. This area is among the largest and richest chromite masses of the world. We compared the performance of CNN to classical derivative approaches.

  2. A universal concept based on cellular neural networks for ultrafast and flexible solving of differential equations.

    PubMed

    Chedjou, Jean Chamberlain; Kyamakya, Kyandoghere

    2015-04-01

    This paper develops and validates a comprehensive and universally applicable computational concept for solving nonlinear differential equations (NDEs) through a neurocomputing concept based on cellular neural networks (CNNs). High-precision, stability, convergence, and lowest-possible memory requirements are ensured by the CNN processor architecture. A significant challenge solved in this paper is that all these cited computing features are ensured in all system-states (regular or chaotic ones) and in all bifurcation conditions that may be experienced by NDEs.One particular quintessence of this paper is to develop and demonstrate a solver concept that shows and ensures that CNN processors (realized either in hardware or in software) are universal solvers of NDE models. The solving logic or algorithm of given NDEs (possible examples are: Duffing, Mathieu, Van der Pol, Jerk, Chua, Rössler, Lorenz, Burgers, and the transport equations) through a CNN processor system is provided by a set of templates that are computed by our comprehensive templates calculation technique that we call nonlinear adaptive optimization. This paper is therefore a significant contribution and represents a cutting-edge real-time computational engineering approach, especially while considering the various scientific and engineering applications of this ultrafast, energy-and-memory-efficient, and high-precise NDE solver concept. For illustration purposes, three NDE models are demonstratively solved, and related CNN templates are derived and used: the periodically excited Duffing equation, the Mathieu equation, and the transport equation. PMID:25794380

  3. Mapping the Vif-A3G interaction using peptide arrays: a basis for anti-HIV lead peptides.

    PubMed

    Reingewertz, Tali H; Britan-Rosich, Elena; Rotem-Bamberger, Shahar; Viard, Mathias; Jacobs, Amy; Miller, Abigail; Lee, Ji Youn; Hwang, Jeeseong; Blumenthal, Robert; Kotler, Moshe; Friedler, Assaf

    2013-06-15

    Human apolipoprotein-B mRNA-editing catalytic polypeptide-like 3G (A3G) is a cytidine deaminase that restricts retroviruses, endogenous retro-elements and DNA viruses. A3G plays a key role in the anti-HIV-1 innate cellular immunity. The HIV-1 Vif protein counteracts A3G mainly by leading A3G towards the proteosomal machinery and by direct inhibition of its enzymatic activity. Both activities involve direct interaction between Vif and A3G. Disrupting the interaction between A3G and Vif may rescue A3G antiviral activity and inhibit HIV-1 propagation. Here, mapping the interaction sites between A3G and Vif by peptide array screening revealed distinct regions in Vif important for A3G binding, including the N-terminal domain (NTD), C-terminal domain (CTD) and residues 83-99. The Vif-binding sites in A3G included 12 different peptides that showed strong binding to either full-length Vif, Vif CTD or both. Sequence similarity was found between Vif-binding peptides from the A3G CTD and NTD. A3G peptides were synthesized and tested for their ability to counteract Vif action. A3G 211-225 inhibited HIV-1 replication in cell culture and impaired Vif dependent A3G degradation. In vivo co-localization of full-length Vif with A3G 211-225 was demonstrated by use of FRET. This peptide has the potential to serve as an anti-HIV-1 lead compound. Our results suggest a complex interaction between Vif and A3G that is mediated by discontinuous binding regions with different affinities. PMID:23545135

  4. Spatio-temporal analysis of brain electrical activity in epilepsy based on cellular nonlinear networks

    NASA Astrophysics Data System (ADS)

    Gollas, Frank; Tetzlaff, Ronald

    2009-05-01

    Epilepsy is the most common chronic disorder of the nervous system. Generally, epileptic seizures appear without foregoing sign or warning. The problem of detecting a possible pre-seizure state in epilepsy from EEG signals has been addressed by many authors over the past decades. Different approaches of time series analysis of brain electrical activity already are providing valuable insights into the underlying complex dynamics. But the main goal the identification of an impending epileptic seizure with a sufficient specificity and reliability, has not been achieved up to now. An algorithm for a reliable, automated prediction of epileptic seizures would enable the realization of implantable seizure warning devices, which could provide valuable information to the patient and time/event specific drug delivery or possibly a direct electrical nerve stimulation. Cellular Nonlinear Networks (CNN) are promising candidates for future seizure warning devices. CNN are characterized by local couplings of comparatively simple dynamical systems. With this property these networks are well suited to be realized as highly parallel, analog computer chips. Today available CNN hardware realizations exhibit a processing speed in the range of TeraOps combined with low power consumption. In this contribution new algorithms based on the spatio-temporal dynamics of CNN are considered in order to analyze intracranial EEG signals and thus taking into account mutual dependencies between neighboring regions of the brain. In an identification procedure Reaction-Diffusion CNN (RD-CNN) are determined for short segments of brain electrical activity, by means of a supervised parameter optimization. RD-CNN are deduced from Reaction-Diffusion Systems, which usually are applied to investigate complex phenomena like nonlinear wave propagation or pattern formation. The Local Activity Theory provides a necessary condition for emergent behavior in RD-CNN. In comparison linear spatio

  5. Design and simulation of cellular nonlinear networks using single-electron tunneling transistor technology

    NASA Astrophysics Data System (ADS)

    Gerousis, Costa P.

    It is currently predicted that semiconductor device scaling will end at the 22-nm device feature size (7 nm physical channel length) according to the International Technology Roadmap for Semiconductors. The main challenge is then to develop innovative technologies that will extend the scaling beyond roadmap projection. Any new technology must be well matched with complementary metal oxide semiconductor (CMOS) technology and scaleable beyond CMOS scaling projections and must provide low-power high-speed signal processing. Nanotechnology will become an appealing option for developing devices for integrated circuits with dimensions and performances well beyond roadmap predictions. Such devices, based on the controllable transfer of charge between dots or 'islands', can take advantage of the quantum mechanical effects, such as tunneling and energy quantization, which would normally occur at the nanometer scale. An outstanding challenge is in arranging such nanodevices in new architectures that can be integrated on a single chip. In particular, locally interconnected architectures are believed to be necessary to alleviate the problems associated with increasing interconnect length and complexity in ultra-dense circuits. The goal of this work is to investigate the use of nanoelectronic structures in cellular non-linear network (CNN) architectures for potential application in future high-density and low-power CMOS-nanodevice hybrid circuits. The operation of the single-electron tunneling (SET) transistor is first reviewed, followed by a discussion of simple CNN linear architectures using a SET inverter topology as the basis for the non-linear transfer characteristics for individual cells to be used in analog processing arrays for image-processing applications. The basic SET CNN cell acts as a summing node that is capacitively coupled to the inputs and outputs of nearest neighbor cells. Monte Carlo simulation results are used to show CNN-like behavior in attempting to

  6. Implementation of a cellular neural network-based segmentation algorithm on the bio-inspired vision system

    NASA Astrophysics Data System (ADS)

    Karabiber, Fethullah; Grassi, Giuseppe; Vecchio, Pietro; Arik, Sabri; Yalcin, M. Erhan

    2011-01-01

    Based on the cellular neural network (CNN) paradigm, the bio-inspired (bi-i) cellular vision system is a computing platform consisting of state-of-the-art sensing, cellular sensing-processing and digital signal processing. This paper presents the implementation of a novel CNN-based segmentation algorithm onto the bi-i system. The experimental results, carried out for different benchmark video sequences, highlight the feasibility of the approach, which provides a frame rate of about 26 frame/sec. Comparisons with existing CNN-based methods show that, even though these methods are from two to six times faster than the proposed one, the conceived approach is more accurate and, consequently, represents a satisfying trade-off between real-time requirements and accuracy.

  7. Impedance matching network for high frequency ultrasonic transducer for cellular applications.

    PubMed

    Kim, Min Gon; Yoon, Sangpil; Kim, Hyung Ham; Shung, K Kirk

    2016-02-01

    An approach for the design of an impedance matching network (IMN) for high frequency ultrasonic transducers with large apertures based on impedance analysis for cellular applications is presented in this paper. The main objectives were to maximize energy transmission from the excitation source to the ultrasonic transducers for cell manipulation and to achieve low input parameters for the safe operation of an ultrasonic transducer because the piezoelectric material in high frequency ultrasonic transducers is prone to breakage due to its being extremely thin. Two ultrasonic transducers, which were made of lithium niobate single crystal with the thickness of 15 μm, having apertures of 4.3 mm (fnumber=1.23) and 2.6mm (fnumber=0.75) were tested. L-type IMN was selected for high sensitivity and compact design of the ultrasonic transducers. The target center frequency was chosen as the frequency where the electrical admittance (|Y|) and phase angle (θz) from impedance analysis was maximal and zero, respectively. The reference center frequency and reference echo magnitude were selected as the center frequency and echo magnitude, measured by pulse-echo testing, of the ultrasonic transducer without IMN. Initial component values and topology of IMN were determined using the Smith chart, and pulse-echo testing was analyzed to verify the performance of the ultrasonic transducers with and without IMN. After several iterations between changing component values and topology of IMN, and pulse-echo measurement of the ultrasonic transducer with IMN, optimized component values and topology of IMN were chosen when the measured center frequency from pulse-echo testing was comparable to the target frequency, and the measured echo magnitude was at least 30% larger than the reference echo magnitude. Performance of an ultrasonic transducer with and without IMN was tested by observing a tangible dent on the surface of a plastic petridish and single cell response after an acoustic pulse was

  8. Intrinsic noise, dissipation cost, and robustness of cellular networks: The underlying energy landscape of MAPK signal transduction

    PubMed Central

    Lapidus, Saul; Han, Bo; Wang, Jin

    2008-01-01

    We develop a probabilistic method for analyzing global features of a cellular network under intrinsic statistical fluctuations, which is important when there are finite numbers of molecules. By making a self-consistent mean field approximation of splitting the variables in order to reduce the large number of degrees of freedom, which is reasonable for a not very strongly interacting network, we discovered that the underlying energy landscape of the mitogen-activated protein kinases (MAPKs) signal transduction network (with experimentally measured or inferred parameters such as chemical reaction rate coefficients in the network) is funneled toward a global minimum characterized by the nonequilibrium steady-state fixed point of the system at the end of the signal transduction process. For this system, we also show that the energy landscape is robust against intrinsic fluctuations and random perturbation to the inherent chemical reaction rates. The ratio of the slope versus the roughness of the energy landscape becomes a quantitative measure of robustness and stability of the network. Furthermore, we quantify the dissipation cost of this nonequilibrium system through entropy production, caused by the nonequilibrium flux in the system. We found that a lower dissipation cost corresponds to a more robust network. This least dissipation property might provide a design principle for robust and functional networks. Finally, we find the possibility of bistable and oscillatory-like solutions, which are important for cell fate decisions, upon perturbations. The method described here can be used in a variety of biological networks. PMID:18420822

  9. Geometric phase transition in the cellular network of the pancreatic islets may underlie the onset of type 1diabetes

    NASA Astrophysics Data System (ADS)

    Wang, Xujing

    Living systems are characterized by complexity in structure and emergent dynamic orders. In many aspects the onset of a chronic disease resembles phase transition in a dynamic system: quantitative changes accumulate largely unnoticed until a critical threshold is reached, which causes abrupt qualitative changes of the system. In this study we investigate this idea in a real example, the insulin-producing pancreatic islet β-cells and the onset of type 1 diabetes. Within each islet, the β-cells are electrically coupled to each other, and function as a network with synchronized actions. Using percolation theory we show how normal islet function is intrinsically linked to network connectivity, and the critical point where the islet cellular network loses site percolation, is consistent with laboratory and clinical observations of the threshold β-cell loss that causes islet functional failure. Numerical simulations confirm that the islet cellular network needs to be percolated for β-cells to synchronize. Furthermore, the interplay between site percolation and bond strength predicts the existence of a transient phase of islet functional recovery after disease onset and introduction of treatment, potentially explaining a long time mystery in the clinical study of type 1 diabetes: the honeymoon phenomenon. Based on these results, we hypothesized that the onset of T1D may be the result of a phase transition of the islet β-cell network. We further discuss the potential applications in identifying disease-driving factors, and the critical parameters that are predictive of disease onset.

  10. An asynchronous communication system based on the hyperchaotic system of 6th-order cellular neural network

    NASA Astrophysics Data System (ADS)

    Wang, Xingyuan; Xu, Bing; Luo, Chao

    2012-11-01

    This paper proposes a novel asynchronous communication scheme. Based on this scheme, a model using the hyperchaotic system of 6th-order Cellular Neural Network (CNN) is designed. This scheme enhances the security of asynchronous communication compared to the conventional ones. It is noteworthy that the proposed communication scheme does not depend on synchronization, and almost all chaotic systems can be involved in this scheme. Numerical simulations show the effectiveness of this scheme.

  11. Mobile telephones: a comparison of radiated power between 3G VoIP calls and 3G VoCS calls.

    PubMed

    Jovanovic, Dragan; Bragard, Guillaume; Picard, Dominique; Chauvin, Sébastien

    2015-01-01

    The purpose of this study is to assess the mean RF power radiated by mobile telephones during voice calls in 3G VoIP (Voice over Internet Protocol) using an application well known to mobile Internet users, and to compare it with the mean power radiated during voice calls in 3G VoCS (Voice over Circuit Switch) on a traditional network. Knowing that the specific absorption rate (SAR) is proportional to the mean radiated power, the user's exposure could be clearly identified at the same time. Three 3G (High Speed Packet Access) smartphones from three different manufacturers, all dual-band for GSM (900 MHz, 1800 MHz) and dual-band for UMTS (900 MHz, 1950 MHz), were used between 28 July and 04 August 2011 in Paris (France) to make 220 two-minute calls on a mobile telephone network with national coverage. The places where the calls were made were selected in such a way as to describe the whole range of usage situations of the mobile telephone. The measuring equipment, called "SYRPOM", recorded the radiation power levels and the frequency bands used during the calls with a sampling rate of 20,000 per second. In the framework of this study, the mean normalised power radiated by a telephone in 3G VoIP calls was evaluated at 0.75% maximum power of the smartphone, compared with 0.22% in 3G VoCS calls. The very low average power levels associated with use of 3G devices with VoIP or VoCS support the view that RF exposure resulting from their use is far from exceeding the basic restrictions of current exposure limits in terms of SAR. PMID:25352159

  12. HIV-1 Vif binds to APOBEC3G mRNA and inhibits its translation

    PubMed Central

    Mercenne, Gaëlle; Bernacchi, Serena; Richer, Delphine; Bec, Guillaume; Henriet, Simon; Paillart, Jean-Christophe; Marquet, Roland

    2010-01-01

    The HIV-1 viral infectivity factor (Vif) allows productive infection of non-permissive cells (including most natural HIV-1 targets) by counteracting the cellular cytosine deaminases APOBEC-3G (hA3G) and hA3F. The Vif-induced degradation of these restriction factors by the proteasome has been extensively studied, but little is known about the translational repression of hA3G and hA3F by Vif, which has also been proposed to participate in Vif function. Here, we studied Vif binding to hA3G mRNA and its role in translational repression. Filter binding assays and fluorescence titration curves revealed that Vif tightly binds to hA3G mRNA. Vif overall binding affinity was higher for the 3′UTR than for the 5′UTR, even though this region contained at least one high affinity Vif binding site (apparent Kd = 27 ± 6 nM). Several Vif binding sites were identified in 5′ and 3′UTRs using RNase footprinting. In vitro translation evidenced that Vif inhibited hA3G translation by two mechanisms: a main time-independent process requiring the 5′UTR and an additional time-dependent, UTR-independent process. Results using a Vif protein mutated in the multimerization domain suggested that the molecular mechanism of translational control is more complicated than a simple physical blockage of scanning ribosomes. PMID:19910370

  13. HIV-1 Vif binds to APOBEC3G mRNA and inhibits its translation.

    PubMed

    Mercenne, Gaëlle; Bernacchi, Serena; Richer, Delphine; Bec, Guillaume; Henriet, Simon; Paillart, Jean-Christophe; Marquet, Roland

    2010-01-01

    The HIV-1 viral infectivity factor (Vif) allows productive infection of non-permissive cells (including most natural HIV-1 targets) by counteracting the cellular cytosine deaminases APOBEC-3G (hA3G) and hA3F. The Vif-induced degradation of these restriction factors by the proteasome has been extensively studied, but little is known about the translational repression of hA3G and hA3F by Vif, which has also been proposed to participate in Vif function. Here, we studied Vif binding to hA3G mRNA and its role in translational repression. Filter binding assays and fluorescence titration curves revealed that Vif tightly binds to hA3G mRNA. Vif overall binding affinity was higher for the 3'UTR than for the 5'UTR, even though this region contained at least one high affinity Vif binding site (apparent K(d) = 27 +/- 6 nM). Several Vif binding sites were identified in 5' and 3'UTRs using RNase footprinting. In vitro translation evidenced that Vif inhibited hA3G translation by two mechanisms: a main time-independent process requiring the 5'UTR and an additional time-dependent, UTR-independent process. Results using a Vif protein mutated in the multimerization domain suggested that the molecular mechanism of translational control is more complicated than a simple physical blockage of scanning ribosomes. PMID:19910370

  14. Mechanical models of the cellular cytoskeletal network for the analysis of intracellular mechanical properties and force distributions: a review.

    PubMed

    Chen, Ting-Jung; Wu, Chia-Ching; Su, Fong-Chin

    2012-12-01

    The cytoskeleton, which is the major mechanical component of cells, supports the cell body and regulates the cellular motility to assist the cell in performing its biological functions. Several cytoskeletal network models have been proposed to investigate the mechanical properties of cells. This review paper summarizes these models with a focus on the prestressed cable network, the semi-flexible chain network, the open-cell foam, the tensegrity, and the granular models. The components, material parameters, types of connection joints, tension conditions, and the advantages and disadvantages of each model are evaluated from a structural and biological point of view. The underlying mechanisms that are associated with the morphological changes of spreading cells are expected to be simulated using a cytoskeletal model; however, it is still paid less attention most likely due to the lack of a suitable cytoskeletal model that can accurately model the spreading process. In this review article, the established cytoskeletal models are hoped to provide useful information for the development of future cytoskeletal models with different degrees of cell attachment for the study of the mechanical mechanisms underlying the cellular behaviors in response to external stimulations. PMID:23062682

  15. Position and Velocity Tracking in Cellular Networks Using the Kalman Filter

    SciTech Connect

    Olama, Mohammed M; Djouadi, Seddik M; Kuruganti, Phani Teja

    2009-01-01

    Access to the right information anytime, anywhere is becoming the new driving force for the information technology revolution. The 'right' information's relevance is based on the user's profile and his/her current geographical position and/or time. Location Based Service (LBS) is an innovative technology that provides information or makes information available based on the geographical location of the mobile user. Analysts predict that LBSs will lead to new applications, generating billions of US dollars worldwide (Leite, 2001; Searle, 2001). The need for an efficient and accurate mobile station (MS) positioning system is growing day by day. The ability to pinpoint the location of an individual has an obvious and vital value in the context of emergency services (Chan, 2003; Olama et al., 2008). Pinpointing the location of people and other valuable assets also opens the door to a new world of previously unimagined information services and m-commerce probabilities. For example, availability of services like 'Where is the nearest ATM?', 'Check traffic conditions on the highway on my route', 'Find a parking lot nearby', as well as answers to 'Where is my advisor?', and 'Where is my car?' will be an everyday rule in our lives (Charalambous & Panayiotou, 2004). A technology independent LBS architecture can be considered as comprised by three main parts (Girodon, 2002): A user requesting information, a mobile network operator and its partners, and several content providers (e.g. data, maps). The subscriber requests a personalized service dependant on his geographic location. The system will ask the Location Services Manager (which is in charge of handling requests, i.e., send/receive to the Location Calculator and the Content Providers) to pinpoint the location of the mobile. The Location Services Manager (LSM), using the Location Calculator, will ask the Content Provider (CP) to supply qualified information according to the mobile's geographical position. The LSM will

  16. Chrysler improved numerical differencing analyzer for third generation computers CINDA-3G

    NASA Technical Reports Server (NTRS)

    Gaski, J. D.; Lewis, D. R.; Thompson, L. R.

    1972-01-01

    New and versatile method has been developed to supplement or replace use of original CINDA thermal analyzer program in order to take advantage of improved systems software and machine speeds of third generation computers. CINDA-3G program options offer variety of methods for solution of thermal analog models presented in network format.

  17. Human APOBEC3G incorporation into murine leukemia virus particles

    SciTech Connect

    Kremer, Melanie; Schnierle, Barbara S. . E-mail: schba@pei.de

    2005-06-20

    The human APOBEC3G protein exhibits broad antiretroviral activity against a variety of retroviruses. It is packaged into viral particles and executes its antiviral function in the target cell. The packaging of APOBEC3G into different viral particles requires a mechanism that confers this promiscuity. Here, APOBEC3G incorporation into murine leukemia virus (MLV) was studied using retroviral vectors. APOBEC3G uptake did not require either its cytidine deaminase activity or the presence of a retroviral vector genome. Results from immunoprecipitation and co-localization studies of APOBEC3G with a MLV Gag-CFP (cyan fluorescent protein) fusion protein imply an interaction between both proteins. RNase A treatment did not inhibit the co-precipitation of Gag-CFP and APOBEC3G, suggesting that the interaction is RNA independent. Like human immunodeficiency virus (HIV) Gag, the MLV Gag precursor protein appears to interact with APOBEC3G, indicating that Gag contains conserved structures which are used to encapsidate APOBEC3G into different retroviral particles.

  18. Comparative analysis of Salmonella susceptibility and tolerance to the biocide chlorhexidine identifies a complex cellular defense network.

    PubMed

    Condell, Orla; Power, Karen A; Händler, Kristian; Finn, Sarah; Sheridan, Aine; Sergeant, Kjell; Renaut, Jenny; Burgess, Catherine M; Hinton, Jay C D; Nally, Jarlath E; Fanning, Séamus

    2014-01-01

    Chlorhexidine is one of the most widely used biocides in health and agricultural settings as well as in the modern food industry. It is a cationic biocide of the biguanide class. Details of its mechanism of action are largely unknown. The frequent use of chlorhexidine has been questioned recently, amidst concerns that an overuse of this compound may select for bacteria displaying an altered susceptibility to antimicrobials, including clinically important anti-bacterial agents. We generated a Salmonella enterica serovar Typhimurium isolate (ST24(CHX)) that exhibited a high-level tolerant phenotype to chlorhexidine, following several rounds of in vitro selection, using sub-lethal concentrations of the biocide. This mutant showed altered suceptibility to a panel of clinically important antimicrobial compounds. Here we describe a genomic, transcriptomic, proteomic, and phenotypic analysis of the chlorhexidine tolerant S. Typhimurium compared with its isogenic sensitive progenitor. Results from this study describe a chlorhexidine defense network that functions in both the reference chlorhexidine sensitive isolate and the tolerant mutant. The defense network involved multiple cell targets including those associated with the synthesis and modification of the cell wall, the SOS response, virulence, and a shift in cellular metabolism toward anoxic pathways, some of which were regulated by CreB and Fur. In addition, results indicated that chlorhexidine tolerance was associated with more extensive modifications of the same cellular processes involved in this proposed network, as well as a divergent defense response involving the up-regulation of additional targets such as the flagellar apparatus and an altered cellular phosphate metabolism. These data show that sub-lethal concentrations of chlorhexidine induce distinct changes in exposed Salmonella, and our findings provide insights into the mechanisms of action and tolerance to this biocidal agent. PMID:25136333

  19. Comparative analysis of Salmonella susceptibility and tolerance to the biocide chlorhexidine identifies a complex cellular defense network

    PubMed Central

    Condell, Orla; Power, Karen A.; Händler, Kristian; Finn, Sarah; Sheridan, Aine; Sergeant, Kjell; Renaut, Jenny; Burgess, Catherine M.; Hinton, Jay C. D.; Nally, Jarlath E.; Fanning, Séamus

    2014-01-01

    Chlorhexidine is one of the most widely used biocides in health and agricultural settings as well as in the modern food industry. It is a cationic biocide of the biguanide class. Details of its mechanism of action are largely unknown. The frequent use of chlorhexidine has been questioned recently, amidst concerns that an overuse of this compound may select for bacteria displaying an altered susceptibility to antimicrobials, including clinically important anti-bacterial agents. We generated a Salmonella enterica serovar Typhimurium isolate (ST24CHX) that exhibited a high-level tolerant phenotype to chlorhexidine, following several rounds of in vitro selection, using sub-lethal concentrations of the biocide. This mutant showed altered suceptibility to a panel of clinically important antimicrobial compounds. Here we describe a genomic, transcriptomic, proteomic, and phenotypic analysis of the chlorhexidine tolerant S. Typhimurium compared with its isogenic sensitive progenitor. Results from this study describe a chlorhexidine defense network that functions in both the reference chlorhexidine sensitive isolate and the tolerant mutant. The defense network involved multiple cell targets including those associated with the synthesis and modification of the cell wall, the SOS response, virulence, and a shift in cellular metabolism toward anoxic pathways, some of which were regulated by CreB and Fur. In addition, results indicated that chlorhexidine tolerance was associated with more extensive modifications of the same cellular processes involved in this proposed network, as well as a divergent defense response involving the up-regulation of additional targets such as the flagellar apparatus and an altered cellular phosphate metabolism. These data show that sub-lethal concentrations of chlorhexidine induce distinct changes in exposed Salmonella, and our findings provide insights into the mechanisms of action and tolerance to this biocidal agent. PMID:25136333

  20. Delay-dependent exponential passivity of uncertain cellular neural networks with discrete and distributed time-varying delays.

    PubMed

    Du, Yuanhua; Zhong, Shouming; Xu, Jia; Zhou, Nan

    2015-05-01

    This paper is concerned with the delay-dependent exponential passivity analysis issue for uncertain cellular neural networks with discrete and distributed time-varying delays. By decomposing the delay interval into multiple equidistant subintervals and multiple nonuniform subintervals, a suitable augmented Lyapunov-Krasovskii functionals are constructed on these intervals. A set of novel sufficient conditions are obtained to guarantee the exponential passivity analysis issue for the considered system. Finally, two numerical examples are provided to demonstrate the effectiveness of the proposed results. PMID:25702046

  1. Identification of a Novel HIV-1 Inhibitor Targeting Vif-dependent Degradation of Human APOBEC3G Protein*

    PubMed Central

    Pery, Erez; Sheehy, Ann; Nebane, N. Miranda; Brazier, Andrew Jay; Misra, Vikas; Rajendran, Kottampatty S.; Buhrlage, Sara J.; Mankowski, Marie K.; Rasmussen, Lynn; White, E. Lucile; Ptak, Roger G.; Gabuzda, Dana

    2015-01-01

    APOBEC3G (A3G) is a cellular cytidine deaminase that restricts HIV-1 replication by inducing G-to-A hypermutation in viral DNA and by deamination-independent mechanisms. HIV-1 Vif binds to A3G, resulting in its degradation via the 26 S proteasome. Therefore, this interaction represents a potential therapeutic target. To identify compounds that inhibit interaction between A3G and HIV-1 Vif in a high throughput format, we developed a homogeneous time-resolved fluorescence resonance energy transfer assay. A 307,520 compound library from the NIH Molecular Libraries Small Molecule Repository was screened. Secondary screens to evaluate dose-response performance and off-target effects, cell-based assays to identify compounds that attenuate Vif-dependent degradation of A3G, and assays testing antiviral activity in peripheral blood mononuclear cells and T cells were employed. One compound, N.41, showed potent antiviral activity in A3G(+) but not in A3G(−) T cells and had an IC50 as low as 8.4 μm and a TC50 of >100 μm when tested against HIV-1Ba-L replication in peripheral blood mononuclear cells. N.41 inhibited the Vif-A3G interaction and increased cellular A3G levels and incorporation of A3G into virions, thereby attenuating virus infectivity in a Vif-dependent manner. N.41 activity was also species- and Vif-dependent. Preliminary structure-activity relationship studies suggest that a hydroxyl moiety located at a phenylamino group is critical for N.41 anti-HIV activity and identified N.41 analogs with better potency (IC50 as low as 4.2 μm). These findings identify a new lead compound that attenuates HIV replication by liberating A3G from Vif regulation and increasing its innate antiviral activity. PMID:25724652

  2. Exact quantification of cellular robustness in genome-scale metabolic networks

    PubMed Central

    Gerstl, Matthias P.; Klamt, Steffen; Jungreuthmayer, Christian; Zanghellini, Jürgen

    2016-01-01

    Motivation: Robustness, the ability of biological networks to uphold their functionality in spite of perturbations, is a key characteristic of all living systems. Although several theoretical approaches have been developed to formalize robustness, it still eludes an exact quantification. Here, we present a rigorous and quantitative approach for the structural robustness of metabolic networks by measuring their ability to tolerate random reaction (or gene) knockouts. Results: In analogy to reliability theory, based on an explicit consideration of all possible knockout sets, we exactly quantify the probability of failure for a given network function (e.g. growth). This measure can be computed if the network’s minimal cut sets (MSCs) are known. We show that even in genome-scale metabolic networks the probability of (network) failure can be reliably estimated from MSCs with lowest cardinalities. We demonstrate the applicability of our theory by analyzing the structural robustness of multiple Enterobacteriaceae and Blattibacteriaceae and show a dramatically low structural robustness for the latter. We find that structural robustness develops from the ability to proliferate in multiple growth environments consistent with experimentally found knowledge. Conclusion: The probability of (network) failure provides thus a reliable and easily computable measure of structural robustness and redundancy in (genome-scale) metabolic networks. Availability and implementation: Source code is available under the GNU General Public License at https://github.com/mpgerstl/networkRobustnessToolbox. Contact: juergen.zanghellini@boku.ac.at Supplementary information: Supplementary data are available at Bioinformatics online. PMID:26543173

  3. The Speckle Noise Reduction and the Boundary Enhancement on Medical Ultrasound Images using the Cellular Neural Networks

    NASA Astrophysics Data System (ADS)

    Park, Hyunkyung; Miyazaki, Ryota; Nishimura, Toshihiro; Tamaki, Yasuhiro

    The purpose is to remove the speckle noise and to emphasize the boundary of a tumor by filtering based on the intensity difference in the medical ultrasound images. The proposed method is evaluated using numerical phantom simulating ultrasound B-mode images, and the effect is confirmed by applying to medical ultrasound images. Therefore, some important features such as tissue boundaries and small tumors may be overlooked. A CNN (cellular neural networks) for the speckle reduction and the edge enhancement are proposed in this paper. A CNN which is a kind of recurrent neural network can deal with images by the weight of neurons called a cell. It could be obtained more detail images recognition compared with the previous studies. A determination template parameters of the CNN for ultrasound image processing is discussed. The experimental results show effectiveness of applying the proposed method to boundary enhancement and the speckle reduction of medical ultrasound image.

  4. Multi-Hop Link Capacity of Multi-Route Multi-Hop MRC Diversity for a Virtual Cellular Network

    NASA Astrophysics Data System (ADS)

    Daou, Imane; Kudoh, Eisuke; Adachi, Fumiyuki

    In virtual cellular network (VCN), proposed for high-speed mobile communications, the signal transmitted from a mobile terminal is received by some wireless ports distributed in each virtual cell and relayed to the central port that acts as a gateway to the core network. In this paper, we apply the multi-route MHMRC diversity in order to decrease the transmit power and increase the multi-hop link capacity. The transmit power, the interference power and the link capacity are evaluated for DS-CDMA multi-hop VCN by computer simulation. The multi-route MHMRC diversity can be applied to not only DS-CDMA but also other access schemes (i. e. MC-CDMA, OFDM, etc.).

  5. Mitigating Handoff Call Dropping in Wireless Cellular Networks: A Call Admission Control Technique

    NASA Astrophysics Data System (ADS)

    Ekpenyong, Moses Effiong; Udoh, Victoria Idia; Bassey, Udoma James

    2016-06-01

    Handoff management has been an important but challenging issue in the field of wireless communication. It seeks to maintain seamless connectivity of mobile users changing their points of attachment from one base station to another. This paper derives a call admission control model and establishes an optimal step-size coefficient (k) that regulates the admission probability of handoff calls. An operational CDMA network carrier was investigated through the analysis of empirical data collected over a period of 1 month, to verify the performance of the network. Our findings revealed that approximately 23 % of calls in the existing system were lost, while 40 % of the calls (on the average) were successfully admitted. A simulation of the proposed model was then carried out under ideal network conditions to study the relationship between the various network parameters and validate our claim. Simulation results showed that increasing the step-size coefficient degrades the network performance. Even at optimum step-size (k), the network could still be compromised in the presence of severe network crises, but our model was able to recover from these problems and still functions normally.

  6. APOBEC3G impairs the multimerization of the HIV-1 Vif protein in living cells.

    PubMed

    Batisse, Julien; Guerrero, Santiago Xavier; Bernacchi, Serena; Richert, Ludovic; Godet, Julien; Goldschmidt, Valérie; Mély, Yves; Marquet, Roland; de Rocquigny, Hugues; Paillart, Jean-Christophe

    2013-06-01

    The HIV-1 viral infectivity factor (Vif) is a small basic protein essential for viral fitness and pathogenicity. Vif allows productive infection in nonpermissive cells, including most natural HIV-1 target cells, by counteracting the cellular cytosine deaminases APOBEC3G (apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3G [A3G]) and A3F. Vif is also associated with the viral assembly complex and packaged into viral particles through interactions with the viral genomic RNA and the nucleocapsid domain of Pr55(Gag). Recently, we showed that oligomerization of Vif into high-molecular-mass complexes induces Vif folding and influences its binding to high-affinity RNA binding sites present in the HIV genomic RNA. To get further insight into the role of Vif multimerization in viral assembly and A3G repression, we used fluorescence lifetime imaging microscopy (FLIM)- and fluorescence resonance energy transfer (FRET)-based assays to investigate Vif-Vif interactions in living cells. By using two N-terminally tagged Vif proteins, we show that Vif-Vif interactions occur in living cells. This oligomerization is strongly reduced when the putative Vif multimerization domain ((161)PPLP(164)) is mutated, indicating that this domain is crucial, but that regions outside this motif also participate in Vif oligomerization. When coexpressed together with Pr55(Gag), Vif is largely relocated to the cell membrane, where Vif oligomerization also occurs. Interestingly, wild-type A3G strongly interferes with Vif multimerization, contrary to an A3G mutant that does not bind to Vif. These findings confirm that Vif oligomerization occurs in living cells partly through its C-terminal motif and suggest that A3G may target and perturb the Vif oligomerization state to limit its functions in the cell. PMID:23576497

  7. APOBEC3G Impairs the Multimerization of the HIV-1 Vif Protein in Living Cells

    PubMed Central

    Batisse, Julien; Guerrero, Santiago Xavier; Bernacchi, Serena; Richert, Ludovic; Godet, Julien; Goldschmidt, Valérie; Mély, Yves; Marquet, Roland; de Rocquigny, Hugues

    2013-01-01

    The HIV-1 viral infectivity factor (Vif) is a small basic protein essential for viral fitness and pathogenicity. Vif allows productive infection in nonpermissive cells, including most natural HIV-1 target cells, by counteracting the cellular cytosine deaminases APOBEC3G (apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3G [A3G]) and A3F. Vif is also associated with the viral assembly complex and packaged into viral particles through interactions with the viral genomic RNA and the nucleocapsid domain of Pr55Gag. Recently, we showed that oligomerization of Vif into high-molecular-mass complexes induces Vif folding and influences its binding to high-affinity RNA binding sites present in the HIV genomic RNA. To get further insight into the role of Vif multimerization in viral assembly and A3G repression, we used fluorescence lifetime imaging microscopy (FLIM)- and fluorescence resonance energy transfer (FRET)-based assays to investigate Vif-Vif interactions in living cells. By using two N-terminally tagged Vif proteins, we show that Vif-Vif interactions occur in living cells. This oligomerization is strongly reduced when the putative Vif multimerization domain (161PPLP164) is mutated, indicating that this domain is crucial, but that regions outside this motif also participate in Vif oligomerization. When coexpressed together with Pr55Gag, Vif is largely relocated to the cell membrane, where Vif oligomerization also occurs. Interestingly, wild-type A3G strongly interferes with Vif multimerization, contrary to an A3G mutant that does not bind to Vif. These findings confirm that Vif oligomerization occurs in living cells partly through its C-terminal motif and suggest that A3G may target and perturb the Vif oligomerization state to limit its functions in the cell. PMID:23576497

  8. Resistance of human T cell leukemia virus type 1 to APOBEC3G restriction is mediated by elements in nucleocapsid

    PubMed Central

    Derse, David; Hill, Shawn A.; Princler, Gerald; Lloyd, Patricia; Heidecker, Gisela

    2007-01-01

    Human T cell leukemia virus type 1 (HTLV-1) has evolved a remarkable strategy to thwart the antiviral effects of the cellular cytidine deaminase APOBEC3G (hA3G). HTLV-1 infects T lymphocytes in vivo, where, like HIV-1, it is likely to encounter hA3G. HIV-1 counteracts the innate antiviral activity of hA3G by producing an accessory protein, Vif, which hastens the degradation of hA3G. In contrast, HTLV-1 does not encode a Vif homologue; instead, HTLV-1 has evolved a cis-acting mechanism to prevent hA3G restriction. We demonstrate here that a peptide motif in the C terminus of the HTLV-1 nucleocapsid (NC) domain inhibits hA3G packaging into nascent virions. Mutation of amino acids within this region resulted in increased levels of hA3G incorporation into virions and increased susceptibility to hA3G restriction. Elements within the C-terminal extension of the NC domain are highly conserved among the primate T cell leukemia viruses, but this extension is absent in all other retroviral NC proteins. PMID:17299050

  9. Beta Cell Formation in vivo Through Cellular Networking, Integration and Processing (CNIP) in Wild Type Adult Mice.

    PubMed

    Doiron, Bruno; Hu, Wenchao; DeFronzo, Ralph A

    2016-01-01

    Insulin replacement therapy is essential in type 1 diabetic individuals and is required in ~40- 50% of type 2 diabetics during their lifetime. Prior attempts at beta cell regeneration have relied upon pancreatic injury to induce beta cell proliferation, dedifferentiation and activation of the embryonic pathway, or stem cell replacement. We report an alternative method to transform adult non-stem (somatic) cells into pancreatic beta cells. The Cellular Networking, Integration and Processing (CNIP) approach targets cellular mechanisms involved in pancreatic function in the organ's adult state and utilizes a synergistic mechanism that integrates three important levels of cellular regulation to induce beta cell formation: (i) glucose metabolism, (ii) membrane receptor function, and (iii) gene transcription. The aim of the present study was to induce pancreatic beta cell formation in vivo in adult animals without stem cells and without dedifferentiating cells to recapitulate the embryonic pathway as previously published (1-3). Our results employing CNIP demonstrate that: (i) insulin secreting cells can be generated in adult pancreatic tissue in vivo and circumvent the problem of generating endocrine (glucagon and somatostatin) cells that exert deleterious effects on glucose homeostasis, and (ii) longterm normalization of glucose tolerance and insulin secretion can be achieved in a wild type diabetic mouse model. The CNIP cocktail has the potential to be used as a preventative or therapeutic treatment or cure for both type 1 and type 2 diabetes. PMID:26696016

  10. A cardiac electrical activity model based on a cellular automata system in comparison with neural network model.

    PubMed

    Khan, Muhammad Sadiq Ali; Yousuf, Sidrah

    2016-03-01

    Cardiac Electrical Activity is commonly distributed into three dimensions of Cardiac Tissue (Myocardium) and evolves with duration of time. The indicator of heart diseases can occur randomly at any time of a day. Heart rate, conduction and each electrical activity during cardiac cycle should be monitor non-invasively for the assessment of "Action Potential" (regular) and "Arrhythmia" (irregular) rhythms. Many heart diseases can easily be examined through Automata model like Cellular Automata concepts. This paper deals with the different states of cardiac rhythms using cellular automata with the comparison of neural network also provides fast and highly effective stimulation for the contraction of cardiac muscles on the Atria in the result of genesis of electrical spark or wave. The specific formulated model named as "States of automaton Proposed Model for CEA (Cardiac Electrical Activity)" by using Cellular Automata Methodology is commonly shows the three states of cardiac tissues conduction phenomena (i) Resting (Relax and Excitable state), (ii) ARP (Excited but Absolutely refractory Phase i.e. Excited but not able to excite neighboring cells) (iii) RRP (Excited but Relatively Refractory Phase i.e. Excited and able to excite neighboring cells). The result indicates most efficient modeling with few burden of computation and it is Action Potential during the pumping of blood in cardiac cycle. PMID:27087101

  11. The dynamic and geometric phase transition in the cellular network of pancreatic islet

    NASA Astrophysics Data System (ADS)

    Wang, Xujing

    2013-03-01

    The pancreatic islet is a micro-organ that contains several thousands of endocrine cells, majority of which being the insulin releasing β - cells . - cellsareexcitablecells , andarecoupledtoeachother through gap junctional channels. Here, using percolation theory, we investigate the role of network structure in determining the dynamics of the β-cell network. We show that the β-cell synchronization depends on network connectivity. More specifically, as the site occupancy is reducing, initially the β-cell synchronization is barely affected, until it reaches around a critical value, where the synchronization exhibit a sudden rapid decline, followed by an slow exponential tail. This critical value coincides with the critical site open probability for percolation transition. The dependence over bond strength is similar, exhibiting critical-behavior like dependence around a certain value of bond strength. These results suggest that the β-cell network undergoes a dynamic phase transition when the network is percolated. We further apply the findings to study diabetes. During the development of diabetes, the β - cellnetworkconnectivitydecreases . Siteoccupancyreducesfromthe reducing β-cell mass, and the bond strength is increasingly impaired from β-cell stress and chronic hyperglycemia. We demonstrate that the network dynamics around the percolation transition explain the disease dynamics around onset, including a long time mystery in diabetes, the honeymoon phenomenon.

  12. Mobile Virtual Private Networking

    NASA Astrophysics Data System (ADS)

    Pulkkis, Göran; Grahn, Kaj; Mårtens, Mathias; Mattsson, Jonny

    Mobile Virtual Private Networking (VPN) solutions based on the Internet Security Protocol (IPSec), Transport Layer Security/Secure Socket Layer (SSL/TLS), Secure Shell (SSH), 3G/GPRS cellular networks, Mobile IP, and the presently experimental Host Identity Protocol (HIP) are described, compared and evaluated. Mobile VPN solutions based on HIP are recommended for future networking because of superior processing efficiency and network capacity demand features. Mobile VPN implementation issues associated with the IP protocol versions IPv4 and IPv6 are also evaluated. Mobile VPN implementation experiences are presented and discussed.

  13. A modified size-dependent core-shell model and its application in the wave propagation of square cellular networks

    NASA Astrophysics Data System (ADS)

    Xu, Xiao-Jian; Wang, Ya-Chuan; Wang, Bo; Zhang, Kai

    2016-06-01

    We propose a modified core-shell model to depict the size-dependent elastic properties of materials with several different cross-sections. By using the Young-Laplace equation, a modified Euler-Bernoulli equation, which has taken a power-law relation between the bulk and surface moduli into account, is derived. A finite element method of the modified Euler-Bernoulli equation is formulated, and assembled to investigate the dispersion relations of the infinite two-dimensional periodic square cellular networks. The effectiveness of the proposed core-shell model is verified by comparing with results of the experiments and the molecular dynamics simulations available in the literature. Numerical results show that surface effects play an important role on the cellular networks with small diameters, large aspect ratios and high wave frequencies. Meanwhile, the analytical expressions for the size-dependent elastic modulus may be useful for the study of the size-dependent elasticity of materials and structures at small length scales.

  14. Robust synchronization analysis in nonlinear stochastic cellular networks with time-varying delays, intracellular perturbations and intercellular noise.

    PubMed

    Chen, Po-Wei; Chen, Bor-Sen

    2011-08-01

    Naturally, a cellular network consisted of a large amount of interacting cells is complex. These cells have to be synchronized in order to emerge their phenomena for some biological purposes. However, the inherently stochastic intra and intercellular interactions are noisy and delayed from biochemical processes. In this study, a robust synchronization scheme is proposed for a nonlinear stochastic time-delay coupled cellular network (TdCCN) in spite of the time-varying process delay and intracellular parameter perturbations. Furthermore, a nonlinear stochastic noise filtering ability is also investigated for this synchronized TdCCN against stochastic intercellular and environmental disturbances. Since it is very difficult to solve a robust synchronization problem with the Hamilton-Jacobi inequality (HJI) matrix, a linear matrix inequality (LMI) is employed to solve this problem via the help of a global linearization method. Through this robust synchronization analysis, we can gain a more systemic insight into not only the robust synchronizability but also the noise filtering ability of TdCCN under time-varying process delays, intracellular perturbations and intercellular disturbances. The measures of robustness and noise filtering ability of a synchronized TdCCN have potential application to the designs of neuron transmitters, on-time mass production of biochemical molecules, and synthetic biology. Finally, a benchmark of robust synchronization design in Escherichia coli repressilators is given to confirm the effectiveness of the proposed methods. PMID:21624379

  15. Coverage Extension and Balancing the Transmitted Power of the Moving Relay Node at LTE-A Cellular Network

    PubMed Central

    Aldhaibani, Jaafar A.; Yahya, Abid; Ahmad, R. Badlishah

    2014-01-01

    The poor capacity at cell boundaries is not enough to meet the growing demand and stringent design which required high capacity and throughput irrespective of user's location in the cellular network. In this paper, we propose new schemes for an optimum fixed relay node (RN) placement in LTE-A cellular network to enhance throughput and coverage extension at cell edge region. The proposed approach mitigates interferences between all nodes and ensures optimum utilization with the optimization of transmitted power. Moreover, we proposed a new algorithm to balance the transmitted power of moving relay node (MR) over cell size and providing required SNR and throughput at the users inside vehicle along with reducing the transmitted power consumption by MR. The numerical analysis along with the simulation results indicates that an improvement in capacity for users is 40% increment at downlink transmission from cell capacity. Furthermore, the results revealed that there is saving nearly 75% from transmitted power in MR after using proposed balancing algorithm. ATDI simulator was used to verify the numerical results, which deals with real digital cartographic and standard formats for terrain. PMID:24672378

  16. The role of glutathione reductase and related enzymes on cellular redox homoeostasis network.

    PubMed

    Couto, Narciso; Wood, Jennifer; Barber, Jill

    2016-06-01

    In this review article we examine the role of glutathione reductase in the regulation, modulation and maintenance of cellular redox homoeostasis. Glutathione reductase is responsible for maintaining the supply of reduced glutathione; one of the most abundant reducing thiols in the majority of cells. In its reduced form, glutathione plays key roles in the cellular control of reactive oxygen species. Reactive oxygen species act as intracellular and extracellular signalling molecules and complex cross talk between levels of reactive oxygen species, levels of oxidised and reduced glutathione and other thiols, and antioxidant enzymes such as glutathione reductase determine the most suitable conditions for redox control within a cell or for activation of programmed cell death. Additionally, we discuss the translation and expression of glutathione reductase in a number of organisms including yeast and humans. In yeast and human cells, a single gene expresses more than one form of glutathione reductase, destined for residence in the cytoplasm or for translocation to different organelles; in plants, however, two genes encoding this protein have been described. In general, insects and kinetoplastids (a group of protozoa, including Plasmodia and Trypanosoma) do not express glutathione reductase or glutathione biosynthetic enzymes. Instead, they express either the thioredoxin system or the trypanothione system. The thioredoxin system is also present in organisms that have the glutathione system and there may be overlapping functions with cross-talk between the two systems. Finally we evaluate therapeutic targets to overcome oxidative stress associated cellular disorders. PMID:26923386

  17. Analysis of the local organization and dynamics of cellular actin networks

    PubMed Central

    Luo, Weiwei; Yu, Cheng-han; Lieu, Zi Zhao; Allard, Jun; Mogilner, Alex; Sheetz, Michael P.

