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Sample records for 3g cellular networks

  1. Condition monitoring of 3G cellular networks through competitive neural models.

    PubMed

    Barreto, Guilherme A; Mota, João C M; Souza, Luis G M; Frota, Rewbenio A; Aguayo, Leonardo

    2005-09-01

    We develop an unsupervised approach to condition monitoring of cellular networks using competitive neural algorithms. Training is carried out with state vectors representing the normal functioning of a simulated CDMA2000 network. Once training is completed, global and local normality profiles (NPs) are built from the distribution of quantization errors of the training state vectors and their components, respectively. The global NP is used to evaluate the overall condition of the cellular system. If abnormal behavior is detected, local NPs are used in a component-wise fashion to find abnormal state variables. Anomaly detection tests are performed via percentile-based confidence intervals computed over the global and local NPs. We compared the performance of four competitive algorithms [winner-take-all (WTA), frequency-sensitive competitive learning (FSCL), self-organizing map (SOM), and neural-gas algorithm (NGA)] and the results suggest that the joint use of global and local NPs is more efficient and more robust than current single-threshold methods.

  2. Providing QoS guarantee in 3G wireless networks

    NASA Astrophysics Data System (ADS)

    Chuah, MooiChoo; Huang, Min; Kumar, Suresh

    2001-07-01

    The third generation networks and services present opportunities to offer multimedia applications and services that meet end-to-end quality of service requirements. In this article, we present UMTS QoS architecture and its requirements. This includes the definition of QoS parameters, traffic classes, the end-to-end data delivery model, and the mapping of end-to-end services to the services provided by the network elements of the UMTS. End-to-end QoS of a user flow is achieved by the combination of the QoS control over UMTS Domain and the IP core Network. In the Third Generation Wireless network, UMTS bearer service manager is responsible to manage radio and transport resources to QoS-enabled applications. The UMTS bearer service consists of the Radio Access Bearer Service between Mobile Terminal and SGSN and Core Network bearer service between SGSN and GGSN. The Radio Access Bearer Service is further realized by the Radio Bearer Service (mostly air interface) and Iu bearer service. For the 3G air interface, one can provide differentiated QoS via intelligent burst allocation scheme, adaptive spreading factor control and weighted fair queueing scheduling algorithms. Next, we discuss the requirements for the transport technologies in the radio access network to provide differentiated QoS to multiple classes of traffic. We discuss both ATM based and IP based transport solutions. Last but not least, we discuss how QoS mechanism is provided in the core network to ensure e2e quality of service requirements. We discuss how mobile terminals that use RSVP as QoS signaling mechanisms can be are supported in the 3G network which may implement only IETF diffserv mechanism. . We discuss how one can map UMTS QoS classes with IETF diffserv code points. We also discuss 2G/3G handover scenarios and how the 2G/3G QoS parameters can be mapped.

  3. Network planning study of the metro-optical-network-oriented 3G application

    NASA Astrophysics Data System (ADS)

    Gong, Qian; Xu, Rong; Lin, Jin Tong

    2005-02-01

    To compare with the 2G mobile communication, 3G technologies can supply the perfect service scope and performance. 3G is the trend of the mobile communication. So now to build the transmission network, it is needed to consider how the transmission network to support the 3G applications. For the 3G network architecture, it include the 2 part: Utran access network and core network. So the metro optical network should consider how to build the network to adapt the 3G applications. Include the metro core and access layer. In the metro core, we should consider the network should evolved towards the Mesh architecture with ASON function to realize the fast protection and restoration, quick end-to-end service provision, and high capacity cross-connect matrix etc. In the access layer, the network should have the ability to access the 3G services such as ATM interface with IMA function. In addition, the traffic grooming should be provided to improve the bandwidth utility. In this paper, first we present the MCC network situation, the network planning model will be introduced. Then we present the topology architecture, node capacity and traffic forecast. At last, based on our analysis, we will give a total solution to MCC to build their metro optical network toward to the mesh network with the consideration of 3G services.

  4. Measurements-based performance evaluation of 3G wireless networks supporting m-health services

    NASA Astrophysics Data System (ADS)

    Wac, Katarzyna E.; Bults, Richard; van Halteren, Aart; Konstantas, Dimitri; Nicola, Victor F.