    2013-01-01

    A ctin filaments, with the aid of multiple accessory proteins, self-assemble into a variety of network patterns. We studied the organization and dynamics of the actin network in nonadhesive regions of cells bridging fibronectin-coated adhesive strips. The network was formed by actin nodes associated with and linked by myosin II and containing the formin disheveled-associated activator of morphogenesis 1 (DAAM1) and the cross-linker filamin A (FlnA). After Latrunculin A (LatA) addition, actin nodes appeared to be more prominent and demonstrated drift-diffusion motion. Superresolution microscopy revealed that, in untreated cells, DAAM1 formed patches with a similar spatial arrangement to the actin nodes. Node movement (diffusion coefficient and velocity) in LatA-treated cells was dependent on the level and activity of myosin IIA, DAAM1, and FlnA. Based on our results, we developed a computational model of the dynamic formin-filamin-actin asters that can self-organize into a contractile actomyosin network. We suggest that such networks are critical for connecting distant parts of the cell to maintain the mechanical coherence of the cytoplasm. PMID:24081490

  18. Analysis of the local organization and dynamics of cellular actin networks.

    PubMed

    Luo, Weiwei; Yu, Cheng-han; Lieu, Zi Zhao; Allard, Jun; Mogilner, Alex; Sheetz, Michael P; Bershadsky, Alexander D

    2013-09-30

    Actin filaments, with the aid of multiple accessory proteins, self-assemble into a variety of network patterns. We studied the organization and dynamics of the actin network in nonadhesive regions of cells bridging fibronectin-coated adhesive strips. The network was formed by actin nodes associated with and linked by myosin II and containing the formin disheveled-associated activator of morphogenesis 1 (DAAM1) and the cross-linker filamin A (FlnA). After Latrunculin A (LatA) addition, actin nodes appeared to be more prominent and demonstrated drift-diffusion motion. Superresolution microscopy revealed that, in untreated cells, DAAM1 formed patches with a similar spatial arrangement to the actin nodes. Node movement (diffusion coefficient and velocity) in LatA-treated cells was dependent on the level and activity of myosin IIA, DAAM1, and FlnA. Based on our results, we developed a computational model of the dynamic formin-filamin-actin asters that can self-organize into a contractile actomyosin network. We suggest that such networks are critical for connecting distant parts of the cell to maintain the mechanical coherence of the cytoplasm. PMID:24081490

  19. EIF3G is associated with narcolepsy across ethnicities.

    PubMed

    Holm, Anja; Lin, Ling; Faraco, Juliette; Mostafavi, Sara; Battle, Alexis; Zhu, Xiaowei; Levinson, Douglas F; Han, Fang; Gammeltoft, Steen; Jennum, Poul; Mignot, Emmanuel; Kornum, Birgitte R

    2015-11-01

    Type 1 narcolepsy, an autoimmune disease affecting hypocretin (orexin) neurons, is strongly associated with HLA-DQB1*06:02. Among polymorphisms associated with the disease is single-nucleotide polymorphism rs2305795 (c.*638G>A) located within the P2RY11 gene. P2RY11 is in a region of synteny conserved in mammals and zebrafish containing PPAN, EIF3G and DNMT1 (DNA methyltransferase 1). As mutations in DNMT1 cause a rare dominant form of narcolepsy in association with deafness, cerebellar ataxia and dementia, we questioned whether the association with P2RY11 in sporadic narcolepsy could be secondary to linkage disequilibrium with DNMT1. Based on genome-wide association data from two cohorts of European and Chinese ancestry, we found that the narcolepsy association signal drops sharply between P2RY11/EIF3G and DNMT1, suggesting that the association with narcolepsy does not extend into the DNMT1 gene region. Interestingly, using transethnic mapping, we identified a novel single-nucleotide polymorphism rs3826784 (c.596-260A>G) in the EIF3G gene also associated with narcolepsy. The disease-associated allele increases EIF3G mRNA expression. EIF3G is located in the narcolepsy risk locus and EIF3G expression correlates with PPAN and P2RY11 expression. This suggests shared regulatory mechanisms that might be affected by the polymorphism and are of relevance to narcolepsy. PMID:25669430

  20. Rainfall measurements from cellular networks microwave links : an alternative ground reference for satellite validation and hydrology in Africa .

    NASA Astrophysics Data System (ADS)

    Gosset, Marielle; cazenave, frederic; Zougmore, françois; Doumounia, Ali; kacou, Modeste

    2015-04-01

    In many part of the Tropics the ground based gauge networks are sparse, often degrading and accessing this data for monitoring rainfall or for validating satellite products is sometime difficult. Here, an alternative rainfall measuring technique is proposed and tested in West Africa. It is based on using commercial microwave links from cellular telephone networks to detect and quantify rainfall. Rainfall monitoring based on commercial terrestrial microwave links has been tested for the first time in Burkina Faso, in Sahel. The rainfall regime is characterized by intense rainfall intensities brought by mesoscale Convective systems (MCS), generated by deep organized convection. The region is subjected to drought as well as dramatic floods associated with the intense rainfall provided by a few MCSs. The hydrometeorological risk is increasing and need to be monitored. In collaboration with the national cellular phone operator, Telecel Faso, the attenuation on 29 km long microwave links operating at 7 GHz was monitored at 1s time rate for the monsoon season 2012. The time series of attenuation is transformed into rain rates and compared with rain gauge data. The method is successful in quantifying rainfall: 95% of the rainy days are detected. The correlation with the daily raingauge series is 0.8 and the season bias is 5%. The correlation at the 5 min time step within each event is also high. We will present the quantitative results, discuss the uncertainties and compare the time series and the 2D maps with those derived from a polarimetric radar. The results demonstrate the potential interest of exploiting national and regional wireless telecommunication networks to provide rainfall maps for various applications : urban hydrology, agro-hydrological risk monitoring, satellite validation and development of combined rainfall products. We will also present the outcome of the first international Rain Cell Africa workshop held in Ouagadougou early 2015.

  1. R&D on wireless broadband communication systems: new generation ubiquitous mobile network

    NASA Astrophysics Data System (ADS)

    Ogawa, Hiroyo

    2007-09-01

    R&D on new generation mobile network has attracted a growing interest over the world on the background of rapid market growth for 2nd and 3rd - generation cellular networks and wireless LANs/MANs. The National Institute of Information and Communications Technology (NICT) has been carried out the New Generation Mobile Network Project from April 2002 to March 2006, and has developed fundamental technologies to enable seamless and secure integration of various wireless access networks such as existing cellular networks, wireless LANs, home networks, intelligent transport systems (ITS), the Beyond-3G (B3G) cellular and other wireless access systems. From April 2006, Ubiquitous Mobile Network project focused on cognitive radio technology and integrated seamless networking technology was started. This paper overviews the achievement and the future plan of these projects.

  2. An Experimental Performance Comparison of 3G and Wi-Fi

    NASA Astrophysics Data System (ADS)

    Gass, Richard; Diot, Christophe

    Mobile Internet users have two options for connectivity: pay premium fees to utilize 3G or wander around looking for open Wi-Fi access points. We perform an experimental evaluation of the amount of data that can be pushed to and pulled from the Internet on 3G and open Wi-Fi access points while on the move. This side-by-side comparison is carried out at both driving and walking speeds in an urban area using standard devices. We show that significant amounts of data can be transferred opportunistically without the need of always being connected to the network. We also show that Wi-Fi mostly suffers from not being able to exploit short contacts with access points but performs comparably well against 3G when downloading and even significantly better while uploading data.

  3. From Cellular Attractor Selection to Adaptive Signal Control for Traffic Networks.

    PubMed

    Tian, Daxin; Zhou, Jianshan; Sheng, Zhengguo; Wang, Yunpeng; Ma, Jianming

    2016-01-01

    The management of varying traffic flows essentially depends on signal controls at intersections. However, design an optimal control that considers the dynamic nature of a traffic network and coordinates all intersections simultaneously in a centralized manner is computationally challenging. Inspired by the stable gene expressions of Escherichia coli in response to environmental changes, we explore the robustness and adaptability performance of signalized intersections by incorporating a biological mechanism in their control policies, specifically, the evolution of each intersection is induced by the dynamics governing an adaptive attractor selection in cells. We employ a mathematical model to capture such biological attractor selection and derive a generic, adaptive and distributed control algorithm which is capable of dynamically adapting signal operations for the entire dynamical traffic network. We show that the proposed scheme based on attractor selection can not only promote the balance of traffic loads on each link of the network but also allows the global network to accommodate dynamical traffic demands. Our work demonstrates the potential of bio-inspired intelligence emerging from cells and provides a deep understanding of adaptive attractor selection-based control formation that is useful to support the designs of adaptive optimization and control in other domains. PMID:26972968

  4. From Cellular Attractor Selection to Adaptive Signal Control for Traffic Networks

    PubMed Central

    Tian, Daxin; Zhou, Jianshan; Sheng, Zhengguo; Wang, Yunpeng; Ma, Jianming

    2016-01-01

    The management of varying traffic flows essentially depends on signal controls at intersections. However, design an optimal control that considers the dynamic nature of a traffic network and coordinates all intersections simultaneously in a centralized manner is computationally challenging. Inspired by the stable gene expressions of Escherichia coli in response to environmental changes, we explore the robustness and adaptability performance of signalized intersections by incorporating a biological mechanism in their control policies, specifically, the evolution of each intersection is induced by the dynamics governing an adaptive attractor selection in cells. We employ a mathematical model to capture such biological attractor selection and derive a generic, adaptive and distributed control algorithm which is capable of dynamically adapting signal operations for the entire dynamical traffic network. We show that the proposed scheme based on attractor selection can not only promote the balance of traffic loads on each link of the network but also allows the global network to accommodate dynamical traffic demands. Our work demonstrates the potential of bio-inspired intelligence emerging from cells and provides a deep understanding of adaptive attractor selection-based control formation that is useful to support the designs of adaptive optimization and control in other domains. PMID:26972968

  5. From Cellular Attractor Selection to Adaptive Signal Control for Traffic Networks

    NASA Astrophysics Data System (ADS)

    Tian, Daxin; Zhou, Jianshan; Sheng, Zhengguo; Wang, Yunpeng; Ma, Jianming

    2016-03-01

    The management of varying traffic flows essentially depends on signal controls at intersections. However, design an optimal control that considers the dynamic nature of a traffic network and coordinates all intersections simultaneously in a centralized manner is computationally challenging. Inspired by the stable gene expressions of Escherichia coli in response to environmental changes, we explore the robustness and adaptability performance of signalized intersections by incorporating a biological mechanism in their control policies, specifically, the evolution of each intersection is induced by the dynamics governing an adaptive attractor selection in cells. We employ a mathematical model to capture such biological attractor selection and derive a generic, adaptive and distributed control algorithm which is capable of dynamically adapting signal operations for the entire dynamical traffic network. We show that the proposed scheme based on attractor selection can not only promote the balance of traffic loads on each link of the network but also allows the global network to accommodate dynamical traffic demands. Our work demonstrates the potential of bio-inspired intelligence emerging from cells and provides a deep understanding of adaptive attractor selection-based control formation that is useful to support the designs of adaptive optimization and control in other domains.

  6. Actin-binding proteins: the long road to understanding the dynamic landscape of cellular actin networks.

    PubMed

    Lappalainen, Pekka

    2016-08-15

    The actin cytoskeleton supports a vast number of cellular processes in nonmuscle cells. It is well established that the organization and dynamics of the actin cytoskeleton are controlled by a large array of actin-binding proteins. However, it was only 40 years ago that the first nonmuscle actin-binding protein, filamin, was identified and characterized. Filamin was shown to bind and cross-link actin filaments into higher-order structures and contribute to phagocytosis in macrophages. Subsequently many other nonmuscle actin-binding proteins were identified and characterized. These proteins regulate almost all steps of the actin filament assembly and disassembly cycles, as well as the arrangement of actin filaments into diverse three-dimensional structures. Although the individual biochemical activities of most actin-regulatory proteins are relatively well understood, knowledge of how these proteins function together in a common cytoplasm to control actin dynamics and architecture is only beginning to emerge. Furthermore, understanding how signaling pathways and mechanical cues control the activities of various actin-binding proteins in different cellular, developmental, and pathological processes will keep researchers busy for decades. PMID:27528696

  7. A Single-Chip 8-Band CMOS Transceiver for 3G Cellular Systems with Digital Interface

    NASA Astrophysics Data System (ADS)

    Yoshida, Hiroshi; Toyoda, Takehiko; Tsurumi, Hiroshi; Itoh, Nobuyuki

    In this paper, a single-chip dual-mode 8-band 130nm CMOS transceiver including A/D/A converters and digital filters with 312MHz LVDS interface is presented. For a transmitter chain, linear direct quadrature modulation architecture is introduced for both W-CDMA/HSDPA (High Speed Uplink Packet Access) and for GSM/EDGE. Analog baseband LPFs and quadrature modulators are commonly used both for GSM and for EDGE. For a direct conversion receiver chain, ABB (Analog Base-Band) blocks, i.e., LPFs and VGAs, delta-sigma A/D converters, and FIR filters are commonly used for W-CDMA/HSDPA (High Speed Downlink Packet Access) and GSM/EDGE to reduce chip area. Their characteristics can be reconfigured by register-based control sequence. The receiver chain also includes high-speed DC offset cancellers both in analog and in digital stage, and the self-contained AGC controller, whose parameters such as time constant are programmable to be free from DBB (Digital Base-Band) control. The transceiver also includes wide-range VCOs and fractional PLLs, an LVDS driver and receiver for high-speed digital interface of 312MHz. Measured results reveal that the transceiver satisfies 3GPP specifications for W-CDMA/HSPA (High Speed Packet Access) and GSM/EDGE.

  8. Inhibition of a NEDD8 Cascade Restores Restriction of HIV by APOBEC3G

    PubMed Central

    Crosby, David C.; Kim, Dong Young; Kwon, Eunju; Yen, Linda; Cartozo, Nathalie Caretta; Li, Ming; Jäger, Stefanie; Mason-Herr, Jeremy; Hayashi, Fumiaki; Yokoyama, Shigeyuki; Krogan, Nevan J.; Harris, Reuben S.; Peterlin, Boris Matija; Gross, John D.

    2012-01-01

    Cellular restriction factors help to defend humans against human immunodeficiency virus (HIV). HIV accessory proteins hijack at least three different Cullin-RING ubiquitin ligases, which must be activated by the small ubiquitin-like protein NEDD8, in order to counteract host cellular restriction factors. We found that conjugation of NEDD8 to Cullin-5 by the NEDD8-conjugating enzyme UBE2F is required for HIV Vif-mediated degradation of the host restriction factor APOBEC3G (A3G). Pharmacological inhibition of the NEDD8 E1 by MLN4924 or knockdown of either UBE2F or its RING-protein binding partner RBX2 bypasses the effect of Vif, restoring the restriction of HIV by A3G. NMR mapping and mutational analyses define specificity determinants of the UBE2F NEDD8 cascade. These studies demonstrate that disrupting host NEDD8 cascades presents a novel antiretroviral therapeutic approach enhancing the ability of the immune system to combat HIV. PMID:23300442

  9. Biological pattern generation: the cellular and computational logic of networks in motion.

    PubMed

    Grillner, Sten

    2006-12-01

    In 1900, Ramón y Cajal advanced the neuron doctrine, defining the neuron as the fundamental signaling unit of the nervous system. Over a century later, neurobiologists address the circuit doctrine: the logic of the core units of neuronal circuitry that control animal behavior. These are circuits that can be called into action for perceptual, conceptual, and motor tasks, and we now need to understand whether there are coherent and overriding principles that govern the design and function of these modules. The discovery of central motor programs has provided crucial insight into the logic of one prototypic set of neural circuits: those that generate motor patterns. In this review, I discuss the mode of operation of these pattern generator networks and consider the neural mechanisms through which they are selected and activated. In addition, I will outline the utility of computational models in analysis of the dynamic actions of these motor networks. PMID:17145498

  10. Mobility-Aware Caching and Computation Offloading in 5G Ultra-Dense Cellular Networks.

    PubMed

    Chen, Min; Hao, Yixue; Qiu, Meikang; Song, Jeungeun; Wu, Di; Humar, Iztok

    2016-01-01

    Recent trends show that Internet traffic is increasingly dominated by content, which is accompanied by the exponential growth of traffic. To cope with this phenomena, network caching is introduced to utilize the storage capacity of diverse network devices. In this paper, we first summarize four basic caching placement strategies, i.e., local caching, Device-to-Device (D2D) caching, Small cell Base Station (SBS) caching and Macrocell Base Station (MBS) caching. However, studies show that so far, much of the research has ignored the impact of user mobility. Therefore, taking the effect of the user mobility into consideration, we proposes a joint mobility-aware caching and SBS density placement scheme (MS caching). In addition, differences and relationships between caching and computation offloading are discussed. We present a design of a hybrid computation offloading and support it with experimental results, which demonstrate improved performance in terms of energy cost. Finally, we discuss the design of an incentive mechanism by considering network dynamics, differentiated user's quality of experience (QoE) and the heterogeneity of mobile terminals in terms of caching and computing capabilities. PMID:27347975

  11. Mobility-Aware Caching and Computation Offloading in 5G Ultra-Dense Cellular Networks

    PubMed Central

    Chen, Min; Hao, Yixue; Qiu, Meikang; Song, Jeungeun; Wu, Di; Humar, Iztok

    2016-01-01

    Recent trends show that Internet traffic is increasingly dominated by content, which is accompanied by the exponential growth of traffic. To cope with this phenomena, network caching is introduced to utilize the storage capacity of diverse network devices. In this paper, we first summarize four basic caching placement strategies, i.e., local caching, Device-to-Device (D2D) caching, Small cell Base Station (SBS) caching and Macrocell Base Station (MBS) caching. However, studies show that so far, much of the research has ignored the impact of user mobility. Therefore, taking the effect of the user mobility into consideration, we proposes a joint mobility-aware caching and SBS density placement scheme (MS caching). In addition, differences and relationships between caching and computation offloading are discussed. We present a design of a hybrid computation offloading and support it with experimental results, which demonstrate improved performance in terms of energy cost. Finally, we discuss the design of an incentive mechanism by considering network dynamics, differentiated user’s quality of experience (QoE) and the heterogeneity of mobile terminals in terms of caching and computing capabilities. PMID:27347975

  12. Cellular location and major terminal networks of the orexinergic system in the brain of two megachiropterans.

    PubMed

    Dell, Leigh-Anne; Kruger, Jean-Leigh; Pettigrew, John D; Manger, Paul R

    2013-11-01

    The present study describes the distribution of orexin-A immunoreactive neurons and their terminal networks in the brains of two species of megachiropterans. In general the organization of the orexinergic system in the mammalian brain is conserved across species, but as one of two groups of mammals that fly and have a high metabolic rate, it was of interest to determine whether there were any specific differences in the organization of this system in the megachiropterans. Orexinergic neurons were limited in distribution to the hypothalamus, and formed three distinct clusters, or nuclei, a main cluster with a perifornical location, a zona incerta cluster in the dorsolateral hypothalamus and an optic tract cluster in the ventrolateral hypothalamus. The nuclear parcellation of the orexinergic system in the megachiropterans is similar to that seen in many mammals, but differs from the microchiropterans where the optic tract cluster is absent. The terminal networks of the orexinergic neurons in the megachiropterans was similar to that seen in a range of mammalian species, with significant terminal networks being found in the hypothalamus, cholinergic pedunculopontine and laterodorsal tegemental nuclei, the noradrenergic locus coeruleus complex, all serotonergic nuclei, the paraventricular nuclei of the epithalamus and adjacent to the habenular nuclei. While the megachiropteran orexinergic system is typically mammalian in form, it does differ from that reported for microchiropterans, and thus provides an additional neural character arguing for independent evolution of these two chiropteran suborders. PMID:24041616

  13. Cellular and circuit models of increased resting-state network gamma activity in schizophrenia.

    PubMed

    White, R S; Siegel, S J

    2016-05-01

    Schizophrenia (SCZ) is a disorder characterized by positive symptoms (hallucinations, delusions), negative symptoms (blunted affect, alogia, reduced sociability, and anhedonia), as well as persistent cognitive deficits (memory, concentration, and learning). While the biology underlying subjective experiences is difficult to study, abnormalities in electroencephalographic (EEG) measures offer a means to dissect potential circuit and cellular changes in brain function. EEG is indispensable for studying cerebral information processing due to the introduction of techniques for the decomposition of event-related activity into its frequency components. Specifically, brain activity in the gamma frequency range (30-80Hz) is thought to underlie cognitive function and may be used as an endophenotype to aid in diagnosis and treatment of SCZ. In this review we address evidence indicating that there is increased resting-state gamma power in SCZ. We address how modeling this aspect of the illness in animals may help treatment development as well as providing insights into the etiology of SCZ. PMID:26577758

  14. From molecular interaction to acute promyelocytic leukemia: Calculating leukemogenesis and remission from endogenous molecular-cellular network.

    PubMed

    Yuan, Ruoshi; Zhu, Xiaomei; Radich, Jerald P; Ao, Ping

    2016-01-01

    Acute promyelocytic leukemia (APL) remains the best example of a malignancy that can be cured clinically by differentiation therapy. We demonstrate that APL may emerge from a dynamical endogenous molecular-cellular network obtained from normal, non-cancerous molecular interactions such as signal transduction and translational regulation under physiological conditions. This unifying framework, which reproduces APL, normal progenitor, and differentiated granulocytic phenotypes as different robust states from the network dynamics, has the advantage to study transition between these states, i.e. critical drivers for leukemogenesis and targets for differentiation. The simulation results quantitatively reproduce microarray profiles of NB4 and HL60 cell lines in response to treatment and normal neutrophil differentiation, and lead to new findings such as biomarkers for APL and additional molecular targets for arsenic trioxide therapy. The modeling shows APL and normal states mutually suppress each other, both in "wiring" and in dynamical cooperation. Leukemogenesis and recovery under treatment may be a consequence of spontaneous or induced transitions between robust states, through "passes" or "dragging" by drug effects. Our approach rationalizes leukemic complexity and constructs a platform towards extending differentiation therapy by performing "dry" molecular biology experiments. PMID:27098097

  15. From molecular interaction to acute promyelocytic leukemia: Calculating leukemogenesis and remission from endogenous molecular-cellular network

    PubMed Central

    Yuan, Ruoshi; Zhu, Xiaomei; Radich, Jerald P.; Ao, Ping

    2016-01-01

    Acute promyelocytic leukemia (APL) remains the best example of a malignancy that can be cured clinically by differentiation therapy. We demonstrate that APL may emerge from a dynamical endogenous molecular-cellular network obtained from normal, non-cancerous molecular interactions such as signal transduction and translational regulation under physiological conditions. This unifying framework, which reproduces APL, normal progenitor, and differentiated granulocytic phenotypes as different robust states from the network dynamics, has the advantage to study transition between these states, i.e. critical drivers for leukemogenesis and targets for differentiation. The simulation results quantitatively reproduce microarray profiles of NB4 and HL60 cell lines in response to treatment and normal neutrophil differentiation, and lead to new findings such as biomarkers for APL and additional molecular targets for arsenic trioxide therapy. The modeling shows APL and normal states mutually suppress each other, both in “wiring” and in dynamical cooperation. Leukemogenesis and recovery under treatment may be a consequence of spontaneous or induced transitions between robust states, through “passes” or “dragging” by drug effects. Our approach rationalizes leukemic complexity and constructs a platform towards extending differentiation therapy by performing “dry” molecular biology experiments. PMID:27098097

  16. TRPV1 mediates cellular uptake of anandamide and thus promotes endothelial cell proliferation and network-formation

    PubMed Central

    Hofmann, Nicole A.; Barth, Sonja; Waldeck-Weiermair, Markus; Klec, Christiane; Strunk, Dirk; Malli, Roland; Graier, Wolfgang F.

    2014-01-01

    ABSTRACT Anandamide (N-arachidonyl ethanolamide, AEA) is an endogenous cannabinoid that is involved in various pathological conditions, including cardiovascular diseases and tumor-angiogenesis. Herein, we tested the involvement of classical cannabinoid receptors (CBRs) and the Ca2+-channel transient receptor potential vanilloid 1 (TRPV1) on cellular AEA uptake and its effect on endothelial cell proliferation and network-formation. Uptake of the fluorescence-labeled anandamide (SKM4-45-1) was monitored in human endothelial colony-forming cells (ECFCs) and a human endothelial-vein cell line (EA.hy926). Involvement of the receptors during AEA translocation was determined by selective pharmacological inhibition (AM251, SR144528, CID16020046, SB366791) and molecular interference by TRPV1-selective siRNA-mediated knock-down and TRPV1 overexpression. We show that exclusively TRPV1 contributes essentially to AEA transport into endothelial cells in a Ca2+-independent manner. This TRPV1 function is a prerequisite for AEA-induced endothelial cell proliferation and network-formation. Our findings point to a so far unknown moonlighting function of TRPV1 as Ca2+-independent contributor/regulator of AEA uptake. We propose TRPV1 as representing a promising target for development of pharmacological therapies against AEA-triggered endothelial cell functions, including their stimulatory effect on tumor-angiogenesis. PMID:25395667

  17. The p53 network: Cellular and systemic DNA damage responses in aging and cancer

    PubMed Central

    Reinhardt, H. Christian; Schumacher, Björn

    2014-01-01

    Genome instability contributes to cancer development and accelerates age-related pathologies as evidenced by a variety of congenital cancer susceptibility and progeroid syndromes that are caused by defects in genome maintenance mechanisms. DNA damage response pathways that are mediated through the tumor suppressor p53 play an important role in the cell intrinsic responses to genome instability, including a transient cell cycle arrest, senescence and apoptosis. Both senescence and apoptosis are powerful tumor suppressive pathways preventing the uncontrolled proliferation of transformed cells. However, both pathways can potentially deplete stem and progenitor cell pools, thus promoting tissue degeneration and organ failure, which are both hallmarks of aging. p53 signaling is also involved in mediating non-cell autonomous interactions with the innate immune system and in the systemic adjustments during the aging process. The network of p53 target genes thus functions as an important regulator of cancer prevention and the physiology of aging. PMID:22265392

  18. Evolving gene regulation networks into cellular networks guiding adaptive behavior: an outline how single cells could have evolved into a centralized neurosensory system

    PubMed Central

    Fritzsch, Bernd; Jahan, Israt; Pan, Ning; Elliott, Karen L.

    2014-01-01

    Understanding the evolution of the neurosensory system of man, able to reflect on its own origin, is one of the major goals of comparative neurobiology. Details of the origin of neurosensory cells, their aggregation into central nervous systems and associated sensory organs, their localized patterning into remarkably different cell types aggregated into variably sized parts of the central nervous system begin to emerge. Insights at the cellular and molecular level begin to shed some light on the evolution of neurosensory cells, partially covered in this review. Molecular evidence suggests that high mobility group (HMG) proteins of pre-metazoans evolved into the definitive Sox [SRY (sex determining region Y)-box] genes used for neurosensory precursor specification in metazoans. Likewise, pre-metazoan basic helix-loop-helix (bHLH) genes evolved in metazoans into the group A bHLH genes dedicated to neurosensory differentiation in bilaterians. Available evidence suggests that the Sox and bHLH genes evolved a cross-regulatory network able to synchronize expansion of precursor populations and their subsequent differentiation into novel parts of the brain or sensory organs. Molecular evidence suggests metazoans evolved patterning gene networks early and not dedicated to neuronal development. Only later in evolution were these patterning gene networks tied into the increasing complexity of diffusible factors, many of which were already present in pre-metazoans, to drive local patterning events. It appears that the evolving molecular basis of neurosensory cell development may have led, in interaction with differentially expressed patterning genes, to local network modifications guiding unique specializations of neurosensory cells into sensory organs and various areas of the central nervous system. PMID:25416504

  19. Structurally Dynamic Cellular Networks as Models for Planck Scale Physics and the Quantum Vacuum

    NASA Astrophysics Data System (ADS)

    Requardt, Manfred

    Starting from the working hypothesis that both physics and the corresponding mathematics have to be described by means of discrete concepts on the Planck scale, one of the many problems one has to face in this enterprise is to find the discrete protoforms of the building blocks of our ordinary continuum physics and mathematics. We regard these continuum concepts and continuum space-time (S-T) in particular as being emergent, coarse-grained and derived relative to an underlying erratic and disordered microscopic substratum which is expected to play by quite different rules. A central role in our analysis is played by a geometric renormalization group which creates (among other things) a kind of sparse translocal network of correlations in classical continuous space-time and underlies in our view such mysterious phenomena as holography and the black hole entropy-area law. The same point of view holds for quantum theory which we also regard as a low-energy, coarse-grained continuum theory, being emergent from something more fundamental.

  20. A Dynamic Programming Approach for Base Station Sleeping in Cellular Networks

    NASA Astrophysics Data System (ADS)

    Gong, Jie; Zhou, Sheng; Niu, Zhisheng

    The energy consumption of the information and communication technology (ICT) industry, which has become a serious problem, is mostly due to the network infrastructure rather than the mobile terminals. In this paper, we focus on reducing the energy consumption of base stations (BSs) by adjusting their working modes (active or sleep). Specifically, the objective is to minimize the energy consumption while satisfying quality of service (QoS, e.g., blocking probability) requirement and, at the same time, avoiding frequent mode switching to reduce signaling and delay overhead. The problem is modeled as a dynamic programming (DP) problem, which is NP-hard in general. Based on cooperation among neighboring BSs, a low-complexity algorithm is proposed to reduce the size of state space as well as that of action space. Simulations demonstrate that, with the proposed algorithm, the active BS pattern well meets the time variation and the non-uniform spatial distribution of system traffic. Moreover, the tradeoff between the energy saving from BS sleeping and the cost of switching is well balanced by the proposed scheme.

  1. Ultra-Porous Nanoparticle Networks: A Biomimetic Coating Morphology for Enhanced Cellular Response and Infiltration

    PubMed Central

    Nasiri, Noushin; Ceramidas, Anthony; Mukherjee, Shayanti; Panneerselvan, Anitha; Nisbet, David R.; Tricoli, Antonio

    2016-01-01

    Orthopedic treatments are amongst the most common cause of surgery and are responsible for a large share of global healthcare expenditures. Engineering materials that can hasten bone integration will improve the quality of life of millions of patients per year and reduce associated medical costs. Here, we present a novel hierarchical biomimetic coating that mimics the inorganic constituent of mammalian bones with the aim of improving osseointegration of metallic implants. We exploit the thermally-driven self-organization of metastable core-shell nanoparticles during their aerosol self-assembly to rapidly fabricate robust, ultra-porous nanoparticle networks (UNN) of crystalline hydroxyapatite (HAp). Comparative analysis of the response of osteoblast cells to the ultra-porous nanostructured HAp surfaces and to the spin coated HAp surfaces revealed superior osseointegrative properties of the UNN coatings with significant cell and filopodia infiltration. This flexible synthesis approach for the engineering of UNN HAp coatings on titanium implants provides a platform technology to study the bone-implant interface for improved osseointegration and osteoconduction. PMID:27076035

  2. Incorporation of aggrecan in interpenetrating network hydrogels to improve cellular performance for cartilage tissue engineering.

    PubMed

    Ingavle, Ganesh C; Frei, Anthony W; Gehrke, Stevin H; Detamore, Michael S

    2013-06-01

    Interpenetrating network (IPN) hydrogels were recently introduced to the cartilage tissue engineering literature, with the approach of encapsulating cells in thermally gelling agarose that is then soaked in a poly(ethylene glycol) diacrylate (PEGDA) solution, which is then photopolymerized. These IPNs possess significantly enhanced mechanical performance desirable for cartilage regeneration, potentially allowing patients to return to weight-bearing activities quickly after surgical implantation. In an effort to improve cell viability and performance, inspiration was drawn from previous studies that have elicited positive chondrogenic responses to aggrecan, the proteoglycan largely responsible for the compressive stiffness of cartilage. Aggrecan was incorporated into the IPNs in conservative concentrations (40 μg/mL), and its effect was contrasted with the incorporation of chondroitin sulfate (CS), the primary glycosaminoglycan associated with aggrecan. Aggrecan was incorporated by physical entrapment within agarose and methacrylated CS was incorporated by copolymerization with PEGDA. The IPNs incorporating aggrecan or CS exhibited over 50% viability with encapsulated chondrocytes after 6 weeks. Both aggrecan and CS improved cell viability by 15.6% and 20%, respectively, relative to pure IPNs at 6 weeks culture time. In summary, we have introduced the novel approach of including a raw material from cartilage, namely aggrecan, to serve as a bioactive signal to cells encapsulated in IPN hydrogels for cartilage tissue engineering, which led to improved performance of encapsulated chondrocytes. PMID:23379843

  3. Ultra-Porous Nanoparticle Networks: A Biomimetic Coating Morphology for Enhanced Cellular Response and Infiltration.

    PubMed

    Nasiri, Noushin; Ceramidas, Anthony; Mukherjee, Shayanti; Panneerselvan, Anitha; Nisbet, David R; Tricoli, Antonio

    2016-01-01

    Orthopedic treatments are amongst the most common cause of surgery and are responsible for a large share of global healthcare expenditures. Engineering materials that can hasten bone integration will improve the quality of life of millions of patients per year and reduce associated medical costs. Here, we present a novel hierarchical biomimetic coating that mimics the inorganic constituent of mammalian bones with the aim of improving osseointegration of metallic implants. We exploit the thermally-driven self-organization of metastable core-shell nanoparticles during their aerosol self-assembly to rapidly fabricate robust, ultra-porous nanoparticle networks (UNN) of crystalline hydroxyapatite (HAp). Comparative analysis of the response of osteoblast cells to the ultra-porous nanostructured HAp surfaces and to the spin coated HAp surfaces revealed superior osseointegrative properties of the UNN coatings with significant cell and filopodia infiltration. This flexible synthesis approach for the engineering of UNN HAp coatings on titanium implants provides a platform technology to study the bone-implant interface for improved osseointegration and osteoconduction. PMID:27076035

  4. Evidence for progressive reduction and loss of telocytes in the dermal cellular network of systemic sclerosis.

    PubMed

    Manetti, Mirko; Guiducci, Serena; Ruffo, Martina; Rosa, Irene; Faussone-Pellegrini, Maria Simonetta; Matucci-Cerinic, Marco; Ibba-Manneschi, Lidia

    2013-04-01

    Telocytes, a peculiar type of stromal cells, have been recently identified in a variety of tissues and organs, including human skin. Systemic sclerosis (SSc, scleroderma) is a complex connective tissue disease characterized by fibrosis of the skin and internal organs. We presently investigated telocyte distribution and features in the skin of SSc patients compared with normal skin. By an integrated immunohistochemical and transmission electron microscopy approach, we confirmed that telocytes were present in human dermis, where they were mainly recognizable by their typical ultrastructural features and were immunophenotypically characterized by CD34 expression. Our findings also showed that dermal telocytes were immunophenotypically negative for CD31/PECAM-1 (endothelial cells), α-SMA (myofibroblasts, pericytes, vascular smooth muscle cells), CD11c (dendritic cells, macrophages), CD90/Thy-1 (fibroblasts) and c-kit/CD117 (mast cells). In normal skin, telocytes were organized to form three-dimensional networks distributed among collagen bundles and elastic fibres, and surrounded microvessels, nerves and skin adnexa (hair follicles, sebaceous and sweat glands). Telocytes displayed severe ultrastructural damages (swollen mitochondria, cytoplasmic vacuolization, lipofuscinic bodies) suggestive of ischaemia-induced cell degeneration and were progressively lost from the clinically affected skin of SSc patients. Telocyte damage and loss evolved differently according to SSc subsets and stages, being more rapid and severe in diffuse SSc. Briefly, in human skin telocytes are a distinct stromal cell population. In SSc skin, the progressive loss of telocytes might (i) contribute to the altered three-dimensional organization of the extracellular matrix, (ii) reduce the control of fibroblast, myofibroblast and mast cell activity, and (iii) impair skin regeneration and/or repair. PMID:23444845

  5. Mapping the Hsp90 Genetic Network Reveals Ergosterol Biosynthesis and Phosphatidylinositol-4-Kinase Signaling as Core Circuitry Governing Cellular Stress

    PubMed Central

    O’Meara, Teresa R.; Valaei, Seyedeh Fereshteh; Diezmann, Stephanie; Cowen, Leah E.

    2016-01-01

    Candida albicans is a leading human fungal pathogen that causes life-threatening systemic infections. A key regulator of C. albicans stress response, drug resistance, morphogenesis, and virulence is the molecular chaperone Hsp90. Targeting Hsp90 provides a powerful strategy to treat fungal infections, however, the therapeutic utility of current inhibitors is compromised by toxicity due to inhibition of host Hsp90. To identify components of the Hsp90-dependent circuitry governing virulence and drug resistance that are sufficiently divergent for selective targeting in the pathogen, we pioneered chemical genomic profiling of the Hsp90 genetic network in C. albicans. Here, we screen mutant collections covering ~10% of the genome for hypersensitivity to Hsp90 inhibition in multiple environmental conditions. We identify 158 HSP90 chemical genetic interactors, most of which are important for growth only in specific environments. We discovered that the sterol C-22 desaturase gene ERG5 and the phosphatidylinositol-4-kinase (PI4K) gene STT4 are HSP90 genetic interactors under multiple conditions, suggesting a function upstream of Hsp90. By systematic analysis of the ergosterol biosynthetic cascade, we demonstrate that defects in ergosterol biosynthesis induce cellular stress that overwhelms Hsp90’s functional capacity. By analysis of the phosphatidylinositol pathway, we demonstrate that there is a genetic interaction between the PI4K Stt4 and Hsp90. We also establish that Stt4 is required for normal actin polarization through regulation of Wal1, and suggest a model in which defects in actin remodeling induces stress that creates a cellular demand for Hsp90 that exceeds its functional capacity. Consistent with this model, actin inhibitors are synergistic with Hsp90 inhibitors. We highlight new connections between Hsp90 and virulence traits, demonstrating that Erg5 and Stt4 enable activation of macrophage pyroptosis. This work uncovers novel circuitry regulating Hsp90

  6. Mapping the Hsp90 Genetic Network Reveals Ergosterol Biosynthesis and Phosphatidylinositol-4-Kinase Signaling as Core Circuitry Governing Cellular Stress.

    PubMed

    O'Meara, Teresa R; Veri, Amanda O; Polvi, Elizabeth J; Li, Xinliu; Valaei, Seyedeh Fereshteh; Diezmann, Stephanie; Cowen, Leah E

    2016-06-01

    Candida albicans is a leading human fungal pathogen that causes life-threatening systemic infections. A key regulator of C. albicans stress response, drug resistance, morphogenesis, and virulence is the molecular chaperone Hsp90. Targeting Hsp90 provides a powerful strategy to treat fungal infections, however, the therapeutic utility of current inhibitors is compromised by toxicity due to inhibition of host Hsp90. To identify components of the Hsp90-dependent circuitry governing virulence and drug resistance that are sufficiently divergent for selective targeting in the pathogen, we pioneered chemical genomic profiling of the Hsp90 genetic network in C. albicans. Here, we screen mutant collections covering ~10% of the genome for hypersensitivity to Hsp90 inhibition in multiple environmental conditions. We identify 158 HSP90 chemical genetic interactors, most of which are important for growth only in specific environments. We discovered that the sterol C-22 desaturase gene ERG5 and the phosphatidylinositol-4-kinase (PI4K) gene STT4 are HSP90 genetic interactors under multiple conditions, suggesting a function upstream of Hsp90. By systematic analysis of the ergosterol biosynthetic cascade, we demonstrate that defects in ergosterol biosynthesis induce cellular stress that overwhelms Hsp90's functional capacity. By analysis of the phosphatidylinositol pathway, we demonstrate that there is a genetic interaction between the PI4K Stt4 and Hsp90. We also establish that Stt4 is required for normal actin polarization through regulation of Wal1, and suggest a model in which defects in actin remodeling induces stress that creates a cellular demand for Hsp90 that exceeds its functional capacity. Consistent with this model, actin inhibitors are synergistic with Hsp90 inhibitors. We highlight new connections between Hsp90 and virulence traits, demonstrating that Erg5 and Stt4 enable activation of macrophage pyroptosis. This work uncovers novel circuitry regulating Hsp90

  7. Mathematical model of the SH-3G helicopter

    NASA Technical Reports Server (NTRS)

    Phillips, J. D.

    1982-01-01

    A mathematical model of the Sikorsky SH-3G helicopter based on classical nonlinear, quasi-steady rotor theory was developed. The model was validated statically and dynamically by comparison with Navy flight-test data. The model incorporates ad hoc revisions which address the ideal assumptions of classical rotor theory and improve the static trim characteristics to provide a more realistic simulation, while retaining the simplicity of the classical model.

  8. A cellular nonlinear network: real-time technology for the analysis of microfluidic phenomena in blood vessels

    NASA Astrophysics Data System (ADS)

    Sapuppo, F.; Bucolo, M.; Intaglietta, M.; Fortuna, L.; Arena, P.

    2006-02-01

    A new approach to the observation and analysis of dynamic structural and functional parameters in the microcirculation is described. The new non-invasive optical system is based on cellular nonlinear networks (CNNs), highly integrated analogue processor arrays whose processing elements, the cells, interact directly within a finite local neighbourhood. CNNs, thanks to their parallel processing feature and spatially distributed structure, are widely used to solve high-speed image processing and recognition problems and in the description and modelling of biological dynamics through the solution of time continuous partial differential equations (PDEs). They are therefore considered extremely suitable for spatial-temporal dynamic characterization of fluidic phenomena at micrometric to nanometric scales, such as blood flow in microvessels and its interaction with the cells of the vessel wall. A CNN universal machine (CNN-UM) structure was used to implement, via simulation and hardware (ACE16k), the algorithms to determine the functional capillarity density (FCD) and red blood cell velocity (RBCV) in capillaries obtained by intravital microscopy during in vivo experiments on hamsters. The system exploits the moving particles to distinguish the functional capillaries from the stationary background. This information is used to reconstruct a map and to calculate the velocity of the moving objects.

  9. A 181 GOPS AKAZE Accelerator Employing Discrete-Time Cellular Neural Networks for Real-Time Feature Extraction

    PubMed Central

    Jiang, Guangli; Liu, Leibo; Zhu, Wenping; Yin, Shouyi; Wei, Shaojun

    2015-01-01

    This paper proposes a real-time feature extraction VLSI architecture for high-resolution images based on the accelerated KAZE algorithm. Firstly, a new system architecture is proposed. It increases the system throughput, provides flexibility in image resolution, and offers trade-offs between speed and scaling robustness. The architecture consists of a two-dimensional pipeline array that fully utilizes computational similarities in octaves. Secondly, a substructure (block-serial discrete-time cellular neural network) that can realize a nonlinear filter is proposed. This structure decreases the memory demand through the removal of data dependency. Thirdly, a hardware-friendly descriptor is introduced in order to overcome the hardware design bottleneck through the polar sample pattern; a simplified method to realize rotation invariance is also presented. Finally, the proposed architecture is designed in TSMC 65 nm CMOS technology. The experimental results show a performance of 127 fps in full HD resolution at 200 MHz frequency. The peak performance reaches 181 GOPS and the throughput is double the speed of other state-of-the-art architectures. PMID:26404305

  10. Decoding genome-wide GadEWX-transcriptional regulatory networks reveals multifaceted cellular responses to acid stress in Escherichia coli.

    PubMed

    Seo, Sang Woo; Kim, Donghyuk; O'Brien, Edward J; Szubin, Richard; Palsson, Bernhard O

    2015-01-01

    The regulators GadE, GadW and GadX (which we refer to as GadEWX) play a critical role in the transcriptional regulation of the glutamate-dependent acid resistance (GDAR) system in Escherichia coli K-12 MG1655. However, the genome-wide regulatory role of GadEWX is still unknown. Here we comprehensively reconstruct the genome-wide GadEWX transcriptional regulatory network and RpoS involvement in E. coli K-12 MG1655 under acidic stress. Integrative data analysis reveals that GadEWX regulons consist of 45 genes in 31 transcription units and 28 of these genes were associated with RpoS-binding sites. We demonstrate that GadEWX directly and coherently regulate several proton-generating/consuming enzymes with pairs of negative-feedback loops for pH homeostasis. In addition, GadEWX regulate genes with assorted functions, including molecular chaperones, acid resistance, stress response and other regulatory activities. These results show how GadEWX simultaneously coordinate many cellular processes to produce the overall response of E. coli to acid stress. PMID:26258987

  11. Decoding genome-wide GadEWX-transcriptional regulatory networks reveals multifaceted cellular responses to acid stress in Escherichia coli

    PubMed Central

    Seo, Sang Woo; Kim, Donghyuk; O'Brien, Edward J.; Szubin, Richard; Palsson, Bernhard O.

    2015-01-01

    The regulators GadE, GadW and GadX (which we refer to as GadEWX) play a critical role in the transcriptional regulation of the glutamate-dependent acid resistance (GDAR) system in Escherichia coli K-12 MG1655. However, the genome-wide regulatory role of GadEWX is still unknown. Here we comprehensively reconstruct the genome-wide GadEWX transcriptional regulatory network and RpoS involvement in E. coli K-12 MG1655 under acidic stress. Integrative data analysis reveals that GadEWX regulons consist of 45 genes in 31 transcription units and 28 of these genes were associated with RpoS-binding sites. We demonstrate that GadEWX directly and coherently regulate several proton-generating/consuming enzymes with pairs of negative-feedback loops for pH homeostasis. In addition, GadEWX regulate genes with assorted functions, including molecular chaperones, acid resistance, stress response and other regulatory activities. These results show how GadEWX simultaneously coordinate many cellular processes to produce the overall response of E. coli to acid stress. PMID:26258987

  12. A 181 GOPS AKAZE Accelerator Employing Discrete-Time Cellular Neural Networks for Real-Time Feature Extraction.

    PubMed

    Jiang, Guangli; Liu, Leibo; Zhu, Wenping; Yin, Shouyi; Wei, Shaojun

    2015-01-01

    This paper proposes a real-time feature extraction VLSI architecture for high-resolution images based on the accelerated KAZE algorithm. Firstly, a new system architecture is proposed. It increases the system throughput, provides flexibility in image resolution, and offers trade-offs between speed and scaling robustness. The architecture consists of a two-dimensional pipeline array that fully utilizes computational similarities in octaves. Secondly, a substructure (block-serial discrete-time cellular neural network) that can realize a nonlinear filter is proposed. This structure decreases the memory demand through the removal of data dependency. Thirdly, a hardware-friendly descriptor is introduced in order to overcome the hardware design bottleneck through the polar sample pattern; a simplified method to realize rotation invariance is also presented. Finally, the proposed architecture is designed in TSMC 65 nm CMOS technology. The experimental results show a performance of 127 fps in full HD resolution at 200 MHz frequency. The peak performance reaches 181 GOPS and the throughput is double the speed of other state-of-the-art architectures. PMID:26404305

  13. Investigating the specific core genetic-and-epigenetic networks of cellular mechanisms involved in human aging in peripheral blood mononuclear cells

    PubMed Central

    Li, Cheng-Wei; Wang, Wen-Hsin; Chen, Bor-Sen

    2016-01-01

    Aging is an inevitable part of life for humans, and slowing down the aging process has become a main focus of human endeavor. Here, we applied a systems biology approach to construct protein-protein interaction networks, gene regulatory networks, and epigenetic networks, i.e. genetic and epigenetic networks (GENs), of elderly individuals and young controls. We then compared these GENs to extract aging mechanisms using microarray data in peripheral blood mononuclear cells, microRNA (miRNA) data, and database mining. The core GENs of elderly individuals and young controls were obtained by applying principal network projection to GENs based on Principal Component Analysis. By comparing the core networks, we identified that to overcome the accumulated mutation of genes in the aging process the transcription factor JUN can be activated by stress signals, including the MAPK signaling, T-cell receptor signaling, and neurotrophin signaling pathways through DNA methylation of BTG3, G0S2, and AP2B1 and the regulations of mir-223 let-7d, and mir-130a. We also address the aging mechanisms in old men and women. Furthermore, we proposed that drugs designed to target these DNA methylated genes or miRNAs may delay aging. A multiple drug combination comprising phenylalanine, cholesterol, and palbociclib was finally designed for delaying the aging process. PMID:26895224

  14. Develop 3G Application with The J2ME SATSA API

    NASA Astrophysics Data System (ADS)

    JunWu, Xu; JunLing, Liang

    This paper describes research in the use of the Security and Trust Services API for J2ME (SATSA) to develop mobile applications. for 3G networks. SATSA defines a set of APIs that allows J2ME applications to communicate with and access functionality, secure storage and cryptographic operations provided by security elements such as smart cards and Wireless Identification Modules (WIM). A Java Card application could also work as an authentication module in a J2ME-based e-bank application. The e-bank application would allow its users to access their bank accounts using their cell phones.

  15. Proteomic, cellular, and network analyses reveal new DUSP3 interactions with nucleolar proteins in HeLa cells.

    PubMed

    Panico, Karine; Forti, Fabio Luis

    2013-12-01

    DUSP3 (or Vaccinia virus phosphatase VH1-related; VHR) is a small dual-specificity phosphatase known to dephosphorylate c-Jun N-terminal kinases and extracellular signal-regulated kinases. In human cervical cancer cells, DUSP3 is overexpressed, localizes preferentially to the nucleus, and plays a key role in cellular proliferation and senescence triggering. Other DUSP3 functions are still unknown, as illustrated by recent and unpublished results from our group showing that this enzyme mediates DNA damage response or repair processes. In this study, we sought to identify new interactions between DUSP3 and proteins directly or indirectly involved in or correlated with its biological roles in HeLa cells exposed to gamma or UV radiation. By using GST-DUSP as bait, we pulled down interacting proteins and identified them by LC-MS/MS. Of the 46 proteins obtained, six hits were extensively validated by immune techniques; the proteins Nucleophosmin, HnRNP C1/C2, and Nucleolin were the most promising targets found to directly interact with DUSP3. We then analyzed the DUSP3 interactomes using physical protein-protein interaction networks using our hits as the seed list. The validated hits as well as unvalidated hits fluctuated on the DUSP3 interactomes of HeLa cells, independent of the time post radiation, which confirmed our proteomic and experimental data and clearly showed the proximity of DUSP3 to proteins involved in processes intimately related to DNA repair and senescence, such as Ku70 and Tert, via interactions with nucleolar proteins, which were identified in this study, that regulate DNA/RNA structure and functions. PMID:24245651

  16. Modeling land use and land cover changes in a vulnerable coastal region using artificial neural networks and cellular automata.

    PubMed

    Qiang, Yi; Lam, Nina S N

    2015-03-01

    As one of the most vulnerable coasts in the continental USA, the Lower Mississippi River Basin (LMRB) region has endured numerous hazards over the past decades. The sustainability of this region has drawn great attention from the international, national, and local communities, wanting to understand how the region as a system develops under intense interplay between the natural and human factors. A major problem in this deltaic region is significant land loss over the years due to a combination of natural and human factors. The main scientific and management questions are what factors contribute to the land use land cover (LULC) changes in this region, can we model the changes, and how would the LULC look like in the future given the current factors? This study analyzed the LULC changes of the region between 1996 and 2006 by utilizing an artificial neural network (ANN) to derive the LULC change rules from 15 human and natural variables. The rules were then used to simulate future scenarios in a cellular automation model. A stochastic element was added in the model to represent factors that were not included in the current model. The analysis was conducted for two sub-regions in the study area for comparison. The results show that the derived ANN models could simulate the LULC changes with a high degree of accuracy (above 92 % on average). A total loss of 263 km(2) in wetlands from 2006 to 2016 was projected, whereas the trend of forest loss will cease. These scenarios provide useful information to decision makers for better planning and management of the region. PMID:25647797

  17. Intracellular interactions between APOBEC3G, RNA, and HIV-1 Gag: APOBEC3G multimerization is dependent on its association with RNA

    PubMed Central

    Friew, Yeshitila N; Boyko, Vitaly; Hu, Wei-Shau; Pathak, Vinay K

    2009-01-01

    Background Host restriction factor APOBEC3G (A3G) blocks human immunodeficiency virus type 1 (HIV-1) replication by G-to-A hypermutation, and by inhibiting DNA synthesis and provirus formation. Previous reports have suggested that A3G is a dimer and its virion incorporation is mediated through interactions with viral or nonviral RNAs and/or HIV-1 Gag. We have now employed a bimolecular fluorescence complementation assay (BiFC) to analyze the intracellular A3G-A3G, A3G-RNA, and A3G-Gag interactions in living cells by reconstitution of yellow fluorescent protein (YFP) from its N- or C-terminal fragments. Results The results obtained with catalytic domain 1 and 2 (CD1 and CD2) mutants indicate that A3G-A3G and A3G-Gag multimerization is dependent on an intact CD1 domain, which is required for RNA binding. A mutant HIV-1 Gag that exhibits reduced RNA binding also failed to reconstitute BiFC with wild-type A3G, indicating a requirement for both HIV-1 Gag and A3G to bind to RNA for their multimerization. Addition of a non-specific RNA binding peptide (P22) to the N-terminus of a CD1 mutant of A3G restored BiFC and virion incorporation, but failed to inhibit viral replication, indicating that the mutations in CD1 resulted in additional defects that interfere with A3G's antiviral activity. Conclusion These studies establish a robust BiFC assay for analysis of intracellular interactions of A3G with other macromolecules. The results indicate that in vivo A3G is a monomer that forms multimers upon binding to RNA. In addition, we observed weak interactions between wild-type A3G molecules and RNA binding-defective mutants of A3G, which could explain previously described protein-protein interactions between purified A3G molecules. PMID:19497112

  18. Stackelberg Game Based Power Allocation for Physical Layer Security of Device-to-device Communication Underlaying Cellular Networks

    NASA Astrophysics Data System (ADS)

    Qu, Junyue; Cai, Yueming; Wu, Dan; Chen, Hualiang

    2014-05-01

    The problem of power allocation for device-to-device (D2D) underlay communication to improve physical layer security is addressed. Specifically, to improve the secure communication of the cellular users, we introduce a Stackelberg game for allocating the power of the D2D link under a total power constraint and a rate constraint at the D2D pair. In the introduced Stackelberg game the D2D pair works as a seller and the cellular UEs work as buyers. Firstly, because the interference signals from D2D pair are unknown to both the legitimate receiver and the illegitimate eavesdropper, it is possible that a cellular UE decline to participate in the introduced Stackelberg game. So the condition under which a legitimate user will participate in the introduced Stackelberg game is discussed. Then, based on the Stackelberg game, we propose a semi-distributed power allocation algorithm, which is proved to conclude after finite-time iterations. In the end, some simulations are presented to verify the performance improvement in the physical layer security of cellular UEs using the proposed power allocation algorithm. We can determine that with the proposed algorithm, while the D2D pair's communication demand is met, the physical layer security of cellular UEs can be improved.

  19. Cellular resilience.

    PubMed

    Smirnova, Lena; Harris, Georgina; Leist, Marcel; Hartung, Thomas

    2015-01-01

    Cellular resilience describes the ability of a cell to cope with environmental changes such as toxicant exposure. If cellular metabolism does not collapse directly after the hit or end in programmed cell death, the ensuing stress responses promote a new homeostasis under stress. The processes of reverting "back to normal" and reversal of apoptosis ("anastasis") have been studied little at the cellular level. Cell types show astonishingly similar vulnerability to most toxicants, except for those that require a very specific target, metabolism or mechanism present only in specific cell types. The majority of chemicals triggers "general cytotoxicity" in any cell at similar concentrations. We hypothesize that cells differ less in their vulnerability to a given toxicant than in their resilience (coping with the "hit"). In many cases, cells do not return to the naive state after a toxic insult. The phenomena of "pre-conditioning", "tolerance" and "hormesis" describe this for low-dose exposures to toxicants that render the cell more resistant to subsequent hits. The defense and resilience programs include epigenetic changes that leave a "memory/scar" - an alteration as a consequence of the stress the cell has experienced. These memories might have long-term consequences, both positive (resistance) and negative, that contribute to chronic and delayed manifestations of hazard and, ultimately, disease. This article calls for more systematic analyses of how cells cope with toxic perturbations in the long-term after stressor withdrawal. A technical prerequisite for these are stable (organotypic) cultures and a characterization of stress response molecular networks. PMID:26536287

  20. Multiscale modeling of cellular epigenetic states: stochasticity in molecular networks, chromatin folding in cell nuclei, and tissue pattern formation of cells

    PubMed Central

    Liang, Jie; Cao, Youfang; Gürsoy, Gamze; Naveed, Hammad; Terebus, Anna; Zhao, Jieling

    2016-01-01

    Genome sequences provide the overall genetic blueprint of cells, but cells possessing the same genome can exhibit diverse phenotypes. There is a multitude of mechanisms controlling cellular epigenetic states and that dictate the behavior of cells. Among these, networks of interacting molecules, often under stochastic control, depending on the specific wirings of molecular components and the physiological conditions, can have a different landscape of cellular states. In addition, chromosome folding in three-dimensional space provides another important control mechanism for selective activation and repression of gene expression. Fully differentiated cells with different properties grow, divide, and interact through mechanical forces and communicate through signal transduction, resulting in the formation of complex tissue patterns. Developing quantitative models to study these multi-scale phenomena and to identify opportunities for improving human health requires development of theoretical models, algorithms, and computational tools. Here we review recent progress made in these important directions. PMID:27480462

  1. Global Exponential Stability of Almost Periodic Solution for Neutral-Type Cohen-Grossberg Shunting Inhibitory Cellular Neural Networks with Distributed Delays and Impulses

    PubMed Central

    Xu, Lijun; Jiang, Qi; Gu, Guodong

    2016-01-01

    A kind of neutral-type Cohen-Grossberg shunting inhibitory cellular neural networks with distributed delays and impulses is considered. Firstly, by using the theory of impulsive differential equations and the contracting mapping principle, the existence and uniqueness of the almost periodic solution for the above system are obtained. Secondly, by constructing a suitable Lyapunov functional, the global exponential stability of the unique almost periodic solution is also investigated. The work in this paper improves and extends some results in recent years. As an application, an example and numerical simulations are presented to demonstrate the feasibility and effectiveness of the main results. PMID:27190502

  2. Anticipatory grip force between 1 and 3g

    NASA Astrophysics Data System (ADS)

    White, Olivier; Van Loon, ing.. Jack J. W. A.; Thonnard, Jean-Louis; Hermsdorfer, Joachim; Lefevre, Philippe

    One remarkable capacity of utilizing common tools appropriately as soon as we grasp them relies on the ability to determine in advance the grip force (GF) required to handle them in relation to their mechanical properties and the surrounding environment. This anticipatory strategy avoids the uncompressible delays in the feedback system. The predictive control of GF is made possible because the nervous system can learn, store and then select the internal representations of the dynamics of innumerable objects, known as internal models. Beside this flexibility, the nervous system's ability to learn different task dynamics is often limited in classical robotic experiments The environment itself can be profoundly modified in altered gravity or centrifugation. The few studies that investigated motor adaptation in such contexts did not consider the interaction between gravitational phases and even less the transitions across environments. Here, we tested subject's abilities to adapt to levels of gravitational fields generated by a human centrifuge. In Experiment 1, seven subjects performed 4 lifting trials in each gravitational phase (1 to 2.5g and then 2.5 to 1g by steps of 0.5g) with a 0.12 kg instrumented object. In Experiment 2, six subjects performed vertical oscillations of the object during transitions between 1 and 3g (0.5g steps, ascending and descending phases, profile repeated twice). We continuously measured GF, load force (LF) and ambient gravity. We hypothesized that participants were able to predictively adjust GF to the new environment. In Experiment 1, participants adjusted their GF proportionally to gravity and decreased GF across trials within a given gravitational environment. Preload phases decreased over time from 300ms to 50ms irrespective of gravity. We quantified the abilities of participants to switch across environments by subtracting GF recorded in the last trial in the current gravity level from GF during the first trial in the new environment

  3. New Markov-Shannon Entropy models to assess connectivity quality in complex networks: from molecular to cellular pathway, Parasite-Host, Neural, Industry, and Legal-Social networks.

    PubMed

    Riera-Fernández, Pablo; Munteanu, Cristian R; Escobar, Manuel; Prado-Prado, Francisco; Martín-Romalde, Raquel; Pereira, David; Villalba, Karen; Duardo-Sánchez, Aliuska; González-Díaz, Humberto

    2012-01-21

    Graph and Complex Network theory is expanding its application to different levels of matter organization such as molecular, biological, technological, and social networks. A network is a set of items, usually called nodes, with connections between them, which are called links or edges. There are many different experimental and/or theoretical methods to assign node-node links depending on the type of network we want to construct. Unfortunately, the use of a method for experimental reevaluation of the entire network is very expensive in terms of time and resources; thus the development of cheaper theoretical methods is of major importance. In addition, different methods to link nodes in the same type of network are not totally accurate in such a way that they do not always coincide. In this sense, the development of computational methods useful to evaluate connectivity quality in complex networks (a posteriori of network assemble) is a goal of major interest. In this work, we report for the first time a new method to calculate numerical quality scores S(L(ij)) for network links L(ij) (connectivity) based on the Markov-Shannon Entropy indices of order k-th (θ(k)) for network nodes. The algorithm may be summarized as follows: (i) first, the θ(k)(j) values are calculated for all j-th nodes in a complex network already constructed; (ii) A Linear Discriminant Analysis (LDA) is used to seek a linear equation that discriminates connected or linked (L(ij)=1) pairs of nodes experimentally confirmed from non-linked ones (L(ij)=0); (iii) the new model is validated with external series of pairs of nodes; (iv) the equation obtained is used to re-evaluate the connectivity quality of the network, connecting/disconnecting nodes based on the quality scores calculated with the new connectivity function. This method was used to study different types of large networks. The linear models obtained produced the following results in terms of overall accuracy for network reconstruction

  4. APOBEC3G Complexes Decrease Human Immunodeficiency Virus Type 1 Production ▿

    PubMed Central

    Martin, Kenneth L.; Johnson, Megan; D'Aquila, Richard T.

    2011-01-01

    APOBEC3G (A3G) is packaged into human immunodeficiency virus type 1 (HIV-1) virions unless HIV-1 virion infectivity factor (Vif) counteracts it. Virion A3G restricts HIV-1 reverse transcription and integration in target cells. Some A3G in producer cells colocalizes with specific cytoplasmic structures, in what are called “A3G complexes” here. Functional effects of producer cell A3G complexes on HIV-1 replication were studied. HeLa cells were cotransfected with HIV-1 constructs producing pseudoviruses, as well as either wild-type (WT) A3G or a mutant A3G (C97A, Y124A, W127A, or D128K A3G). Pseudovirus particle production was decreased from cells expressing any of the A3Gs that formed complexes by 24 h after transfection, relative to cells with C97A A3G that did not form detectable A3G complexes by 24 h or A3G-negative cells. The intracellular HIV-1 Gag half-life was shorter in cells containing A3G complexes than in those lacking complexes. HIV-1 virion output was decreased in a single round of replication from a T cell line containing A3G complexes (CEM cells) after infection with Vif-negative HIV-1, compared to Vif-positive HIV-1 that depleted A3G. Levels of production of Vif-negative and Vif-positive virus were similar from cells not containing A3G (CEM-SS cells). Knockdown of the mRNA processing body (P-body) component RCK/p54, eliminated A3G complex formation, and increased HIV-1 production. We conclude that endogenous A3G complexes in producer cells decrease HIV-1 production if not degraded by Vif. PMID:21752914

  5. Simultaneous generation of 3G and millimeter-wave signals using a dual-electrode MZM in ROF systems

    NASA Astrophysics Data System (ADS)

    Ying, Xiang-yue; Xu, Tie-feng; Liu, Tai-jun; Nie, Qiu-hua; Wen, Hua-feng; Li, Jun

    2015-07-01

    A novel radio-over-fiber (ROF) scheme to simultaneously generate and transmit the 3rd generation telecommunication (3G) and millimeter-wave (MMW) signals by using a single dual-electrode Mach-Zehnder modulator (MZM) is proposed. There is no apparent nonlinearity induced by the ROF system. By employing this analog ROF signal transmission technique, highly transparent fiber-wireless convergence networks can be realized, which are ideal for multi-standard wireless system operation.

  6. Interaction between cellular voltage-sensitive conductance and network parameters in a model of neocortex can generate epileptiform bursting.

    SciTech Connect

    van Drongelen, W.; Lee, H. C.; Koch, H.; Elsen, F.; Carroll, M. S.; Hereld, M.; Stevens, R. L.; Mathematics and Computer Science; Univ. of Chicago

    2004-01-01

    We examined the effects of both intrinsic neuronal membrane properties and network parameters on oscillatory activity in a model of neocortex. A scalable network model with six different cell types was built with the pGENESIS neural simulator. The neocortical network consisted of two types of pyramidal cells and four types of inhibitory interneurons. All cell types contained both fast sodium and delayed rectifier potassium channels for generation of action potentials. A subset of the pyramidal neurons contained an additional slow inactivating (persistent) sodium current (NaP). The neurons with the NaP current showed spontaneous bursting activity in the absence of external stimulation. The model also included a routine to calculate a simulated electroencephalogram (EEG) trace from the population activity. This revealed emergent network behavior which ranged from desynchronized activity to different types of seizure-like bursting patterns. At settings with weaker excitatory network effects, the propensity to generate seizure-like behavior increased. Strong excitatory network connectivity destroyed oscillatory behavior, whereas weak connectivity enhanced the relative importance of the spontaneously bursting cells. Our findings are in contradiction with the general opinion that strong excitatory synaptic and/or insufficient inhibition effects are associated with seizure initiation, but are in agreement with previously reported behavior in neocortex.

  7. Identification of a molecular signaling network that regulates a cellular necrotic cell death pathway by a genome wide siRNA screen

    PubMed Central

    Hitomi, Junichi; Christofferson, Dana E.; Ng, Aylwin; Yao, Jianhua; Degterev, Alexei; Xavier, Ramnik J.; Yuan, Junying

    2009-01-01

    Stimulation of death receptors by agonists such as FasL and TNFα activates apoptotic cell death in apoptotic competent conditions or a type of necrotic cell death dependent on RIP1 kinase, termed necroptosis, in apoptotic deficient conditions. In a genome-wide siRNA screen for regulators of necroptosis, we identify a set of 432 genes that regulate necroptosis, a subset of 32 genes that act downstream and/or as regulators of RIP1 kinase, 32 genes required for death receptor mediated apoptosis, and 7 genes involved in both necroptosis and apoptosis. We show that the expression of subsets of the 432 genes are enriched in the immune and nervous systems, and cellular sensitivity to necroptosis is regulated by an extensive signaling network mediating innate immunity. Interestingly, Bmf, a BH3-only Bcl-2 family member, is required for death receptor-induced necroptosis. Our study defines a cellular signaling network that regulates necroptosis and the molecular bifurcation that controls apoptosis and necroptosis. PMID:19109899

  8. Equine Infectious Anemia Virus Gag Assembly and Export Are Directed by Matrix Protein through trans-Golgi Networks and Cellular Vesicles

    PubMed Central

    Zhang, Zeli; Ma, Jian; Zhang, Xiang; Su, Chao; Yao, Qiu-Cheng

    2015-01-01

    ABSTRACT Gag intracellular assembly and export are very important processes for lentiviruses replication. Previous studies have demonstrated that equine infectious anemia virus (EIAV) matrix (MA) possesses distinct phosphoinositide affinity compared with HIV-1 MA and that phosphoinositide-mediated targeting to peripheral and internal membranes is a critical factor in EIAV assembly and release. In this study, we compared the cellular assembly sites of EIAV and HIV-1. We observed that the assembly of EIAV particles occurred on interior cellular membranes, while HIV-1 was targeted to the plasma membrane (PM) for assembly. Then, we determined that W7 and K9 in the EIAV MA N terminus were essential for Gag assembly and release but did not affect the cellular distribution of Gag. The replacement of EIAV MA with HIV-1 MA directed chimeric Gag to the PM but severely impaired Gag release. MA structural analysis indicated that the EIAV and HIV-1 MAs had similar spatial structures but that helix 1 of the EIAV MA was closer to loop 2. Further investigation indicated that EIAV Gag accumulated in the trans-Golgi network (TGN) but not the early and late endosomes. The 9 N-terminal amino acids of EIAV MA harbored the signal that directed Gag to the TGN membrane system. Additionally, we demonstrated that EIAV particles were transported to the extracellular space by the cellular vesicle system. This type of EIAV export was not associated with multivesicular bodies or microtubule depolymerization but could be inhibited by the actin-depolymerizing drug cytochalasin D, suggesting that dynamic actin depolymerization may be associated with EIAV production. IMPORTANCE In previous studies, EIAV Gag was reported to localize to both the cell interior and the plasma membrane. Here, we demonstrate that EIAV likely uses the TGN as the assembly site in contrast to HIV-1, which is targeted to the PM for assembly. These distinct assembly features are determined by the MA domain. We also identified

  9. System-Level Insights into the Cellular Interactome of a Non-Model Organism: Inferring, Modelling and Analysing Functional Gene Network of Soybean (Glycine max)

    PubMed Central

    Xu, Yungang; Guo, Maozu; Zou, Quan; Liu, Xiaoyan; Wang, Chunyu; Liu, Yang

    2014-01-01

    Cellular interactome, in which genes and/or their products interact on several levels, forming transcriptional regulatory-, protein interaction-, metabolic-, signal transduction networks, etc., has attracted decades of research focuses. However, such a specific type of network alone can hardly explain the various interactive activities among genes. These networks characterize different interaction relationships, implying their unique intrinsic properties and defects, and covering different slices of biological information. Functional gene network (FGN), a consolidated interaction network that models fuzzy and more generalized notion of gene-gene relations, have been proposed to combine heterogeneous networks with the goal of identifying functional modules supported by multiple interaction types. There are yet no successful precedents of FGNs on sparsely studied non-model organisms, such as soybean (Glycine max), due to the absence of sufficient heterogeneous interaction data. We present an alternative solution for inferring the FGNs of soybean (SoyFGNs), in a pioneering study on the soybean interactome, which is also applicable to other organisms. SoyFGNs exhibit the typical characteristics of biological networks: scale-free, small-world architecture and modularization. Verified by co-expression and KEGG pathways, SoyFGNs are more extensive and accurate than an orthology network derived from Arabidopsis. As a case study, network-guided disease-resistance gene discovery indicates that SoyFGNs can provide system-level studies on gene functions and interactions. This work suggests that inferring and modelling the interactome of a non-model plant are feasible. It will speed up the discovery and definition of the functions and interactions of other genes that control important functions, such as nitrogen fixation and protein or lipid synthesis. The efforts of the study are the basis of our further comprehensive studies on the soybean functional interactome at the genome

  10. Crystal structures of APOBEC3G N-domain alone and its complex with DNA

    PubMed Central

    Xiao, Xiao; Li, Shu-Xing; Yang, Hanjing; Chen, Xiaojiang S.

    2016-01-01

    APOBEC3G (A3G) is a potent restriction factor of HIV-1. The N-terminal domain of A3G (A3G-CD1) is responsible for oligomerization and nucleic acid binding, both of which are essential for anti-HIV activity. As a countermeasure, HIV-1 viral infectivity factor (Vif) binds A3G-CD1 to mediate A3G degradation. The structural basis for the functions of A3G-CD1 remains elusive. Here, we report the crystal structures of a primate A3G-CD1 (rA3G-CD1) alone and in complex with single-stranded DNA (ssDNA). rA3G-CD1 shares a conserved core structure with the previously determined catalytic APOBECs, but displays unique features for surface charge, dimerization and nucleic acid binding. Its co-crystal structure with ssDNA reveals how the conformations of loops and residues surrounding the Zn-coordinated centre (Zn-centre) change upon DNA binding. The dimerization interface of rA3G-CD1 is important for oligomerization, nucleic acid binding and Vif-mediated degradation. These findings elucidate the molecular basis of antiviral mechanism and HIV-Vif targeting of A3G. PMID:27480941

  11. Crystal structures of APOBEC3G N-domain alone and its complex with DNA.

    PubMed

    Xiao, Xiao; Li, Shu-Xing; Yang, Hanjing; Chen, Xiaojiang S

    2016-01-01

    APOBEC3G (A3G) is a potent restriction factor of HIV-1. The N-terminal domain of A3G (A3G-CD1) is responsible for oligomerization and nucleic acid binding, both of which are essential for anti-HIV activity. As a countermeasure, HIV-1 viral infectivity factor (Vif) binds A3G-CD1 to mediate A3G degradation. The structural basis for the functions of A3G-CD1 remains elusive. Here, we report the crystal structures of a primate A3G-CD1 (rA3G-CD1) alone and in complex with single-stranded DNA (ssDNA). rA3G-CD1 shares a conserved core structure with the previously determined catalytic APOBECs, but displays unique features for surface charge, dimerization and nucleic acid binding. Its co-crystal structure with ssDNA reveals how the conformations of loops and residues surrounding the Zn-coordinated centre (Zn-centre) change upon DNA binding. The dimerization interface of rA3G-CD1 is important for oligomerization, nucleic acid binding and Vif-mediated degradation. These findings elucidate the molecular basis of antiviral mechanism and HIV-Vif targeting of A3G. PMID:27480941

  12. Why Are Cortical GABA Neurons Relevant to Internal Focus in Depression? A cross-level model linking cellular, biochemical, and neural network findings

    PubMed Central

    2014-01-01

    Major Depression is a complex and severe psychiatric disorder whose symptomatology encompasses a critical shift in awareness, specifically in the balance from external to internal mental focus. This is reflected by unspecific somatic symptoms and the predominance of the own cognitions manifested in increased self-focus and rumination. We posit here that sufficient empirical data has accumulated to build a coherent biological model that links these psychological concepts and symptom dimensions to observed biochemical, cellular, regional and neural network deficits. Specifically, deficits in inhibitory gamma amino butyric acid (GABA) regulating excitatory cell input/output and local cell circuit processing of information in key brain regions may underlie the shift that is observed in depressed subjects in resting state activities between the perigenual anterior cingulate cortex (PACC) and the dorsolateral prefrontal cortex (DLPFC). This regional dysbalance translates at the network level in a dysbalance between default-mode and executive networks, which psychopathologically surfaces as a shift in focus from external to internal mental content and associated symptoms (See overview in Figure 1). We focus here on primary evidence at each of those levels and on putative mechanistic links between those levels. Apart from its implications for neuropsychiatric disorders, our model provides for the first time a set of hypotheses for cross-level mechanisms of how internal and external mental contents may be constituted and balanced in healthy subjects, and thus also contributes to the neuroscientific debate on the neural correlates of consciousness. PMID:25048001

  13. Multifaceted counter-APOBEC3G mechanisms employed by HIV-1 Vif

    PubMed Central

    Britan-Rosich, Elena; Nowarski, Roni; Kotler, Moshe

    2011-01-01

    In the absence of HIV-1 Vif protein, the host antiviral deaminase APOBEC3G (A3G) restricts the production of infectious HIV-1 by deamination of dC residues in the negative ssDNA produced by reverse transcription. The Vif protein averts the lethal threat of deamination by precluding the packaging of A3G into assembling virions by mediating proteasomal degradation of A3G. In spite of this robust Vif activity, residual A3G molecules that escape degradation and incorporate into newly assembled virions are potentially deleterious to the virus. We hypothesized that virion-associated Vif inhibits A3G enzymatic activity, and therefore prevents lethal mutagenesis of the newly synthesized viral DNA. Here we show that: (i) Vif-proficient HIV-1 particles released from H9 cells contain A3G with lower specific activity compared with Δvif virus associated A3G; (ii) Encapsidated HIV-1 Vif inhibits the deamination activity of recombinant A3G, and (iii) Purified HIV-1 Vif protein and the Vif-derived peptide Vif25-39 inhibit A3G activity in vitro at nanomolar concentrations in an uncompetitive manner. Our results manifest the potentiality of Vif to control the deamination threat in virions or in the pre-integration complexes (PICs) following entry to target cells. Hence, virion-associated Vif could serve as a last line of defense, protecting the virus against A3G anti-viral activity. PMID:21763507

  14. Feasibility Study on a Portable Field Pest Classification System Design Based on DSP and 3G Wireless Communication Technology

    PubMed Central

    Han, Ruizhen; He, Yong; Liu, Fei

    2012-01-01

    This paper presents a feasibility study on a real-time in field pest classification system design based on Blackfin DSP and 3G wireless communication technology. This prototype system is composed of remote on-line classification platform (ROCP), which uses a digital signal processor (DSP) as a core CPU, and a host control platform (HCP). The ROCP is in charge of acquiring the pest image, extracting image features and detecting the class of pest using an Artificial Neural Network (ANN) classifier. It sends the image data, which is encoded using JPEG 2000 in DSP, to the HCP through the 3G network at the same time for further identification. The image transmission and communication are accomplished using 3G technology. Our system transmits the data via a commercial base station. The system can work properly based on the effective coverage of base stations, no matter the distance from the ROCP to the HCP. In the HCP, the image data is decoded and the pest image displayed in real-time for further identification. Authentication and performance tests of the prototype system were conducted. The authentication test showed that the image data were transmitted correctly. Based on the performance test results on six classes of pests, the average accuracy is 82%. Considering the different live pests’ pose and different field lighting conditions, the result is satisfactory. The proposed technique is well suited for implementation in field pest classification on-line for precision agriculture. PMID:22736996

  15. Feasibility study on a portable field pest classification system design based on DSP and 3G wireless communication technology.

    PubMed

    Han, Ruizhen; He, Yong; Liu, Fei

    2012-01-01

    This paper presents a feasibility study on a real-time in field pest classification system design based on Blackfin DSP and 3G wireless communication technology. This prototype system is composed of remote on-line classification platform (ROCP), which uses a digital signal processor (DSP) as a core CPU, and a host control platform (HCP). The ROCP is in charge of acquiring the pest image, extracting image features and detecting the class of pest using an Artificial Neural Network (ANN) classifier. It sends the image data, which is encoded using JPEG 2000 in DSP, to the HCP through the 3G network at the same time for further identification. The image transmission and communication are accomplished using 3G technology. Our system transmits the data via a commercial base station. The system can work properly based on the effective coverage of base stations, no matter the distance from the ROCP to the HCP. In the HCP, the image data is decoded and the pest image displayed in real-time for further identification. Authentication and performance tests of the prototype system were conducted. The authentication test showed that the image data were transmitted correctly. Based on the performance test results on six classes of pests, the average accuracy is 82%. Considering the different live pests' pose and different field lighting conditions, the result is satisfactory. The proposed technique is well suited for implementation in field pest classification on-line for precision agriculture. PMID:22736996

  16. APOBEC3G exerts tumor suppressive effects in human hepatocellular carcinoma.

    PubMed

    Chang, Li-Ching; Kuo, Ting-Yin; Liu, Ching-Wen; Chen, Yaw-Sen; Lin, Hsi-Hsun; Wu, Pei-Fung

    2014-04-01

    In this study, we collected 44 hepatitis B virus surface antigen positivity HBsAg (+) tumor and nontumor hepatocellular tissues from hepatocellular carcinoma (HCC) patients during hepatectomy, and quantified the APOBEC3G (A3G) mRNA by using a real-time PCR. Our results showed higher expression of A3G mRNA in the nontumor tissues than in the tumor tissues of the HBsAg (+) HCC patients. To further investigate this phenomenon, we constructed a pLV-A3G vector and transfected it into the human HCC cell line, Hep 3B. The results of an immunofluorescence analysis showed the overexpression of A3G in the cytoplasm. We then evaluated A3G cytotoxicity by using a cell viability assay (MTS assay), the results of which showed that Hep 3B cell viability was 88 and 58% after the transfection of pLV and pLV-A3G, respectively, indicating the growth inhibitory effects of A3G on Hep 3B cells. To further evaluate the tumor suppressive effects of A3G, we used a plastic pipette tip to scratch Hep 3B cells grown on a culture dish (to 70-80% confluence) after transfection with pLV-A3G. Our data indicated a ratio of wound closure of 100% in the control cells and in the pLV-expressing cells, compared with 43% in the pLV-A3G-overexpressing cells, 72 h after the wound scratch, as observed using phase-contrast microscopy. These results indicated that A3G inhibits wound healing in Hep 3B cells. Overall, our results suggest that A3G inhibits the growth of human hepatoma cells. PMID:24500029

  17. Perturbation of cellular proteostasis networks identifies pathways that modulate precursor and intermediate but not mature levels of frataxin

    PubMed Central

    Nabhan, Joseph F.; Gooch, Renea L.; Piatnitski Chekler, Eugene L.; Pierce, Betsy; Bulawa, Christine E.

    2015-01-01

    Friedreich’s Ataxia is a genetic disease caused by expansion of an intronic trinucleotide repeat in the frataxin (FXN) gene yielding diminished FXN expression and consequently disease. Since increasing FXN protein levels is desirable to ameliorate pathology, we explored the role of major cellular proteostasis pathways and mitochondrial proteases in FXN processing and turnover. We targeted p97/VCP, the ubiquitin proteasome pathway (UPP), and autophagy with chemical inhibitors in cell lines and patient-derived cells. p97 inhibition by DBeQ increased precursor FXN levels, while UPP and autophagic flux modulators had variable effects predominantly on intermediate FXN. Our data suggest that these pathways cannot be modulated to influence mature functional FXN levels. We also targeted known mitochondrial proteases by RNA interference and discovered a novel protease PITRM1 that regulates intermediate FXN levels. Treatment with the aforementioned chemical and genetic modulators did not have a differential effect in patient cells containing lower amounts of FXN. Interestingly, a number of treatments caused a change in total amount of FXN protein, without an effect on mature FXN. Our results imply that regulation of FXN protein levels is complex and that total amounts can be modulated chemically and genetically without altering the absolute amount of mature FXN protein. PMID:26671574

  18. C/EBPγ Is a Critical Regulator of Cellular Stress Response Networks through Heterodimerization with ATF4.

    PubMed

    Huggins, Christopher J; Mayekar, Manasi K; Martin, Nancy; Saylor, Karen L; Gonit, Mesfin; Jailwala, Parthav; Kasoji, Manjula; Haines, Diana C; Quiñones, Octavio A; Johnson, Peter F

    2016-03-01

    The integrated stress response (ISR) controls cellular adaptations to nutrient deprivation, redox imbalances, and endoplasmic reticulum (ER) stress. ISR genes are upregulated in stressed cells, primarily by the bZIP transcription factor ATF4 through its recruitment to cis-regulatory C/EBP:ATF response elements (CAREs) together with a dimeric partner of uncertain identity. Here, we show that C/EBPγ:ATF4 heterodimers, but not C/EBPβ:ATF4 dimers, are the predominant CARE-binding species in stressed cells. C/EBPγ and ATF4 associate with genomic CAREs in a mutually dependent manner and coregulate many ISR genes. In contrast, the C/EBP family members C/EBPβ and C/EBP homologous protein (CHOP) were largely dispensable for induction of stress genes. Cebpg(-/-) mouse embryonic fibroblasts (MEFs) proliferate poorly and exhibit oxidative stress due to reduced glutathione levels and impaired expression of several glutathione biosynthesis pathway genes. Cebpg(-/-) mice (C57BL/6 background) display reduced body size and microphthalmia, similar to ATF4-null animals. In addition, C/EBPγ-deficient newborns die from atelectasis and respiratory failure, which can be mitigated by in utero exposure to the antioxidant, N-acetyl-cysteine. Cebpg(-/-) mice on a mixed strain background showed improved viability but, upon aging, developed significantly fewer malignant solid tumors than WT animals. Our findings identify C/EBPγ as a novel antioxidant regulator and an obligatory ATF4 partner that controls redox homeostasis in normal and cancerous cells. PMID:26667036

  19. Cellular Protein WDR11 Interacts with Specific Herpes Simplex Virus Proteins at the trans-Golgi Network To Promote Virus Replication

    PubMed Central

    Taylor, Kathryne E.

    2015-01-01

    ABSTRACT It has recently been proposed that the herpes simplex virus (HSV) protein ICP0 has cytoplasmic roles in blocking antiviral signaling and in promoting viral replication in addition to its well-known proteasome-dependent functions in the nucleus. However, the mechanisms through which it produces these effects remain unclear. While investigating this further, we identified a novel cytoplasmic interaction between ICP0 and the poorly characterized cellular protein WDR11. During an HSV infection, WDR11 undergoes a dramatic change in localization at late times in the viral replication cycle, moving from defined perinuclear structures to a dispersed cytoplasmic distribution. While this relocation was not observed during infection with viruses other than HSV-1 and correlated with efficient HSV-1 replication, the redistribution was found to occur independently of ICP0 expression, instead requiring viral late gene expression. We demonstrate for the first time that WDR11 is localized to the trans-Golgi network (TGN), where it interacts specifically with some, but not all, HSV virion components, in addition to ICP0. Knockdown of WDR11 in cultured human cells resulted in a modest but consistent decrease in yields of both wild-type and ICP0-null viruses, in the supernatant and cell-associated fractions, without affecting viral gene expression. Although further study is required, we propose that WDR11 participates in viral assembly and/or secondary envelopment. IMPORTANCE While the TGN has been proposed to be the major site of HSV-1 secondary envelopment, this process is incompletely understood, and in particular, the role of cellular TGN components in this pathway is unknown. Additionally, little is known about the cellular functions of WDR11, although the disruption of this protein has been implicated in multiple human diseases. Therefore, our finding that WDR11 is a TGN-resident protein that interacts with specific viral proteins to enhance viral yields improves both

  20. Hybrid alginate-polyester bimodal network hydrogel for tissue engineering--Influence of structured water on long-term cellular growth.

    PubMed

    Finosh, G T; Jayabalan, M; Vandana, S; Raghu, K G

    2015-11-01

    The development of biodegradable scaffolds (which promote cell-binding, proliferation, long-term cell viability and required biomechanical stability) for cardiac tissue engineering is a challenge. In this study, biosynthetic amphiphilic hybrid hydrogels were prepared using a graft comacromer of natural polysaccharide alginate and synthetic polyester polypropylene fumarate (PPF). Monomodal network hydrogel (HPAS-NO) and bimodal network hydrogel (HPAS-AA) were prepared. Between the two hydrogels, HPAS-AA hydrogel excels over the HPAS-NO hydrogel. HPAS-AA hydrogel is mechanically more stable in the culture medium and undergoes gradual degradation in vitro in PBS (phosphate buffered saline). HPAS-AA contains nano-porous structure and acquires structured water (non-freezing-bound water) (53.457%) along with free water (11.773%). It absorbs more plasma proteins and prevents platelet adsorption and hemolysis when contacted with blood. HPAS-AA hydrogel is cytocompatible and promote 3D cell growth (≈ 70%) of L929 fibroblast even after 18 days and H9C2 cardiomyoblasts. The enhanced and long-term cellular growth of HPAS-AA hydrogel is attributed to the cell responsive features of structured water. HPAS-AA hydrogel can be a better candidate for cardiac tissue engineering applications. PMID:25843368

  1. Tumultuous Relationship between the Human Immunodeficiency Virus Type 1 Viral Infectivity Factor (Vif) and the Human APOBEC-3G and APOBEC-3F Restriction Factors

    PubMed Central

    Henriet, Simon; Mercenne, Gaëlle; Bernacchi, Serena; Paillart, Jean-Christophe; Marquet, Roland

    2009-01-01

    Summary: The viral infectivity factor (Vif) is dispensable for human immunodeficiency virus type 1 (HIV-1) replication in so-called permissive cells but is required for replication in nonpermissive cell lines and for pathogenesis. Virions produced in the absence of Vif have an aberrant morphology and an unstable core and are unable to complete reverse transcription. Recent studies demonstrated that human APOBEC-3G (hA3G) and APOBEC-3F (hA3F), which are selectively expressed in nonpermissive cells, possess strong anti-HIV-1 activity and are sufficient to confer a nonpermissive phenotype. Vif induces the degradation of hA3G and hA3F, suggesting that its main function is to counteract these cellular factors. Most studies focused on the hypermutation induced by the cytidine deaminase activity of hA3G and hA3F and on their Vif-induced degradation by the proteasome. However, recent studies suggested that several mechanisms are involved both in the antiviral activity of hA3G and hA3F and in the way Vif counteracts these antiviral factors. Attempts to reconcile the studies involving Vif in virus assembly and stability with these recent findings suggest that hA3G and hA3F partially exert their antiviral activity independently of their catalytic activity by destabilizing the viral core and the reverse transcription complex, possibly by interfering with the assembly and/or maturation of the viral particles. Vif could then counteract hA3G and hA3F by excluding them from the viral assembly intermediates through competition for the viral genomic RNA, by regulating the proteolytic processing of Pr55Gag, by enhancing the efficiency of the reverse transcription process, and by inhibiting the enzymatic activities of hA3G and hA3F. PMID:19487726

  2. Tumultuous relationship between the human immunodeficiency virus type 1 viral infectivity factor (Vif) and the human APOBEC-3G and APOBEC-3F restriction factors.

    PubMed

    Henriet, Simon; Mercenne, Gaëlle; Bernacchi, Serena; Paillart, Jean-Christophe; Marquet, Roland

    2009-06-01

    The viral infectivity factor (Vif) is dispensable for human immunodeficiency virus type 1 (HIV-1) replication in so-called permissive cells but is required for replication in nonpermissive cell lines and for pathogenesis. Virions produced in the absence of Vif have an aberrant morphology and an unstable core and are unable to complete reverse transcription. Recent studies demonstrated that human APOBEC-3G (hA3G) and APOBEC-3F (hA3F), which are selectively expressed in nonpermissive cells, possess strong anti-HIV-1 activity and are sufficient to confer a nonpermissive phenotype. Vif induces the degradation of hA3G and hA3F, suggesting that its main function is to counteract these cellular factors. Most studies focused on the hypermutation induced by the cytidine deaminase activity of hA3G and hA3F and on their Vif-induced degradation by the proteasome. However, recent studies suggested that several mechanisms are involved both in the antiviral activity of hA3G and hA3F and in the way Vif counteracts these antiviral factors. Attempts to reconcile the studies involving Vif in virus assembly and stability with these recent findings suggest that hA3G and hA3F partially exert their antiviral activity independently of their catalytic activity by destabilizing the viral core and the reverse transcription complex, possibly by interfering with the assembly and/or maturation of the viral particles. Vif could then counteract hA3G and hA3F by excluding them from the viral assembly intermediates through competition for the viral genomic RNA, by regulating the proteolytic processing of Pr55(Gag), by enhancing the efficiency of the reverse transcription process, and by inhibiting the enzymatic activities of hA3G and hA3F. PMID:19487726

  3. A novel podocyte gene, semaphorin 3G, protects glomerular podocyte from lipopolysaccharide-induced inflammation

    PubMed Central

    Ishibashi, Ryoichi; Takemoto, Minoru; Akimoto, Yoshihiro; Ishikawa, Takahiro; He, Peng; Maezawa, Yoshiro; Sakamoto, Kenichi; Tsurutani, Yuya; Ide, Shintaro; Ide, Kana; Kawamura, Harukiyo; Kobayashi, Kazuki; Tokuyama, Hirotake; Tryggvason, Karl; Betsholtz, Christer; Yokote, Koutaro

    2016-01-01

    Kidney diseases including diabetic nephropathy have become huge medical problems, although its precise mechanisms are still far from understood. In order to increase our knowledge about the patho-physiology of kidney, we have previously identified >300 kidney glomerulus-enriched transcripts through large-scale sequencing and microarray profiling of the mouse glomerular transcriptome. One of the glomerulus-specific transcripts identified was semaphorin 3G (Sema3G) which belongs to the semaphorin family. The aim of this study was to analyze both the in vivo and in vitro functions of Sema3G in the kidney. Sema3G was expressed in glomerular podocytes. Although Sema3G knockout mice did not show obvious glomerular defects, ultrastructural analyses revealed partially aberrant podocyte foot processes structures. When these mice were injected with lipopolysaccharide to induce acute inflammation or streptozotocin to induce diabetes, the lack of Sema3G resulted in increased albuminuria. The lack of Sema3G in podocytes also enhanced the expression of inflammatory cytokines including chemokine ligand 2 and interleukin 6. On the other hand, the presence of Sema3G attenuated their expression through the inhibition of lipopolysaccharide-induced Toll like receptor 4 signaling. Taken together, our results surmise that the Sema3G protein is secreted by podocytes and protects podocytes from inflammatory kidney diseases and diabetic nephropathy. PMID:27180624

  4. A novel podocyte gene, semaphorin 3G, protects glomerular podocyte from lipopolysaccharide-induced inflammation.

    PubMed

    Ishibashi, Ryoichi; Takemoto, Minoru; Akimoto, Yoshihiro; Ishikawa, Takahiro; He, Peng; Maezawa, Yoshiro; Sakamoto, Kenichi; Tsurutani, Yuya; Ide, Shintaro; Ide, Kana; Kawamura, Harukiyo; Kobayashi, Kazuki; Tokuyama, Hirotake; Tryggvason, Karl; Betsholtz, Christer; Yokote, Koutaro

    2016-01-01

    Kidney diseases including diabetic nephropathy have become huge medical problems, although its precise mechanisms are still far from understood. In order to increase our knowledge about the patho-physiology of kidney, we have previously identified >300 kidney glomerulus-enriched transcripts through large-scale sequencing and microarray profiling of the mouse glomerular transcriptome. One of the glomerulus-specific transcripts identified was semaphorin 3G (Sema3G) which belongs to the semaphorin family. The aim of this study was to analyze both the in vivo and in vitro functions of Sema3G in the kidney. Sema3G was expressed in glomerular podocytes. Although Sema3G knockout mice did not show obvious glomerular defects, ultrastructural analyses revealed partially aberrant podocyte foot processes structures. When these mice were injected with lipopolysaccharide to induce acute inflammation or streptozotocin to induce diabetes, the lack of Sema3G resulted in increased albuminuria. The lack of Sema3G in podocytes also enhanced the expression of inflammatory cytokines including chemokine ligand 2 and interleukin 6. On the other hand, the presence of Sema3G attenuated their expression through the inhibition of lipopolysaccharide-induced Toll like receptor 4 signaling. Taken together, our results surmise that the Sema3G protein is secreted by podocytes and protects podocytes from inflammatory kidney diseases and diabetic nephropathy. PMID:27180624

  5. APOBEC3G Interacts with ssDNA by Two Modes: AFM Studies

    NASA Astrophysics Data System (ADS)

    Shlyakhtenko, Luda S.; Dutta, Samrat; Banga, Jaspreet; Li, Ming; Harris, Reuben S.; Lyubchenko, Yuri L.

    2015-10-01

    APOBEC3G (A3G) protein has antiviral activity against HIV and other pathogenic retroviruses. A3G has two domains: a catalytic C-terminal domain (CTD) that deaminates cytidine, and a N-terminal domain (NTD) that binds to ssDNA. Although abundant information exists about the biological activities of A3G protein, the interplay between sequence specific deaminase activity and A3G binding to ssDNA remains controversial. We used the topographic imaging and force spectroscopy modalities of Atomic Force Spectroscopy (AFM) to characterize the interaction of A3G protein with deaminase specific and nonspecific ssDNA substrates. AFM imaging demonstrated that A3G has elevated affinity for deaminase specific ssDNA than for nonspecific ssDNA. AFM force spectroscopy revealed two distinct binding modes by which A3G interacts with ssDNA. One mode requires sequence specificity, as demonstrated by stronger and more stable complexes with deaminase specific ssDNA than with nonspecific ssDNA. Overall these observations enforce prior studies suggesting that both domains of A3G contribute to the sequence specific binding of ssDNA.

  6. Stoichiometry of the antiviral protein APOBEC3G in HIV-1 virions.

    PubMed

    Xu, Hongzhan; Chertova, Elena; Chen, Jianbo; Ott, David E; Roser, James D; Hu, Wei-Shau; Pathak, Vinay K

    2007-04-10

    A host cytidine deaminase, APOBEC3G (A3G), inhibits replication of human immunodeficiency virus type 1 (HIV-1) by incorporating into virions in the absence of the virally encoded Vif protein (Deltavif virions), at least in part by causing G-to-A hypermutation. To gain insight into the antiretroviral function of A3G, we determined the quantities of A3G molecules that are incorporated in Deltavif virions. We combined three experimental approaches-reversed-phase high-pressure liquid chromatography (HPLC), scintillation proximity assay (SPA), and quantitative immunoblotting-to determine the molar ratio of A3G to HIV-1 capsid protein in Deltavif virions. Our studies revealed that the amount of the A3G incorporated into Deltavif virions was proportional to the level of its expression in the viral producing cells, and the ratio of the A3G to Gag in the Deltavif virions produced from activated human peripheral blood mononuclear cells (PBMC) was approximately 1:439. Based on previous estimates of the stoichiometry of HIV-1 Gag in virions (1400-5000), we conclude that approximately 7 (+/-4) molecules of A3G are incorporated into Deltavif virions produced from human PBMCs. These results indicate that virion incorporation of only a few molecules of A3G is sufficient to inhibit HIV-1 replication. PMID:17126871

  7. Irregular Cellular Learning Automata.

    PubMed

    Esnaashari, Mehdi; Meybodi, Mohammad Reza

    2015-08-01

    Cellular learning automaton (CLA) is a recently introduced model that combines cellular automaton (CA) and learning automaton (LA). The basic idea of CLA is to use LA to adjust the state transition probability of stochastic CA. This model has been used to solve problems in areas such as channel assignment in cellular networks, call admission control, image processing, and very large scale integration placement. In this paper, an extension of CLA called irregular CLA (ICLA) is introduced. This extension is obtained by removing the structure regularity assumption in CLA. Irregularity in the structure of ICLA is needed in some applications, such as computer networks, web mining, and grid computing. The concept of expediency has been introduced for ICLA and then, conditions under which an ICLA becomes expedient are analytically found. PMID:25291810

  8. APOBEC3G ubiquitination by Nedd4-1 favors its packaging into HIV-1 particles.

    PubMed

    Dussart, Sylvie; Douaisi, Marc; Courcoul, Marianne; Bessou, Gilles; Vigne, Robert; Decroly, Etienne

    2005-01-21

    APOBEC3G is a cytidine deaminase that limits the replication of many retroviruses. This antiviral host factor is packaged into retrovirus particles, where it targets single-stranded DNA generated during reverse transcription and induces up to 2% of G-to-A mutations, which are lethal for the HIV-1 provirus. Vif protein counteracts this antiviral factor by decreasing its packaging into lentivirus particles. Here, we demonstrate that Nedd4-1, an HECT E3 ubiquitin ligase, interacts with APOBEC3G, through its WW2 and WW3 domains. As a result of this interaction, APOBEC3G undergoes post-translational modification by addition of ubiquitin moieties. Accordingly, we demonstrate that the dominant negative Nedd4-1 C/S form prevents APOBEC3G ubiquitination. Moreover, the packaging of APOBEC3G into Pr55 Gag virus-like particles and into HIV-1 virions is reduced when Nedd4-1 C/S is expressed. During HIV-1 viral production in the presence of APOBEC3G, Nedd4-1 C/S restores partially the infectivity of Deltavif HIV-1. We conclude that the ubiquitination of APOBEC3G by Nedd4-1 favors its targeting to the virus assembly site where APOBEC3G interacts with Gag and is packaged into HIV-1 particles in the absence of Vif. PMID:15581898

  9. APOBEC3G has the ability to programme T cell plasticity.

    PubMed

    Garg, Anuradha; Kaul, Deepak

    2016-07-01

    Recently Apolipoprotein B mRNA editing enzyme, Catalytic Polypeptide-like 3G (APOBEC3G) biology has assumed importance because of its role in oncogenesis. In this context, the present study was addressed to understand the immune-modulatory role of APOBEC3G through its effect upon the T-cell plasticity phenomenon. Such an attempt revealed that APOBEC3G has the inherent capacity to regulate genes coding for STAT3, NF-κB, CCL5, IL-6, IL-4, IFN-γ, IL-10 and IL-17 coupled with downregulation of Treg cells within human peripheral blood mononuclear cells (PBMCs) without any noticeable influence upon CD4(+) and CD8(+) cell number. On the basis of these findings, we propose that APOBEC3G has the ability to induce T cell plasticity and modulate immune response. PMID:27282578

  10. Atomic Force Microscopy Studies of APOBEC3G Oligomerization and Dynamics

    PubMed Central

    Shlyakhtenko, Luda S.; Lushnikov, Alexander Y.; Miyagi, Atsushi; Li, Ming; Harris, Reuben S.; Lyubchenko, Yuri L.