    2004-12-01

    The emergence of 3G networks gives rise to new mobile services in many different areas of our daily life. Examples of demanding mobile services are mobile-healthcare (i.e. m-health) services allowing the continuous monitoring of a patient"s vital signs. However, a prerequisite for the successful deployment of m-health services are appropriate performance characteristics of transport services offered by an underlying wireless network (e.g. 3G). In this direction, the EU MobiHealth project targeted the evaluation of 3G networks and their ability to support demanding m-health services. The project developed and trialled a patient monitoring system, evaluating at the same time the network"s performance. This paper presents measurements based performance evaluation methodology developed and applied to assess network performance from an end-user perspective. In addition, it presents the (selected) speed-related evaluation (best-case scenario) results collected during the project. Our measurements show the dynamicity in the performance of 3G networks and phenomena negatively influencing this performance. Based on the evaluation results, we conclude that in-spite of certain shortcomings of existing 3G networks, they are suitable to support a significant set of m-health services. A set of recommendations provide a road map for both operators and service developers for design and deployment of m-health services.

  5. Measurements-based performance evaluation of 3G wireless networks supporting m-health services

    NASA Astrophysics Data System (ADS)

    Wac, Katarzyna E.; Bults, Richard; van Halteren, Aart; Konstantas, Dimitri; Nicola, Victor F.

    2005-01-01

    The emergence of 3G networks gives rise to new mobile services in many different areas of our daily life. Examples of demanding mobile services are mobile-healthcare (i.e. m-health) services allowing the continuous monitoring of a patient"s vital signs. However, a prerequisite for the successful deployment of m-health services are appropriate performance characteristics of transport services offered by an underlying wireless network (e.g. 3G). In this direction, the EU MobiHealth project targeted the evaluation of 3G networks and their ability to support demanding m-health services. The project developed and trialled a patient monitoring system, evaluating at the same time the network's performance. This paper presents measurements based performance evaluation methodology developed and applied to assess network performance from an end-user perspective. In addition, it presents the (selected) speed-related evaluation (best-case scenario) results collected during the project. Our measurements show the dynamicity in the performance of 3G networks and phenomena negatively influencing this performance. Based on the evaluation results, we conclude that in-spite of certain shortcomings of existing 3G networks, they are suitable to support a significant set of m-health services. A set of recommendations provide a road map for both operators and service developers for design and deployment of m-health services.

  6. Output power distributions of terminals in a 3G mobile communication network.

    PubMed

    Persson, Tomas; Törnevik, Christer; Larsson, Lars-Eric; Lovén, Jan

    2012-05-01

    The objective of this study was to examine the distribution of the output power of mobile phones and other terminals connected to a 3G network in Sweden. It is well known that 3G terminals can operate with very low output power, particularly for voice calls. Measurements of terminal output power were conducted in the Swedish TeliaSonera 3G network in November 2008 by recording network statistics. In the analysis, discrimination was made between rural, suburban, urban, and dedicated indoor networks. In addition, information about terminal output power was possible to collect separately for voice and data traffic. Information from six different Radio Network Controllers (RNCs) was collected during at least 1 week. In total, more than 800000 h of voice calls were collected and in addition to that a substantial amount of data traffic. The average terminal output power for 3G voice calls was below 1 mW for any environment including rural, urban, and dedicated indoor networks. This is <1% of the maximum available output power. For data applications the average output power was about 6-8 dB higher than for voice calls. For rural areas the output power was about 2 dB higher, on average, than in urban areas.

  7. Investigation of 3G radio network topologies considering performance and exposure aspects

    NASA Astrophysics Data System (ADS)

    Buddendick, H.; Wertz, P.; Eibert, T. F.; Landstorfer, F. M.; Wölfle, G.

    2007-06-01

    Five different radio network topologies, in the following referred to as "scenario", have been analyzed with regard to their capability to cover a medium size city with 3G mobile services. T-Mobile launched this study to assess different radio network topologies in terms of exposure. Thus, the main focus is to examine if, for exposure reasons, a medium size city can be covered with outer-city located sites. The radio network topologies discussed in this paper can generally be divided into two categories: In category one, the sites are located in the city, and in the other, the sites are located outside of the built-up area. In both cases the number of sites per scenario varies, and additionally the antenna height and site distance to the built-up area vary for the second category. The investigations are performed with a ray optical propagation model based on 3-D building data and a dynamic 3G network simulator. A mix of four services and a realistic spatial traffic distribution based on land usage is assumed. The performance of the scenarios, assessed by the evaluation of coverage and capacity, is examined together with the exposure. It is shown that network topologies with sites located only outside the city are not an adequate solution due to capacity constraints and coverage problems with high data services. A promising network topology is a reduced set of inner-city sites with higher order sectorization.