    2013-01-01

    The DNA cytosine deaminase APOBEC3G (A3G) is a two-domain protein that binds single-stranded DNA (ssDNA) largely through its N-terminal domain and catalyzes deamination using its C-terminal domain. A3G is considered an innate immune effector protein, with a natural capacity to block the replication of retroviruses such as HIV and retrotransposons. However, knowledge about its biophysical properties and mechanism of interaction with DNA are still limited. Oligomerization is one of these unclear issues. What is the stoichiometry of the free protein? What are the factors defining the oligomeric state of the protein? How does the protein oligomerization change upon DNA binding? How stable are protein oligomers? We address these questions here using atomic force microscopy (AFM) to directly image A3G protein in a free-state and in complexes with DNA, and using time-lapse AFM imaging to characterize the dynamics of A3G oligomers. We found that the formation of oligomers is an inherent property of A3G and that the yield of oligomers depends on the protein concentration. Oligomerization of A3G in complexes with ssDNA follows a similar pattern: the higher the protein concentrations the larger oligomers sizes. The specificity of A3G binding to ssDNA does not depend on stoichiometry. The binding of large A3G oligomers requires a longer ssDNA substrate; therefore, much smaller oligomers form complexes with short ssDNA. A3G oligomers dissociate spontaneously into monomers and this process primarily occurs through a monomer dissociation pathway. PMID:24055458

  11. Review of quantitative phase-digital holographic microscopy: promising novel imaging technique to resolve neuronal network activity and identify cellular biomarkers of psychiatric disorders

    PubMed Central

    Marquet, Pierre; Depeursinge, Christian; Magistretti, Pierre J.

    2014-01-01

    Abstract. Quantitative phase microscopy (QPM) has recently emerged as a new powerful quantitative imaging technique well suited to noninvasively explore a transparent specimen with a nanometric axial sensitivity. In this review, we expose the recent developments of quantitative phase-digital holographic microscopy (QP-DHM). Quantitative phase-digital holographic microscopy (QP-DHM) represents an important and efficient quantitative phase method to explore cell structure and dynamics. In a second part, the most relevant QPM applications in the field of cell biology are summarized. A particular emphasis is placed on the original biological information, which can be derived from the quantitative phase signal. In a third part, recent applications obtained, with QP-DHM in the field of cellular neuroscience, namely the possibility to optically resolve neuronal network activity and spine dynamics, are presented. Furthermore, potential applications of QPM related to psychiatry through the identification of new and original cell biomarkers that, when combined with a range of other biomarkers, could significantly contribute to the determination of high risk developmental trajectories for psychiatric disorders, are discussed. PMID:26157976

  12. Image processing with cellular nonlinear networks implemented on field-programmable gate arrays for real-time applications in nuclear fusion

    SciTech Connect

    Palazzo, S.; Vagliasindi, G.; Arena, P.; Murari, A.; Mazon, D.; De Maack, A.; Collaboration: JET-EFDA Contributors

    2010-08-15

    In the past years cameras have become increasingly common tools in scientific applications. They are now quite systematically used in magnetic confinement fusion, to the point that infrared imaging is starting to be used systematically for real-time machine protection in major devices. However, in order to guarantee that the control system can always react rapidly in case of critical situations, the time required for the processing of the images must be as predictable as possible. The approach described in this paper combines the new computational paradigm of cellular nonlinear networks (CNNs) with field-programmable gate arrays and has been tested in an application for the detection of hot spots on the plasma facing components in JET. The developed system is able to perform real-time hot spot recognition, by processing the image stream captured by JET wide angle infrared camera, with the guarantee that computational time is constant and deterministic. The statistical results obtained from a quite extensive set of examples show that this solution approximates very well an ad hoc serial software algorithm, with no false or missed alarms and an almost perfect overlapping of alarm intervals. The computational time can be reduced to a millisecond time scale for 8 bit 496x560-sized images. Moreover, in our implementation, the computational time, besides being deterministic, is practically independent of the number of iterations performed by the CNN - unlike software CNN implementations.

  13. Conformational distribution of baclofen analogues by 1H and 13C NMR analysis and ab initio HF MO STO-3G or STO-3G* calculations

    NASA Astrophysics Data System (ADS)

    Vaccher, Claude; Berthelot, Pascal; Debaert, Michel; Vermeersch, Gaston; Guyon, René; Pirard, Bernard; Vercauteren, Daniel P.; Dory, Magdalena; Evrard, Guy; Durant, François

    1993-12-01

    The conformations of 3-(substituted furan-2-yl) and 3-(substituted thien-2-yl)-γ-aminobutyric acid 1-9 in solution (D 2O) are estimated from high-resolution (300 MHz) 1H NMR coupling data. Conformations and populations of conformers are calculated by means of a modified Karplus-like relationship for the vicinal coupling constants. The results are compared with X-ray crystallographic investigations (torsion angles) and ab initio HF MO ST-3G or STO-3G* calculations. 1H NMR spectral analysis shows how 1-9 in solution retain the preferred g- conformation around the C3C4 bond, as found in the solid state, while a partial rotation is set up around the C2C3 bond: the conformations about C2C3 are all highly populated in solution. The 13C spin-lattice relaxation times are also discussed.

  14. Exposure assessment of one-year-old child to 3G tablet in uplink mode and to 3G femtocell in downlink mode using polynomial chaos decomposition

    NASA Astrophysics Data System (ADS)

    Liorni, I.; Parazzini, M.; Varsier, N.; Hadjem, A.; Ravazzani, P.; Wiart, J.

    2016-04-01

    So far, the assessment of the exposure of children, in the ages 0-2 years old, to relatively new radio-frequency (RF) technologies, such as tablets and femtocells, remains an open issue. This study aims to analyse the exposure of a one year-old child to these two sources, tablets and femtocells, operating in uplink (tablet) and downlink (femtocell) modes, respectively. In detail, a realistic model of an infant has been used to model separately the exposures due to (i) a 3G tablet emitting at the frequency of 1940 MHz (uplink mode) placed close to the body and (ii) a 3G femtocell emitting at 2100 MHz (downlink mode) placed at a distance of at least 1 m from the infant body. For both RF sources, the input power was set to 250 mW. The variability of the exposure due to the variation of the position of the RF sources with respect to the infant body has been studied by stochastic dosimetry, based on polynomial chaos to build surrogate models of both whole-body and tissue specific absorption rate (SAR), which makes it easy and quick to investigate the exposure in a full range of possible positions of the sources. The major outcomes of the study are: (1) the maximum values of the whole-body SAR (WB SAR) have been found to be 9.5 mW kg-1 in uplink mode and 65 μW kg-1 in downlink mode, i.e. within the limits of the ICNIRP 1998 Guidelines; (2) in both uplink and downlink mode the highest SAR values were approximately found in the same tissues, i.e. in the skin, eye and penis for the whole-tissue SAR and in the bone, skin and muscle for the peak SAR; (3) the change in the position of both the 3G tablet and the 3G femtocell significantly influences the infant exposure.

  15. Exposure assessment of one-year-old child to 3G tablet in uplink mode and to 3G femtocell in downlink mode using polynomial chaos decomposition.

    PubMed

    Liorni, I; Parazzini, M; Varsier, N; Hadjem, A; Ravazzani, P; Wiart, J

    2016-04-21

    So far, the assessment of the exposure of children, in the ages 0-2 years old, to relatively new radio-frequency (RF) technologies, such as tablets and femtocells, remains an open issue. This study aims to analyse the exposure of a one year-old child to these two sources, tablets and femtocells, operating in uplink (tablet) and downlink (femtocell) modes, respectively. In detail, a realistic model of an infant has been used to model separately the exposures due to (i) a 3G tablet emitting at the frequency of 1940 MHz (uplink mode) placed close to the body and (ii) a 3G femtocell emitting at 2100 MHz (downlink mode) placed at a distance of at least 1 m from the infant body. For both RF sources, the input power was set to 250 mW. The variability of the exposure due to the variation of the position of the RF sources with respect to the infant body has been studied by stochastic dosimetry, based on polynomial chaos to build surrogate models of both whole-body and tissue specific absorption rate (SAR), which makes it easy and quick to investigate the exposure in a full range of possible positions of the sources. The major outcomes of the study are: (1) the maximum values of the whole-body SAR (WB SAR) have been found to be 9.5 mW kg(-1) in uplink mode and 65 μW kg(-1) in downlink mode, i.e. within the limits of the ICNIRP 1998 Guidelines; (2) in both uplink and downlink mode the highest SAR values were approximately found in the same tissues, i.e. in the skin, eye and penis for the whole-tissue SAR and in the bone, skin and muscle for the peak SAR; (3) the change in the position of both the 3G tablet and the 3G femtocell significantly influences the infant exposure. PMID:27027265

  16. At3g08030 transcript: a molecular marker of seed ageing

    PubMed Central

    Garza-Caligaris, Luz Elena; Avendaño-Vázquez, Aida Odette; Alvarado-López, Sandra; Zúñiga-Sánchez, Esther; Orozco-Segovia, Alma; Pérez-Ruíz, Rigoberto V.; Gamboa-deBuen, Alicia

    2012-01-01

    Background and Aims Prolonged storage generally reduces seed viability and vigour, although the rate of deterioration varies among species and environmental conditions. Here, we suggest a possible ageing molecular marker: At3g08030 mRNA. At3g08030 is a member of the DUF642 highly conserved family of cell-wall-associated proteins that is specific for spermatophytes. Methods At3g08030 expression was performed by RT-PCR and qRT-PCR analysis in seed samples differing in their rate of germination and final germination following a matrix priming and/or controlled deterioration (rapid ageing) treatment. Key Results The At3g08030 gene transcript was present during the entire Arabidopsis thaliana plant life cycle and in seeds, during maturation, the ripening period and after germination. Matrix priming treatment increased the rate of germination of control seeds and seeds aged by controlled deterioration. Priming treatments also increased At3g08030 expression. To determine whether the orthologues of this gene are also age markers in other plant species, At3g08030 was cloned in two wild species, Ceiba aesculifolia and Wigandia urens. As in A. thaliana, the At3g08030 transcript was not present in aged seeds of the tested species but was present in recently shed seeds. A reduction in germination performance of the aged seeds under salt stress was determined by germination assays. Conclusions At3g08030 mRNA detection in a dry seed lot has potential for use as a molecular marker for germination performance in a variety of plant species. PMID:22975286

  17. Cellular Homeostasis and Aging.

    PubMed

    Hartl, F Ulrich

    2016-06-01

    Aging and longevity are controlled by a multiplicity of molecular and cellular signaling events that interface with environmental factors to maintain cellular homeostasis. Modulation of these pathways to extend life span, including insulin-like signaling and the response to dietary restriction, identified the cellular machineries and networks of protein homeostasis (proteostasis) and stress resistance pathways as critical players in the aging process. A decline of proteostasis capacity during aging leads to dysfunction of specific cell types and tissues, rendering the organism susceptible to a range of chronic diseases. This volume of the Annual Review of Biochemistry contains a set of two reviews addressing our current understanding of the molecular mechanisms underlying aging in model organisms and humans. PMID:27050288

  18. Oral immunization of mice with recombinant rabies vaccine strain (ERAG3G) induces complete protection

    PubMed Central

    2015-01-01

    Purpose New rabies vaccine bait for both pets and raccoon dogs residing in Korea is needed to eradicate rabies infection among animals. In this study, we constructed a recombinant rabies virus (RABV), the ERAG3G strain, using a reverse genetics system. Then we investigated the efficacy of this strain in mice after oral administration and the safety of this strain in cats after intramuscular administration. Materials and Methods The ERAG3G strain was rescued in BHK/T7-9 cells using the full-length genome mutated at the amino acid position 333 of the glycoprotein gene of RABV and helper plasmids. Four-week-old mice underwent one or two oral administrations of the ERAG3G strain and were challenged with the highly virulent RABV strain CVSN2c 14 days after the second administration. Clinical symptoms were observed and body weights were measured every day after the challenge. Results All mice showed complete protection against virulent RABV. In addition, cats intramuscularly inoculated with the ERAG3G strain showed high antibody titers ranging from 2.62 to 23.9 IU/mL at 28-day postinoculation. Conclusion The oral immunization of the ERAG3G strain plays an important role in conferring complete protection in mice, and intramuscular inoculation of the ERAG3G strain induces the formation of anti-rabies neutralizing antibody in cats. PMID:25648184

  19. Different Modes of Retrovirus Restriction by Human APOBEC3A and APOBEC3G In Vivo

    PubMed Central

    Stavrou, Spyridon; Crawford, Daniel; Blouch, Kristin; Browne, Edward P.; Kohli, Rahul M.; Ross, Susan R.

    2014-01-01

    The apolipoprotein B editing complex 3 (A3) cytidine deaminases are among the most highly evolutionarily selected retroviral restriction factors, both in terms of gene copy number and sequence diversity. Primate genomes encode seven A3 genes, and while A3F and 3G are widely recognized as important in the restriction of HIV, the role of the other genes, particularly A3A, is not as clear. Indeed, since human cells can express multiple A3 genes, and because of the lack of an experimentally tractable model, it is difficult to dissect the individual contribution of each gene to virus restriction in vivo. To overcome this problem, we generated human A3A and A3G transgenic mice on a mouse A3 knockout background. Using these mice, we demonstrate that both A3A and A3G restrict infection by murine retroviruses but by different mechanisms: A3G was packaged into virions and caused extensive deamination of the retrovirus genomes while A3A was not packaged and instead restricted infection when expressed in target cells. Additionally, we show that a murine leukemia virus engineered to express HIV Vif overcame the A3G-mediated restriction, thereby creating a novel model for studying the interaction between these proteins. We have thus developed an in vivo system for understanding how human A3 proteins use different modes of restriction, as well as a means for testing therapies that disrupt HIV Vif-A3G interactions. PMID:24851906

  20. Modified SNOW 3G: Stream cipher algorithm using piecewise linear chaotic map

    NASA Astrophysics Data System (ADS)

    Wasi, Muhammad Arif Ali; Windarta, Susila

    2016-02-01

    SNOW 3G is a synchronous stream cipher developed by Thomas Johansson and Patrik Ekhdal at Lund University. In 2006, it was chosen as the main part of the second set of Universal Mobile Telecommunications System (UMTS) confidentiality and integrity algorithms [2]. In 2008, Patrik Böhm published a report entitled "Statistical Evaluation of Stream Cipher SNOW 3G". He tested the randomness properties of SNOW 3G key stream generator. Böhm using NIST statistical test suite as randomness test tool with three kinds of test, i.e. long key stream data set, short key stream data set, and initialization vector data set. The result of the report shows that from three kind of tests, only short key stream data set has not passed eight randomness tests. He state that the suggests SNOW 3G fail because there is a weakness in the initialization of the cipher. In this paper we modify SNOW 3G algorithm using piecewise linear chaotic map (PLCM) on the key initialization mode and keystream generation mode. We use the same statistical test that have been used by Böhm [5]. The experiment shows that modified SNOW 3G stream cipher algorithm has passed all the statistical test. The results prove that PLCM impact on algorithm's randomness.

  1. Crystal structure of the anti-viral APOBEC3G catalytic domain and functional implications

    SciTech Connect

    Holden, Lauren G.; Prochnow, Courtney; Chang, Y. Paul; Bransteitter, Ronda; Chelico, Linda; Sen, Udayaditya; Stevens, Raymond C.; Goodman, Myron F.; Chen, Xiaojiang S.

    2009-04-07

    The APOBEC family members are involved in diverse biological functions. APOBEC3G restricts the replication of human immunodeficiency virus (HIV), hepatitis B virus and retroelements by cytidine deamination on single-stranded DNA or by RNA binding. Here we report the high-resolution crystal structure of the carboxy-terminal deaminase domain of APOBEC3G (APOBEC3G-CD2) purified from Escherichia coli. The APOBEC3G-CD2 structure has a five-stranded {beta}-sheet core that is common to all known deaminase structures and closely resembles the structure of another APOBEC protein, APOBEC2. A comparison of APOBEC3G-CD2 with other deaminase structures shows a structural conservation of the active-site loops that are directly involved in substrate binding. In the X-ray structure, these APOBEC3G active-site loops form a continuous 'substrate groove' around the active centre. The orientation of this putative substrate groove differs markedly (by 90 degrees) from the groove predicted by the NMR structure. We have introduced mutations around the groove, and have identified residues involved in substrate specificity, single-stranded DNA binding and deaminase activity. These results provide a basis for understanding the underlying mechanisms of substrate specificity for the APOBEC family.

  2. Human APOBEC3G drives HIV-1 evolution and the development of drug resistance

    SciTech Connect

    Bhattacharya, Tamoy; Kim, Eun - Young; Koning, Fransje; Malim, Michael; Wolinsky, Steven M

    2008-01-01

    Human APOBEC3G (hA3G) is an innate virus restriction factor that induces deamination of specific cytidine residues in single-stranded human immunodeficiency virus type 1 (HIV-1) DNA. Whereas destructive hA3G editing leads to a profound loss of HIV-1 infectivity, more limited editing could be a source of adaptation and diversification. Here we show that the presence of hA3G in T-cells can drive the development of diversity in HIV-1 populations and that under selection pressure imposed by the nucleotide analog reverse transcriptase inhibitor 3TC ((-)2',3'-dideoxy-3'-thiacytidine), a single point mutation that confers 3TC resistance, methionine 184 to isoleucine (M1841), emerges rapidly and reaches fixation. These results provide strong evidence that mutation by hA3G is an important source of genetic variation on which natural selection acts to shape the structure of the viral population and drive the tempo of HIV-1 evolution.

  3. Gene duplication and neofunctionalization: POLR3G and POLR3GL

    PubMed Central

    Renaud, Marianne; Praz, Viviane; Vieu, Erwann; Florens, Laurence; Washburn, Michael P.; l'Hôte, Philippe; Hernandez, Nouria

    2014-01-01

    RNA polymerase III (Pol III) occurs in two versions, one containing the POLR3G subunit and the other the closely related POLR3GL subunit. It is not clear whether these two Pol III forms have the same function, in particular whether they recognize the same target genes. We show that the POLR3G and POLR3GL genes arose from a DNA-based gene duplication, probably in a common ancestor of vertebrates. POLR3G- as well as POLR3GL-containing Pol III are present in cultured cell lines and in normal mouse liver, although the relative amounts of the two forms vary, with the POLR3G-containing Pol III relatively more abundant in dividing cells. Genome-wide chromatin immunoprecipitations followed by high-throughput sequencing (ChIP-seq) reveal that both forms of Pol III occupy the same target genes, in very constant proportions within one cell line, suggesting that the two forms of Pol III have a similar function with regard to specificity for target genes. In contrast, the POLR3G promoter—not the POLR3GL promoter—binds the transcription factor MYC, as do all other promoters of genes encoding Pol III subunits. Thus, the POLR3G/POLR3GL duplication did not lead to neo-functionalization of the gene product (at least with regard to target gene specificity) but rather to neo-functionalization of the transcription units, which acquired different mechanisms of regulation, thus likely affording greater regulation potential to the cell. PMID:24107381

  4. In utero and lactational dioxin exposure induces Sema3b and Sema3g gene expression in the developing mouse brain.

    PubMed

    Kimura, Eiki; Endo, Toshihiro; Yoshioka, Wataru; Ding, Yunjie; Ujita, Waka; Kakeyama, Masaki; Tohyama, Chiharu

    2016-07-22

    In the developing mammalian brain, neural network formation is regulated by complex signaling cascades. In utero and lactational dioxin exposure is known to induce higher brain function abnormalities and dendritic growth disruption in rodents. However, it is unclear whether perinatal dioxin exposure affects the expression of genes involved in neural network formation. Therefore, we investigated changes in gene expression in the brain regions of developing mice born to dams administered 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD; dose: 0, 0.6, or 3.0 μg/kg) on gestational day 12.5. Quantitative RT-PCR showed that TCDD exposure induced Ahrr expression in the cerebral cortex, hippocampus, and olfactory bulb of 3-day-old mice. Gene microarray analysis indicated that the mRNA expression levels of Sema3b and Sema3g, which encode proteins that are known to control axonal projections, were elevated in the olfactory bulb of TCDD-exposed mice, and the induction of these genes was observed during a 2-week postnatal period. Increased Sema3g expression was also observed in the brain but not in the kidney, liver, lung, and spleen of TCDD-exposed neonatal mice. These results indicate that the Sema3b and Sema3g genes are sensitive to brain-specific induction by dioxin exposure, which may disrupt neural network formation in the mammalian nervous system, thereby leading to abnormal higher brain function in adulthood. PMID:27178212

  5. 28 CFR 5.306 - Exemption under section 3(g) of the Act.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 28 Judicial Administration 1 2010-07-01 2010-07-01 false Exemption under section 3(g) of the Act. 5.306 Section 5.306 Judicial Administration DEPARTMENT OF JUSTICE ADMINISTRATION AND ENFORCEMENT OF... officials other than in the course of judicial proceedings, criminal or civil law enforcement...

  6. Crystal Structure of the APOBEC3G Catalytic Domain Reveals Potential Oligomerization Interfaces

    SciTech Connect

    Shandilya, Shivender M.D.; Nalam, Madhavi N.L.; Nalivaika, Ellen A.; Gross, Phillip J.; Valesano, Johnathan C.; Shindo, Keisuke; Li, Ming; Munson, Mary; Royer, William E.; Harjes, Elena; Kono, Takahide; Matsuo, Hiroshi; Harris, Reuben S.; Somasundaran, Mohan; Schiffer, Celia A.

    2010-02-11

    APOBEC3G is a DNA cytidine deaminase that has antiviral activity against HIV-1 and other pathogenic viruses. In this study the crystal structure of the catalytically active C-terminal domain was determined to 2.25 {angstrom}. This structure corroborates features previously observed in nuclear magnetic resonance (NMR) studies, a bulge in the second {beta} strand and a lengthening of the second {alpha} helix. Oligomerization is postulated to be critical for the function of APOBEC3G. In this structure, four extensive intermolecular interfaces are observed, suggesting potential models for APOBEC3G oligomerization. The structural and functional significance of these interfaces was probed by solution NMR and disruptive variants were designed and tested for DNA deaminase and anti-HIV activities. The variant designed to disrupt the most extensive interface lost both activities. NMR solution data provides evidence that another interface, which coordinates a novel zinc site, also exists. Thus, the observed crystallographic interfaces of APOBEC3G may be important for both oligomerization and function.

  7. 78 FR 42107 - Certain Wireless Devices With 3G Capabilities and Components Thereof; Notice of Request for...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-07-15

    ... From the Federal Register Online via the Government Publishing Office INTERNATIONAL TRADE COMMISSION Certain Wireless Devices With 3G Capabilities and Components Thereof; Notice of Request for... certain wireless devices with 3G capabilities and components thereof imported by respondents...

  8. 78 FR 8191 - Certain Wireless Devices With 3G and/or 4G Capabilities and Components Thereof; Institution of...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-02-05

    ... COMMISSION Certain Wireless Devices With 3G and/or 4G Capabilities and Components Thereof; Institution of... certain wireless devices with 3G and/or 4G capabilities and components thereof by reason of infringement... wireless devices with 3G and/or 4G capabilities and components thereof by reason of infringement of one...

  9. 76 FR 54252 - In the Matter of Certain Wireless Devices With 3G Capabilities and Components Thereof; Notice of...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-08-31

    ... COMMISSION In the Matter of Certain Wireless Devices With 3G Capabilities and Components Thereof; Notice of... importation, and the sale within the United States after importation of certain wireless devices with 3G... after ] importation of certain wireless devices with 3G capabilities and components thereof...

  10. HIV-1 Adapts To Replicate in Cells Expressing Common Marmoset APOBEC3G and BST2

    PubMed Central

    Fernández-Oliva, Alberto; Finzi, Andrés; Haim, Hillel; Menéndez-Arias, Luis; Sodroski, Joseph

    2015-01-01

    ABSTRACT Previous studies have shown that a major block to HIV-1 replication in common marmosets operates at the level of viral entry and that this block can be overcome by adaptation of the virus in tissue-cultured cells. However, our current studies indicate that HIV-1 encounters additional postentry blocks in common marmoset peripheral blood mononuclear cells. Here, we show that the common marmoset APOBEC3G (A3G) and BST2 proteins block HIV-1 in cell cultures. Using a directed-evolution method that takes advantage of the natural ability of HIV-1 to mutate during replication, we have been able to overcome these blocks in tissue-cultured cells. In the adapted viruses, specific changes were observed in gag, vif, env, and nef. The contribution of these changes to virus replication in the presence of the A3G and BST2 restriction factors was studied. We found that certain amino acid changes in Vif and Env that arise during adaptation to marmoset A3G and BST2 allow the virus to replicate in the presence of these restriction factors. The changes in Vif reduce expression levels and encapsidation of marmoset APOBEC3G, while the changes in Env increase viral fitness and discretely favor cell-to-cell transmission of the virus, allowing viral escape from these restriction factors. IMPORTANCE HIV-1 can infect only humans and chimpanzees. The main reason for this narrow tropism is the presence in many species of dominant-acting factors, known as restriction factors, that block viral replication in a species-specific way. We have been exploring the blocks to HIV-1 in common marmosets, with the ultimate goal of developing a new animal model of HIV-1 infection in these monkeys. In this study, we observed that common marmoset APOBEC3G and BST2, two known restriction factors, are able to block HIV-1 in cell cultures. We have adapted HIV-1 to replicate in the presence of these restriction factors and have characterized the mechanisms of escape. These studies can help in the

  11. Reg3g overexpression promotes β cell regeneration and induces immune tolerance in nonobese-diabetic mouse model.

    PubMed

    Xia, Fei; Cao, Hui; Du, Jiao; Liu, Xiulan; Liu, Yang; Xiang, Ming

    2016-06-01

    The regenerating islet-derived gene was first isolated in regenerated pancreas tissues, greatly contributing to β cell regeneration. It is an anti-inflammatory in response to cellular stress. This encouraged us to investigate the exact role of a novel member of Reg family, regenerating islet-derived gene γ, in type 1 diabetes of nonobese-diabetic mice. For this, Reg3g gene was overexpressed in pancreatic islets, and conferred beneficial effects on β cell regeneration through activating the Janus kinase 2/signal transducer and activator of transcription 3/nuclear factor κB signaling pathway. Lentiviral vector-encoding regenerating islet-derived gene γ treatment also decreased lymphocyte infiltrates of the intra-islet and peri-islet by inducing both differentiation of regulatory T cell and immature dendritic cells of tolerogenic properties, which attenuated autoimmunity. This treatment further contributed to rebalanced levels of type 1/2 helper T cell cytokines and elevated α1-antitrypsin levels in the serum. These results were not observed in phosphate-buffered saline-treated mice or in lentivirus-control mice. We have shown, for the first time, to our knowledge, that regenerating islet-derived gene γ promotes β cell regeneration and preserves β cells from autoimmunity damage by increasing regulatory T cell differentiation and inducing tolerated dendritic cells. This regenerating islet-derived gene γ infusion could probably be developed into an optimal gene therapy for the prevention and reversal of type 1 diabetes. PMID:26667474

  12. APOBEC3G Variants and Protection against HIV-1 Infection in Burkina Faso.

    PubMed

    Compaore, Tegwinde Rebeca; Soubeiga, Serge Theophile; Ouattara, Abdoul Karim; Obiri-Yeboah, Dorcas; Tchelougou, Damehan; Maiga, Mamoudou; Assih, Maleki; Bisseye, Cyrille; Bakouan, Didier; Compaore, Issaka Pierre; Dembele, Augustine; Martinson, Jeremy; Simpore, Jacques

    2016-01-01

    Studies on host factors, particularly the APOBEC3G gene, have previously found an association with AIDS progression in some populations and against some HIV-1 strains but not others. Our study had two main objectives: firstly, to screen a population from Burkina Faso for three variants of APOBEC3G previously described, and secondly to analyze the effect of these three variants and their haplotypes on HIV-1 infection with Circulating Recombinant Forms (CRFs) present in Burkina Faso. This case control study involved 708 seropositive and seronegative individuals. Genotyping was done by the TaqMan allelic discrimination method. Minor allele frequencies of rs6001417 (p<0.05), rs8177832 (P<0.05), and rs35228531 (P<0.001) were higher in seronegative subjects. The rs6001417 and rs8177832 SNPs were associated with HIV-1 infection in an additive model (P<0.01). Furthermore the SNP rs35228531 was also associated with HIV-1 infection in a dominant model (P<0.001). Odds ratio analysis of genotypes and alleles of the different APOBEC3G variants showed that there is a strong association between the minor genetic variants, genotype of the three SNPs, and HIV-1 status. Haplotype analysis demonstrated that rs6001417, rs8177832, and rs35228531 are in linkage disequilibrium. The haplotype GGT from the rs6001417, rs8177832 and rs35228531 respectively has a protective effect OR = 0.54 [0.43-0.68] with P<0.001. There was also associations between the haplotypes GGC OR = 1.6 [1.1;-2.3] P<0.05, and CGC OR = 5.21 [2.4-11.3] P<0.001, which increase the risk of infection by HIV-1 from almost two (2) to five (5) fold. This study demonstrates an association of rs6001417, rs8177832, and rs35228531 of APOBEC3G with HIV-1 infection in a population from Burkina Faso. PMID:26741797

  13. Preliminary Analysis of the efficacy of Artificial neural Network (ANN) and Cellular Automaton (CA) based Land Use Models in Urban Land-Use Planning

    NASA Astrophysics Data System (ADS)

    Harun, R.

    2013-05-01

    This research provides an opportunity of collaboration between urban planners and modellers by providing a clear theoretical foundations on the two most widely used urban land use models, and assessing the effectiveness of applying the models in urban planning context. Understanding urban land cover change is an essential element for sustainable urban development as it affects ecological functioning in urban ecosystem. Rapid urbanization due to growing inclination of people to settle in urban areas has increased the complexities in predicting that at what shape and size cities will grow. The dynamic changes in the spatial pattern of urban landscapes has exposed the policy makers and environmental scientists to great challenge. But geographic science has grown in symmetry to the advancements in computer science. Models and tools are developed to support urban planning by analyzing the causes and consequences of land use changes and project the future. Of all the different types of land use models available in recent days, it has been found by researchers that the most frequently used models are Cellular Automaton (CA) and Artificial Neural Networks (ANN) models. But studies have demonstrated that the existing land use models have not been able to meet the needs of planners and policy makers. There are two primary causes identified behind this prologue. First, there is inadequate understanding of the fundamental theories and application of the models in urban planning context i.e., there is a gap in communication between modellers and urban planners. Second, the existing models exclude many key drivers in the process of simplification of the complex urban system that guide urban spatial pattern. Thus the models end up being effective in assessing the impacts of certain land use policies, but cannot contribute in new policy formulation. This paper is an attempt to increase the knowledge base of planners on the most frequently used land use model and also assess the

  14. Ubiquitin-fusion as a strategy to modulate protein half-life: A3G antiviral activity revisited

    SciTech Connect

    Cadima-Couto, Iris; Freitas-Vieira, Acilino; Nowarski, Roni; Britan-Rosich, Elena; Kotler, Moshe; Goncalves, Joao

    2009-10-25

    The human APOBEC3G (A3G) is a potent inhibitor of HIV-1 replication and its activity is suppressed by HIV-1 virion infectivity factor (Vif). Vif neutralizes A3G mainly by inducing its degradation in the proteasome and blocking its incorporation into HIV-1 virions. Assessing the time needed for A3G incorporation into virions is, therefore, important to determine how quickly Vif must act to induce its degradation. We show that modelling the intracellular half-life of A3G can induce its Vif-independent targeting to the ubiquitin-proteasome system. By using various amino acids (X) in a cleavable ubiquitin-X-A3G fusion, we demonstrate that the half-life (t1/2) of X-A3G can be manipulated. We show that A3G molecules with a half-life of 13 min are incorporated into virions, whereas those with a half-life shorter than 5 min were not. The amount of X-A3G incorporated into virions increases from 13 min (Phe-A3G) to 85 min (Asn-A3G) and remains constant after this time period. Interestingly, despite the presence of similar levels of Arg-A3G (t1/2 = 28 min) and Asp-A3G (t1/2 = 65 min) into HIV-1 DELTAvif virions, inhibition of viral infectivity was only evident in the presence of A3G proteins with a longer half-life (t1/2 >= 65 min).

  15. Networks.

    ERIC Educational Resources Information Center

    Maughan, George R.; Petitto, Karen R.; McLaughlin, Don

    2001-01-01

    Describes the connectivity features and options of modern campus communication and information system networks, including signal transmission (wire-based and wireless), signal switching, convergence of networks, and network assessment variables, to enable campus leaders to make sound future-oriented decisions. (EV)

  16. APOBEC3G Variants and Protection against HIV-1 Infection in Burkina Faso

    PubMed Central

    Compaore, Tegwinde Rebeca; Soubeiga, Serge Theophile; Ouattara, Abdoul Karim; Obiri-Yeboah, Dorcas; Tchelougou, Damehan; Maiga, Mamoudou; Assih, Maleki; Bisseye, Cyrille; Bakouan, Didier; Compaore, Issaka Pierre; Dembele, Augustine; Martinson, Jeremy; Simpore, Jacques

    2016-01-01

    Studies on host factors, particularly the APOBEC3G gene, have previously found an association with AIDS progression in some populations and against some HIV-1 strains but not others. Our study had two main objectives: firstly, to screen a population from Burkina Faso for three variants of APOBEC3G previously described, and secondly to analyze the effect of these three variants and their haplotypes on HIV-1 infection with Circulating Recombinant Forms (CRFs) present in Burkina Faso. This case control study involved 708 seropositive and seronegative individuals. Genotyping was done by the TaqMan allelic discrimination method. Minor allele frequencies of rs6001417 (p<0.05), rs8177832 (P<0.05), and rs35228531 (P<0.001) were higher in seronegative subjects. The rs6001417 and rs8177832 SNPs were associated with HIV-1 infection in an additive model (P<0.01). Furthermore the SNP rs35228531 was also associated with HIV-1 infection in a dominant model (P<0.001). Odds ratio analysis of genotypes and alleles of the different APOBEC3G variants showed that there is a strong association between the minor genetic variants, genotype of the three SNPs, and HIV-1 status. Haplotype analysis demonstrated that rs6001417, rs8177832, and rs35228531 are in linkage disequilibrium. The haplotype GGT from the rs6001417, rs8177832 and rs35228531 respectively has a protective effect OR = 0.54 [0.43–0.68] with P<0.001. There was also associations between the haplotypes GGC OR = 1.6 [1.1;-2.3] P<0.05, and CGC OR = 5.21 [2.4–11.3] P<0.001, which increase the risk of infection by HIV-1 from almost two (2) to five (5) fold. This study demonstrates an association of rs6001417, rs8177832, and rs35228531 of APOBEC3G with HIV-1 infection in a population from Burkina Faso. PMID:26741797

  17. Atomic force microscopy studies provide direct evidence for dimerization of the HIV restriction factor APOBEC3G.

    PubMed

    Shlyakhtenko, Luda S; Lushnikov, Alexander Y; Li, Ming; Lackey, Lela; Harris, Reuben S; Lyubchenko, Yuri L

    2011-02-01

    APOBEC3G (A3G) is an antiviral protein that binds RNA and single-stranded DNA (ssDNA). The oligomerization state of A3G is likely to be influenced by these nucleic acid interactions. We applied the power of nanoimaging atomic force microscopy technology to characterize the role of ssDNA in A3G oligomerization. We used recombinant human A3G prepared from HEK-293 cells and specially designed DNA substrates that enable free A3G to be distinguished unambiguously from DNA-bound protein complexes. This DNA substrate can be likened to a molecular ruler because it consists of a 235-bp double-stranded DNA visual tag spliced to a 69-nucleotide ssDNA substrate. This hybrid substrate enabled us to use volume measurements to determine A3G stoichiometry in both free and ssDNA-bound states. We observed that free A3G is primarily monomeric, whereas ssDNA-complexed A3G is mostly dimeric. A3G stoichiometry increased slightly with the addition of Mg(2+), but dimers still predominated when Mg(2+) was depleted. A His-248/His-250 Zn(2+)-mediated intermolecular bridge was observed in a catalytic domain crystal structure (Protein Data Bank code 3IR2); however, atomic force microscopy analyses showed that the stoichiometry of the A3G-ssDNA complexes changed insignificantly when these residues were mutated to Ala. We conclude that A3G exchanges between oligomeric forms in solution with monomers predominating and that this equilibrium shifts toward dimerization upon binding ssDNA. PMID:21123176

  18. Production of ethanol 3G from Kappaphycus alvarezii: evaluation of different process strategies.

    PubMed

    Hargreaves, Paulo Iiboshi; Barcelos, Carolina Araújo; da Costa, Antonio Carlos Augusto; Pereira, Nei

    2013-04-01

    This study evaluated the potential of Kappaphycus alvarezii as feedstock for ethanol production, i.e. ethanol 3G. First, aquatic biomass was subjected to a diluted acid pretreatment. This acid pretreatment generated two streams--a galactose-containing liquid fraction and a cellulose-containing solid fraction, which were investigated to determine their fermentability with the following strategies: a single-stream process (simultaneous saccharification and co-fermentation (SSCF) of both fractions altogether), which achieved 64.3 g L(-1) of ethanol, and a two-stream process (fractions were fermented separately), which resulted in 38 g L(-1) of ethanol from the liquid fraction and 53.0 g L(-1) from the simultaneous saccharification and fermentation (SSF) of the solid fraction. Based on the average fermentable carbohydrate concentration, it was possible to obtain 105 L of ethanol per ton of dry seaweed. These preliminaries results indicate that the use of the macro-algae K. alvarezii has a good potential feedstock for bioethanol production. PMID:23500583

  19. Research of the Heart Information Monitoring Robert Based on the 3G Wireless Communication Platform

    NASA Astrophysics Data System (ADS)

    Zhang, Fuli; Yang, Huazhe; Li, Gensong; Hong, Yang; Hu, Qingzhe

    Electrocardiogram (ECG) of a person can be recorded and the diagnostic results can be displayed through touching the heart information monitoring Robert. In addition, the heart rate, phonocardiogram (PCG) and the dynamic three-dimensional echocardiography can also be displayed synchronously. Then the difficult ECG can be transmitted to the service center through 3G wireless communication center, followed by diagnosing the ECG by doctors and transmitting the feedback diagnostic results. I-lead ECG of the person can be recorded by the amplification circuit with high gain and low noise. Then, the heart rate and output phonocardiogram are displayed and the model of heart beat are started to trace through the recognition of R wave. Finally, the difficult ECG is transmitted to the service center via 3G communication chips. The displayed ECG is clear, and the stimulated heart beat is synchronous with that of the person. Furthermore, ECG received by the service center is in accordance with the one recorded by the Robert.

  20. A remote patient monitoring system using a Java-enabled 3G mobile phone.

    PubMed

    Zhang, Pu; Kogure, Yuichi; Matsuoka, Hiroki; Akutagawa, Masatake; Kinouchi, Yohsuke; Zhang, Qinyu

    2007-01-01

    Telemedicine systems have become an important supporting for the medical staffs. As the development of the mobile phones, it is possible to apply the mobile phones to be a part of telemedicine systems. We developed an innovative Remote Patient Monitoring System using a Java-enabled 3G mobile phone. By using this system, doctors can monitor the vital biosignals of patients in ICU/CCU, such as ECG, RESP, SpO2, EtCO2 and so on by using the real-time waveform and data monitoring and list trend data monitoring functions of installed Java jiglet application on the mobile phone. Futhermore, doctors can check the patients' information by using the patient information checking function. The 3G mobile phone used has the ability to implement the application as the same time as being used to mak a voice call. Therefore, the doctor can get more and more information both from the browsing the screen of the mobile phone and the communicating with the medical staffs who are beside the patients and the monitors. The system can be conducted to evaluate the diagnostic accuracy, efficiency, and safety of telediagnosis. PMID:18002804

  1. Networking.

    ERIC Educational Resources Information Center

    Duvall, Betty

    Networking is an information giving and receiving system, a support system, and a means whereby women can get ahead in careers--either in new jobs or in current positions. Networking information can create many opportunities: women can talk about how other women handle situations and tasks, and previously established contacts can be used in…

  2. Integrative omics reveals MYCN as a global suppressor of cellular signalling and enables network-based therapeutic target discovery in neuroblastoma.

    PubMed

    Duffy, David J; Krstic, Aleksandar; Halasz, Melinda; Schwarzl, Thomas; Fey, Dirk; Iljin, Kristiina; Mehta, Jai Prakash; Killick, Kate; Whilde, Jenny; Turriziani, Benedetta; Haapa-Paananen, Saija; Fey, Vidal; Fischer, Matthias; Westermann, Frank; Henrich, Kai-Oliver; Bannert, Steffen; Higgins, Desmond G; Kolch, Walter

    2015-12-22

    Despite intensive study, many mysteries remain about the MYCN oncogene's functions. Here we focus on MYCN's role in neuroblastoma, the most common extracranial childhood cancer. MYCN gene amplification occurs in 20% of cases, but other recurrent somatic mutations are rare. This scarcity of tractable targets has hampered efforts to develop new therapeutic options. We employed a multi-level omics approach to examine MYCN functioning and identify novel therapeutic targets for this largely un-druggable oncogene. We used systems medicine based computational network reconstruction and analysis to integrate a range of omic techniques: sequencing-based transcriptomics, genome-wide chromatin immunoprecipitation, siRNA screening and interaction proteomics, revealing that MYCN controls highly connected networks, with MYCN primarily supressing the activity of network components. MYCN's oncogenic functions are likely independent of its classical heterodimerisation partner, MAX. In particular, MYCN controls its own protein interaction network by transcriptionally regulating its binding partners.Our network-based approach identified vulnerable therapeutically targetable nodes that function as critical regulators or effectors of MYCN in neuroblastoma. These were validated by siRNA knockdown screens, functional studies and patient data. We identified β-estradiol and MAPK/ERK as having functional cross-talk with MYCN and being novel targetable vulnerabilities of MYCN-amplified neuroblastoma. These results reveal surprising differences between the functioning of endogenous, overexpressed and amplified MYCN, and rationalise how different MYCN dosages can orchestrate cell fate decisions and cancerous outcomes. Importantly, this work describes a systems-level approach to systematically uncovering network based vulnerabilities and therapeutic targets for multifactorial diseases by integrating disparate omic data types. PMID:26673823

  3. Integrative omics reveals MYCN as a global suppressor of cellular signalling and enables network-based therapeutic target discovery in neuroblastoma

    PubMed Central

    Fey, Dirk; Iljin, Kristiina; Mehta, Jai Prakash; Killick, Kate; Whilde, Jenny; Turriziani, Benedetta; Haapa-Paananen, Saija; Fey, Vidal; Fischer, Matthias; Westermann, Frank; Henrich, Kai-Oliver; Bannert, Steffen; Higgins, Desmond G.; Kolch, Walter

    2015-01-01

    Despite intensive study, many mysteries remain about the MYCN oncogene's functions. Here we focus on MYCN's role in neuroblastoma, the most common extracranial childhood cancer. MYCN gene amplification occurs in 20% of cases, but other recurrent somatic mutations are rare. This scarcity of tractable targets has hampered efforts to develop new therapeutic options. We employed a multi-level omics approach to examine MYCN functioning and identify novel therapeutic targets for this largely un-druggable oncogene. We used systems medicine based computational network reconstruction and analysis to integrate a range of omic techniques: sequencing-based transcriptomics, genome-wide chromatin immunoprecipitation, siRNA screening and interaction proteomics, revealing that MYCN controls highly connected networks, with MYCN primarily supressing the activity of network components. MYCN's oncogenic functions are likely independent of its classical heterodimerisation partner, MAX. In particular, MYCN controls its own protein interaction network by transcriptionally regulating its binding partners. Our network-based approach identified vulnerable therapeutically targetable nodes that function as critical regulators or effectors of MYCN in neuroblastoma. These were validated by siRNA knockdown screens, functional studies and patient data. We identified β-estradiol and MAPK/ERK as having functional cross-talk with MYCN and being novel targetable vulnerabilities of MYCN-amplified neuroblastoma. These results reveal surprising differences between the functioning of endogenous, overexpressed and amplified MYCN, and rationalise how different MYCN dosages can orchestrate cell fate decisions and cancerous outcomes. Importantly, this work describes a systems-level approach to systematically uncovering network based vulnerabilities and therapeutic targets for multifactorial diseases by integrating disparate omic data types. PMID:26673823

  4. Adaptive stochastic cellular automata: Applications

    NASA Astrophysics Data System (ADS)

    Qian, S.; Lee, Y. C.; Jones, R. D.; Barnes, C. W.; Flake, G. W.; O'Rourke, M. K.; Lee, K.; Chen, H. H.; Sun, G. Z.; Zhang, Y. Q.; Chen, D.; Giles, C. L.

    1990-09-01

    The stochastic learning cellular automata model has been applied to the problem of controlling unstable systems. Two example unstable systems studied are controlled by an adaptive stochastic cellular automata algorithm with an adaptive critic. The reinforcement learning algorithm and the architecture of the stochastic CA controller are presented. Learning to balance a single pole is discussed in detail. Balancing an inverted double pendulum highlights the power of the stochastic CA approach. The stochastic CA model is compared to conventional adaptive control and artificial neural network approaches.