  8. Providing end-to-end QoS for multimedia applications in 3G wireless networks

    NASA Astrophysics Data System (ADS)

    Guo, Katherine; Rangarajan, Samapth; Siddiqui, M. A.; Paul, Sanjoy

    2003-11-01

    As the usage of wireless packet data services increases, wireless carriers today are faced with the challenge of offering multimedia applications with QoS requirements within current 3G data networks. End-to-end QoS requires support at the application, network, link and medium access control (MAC) layers. We discuss existing CDMA2000 network architecture and show its shortcomings that prevent supporting multiple classes of traffic at the Radio Access Network (RAN). We then propose changes in RAN within the standards framework that enable support for multiple traffic classes. In addition, we discuss how Session Initiation Protocol (SIP) can be augmented with QoS signaling for supporting end-to-end QoS. We also review state of the art scheduling algorithms at the base station and provide possible extensions to these algorithms to support different classes of traffic as well as different classes of users.

  9. Transcoding-Based Error-Resilient Video Adaptation for 3G Wireless Networks

    NASA Astrophysics Data System (ADS)

    Eminsoy, Sertac; Dogan, Safak; Kondoz, Ahmet M.

    2007-12-01

    Transcoding is an effective method to provide video adaptation for heterogeneous internetwork video access and communication environments, which require the tailoring (i.e., repurposing) of coded video properties to channel conditions, terminal capabilities, and user preferences. This paper presents a video transcoding system that is capable of applying a suite of error resilience tools on the input compressed video streams while controlling the output rates to provide robust communications over error-prone and bandwidth-limited 3G wireless networks. The transcoder is also designed to employ a new adaptive intra-refresh algorithm, which is responsive to the detected scene activity inherently embedded into the video content and the reported time-varying channel error conditions of the wireless network. Comprehensive computer simulations demonstrate significant improvements in the received video quality performances using the new transcoding architecture without an extra computational cost.

  10. TTCN-3 Based Conformance Testing of Mobile Broadcast Business Management System in 3G Networks

    NASA Astrophysics Data System (ADS)

    Wang, Zhiliang; Yin, Xia; Xiang, Yang; Zhu, Ruiping; Gao, Shirui; Wu, Xin; Liu, Shijian; Gao, Song; Zhou, Li; Li, Peng

    Mobile broadcast service is one of the emerging most important new services in 3G networks. To better operate and manage mobile broadcast services, mobile broadcast business management system (MBBMS) should be designed and developed. Such a system, with its distributed nature, complicated XML data and security mechanism, faces many challenges in testing technology. In this paper, we study the conformance testing methodology of MBBMS, and design and implement a MBBMS protocol conformance testing tool based on TTCN-3, a standardized test description language that can be used in black-box testing of reactive and distributed system. In this methodology and testing tool, we present a semi-automatic XML test data generation method of TTCN-3 test suite and use HMSC model to help the design of test suite. In addition, we also propose an integrated testing method for hierarchical MBBMS security architecture. This testing tool has been used in industrial level’s testing.

  11. 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.

  12. The double-domain cytidine deaminase APOBEC3G is a cellular site-specific RNA editing enzyme

    PubMed Central

    Sharma, Shraddha; Patnaik, Santosh K.; Taggart, Robert T.; Baysal, Bora E.

    2016-01-01

    APOBEC3G is a cytidine deaminase with two homologous domains and restricts retroelements and HIV-1. APOBEC3G deaminates single-stranded DNAs via its C-terminal domain, whereas the N-terminal domain is considered non-catalytic. Although APOBEC3G is known to bind RNAs, APOBEC3G-mediated RNA editing has not been observed. We recently discovered RNA editing by the single-domain enzyme APOBEC3A in innate immune cells. To determine if APOBEC3G is capable of RNA editing, we transiently expressed APOBEC3G in the HEK293T cell line and performed transcriptome-wide RNA sequencing. We show that APOBEC3G causes site-specific C-to-U editing of mRNAs from over 600 genes. The edited cytidines are often flanked by inverted repeats, but are largely distinct from those deaminated by APOBEC3A. We verified protein-recoding RNA editing of selected genes including several that are known to be involved in HIV-1 infectivity. APOBEC3G co-purifies with highly edited mRNA substrates. We find that conserved catalytic residues in both cytidine deaminase domains are required for RNA editing. Our findings demonstrate the novel RNA editing function of APOBEC3G and suggest a role for the N-terminal domain in RNA editing. PMID:27974822

  13. The double-domain cytidine deaminase APOBEC3G is a cellular site-specific RNA editing enzyme.

    PubMed

    Sharma, Shraddha; Patnaik, Santosh K; Taggart, Robert T; Baysal, Bora E

    2016-12-15

    APOBEC3G is a cytidine deaminase with two homologous domains and restricts retroelements and HIV-1. APOBEC3G deaminates single-stranded DNAs via its C-terminal domain, whereas the N-terminal domain is considered non-catalytic. Although APOBEC3G is known to bind RNAs, APOBEC3G-mediated RNA editing has not been observed. We recently discovered RNA editing by the single-domain enzyme APOBEC3A in innate immune cells. To determine if APOBEC3G is capable of RNA editing, we transiently expressed APOBEC3G in the HEK293T cell line and performed transcriptome-wide RNA sequencing. We show that APOBEC3G causes site-specific C-to-U editing of mRNAs from over 600 genes. The edited cytidines are often flanked by inverted repeats, but are largely distinct from those deaminated by APOBEC3A. We verified protein-recoding RNA editing of selected genes including several that are known to be involved in HIV-1 infectivity. APOBEC3G co-purifies with highly edited mRNA substrates. We find that conserved catalytic residues in both cytidine deaminase domains are required for RNA editing. Our findings demonstrate the novel RNA editing function of APOBEC3G and suggest a role for the N-terminal domain in RNA editing.

  14. 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.

  15. Portable emergency telemedicine system over wireless broadband and 3G networks.

    PubMed

    Hong, SungHye; Kim, SangYong; Kim, JungChae; Lim, DongKyu; Jung, SeokMyung; Kim, DongKeun; Yoo, Sun K

    2009-01-01

    The telemedicine system aims at monitoring patients remotely without limit in time and space. However the existing telemedicine systems exchange medical information simply in a specified location. Due to increasing speed in processing data and expanding bandwidth of wireless networks, it is possible to perform telemedicine services on personal digital assistants (PDA). In this paper, a telemedicine system on PDA was developed using wideband mobile networks such as Wi-Fi, HSDPA, and WiBro for high speed bandwidths. This system enables to utilize and exchange variety and reliable patient information of video, biosignals, chatting messages, and triage data. By measuring bandwidths of individual data of the system over wireless networks, and evaluating the performance of this system using PDA, we demonstrated the feasibility of the designed portable emergency telemedicine system.

  16. 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

  17. Complexity, dynamic cellular network, and tumorigenesis.

    PubMed

    Waliszewski, P

    1997-01-01

    A holistic approach to tumorigenesis is proposed. The main element of the model is the existence of dynamic cellular network. This network comprises a molecular and an energetistic structure of a cell connected through the multidirectional flow of information. The interactions within dynamic cellular network are complex, stochastic, nonlinear, and also involve quantum effects. From this non-reductionist perspective, neither tumorigenesis can be limited to the genetic aspect, nor the initial event must be of molecular nature, nor mutations and epigenetic factors are mutually exclusive, nor a link between cause and effect can be established. Due to complexity, an unstable stationary state of dynamic cellular network rather than a group of unrelated genes determines the phenotype of normal and transformed cells. This implies relativity of tumor suppressor genes and oncogenes. A bifurcation point is defined as an unstable state of dynamic cellular network leading to the other phenotype-stationary state. In particular, the bifurcation point may be determined by a change of expression of a single gene. Then, the gene is called bifurcation point gene. The unstable stationary state facilitates the chaotic dynamics. This may result in a fractal dimension of both normal and tumor tissues. The co-existence of chaotic dynamics and complexity is the essence of cellular processes and shapes differentiation, morphogenesis, and tumorigenesis. In consequence, tumorigenesis is a complex, unpredictable process driven by the interplay between self-organisation and selection.