  5. SIMULATION OF GENERAL ANESTHESIA ON THE "SIMMAN 3G" AND ITS EFFICIENCY.

    PubMed

    Potapov, A F; Matveev, A S; Ignatiev, V G; Ivanova, A A; Aprosimov, L A

    2015-01-01

    In recent years in medical educational process new innovative technologies are widely used with computer simulation, providing the reality of medical intervations and procedures. Practice-training teaching with using of simulation allows to improve the efficiency of learning material at the expense of creating imaginary professional activity and leading barring material to practical activity. The arm of the investigation is evaluation of the students training efficiency at the Medical Institute on the topic "General Anesthesia with using a modern simulation "SimMan 3 G". The material of the investigation is the results, carried out on the basis of the Centre of Practical skills and medical virtual educational technologies (Simulation Centre) at the Medical Institute of NEFU by M.K. Ammosov. The Object of the investigation was made up by 55 students of the third (3) course of the Faculty of General Medicine of the Medical Institute of NEFU. The investigation was hold during practical trainings (April-May 2014) of the General Surgery Department on the topic "General Anesthesia". A simulation practical course "General Anesthesia" consisted of 12 academic hours. Practical training was carried out using instruments, equipments and facilities to install anesthesia on the SimMan 3G with shooting the process and further discussions of the results. The methods of the investigations were the appreciation of students background knowledge before and after practical training (by 5 points scale) and the analysis of the results. The results of the investigation showed that before the practical course only 23 students (41.8%) had dot positive marks: "Good"--7 students (12.7%) and "Satisfactory"--16 (29.1%) students. The rest 22 (58.2%) students had bad results. The practical trainings using real instruments, equipments and facilities with imitation of installation of preparations for introductory anesthesia, main analgesics and muscle relaxants showed a patients reaction on the

  6. Clustered mutations in hominid genome evolution are consistent with APOBEC3G enzymatic activity.

    PubMed

    Pinto, Yishay; Gabay, Orshay; Arbiza, Leonardo; Sams, Aaron J; Keinan, Alon; Levanon, Erez Y

    2016-05-01

    The gradual accumulation of mutations by any of a number of mutational processes is a major driving force of divergence and evolution. Here, we investigate a potentially novel mutational process that is based on the activity of members of the AID/APOBEC family of deaminases. This gene family has been recently shown to introduce-in multiple types of cancer-enzyme-induced clusters of co-occurring somatic mutations caused by cytosine deamination. Going beyond somatic mutations, we hypothesized that APOBEC3-following its rapid expansion in primates-can introduce unique germline mutation clusters that can play a role in primate evolution. In this study, we tested this hypothesis by performing a comprehensive comparative genomic screen for APOBEC3-induced mutagenesis patterns across different hominids. We detected thousands of mutation clusters introduced along primate evolution which exhibit features that strongly fit the known patterns of APOBEC3G mutagenesis. These results suggest that APOBEC3G-induced mutations have contributed to the evolution of all genomes we studied. This is the first indication of site-directed, enzyme-induced genome evolution, which played a role in the evolution of both modern and archaic humans. This novel mutational mechanism exhibits several unique features, such as its higher tendency to mutate transcribed regions and regulatory elements and its ability to generate clusters of concurrent point mutations that all occur in a single generation. Our discovery demonstrates the exaptation of an anti-viral mechanism as a new source of genomic variation in hominids with a strong potential for functional consequences. PMID:27056836

  7. Clustered mutations in hominid genome evolution are consistent with APOBEC3G enzymatic activity

    PubMed Central

    Pinto, Yishay; Gabay, Orshay; Arbiza, Leonardo; Sams, Aaron J.; Keinan, Alon

    2016-01-01

    The gradual accumulation of mutations by any of a number of mutational processes is a major driving force of divergence and evolution. Here, we investigate a potentially novel mutational process that is based on the activity of members of the AID/APOBEC family of deaminases. This gene family has been recently shown to introduce—in multiple types of cancer—enzyme-induced clusters of co-occurring somatic mutations caused by cytosine deamination. Going beyond somatic mutations, we hypothesized that APOBEC3—following its rapid expansion in primates—can introduce unique germline mutation clusters that can play a role in primate evolution. In this study, we tested this hypothesis by performing a comprehensive comparative genomic screen for APOBEC3-induced mutagenesis patterns across different hominids. We detected thousands of mutation clusters introduced along primate evolution which exhibit features that strongly fit the known patterns of APOBEC3G mutagenesis. These results suggest that APOBEC3G-induced mutations have contributed to the evolution of all genomes we studied. This is the first indication of site-directed, enzyme-induced genome evolution, which played a role in the evolution of both modern and archaic humans. This novel mutational mechanism exhibits several unique features, such as its higher tendency to mutate transcribed regions and regulatory elements and its ability to generate clusters of concurrent point mutations that all occur in a single generation. Our discovery demonstrates the exaptation of an anti-viral mechanism as a new source of genomic variation in hominids with a strong potential for functional consequences. PMID:27056836

  8. Structure at 1.6 Å resolution of the protein from gene locus At3g22680 from Arabidopsis thaliana

    SciTech Connect

    Allard, Simon T. M.; Bingman, Craig A.; Johnson, Kenneth A.; Wesenberg, Gary E.; Bitto, Eduard; Jeon, Won Bae; Phillips, George N. Jr

    2005-07-01

    The crystal structure of the 18 kDa At3g22680 gene product from A. thaliana was determined at 1.6 Å resolution. At3g22680 shows no structural homology to any other known proteins and represents a new fold in protein conformational space. The gene product of At3g22680 from Arabidopsis thaliana codes for a protein of unknown function. The crystal structure of the At3g22680 gene product was determined by multiple-wavelength anomalous diffraction and refined to an R factor of 16.0% (R{sub free} = 18.4%) at 1.60 Å resolution. The refined structure shows one monomer in the asymmetric unit, with one molecule of the non-denaturing detergent CHAPS (3-[(3-cholamidopropyl)dimethylammonio]-1-propane sulfonate) tightly bound. Protein At3g22680 shows no structural homology to any other known proteins and represents a new fold in protein conformation space.

  9. Engineering Cellular Metabolism.

    PubMed

    Nielsen, Jens; Keasling, Jay D

    2016-03-10

    Metabolic engineering is the science of rewiring the metabolism of cells to enhance production of native metabolites or to endow cells with the ability to produce new products. The potential applications of such efforts are wide ranging, including the generation of fuels, chemicals, foods, feeds, and pharmaceuticals. However, making cells into efficient factories is challenging because cells have evolved robust metabolic networks with hard-wired, tightly regulated lines of communication between molecular pathways that resist efforts to divert resources. Here, we will review the current status and challenges of metabolic engineering and will discuss how new technologies can enable metabolic engineering to be scaled up to the industrial level, either by cutting off the lines of control for endogenous metabolism or by infiltrating the system with disruptive, heterologous pathways that overcome cellular regulation. PMID:26967285

  10. Integration of mobile satellite and cellular systems

    NASA Technical Reports Server (NTRS)

    Drucker, Elliott H.; Estabrook, Polly; Pinck, Deborah; Ekroot, Laura

    1993-01-01

    By integrating the ground based infrastructure component of a mobile satellite system with the infrastructure systems of terrestrial 800 MHz cellular service providers, a seamless network of universal coverage can be established. Users equipped for both cellular and satellite service can take advantage of a number of features made possible by such integration, including seamless handoff and universal roaming. To provide maximum benefit at lowest posible cost, the means by which these systems are integrated must be carefully considered. Mobile satellite hub stations must be configured to efficiently interface with cellular Mobile Telephone Switching Offices (MTSO's), and cost effective mobile units that provide both cellular and satellite capability must be developed.

  11. Docking studies and network analyses reveal capacity of compounds from Kandelia rheedii to strengthen cellular immunity by interacting with host proteins during tuberculosis infection

    PubMed Central

    Zaman, Aubhishek

    2012-01-01

    Kandelia rheedii (locally known as Guria or Rasunia), widely found and used in Indian subcontinent, is a well-known herbal cure to tuberculosis. However, neither the mechanism nor the active components of the plant extract responsible for mediating this action has yet been confirmed. Here in this study, molecular interactions of three compounds (emodin, fusaric acid and skyrin) from the plant extract with the host protein targets (casein kinase (CSNK), estrogen receptor (ERBB), dopamine β-hydroxylase (DBH) and glucagon receptor (Gcgr)) has been found. These protein targets are known to be responsible for strengthening cellular immunity against Mycobacteria tuberculosis. The specific interactions of these three compounds with the respective protein targets have been discussed here. The insights from study should further help us designing molecular medicines against tuberculosis. PMID:23275699

  12. Inactivation of yeast hexokinase by Cibacron Blue 3G-A: spectral, kinetic and structural investigations.

    PubMed Central

    Puri, R N; Roskoski, R

    1994-01-01

    Yeast hexokinase, a homodimer (100 kDa), is an important enzyme in the glycolytic pathway. Although Cibacron Blue 3G-A (Reactive Blue 2) has been previously shown to inactivate yeast hexokinase, no comprehensive study exists concerning the nature of interaction(s) between hexokinase and the blue dye. A comparison of the computer-generated three-dimensional (3D) representations showed considerable overlap of the purine ring of ATP, a nucleotide substrate of hexokinase, with the hydrophobic anthraquinone moiety of the blue dye. The visible spectrum of the blue dye showed a characteristic absorption band centred at 628 nm. The visible difference spectrum of increasing concentration of the dye and the same concentrations of the dye plus a fixed concentration of hexokinase exhibited a maximum, a minimum and an isobestic point at 683, 585, and 655 nm respectively. The visible difference spectrum of the blue dye and the dye in 50% ethylene glycol showed a maximum and a minimum at 660 and 570 nm respectively. The visible difference spectrum of the blue dye in the presence of the dye and hexokinase modified at the active site by pyridoxal phosphate, iodoacetamide and o-phthalaldehyde was devoid of bands characteristic of the hexokinase-blue dye complex. Size-exclusion-chromatographic studies in the absence or presence of guanidinium chloride showed that the enzyme inactivated by the blue dye was co-eluted with the unmodified enzyme. The dialysis residue obtained after extensive dialysis of the gel-filtered complex, against a buffer of high ionic strength, showed an absorption maximum at 655 nm characteristic of the dye-enzyme complex. Inactivation data when analysed by 'Kitz-Wilson'-type kinetics for an irreversible inhibitor, yielded values of 0.05 min-1 and 92 microM for maximum rate of inactivation (k3) and dissociation constant (Kd) for the enzyme-dye complex respectively. Sugar and nucleotide substrates protected hexokinase against inactivation by the blue dye. About 2

  13. HBsAg blocks TYPE I IFN induced up-regulation of A3G through inhibition of STAT3.

    PubMed

    Xu, Fengchao; Song, Hongxiao; Li, Na; Tan, Guangyun

    2016-04-22

    Interferon (IFN) is a regularly utilized therapeutic for the treatment of chronic hepatitis B and appears to induce superior HBeAg seroconversion comparing nucleos/tide analogs. However, the mechanisms underlying IFN inhibition of HBV replication, as well as poor responses to IFN are unclear. Apobec3G has been reported to be involved in regulating HBV replication. In this study, we investigated Apobec3G expression and regulatory pathways during HBV infection. We show that over-expression of A3G leads to inhibition of HBV replication. We also show that IFN induces a significant increase in A3G protein expression, which is associated with STAT3 activation. We further show that A3G expression in HBV patients is lower compared to non-infected controls, possibly by HBsAg which inhibits IFN induced A3G up-regulation in a dose dependent manner. This process is likely mediated through inhibition of STAT3-Ser727 phosphorylation. The results presented in this study indicate that STAT3 plays an important role in IFN-induced A3G production, and HBsAg may correlated with poor response to IFN treatment. PMID:27003258

  14. APOBEC3G inhibits HIV-1 RNA elongation by inactivating the viral trans-activation response element.

    PubMed

    Nowarski, Roni; Prabhu, Ponnandy; Kenig, Edan; Smith, Yoav; Britan-Rosich, Elena; Kotler, Moshe

    2014-07-29

    Deamination of cytidine residues in viral DNA is a major mechanism by which APOBEC3G (A3G) inhibits vif-deficient human immunodeficiency virus type 1 (HIV-1) replication. dC-to-dU transition following RNase-H activity leads to viral cDNA degradation, production of non-functional proteins, formation of undesired stop codons and decreased viral protein synthesis. Here, we demonstrate that A3G provides an additional layer of defense against HIV-1 infection dependent on inhibition of proviral transcription. HIV-1 transcription elongation is regulated by the trans-activation response (TAR) element, a short stem-loop RNA structure required for elongation factors binding. Vif-deficient HIV-1-infected cells accumulate short viral transcripts and produce lower amounts of full-length HIV-1 transcripts due to A3G deamination of the TAR apical loop cytidine, highlighting the requirement for TAR loop integrity in HIV-1 transcription. We further show that free single-stranded DNA (ssDNA) termini are not essential for A3G activity and a gap of CCC motif blocked with juxtaposed DNA or RNA on either or 3'+5' ends is sufficient for A3G deamination. These results identify A3G as an efficient mutator and that deamination of (-)SSDNA results in an early block of HIV-1 transcription. PMID:24859335

  15. APOBEC3G Inhibits HIV-1 RNA Elongation by Inactivating the Viral Trans-Activation Response Element

    PubMed Central

    Nowarski, Roni; Prabhu, Ponnandy; Kenig, Edan; Smith, Yoav; Britan-Rosich, Elena; Kotler, Moshe

    2014-01-01

    Deamination of cytidine residues in viral DNA (vDNA) is a major mechanism by which APOBEC3G (A3G) inhibits vif-deficient HIV-1 replication. dC to dU transition following RNase-H activity leads to viral cDNA degradation, production of non-functional proteins, formation of undesired stop codons and decreased viral protein synthesis. Here we demonstrate that A3G provides an additional layer of defence against HIV-1 infection dependent on inhibition of proviral transcription. HIV-1 transcription elongation is regulated by the trans-activation response (TAR) element, a short stem-loop RNA structure required for elongation factors binding. Vif-deficient HIV-1-infected cells accumulate short viral transcripts and produce lower amounts of full-length HIV-1 transcripts due to A3G deamination of the TAR apical loop cytidine, highlighting the requirement for TAR loop integrity in HIV-1 transcription. Finally, we show that free ssDNA termini are not essential for A3G activity and a gap of CCC motif blocked with juxtaposed DNA or RNA on either or 3′+5′ ends is sufficient for A3G deamination, identifying A3G as an efficient mutator, and that deamination of (−)SSDNA results in an early block of HIV-1 transcription. PMID:24859335

  16. Estimating the fraction of progeny virions that must incorporate APOBEC3G for suppression of productive HIV-1 infection

    SciTech Connect

    Thangavelu, Pulari U.; Gupta, Vipul; Dixit, Narendra M.

    2014-01-20

    The contest between the host factor APOBEC3G (A3G) and the HIV-1 protein Vif presents an attractive target of intervention. The extent to which the A3G–Vif interaction must be suppressed to tilt the balance in favor of A3G remains unknown. We employed stochastic simulations and mathematical modeling of the within-host dynamics and evolution of HIV-1 to estimate the fraction of progeny virions that must incorporate A3G to render productive infection unsustainable. Using three different approaches, we found consistently that a transition from sustained infection to suppression of productive infection occurred when the latter fraction exceeded ∼0.8. The transition was triggered by A3G-induced hypermutations that led to premature stop codons compromising viral production and was consistent with driving the basic reproductive number, R{sub 0}, below unity. The fraction identified may serve as a quantitative guideline for strategies targeting the A3G–Vif axis. - Highlights: • We perform simulations and mathematical modeling of the role of APOBEC3G in suppressing HIV-1 infection. • In three distinct ways, we estimate that when over 80% of progeny virions carry APOBEC3G, productive HIV-1 infection would be suppressed. • Our estimate of this critical fraction presents quantitative guidelines for strategies targeting the APOBEC3G–Vif axis.

  17. Fluorescence in situ hybridization mapping of the mouse platelet endothelial cell adhesion molecule-1 (PECAM1) to mouse chromosome 6, region F3-G1

    SciTech Connect

    Xie, Yong; Muller, W.A.

    1996-10-15

    Human platelet/endothelial cell adhesion molecule-1 (PECAM1), an important member of the immunoglobulin gene superfamily, is widely distributed on cells of the vascular system and mediates cellular interactions through both homophilic and heterophilic adhesive mechanisms. The function of PECAM1 in vitro has begun to be understood, but its function in vivo is yet to be established. To study the function of PECAM1 in vivo, its mouse counterpart was identified and its cDNA gene isolated and characterized. In this study, the mouse chromosomal localization was determined for the mouse gene encoding Pecam. Fluorescence in situ hybridization was used to map the Pecam gene on mouse chromosome 6, region F3-G1. 12 refs., 2 figs.

  18. Cellular mechanics and motility

    NASA Astrophysics Data System (ADS)

    Hénon, Sylvie; Sykes, Cécile

    2015-10-01

    cross-linked or branched networks. It is a highly dynamical system in which filaments are able to elongate or slide one on the other with the contribution of very active cellular proteins like molecular motors. The versatile properties of this cytoskeleton ensure the diversity of mechanical behaviors to explain cell rigidity as well as cell motility.

  19. Extension of RAPTOR-M3G to r-θ-z Geometry for Use in Reactor Dosimetry Applications

    NASA Astrophysics Data System (ADS)

    Hunter, Melissa A.; Longoni, Gianluca; Anderson, Stanwood L.

    2009-08-01

    The RAPTOR-M3G (RApid Parallel Transport Of Radiation - Multiple 3-D Geometries) is a new deterministic radiation transport code that was originally developed for x-y-z geometry. The development of the r-θ-z version of RAPTOR-M3G and its application to determine ex-vessel neutron dosimetry responses in the cavity of a typical 2-loop pressurized water reactor is presented. The neutron dosimetry responses determined from RAPTOR-M3G and TORT 3-D r-θ-z calculations are compared to actual measured responses.

  20. EEG Changes Due to Experimentally Induced 3G Mobile Phone Radiation

    PubMed Central

    Roggeveen, Suzanne; van Os, Jim; Viechtbauer, Wolfgang; Lousberg, Richel

    2015-01-01

    The aim of this study was to investigate whether a 15-minute placement of a 3G dialing mobile phone causes direct changes in EEG activity compared to the placement of a sham phone. Furthermore, it was investigated whether placement of the mobile phone on the ear or the heart would result in different outcomes. Thirty-one healthy females participated. All subjects were measured twice: on one of the two days the mobile phone was attached to the ear, the other day to the chest. In this single-blind, cross-over design, assessments in the sham phone condition were conducted directly preceding and following the mobile phone exposure. During each assessment, EEG activity and radiofrequency radiation were recorded jointly. Delta, theta, alpha, slowbeta, fastbeta, and gamma activity was computed. The association between radiation exposure and the EEG was tested using multilevel random regression analyses with radiation as predictor of main interest. Significant radiation effects were found for the alpha, slowbeta, fastbeta, and gamma bands. When analyzed separately, ear location of the phone was associated with significant results, while chest placement was not. The results support the notion that EEG alterations are associated with mobile phone usage and that the effect is dependent on site of placement. Further studies are required to demonstrate the physiological relevance of these findings. PMID:26053854

  1. Fish otolith growth in 1g and 3g depends on the gravity vector.

    PubMed

    Anken, R H; Werner, K; Breuer, J; Rahmann, H

    2000-01-01

    Size and asymmetry (size difference between the left and the right side) as well as calcium (Ca) content of inner ear otoliths of larval cichlid fish Oreochromis mossambicus were determined after a long-term stay at hypergravity conditions (3g; centrifuge). Both utricular and saccular otoliths (lapilli and sagittae, respectively) were significantly smaller after hyper-g exposure as compared to parallely raised 1g-control specimens and the absolute amount of otolith-Ca was diminished. The asymmetry of sagittae was significantly increased in the experimental animals, whereas the respective asymmetry concerning lapilli was markedly decreased. In the course of another experiment larvae were raised in aquarium hatch baskets, from which one was placed directly above aeration equipment which resulted in random water circulation shifting the fish around ("shifted" specimens). The lapillar asymmetry of the "stationary" specimens showed a highly significant increase during early development when larvae were forced to lay on their sides due to their prominent yolk-sacs. In later developmental stages, when they began to swim freely, a dramatic decrease in lapillar asymmetry was apparent. Taken together with own previous findings according to which otolith growth stops after vestibular nerve transaction, the results presented here suggest that the growth and the development of bilateral asymmetry of otoliths is guided by the environmental gravity vector, obviously involving a feedback loop between the brain and the inner ear. PMID:11542852

  2. Fish Otolith Growth in 1g and 3g Depends on the Gravity Vector

    NASA Astrophysics Data System (ADS)

    Anken, R. H.; Werner, K.; Breuer, J.; Rahmann, H.

    Size and asymmetry (size difference between the left and the right side) as well as calcium (Ca) content of inner ear otoliths of larval cichlid fish Oreochromis mossambicus were determined after a long-term stay at hypergravity conditions (3g; centrifuge). Both utricular and saccular otoliths (lapilli and sagittae, respectively) were significantly smaller after hyper-g exposure as compared to parallely raised 1g-control specimens and the absolute amount of otolith-Ca was diminished. The asymmetry of sagittae was significantly increased in the experimental animals, whereas the respective asymmetry concerning lapilli was markedly decreased. In the course of another experiment, larvae were raised in aquarium hatch baskets, from which one was placed directly above aeration equipment, which resulted in random water circulation shifting the fish around (``shifted'' specimens). The lapillar asymmetry of the ``stationary'' specimens showed a highly significant increase during early development when larvae were forced to lay on their sides due to their prominent yolk-sacs. In later developmental stages, when they began to swim freely, a dramatic decrease in lapillar asymmetry was apparent. Taken together with own previous findings according to which otolith growth stops after vestibular nerve transection, the results presented here suggest that the growth and the development of bilateral asymmetry of otoliths is guided by the environmental gravity vector, obviously involving a feedback loop between the brain and the inner ear

  3. Morphometry of fish inner ear otoliths after development at 3g hypergravity.

    PubMed

    Anken, R H; Kappel, T; Rahmann, H

    1998-07-01

    Size and asymmetry (size difference between the left and right sides) of inner ear otoliths of larval cichlid fish were determined after a long-term stay in moderate hypergravity conditions (3g; centrifuge), in the course of which the animals completed their ontogenetic development from hatch to freely swimming. Neither the normal morphogenetic development nor the timely onset and gain of performance of swimming behaviour were impaired by the experimental conditions. However, both utricular and saccular otoliths (lapilli and sagittae, respectively) were significantly smaller after hyper-g exposure compared to 1g control specimens raised in parallel. The asymmetry of sagittae was significantly increased in the experimental animals, whereas the respective asymmetry of lapilli was pronouncedly decreased compared with the 1g controls. These findings suggest that growth and development of bilateral asymmetry of otoliths are guided by the environmental gravity vector. Some of the hyper-g animals revealed a kinetotic behaviour on transfer to normal 1g earth conditions, which was similar to the behaviour observed in previous experiments on the transfer from 1g to microgravity (parabolic aircraft flights). The lapillar asymmetry of kinetotic samples was found to be significantly higher than that of normally behaving experimental specimens. No differences in asymmetry of sagittae were obtained between the two groups. This supports an earlier theoretical concept, according to which human static space sickness might be based on asymmetric utricular otoliths. PMID:9726679

  4. SMAC: A soft MAC to reduce control overhead and latency in CDMA-based AMI networks

    DOE PAGESBeta

    Garlapati, Shravan; Kuruganti, Teja; Buehrer, Michael R.; Reed, Jeffrey H.

    2015-10-26

    The utilization of state-of-the-art 3G cellular CDMA technologies in a utility owned AMI network results in a large amount of control traffic relative to data traffic, increases the average packet delay and hence are not an appropriate choice for smart grid distribution applications. Like the CDG, we consider a utility owned cellular like CDMA network for smart grid distribution applications and classify the distribution smart grid data as scheduled data and random data. Also, we propose SMAC protocol, which changes its mode of operation based on the type of the data being collected to reduce the data collection latency andmore » control overhead when compared to 3G cellular CDMA2000 MAC. The reduction in the data collection latency and control overhead aids in increasing the number of smart meters served by a base station within the periodic data collection interval, which further reduces the number of base stations needed by a utility or reduces the bandwidth needed to collect data from all the smart meters. The reduction in the number of base stations and/or the reduction in the data transmission bandwidth reduces the CAPital EXpenditure (CAPEX) and OPerational EXpenditure (OPEX) of the AMI network. Finally, the proposed SMAC protocol is analyzed using markov chain, analytical expressions for average throughput and average packet delay are derived, and simulation results are also provided to verify the analysis.« less

  5. SMAC: A soft MAC to reduce control overhead and latency in CDMA-based AMI networks

    SciTech Connect

    Garlapati, Shravan; Kuruganti, Teja; Buehrer, Michael R.; Reed, Jeffrey H.

    2015-10-26

    The utilization of state-of-the-art 3G cellular CDMA technologies in a utility owned AMI network results in a large amount of control traffic relative to data traffic, increases the average packet delay and hence are not an appropriate choice for smart grid distribution applications. Like the CDG, we consider a utility owned cellular like CDMA network for smart grid distribution applications and classify the distribution smart grid data as scheduled data and random data. Also, we propose SMAC protocol, which changes its mode of operation based on the type of the data being collected to reduce the data collection latency and control overhead when compared to 3G cellular CDMA2000 MAC. The reduction in the data collection latency and control overhead aids in increasing the number of smart meters served by a base station within the periodic data collection interval, which further reduces the number of base stations needed by a utility or reduces the bandwidth needed to collect data from all the smart meters. The reduction in the number of base stations and/or the reduction in the data transmission bandwidth reduces the CAPital EXpenditure (CAPEX) and OPerational EXpenditure (OPEX) of the AMI network. Finally, the proposed SMAC protocol is analyzed using markov chain, analytical expressions for average throughput and average packet delay are derived, and simulation results are also provided to verify the analysis.

  6. Analysis of train movement dynamics under various temporal-spatial constraints in fixed-block railway network using extended cellular automaton model

    NASA Astrophysics Data System (ADS)

    Zhou, Yonghua; Zhang, Zhenlin; Liu, Deng

    2014-03-01

    In the fixed-block railway traffic, the trains adjust their speeds in view of their preceding allowable spaces caused by their respective front adjacent trains or specified by scheduling commands. The railway lines have the line-type speed limits within some block sections and the point-type ones at the terminals of block sections. Those speed limits originate from line conditions, scheduling commands and indications of signal equipment. This paper attempts to in detail reveal the train movement mechanism synthetically considering those temporal-spatial constraints. The proposed train movement model defines four kinds of target points and utilizes them to successively engender the instantaneous target points with their corresponding target speeds. It adopts the rule-based description mechanism in cellular automata (CA) but with continuous spaces to replicate restrictive, autonomous and synergistic behaviors of and among trains. The selections of accelerations and decelerations are based upon the data models of practical acceleration and deceleration processes; thereupon, the model is data-driven. The analysis of train movement dynamics through case studies demonstrates that the extended CA model can reproduce the train movement mechanism of grading speed control to satisfy the aforementioned temporal-spatial constraints. The model is applicable to represent the as-is or should-be states of train movements when adjustable parameters are properly configured.

  7. A single immunization with recombinant rabies virus (ERAG3G) confers complete protection against rabies in mice

    PubMed Central

    2014-01-01

    Purpose New alternative bait rabies vaccines applicable to pet dogs and wild animals are needed to eradicate rabies in Korea. In this study, recombinant rabies virus, ERAG3G strain was constructed using reverse genetic system and the safety, efficacy and immunogenicity of the ERAG3G strain was evaluated in mice and dogs. Materials and Methods Using the full-length genome mutated amino acid at position 333 of glycoprotein of rabies virus (RABV) and helper plasmids, the ERAG3G strain was rescued in BHK/T7-9 cells successfully. Mice were inoculated with the ERAG3G strain for safety and efficacy. Safety and immunogenicity of the dog inoculated with the ERAG3G strain (1 mL, 108.0 FAID50/mL) via intramuscular route was evaluated for 28 days after inoculation. Results The ERAG3G strain rescued by reverse genetic system was propagated well in the mouse neuroblastoma cells revealing titer of 108.5 FAID50/mL and was not pathogenic to 4- or 6-week-old mice that received by intramuscular or intracranical route. Immunization with the ERAG3G strain conferred complete protection from lethal RABV in mice. Dogs inoculated with the vaccine candidate via intramuscular route showed high neutralizing antibody titer ranging from 2.62 to 23.9 IU/mL at 28 days postinoculation. Conclusion Our findings suggest that the ERAG3G strain plays an important role in inducing protective efficacy in mice and causes to arise anti-rabies neutralizing antibody in dogs. PMID:25003091

  8. A Non-Stationary 1981-2012 AVHRR NDVI(sub 3g) Time Series

    NASA Technical Reports Server (NTRS)

    Pinzon, Jorge E.; Tucker, Compton J.

    2014-01-01

    The NDVI(sub 3g) time series is an improved 8-km normalized difference vegetation index (NDVI) data set produced from Advanced Very High Resolution Radiometer (AVHRR) instruments that extends from 1981 to the present. The AVHRR instruments have flown or are flying on fourteen polar-orbiting meteorological satellites operated by the National Oceanic and Atmospheric Administration (NOAA) and are currently flying on two European Organization for the Exploitation of Meteorological Satellites (EUMETSAT) polar-orbiting meteorological satellites, MetOp-A and MetOp-B. This long AVHRR record is comprised of data from two different sensors: the AVHRR/2 instrument that spans July 1981 to November 2000 and the AVHRR/3 instrument that continues these measurements from November 2000 to the present. The main difficulty in processing AVHRR NDVI data is to properly deal with limitations of the AVHRR instruments. Complicating among-instrument AVHRR inter-calibration of channels one and two is the dual gain introduced in late 2000 on the AVHRR/3 instruments for both these channels. We have processed NDVI data derived from the Sea-Viewing Wide Field-of-view Sensor (SeaWiFS) from 1997 to 2010 to overcome among-instrument AVHRR calibration difficulties. We use Bayesian methods with high quality well-calibrated SeaWiFS NDVI data for deriving AVHRR NDVI calibration parameters. Evaluation of the uncertainties of our resulting NDVI values gives an error of plus or minus 0.005 NDVI units for our 1981 to present data set that is independent of time within our AVHRR NDVI continuum and has resulted in a non-stationary climate data set.

  9. ASK1 restores the antiviral activity of APOBEC3G by disrupting HIV-1 Vif-mediated counteraction

    PubMed Central

    Miyakawa, Kei; Matsunaga, Satoko; Kanou, Kazuhiko; Matsuzawa, Atsushi; Morishita, Ryo; Kudoh, Ayumi; Shindo, Keisuke; Yokoyama, Masaru; Sato, Hironori; Kimura, Hirokazu; Tamura, Tomohiko; Yamamoto, Naoki; Ichijo, Hidenori; Takaori-Kondo, Akifumi; Ryo, Akihide

    2015-01-01

    APOBEC3G (A3G) is an innate antiviral restriction factor that strongly inhibits the replication of human immunodeficiency virus type 1 (HIV-1). An HIV-1 accessory protein, Vif, hijacks the host ubiquitin–proteasome system to execute A3G degradation. Identification of the host pathways that obstruct the action of Vif could provide a new strategy for blocking viral replication. We demonstrate here that the host protein ASK1 (apoptosis signal-regulating kinase 1) interferes with the counteraction by Vif and revitalizes A3G-mediated viral restriction. ASK1 binds the BC-box of Vif, thereby disrupting the assembly of the Vif–ubiquitin ligase complex. Consequently, ASK1 stabilizes A3G and promotes its incorporation into viral particles, ultimately reducing viral infectivity. Furthermore, treatment with the antiretroviral drug AZT (zidovudine) induces ASK1 expression and restores the antiviral activity of A3G in HIV-1-infected cells. This study thus demonstrates a distinct function of ASK1 in restoring the host antiviral system that can be enhanced by AZT treatment. PMID:25901786

  10. Nuclear distribution of eIF3g and its interacting nuclear proteins in breast cancer cells

    PubMed Central

    ZHENG, QIAOLI; LIU, HAO; YE, JINGJIA; ZHANG, HUI; JIA, ZHENYU; CAO, JIANG

    2016-01-01

    Eukaryotic translation initiation factor 3 subunit g (eIF3g) is a core subunit of the eukaryotic translation initiation factor 3 complex, and is important in the initiation of translation. It is also involved in caspase-mediated apoptosis, and is upregulated in multidrug-resistant cancer cells. In the present study, the nuclear distribution of eIF3g was determined by performing co-immunoprecipitation of proteins that potentially interact with eIF3g in the nucleus. Mass spectrometry characterization showed that three proteins, heterogeneous nuclear ribonucleoprotein U/scaffold attachment factor A, HSZFP36/zinc finger protein 823 and β-actin, were among the candidate eIF3g-interacting proteins in the nucleus. The protein-protein interaction was further confirmed by cross-linking and a glutathione S-transferase pull-down assay, followed by western blotting. The co-localization of these proteins was determined by confocal microscopy. These findings provide novel insight into the possible functions of eIF3g in the nucleus and serves as an important first step for further investigation of the roles of eIF3g in cancer development. PMID:26935993

  11. First-In-Class Small Molecule Inhibitors of the Single-Strand DNA Cytosine Deaminase APOBEC3G

    SciTech Connect

    Li, Ming; Shandilya, Shivender M.D.; Carpenter, Michael A.; Rathore, Anurag; Brown, William L.; Perkins, Angela L.; Harki, Daniel A.; Solberg, Jonathan; Hook, Derek J.; Pandey, Krishan K.; Parniak, Michael A.; Johnson, Jeffrey R.; Krogan, Nevan J.; Somasundaran, Mohan; Ali, Akbar; Schiffer, Celia A.; Harris, Reuben S.

    2012-04-04

    APOBEC3G is a single-stranded DNA cytosine deaminase that comprises part of the innate immune response to viruses and transposons. Although APOBEC3G is the prototype for understanding the larger mammalian polynucleotide deaminase family, no specific chemical inhibitors exist to modulate its activity. High-throughput screening identified 34 compounds that inhibit APOBEC3G catalytic activity. Twenty of 34 small molecules contained catechol moieties, which are known to be sulfhydryl reactive following oxidation to the orthoquinone. Located proximal to the active site, C321 was identified as the binding site for the inhibitors by a combination of mutational screening, structural analysis, and mass spectrometry. Bulkier substitutions C321-to-L, F, Y, or W mimicked chemical inhibition. A strong specificity for APOBEC3G was evident, as most compounds failed to inhibit the related APOBEC3A enzyme or the unrelated enzymes E. coli uracil DNA glycosylase, HIV-1 RNase H, or HIV-1 integrase. Partial, but not complete, sensitivity could be conferred to APOBEC3A by introducing the entire C321 loop from APOBEC3G. Thus, a structural model is presented in which the mechanism of inhibition is both specific and competitive, by binding a pocket adjacent to the APOBEC3G active site, reacting with C321, and blocking access to substrate DNA cytosines.

  12. Robustness of networks of networks with degree-degree correlation

    NASA Astrophysics Data System (ADS)

    Min, Byungjoon; Canals, Santiago; Makse, Hernan

    Many real-world complex systems ranging from critical infrastructure and transportation networks to living systems including brain and cellular networks are not formed by an isolated network but by a network of networks. Randomly coupled networks with interdependency between different networks may easily result in abrupt collapse. Here, we seek a possible explanation of stable functioning in natural networks of networks including functional brain networks. Specifically, we analyze the robustness of networks of networks focused on one-to-many interconnections between different networks and degree-degree correlation. Implication of the network robustness on functional brain networks of rats is also discussed.

  13. PHY and MAC Layer Design of Hybrid Spread Spectrum Based Smart Meter Network

    SciTech Connect

    Kuruganti, Phani Teja

    2012-01-01

    The smart grid is a combined process of revitalizing the traditional power grid applications and introducing new applications to improve the efficiency of power generation, transmission and distribution. This can be achieved by leveraging advanced communication and networking technologies. Therefore the selection of the appropriate communication technology for different smart grid applications has been debated a lot in the recent past. After comparing different possible technologies, a recent research study has arrived at a conclusion that the 3G cellular technology is the right choice for distribution side smart grid applications like smart metering, advanced distribution automation and demand response management system. In this paper, we argue that the current 3G/4G cellular technologies are not an appropriate choice for smart grid distribution applications and propose a Hybrid Spread Spectrum (HSS) based Advanced Metering Infrastructure (AMI) as one of the alternatives to 3G/4G technologies. We present a preliminary PHY and MAC layer design of a HSS based AMI network and evaluate their performance using matlab and NS2 simulations. Also, we propose a time hierarchical scheme that can significantly reduce the volume of random access traffic generated during blackouts and the delay in power outage reporting.

  14. Female sex steroids and glia cells: Impact on multiple sclerosis lesion formation and fine tuning of the local neurodegenerative cellular network.

    PubMed

    Kipp, Markus; Hochstrasser, Tanja; Schmitz, Christoph; Beyer, Cordian

    2016-08-01

    Multiple sclerosis (MS) is a chronic inflammatory and demyelinating disease that shows a female-to-male gender prevalence and alleviation of disease activity during late stage pregnancy. In MS-related animal models, sex steroids ameliorate symptoms and protect from demyelination and neuronal damage. Underlying mechanisms of these protective avenues are continuously discovered, in part by using novel transgenic animal models. In this review article, we highlight the regulation of glia cell function by female sex steroids. We specifically focus on the relevance of glia cells for immune cell recruitment into the central nervous system and show how estrogen and progesterone can modulate these cell-cell communication pathways. Since MS is considered to have a strong neurodegenerative component, principal neuroprotective mechanisms, exerted by sex-steroids will be discussed as well. Activation of steroid receptors might not just act as immunosuppressant but at the same time harmonize brain-intrinsic networks to dampen neurodegeneration and, thus, disease progression in MS. PMID:26698019

  15. Cellular Stress Responses and Monitored Cellular Activities.

    PubMed

    Sawa, Teiji; Naito, Yoshifumi; Kato, Hideya; Amaya, Fumimasa

    2016-08-01

    To survive, organisms require mechanisms that enable them to sense changes in the outside environment, introduce necessary responses, and resist unfavorable distortion. Consequently, through evolutionary adaptation, cells have become equipped with the apparatus required to monitor their fundamental intracellular processes and the mechanisms needed to try to offset malfunction without receiving any direct signals from the outside environment. It has been shown recently that eukaryotic cells are equipped with a special mechanism that monitors their fundamental cellular functions and that some pathogenic proteobacteria can override this monitoring mechanism to cause harm. The monitored cellular activities involved in the stressed intracellular response have been researched extensively in Caenorhabditis elegans, where discovery of an association between key mitochondrial activities and innate immune responses was named "cellular associated detoxification and defenses (cSADD)." This cellular surveillance pathway (cSADD) oversees core cellular activities such as mitochondrial respiration and protein transport into mitochondria, detects xenobiotics and invading pathogens, and activates the endocrine pathways controlling behavior, detoxification, and immunity. The cSADD pathway is probably associated with cellular responses to stress in human inflammatory diseases. In the critical care field, the pathogenesis of lethal inflammatory syndromes (e.g., respiratory distress syndromes and sepsis) involves the disturbance of mitochondrial respiration leading to cell death. Up-to-date knowledge about monitored cellular activities and cSADD, especially focusing on mitochondrial involvement, can probably help fill a knowledge gap regarding the pathogenesis of lethal inflammatory syndromes in the critical care field. PMID:26954943

  16. Cellular Phone Towers

    MedlinePlus

    ... the call. How are people exposed to the energy from cellular phone towers? As people use cell ... where people can be exposed to them. The energy from a cellular phone tower antenna, like that ...

  17. Identification of a Protein Network Interacting with TdRF1, a Wheat RING Ubiquitin Ligase with a Protective Role against Cellular Dehydration1[C][W

    PubMed Central

    Guerra, Davide; Mastrangelo, Anna Maria; Lopez-Torrejon, Gema; Marzin, Stephan; Schweizer, Patrick; Stanca, Antonio Michele; del Pozo, Juan Carlos; Cattivelli, Luigi; Mazzucotelli, Elisabetta

    2012-01-01

    Plants exploit ubiquitination to modulate the proteome with the final aim to ensure environmental adaptation and developmental plasticity. Ubiquitination targets are specifically driven to degradation through the action of E3 ubiquitin ligases. Genetic analyses have indicated wide functions of ubiquitination in plant life; nevertheless, despite the large number of predicted E3s, only a few of them have been characterized so far, and only a few ubiquitination targets are known. In this work, we characterized durum wheat (Triticum durum) RING Finger1 (TdRF1) as a durum wheat nuclear ubiquitin ligase. Moreover, its barley (Hordeum vulgare) homolog was shown to protect cells from dehydration stress. A protein network interacting with TdRF1 has been defined. The transcription factor WHEAT BEL1-TYPE HOMEODOMAIN1 (WBLH1) was degraded in a TdRF1-dependent manner through the 26S proteasome in vivo, the mitogen-activated protein kinase TdWNK5 [for Triticum durum WITH NO LYSINE (K)5] was able to phosphorylate TdRF1 in vitro, and the RING-finger protein WHEAT VIVIPAROUS-INTERACTING PROTEIN2 (WVIP2) was shown to have a strong E3 ligase activity. The genes coding for the TdRF1 interactors were all responsive to cold and/or dehydration stress, and a negative regulative function in dehydration tolerance was observed for the barley homolog of WVIP2. A role in the control of plant development was previously known, or predictable based on homology, for wheat BEL1-type homeodomain1(WBLH1). Thus, TdRF1 E3 ligase might act regulating the response to abiotic stress and remodeling plant development in response to environmental constraints. PMID:22167118

  18. SPT-3G: a next-generation cosmic microwave background polarization experiment on the South Pole telescope

    NASA Astrophysics Data System (ADS)

    Benson, B. A.; Ade, P. A. R.; Ahmed, Z.; Allen, S. W.; Arnold, K.; Austermann, J. E.; Bender, A. N.; Bleem, L. E.; Carlstrom, J. E.; Chang, C. L.; Cho, H. M.; Cliche, J. F.; Crawford, T. M.; Cukierman, A.; de Haan, T.; Dobbs, M. A.; Dutcher, D.; Everett, W.; Gilbert, A.; Halverson, N. W.; Hanson, D.; Harrington, N. L.; Hattori, K.; Henning, J. W.; Hilton, G. C.; Holder, G. P.; Holzapfel, W. L.; Irwin, K. D.; Keisler, R.; Knox, L.; Kubik, D.; Kuo, C. L.; Lee, A. T.; Leitch, E. M.; Li, D.; McDonald, M.; Meyer, S. S.; Montgomery, J.; Myers, M.; Natoli, T.; Nguyen, H.; Novosad, V.; Padin, S.; Pan, Z.; Pearson, J.; Reichardt, C.; Ruhl, J. E.; Saliwanchik, B. R.; Simard, G.; Smecher, G.; Sayre, J. T.; Shirokoff, E.; Stark, A. A.; Story, K.; Suzuki, A.; Thompson, K. L.; Tucker, C.; Vanderlinde, K.; Vieira, J. D.; Vikhlinin, A.; Wang, G.; Yefremenko, V.; Yoon, K. W.

    2014-07-01

    We describe the design of a new polarization sensitive receiver, spt-3g, for the 10-meter South Pole Telescope (spt). The spt-3g receiver will deliver a factor of ~20 improvement in mapping speed over the current receiver, spt-pol. The sensitivity of the spt-3g receiver will enable the advance from statistical detection of B-mode polarization anisotropy power to high signal-to-noise measurements of the individual modes, i.e., maps. This will lead to precise (~0.06 eV) constraints on the sum of neutrino masses with the potential to directly address the neutrino mass hierarchy. It will allow a separation of the lensing and inflationary B-mode power spectra, improving constraints on the amplitude and shape of the primordial signal, either through spt-3g data alone or in combination with bicep2/keck, which is observing the same area of sky. The measurement of small-scale temperature anisotropy will provide new constraints on the epoch of reionization. Additional science from the spt-3g survey will be significantly enhanced by the synergy with the ongoing optical Dark Energy Survey (des), including: a 1% constraint on the bias of optical tracers of large-scale structure, a measurement of the differential Doppler signal from pairs of galaxy clusters that will test General Relativity on ~200Mpc scales, and improved cosmological constraints from the abundance of clusters of galaxies

  19. The Vaporization of B2O3(l) to B2O3(g) and B2O2(g)

    NASA Technical Reports Server (NTRS)

    Jacobson, Nathan S.; Myers, Dwight L.

    2011-01-01

    The vaporization of B2O3 in a reducing environment leads to formation of both B2O3(g) and B2O2(g). While formation of B2O3(g) is well understood, many questions about the formation of B2O2(g) remain. Previous studies using B(s) + B2O3(l) have led to inconsistent thermodynamic data. In this study, it was found that after heating, B(s) and B2O3(l) appear to separate and variations in contact area likely led to the inconsistent vapor pressures of B2O2(g). To circumvent this problem, an activity of boron is fixed with a two-phase mixture of FeB and Fe2B. Both second and third law enthalpies of formation were measured for B2O2(g) and B2O3(g). From these the enthalpies of formation at 298.15 K are calculated to be -479.9 +/- 41.5 kJ/mol for B2O2(g) and -833.4 +/- 13.1 kJ/mol for B2O3(g). Ab initio calculations to determine the enthalpies of formation of B2O2(g) and B2O3(g) were conducted using the W1BD composite method and show good agreement with the experimental values.

  20. Wrinkling in Cellular Structured Composites

    NASA Astrophysics Data System (ADS)

    Kaynia, Narges; Li, Yaning; Boyce, Mary C.

    2013-03-01

    Many structured composites found in nature possess undulating and wrinkled interfacial layers that regulate mechanical, chemical, acoustic, adhesive, thermal, electrical and optical functions of the material. This research focused on the formation of wrinkling patterns in cellular structured composites and the effect of the wrinkling pattern on the overall structural response. The cellular composites consisted of stiffer interfacial layers constructing a network submerged in a soft matrix. Analytical and finite element models were developed to capture various aspects of the wrinkling mechanism. The characteristics of the undulation patterns and the instability modes were investigated as functions of model geometry and material composition. Mechanical experiments were designed to further explore the modeling results. The cellular composite samples were fabricated by using different types of elastomers and by varying the geometry and the material properties. The experimental and numerical results were consistent with the analytical predictions. The results in this research improve understanding of the mechanisms governing the undulation pattern formation in cellular composites and can be used to enable on-demand tunability of different functions to provide, among others, active control of wave propagation, mechanical stiffness and deformation, and material swelling and growth.

  1. Hierarchical cellular materials

    SciTech Connect

    Gibson, L.J.

    1991-01-01

    In this paper a method for estimating the contributions of both the composite and the cellular microstructures to the overall material properties and the mechanical efficiency of natural cellular solids will be described. The method will be demonstrated by focusing on the Young's modulus; similar techniques can be used for other material properties. The results suggest efficient microstructures for engineered cellular materials.

  2. Hierarchical cellular materials

    SciTech Connect

    Gibson, L.J.

    1991-12-31

    In this paper a method for estimating the contributions of both the composite and the cellular microstructures to the overall material properties and the mechanical efficiency of natural cellular solids will be described. The method will be demonstrated by focusing on the Young`s modulus; similar techniques can be used for other material properties. The results suggest efficient microstructures for engineered cellular materials.

  3. Passive Noise Filtering by Cellular Compartmentalization.

    PubMed

    Stoeger, Thomas; Battich, Nico; Pelkmans, Lucas

    2016-03-10

    Chemical reactions contain an inherent element of randomness, which presents itself as noise that interferes with cellular processes and communication. Here we discuss the ability of the spatial partitioning of molecular systems to filter and, thus, remove noise, while preserving regulated and predictable differences between single living cells. In contrast to active noise filtering by network motifs, cellular compartmentalization is highly effective and easily scales to numerous systems without requiring a substantial usage of cellular energy. We will use passive noise filtering by the eukaryotic cell nucleus as an example of how this increases predictability of transcriptional output, with possible implications for the evolution of complex multicellularity. PMID:26967282

  4. Thermodynamics of cellular statistical inference

    NASA Astrophysics Data System (ADS)

    Lang, Alex; Fisher, Charles; Mehta, Pankaj

    2014-03-01

    Successful organisms must be capable of accurately sensing the surrounding environment in order to locate nutrients and evade toxins or predators. However, single cell organisms face a multitude of limitations on their accuracy of sensing. Berg and Purcell first examined the canonical example of statistical limitations to cellular learning of a diffusing chemical and established a fundamental limit to statistical accuracy. Recent work has shown that the Berg and Purcell learning limit can be exceeded using Maximum Likelihood Estimation. Here, we recast the cellular sensing problem as a statistical inference problem and discuss the relationship between the efficiency of an estimator and its thermodynamic properties. We explicitly model a single non-equilibrium receptor and examine the constraints on statistical inference imposed by noisy biochemical networks. Our work shows that cells must balance sample number, specificity, and energy consumption when performing statistical inference. These tradeoffs place significant constraints on the practical implementation of statistical estimators in a cell.

  5. Peroxisome Metabolism and Cellular Aging

    PubMed Central

    Titorenko, Vladimir I.; Terlecky, Stanley R.

    2010-01-01

    The essential role of peroxisomes in fatty acid oxidation, anaplerotic metabolism, and hydrogen peroxide turnover is well established. Recent findings suggest these and other related biochemical processes governed by the organelle may also play a critical role in regulating cellular aging. The goal of this review is to summarize and integrate into a model, the evidence that peroxisome metabolism actually helps define the replicative and chronological age of a eukaryotic cell. In this model, peroxisomal reactive oxygen species (ROS) are seen as altering organelle biogenesis and function, and eliciting changes in the dynamic communication networks that exist between peroxisomes and other cellular compartments. At low levels, peroxisomal ROS activate an anti-aging program in the cell; at concentrations beyond a specific threshold, a pro-aging course is triggered. PMID:21083858

  6. Vehicular ad hoc network for a surveillance system using multifrequency band enhancement

    NASA Astrophysics Data System (ADS)

    Bunruangses, Montree; Sunat, Khamron; Mitatha, Somsak; Yupapin, Preecha P.

    2010-09-01

    We present a new design of a surveillance system via a vehicular ad hoc network (VANET) integrated by a 3-G or 4-G cellular wireless network. We propose dense wavelength division multiplexing wavelength enhancement for increasing the channel capacity and signal security. Increase in the number of channels can be obtained by increasing the wavelength density. Signal security is introduced by a specific wavelength filter controlled by the central operator. Optical communication wavelength enhancement is reviewed. The advantage of this proposed system is that it can easily be implemented and incorporated into the existing communication link in either a cellular or ad hoc wireless system, where signal security and hence privacy can be provided.

  7. Knee-ligament loading properties as influenced by gravity. I - Junction with bone of 3-G rodents

    NASA Technical Reports Server (NTRS)

    Wunder, C. C.; Matthes, R. D.; Tipton, C. M.

    1982-01-01

    The effect of 3-G conditions on the bone-to-ligament junctions of the knee is studied in rats. Results following chronic 3-G centrifugation of rats show that their bone-to-ligament junctions exhibited a force-sustaining capacity (F) which was 95 + or - 12% of the value for the control group. However, F was actually 29 + or - 5% greater for centrifuged rats than for control rats of comparable size, as the experimental animals grew to smaller body mass. It is concluded that gravity determines part of the magnitude of F, and therefore this value will probably be weaker after development in a weightless environment.

  8. Oligomerization transforms human APOBEC3G from an efficient enzyme to a slowly dissociating nucleic acid-binding protein.

    PubMed

    Chaurasiya, Kathy R; McCauley, Micah J; Wang, Wei; Qualley, Dominic F; Wu, Tiyun; Kitamura, Shingo; Geertsema, Hylkje; Chan, Denise S B; Hertz, Amber; Iwatani, Yasumasa; Levin, Judith G; Musier-Forsyth, Karin; Rouzina, Ioulia; Williams, Mark C

    2014-01-01

    The human APOBEC3 proteins are a family of DNA-editing enzymes that play an important role in the innate immune response against retroviruses and retrotransposons. APOBEC3G is a member of this family that inhibits HIV-1 replication in the absence of the viral infectivity factor Vif. Inhibition of HIV replication occurs by both deamination of viral single-stranded DNA and a deamination-independent mechanism. Efficient deamination requires rapid binding to and dissociation from ssDNA. However, a relatively slow dissociation rate is required for the proposed deaminase-independent roadblock mechanism in which APOBEC3G binds the viral template strand and blocks reverse transcriptase-catalysed DNA elongation. Here, we show that APOBEC3G initially binds ssDNA with rapid on-off rates and subsequently converts to a slowly dissociating mode. In contrast, an oligomerization-deficient APOBEC3G mutant did not exhibit a slow off rate. We propose that catalytically active monomers or dimers slowly oligomerize on the viral genome and inhibit reverse transcription. PMID:24345943

  9. Oligomerization transforms human APOBEC3G from an efficient enzyme to a slowly dissociating nucleic acid binding protein

    PubMed Central

    Chaurasiya, Kathy R.; McCauley, Micah J.; Wang, Wei; Qualley, Dominic F.; Wu, Tiyun; Kitamura, Shingo; Geertsema, Hylkje; Chan, Denise S.B.; Hertz, Amber; Iwatani, Yasumasa; Levin, Judith G.; Musier-Forsyth, Karin; Rouzina, Ioulia; Williams, Mark C.

    2014-01-01

    The human APOBEC3 proteins are a family of DNA-editing enzymes that play an important role in the innate immune response and have broad activity against retroviruses and retrotransposons. APOBEC3G is a member of this family that inhibits HIV-1 replication in the absence of the viral infectivity factor Vif. Inhibition of HIV replication occurs by both deamination of viral single-stranded DNA and a deamination-independent mechanism. Efficient deamination requires rapid binding to and dissociation from ssDNA. However, a relatively slow dissociation rate is required for the proposed deaminase-independent roadblock mechanism in which APOBEC3G binds the viral template strand and blocks reverse transcriptase-catalyzed DNA elongation. Here we show that APOBEC3G initially binds ssDNA with rapid on-off rates and subsequently converts to a slowly dissociating mode. In contrast, an oligomerization-deficient APOBEC3G mutant did not exhibit a slow off rate. We propose that catalytically active monomers or dimers slowly oligomerize on the viral genome and inhibit reverse transcription. PMID:24345943

  10. Reactor Dosimetry Applications Using RAPTOR-M3G:. a New Parallel 3-D Radiation Transport Code

    NASA Astrophysics Data System (ADS)

    Longoni, Gianluca; Anderson, Stanwood L.

    2009-08-01

    The numerical solution of the Linearized Boltzmann Equation (LBE) via the Discrete Ordinates method (SN) requires extensive computational resources for large 3-D neutron and gamma transport applications due to the concurrent discretization of the angular, spatial, and energy domains. This paper will discuss the development RAPTOR-M3G (RApid Parallel Transport Of Radiation - Multiple 3D Geometries), a new 3-D parallel radiation transport code, and its application to the calculation of ex-vessel neutron dosimetry responses in the cavity of a commercial 2-loop Pressurized Water Reactor (PWR). RAPTOR-M3G is based domain decomposition algorithms, where the spatial and angular domains are allocated and processed on multi-processor computer architectures. As compared to traditional single-processor applications, this approach reduces the computational load as well as the memory requirement per processor, yielding an efficient solution methodology for large 3-D problems. Measured neutron dosimetry responses in the reactor cavity air gap will be compared to the RAPTOR-M3G predictions. This paper is organized as follows: Section 1 discusses the RAPTOR-M3G methodology; Section 2 describes the 2-loop PWR model and the numerical results obtained. Section 3 addresses the parallel performance of the code, and Section 4 concludes this paper with final remarks and future work.

  11. Oligomerization transforms human APOBEC3G from an efficient enzyme to a slowly dissociating nucleic acid-binding protein

    NASA Astrophysics Data System (ADS)

    Chaurasiya, Kathy R.; McCauley, Micah J.; Wang, Wei; Qualley, Dominic F.; Wu, Tiyun; Kitamura, Shingo; Geertsema, Hylkje; Chan, Denise S. B.; Hertz, Amber; Iwatani, Yasumasa; Levin, Judith G.; Musier-Forsyth, Karin; Rouzina, Ioulia; Williams, Mark C.

    2014-01-01

    The human APOBEC3 proteins are a family of DNA-editing enzymes that play an important role in the innate immune response against retroviruses and retrotransposons. APOBEC3G is a member of this family that inhibits HIV-1 replication in the absence of the viral infectivity factor Vif. Inhibition of HIV replication occurs by both deamination of viral single-stranded DNA and a deamination-independent mechanism. Efficient deamination requires rapid binding to and dissociation from ssDNA. However, a relatively slow dissociation rate is required for the proposed deaminase-independent roadblock mechanism in which APOBEC3G binds the viral template strand and blocks reverse transcriptase-catalysed DNA elongation. Here, we show that APOBEC3G initially binds ssDNA with rapid on-off rates and subsequently converts to a slowly dissociating mode. In contrast, an oligomerization-deficient APOBEC3G mutant did not exhibit a slow off rate. We propose that catalytically active monomers or dimers slowly oligomerize on the viral genome and inhibit reverse transcription.

  12. APOBEC3G generates nonsense mutations in human T-cell leukemia virus type 1 proviral genomes in vivo.

    PubMed

    Fan, Jun; Ma, Guangyong; Nosaka, Kisato; Tanabe, Junko; Satou, Yorifumi; Koito, Atsushi; Wain-Hobson, Simon; Vartanian, Jean-Pierre; Matsuoka, Masao

    2010-07-01

    Human T-cell leukemia virus type 1 (HTLV-1) induces cell proliferation after infection, leading to efficient transmission by cell-to-cell contact. After a long latent period, a fraction of carriers develop adult T-cell leukemia (ATL). Genetic changes in the tax gene in ATL cells were reported in about 10% of ATL cases. To determine genetic changes that may occur throughout the provirus, we determined the entire sequence of the HTLV-1 provirus in 60 ATL cases. Abortive genetic changes, including deletions, insertions, and nonsense mutations, were frequent in all viral genes except the HBZ gene, which is transcribed from the minus strand of the virus. G-to-A base substitutions were the most frequent mutations in ATL cells. The sequence context of G-to-A mutations was in accordance with the preferred target sequence of human APOBEC3G (hA3G). The target sequences of hA3G were less frequent in the plus strand of the HBZ coding region than in other coding regions of the HTLV-1 provirus. Nonsense mutations in viral genes including tax were also observed in proviruses from asymptomatic carriers, indicating that these mutations were generated during reverse transcription and prior to oncogenesis. The fact that hA3G targets the minus strand during reverse transcription explains why the HBZ gene is not susceptible to such nonsense mutations. HTLV-1-infected cells likely take advantage of hA3G to escape from the host immune system by losing expression of viral proteins. PMID:20463074

  13. Fundamental Limits to Cellular Sensing

    NASA Astrophysics Data System (ADS)

    ten Wolde, Pieter Rein; Becker, Nils B.; Ouldridge, Thomas E.; Mugler, Andrew

    2016-03-01

    In recent years experiments have demonstrated that living cells can measure low chemical concentrations with high precision, and much progress has been made in understanding what sets the fundamental limit to the precision of chemical sensing. Chemical concentration measurements start with the binding of ligand molecules to receptor proteins, which is an inherently noisy process, especially at low concentrations. The signaling networks that transmit the information on the ligand concentration from the receptors into the cell have to filter this receptor input noise as much as possible. These networks, however, are also intrinsically stochastic in nature, which means that they will also add noise to the transmitted signal. In this review, we will first discuss how the diffusive transport and binding of ligand to the receptor sets the receptor correlation time, which is the timescale over which fluctuations in the state of the receptor, arising from the stochastic receptor-ligand binding, decay. We then describe how downstream signaling pathways integrate these receptor-state fluctuations, and how the number of receptors, the receptor correlation time, and the effective integration time set by the downstream network, together impose a fundamental limit on the precision of sensing. We then discuss how cells can remove the receptor input noise while simultaneously suppressing the intrinsic noise in the signaling network. We describe why this mechanism of time integration requires three classes (groups) of resources—receptors and their integration time, readout molecules, energy—and how each resource class sets a fundamental sensing limit. We also briefly discuss the scheme of maximum-likelihood estimation, the role of receptor cooperativity, and how cellular copy protocols differ from canonical copy protocols typically considered in the computational literature, explaining why cellular sensing systems can never reach the Landauer limit on the optimal trade

  14. 78 FR 958 - Certain Wireless Devices With 3G and/or 4G Capabilities and Components Thereof Notice of Receipt...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-01-07

    ... COMMISSION Certain Wireless Devices With 3G and/or 4G Capabilities and Components Thereof Notice of Receipt... Commission has received a complaint entitled Certain Wireless Devices with 3G and/or 4G Capabilities and... importation, and the sale within the United States after importation of certain wireless devices with 3g...

  15. SonTek SL3G Side-Looking Doppler Current Meter application in Complex Flow Conditions

    NASA Astrophysics Data System (ADS)

    Wagenaar, D.

    2014-12-01

    The SonTek Argonaut SL Side-Looking Doppler Current Meters are well established products in the measurement of real-time water velocity in open channels. With the development of acoustic doppler technology the decision was made to incorporate latest technology in the Argonaut SL and hence the SonTek SL3G was born.The SonTek SL3G Acoustic Doppler instrument incorporates a number of innovations that improves velocity measurements and quality assurance of data for Side-Looking Doppler Current Meters. SmartPulseHD was originally introduced with the launch of the SonTek M9/S5 RiverSurveyor Acoustic Doppler Instruments and the increased accuracy and resolution of velocity measurements made it obvious to include into the new SL3G instruments. SmartPulseHD continuously tracks the water conditions and selects the optimum processing configuration required using multiple ping types and processing techniques. The new SL3G design makes it the smallest Side Looking Acoustic Doppler Velocity Meter on the market reducing flow disturbance caused by the instrument and the distance of first measurement cell from boundary.The application of the SL3G Acoustic Doppler instrument is designed for complex flow conditions where the use of conventional stage-discharge relationships is economically not viable and therefore requires the use of velocity index methodology. The case-study presented in this paper is situated in the Colorado River downstream of Imperial Dam affected by controlled releases, drainage from adjacent irrigation areas and backwater from a weir situated downstream of the monitoring site. The paper analyses the relationship between measured mean velocity and index velocity and if additional variables such as stage and or Y-velocity need to be incorporated in the development of the index velocity rating. In addition, to determine the variables impacting on the index velocity rating, the index velocity applied will be evaluated by the best linear relationship between the

  16. Crystal Structure of DNA Cytidine Deaminase ABOBEC3G Catalytic Deamination Domain Suggests a Binding Mode of Full-length Enzyme to Single-stranded DNA*

    PubMed Central

    Lu, Xiuxiu; Zhang, Tianlong; Xu, Zeng; Liu, Shanshan; Zhao, Bin; Lan, Wenxian; Wang, Chunxi; Ding, Jianping; Cao, Chunyang

    2015-01-01

    APOBEC3G (A3G) is a DNA cytidine deaminase (CD) that demonstrates antiviral activity against human immunodeficiency virus 1 (HIV-1) and other pathogenic virus. It has an inactive N-terminal CD1 virus infectivity factor (Vif) protein binding domain (A3G-CD1) and an actively catalytic C-terminal CD2 deamination domain (A3G-CD2). Although many studies on the structure of A3G-CD2 and enzymatic properties of full-length A3G have been reported, the mechanism of how A3G interacts with HIV-1 single-stranded DNA (ssDNA) is still not well characterized. Here, we reported a crystal structure of a novel A3G-CD2 head-to-tail dimer (in which the N terminus of the monomer H (head) interacts with the C terminus of monomer T (tail)), where a continuous DNA binding groove was observed. By constructing the A3G-CD1 structural model, we found that its overall fold was almost identical to that of A3G-CD2. We mutated the residues located in or along the groove in monomer H and the residues in A3G-CD1 that correspond to those seated in or along the groove in monomer T. Then, by performing enzymatic assays, we confirmed the reported key elements and the residues in A3G necessary to the catalytic deamination. Moreover, we identified more than 10 residues in A3G essential to DNA binding and deamination reaction. Therefore, this dimer structure may represent a structural model of full-length A3G, which indicates a possible binding mode of A3G to HIV-1 ssDNA. PMID:25542899

  17. Crystal structure of DNA cytidine deaminase ABOBEC3G catalytic deamination domain suggests a binding mode of full-length enzyme to single-stranded DNA.

    PubMed

    Lu, Xiuxiu; Zhang, Tianlong; Xu, Zeng; Liu, Shanshan; Zhao, Bin; Lan, Wenxian; Wang, Chunxi; Ding, Jianping; Cao, Chunyang

    2015-02-13

    APOBEC3G (A3G) is a DNA cytidine deaminase (CD) that demonstrates antiviral activity against human immunodeficiency virus 1 (HIV-1) and other pathogenic virus. It has an inactive N-terminal CD1 virus infectivity factor (Vif) protein binding domain (A3G-CD1) and an actively catalytic C-terminal CD2 deamination domain (A3G-CD2). Although many studies on the structure of A3G-CD2 and enzymatic properties of full-length A3G have been reported, the mechanism of how A3G interacts with HIV-1 single-stranded DNA (ssDNA) is still not well characterized. Here, we reported a crystal structure of a novel A3G-CD2 head-to-tail dimer (in which the N terminus of the monomer H (head) interacts with the C terminus of monomer T (tail)), where a continuous DNA binding groove was observed. By constructing the A3G-CD1 structural model, we found that its overall fold was almost identical to that of A3G-CD2. We mutated the residues located in or along the groove in monomer H and the residues in A3G-CD1 that correspond to those seated in or along the groove in monomer T. Then, by performing enzymatic assays, we confirmed the reported key elements and the residues in A3G necessary to the catalytic deamination. Moreover, we identified more than 10 residues in A3G essential to DNA binding and deamination reaction. Therefore, this dimer structure may represent a structural model of full-length A3G, which indicates a possible binding mode of A3G to HIV-1 ssDNA. PMID:25542899

  18. Modelling cellular behaviour

    NASA Astrophysics Data System (ADS)

    Endy, Drew; Brent, Roger

    2001-01-01

    Representations of cellular processes that can be used to compute their future behaviour would be of general scientific and practical value. But past attempts to construct such representations have been disappointing. This is now changing. Increases in biological understanding combined with advances in computational methods and in computer power make it possible to foresee construction of useful and predictive simulations of cellular processes.

  19. The 2100MHz radiofrequency radiation of a 3G-mobile phone and the DNA oxidative damage in brain.

    PubMed

    Sahin, Duygu; Ozgur, Elcin; Guler, Goknur; Tomruk, Arın; Unlu, Ilhan; Sepici-Dinçel, Aylin; Seyhan, Nesrin

    2016-09-01

    We aimed to evaluate the effect of 2100MHz radiofrequency radiation emitted by a generator, simulating a 3G-mobile phone on the brain of rats during 10 and 40 days of exposure. The female rats were randomly divided into four groups. Group I; exposed to 3G modulated 2100MHz RFR signal for 6h/day, 5 consecutive days/wk for 2 weeks, group II; control 10 days, were kept in an inactive exposure set-up for 6h/day, 5 consecutive days/wk for 2 weeks, group III; exposed to 3G modulated 2100MHz RFR signal for 6h/day, 5 consecutive days/wk for 8 weeks and group IV; control 40 days, were kept in an inactive exposure set-up for 6h/day, 5 consecutive days/wk for 8 weeks. After the genomic DNA content of brain was extracted, oxidative DNA damage (8-hydroxy-2'deoxyguanosine, pg/mL) and malondialdehyde (MDA, nmoL/g tissue) levels were determined. Our main finding was the increased oxidative DNA damage to brain after 10 days of exposure with the decreased oxidative DNA damage following 40 days of exposure compared to their control groups. Besides decreased lipid peroxidation end product, MDA, was observed after 40 days of exposure. The measured decreased quantities of damage during the 40 days of exposure could be the means of adapted and increased DNA repair mechanisms. PMID:26775761

  20. Catalytic Analysis of APOBEC3G Involving Real-Time NMR Spectroscopy Reveals Nucleic Acid Determinants for Deamination

    PubMed Central

    Kamba, Keisuke; Nagata, Takashi; Katahira, Masato

    2015-01-01

    APOBEC3G (A3G) is a single-stranded DNA-specific cytidine deaminase that preferentially converts cytidine to uridine at the third position of triplet cytosine (CCC) hotspots. A3G restricts the infectivity of viruses, such as HIV-1, by targeting CCC hotspots scattered through minus DNA strands, reverse-transcribed from genomic RNA. Previously, we developed a real-time NMR method and elucidated the origin of the 3'→5' polarity of deamination of DNA by the C-terminal domain of A3G (CD2), which is a phenomenon by which a hotspot located closer to the 5'-end is deaminated more effectively than one less close to the 5'-end, through quantitative analysis involving nonspecific binding to and sliding along DNA. In the present study we applied the real-time NMR method to analyze the catalytic activity of CD2 toward DNA oligonucleotides containing a nucleotide analog at a single or multiple positions. Analyses revealed the importance of the sugar and base moieties throughout the consecutive 5 nucleotides, the CCC hotspot being positioned at the center. It was also shown that the sugar or base moieties of the nucleotides outside this 5 nucleotide recognition sequence are also relevant as to CD2's activity. Analyses involving DNA oligonucleotides having two CCC hotspots linked by a long sequence of either deoxyribonucleotides, ribonucleotides or abasic deoxyribonucleotides suggested that the phosphate backbone is required for CD2 to slide along the DNA strand and to exert the 3'→5' polarity. Examination of the effects of different salt concentrations on the 3'→5' polarity indicated that the higher the salt concentration, the less prominent the 3'→5' polarity. This is most likely the result of alleviation of sliding due to a decrease in the affinity of CD2 with the phosphate backbone at high salt concentrations. We also investigated the reactivity of substrates containing 5-methylcytidine (5mC) or 5-hydroxymethylcytidine, and found that A3G exhibited low activity toward

  1. Cellular Reflectarray Antenna

    NASA Technical Reports Server (NTRS)

    Romanofsky, Robert R.

    2010-01-01

    The cellular reflectarray antenna is intended to replace conventional parabolic reflectors that must be physically aligned with a particular satellite in geostationary orbit. These arrays are designed for specified geographical locations, defined by latitude and longitude, each called a "cell." A particular cell occupies nominally 1,500 square miles (3,885 sq. km), but this varies according to latitude and longitude. The cellular reflectarray antenna designed for a particular cell is simply positioned to align with magnetic North, and the antenna surface is level (parallel to the ground). A given cellular reflectarray antenna will not operate in any other cell.

  2. Increased expression with differential subcellular location of cytidine deaminase APOBEC3G in human CD4(+) T-cell activation and dendritic cell maturation.

    PubMed

    Oliva, Harold; Pacheco, Rodrigo; Martinez-Navio, José M; Rodríguez-García, Marta; Naranjo-Gómez, Mar; Climent, Núria; Prado, Carolina; Gil, Cristina; Plana, Montserrat; García, Felipe; Miró, José M; Franco, Rafael; Borras, Francesc E; Navaratnam, Naveenan; Gatell, José M; Gallart, Teresa

    2016-08-01

    APOBEC3G (apolipoprotein B mRNA editing enzyme catalytic polypeptide-like 3G; A3G) is an innate defense protein showing activity against retroviruses and retrotransposons. Activated CD4(+) T cells are highly permissive for HIV-1 replication, whereas resting CD4(+) T cells are refractory. Dendritic cells (DCs), especially mature DCs, are also refractory. We investigated whether these differences could be related to a differential A3G expression and/or subcellular distribution. We found that A3G mRNA and protein expression is very low in resting CD4(+) T cells and immature DCs, but increases strongly following T-cell activation and DC maturation. The Apo-7 anti-A3G monoclonal antibody (mAb), which was specifically developed, confirmed these differences at the protein level and disclosed that A3G is mainly cytoplasmic in resting CD4(+) T cells and immature DCs. Nevertheless, A3G translocates to the nucleus in activated-proliferating CD4(+) T cells, yet remaining cytoplasmic in matured DCs, a finding confirmed by immunoblotting analysis of cytoplasmic and nuclear fractions. Apo-7 mAb was able to immunoprecipitate endogenous A3G allowing to detect complexes with numerous proteins in activated-proliferating but not in resting CD4(+) T cells. The results show for the first time the nuclear translocation of A3G in activated-proliferating CD4(+) T cells. PMID:26987686

  3. CELLULAR MAGNESIUM HOMEOSTASIS

    PubMed Central

    Romani, Andrea M.P.

    2011-01-01

    Magnesium, the second most abundant cellular cation after potassium, is essential to regulate numerous cellular functions and enzymes, including ion channels, metabolic cycles, and signaling pathways, as attested by more than 1000 entries in the literature. Despite significant recent progress, however, our understanding of how cells regulate Mg2+ homeostasis and transport still remains incomplete. For example, the occurrence of major fluxes of Mg2+ in either direction across the plasma membrane of mammalian cells following metabolic or hormonal stimuli has been extensively documented. Yet, the mechanisms ultimately responsible for magnesium extrusion across the cell membrane have not been cloned. Even less is known about the regulation in cellular organelles. The present review is aimed at providing the reader with a comprehensive and up-to-date understanding of the mechanisms enacted by eukaryotic cells to regulate cellular Mg2+ homeostasis and how these mechanisms are altered under specific pathological conditions. PMID:21640700

  4. The C3G/Rap1 pathway promotes secretion of MMP-2 and MMP-9 and is involved in serous ovarian cancer metastasis.

    PubMed

    Che, Ya-Ling; Luo, Shu-Juan; Li, Gang; Cheng, Min; Gao, Yi-Meng; Li, Xue-Mei; Dai, Jie-Min; He, Huan; Wang, Jin; Peng, Hui-Juan; Zhang, Yu; Li, Wen-Yan; Wang, Hui; Liu, Bin; Linghu, Hua

    2015-04-10

    Complete resection is pivotal to improve survival to epithelial ovarian cancer (EOC). Crk SH3-domain-binding guanine nucleotide-releasing factor (C3G) is involved in multiple signaling pathways and it has opposite roles in different cancers. The present study aimed to identify C3G expression in ovarian tissue samples from patients with EOC and to explore its association with tumor grade. Eighty-seven archival paraffin-embedded, formalin-fixed, ovarian cancer tissues with serous histology were stained for C3G by immunohistochemistry. To evaluate the contribution of C3G to Rap1 activity, 36 patients with serous ovarian cancer (SOC) were investigated. Additionally, C3G was knocked down in SKOV3 and HEY cells. C3G regulated Rap1 activity and high Rap1 activity was correlated with poor differentiation, advanced FIGO stage, and unsuccessful cytoreductive surgery of SOC. Knockdown of C3G suppressed cell invasion, intravasation and extravasation, and reduced Rap1 activity and secretion of matrix metalloproteinase (MMP)-2 and MMP-9. C3G-mediated activation of Rap1 could direct the tumor pattern of human SOC by promoting the secretion of MMP-2 and MMP-9. These results suggest that C3G is involved in the metastatic spread of EOC. PMID:25617801

  5. Fabrication of large dual-polarized multichroic TES bolometer arrays for CMB measurements with the SPT-3G camera

    NASA Astrophysics Data System (ADS)

    Posada, C. M.; Ade, P. A. R.; Ahmed, Z.; Arnold, K.; Austermann, J. E.; Bender, A. N.; Bleem, L. E.; Benson, B. A.; Byrum, K.; Carlstrom, J. E.; Chang, C. L.; Cho, H. M.; Ciocys, S. T.; Cliche, J. F.; Crawford, T. M.; Cukierman, A.; Czaplewski, D.; Ding, J.; Divan, R.; de Haan, T.; Dobbs, M. A.; Dutcher, D.; Everett, W.; Gilbert, A.; Halverson, N. W.; Harrington, N. L.; Hattori, K.; Henning, J. W.; Hilton, G. C.; Holzapfel, W. L.; Hubmayr, J.; Irwin, K. D.; Jeong, O.; Keisler, R.; Kubik, D.; Kuo, C. L.; Lee, A. T.; Leitch, E. M.; Lendinez, S.; Meyer, S. S.; Miller, C. S.; Montgomery, J.; Myers, M.; Nadolski, A.; Natoli, T.; Nguyen, H.; Novosad, V.; Padin, S.; Pan, Z.; Pearson, J.; Ruhl, J. E.; Saliwanchik, B. R.; Smecher, G.; Sayre, J. T.; Shirokoff, E.; Stan, L.; Stark, A. A.; Sobrin, J.; Story, K.; Suzuki, A.; Thompson, K. L.; Tucker, C.; Vanderlinde, K.; Vieira, J. D.; Wang, G.; Whitehorn, N.; Yefremenko, V.; Yoon, K. W.; Ziegler, K. E.

    2015-09-01

    This work presents the procedures used at Argonne National Laboratory to fabricate large arrays of multichroic transition-edge sensor (TES) bolometers for cosmic microwave background (CMB) measurements. These detectors will be assembled into the focal plane for the SPT-3G camera, the third generation CMB camera to be installed in the South Pole Telescope. The complete SPT-3G camera will have approximately 2690 pixels, for a total of 16 140 TES bolometric detectors. Each pixel is comprised of a broad-band sinuous antenna coupled to a Nb microstrip line. In-line filters are used to define the different bands before the millimeter-wavelength signal is fed to the respective Ti/Au TES bolometers. There are six TES bolometer detectors per pixel, which allow for measurements of three band-passes (95, 150 and 220 GHz) and two polarizations. The steps involved in the monolithic fabrication of these detector arrays are presented here in detail. Patterns are defined using a combination of stepper and contact lithography. The misalignment between layers is kept below 200 nm. The overall fabrication involves a total of 16 processes, including reactive and magnetron sputtering, reactive ion etching, inductively coupled plasma etching and chemical etching.

  6. Architected Cellular Materials

    NASA Astrophysics Data System (ADS)

    Schaedler, Tobias A.; Carter, William B.

    2016-07-01

    Additive manufacturing enables fabrication of materials with intricate cellular architecture, whereby progress in 3D printing techniques is increasing the possible configurations of voids and solids ad infinitum. Examples are microlattices with graded porosity and truss structures optimized for specific loading conditions. The cellular architecture determines the mechanical properties and density of these materials and can influence a wide range of other properties, e.g., acoustic, thermal, and biological properties. By combining optimized cellular architectures with high-performance metals and ceramics, several lightweight materials that exhibit strength and stiffness previously unachievable at low densities were recently demonstrated. This review introduces the field of architected materials; summarizes the most common fabrication methods, with an emphasis on additive manufacturing; and discusses recent progress in the development of architected materials. The review also discusses important applications, including lightweight structures, energy absorption, metamaterials, thermal management, and bioscaffolds.

  7. Approaches to Biosimulation of Cellular Processes

    PubMed Central

    Westerhoff, H. V.

    2006-01-01

    Modelling and simulation are at the heart of the rapidly developing field of systems biology. This paper reviews various types of models, simulation methods, and theoretical approaches that are presently being used in the quantitative description of cellular processes. We first describe how molecular interaction networks can be represented by means of stoichiometric, topological and kinetic models. We briefly discuss the formulation of kinetic models using mesoscopic (stochastic) or macroscopic (continuous) approaches, and we go on to describe how detailed models of molecular interaction networks (silicon cells) can be constructed on the basis of experimentally determined kinetic parameters for cellular processes. We show how theory can help in analyzing models by applying control analysis to a recently published silicon cell model. Finally, we review some of the theoretical approaches available to analyse kinetic models and experimental data, respectively. PMID:19669467

  8. A Hydrodynamic Analysis of APOBEC3G Reveals a Monomer-Dimer-Tetramer Self-Association that has Implications for Anti-HIV Function†

    PubMed Central

    Salter, Jason D.; Krucinska, Jolanta; Raina, Jay; Smith, Harold C.; Wedekind, Joseph E.

    2009-01-01

    The innate antiviral factor APOBEC3G (A3G) possesses RNA binding activity and deaminates HIV-1 DNA. High-molecular-mass forms of A3G can be isolated from a variety of cell types, but exhibit limited deaminase activity relative to low-molecular-mass species prepared under RNA-depleted conditions. To investigate the fundamental oligomeric state and shape of A3G, we conducted sedimentation velocity analyses of the pure enzyme under RNA-deficient conditions. The results reveal a predominant dimer in equilibrium with minor monomeric and tetrameric species. Hydrodynamic modeling of the dimer supports an extended cylindrical shape that assembles into an elongated tetramer. Overall, the results provide physical restraints for the A3G quaternary structure that have implications for modulating antiviral function. PMID:19839647

  9. Genetic Dominance & Cellular Processes

    ERIC Educational Resources Information Center

    Seager, Robert D.

    2014-01-01

    In learning genetics, many students misunderstand and misinterpret what "dominance" means. Understanding is easier if students realize that dominance is not a mechanism, but rather a consequence of underlying cellular processes. For example, metabolic pathways are often little affected by changes in enzyme concentration. This means that…

  10. Teaching cellular engineering.

    PubMed

    Hammer, Daniel A; Waugh, Richard E

    2006-02-01

    Cellular engineering is one of the fastest growing subdisciplines in the field of Biomedical Engineering. It involves the application of engineering analysis to understand and control cellular behavior, with the ultimate objective of developing novel therapeutic or diagnostic approaches for the clinic or harnessing cellular function for commercial applications. Well-educated students in this area need strong foundational knowledge in engineering science, chemistry, and cell and molecular biology. In undergraduate curricula, the challenge is to include essential engineering skills plus appropriate levels of training in chemistry and biology while satisfying accreditation-mandated breadth in engineering training. At the graduate level, educators must accommodate students with diverse backgrounds and provide them with both a state-of-the-art understanding of the life sciences and the most advanced engineering skills. Engineering curricular content should include mechanics and materials, physical chemistry, transport phenomena, and control theory. Training from faculty with appointments and research programs in the life sciences is generally recommended, and additional life science content should also be integrated within the engineering curriculum. A capstone course in cellular engineering that includes opportunities for students to have hands-on experiences with state-of-the-art laboratory techniques is highly recommended. PMID:16450196

  11. Auxin and Cellular Elongation.

    PubMed

    Velasquez, Silvia Melina; Barbez, Elke; Kleine-Vehn, Jürgen; Estevez, José M

    2016-03-01

    Auxin is a crucial growth regulator in plants. However, a comprehensive understanding of how auxin induces cell expansion is perplexing, because auxin acts in a concentration- and cell type-dependent manner. Consequently, it is desirable to focus on certain cell types to exemplify the underlying growth mechanisms. On the other hand, plant tissues display supracellular growth (beyond the level of single cells); hence, other cell types might compromise the growth of a certain tissue. Tip-growing cells do not display neighbor-induced growth constraints and, therefore, are a valuable source of information for growth-controlling mechanisms. Here, we focus on auxin-induced cellular elongation in root hairs, exposing a mechanistic view of plant growth regulation. We highlight a complex interplay between auxin metabolism and transport, steering root hair development in response to internal and external triggers. Auxin signaling modules and downstream cascades of transcription factors define a developmental program that appears rate limiting for cellular growth. With this knowledge in mind, the root hair cell is a very suitable model system in which to dissect cellular effectors required for cellular expansion. PMID:26787325

  12. The New Cellular Immunology

    ERIC Educational Resources Information Center

    Claman, Henry N.

    1973-01-01

    Discusses the nature of the immune response and traces many of the discoveries that have led to the present state of knowledge in immunology. The new cellular immunology is directing its efforts toward improving health by proper manipulation of the immune mechanisms of the body. (JR)

  13. Statistical properties of cellular automata in the context of learning and recognition: Part 1, Introduction

    SciTech Connect

    Gutowitz, H.A.

    1988-11-17

    In this lecture the map from a cellular automaton to a sequence of analytical approximations called the local structure theory is described. Connections are drawn between cellular automata and neural network models. It is suggested that the process by which a cellular automaton holds particular probability measures invariant is an appropriate model for biological memory. 20 figs.

  14. Fabrication of cellular materials

    NASA Astrophysics Data System (ADS)

    Prud'homme, Robert K.; Aksay, Ilhan A.; Garg, Rajeev

    1996-02-01

    Nature uses cellular materials in applications requiring strength while, simultaneously, minimizing raw materials requirements. Minimizing raw materials is efficient both in terms of the energy expended by the organism to synthesize the structure and in terms of the strength- to-weight ratio of the structure. Wood is the most obvious example of cellular bio-materials, and it is the focus of other presentations in this symposium. The lightweight bone structure of birds is another excellent example where weight is a key criterion. The anchoring foot of the common muscle [Mytilus edulis] whereby it attaches itself to objects is a further example of a biological system that uses a foam to fill space and yet conserve on raw materials. In the case of the muscle the foam is water filled and the foot structure distributes stress over a larger area so that the strength of the byssal thread from which it is suspended is matched to the strength of interfacial attachment of the foot to a substrate. In these examples the synthesis and fabrication of the cellular material is directed by intercellular, genetically coded, biochemical reactions. The resulting cell sizes are microns in scale. Cellular materials at the next larger scale are created by organisms at the next higher level of integration. For example an African tree frog lays her eggs in a gas/fluid foam sack she builds on a branch overhanging a pond. The outside of the foam sack hardens in the sun and prevents water evaporation. The foam structure minimizes the amount of fluid that needs to be incorporated into the sack and minimizes its weight. However, as far as the developing eggs are concerned, they are in an aqueous medium, i.e. the continuous fluid phase of the foam. After precisely six days the eggs hatch, and the solidified outer wall re-liquefies and dumps the emerging tadpoles into the pond below. The bee honeycomb is an example of a cellular material with exquisite periodicity at millimeter length scales. The

  15. Integration of cellular signals in chattering environments.

    PubMed

    Rué, P; Domedel-Puig, N; Garcia-Ojalvo, J; Pons, A J

    2012-09-01

    Cells are constantly exposed to fluctuating environmental conditions. External signals are sensed, processed and integrated by cellular signal transduction networks, which translate input signals into specific cellular responses by means of biochemical reactions. These networks have a complex nature, and we are still far from having a complete characterization of the process through which they integrate information, specially given the noisy environment in which that information is embedded. Guided by the many instances of constructive influences of noise that have been reported in the physical sciences in the last decades, here we explore how multiple signals are integrated in an eukaryotic cell in the presence of background noise, or chatter. To that end, we use a Boolean model of a typical human signal transduction network. Despite its complexity, we find that the network is able to display simple patterns of signal integration. Furthermore, our computational analysis shows that these integration patterns depend on the levels of fluctuating background activity carried by other cell inputs. Taken together, our results indicate that signal integration is sensitive to environmental fluctuations, and that this background noise effectively determines the information integration capabilities of the cell. PMID:22584015

  16. Cellular growth in biofilms

    SciTech Connect

    Wood, B.D.; Whitaker, S.

    1999-09-20

    In this paper the authors develop a macroscopic evolutionary equation for the growth of the cellular phase starting from a microscopic description of mass transport and a simple structured model for product formation. The methods of continuum mechanics and volume averaging are used to develop the macroscopic representation by carefully considering the fluxes of chemical species that pertain to cell growth. The concept of structured models is extended to include the transport of reacting chemical species at the microscopic scale. The resulting macroscopic growth model is similar in form to previously published models for the transport of a single substrate and electron donor and for the production of cellular mass and exopolymer. The method of volume averaging indicated under what conditions the developed growth model is valid and provides an explicit connection between the relevant microscopic model parameters and their corresponding macroscopic counterparts.

  17. Cellular dysfunction in sepsis.

    PubMed

    Singer, Mervyn

    2008-12-01

    Cellular dysfunction is a commonplace sequelum of sepsis and other systemic inflammatory conditions. Impaired energy production (related to mitochondrial inhibition, damage, and reduced protein turnover) appears to be a core mechanism underlying the development of organ dysfunction. The reduction in energy availability appears to trigger a metabolic shutdown that impairs normal functioning of the cell. This may well represent an adaptive mechanism analogous to hibernation that prevents a massive degree of cell death and thus enables eventual recovery in survivors. PMID:18954700

  18. Radiolabeled cellular blood elements

    SciTech Connect

    Thakur, M.L.; Ezikowitz, M.D.; Hardeman, M.R.

    1985-01-01

    This book contains papers delivered by guest lectures and participants at the Advanced Study Institute's colloquium on Radiolabeled Cellular Blood Elements at Maratea, Italy on August 29, to September 9, 1982. The book includes chapters on basic cell physiology and critical reviews of data and experience in the preparation and use of radiolabeled cells, as well as reports on very recent developments, from a faculty that included experts on cell physiology in health and disease and on the technology of in vivo labeling.

  19. Biochemical Basis of Immunological and Retroviral Responses to DNA-targeted Cytosine Deamination by Activation-induced Cytidine Deaminase and APOBEC3G*

    PubMed Central

    Chelico, Linda; Pham, Phuong; Petruska, John; Goodman, Myron F.

    2009-01-01

    Activation-induced cytidine deaminase (AID) and APOBEC3G catalyze deamination of cytosine to uracil on single-stranded DNA, thereby setting in motion a regulated hypermutagenic process essential for human well-being. However, if regulation fails, havoc ensues. AID plays a central role in the synthesis of high affinity antibodies, and APOBEC3G inactivates human immunodeficiency virus-1. This minireview highlights biochemical and structural properties of AID and APOBEC3G, showing how studies using the purified enzymes provide valuable insight into the considerably more complex biology governing antibody generation and human immunodeficiency virus inactivation. PMID:19684020

  20. Predictability in cellular automata.

    PubMed

    Agapie, Alexandru; Andreica, Anca; Chira, Camelia; Giuclea, Marius

    2014-01-01

    Modelled as finite homogeneous Markov chains, probabilistic cellular automata with local transition probabilities in (0, 1) always posses a stationary distribution. This result alone is not very helpful when it comes to predicting the final configuration; one needs also a formula connecting the probabilities in the stationary distribution to some intrinsic feature of the lattice configuration. Previous results on the asynchronous cellular automata have showed that such feature really exists. It is the number of zero-one borders within the automaton's binary configuration. An exponential formula in the number of zero-one borders has been proved for the 1-D, 2-D and 3-D asynchronous automata with neighborhood three, five and seven, respectively. We perform computer experiments on a synchronous cellular automaton to check whether the empirical distribution obeys also that theoretical formula. The numerical results indicate a perfect fit for neighbourhood three and five, which opens the way for a rigorous proof of the formula in this new, synchronous case. PMID:25271778

  1. Probabilistic cellular automata.

    PubMed

    Agapie, Alexandru; Andreica, Anca; Giuclea, Marius

    2014-09-01

    Cellular automata are binary lattices used for modeling complex dynamical systems. The automaton evolves iteratively from one configuration to another, using some local transition rule based on the number of ones in the neighborhood of each cell. With respect to the number of cells allowed to change per iteration, we speak of either synchronous or asynchronous automata. If randomness is involved to some degree in the transition rule, we speak of probabilistic automata, otherwise they are called deterministic. With either type of cellular automaton we are dealing with, the main theoretical challenge stays the same: starting from an arbitrary initial configuration, predict (with highest accuracy) the end configuration. If the automaton is deterministic, the outcome simplifies to one of two configurations, all zeros or all ones. If the automaton is probabilistic, the whole process is modeled by a finite homogeneous Markov chain, and the outcome is the corresponding stationary distribution. Based on our previous results for the asynchronous case-connecting the probability of a configuration in the stationary distribution to its number of zero-one borders-the article offers both numerical and theoretical insight into the long-term behavior of synchronous cellular automata. PMID:24999557

  2. Quantum cellular automata

    NASA Astrophysics Data System (ADS)

    Porod, Wolfgang; Lent, Craig S.; Bernstein, Gary H.

    1994-06-01

    The Notre Dame group has developed a new paradigm for ultra-dense and ultra-fast information processing in nanoelectronic systems. These Quantum Cellular Automata (QCA's) are the first concrete proposal for a technology based on arrays of coupled quantum dots. The basic building block of these cellular arrays is the Notre Dame Logic Cell, as it has been called in the literature. The phenomenon of Coulomb exclusion, which is a synergistic interplay of quantum confinement and Coulomb interaction, leads to a bistable behavior of each cell which makes possible their use in large-scale cellular arrays. The physical interaction between neighboring cells has been exploited to implement logic functions. New functionality may be achieved in this fashion, and the Notre Dame group invented a versatile majority logic gate. In a series of papers, the feasibility of QCA wires, wire crossing, inverters, and Boolean logic gates was demonstrated. A major finding is that all logic functions may be integrated in a hierarchial fashion which allows the design of complicated QCA structures. The most complicated system which was simulated to date is a one-bit full adder consisting of some 200 cells. In addition to exploring these new concepts, efforts are under way to physically realize such structures both in semiconductor and metal systems. Extensive modeling work of semiconductor quantum dot structures has helped identify optimum design parameters for QCA experimental implementations.

  3. Decolorization of the anthraquinone dye Cibacron Blue 3G-A with immobilized Coprinus cinereus in fluidized bed bioreactor.

    PubMed

    Moutaouakkil, A; Blaghen, M

    2011-01-01

    Coprinus cinereus, which was able to decolorize the anthraquinone dye Cibacron Blue 3G-A (CB) enzymatically, was used as a biocatalyst for the decolorization of synthetic solutions containing this reactive dye. Coprinus cinereus was immobilized in both calcium alginate and polyacrylamide gels, and was used for the decolorization of CB from synthetic water by using a fluidized bed bioreactor. The highest specific decolorization rate was obtained when Coprinus cinereus was entrapped in calcium alginate beads, and was of about 3.84 mg g(-1) h(-1) with a 50% conversion time (t1/2) of about 2.60 h. Moreover, immobilized fungal biomass in calcium alginate continuously decolorized CB even after 7 repeated experiments without significant loss of activity, while polyacrylamide-immobilized fungal biomass retained only 67% of its original activity. The effects of some physicochemical parameters such as temperature, pH and dye concentration on decolorization performance of isolated fungal strain were also investigated. PMID:21438473

  4. VizieR Online Data Catalog: ISOCAM survey of Serpens/G3-G6 (Djupvik+, 2006)

    NASA Astrophysics Data System (ADS)

    Djupvik, A. A.; Andre, P.; Bontemps, S.; Motte, F.; Olofsson, G.; Gaalfalk, M.; Floren, H.-G.

    2006-08-01

    We present results from an ISOCAM survey in the two broadband filters LW2 (5-8.5um) and LW3 (12-18um) of a 19'x16' field called Serp_NH3 centred on the optical group Serpens/G3-G6. A total of 186 sources were detected in the 6.7um band and/or the 14.3um band to a limiting sensitivity of ~2mJy. These have been cross-correlated with the 2MASS catalogue and are all listed in table1. Deep follow-up photometry in the Ks band obtained with Arnica at the Nordic Optical Telescope (NOT) is listed in table2. Deep L' band photometry of selected sources using SIRCA at the NOT is listed in table3. Continuum emission at 1.3mm and 3.6cm was observed with IRAM and VLA, respectively, and deep imaging in the 2.12um S(1) line of H2 was obtained with NOTCam at the NOT. We find strong evidence for a stellar population of 31 Class II sources (listed in table5), 5 flat-spectrum sources, 5 Class I sources (listed in table4), and two Class 0 sources. Our method does not sample the Class III sources. (3 data files).

  5. SensorWeb 3G: Extending On-Orbit Sensor Capabilities to Enable Near Realtime User Configurability

    NASA Technical Reports Server (NTRS)

    Mandl, Daniel; Cappelaere, Pat; Frye, Stuart; Sohlberg, Rob; Ly, Vuong; Chien, Steve; Tran, Daniel; Davies, Ashley; Sullivan, Don; Ames, Troy; Witt, Ken; Stanley, Jason

    2010-01-01

    This research effort prototypes an implementation of a standard interface, Web Coverage Processing Service (WCPS), which is an Open Geospatial Consortium(OGC) standard, to enable users to define, test, upload and execute algorithms for on-orbit sensor systems. The user is able to customize on-orbit data products that result from raw data streaming from an instrument. This extends the SensorWeb 2.0 concept that was developed under a previous Advanced Information System Technology (AIST) effort in which web services wrap sensors and a standardized Extensible Markup Language (XML) based scripting workflow language orchestrates processing steps across multiple domains. SensorWeb 3G extends the concept by providing the user controls into the flight software modules associated with on-orbit sensor and thus provides a degree of flexibility which does not presently exist. The successful demonstrations to date will be presented, which includes a realistic HyspIRI decadal mission testbed. Furthermore, benchmarks that were run will also be presented along with future demonstration and benchmark tests planned. Finally, we conclude with implications for the future and how this concept dovetails into efforts to develop "cloud computing" methods and standards.

  6. Femur-bending properties as influenced by gravity. I - Ultimate load and moment for 3-G rats

    NASA Technical Reports Server (NTRS)

    Wunder, C. C.; Welch, R. C.; Glade, R.; Fleming, B. P.; Cook, K. M.

    1977-01-01

    Fresh experimental bones can withstand greater bending forces and moments after 1.0 to 2.5 weeks of 3-G exposure. This appears more attributable to a 50% greater strength of bone material than to effects upon size or shape, and is most measurable for animals of 5 to 8 weeks of age. Experimental bone material seems to grow to its mature level at a younger age rather then there being so marked an effect upon the mature level itself. We simulated 3.1 G by chronic centrifugation of 66 albino rats and compared them to 63 1-G controls. Extrapolation of the simplest mathematical description of the present results to weaker, zero-G bones could be tested by a total of 60 space-based control and experimental animals. A flight of only 15 animals would be necessary for comparison to ground-based control animals. This is consistent with reports of bone demineralization during space-flight. In light of the differences in bone histology, however, extrapolation of these results to humans would be premature and, if at all applicable, are most likely to be so for children rather than adults.

  7. Inter-Cellular Forces Orchestrate Contact Inhibition of Locomotion

    PubMed Central

    Davis, John R.; Luchici, Andrei; Mosis, Fuad; Thackery, James; Salazar, Jesus A.; Mao, Yanlan; Dunn, Graham A.; Betz, Timo; Miodownik, Mark; Stramer, Brian M.

    2015-01-01

    Summary Contact inhibition of locomotion (CIL) is a multifaceted process that causes many cell types to repel each other upon collision. During development, this seemingly uncoordinated reaction is a critical driver of cellular dispersion within embryonic tissues. Here, we show that Drosophila hemocytes require a precisely orchestrated CIL response for their developmental dispersal. Hemocyte collision and subsequent repulsion involves a stereotyped sequence of kinematic stages that are modulated by global changes in cytoskeletal dynamics. Tracking actin retrograde flow within hemocytes in vivo reveals synchronous reorganization of colliding actin networks through engagement of an inter-cellular adhesion. This inter-cellular actin-clutch leads to a subsequent build-up in lamellar tension, triggering the development of a transient stress fiber, which orchestrates cellular repulsion. Our findings reveal that the physical coupling of the flowing actin networks during CIL acts as a mechanotransducer, allowing cells to haptically sense each other and coordinate their behaviors. PMID:25799385

  8. A synthetic biology approach to understanding cellular information processing

    PubMed Central

    Riccione, Katherine A; Smith, Robert P; Lee, Anna J; You, Lingchong

    2012-01-01

    The survival of cells and organisms requires proper responses to environmental signals. These responses are governed by cellular networks, which serve to process diverse environmental cues. Biological networks often contain recurring network topologies called ‘motifs’. It has been recognized that the study of such motifs allows one to predict the response of a biological network, and thus cellular behavior. However, studying a single motif in complete isolation of all other network motifs in a natural setting is difficult. Synthetic biology has emerged as a powerful approach to understanding the dynamic properties of network motifs. In addition to testing existing theoretical predictions, construction and analysis of synthetic gene circuits has led to the discovery of novel motif dynamics such as how the combination of simple motifs can lead to autonomous dynamics or how noise in transcription and translation can affect the dynamics of a motif. Here, we review developments in synthetic biology as they pertain to increasing our understanding of cellular information processing. We highlight several types of dynamic behaviors that diverse motifs can generate, including the control of input/output responses, the generation of autonomous spatial and temporal dynamics, as well as the influence of noise in motif dynamics and cellular behavior. PMID:23411668

  9. Capacity Limit, Link Scheduling and Power Control in Wireless Networks

    ERIC Educational Resources Information Center

    Zhou, Shan

    2013-01-01

    The rapid advancement of wireless technology has instigated the broad deployment of wireless networks. Different types of networks have been developed, including wireless sensor networks, mobile ad hoc networks, wireless local area networks, and cellular networks. These networks have different structures and applications, and require different…

  10. Specific absorption rate variation in a brain phantom due to exposure by a 3G mobile phone: problems in dosimetry.

    PubMed

    Behari, J; Nirala, Jay Prakash

    2013-12-01

    A specific absorption rate (SAR) measurements system has been developed for compliance testing of personal mobile phone in a brain phantom material contained in a Perspex box. The volume of the box has been chosen corresponding to the volume of a small rat and illuminated by a 3G mobile phone frequency (1718.5 MHz), and the emitted radiation directed toward brain phantom .The induced fields in the phantom material are measured. Set up to lift the plane carrying the mobile phone is run by a pulley whose motion is controlled by a stepper motor. The platform is made to move at a pre-determined rate of 2 degrees per min limited up to 20 degrees. The measured data for induced fields in various locations are used to compute corresponding SAR values and inter comparison obtained. These data are also compared with those when the mobile phone is placed horizontally with respect to the position of the animal. The SAR data is also experimentally obtained by measuring a rise in temperature due to this mobile exposures and data compared with those obtained in the previous set. To seek a comparison with the safety criteria same set of measurements are performed in 10 g phantom material contained in a cubical box. These results are higher than those obtained with the knowledge of induced field measurements. It is concluded that SAR values are sensitive to the angular position of the moving platform and are well below the safety criteria prescribed for human exposure. The data are suggestive of having a fresh look to understand the mode of electromagnetic field -bio interaction. PMID:24579373

  11. The influence of leaf-atmosphere NH3(g ) exchange on the isotopic composition of nitrogen in plants and the atmosphere.

    PubMed

    Johnson, Jennifer E; Berry, Joseph A

    2013-10-01

    The distribution of nitrogen isotopes in the biosphere has the potential to offer insights into the past, present and future of the nitrogen cycle, but it is challenging to unravel the processes controlling patterns of mixing and fractionation. We present a mathematical model describing a previously overlooked process: nitrogen isotope fractionation during leaf-atmosphere NH3(g ) exchange. The model predicts that when leaf-atmosphere exchange of NH3(g ) occurs in a closed system, the atmospheric reservoir of NH3(g ) equilibrates at a concentration equal to the ammonia compensation point and an isotopic composition 8.1‰ lighter than nitrogen in protein. In an open system, when atmospheric concentrations of NH3(g ) fall below or rise above the compensation point, protein can be isotopically enriched by net efflux of NH3(g ) or depleted by net uptake. Comparison of model output with existing measurements in the literature suggests that this process contributes to variation in the isotopic composition of nitrogen in plants as well as NH3(g ) in the atmosphere, and should be considered in future analyses of nitrogen isotope circulation. The matrix-based modelling approach that is introduced may be useful for quantifying isotope dynamics in other complex systems that can be described by first-order kinetics. PMID:23452149

  12. Formin’ cellular structures

    PubMed Central

    Bogdan, Sven; Schultz, Jörg; Grosshans, Jörg

    2014-01-01

    Members of the Diaphanous (Dia) protein family are key regulators of fundamental actin driven cellular processes, which are conserved from yeast to humans. Researchers have uncovered diverse physiological roles in cell morphology, cell motility, cell polarity, and cell division, which are involved in shaping cells into tissues and organs. The identification of numerous binding partners led to substantial progress in our understanding of the differential functions of Dia proteins. Genetic approaches and new microscopy techniques allow important new insights into their localization, activity, and molecular principles of regulation. PMID:24719676

  13. Control of cellular automata

    NASA Astrophysics Data System (ADS)

    Bagnoli, Franco; Rechtman, Raúl; El Yacoubi, Samira

    2012-12-01

    We study the problem of master-slave synchronization and control of totalistic cellular automata. The synchronization mechanism is that of setting a fraction of sites of the slave system equal to those of the master one (pinching synchronization). The synchronization observable is the distance between the two configurations. We present three control strategies that exploit local information (the number of nonzero first-order Boolean derivatives) in order to choose the sites to be synchronized. When no local information is used, we speak of simple pinching synchronization. We find the critical properties of control and discuss the best control strategy compared with simple synchronization.

  14. Efficiency of cellular information processing

    NASA Astrophysics Data System (ADS)

    Barato, Andre C.; Hartich, David; Seifert, Udo

    2014-10-01

    We show that a rate of conditional Shannon entropy reduction, characterizing the learning of an internal process about an external process, is bounded by the thermodynamic entropy production. This approach allows for the definition of an informational efficiency that can be used to study cellular information processing. We analyze three models of increasing complexity inspired by the Escherichia coli sensory network, where the external process is an external ligand concentration jumping between two values. We start with a simple model for which ATP must be consumed so that a protein inside the cell can learn about the external concentration. With a second model for a single receptor we show that the rate at which the receptor learns about the external environment can be nonzero even without any dissipation inside the cell since chemical work done by the external process compensates for this learning rate. The third model is more complete, also containing adaptation. For this model we show inter alia that a bacterium in an environment that changes at a very slow time-scale is quite inefficient, dissipating much more than it learns. Using the concept of a coarse-grained learning rate, we show for the model with adaptation that while the activity learns about the external signal the option of changing the methylation level increases the concentration range for which the learning rate is substantial.

  15. Spectrum survey for reliable communications of cognitive radio based smart grid network

    NASA Astrophysics Data System (ADS)

    Farah Aqilah, Wan; Jayavalan, Shanjeevan; Mohd Aripin, Norazizah; Mohamad, Hafizal; Ismail, Aiman

    2013-06-01

    The smart grid (SG) system is expected to involve huge amount of data with different levels of priorities to different applications or users. The traditional grid which tend to deploy propriety networks with limited coverage and bandwidth, is not sufficient to support large scale SG network. Cognitive radio (CR) is a promising communication platform for SG network by utilizing potentially all available spectrum resources, subject to interference constraint. In order to develop a reliable communication framework for CR based SG network, thorough investigations on the current radio spectrum are required. This paper presents the spectrum utilization in Malaysia, specifically in the UHF/VHF bands, cellular (GSM 900, GSM 1800 and 3G), WiMAX, ISM and LTE band. The goal is to determine the potential spectrum that can be exploit by the CR users in the SG network. Measurements was conducted for 24 hours to quantify the average spectrum usage and the amount of available bandwidth. The findings in this paper are important to provide insight of actual spectrum utilization prior to developing a reliable communication platform for CR based SG network.

  16. GENE EXPRESSION NETWORKS

    EPA Science Inventory

    "Gene expression network" is the term used to describe the interplay, simple or complex, between two or more gene products in performing a specific cellular function. Although the delineation of such networks is complicated by the existence of multiple and subtle types of intera...

  17. Contribution of APOBEC3G/F activity to the development of low-abundance drug-resistant human immunodeficiency virus type 1 variants.

    PubMed

    Noguera-Julian, M; Cozzi-Lepri, A; Di Giallonardo, F; Schuurman, R; Däumer, M; Aitken, S; Ceccherini-Silberstein, F; D'Arminio Monforte, A; Geretti, A M; Booth, C L; Kaiser, R; Michalik, C; Jansen, K; Masquelier, B; Bellecave, P; Kouyos, R D; Castro, E; Furrer, H; Schultze, A; Günthard, H F; Brun-Vezinet, F; Metzner, K J; Paredes, R

    2016-02-01

    Plasma drug-resistant minority human immunodeficiency virus type 1 variants (DRMVs) increase the risk of virological failure to first-line non-nucleoside reverse transcriptase inhibitor antiretroviral therapy (ART). The origin of DRMVs in ART-naive patients, however, remains unclear. In a large pan-European case-control study investigating the clinical relevance of pre-existing DRMVs using 454 pyrosequencing, the six most prevalent plasma DRMVs detected corresponded to G-to-A nucleotide mutations (V90I, V106I, V108I, E138K, M184I and M230I). Here, we evaluated if such DRMVs could have emerged from apolipoprotein B mRNA editing enzyme, catalytic polypeptide 3G/F (APOBEC3G/F) activity. Out of 236 ART-naive subjects evaluated, APOBEC3G/F hypermutation signatures were detected in plasma viruses of 14 (5.9%) individuals. Samples with minority E138K, M184I, and M230I mutations, but not those with V90I, V106I or V108I, were significantly associated with APOBEC3G/F activity (Fisher's P < 0.005), defined as the presence of > 0.5% of sample sequences with an APOBEC3G/F signature. Mutations E138K, M184I and M230I co-occurred in the same sequence as APOBEC3G/F signatures in 3/9 (33%), 5/11 (45%) and 4/8 (50%) of samples, respectively; such linkage was not found for V90I, V106I or V108I. In-frame STOP codons were observed in 1.5% of all clonal sequences; 14.8% of them co-occurred with APOBEC3G/F signatures. APOBEC3G/F-associated E138K, M184I and M230I appeared within clonal sequences containing in-frame STOP codons in 2/3 (66%), 5/5 (100%) and 4/4 (100%) of the samples. In a re-analysis of the parent case control study, the presence of APOBEC3G/F signatures was not associated with virological failure. In conclusion, the contribution of APOBEC3G/F editing to the development of DRMVs is very limited and does not affect the efficacy of non-nucleoside reverse transcriptase inhibitor ART. PMID:26482266

  18. Cellular Contraction and Polarization Drive Collective Cellular Motion.

    PubMed

    Notbohm, Jacob; Banerjee, Shiladitya; Utuje, Kazage J C; Gweon, Bomi; Jang, Hwanseok; Park, Yongdoo; Shin, Jennifer; Butler, James P; Fredberg, Jeffrey J; Marchetti, M Cristina

    2016-06-21

    Coordinated motions of close-packed multicellular systems typically generate cooperative packs, swirls, and clusters. These cooperative motions are driven by active cellular forces, but the physical nature of these forces and how they generate collective cellular motion remain poorly understood. Here, we study forces and motions in a confined epithelial monolayer and make two experimental observations: 1) the direction of local cellular motion deviates systematically from the direction of the local traction exerted by each cell upon its substrate; and 2) oscillating waves of cellular motion arise spontaneously. Based on these observations, we propose a theory that connects forces and motions using two internal state variables, one of which generates an effective cellular polarization, and the other, through contractile forces, an effective cellular inertia. In agreement with theoretical predictions, drugs that inhibit contractility reduce both the cellular effective elastic modulus and the frequency of oscillations. Together, theory and experiment provide evidence suggesting that collective cellular motion is driven by at least two internal variables that serve to sustain waves and to polarize local cellular traction in a direction that deviates systematically from local cellular velocity. PMID:27332131

  19. Integrated cellular systems

    NASA Astrophysics Data System (ADS)

    Harper, Jason C.

    The generation of new three-dimensional (3D) matrices that enable integration of biomolecular components and whole cells into device architectures, without adversely altering their morphology or activity, continues to be an expanding and challenging field of research. This research is driven by the promise that encapsulated biomolecules and cells can significantly impact areas as diverse as biocatalysis, controlled delivery of therapeutics, environmental and industrial process monitoring, early warning of warfare agents, bioelectronics, photonics, smart prosthetics, advanced physiological sensors, portable medical diagnostic devices, and tissue/organ replacement. This work focuses on the development of a fundamental understanding of the biochemical and nanomaterial mechanisms that govern the cell directed assembly and integration process. It was shown that this integration process relies on the ability of cells to actively develop a pH gradient in response to evaporation induced osmotic stress, which catalyzes silica condensation within a thin 3D volume surrounding the cells, creating a functional bio/nano interface. The mechanism responsible for introducing functional foreign membrane-bound proteins via proteoliposome addition to the silica-lipid-cell matrix was also determined. Utilizing this new understanding, 3D cellular immobilization capabilities were extended using sol-gel matrices endowed with glycerol, trehalose, and media components. The effects of these additives, and the metabolic phase of encapsulated S. cerivisiase cells, on long-term viability and the rate of inducible gene expression was studied. This enabled the entrapment of cells within a novel microfluidic platform capable of simultaneous colorimetric, fluorescent, and electrochemical detection of a single analyte, significantly improving confidence in the biosensor output. As a complementary approach, multiphoton protein lithography was utilized to engineer 3D protein matrices in which to

  20. Cellular Dynamic Simulator: An Event Driven Molecular Simulation Environment for Cellular Physiology

    PubMed Central

    Byrne, Michael J.; Waxham, M. Neal; Kubota, Yoshihisa

    2010-01-01

    In this paper, we present the Cellular Dynamic Simulator (CDS) for simulating diffusion and chemical reactions within crowded molecular environments. CDS is based on a novel event driven algorithm specifically designed for precise calculation of the timing of collisions, reactions and other events for each individual molecule in the environment. Generic mesh based compartments allow the creation / importation of very simple or detailed cellular structures that exist in a 3D environment. Multiple levels of compartments and static obstacles can be used to create a dense environment to mimic cellular boundaries and the intracellular space. The CDS algorithm takes into account volume exclusion and molecular crowding that may impact signaling cascades in small sub-cellular compartments such as dendritic spines. With the CDS, we can simulate simple enzyme reactions; aggregation, channel transport, as well as highly complicated chemical reaction networks of both freely diffusing and membrane bound multi-protein complexes. Components of the CDS are generally defined such that the simulator can be applied to a wide range of environments in terms of scale and level of detail. Through an initialization GUI, a simple simulation environment can be created and populated within minutes yet is powerful enough to design complex 3D cellular architecture. The initialization tool allows visual confirmation of the environment construction prior to execution by the simulator. This paper describes the CDS algorithm, design implementation, and provides an overview of the types of features available and the utility of those features are highlighted in demonstrations. PMID:20361275

  1. The Cellular Building Blocks of Breathing

    PubMed Central

    Ramirez, J.M.; Doi, A.; Garcia, A.J.; Elsen, F.P.; Koch, H.; Wei, A.D.

    2013-01-01

    Respiratory brainstem neurons fulfill critical roles in controlling breathing: they generate the activity patterns for breathing and contribute to various sensory responses including changes in O2 and CO2. These complex sensorimotor tasks depend on the dynamic interplay between numerous cellular building blocks that consist of voltage-, calcium-, and ATP-dependent ionic conductances, various ionotropic and metabotropic synaptic mechanisms, as well as neuromodulators acting on G-protein coupled receptors and second messenger systems. As described in this review, the sensorimotor responses of the respiratory network emerge through the state-dependent integration of all these building blocks. There is no known respiratory function that involves only a small number of intrinsic, synaptic, or modulatory properties. Because of the complex integration of numerous intrinsic, synaptic, and modulatory mechanisms, the respiratory network is capable of continuously adapting to changes in the external and internal environment, which makes breathing one of the most integrated behaviors. Not surprisingly, inspiration is critical not only in the control of ventilation, but also in the context of “inspiring behaviors” such as arousal of the mind and even creativity. Far-reaching implications apply also to the underlying network mechanisms, as lessons learned from the respiratory network apply to network functions in general. PMID:23720262

  2. Cellular Morphogenesis In Silico

    PubMed Central

    Shinbrot, Troy; Chun, Young; Caicedo-Carvajal, Carlos; Foty, Ramsey

    2009-01-01

    Abstract We describe a model that simulates spherical cells of different types that can migrate and interact either attractively or repulsively. We find that both expected morphologies and previously unreported patterns spontaneously self-assemble. Among the newly discovered patterns are a segmented state of alternating discs, and a “shish-kebab” state, in which one cell type forms a ring around a second type. We show that these unique states result from cellular attraction that increases with distance (e.g., as membranes stretch viscoelastically), and would not be seen in traditional, e.g., molecular, potentials that diminish with distance. Most of the states found computationally have been observed in vitro, and it remains to be established what role these self-assembled states may play in in vivo morphogenesis. PMID:19686642

  3. Genetic and functional characterization of HIV-1 Vif on APOBEC3G degradation: First report of emergence of B/C recombinants from North India

    PubMed Central

    Ronsard, Larance; Raja, Rameez; Panwar, Vaishali; Saini, Sanjesh; Mohankumar, Kumaravel; Sridharan, Subhashree; Padmapriya, Ramamoorthy; Chaudhuri, Suhnrita; Ramachandran, Vishnampettai G; Banerjea, Akhil C

    2015-01-01

    HIV-1 is characterized by high genetic heterogeneity which is a challenge for developing therapeutics. Therefore, it is necessary to understand the extent of genetic variations that HIV is undergoing in North India. The objective of this study was to determine the role of genetic and functional role of Vif on APOBEC3G degradation. Vif is an accessory protein involved in counteracting APOBEC3/F proteins. Genetic analysis of Vif variants revealed that Vif C variants were closely related to South African Vif C whereas Vif B variants and Vif B/C showed distinct geographic locations. This is the first report to show the emergence of Vif B/C in our population. The functional domains, motifs and phosphorylation sites were well conserved. Vif C variants differed in APOBEC3G degradation from Vif B variants. Vif B/C revealed similar levels of APOBEC3G degradation to Vif C confirming the presence of genetic determinants in C-terminal region. High genetic diversity was observed in Vif variants which may cause the emergence of more complex and divergent strains. These results reveal the genetic determinants of Vif in mediating APOBEC3G degradation and highlight the genetic information for the development of anti-viral drugs against HIV. Importance: Vif is an accessory HIV-1 protein which plays significant role in the degradation of human DNA-editing factor APOBEC3G, thereby impeding the antiretroviral activity of APOBEC3G. It is known that certain natural polymorphisms in Vif could degrade APOBEC3G relatively higher rate, suggesting its role in HIV-1 pathogenesis. This is the first report from North India showcasing genetic variations and novel polymorphisms in Vif gene. Subtype C is prevalent in India, but for the first time we observed putative B/C recombinants with a little high ability to degrade APOBEC3G indicating adaptation and evolving nature of virus in our population. Indian Vif C variants were able to degrade APOBEC3G well in comparison to Vif B variants. These

  4. Rapid Cellular Identification by Dynamic Electromechanical Response

    SciTech Connect

    Nikiforov, Maxim; Jesse, Stephen; Kalinin, Sergei V; Reukov, Vladimir V; Vertegel, Alexey; Thompson, Gary L

    2009-01-01

    Coupling between electrical and mechanical phenomena is ubiquitous in living systems. Here, we demonstrate rapid identification of cellular organisms using difference in electromechanical activity in a broad frequency range. Principal component analysis of the dynamic electromechanical response spectra bundled with neural network based recognition provides a robust identification algorithm based on their electromechanical signature, and allows unambiguous differentiation of model Micrococcus Lysodeikticus and Pseudomonas Fluorescens system. This methodology provides a universal pathway for biological identification obviating the need for well-defined analytical models of Scanning Probe Microscopy response.

  5. OTRA-THS MAC to reduce Power Outage Data Collection Latency in a smart meter network

    SciTech Connect

    Garlapati, Shravan K; Kuruganti, Phani Teja; Buehrer, Richard M; Reed, Jeffrey H

    2014-01-01

    The deployment of advanced metering infrastructure by the electric utilities poses unique communication challenges, particularly as the number of meters per aggregator increases. During a power outage, a smart meter tries to report it instantaneously to the electric utility. In a densely populated residential/industrial locality, it is possible that a large number of smart meters simultaneously try to get access to the communication network to report the power outage. If the number of smart meters is very high of the order of tens of thousands (metropolitan areas), the power outage data flooding can lead to Random Access CHannel (RACH) congestion. Several utilities are considering the use of cellular network for smart meter communications. In 3G/4G cellular networks, RACH congestion not only leads to collisions, retransmissions and increased RACH delays, but also has the potential to disrupt the dedicated traffic flow by increasing the interference levels (3G CDMA). In order to overcome this problem, in this paper we propose a Time Hierarchical Scheme (THS) that reduces the intensity of power outage data flooding and power outage reporting delay by 6/7th, and 17/18th when compared to their respective values without THS. Also, we propose an Optimum Transmission Rate Adaptive (OTRA) MAC to optimize the latency in power outage data collection. The analysis and simulation results presented in this paper show that both the OTRA and THS features of the proposed MAC results in a Power Outage Data Collection Latency (PODCL) that is 1/10th of the 4G LTE PODCL.

  6. Structure at 1.6 Å resolution of the protein from gene locus At3g22680 from Arabidopsis thaliana

    PubMed Central

    Allard, Simon T. M.; Bingman, Craig A.; Johnson, Kenneth A.; Wesenberg, Gary E.; Bitto, Eduard; Jeon, Won Bae; Phillips, George N.

    2005-01-01

    The gene product of At3g22680 from Arabidopsis thaliana codes for a protein of unknown function. The crystal structure of the At3g22680 gene product was determined by multiple-wavelength anomalous diffraction and refined to an R factor of 16.0% (R free = 18.4%) at 1.60 Å resolution. The refined structure shows one monomer in the asymmetric unit, with one molecule of the non-denaturing detergent CHAPS {3-[(3-cholamidopropyl)dimethylammonio]-1-propane sulfon­ate} tightly bound. Protein At3g22680 shows no structural homology to any other known proteins and represents a new fold in protein conformation space. PMID:16511118

  7. Cellular telephone-based radiation detection instrument

    DOEpatents

    Craig, William W.; Labov, Simon E.

    2011-06-14

    A network of radiation detection instruments, each having a small solid state radiation sensor module integrated into a cellular phone for providing radiation detection data and analysis directly to a user. The sensor module includes a solid-state crystal bonded to an ASIC readout providing a low cost, low power, light weight compact instrument to detect and measure radiation energies in the local ambient radiation field. In particular, the photon energy, time of event, and location of the detection instrument at the time of detection is recorded for real time transmission to a central data collection/analysis system. The collected data from the entire network of radiation detection instruments are combined by intelligent correlation/analysis algorithms which map the background radiation and detect, identify and track radiation anomalies in the region.

  8. APOBEC3G mRNA expression in exposed seronegative and early stage HIV infected individuals decreases with removal of exposure and with disease progression

    PubMed Central

    Vázquez-Pérez, Joel A; Ormsby, Christopher E; Hernández-Juan, Ramón; Torres, Klintsy J; Reyes-Terán, Gustavo

    2009-01-01

    Background APOBEC3G is an antiretroviral factor that acts by inducing G to A mutations. In this study, we examined the expression of APOBEC3G in uninfected HIV-1 exposed individuals at the time of their partner's diagnosis and one year later. We then compared this expression with that of infected individuals at different disease stages. APOBEC3G mRNA was measured in PBMCs from three groups: healthy controls with no known risk factor to HIV infection (n = 26), exposed uninfected individuals who had unprotected sex with their HIV+ partners for at least 3 months (n = 37), and HIV infected patients at various disease stages (n = 45), including 8 patients with low HIV viral loads < 10,000 copies/mL (LVL) for at least 3 years. Additionally, we obtained sequences from the env, gag, pol, nef, vif and the LTR of the patients' virus. Results Exposed uninfected individuals expressed higher APOBEC3G than healthy controls (3.86 vs. 1.69 relative expression units), and their expression significantly decreased after a year from the HIV diagnosis and subsequent treatment of their partners. Infected individuals showed a positive correlation (Rho = 0.57, p = 0.00006) of APOBEC3G expression with CD4+ T cell count, and a negative correlation with HIV viremia (Rho = -0.54, p = 0.00004). The percentage of G to A mutations had a positive correlation (Rho = 0.43, p = 0.0226) with APOBEC3G expression, and it was higher in LVL individuals than in the other patients (IQR 8.27 to 9.64 vs. 7.06 to 8.1, p = 0.0084). Out of 8 LVLs, 3 had hypermutations, and 4 had premature stop codons only in viral vif. Conclusion The results suggest that exposure to HIV may trigger APOBEC3G expression in PBMCs, in the absence of infection. Additionally, cessation of exposure or advanced disease is associated with decreased APOBEC3G expression. PMID:19254362

  9. Cellular energy metabolism

    SciTech Connect

    Glaser, M.

    1991-06-01

    Studies have been carried out on adenylate kinase which is an important enzyme in determining the concentrations of the adenine nucleotides. An efficient method has been developed to clone mutant adenylate kinase genes in E. coli. Site-specific mutagenesis of the wild type gene also has been used to obtain forms of adenylate kinase with altered amino acids. The wild type and mutant forms of adenylate kinase have been overexpressed and large quantities were readily isolated. The kinetic and fluorescence properties of the different forms of adenylate kinase were characterized. This has led to a new model for the location of the AMP and ATP bindings sites on the enzyme and a proposal for the mechanism of substrate inhibition. Crystals of the wild type enzyme were obtained that diffract to at least 2.3 {angstrom} resolution. Experiments were also initiated to determine the function of adenylate kinase in vivo. In one set of experiments, E. coli strains with mutations in adenylate kinase showed large changes in cellular nucleotides after reaching the stationary phase in a low phosphate medium. This was caused by selective proteolytic degradation of the mutant adenylate kinase caused by phosphate starvation.

  10. Molecular and Cellular Biophysics

    NASA Astrophysics Data System (ADS)

    Jackson, Meyer B.

    2006-01-01

    Molecular and Cellular Biophysics provides advanced undergraduate and graduate students with a foundation in the basic concepts of biophysics. Students who have taken physical chemistry and calculus courses will find this book an accessible and valuable aid in learning how these concepts can be used in biological research. The text provides a rigorous treatment of the fundamental theories in biophysics and illustrates their application with examples. Conformational transitions of proteins are studied first using thermodynamics, and subsequently with kinetics. Allosteric theory is developed as the synthesis of conformational transitions and association reactions. Basic ideas of thermodynamics and kinetics are applied to topics such as protein folding, enzyme catalysis and ion channel permeation. These concepts are then used as the building blocks in a treatment of membrane excitability. Through these examples, students will gain an understanding of the general importance and broad applicability of biophysical principles to biological problems. Offers a unique synthesis of concepts across a wide range of biophysical topics Provides a rigorous theoretical treatment, alongside applications in biological systems Author has been teaching biophysics for nearly 25 years

  11. Electrosurgery with cellular precision.

    PubMed

    Palanker, Daniel V; Vankov, Alexander; Huie, Philip

    2008-02-01

    Electrosurgery, one of the most-often used surgical tools, is a robust but somewhat crude technology that has changed surprisingly little since its invention almost a century ago. Continuous radiofrequency is still used for tissue cutting, with thermal damage extending to hundreds of micrometers. In contrast, lasers developed 70 years later, have been constantly perfected, and the laser-tissue interactions explored in great detail, which has allowed tissue ablation with cellular precision in many laser applications. We discuss mechanisms of tissue damage by electric field, and demonstrate that electrosurgery with properly optimized waveforms and microelectrodes can rival many advanced lasers. Pulsed electric waveforms with burst durations ranging from 10 to 100 micros applied via insulated planar electrodes with 12 microm wide exposed edges produced plasma-mediated dissection of tissues with the collateral damage zone ranging from 2 to 10 microm. Length of the electrodes can vary from micrometers to centimeters and all types of soft tissues-from membranes to cartilage and skin could be dissected in liquid medium and in a dry field. This technology may allow for major improvements in outcomes of the current surgical procedures and development of much more refined surgical techniques. PMID:18270030

  12. Active Cellular Nematics

    NASA Astrophysics Data System (ADS)

    Duclos, Guillaume; Erlenkaemper, Christoph; Garcia, Simon; Yevick, Hannah; Joanny, Jean-François; Silberzan, Pascal; Biology inspired physics at mesoscales Team; Physical approach of biological problems Team

    We study the emergence of a nematic order in a two-dimensional tissue of apolar elongated fibroblast cells. Initially, these cells are very motile and the monolayer is characterized by giant density fluctuations, a signature of far-from-equilibrium systems. As the cell density increases because of proliferation, the cells align with each other forming large perfectly oriented domains while the cellular movements slow down and eventually freeze. Therefore topological defects characteristic of nematic phases remain trapped at long times, preventing the development of infinite domains. By analogy with classical non-active nematics, we have investigated the role of boundaries and we have shown that cells confined in stripes of width smaller than typically 500 µm are perfectly aligned in the stripe direction. Experiments performed in cross-shaped patterns show that both the number of cells and the degree of alignment impact the final orientation. Reference: Duclos G., Garcia S., Yevick H.G. and Silberzan P., ''Perfect nematic order in confined monolayers of spindle-shaped cells'', Soft Matter, 10, 14, 2014

  13. 47 CFR 22.909 - Cellular markets.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 47 Telecommunication 2 2013-10-01 2013-10-01 false Cellular markets. 22.909 Section 22.909... Cellular Radiotelephone Service § 22.909 Cellular markets. Cellular markets are standard geographic areas used by the FCC for administrative convenience in the licensing of cellular systems. Cellular...

  14. 47 CFR 22.909 - Cellular markets.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 47 Telecommunication 2 2014-10-01 2014-10-01 false Cellular markets. 22.909 Section 22.909... Cellular Radiotelephone Service § 22.909 Cellular markets. Cellular markets are standard geographic areas used by the FCC for administrative convenience in the licensing of cellular systems. Cellular...

  15. Elements of the cellular metabolic structure

    PubMed Central

    De la Fuente, Ildefonso M.

    2015-01-01

    A large number of studies have demonstrated the existence of metabolic covalent modifications in different molecular structures, which are able to store biochemical information that is not encoded by DNA. Some of these covalent mark patterns can be transmitted across generations (epigenetic changes). Recently, the emergence of Hopfield-like attractor dynamics has been observed in self-organized enzymatic networks, which have the capacity to store functional catalytic patterns that can be correctly recovered by specific input stimuli. Hopfield-like metabolic dynamics are stable and can be maintained as a long-term biochemical memory. In addition, specific molecular information can be transferred from the functional dynamics of the metabolic networks to the enzymatic activity involved in covalent post-translational modulation, so that determined functional memory can be embedded in multiple stable molecular marks. The metabolic dynamics governed by Hopfield-type attractors (functional processes), as well as the enzymatic covalent modifications of specific molecules (structural dynamic processes) seem to represent the two stages of the dynamical memory of cellular metabolism (metabolic memory). Epigenetic processes appear to be the structural manifestation of this cellular metabolic memory. Here, a new framework for molecular information storage in the cell is presented, which is characterized by two functionally and molecularly interrelated systems: a dynamic, flexible and adaptive system (metabolic memory) and an essentially conservative system (genetic memory). The molecular information of both systems seems to coordinate the physiological development of the whole cell. PMID:25988183

  16. Taming the sphinx: Mechanisms of cellular sphingolipid homeostasis.

    PubMed

    Olson, D K; Fröhlich, F; Farese, R V; Walther, T C

    2016-08-01

    Sphingolipids are important structural membrane components of eukaryotic cells, and potent signaling molecules. As such, their levels must be maintained to optimize cellular functions in different cellular membranes. Here, we review the current knowledge of homeostatic sphingolipid regulation. We describe recent studies in Saccharomyces cerevisiae that have provided insights into how cells sense changes in sphingolipid levels in the plasma membrane and acutely regulate sphingolipid biosynthesis by altering signaling pathways. We also discuss how cellular trafficking has emerged as an important determinant of sphingolipid homeostasis. Finally, we highlight areas where work is still needed to elucidate the mechanisms of sphingolipid regulation and the physiological functions of such regulatory networks, especially in mammalian cells. This article is part of a Special Issue entitled: The cellular lipid landscape edited by Tim P. Levine and Anant K. Menon. PMID:26747648

  17. Material and mechanical factors: new strategy in cellular neurogenesis

    PubMed Central

    Stoll, Hillary; Kwon, Il Keun; Lim, Jung Yul

    2014-01-01

    Since damaged neural circuits are not generally self-recovered, developing methods to stimulate neurogenesis is critically required. Most studies have examined the effects of soluble pharmacological factors on the cellular neurogenesis. On the other hand, it is now recognized that the other extracellular factors, including material and mechanical cues, also have a strong potential to induce cellular neurogenesis. This article will review recent data on the material (chemical patterning, micro/nano-topography, carbon nanotube, graphene) and mechanical (static cue from substrate stiffness, dynamic cue from stretch and flow shear) stimulations of cellular neurogenesis. These approaches may provide new neural regenerative medicine protocols. Scaffolding material templates capable of triggering cellular neurogenesis can be explored in the presence of neurogenesis-stimulatory mechanical environments, and also with conventional soluble factors, to enhance axonal growth and neural network formation in neural tissue engineering. PMID:25422642

  18. Crystal structure of the protein At3g01520, a eukaryotic universal stress protein-like protein from Arabidopsis thaliana in complex with AMP.

    PubMed

    Kim, Do Jin; Bitto, Eduard; Bingman, Craig A; Kim, Hyun-Jung; Han, Byung Woo; Phillips, George N

    2015-07-01

    Members of the universal stress protein (USP) family are conserved in a phylogenetically diverse range of prokaryotes, fungi, protists, and plants and confer abilities to respond to a wide range of environmental stresses. Arabidopsis thaliana contains 44 USP domain-containing proteins, and USP domain is found either in a small protein with unknown physiological function or in an N-terminal portion of a multi-domain protein, usually a protein kinase. Here, we report the first crystal structure of a eukaryotic USP-like protein encoded from the gene At3g01520. The crystal structure of the protein At3g01520 was determined by the single-wavelength anomalous dispersion method and refined to an R factor of 21.8% (Rfree = 26.1%) at 2.5 Å resolution. The crystal structure includes three At3g01520 protein dimers with one AMP molecule bound to each protomer, comprising a Rossmann-like α/β overall fold. The bound AMP and conservation of residues in the ATP-binding loop suggest that the protein At3g01520 also belongs to the ATP-binding USP subfamily members. PMID:25921306

  19. Effects of 2G and 3G mobile phones on human alpha rhythms: Resting EEG in adolescents, young adults, and the elderly.

    PubMed

    Croft, R J; Leung, S; McKenzie, R J; Loughran, S P; Iskra, S; Hamblin, D L; Cooper, N R

    2010-09-01

    The present study was conducted to determine whether adolescents and/or the elderly are more sensitive to mobile phone (MP)-related bioeffects than young adults, and to determine this for both 2nd generation (2G) GSM, and 3rd generation (3G) W-CDMA exposures. To test this, resting alpha activity (8-12 Hz band of the electroencephalogram) was assessed because numerous studies have now reported it to be enhanced by MP exposure. Forty-one 13-15 year olds, forty-two 19-40 year olds, and twenty 55-70 year olds were tested using a double-blind crossover design, where each participant received Sham, 2G and 3G exposures, separated by at least 4 days. Alpha activity, during exposure relative to baseline, was recorded and compared between conditions. Consistent with previous research, the young adults' alpha was greater in the 2G compared to Sham condition, however, no effect was seen in the adolescent or the elderly groups, and no effect of 3G exposures was found in any group. The results provide further support for an effect of 2G exposures on resting alpha activity in young adults, but fail to support a similar enhancement in adolescents or the elderly, or in any age group as a function of 3G exposure. PMID:20564174

  20. Leucocyte cellular adhesion molecules.

    PubMed

    Yong, K; Khwaja, A

    1990-12-01

    Leucocytes express adhesion promoting receptors which mediate cell-cell and cell-matrix interactions. These adhesive interactions are crucial to the regulation of haemopoiesis and thymocyte maturation, the direction and control of leucocyte traffic and migration through tissues, and in the development of immune and non-immune inflammatory responses. Several families of adhesion receptors have been identified (Table). The leucocyte integrin family comprises 3 alpha beta heterodimeric membrane glycoproteins which share a common beta subunit, designated CD18. The alpha subunits of each of the 3 members, lymphocyte function associated antigen-1 (LFA-1), macrophage antigen-1 (Mac-1) and p150,95 are designated CD11a, b and c respectively. These adhesion molecules play a critical part in the immune and inflammatory responses of leucocytes. The leucocyte integrin family is, in turn, part of the integrin superfamily, members of which are evolutionally, structurally and functionally related. Another Integrin subfamily found on leucocytes is the VLA group, so-called because the 'very late activation antigens' VLA-1 and VLA-2 were originally found to appear late in T-cell activation. Members of this family function mainly as extracellular matrix adhesion receptors and are found both on haemopoietic and non-haemopoietic cells. They play a part in diverse cellular functions including tissue organisation, lymphocyte recirculation and T-cell immune responses. A third integrin subfamily, the cytoadhesins, are receptors on platelets and endothelial cells which bind extracellular matrix proteins. A second family of adhesion receptors is the immunoglobulin superfamily, members of which include CD2, LFA-3 and ICAM-1, which participate in T-cell adhesive interactions, and the antigen-specific receptors of T and B cells, CD4, CD8 and the MHC Class I and II molecules. A recently recognised family of adhesion receptors is the selectins, characterised by a common lectin domain. Leucocyte

  1. Origin of cells and network information

    PubMed Central

    Tanabe, Shihori

    2015-01-01

    All cells are derived from one cell, and the origin of different cell types is a subject of curiosity. Cells construct life through appropriately timed networks at each stage of development. Communication among cells and intracellular signaling are essential for cell differentiation and for life processes. Cellular molecular networks establish cell diversity and life. The investigation of the regulation of each gene in the genome within the cellular network is therefore of interest. Stem cells produce various cells that are suitable for specific purposes. The dynamics of the information in the cellular network changes as the status of cells is altered. The components of each cell are subject to investigation. PMID:25914760

  2. Cellular compartmentalization of secondary metabolism

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Fungal secondary metabolism is often considered apart from the essential housekeeping functions of the cell. However, there are clear links between fundamental cellular metabolism and the biochemical pathways leading to secondary metabolite synthesis. Besides utilizing key biochemical precursors sh...

  3. Cellular therapy for haematological malignancies.

    PubMed

    Roddie, P H; Turner, M L

    2002-11-01

    The aim of this review was to summarize the recent progress made in the field of cellular therapeutics in haematological malignancy. The review also examined the role that the National Transfusion Services might play in the manufacture of new cellular therapeutic agents, given both their expertise in the safe provision of blood products and their possession of accredited cell manipulation facilities. Cellular therapy is entering an era in which novel cellular products will find increasing clinical use, particularly in the areas of haematopoietic stem cell transplantation and immunotherapy. The production of novel cell-based therapies, both in Europe and North America, is now under strict regulatory control and therefore collaboration with the National Transfusion Services in the manufacture of these agents may well be beneficial if the production standards demanded by the regulatory authorities are to be fulfilled. PMID:12437515

  4. Comparison of Analysis Results Between 2D/1D Synthesis and RAPTOR-M3G in the Korea Standard Nuclear Plant (KSNP)

    NASA Astrophysics Data System (ADS)

    Joung Lim, Mi; Maeng, Young Jae; Fero, Arnold H.; Anderson, Stanwood L.

    2016-02-01

    The 2D/1D synthesis methodology has been used to calculate the fast neutron (E > 1.0 MeV) exposure to the beltline region of the reactor pressure vessel. This method uses the DORT 3.1 discrete ordinates code and the BUGLE-96 cross-section library based on ENDF/B-VI. RAPTOR-M3G (RApid Parallel Transport Of Radiation-Multiple 3D Geometries) which performs full 3D calculations was developed and is based on domain decomposition algorithms, where the spatial and angular domains are allocated and processed on multi-processor computer architecture. As compared to traditional single-processor applications, this approach reduces the computational load as well as the memory requirement per processor. Both methods are applied to surveillance test results for the Korea Standard Nuclear Plant (KSNP)-OPR (Optimized Power Reactor) 1000 MW. The objective of this paper is to compare the results of the KSNP surveillance program between 2D/1D synthesis and RAPTOR-M3G. Each operating KSNP has a reactor vessel surveillance program consisting of six surveillance capsules located between the core and the reactor vessel in the downcomer region near the reactor vessel wall. In addition to the In-Vessel surveillance program, an Ex-Vessel Neutron Dosimetry (EVND) program has been implemented. In order to estimate surveillance test results, cycle-specific forward transport calculations were performed by 2D/1D synthesis and by RAPTOR-M3G. The ratio between measured and calculated (M/C) reaction rates will be discussed. The current plan is to install an EVND system in all of the Korea PWRs including the new reactor type, APR (Advanced Power Reactor) 1400 MW. This work will play an important role in establishing a KSNP-specific database of surveillance test results and will employ RAPTOR-M3G for surveillance dosimetry location as well as positions in the KSNP reactor vessel.

  5. C3G/Rapgef1 Is Required in Multipolar Neurons for the Transition to a Bipolar Morphology during Cortical Development

    PubMed Central

    Shah, Bhavin; Lutter, Daniela; Bochenek, Magdalena L.; Kato, Katsuhiro; Tsytsyura, Yaroslav; Glyvuk, Natalia; Sakakibara, Akira; Klingauf, Jürgen; Adams, Ralf H.; Püschel, Andreas W.

    2016-01-01

    The establishment of a polarized morphology is essential for the development and function of neurons. During the development of the mammalian neocortex, neurons arise in the ventricular zone (VZ) from radial glia cells (RGCs) and leave the VZ to generate the cortical plate (CP). During their migration, newborn neurons first assume a multipolar morphology in the subventricular zone (SVZ) and lower intermediate zone (IZ). Subsequently, they undergo a multi-to-bipolar (MTB) transition to become bipolar in the upper IZ by developing a leading process and a trailing axon. The small GTPases Rap1A and Rap1B act as master regulators of neural cell polarity in the developing mouse neocortex. They are required for maintaining the polarity of RGCs and directing the MTB transition of multipolar neurons. Here we show that the Rap1 guanine nucleotide exchange factor (GEF) C3G (encoded by the Rapgef1 gene) is a crucial regulator of the MTB transition in vivo by conditionally inactivating the Rapgef1 gene in the developing mouse cortex at different time points during neuronal development. Inactivation of C3G results in defects in neuronal migration, axon formation and cortical lamination. Live cell imaging shows that C3G is required in cortical neurons for both the specification of an axon and the initiation of radial migration by forming a leading process. PMID:27111087

  6. C3G/Rapgef1 Is Required in Multipolar Neurons for the Transition to a Bipolar Morphology during Cortical Development.

    PubMed

    Shah, Bhavin; Lutter, Daniela; Bochenek, Magdalena L; Kato, Katsuhiro; Tsytsyura, Yaroslav; Glyvuk, Natalia; Sakakibara, Akira; Klingauf, Jürgen; Adams, Ralf H; Püschel, Andreas W

    2016-01-01

    The establishment of a polarized morphology is essential for the development and function of neurons. During the development of the mammalian neocortex, neurons arise in the ventricular zone (VZ) from radial glia cells (RGCs) and leave the VZ to generate the cortical plate (CP). During their migration, newborn neurons first assume a multipolar morphology in the subventricular zone (SVZ) and lower intermediate zone (IZ). Subsequently, they undergo a multi-to-bipolar (MTB) transition to become bipolar in the upper IZ by developing a leading process and a trailing axon. The small GTPases Rap1A and Rap1B act as master regulators of neural cell polarity in the developing mouse neocortex. They are required for maintaining the polarity of RGCs and directing the MTB transition of multipolar neurons. Here we show that the Rap1 guanine nucleotide exchange factor (GEF) C3G (encoded by the Rapgef1 gene) is a crucial regulator of the MTB transition in vivo by conditionally inactivating the Rapgef1 gene in the developing mouse cortex at different time points during neuronal development. Inactivation of C3G results in defects in neuronal migration, axon formation and cortical lamination. Live cell imaging shows that C3G is required in cortical neurons for both the specification of an axon and the initiation of radial migration by forming a leading process. PMID:27111087

  7. Mathematical Modeling of Cellular Metabolism.

    PubMed

    Berndt, Nikolaus; Holzhütter, Hermann-Georg

    2016-01-01

    Cellular metabolism basically consists of the conversion of chemical compounds taken up from the extracellular environment into energy (conserved in energy-rich bonds of organic phosphates) and a wide array of organic molecules serving as catalysts (enzymes), information carriers (nucleic acids), and building blocks for cellular structures such as membranes or ribosomes. Metabolic modeling aims at the construction of mathematical representations of the cellular metabolism that can be used to calculate the concentration of cellular molecules and the rates of their mutual chemical interconversion in response to varying external conditions as, for example, hormonal stimuli or supply of essential nutrients. Based on such calculations, it is possible to quantify complex cellular functions as cellular growth, detoxification of drugs and xenobiotic compounds or synthesis of exported molecules. Depending on the specific questions to metabolism addressed, the methodological expertise of the researcher, and available experimental information, different conceptual frameworks have been established, allowing the usage of computational methods to condense experimental information from various layers of organization into (self-) consistent models. Here, we briefly outline the main conceptual frameworks that are currently exploited in metabolism research. PMID:27557541

  8. Incentive Mechanism for P2P Content Sharing over Heterogenous Access Networks

    NASA Astrophysics Data System (ADS)

    Sato, Kenichiro; Hashimoto, Ryo; Yoshino, Makoto; Shinkuma, Ryoichi; Takahashi, Tatsuro

    In peer-to-peer (P2P) content sharing, users can share their content by contributing their own resources to one another. However, since there is no incentive for contributing contents or resources to others, users may attempt to obtain content without any contribution. To motivate users to contribute their resources to the service, incentive-rewarding mechanisms have been proposed. On the other hand, emerging wireless technologies, such as IEEE 802.11 wireless local area networks, beyond third generation (B3G) cellular networks and mobile WiMAX, provide high-speed Internet access for wireless users. Using these high-speed wireless access, wireless users can use P2P services and share their content with other wireless users and with fixed users. However, this diversification of access networks makes it difficult to appropriately assign rewards to each user according to their contributions. This is because the cost necessary for contribution is different in different access networks. In this paper, we propose a novel incentive-rewarding mechanism called EMOTIVER that can assign rewards to users appropriately. The proposed mechanism uses an external evaluator and interactive learning agents. We also investigate a way of appropriately controlling rewards based on the system service's quality and managing policy.

  9. Biomimetic superelastic graphene-based cellular monoliths.

    PubMed

    Qiu, Ling; Liu, Jeffery Z; Chang, Shery L Y; Wu, Yanzhe; Li, Dan

    2012-01-01

    Many applications proposed for graphene require multiple sheets be assembled into a monolithic structure. The ability to maintain structural integrity upon large deformation is essential to ensure a macroscopic material which functions reliably. However, it has remained a great challenge to achieve high elasticity in three-dimensional graphene networks. Here we report that the marriage of graphene chemistry with ice physics can lead to the formation of ultralight and superelastic graphene-based cellular monoliths. Mimicking the hierarchical structure of natural cork, the resulting materials can sustain their structural integrity under a load of >50,000 times their own weight and can rapidly recover from >80% compression. The unique biomimetic hierarchical structure also provides this new class of elastomers with exceptionally high energy absorption capability and good electrical conductivity. The successful synthesis of such fascinating materials paves the way to explore the application of graphene in a self-supporting, structurally adaptive and 3D macroscopic form. PMID:23212370

  10. Analytical Solution of Traffic Cellular Automata Model

    NASA Astrophysics Data System (ADS)

    Lo, Shih-Ching; Hsu, Chia-Hung

    2009-08-01

    Complex traffic system seems to be simulated successfully by cellular automaton (CA) models. Various models are developed to understand single-lane traffic, multilane traffic, lane-changing behavior and network traffic situations. However, the result of CA simulation can only be obtained after massive microscopic computation. Although, the mean field theory (MFT) has been studied to be the approximation of CA model, the MFT can only applied to the simple CA rules or small value of parameters. In this study, we simulate traffic flow by the NaSch model under different combination of parameters, which are maximal speed, dawdling probability and density. After that, the position of critical density, the slope of free-flow and congested regime are observed and modeled due to the simulated data. Finally, the coefficients of the model will be calibrated by the simulated data and the analytical solution of traffic CA is obtained.

  11. Traffic jam dynamics in stochastic cellular automata

    SciTech Connect

    Nagel, K. |; Schreckenberg, M.

    1995-09-01

    Simple models for particles hopping on a grid (cellular automata) are used to simulate (single lane) traffic flow. Despite their simplicity, these models are astonishingly realistic in reproducing start-stop-waves and realistic fundamental diagrams. One can use these models to investigate traffic phenomena near maximum flow. A so-called phase transition at average maximum flow is visible in the life-times of jams. The resulting dynamic picture is consistent with recent fluid-dynamical results by Kuehne/Kerner/Konhaeuser, and with Treiterer`s hysteresis description. This places CA models between car-following models and fluid-dynamical models for traffic flow. CA models are tested in projects in Los Alamos (USA) and in NRW (Germany) for large scale microsimulations of network traffic.

  12. Prenatal Alcohol Exposure and Cellular Differentiation

    PubMed Central

    Veazey, Kylee J.; Muller, Daria; Golding, Michael C.

    2013-01-01

    Exposure to alcohol significantly alters the developmental trajectory of progenitor cells and fundamentally compromises tissue formation (i.e., histogenesis). Emerging research suggests that ethanol can impair mammalian development by interfering with the execution of molecular programs governing differentiation. For example, ethanol exposure disrupts cellular migration, changes cell–cell interactions, and alters growth factor signaling pathways. Additionally, ethanol can alter epigenetic mechanisms controlling gene expression. Normally, lineage-specific regulatory factors (i.e., transcription factors) establish the transcriptional networks of each new cell type; the cell’s identity then is maintained through epigenetic alterations in the way in which the DNA encoding each gene becomes packaged within the chromatin. Ethanol exposure can induce epigenetic changes that do not induce genetic mutations but nonetheless alter the course of fetal development and result in a large array of patterning defects. Two crucial enzyme complexes—the Polycomb and Trithorax proteins—are central to the epigenetic programs controlling the intricate balance between self-renewal and the execution of cellular differentiation, with diametrically opposed functions. Prenatal ethanol exposure may disrupt the functions of these two enzyme complexes, altering a crucial aspect of mammalian differentiation. Characterizing the involvement of Polycomb and Trithorax group complexes in the etiology of fetal alcohol spectrum disorders will undoubtedly enhance understanding of the role that epigenetic programming plays in this complex disorder. PMID:24313167

  13. D1((2)B2g) to D0((2)Au) Fluorescence from the Matrix-Isolated Perylene Cation Following Laser Excitation into the D5(2)B3g) and D2 ((2)B3g) Electronic States

    NASA Technical Reports Server (NTRS)

    Chillier, Xavier D. F.; Stone, Bradley M.; Joblin, Christine; Salama, Farid; Allamandola, Louis J.; DeVincenzi, Donald L. (Technical Monitor)

    2001-01-01

    Fluorescence spectra of the perylene cation, pumped by direct laser excitation via the D(sub 2)((2)B(sub 3g)) (left arrow) D(sub 0)((2)A(sub u)) and D(sub 5)(2)B(sub 3g)) (left arrow) D(sub 0)((2)A(sub u)) transitions, are presented. Direct excitation into the D5 or D2 states is followed by rapid non-radiative relaxation to D1 that, in turn,relaxes radiatively. Excitation spectroscopy across the D(sub 2)((2)B(sub 3g)) (left arrow) D(sub 0)((2)A(sub u)) transition near 730 nm shows that site splitting plays little or no role in determining the spectral substructure in the ion spectra. Tentative assignments for ground state vibrational frequencies are made by comparison of spectral intervals with calculated normal mode frequencies.

  14. D1(2B2g)→D0(2Au) fluorescence from the matrix-isolated perylene cation following laser excitation into the D5(2B3g) and D2(2B3g) electronic states

    NASA Astrophysics Data System (ADS)

    Chillier, Xavier D. F.; Stone, Bradley M.; Joblin, Christine; Salama, Farid; Allamandola, Louis J.

    2002-04-01

    Fluorescence spectra of the perylene cation, isolated in an argon matrix and pumped by direct laser excitation via the D2(2B3g)←D0(2Au) and D5(2B3g)←D0(2Au) transitions, are presented. Direct excitation into the D5 or D2 states is followed by rapid nonradiative relaxation to D1 that, in turn, relaxes radiatively. Excitation spectroscopy across the D2(2B3g)←D0(2Au) transition near 731 nm shows that site splitting plays little or no role in determining the spectral substructure in the ion spectra. Tentative assignments for ground state vibrational frequencies are made by a comparison of spectral intervals with calculated normal mode frequencies, with the strongest IR bands leading to the most intense vibronic bands.

  15. Cellular Decision-Making and Biological Noise: From Microbes to Mammals

    PubMed Central

    Balázsi, Gábor; van Oudenaarden, Alexander; Collins, James J.

    2011-01-01

    Cellular decision-making is the process wherein cells assume different, functionally important and heritable fates without an associated genetic or environmental difference. Such stochastic cell-fate decisions generate non-genetic cellular diversity, which may be critical for metazoan development as well as optimized microbial resource utilization and survival in a fluctuating, frequently stressful environment. Here we review several examples of cellular decision-making from viruses, bacteria, yeast, lower metazoans and mammals, highlighting the role of regulatory network structure and molecular noise. We propose that cellular decision-making is one of at least three key processes underlying development at various scales of biological organization. PMID:21414483

  16. Overview of molecular, cellular, and genetic neurotoxicology.

    PubMed

    Wallace, David R

    2005-05-01

    It has become increasingly evident that the field of neurotoxicology is not only rapidly growing but also rapidly evolving, especially over the last 20 years. As the number of drugs and environmental and bacterial/viral agents with potential neurotoxic properties has grown, the need for additional testing has increased. Only recently has the technology advanced to a level that neurotoxicologic studies can be performed without operating in a "black box." Examination of the effects of agents that are suspected of being toxic can occur on the molecular (protein-protein), cellular (biomarkers, neuronal function), and genetic (polymorphisms) level. Together, these areas help to elucidate the potential toxic profiles of unknown (and in some cases, known) agents. The area of proteomics is one of the fastest growing areas in science and particularly applicable to neurotoxicology. Lubec et al, provide a review of the potential and limitations of proteomics. Proteomics focuses on a more comprehensive view of cellular proteins and provides considerably more information about the effects of toxins on the CNS. Proteomics can be classified into three different focuses: post-translational modification, protein-expression profiling, and protein-network mapping. Together, these methods represent a more complete and powerful image of protein modifications following potential toxin exposure. Cellular neurotoxicology involves many cellular processes including alterations in cellular energy homeostasis, ion homeostasis, intracellular signaling function, and neurotransmitter release, uptake, and storage. The greatest hurdle in cellular neurotoxicology has been the discovery of appropriate biomarkers that are reliable, reproducible, and easy to obtain. There are biomarkers of exposure effect, and susceptibility. Finding the appropriate biomarker for a particular toxin is a daunting task. The appropriate biomarker for a particular toxin is a daunting task. The advantage to biomarker

  17. Continuum representations of cellular solids

    SciTech Connect

    Neilsen, M.K.

    1993-09-01

    Cellular materials consist of interconnected struts or plates which form cells. The struts or plates are constructed from a variety of metals, polymers, ceramics and wood products. Cellular materials are often used in impact limiters for shipping containers to protect the contents from accidental impact events. These materials exhibit a variety of complex behavior when subjected to crushing loads. This research focuses on the development of continuum representations of cellular solids that can be used in the finite element analysis of shipping container accidents. A significant portion of this work is the development of a new methodology to relate localized deformations to appropriate constitutive descriptions. This methodology provides the insight needed to select constitutive descriptions for cellular solids that capture the localized deformations that are observed experimentally. Constitutive relations are developed for two different cellular materials, aluminum honeycomb and polyurethane foam. These constitutive relations are based on plasticity and continuum damage theories. Plasticity is used to describe the permanent deformation exhibited by both aluminum honeycomb and polyurethane foam. Continuum damage is needed to capture the change in elastic parameters due to cracking of the polyurethane cell wall materials. The new constitutive description of polyurethane foam is implemented in both static and dynamic finite element codes, and analytical and numerical predictions are compared with available experimental data.

  18. Parameter-less approaches for interpreting dynamic cellular response

    PubMed Central

    2014-01-01

    Cellular response such as cell signaling is an integral part of information processing in biology. Upon receptor stimulation, numerous intracellular molecules are invoked to trigger the transcription of genes for specific biological purposes, such as growth, differentiation, apoptosis or immune response. How complex are such specialized and sophisticated machinery? Computational modeling is an important tool for investigating dynamic cellular behaviors. Here, I focus on certain types of key signaling pathways that can be interpreted well using simple physical rules based on Boolean logic and linear superposition of response terms. From the examples shown, it is conceivable that for small-scale network modeling, reaction topology, rather than parameter values, is crucial for understanding population-wide cellular behaviors. For large-scale response, non-parametric statistical approaches have proven valuable for revealing emergent properties. PMID:25183996

  19. In Vivo Cellular Reprogramming: The Next Generation.

    PubMed

    Srivastava, Deepak; DeWitt, Natalie

    2016-09-01

    Cellular reprogramming technology has created new opportunities in understanding human disease, drug discovery, and regenerative medicine. While a combinatorial code was initially found to reprogram somatic cells to pluripotency, a "second generation" of cellular reprogramming involves lineage-restricted transcription factors and microRNAs that directly reprogram one somatic cell to another. This technology was enabled by gene networks active during development, which induce global shifts in the epigenetic landscape driving cell fate decisions. A major utility of direct reprogramming is the potential of harnessing resident support cells within damaged organs to regenerate lost tissue by converting them into the desired cell type in situ. Here, we review the progress in direct cellular reprogramming, with a focus on the paradigm of in vivo reprogramming for regenerative medicine, while pointing to hurdles that must be overcome to translate this technology into future therapeutics. PMID:27610565

  20. Aging, Cellular Senescence, and Cancer

    PubMed Central

    Campisi, Judith

    2014-01-01

    For most species, aging promotes a host of degenerative pathologies that are characterized by debilitating losses of tissue or cellular function. However, especially among vertebrates, aging also promotes hyperplastic pathologies, the most deadly of which is cancer. In contrast to the loss of function that characterizes degenerating cells and tissues, malignant (cancerous) cells must acquire new (albeit aberrant) functions that allow them to develop into a lethal tumor. This review discusses the idea that, despite seemingly opposite characteristics, the degenerative and hyperplastic pathologies of aging are at least partly linked by a common biological phenomenon: a cellular stress response known as cellular senescence. The senescence response is widely recognized as a potent tumor suppressive mechanism. However, recent evidence strengthens the idea that it also drives both degenerative and hyper-plastic pathologies, most likely by promoting chronic inflammation. Thus, the senescence response may be the result of antagonistically pleiotropic gene action. PMID:23140366

  1. Aging, cellular senescence, and cancer.

    PubMed

    Campisi, Judith

    2013-01-01

    For most species, aging promotes a host of degenerative pathologies that are characterized by debilitating losses of tissue or cellular function. However, especially among vertebrates, aging also promotes hyperplastic pathologies, the most deadly of which is cancer. In contrast to the loss of function that characterizes degenerating cells and tissues, malignant (cancerous) cells must acquire new (albeit aberrant) functions that allow them to develop into a lethal tumor. This review discusses the idea that, despite seemingly opposite characteristics, the degenerative and hyperplastic pathologies of aging are at least partly linked by a common biological phenomenon: a cellular stress response known as cellular senescence. The senescence response is widely recognized as a potent tumor suppressive mechanism. However, recent evidence strengthens the idea that it also drives both degenerative and hyperplastic pathologies, most likely by promoting chronic inflammation. Thus, the senescence response may be the result of antagonistically pleiotropic gene action. PMID:23140366

  2. Fracture mechanics of cellular glass

    NASA Technical Reports Server (NTRS)

    Zwissler, J. G.; Adams, M. A.

    1981-01-01

    The fracture mechanics of cellular glasses (for the structural substrate of mirrored glass for solr concentrator reflecting panels) are discussed. Commercial and developmental cellular glasses were tested and analyzed using standard testing techniques and models developed from linear fracture mechanics. Two models describing the fracture behavior of these materials were developed. Slow crack growth behavior in cellular glass was found to be more complex than that encountered in dense glasses or ceramics. The crack velocity was found to be strongly dependent upon water vapor transport to the tip of the moving crack. The existence of a static fatigue limit was not conclusively established, however, it is speculated that slow crack growth behavior in Region 1 may be slower, by orders of magnitude, than that found in dense glasses.

  3. Cellular-based preemption system

    NASA Technical Reports Server (NTRS)

    Bachelder, Aaron D. (Inventor)

    2011-01-01

    A cellular-based preemption system that uses existing cellular infrastructure to transmit preemption related data to allow safe passage of emergency vehicles through one or more intersections. A cellular unit in an emergency vehicle is used to generate position reports that are transmitted to the one or more intersections during an emergency response. Based on this position data, the one or more intersections calculate an estimated time of arrival (ETA) of the emergency vehicle, and transmit preemption commands to traffic signals at the intersections based on the calculated ETA. Additional techniques may be used for refining the position reports, ETA calculations, and the like. Such techniques include, without limitation, statistical preemption, map-matching, dead-reckoning, augmented navigation, and/or preemption optimization techniques, all of which are described in further detail in the above-referenced patent applications.

  4. GABAergic Interneurons in the Neocortex: From Cellular Properties to Circuits.

    PubMed

    Tremblay, Robin; Lee, Soohyun; Rudy, Bernardo

    2016-07-20

    Cortical networks are composed of glutamatergic excitatory projection neurons and local GABAergic inhibitory interneurons that gate signal flow and sculpt network dynamics. Although they represent a minority of the total neocortical neuronal population, GABAergic interneurons are highly heterogeneous, forming functional classes based on their morphological, electrophysiological, and molecular features, as well as connectivity and in vivo patterns of activity. Here we review our current understanding of neocortical interneuron diversity and the properties that distinguish cell types. We then discuss how the involvement of multiple cell types, each with a specific set of cellular properties, plays a crucial role in diversifying and increasing the computational power of a relatively small number of simple circuit motifs forming cortical networks. We illustrate how recent advances in the field have shed light onto the mechanisms by which GABAergic inhibition contributes to network operations. PMID:27477017

  5. Methods for Determining the Cellular Functions of Vimentin Intermediate Filaments.

    PubMed

    Ridge, Karen M; Shumaker, Dale; Robert, Amélie; Hookway, Caroline; Gelfand, Vladimir I; Janmey, Paul A; Lowery, Jason; Guo, Ming; Weitz, David A; Kuczmarski, Edward; Goldman, Robert D

    2016-01-01

    The type III intermediate filament protein vimentin was once thought to function mainly as a static structural protein in the cytoskeleton of cells of mesenchymal origin. Now, however, vimentin is known to form a dynamic, flexible network that plays an important role in a number of signaling pathways. Here, we describe various methods that have been developed to investigate the cellular functions of the vimentin protein and intermediate filament network, including chemical disruption, photoactivation and photoconversion, biolayer interferometry, soluble bead binding assay, three-dimensional substrate experiments, collagen gel contraction, optical-tweezer active microrheology, and force spectrum microscopy. Using these techniques, the contributions of vimentin to essential cellular processes can be probed in ever further detail. PMID:26795478

  6. Methods for Determining the Cellular Functions of Vimentin Intermediate Filaments

    PubMed Central

    Ridge, Karen M.; Shumaker, Dale; Robert, Amélie; Hookway, Caroline; Gelfand, Vladimir I.; Janmey, Paul A.; Lowery, Jason; Guo, Ming; Weitz, David A.; Kuczmarski, Edward; Goldman, Robert D.

    2016-01-01

    The type III intermediate filament protein vimentin was once thought to function mainly as a static structural protein in the cytoskeleton of cells of mesenchymal origin. Now, however, vimentin is known to form a dynamic, flexible network that plays an important role in a number of signaling pathways. Here, we describe various methods that have been developed to investigate the cellular functions of the vimentin protein and intermediate filament network, including chemical disruption, photoactivation and photoconversion, biolayer interferometry, soluble bead binding assay, three-dimensional substrate experiments, collagen gel contraction, optical-tweezer active microrheology, and force spectrum microscopy. Using these techniques, the contributions of vimentin to essential cellular processes can be probed in ever further detail. PMID:26795478

  7. Microscopic origin of the 1.3 G{sub 0} conductance observed in oxygen-doped silver quantum point contacts

    SciTech Connect

    Tu, Xingchen; Wang, Minglang; Hou, Shimin; Sanvito, Stefano

    2014-11-21

    Besides the peak at one conductance quantum, G{sub 0}, two additional features at ∼0.4 G{sub 0} and ∼1.3 G{sub 0} have been observed in the conductance histograms of silver quantum point contacts at room temperature in ambient conditions. In order to understand such feature, here we investigate the electronic transport and mechanical properties of clean and oxygen-doped silver atomic contacts by employing the non-equilibrium Green's function formalism combined with density functional theory. Our calculations show that, unlike clean Ag single-atom contacts showing a conductance of 1 G{sub 0}, the low-bias conductance of oxygen-doped Ag atomic contacts depends on the number of oxygen impurities and their binding configuration. When one oxygen atom binds to an Ag monatomic chain sandwiched between two Ag electrodes, the low-bias conductance of the junction always decreases. In contrast, when the number of oxygen impurities is two and the O-O axis is perpendicular to the Ag-Ag axis, the transmission coefficients at the Fermi level are, respectively, calculated to be 1.44 for the junction with Ag(111) electrodes and 1.24 for that with Ag(100) electrodes, both in good agreement with the measured value of ∼1.3 G{sub 0}. The calculated rupture force (1.60 nN for the junction with Ag(111) electrodes) is also consistent with the experimental value (1.66 ± 0.09 nN), confirming that the measured ∼1.3 G{sub 0} conductance should originate from Ag single-atom contacts doped with two oxygen atoms in a perpendicular configuration.

  8. H3.3 G34R mutations in pediatric primitive neuroectodermal tumors of central nervous system (CNS-PNET) and pediatric glioblastomas: possible diagnostic and therapeutic implications?

    PubMed

    Gessi, Marco; Gielen, Gerrit H; Hammes, Jennifer; Dörner, Evelyn; Mühlen, Anja Zur; Waha, Andreas; Pietsch, Torsten

    2013-03-01

    Pediatric glioblastomas recently have been exon sequenced with evidence that approximately 30 % of cases harbour mutations of the histone H3.3 gene. Although studies to determinate their role in risk stratification are on-going, it remains to be determined whether H3.3 mutations could be found in other tumors such as pediatric primitive neuroectodermal tumors of the central nervous system (CNS-PNETs) and whether the presence of H3.3 mutations in glioblastomas could be used as diagnostic tool in their differential diagnosis with CNS-PNETs. We performed a large mutational pyrosequencing-based screening on 123 pediatric glioblastomas and 33 CNS-PNET. The analysis revealed that 39/123 (31.7 %) glioblastomas carry H3.3 mutations. The K27M (AAG → ATG, lysine → methionine) mutation was found in 33 glioblastomas (26 %); the G34R (GGG → AGG, glycine → arginine) was observed in 6 glioblastomas (5.5 %). However, we also identified 4 of 33 cases (11 %) of CNS-PNETs harbouring a H3.3 G34R mutation. Multiplex ligation-dependent probe amplification analysis revealed PDGFR-alpha amplification and EGFR gain in two cases and N-Myc amplification in one case of H3.3 G34R mutated CNS-PNET. None of H3.3 mutated tumors presented a CDKN2A loss. In conclusion, because pediatric patients with glioblastoma and CNS-PNET are treated according to different therapeutic protocols, these findings may raise further concerns about the reliability of the histological diagnosis in the case of an undifferentiated brain tumor harbouring G34R H3.3 mutation. In this view, additional studies are needed to determine whether H3.3 G34 mutated CNS-PNET/glioblastomas may represent a defined tumor subtype. PMID:23354654

  9. Synthetic biology in cellular immunotherapy

    PubMed Central

    Chakravarti, Deboki; Wong, Wilson W.

    2015-01-01

    The adoptive transfer of genetically engineered T cells with cancer-targeting receptors has shown tremendous promise for eradicating tumors in clinical trials. This form of cellular immunotherapy presents a unique opportunity to incorporate advanced systems and synthetic biology approaches to create cancer therapeutics with novel functions. Here, we first review the development of synthetic receptors, switches, and circuits to control the location, duration, and strength of T cell activity against tumors. In addition, we discuss the cellular engineering and genome editing of host cells (or the chassis) to improve the efficacy of cell-based cancer therapeutics, and to reduce the time and cost of manufacturing. PMID:26088008

  10. Global properties of cellular automata

    SciTech Connect

    Jen, E.

    1986-04-01

    Cellular automata are discrete mathematical systems that generate diverse, often complicated, behavior using simple deterministic rules. Analysis of the local structure of these rules makes possible a description of the global properties of the associated automata. A class of cellular automata that generate infinitely many aperoidic temporal sequences is defined,a s is the set of rules for which inverses exist. Necessary and sufficient conditions are derived characterizing the classes of ''nearest-neighbor'' rules for which arbitrary finite initial conditions (i) evolve to a homogeneous state; (ii) generate at least one constant temporal sequence.

  11. Cellular automaton for chimera states

    NASA Astrophysics Data System (ADS)

    García-Morales, Vladimir

    2016-04-01

    A minimalistic model for chimera states is presented. The model is a cellular automaton (CA) which depends on only one adjustable parameter, the range of the nonlocal coupling, and is built from elementary cellular automata and the majority (voting) rule. This suggests the universality of chimera-like behavior from a new point of view: Already simple CA rules based on the majority rule exhibit this behavior. After a short transient, we find chimera states for arbitrary initial conditions, the system spontaneously splitting into stable domains separated by static boundaries, some synchronously oscillating and the others incoherent. When the coupling range is local, nontrivial coherent structures with different periodicities are formed.

  12. Cellular senescence in aging primates.

    PubMed

    Herbig, Utz; Ferreira, Mark; Condel, Laura; Carey, Dee; Sedivy, John M

    2006-03-01

    The aging of organisms is characterized by a gradual functional decline of all organ systems. Mammalian somatic cells in culture display a limited proliferative life span, at the end of which they undergo an irreversible cell cycle arrest known as replicative senescence. Whether cellular senescence contributes to organismal aging has been controversial. We investigated telomere dysfunction, a recently discovered biomarker of cellular senescence, and found that the number of senescent fibroblasts increases exponentially in the skin of aging baboons, reaching >15% of all cells in very old individuals. In addition, the same cells contain activated ataxia-telangiectasia mutated kinase and heterochromatinized nuclei, confirming their senescent status. PMID:16456035

  13. Cellular basis of Alzheimer's disease.

    PubMed

    Bali, Jitin; Halima, Saoussen Ben; Felmy, Boas; Goodger, Zoe; Zurbriggen, Sebastian; Rajendran, Lawrence

    2010-12-01

    Alzheimer's disease (AD) is the most common form of neurodegenerative disease. A characteristic feature of the disease is the presence of amyloid-β (Aβ) which either in its soluble oligomeric form or in the plaque-associated form is causally linked to neurodegeneration. Aβ peptide is liberated from the membrane-spanning -amyloid precursor protein by sequential proteolytic processing employing β- and γ-secretases. All these proteins involved in the production of Aβ peptide are membrane associated and hence, membrane trafficking and cellular compartmentalization play important roles. In this review, we summarize the key cellular events that lead to the progression of AD. PMID:21369424

  14. An Evolutionary Hybrid Cellular Automaton Model of Solid Tumour Growth

    PubMed Central

    Gerlee, P.; Anderson, A.R.A.

    2007-01-01

    We propose a cellular automaton model of solid tumour growth, in which each cell is equipped with a micro-environment response network. This network is modelled using a feed-forward artificial neural network, that takes environmental variables as an input and from these determines the cellular behaviour as the output. The response of the network is determined by connection weights and thresholds in the network, which are subject to mutations when the cells divide. As both available space and nutrients are limited resources for the tumour this gives rise to clonal evolution where only the fittest cells survive. Using this approach we have investigated the impact of the tissue oxygen concentration on the growth and evolutionary dynamics of the tumour. The results show that the oxygen concentration affects the selection pressure, cell population diversity and morphology of the tumour. A low oxygen concentration in the tissue gives rise to a tumour with a fingered morphology that contains aggressive phenotypes with a small apoptotic potential, while a high oxygen concentration in the tissue gives rise to a tumour with a round morphology containing less evolved phenotypes. The tissue oxygen concentration thus affects the tumour at both the morphological level and on the phenotype level. PMID:17374383

  15. Zinc-mediated binding of a low-molecular-weight stabilizer of the host anti-viral factor apolipoprotein B mRNA-editing enzyme, catalytic polypeptide-like 3G.

    PubMed

    Radwan, Mohamed O; Sonoda, Sachiko; Ejima, Tomohiko; Tanaka, Ayumi; Koga, Ryoko; Okamoto, Yoshinari; Fujita, Mikako; Otsuka, Masami

    2016-09-15

    Apolipoprotein B mRNA-editing enzyme, catalytic polypeptide-like 3G (APOBEC3G, A3G), is a human anti-virus restriction protein which works deaminase-dependently and -independently. A3G is known to be ubiquitinated by HIV-1 viral infectivity factor (Vif) protein, leading to proteasomal degradation. A3G contains two zinc ions at the N-terminal domain and the C-terminal domain. Four lysine residues, K(297), K(301), K(303), and K(334), are known to be required for Vif-mediated A3G ubiquitination and degradation. Previously, we reported compound SN-1, a zinc chelator that increases steady-state expression level of A3G in the presence of Vif. In this study, we prepared Biotin-SN-1, a biotinylated derivative of SN-1, to study the SN-1-A3G interaction. A pull-down assay revealed that Biotin-SN-1 bound A3G. A zinc-abstraction experiment indicated that SN-1 binds to the zinc site of A3G. We carried out a SN-1-A3G docking study using molecular operating environment. The calculations revealed that SN-1 binds to the C-terminal domain through Zn(2+), H(216), P(247), C(288), and Y(315). Notably, SN-1-binding covers the H(257), E(259), C(288), and C(291) residues that participate in zinc-mediated deamination, and the ubiquitination regions of A3G. The binding of SN-1 presumably perturbs the secondary structure between C(288) and Y(315), leading to less efficient ubiquitination. PMID:27475536

  16. 3D Encoding of Musical Score Information and the Playback Method Used by the Cellular Phone

    NASA Astrophysics Data System (ADS)

    Kubo, Hitoshi; Sugiura, Akihiko

    Recently, 3G cellular phone that can take a movie has spread by improving the digital camera function. And, 2Dcode has accurate readout and high operability. And it has spread as an information transmission means. However, the symbol is expanded and complicated when information of 2D codes increases. To solve these, 3D code was proposed. But it need the special equipment for readout, and specializes in the enhancing reality feeling technology. Therefore, it is difficult to apply it to the cellular phone. And so, we propose 3D code that can be recognized by the movie shooting function of the cellular phone. And, score information was encoded. We apply Gray Code to the property of music, and encode it. And the effectiveness was verified.

  17. Quantitative Analysis of Cellular Metabolic Dissipative, Self-Organized Structures

    PubMed Central

    de la Fuente, Ildefonso Martínez

    2010-01-01

    One of the most important goals of the postgenomic era is understanding the metabolic dynamic processes and the functional structures generated by them. Extensive studies during the last three decades have shown that the dissipative self-organization of the functional enzymatic associations, the catalytic reactions produced during the metabolite channeling, the microcompartmentalization of these metabolic processes and the emergence of dissipative networks are the fundamental elements of the dynamical organization of cell metabolism. Here we present an overview of how mathematical models can be used to address the properties of dissipative metabolic structures at different organizational levels, both for individual enzymatic associations and for enzymatic networks. Recent analyses performed with dissipative metabolic networks have shown that unicellular organisms display a singular global enzymatic structure common to all living cellular organisms, which seems to be an intrinsic property of the functional metabolism as a whole. Mathematical models firmly based on experiments and their corresponding computational approaches are needed to fully grasp the molecular mechanisms of metabolic dynamical processes. They are necessary to enable the quantitative and qualitative analysis of the cellular catalytic reactions and also to help comprehend the conditions under which the structural dynamical phenomena and biological rhythms arise. Understanding the molecular mechanisms responsible for the metabolic dissipative structures is crucial for unraveling the dynamics of cellular life. PMID:20957111

  18. Cellular Automata and the Humanities.

    ERIC Educational Resources Information Center

    Gallo, Ernest

    1994-01-01

    The use of cellular automata to analyze several pre-Socratic hypotheses about the evolution of the physical world is discussed. These hypotheses combine characteristics of both rigorous and metaphoric language. Since the computer demands explicit instructions for each step in the evolution of the automaton, such models can reveal conceptual…

  19. Gene regulatory networks and the underlying biology of developmental toxicity

    EPA Science Inventory

    Embryonic cells are specified by large-scale networks of functionally linked regulatory genes. Knowledge of the relevant gene regulatory networks is essential for understanding phenotypic heterogeneity that emerges from disruption of molecular functions, cellular processes or sig...

  20. Uracil DNA Glycosylase Is Dispensable for Human Immunodeficiency Virus Type 1 Replication and Does Not Contribute to the Antiviral Effects of the Cytidine Deaminase Apobec3G

    PubMed Central

    Kaiser, Shari M.; Emerman, Michael

    2006-01-01

    It is well established that many host factors are involved in the replication of human immunodeficiency virus (HIV) type 1. One host protein, uracil DNA glycosylase 2 (UNG2), binds to multiple viral proteins and is packaged into HIV type 1 virions. UNG initiates the removal of uracils from DNA, and this has been proposed to be important both for reverse transcription and as a mediator to the antiviral effect of virion-incorporated Apobec3G, a cytidine deaminase that generates numerous uracils in the viral DNA during virus replication. We used a natural human UNG−/− cell line as well as cells that express a potent catalytic active-site inhibitor of UNG to assess the effects of removing UNG activity on HIV infectivity. In both cases, we find UNG2 activity and protein to be completely dispensable for virus replication. Moreover, we find that virion-associated UNG2 does not affect the loss of infectivity caused by Apobec3G. PMID:16378989

  1. Optofluidic Detection for Cellular Phenotyping

    PubMed Central

    Tung, Yi-Chung; Huang, Nien-Tsu; Oh, Bo-Ram; Patra, Bishnubrata; Pan, Chi-Chun; Qiu, Teng; Paul, K. Chu; Zhang, Wenjun; Kurabayashi, Katsuo

    2012-01-01

    Quantitative analysis of the output of processes and molecular interactions within a single cell is highly critical to the advancement of accurate disease screening and personalized medicine. Optical detection is one of the most broadly adapted measurement methods in biological and clinical assays and serves cellular phenotyping. Recently, microfluidics has obtained increasing attention due to several advantages, such as small sample and reagent volumes, very high throughput, and accurate flow control in the spatial and temporal domains. Optofluidics, which is the attempt to integrate optics with microfluidic, shows great promise to enable on-chip phenotypic measurements with high precision, sensitivity, specificity, and simplicity. This paper reviews the most recent developments of optofluidic technologies for cellular phenotyping optical detection. PMID:22854915

  2. Hox Targets and Cellular Functions

    PubMed Central

    Sánchez-Herrero, Ernesto

    2013-01-01

    Hox genes are a group of genes that specify structures along the anteroposterior axis in bilaterians. Although in many cases they do so by modifying a homologous structure with a different (or no) Hox input, there are also examples of Hox genes constructing new organs with no homology in other regions of the body. Hox genes determine structures though the regulation of targets implementing cellular functions and by coordinating cell behavior. The genetic organization to construct or modify a certain organ involves both a genetic cascade through intermediate transcription factors and a direct regulation of targets carrying out cellular functions. In this review I discuss new data from genome-wide techniques, as well as previous genetic and developmental information, to describe some examples of Hox regulation of different cell functions. I also discuss the organization of genetic cascades leading to the development of new organs, mainly using Drosophila melanogaster as the model to analyze Hox function. PMID:24490109

  3. Cellular solidification of transparent monotectics

    NASA Technical Reports Server (NTRS)

    Kaulker, W. F.

    1986-01-01

    Understanding how liquid phase particles are engulfed or pushed during freezing of a monotectic is addressed. The additional complication is that the solid-liquid interface is nonplanar due to constitutional undercooling. Some evidence of particle pushing where the particles are the liquid phase of the montectic was already observed. Cellular freezing of the succinonitrile-glycerol system also occurred. Only a few compositions were tested at that time. The starting materials were not especially pure so that cellular interface observed was likely due to the presence of unkown impurities, the major portion of which was water. Topics addressed include: the effort of modeling the particle pushing process using the computer, establishing an apparatus for the determination of phase diagrams, and the measurement of the temperature gradients with a specimen which will solidify on the temperature gradient microscope stage.

  4. Cellular tagging as a neural network mechanism for behavioural tagging

    PubMed Central

    Nomoto, Masanori; Ohkawa, Noriaki; Nishizono, Hirofumi; Yokose, Jun; Suzuki, Akinobu; Matsuo, Mina; Tsujimura, Shuhei; Takahashi, Yukari; Nagase, Masashi; Watabe, Ayako M.; Kato, Fusao; Inokuchi, Kaoru

    2016-01-01

    Behavioural tagging is the transformation of a short-term memory, induced by a weak experience, into a long-term memory (LTM) due to the temporal association with a novel experience. The mechanism by which neuronal ensembles, each carrying a memory engram of one of the experiences, interact to achieve behavioural tagging is unknown. Here we show that retrieval of a LTM formed by behavioural tagging of a weak experience depends on the degree of overlap with the neuronal ensemble corresponding to a novel experience. The numbers of neurons activated by weak training in a novel object recognition (NOR) task and by a novel context exploration (NCE) task, denoted as overlapping neurons, increases in the hippocampal CA1 when behavioural tagging is successfully achieved. Optical silencing of an NCE-related ensemble suppresses NOR–LTM retrieval. Thus, a population of cells recruited by NOR is tagged and then preferentially incorporated into the memory trace for NCE to achieve behavioural tagging. PMID:27477539

  5. Method for analyzing signaling networks in complex cellular systems.

    PubMed

    Plavec, Ivan; Sirenko, Oksana; Privat, Sylvie; Wang, Yuker; Dajee, Maya; Melrose, Jennifer; Nakao, Brian; Hytopoulos, Evangelos; Berg, Ellen L; Butcher, Eugene C

    2004-02-01

    Now that the human genome has been sequenced, the challenge of assigning function to human genes has become acute. Existing approaches using microarrays or proteomics frequently generate very large volumes of data not directly related to biological function, making interpretation difficult. Here, we describe a technique for integrative systems biology in which: (i) primary cells are cultured under biologically meaningful conditions; (ii) a limited number of biologically meaningful readouts are measured; and (iii) the results obtained under several different conditions are combined for analysis. Studies of human endothelial cells overexpressing different signaling molecules under multiple inflammatory conditions show that this system can capture a remarkable range of functions by a relatively small number of simple measurements. In particular, measurement of seven different protein levels by ELISA under four different conditions is capable of reconstructing pathway associations of 25 different proteins representing four known signaling pathways, implicating additional participants in the NF-kappaBorRAS/mitogen-activated protein kinase pathways and defining additional interactions between these pathways. PMID:14745015

  6. Method for analyzing signaling networks in complex cellular systems

    PubMed Central

    Plavec, Ivan; Sirenko, Oksana; Privat, Sylvie; Wang, Yuker; Dajee, Maya; Melrose, Jennifer; Nakao, Brian; Hytopoulos, Evangelos; Berg, Ellen L.; Butcher, Eugene C.

    2004-01-01

    Now that the human genome has been sequenced, the challenge of assigning function to human genes has become acute. Existing approaches using microarrays or proteomics frequently generate very large volumes of data not directly related to biological function, making interpretation difficult. Here, we describe a technique for integrative systems biology in which: (i) primary cells are cultured under biologically meaningful conditions; (ii) a limited number of biologically meaningful readouts are measured; and (iii) the results obtained under several different conditions are combined for analysis. Studies of human endothelial cells overexpressing different signaling molecules under multiple inflammatory conditions show that this system can capture a remarkable range of functions by a relatively small number of simple measurements. In particular, measurement of seven different protein levels by ELISA under four different conditions is capable of reconstructing pathway associations of 25 different proteins representing four known signaling pathways, implicating additional participants in the NF-κBorRAS/mitogen-activated protein kinase pathways and defining additional interactions between these pathways. PMID:14745015

  7. Cellular networks controlling Th2 polarization in allergy and immunity.

    PubMed

    Kool, Mirjam; Hammad, Hamida; Lambrecht, Bart N

    2012-01-01

    In contrast to the development of Th1 (type 1 T helper cells), Th17 and Treg (regulatory T cells), little is known of the mechanisms governing Th2 development, which is important for immunity to helminths and for us to understand the pathogenesis of allergy. A picture is emerging in which mucosal epithelial cells instruct dendritic cells to promote Th2 responses in the absence of IL-12 (interleukin 12) production and provide instruction through thymic stromal lymphopoieitin (TSLP) or granulocyte-macrophage colony stimulating factor (GM-CSF). At the same time, allergens, helminths and chemical adjuvants elicit the response of innate immune cells like basophils, which provide more polarizing cytokines and IL-4 and reinforce Th2 immunity. This unique communication between cells will only be fully appreciated if we study Th2 immunity in vivo and in a tissue-specific context, and can only be fully understood if we compare several models of Th2 immune response induction. PMID:22403589

  8. Analysis of dosimetry from the H.B. Robinson unit 2 pressure vessel benchmark using RAPTOR-M3G and ALPAN

    SciTech Connect

    Fischer, G.A.

    2011-07-01

    Document available in abstract form only, full text of document follows: The dosimetry from the H. B. Robinson Unit 2 Pressure Vessel Benchmark is analyzed with a suite of Westinghouse-developed codes and data libraries. The radiation transport from the reactor core to the surveillance capsule and ex-vessel locations is performed by RAPTOR-M3G, a parallel deterministic radiation transport code that calculates high-resolution neutron flux information in three dimensions. The cross-section library used in this analysis is the ALPAN library, an Evaluated Nuclear Data File (ENDF)/B-VII.0-based library designed for reactor dosimetry and fluence analysis applications. Dosimetry is evaluated with the industry-standard SNLRML reactor dosimetry cross-section data library. (authors)

  9. New functions developed for ICU/CCU remote monitoring system using a 3G mobile phone and evaluations of the system.

    PubMed

    Zhang, Pu; Kumabe, Akinoubu; Kogure, Yuichi; Akutagawa, Masatake; Kinouchi, Yohsuke; Zhang, Qinyu

    2008-01-01

    As a combination of medical information and Telecommunication technologies, telemedicine plays a more and more important role in supporting doctors to diagnose and taking care of people's daily health. It is also an appropriate means to solve the conflict between aging of population and inadequacy of doctors, which are the actual condition and inevitable developing trend of the society not only in developed countries. In this paper, some new functions are developed for a ICU/CCU Remote Monitoring System using a 3G mobile phone. Furthermore, some evaluations of the system have been implied on several different mobile phones. The system is anticipated to be adopted by hospitals for its accuracy and real-time performance to supporting telediagnosis for patients in ICU/CCU. PMID:19163924

  10. Xtoys: Cellular automata on xwindows

    SciTech Connect

    Creutz, M.

    1995-08-15

    Xtoys is a collection of xwindow programs for demonstrating simulations of various statistical models. Included are xising, for the two dimensional Ising model, xpotts, for the q-state Potts model, xautomalab, for a fairly general class of totalistic cellular automata, xsand, for the Bak-Tang-Wiesenfield model of self organized criticality, and xfires, a simple forest fire simulation. The programs should compile on any machine supporting xwindows.

  11. Synthesis, cytotoxicity and antiviral evaluation of new series of imidazo[4,5-g]quinoline and pyrido[2,3-g]quinoxalinone derivatives.

    PubMed

    Briguglio, Irene; Loddo, Roberta; Laurini, Erik; Fermeglia, Maurizio; Piras, Sandra; Corona, Paola; Giunchedi, Paolo; Gavini, Elisabetta; Sanna, Giuseppina; Giliberti, Gabriele; Ibba, Cristina; Farci, Pamela; La Colla, Paolo; Pricl, Sabrina; Carta, Antonio

    2015-11-13

    Linear aromatic N-tricyclic compounds with promising antiviral activity and minimal cytotoxicity were prepared and analyzed in the last years. Specifically, the pyrido[2,3-g]quinoxalinone nucleus was found endowed with high potency against several pathogenic RNA viruses as etiological agents of important veterinary and human pathologies. Following our research program on new antiviral agents we have designed, synthesized and assayed new series of imidazo[4,5-g]quinoline and pyrido[2,3-g]quinoxalinone derivatives. Lead compounds 1-4 were further modified to enhance their antiviral activity and reduce their cytotoxicity. Thus, different substituents were introduced on N atom at position 1 or the O atom at position 2 of the leads; contextually, several groups were inserted on the nitrogen atom at position 7 of diaminoquinoline intermediates. Title compounds were tested in cell-based assays for cytotoxicity and antiviral activity against RNA virus families containing single-stranded (either positive-sense (ssRNA+) or negative-sense (ssRNA-)), and double-stranded genomes (dsRNA), and against two representatives of DNA virus families. Some derivatives emerged as potential leads for further development as antiviral agents against some viruses of public health significance, such as RSV, Reo, BVDV and HCV. Particularly, compounds 4, 11b, 11c, 13c, 15a, 18 and 21 resulted active against BVDV at concentrations ranging from 1.3 to 5 μM. Compound 21 was also evaluated for its activity on the BVDV RdRp. Compound 4 was also tested as potential anti-HCV compound in a subgenomic replication assay. Molecular simulation results provided a molecular rationale for the anti-BVDV activity of these compounds. PMID:26479028

  12. The 3D-HST Survey: Hubble Space Telescope WFC3/G141 Grism Spectra, Redshifts, and Emission Line Measurements for ~ 100,000 Galaxies

    NASA Astrophysics Data System (ADS)

    Momcheva, Ivelina G.; Brammer, Gabriel B.; van Dokkum, Pieter G.; Skelton, Rosalind E.; Whitaker, Katherine E.; Nelson, Erica J.; Fumagalli, Mattia; Maseda, Michael V.; Leja, Joel; Franx, Marijn; Rix, Hans-Walter; Bezanson, Rachel; Da Cunha, Elisabete; Dickey, Claire; Förster Schreiber, Natascha M.; Illingworth, Garth; Kriek, Mariska; Labbé, Ivo; Ulf Lange, Johannes; Lundgren, Britt F.; Magee, Daniel; Marchesini, Danilo; Oesch, Pascal; Pacifici, Camilla; Patel, Shannon G.; Price, Sedona; Tal, Tomer; Wake, David A.; van der Wel, Arjen; Wuyts, Stijn

    2016-08-01

    We present reduced data and data products from the 3D-HST survey, a 248-orbit HST Treasury program. The survey obtained WFC3 G141 grism spectroscopy in four of the five CANDELS fields: AEGIS, COSMOS, GOODS-S, and UDS, along with WFC3 H 140 imaging, parallel ACS G800L spectroscopy, and parallel I 814 imaging. In a previous paper, we presented photometric catalogs in these four fields and in GOODS-N, the fifth CANDELS field. Here we describe and present the WFC3 G141 spectroscopic data, again augmented with data from GO-1600 in GOODS-N (PI: B. Weiner). We developed software to automatically and optimally extract interlaced two-dimensional (2D) and one-dimensional (1D) spectra for all objects in the Skelton et al. (2014) photometric catalogs. The 2D spectra and the multi-band photometry were fit simultaneously to determine redshifts and emission line strengths, taking the morphology of the galaxies explicitly into account. The resulting catalog has redshifts and line strengths (where available) for 22,548 unique objects down to {{JH}}{IR}≤slant 24 (79,609 unique objects down to {{JH}}{IR}≤slant 26). Of these, 5459 galaxies are at z\\gt 1.5 and 9621 are at 0.7\\lt z\\lt 1.5, where Hα falls in the G141 wavelength coverage. The typical redshift error for {{JH}}{IR}≤slant 24 galaxies is {σ }z≈ 0.003× (1+z), i.e., one native WFC3 pixel. The 3σ limit for emission line fluxes of point sources is 2.1× {10}-17 erg s‑1 cm‑2. All 2D and 1D spectra, as well as redshifts, line fluxes, and other derived parameters, are publicly available.18

  13. Evaluating and Quantifying the Climate-Driven Interannual Variability in Global Inventory Modeling and Mapping Studies (GIMMS) Normalized Difference Vegetation Index (NDVI3g) at Global Scales

    NASA Technical Reports Server (NTRS)

    Zeng, Fanwei; Collatz, George James; Pinzon, Jorge E.; Ivanoff, Alvaro

    2013-01-01

    Satellite observations of surface reflected solar radiation contain informationabout variability in the absorption of solar radiation by vegetation. Understanding thecauses of variability is important for models that use these data to drive land surface fluxesor for benchmarking prognostic vegetation models. Here we evaluated the interannualvariability in the new 30.5-year long global satellite-derived surface reflectance index data,Global Inventory Modeling and Mapping Studies normalized difference vegetation index(GIMMS NDVI3g). Pearsons correlation and multiple linear stepwise regression analyseswere applied to quantify the NDVI interannual variability driven by climate anomalies, andto evaluate the effects of potential interference (snow, aerosols and clouds) on the NDVIsignal. We found ecologically plausible strong controls on NDVI variability by antecedent precipitation and current monthly temperature with distinct spatial patterns. Precipitation correlations were strongest for temperate to tropical water limited herbaceous systemswhere in some regions and seasons 40 of the NDVI variance could be explained byprecipitation anomalies. Temperature correlations were strongest in northern mid- to-high-latitudes in the spring and early summer where up to 70 of the NDVI variance was explained by temperature anomalies. We find that, in western and central North America,winter-spring precipitation determines early summer growth while more recent precipitation controls NDVI variability in late summer. In contrast, current or prior wetseason precipitation anomalies were correlated with all months of NDVI in sub-tropical herbaceous vegetation. Snow, aerosols and clouds as well as unexplained phenomena still account for part of the NDVI variance despite corrections. Nevertheless, this study demonstrates that GIMMS NDVI3g represents real responses of vegetation to climate variability that are useful for global models.

  14. Competitive potential of cellular mobile telecommunications

    SciTech Connect

    Ware, H.

    1983-02-03

    The Federal Communications Commission (FCC) has recently issued rules for the commercial operation of a telecommunications technology not previously in commercial use: the cellular mobile radio. The author has carefully considered the potential for competition between cellular systems and for competition between cellular radio and alternative communications technologies under the regulatory scheme which has been adopted by the FCC. He finds that competition between cellular and wire-line services can be viable if cellular cost and demand data are carefully tracked to avoid market congestion and if cellular or other techniques are not allowed to undercut selected local exchange rates.

  15. Cellular automata simulation of traffic including cars and bicycles

    NASA Astrophysics Data System (ADS)

    Vasic, Jelena; Ruskin, Heather J.

    2012-04-01

    As 'greening' of all aspects of human activity becomes mainstream, transportation science is also increasingly focused around sustainability. Modal co-existence between motorised and non-motorised traffic on urban networks is, in this context, of particular interest for traffic flow modelling. The main modelling problems here are posed by the heterogeneity of vehicles, including size and dynamics, and by the complex interactions at intersections. Herein we address these with a novel technique, based on one-dimensional cellular automata components, for modelling network infrastructure and its occupancy by vehicles. We use this modelling approach, together with a corresponding vehicle behaviour model, to simulate combined car and bicycle traffic for two elemental scenarios-examples of components that would be used in the building of an arbitrary network. Results of simulations performed on these scenarios, (i) a stretch of road and (ii) an intersection causing conflict between cars and bicycles sharing a lane, are presented and analysed.

  16. Antitumor agents 6. Synthesis, structure-activity relationships, and biological evaluation of spiro[imidazolidine-4,3'-thieno[2,3-g]quinoline]-tetraones and spiro[thieno[2,3-g]quinoline-3,5'-[1,2,4]triazinane]-tetraones with potent antiproliferative activity.

    PubMed

    Bolognese, Adele; Correale, Gaetano; Manfra, Michele; Esposito, Anna; Novellino, Ettore; Lavecchia, Antonio

    2008-12-25

    Two series of quinolinquinone derivatives, 2'H-spiro[imidazolidine-4,3'-thieno[2,3-g]quinoline]-2,4',5,9'-tetraones (2a-n) and 2H-spiro[thieno[2,3-g]quinoline-3,5'-[1,2,4]triazinane]-3',4,6',9-tetraones (3a-e), were designed and synthesized using the previously described ethyl 3-amino-4,9-dioxo-2,3,4,9-tetrahydrothieno[2,3-g]quinoline-3-carboxylate (1) as a starting material. All compounds were evaluated for their antiproliferative activity against a panel of representative liquid and solid human tumor cell lines and exhibit IC(50) values in the micromolar/submicromolar range. Series 2 displayed higher cytotoxicity than did series 3. The nature of the substituents on both imidazoline and triazinane N1 nitrogen markedly affected the activity profile of these series. Spectrophotometric and fluorescence measurements as well as unwinding assays performed on the most cytotoxic compounds, 2c, 2g, and 2k, showed that they are nonintercalative DNA agents and inhibit the catalytic activity of Topo II in a concentration-dependent mode. 2g was the most active Topo II inhibitor with activity levels comparable to those of VP-16. PMID:19053767

  17. Interrogating cellular fate decisions with high-throughput arrays of multiplexed cellular communities.

    PubMed

    Chen, Sisi; Bremer, Andrew W; Scheideler, Olivia J; Na, Yun Suk; Todhunter