  18. Inferring cellular networks using probabilistic graphical models.

    PubMed

    Friedman, Nir

    2004-02-06

    High-throughput genome-wide molecular assays, which probe cellular networks from different perspectives, have become central to molecular biology. Probabilistic graphical models are useful for extracting meaningful biological insights from the resulting data sets. These models provide a concise representation of complex cellular networks by composing simpler submodels. Procedures based on well-understood principles for inferring such models from data facilitate a model-based methodology for analysis and discovery. This methodology and its capabilities are illustrated by several recent applications to gene expression data.

  19. 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

  20. 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.

  1. 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

  2. Network motifs modulate druggability of cellular targets

    PubMed Central

    Wu, Fan; Ma, Cong; Tan, Cheemeng

    2016-01-01

    Druggability refers to the capacity of a cellular target to be modulated by a small-molecule drug. To date, druggability is mainly studied by focusing on direct binding interactions between a drug and its target. However, druggability is impacted by cellular networks connected to a drug target. Here, we use computational approaches to reveal basic principles of network motifs that modulate druggability. Through quantitative analysis, we find that inhibiting self-positive feedback loop is a more robust and effective treatment strategy than inhibiting other regulations, and adding direct regulations to a drug-target generally reduces its druggability. The findings are explained through analytical solution of the motifs. Furthermore, we find that a consensus topology of highly druggable motifs consists of a negative feedback loop without any positive feedback loops, and consensus motifs with low druggability have multiple positive direct regulations and positive feedback loops. Based on the discovered principles, we predict potential genetic targets in Escherichia coli that have either high or low druggability based on their network context. Our work establishes the foundation toward identifying and predicting druggable targets based on their network topology. PMID:27824147

  3. 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.

  4. 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.

  5. 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.

  6. 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…

  7. Supporting performance and configuration management of GTE cellular networks

    SciTech Connect

    Tan, Ming; Lafond, C.; Jakobson, G.; Young, G.

    1996-12-31

    GTE Laboratories, in cooperation with GTE Mobilnet, has developed and deployed PERFFEX (PERFormance Expert), an intelligent system for performance and configuration management of cellular networks. PERFEX assists cellular network performance and radio engineers in the analysis of large volumes of cellular network performance and configuration data. It helps them locate and determine the probable causes of performance problems, and provides intelligent suggestions about how to correct them. The system combines an expert cellular network performance tuning capability with a map-based graphical user interface, data visualization programs, and a set of special cellular engineering tools. PERFEX is in daily use at more than 25 GTE Mobile Switching Centers. Since the first deployment of the system in late 1993, PERFEX has become a major GTE cellular network performance optimization tool.

  8. Heterogeneous force network in 3D cellularized collagen networks.

    PubMed

    Liang, Long; Jones, Christopher; Chen, Shaohua; Sun, Bo; Jiao, Yang

    2016-10-25

    Collagen networks play an important role in coordinating and regulating collective cellular dynamics via a number of signaling pathways. Here, we investigate the transmission of forces generated by contractile cells in 3D collagen-I networks. Specifically, the graph (bond-node) representations of collagen networks with collagen concentrations of 1, 2 and 4 mg ml(-1) are derived from confocal microscopy data and used to model the network microstructure. Cell contraction is modeled by applying correlated displacements at specific nodes of the network, representing the focal adhesion sites. A nonlinear elastic model is employed to characterize the mechanical behavior of individual fiber bundles including strain hardening during stretching and buckling under compression. A force-based relaxation method is employed to obtain equilibrium network configurations under cell contraction. We find that for all collagen concentrations, the majority of the forces are carried by a small number of heterogeneous force chains emitted from the contracting cells, which is qualitatively consistent with our experimental observations. The force chains consist of fiber segments that either possess a high degree of alignment before cell contraction or are aligned due to fiber reorientation induced by cell contraction. 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 can support long-range force transmission. The force chains emerge even at very small cell contractions, and the number of force chains increases with increasing cell contraction. At large cell contractions, the fibers close to the cell surface are in the nonlinear regime, and the nonlinear region is localized in a small neighborhood of the cell. In addition, the number of force chains increases with increasing collagen concentration, due to the larger number of focal adhesion sites

  9. Heterogeneous force network in 3D cellularized collagen networks

    NASA Astrophysics Data System (ADS)

    Liang, Long; Jones, Christopher; Chen, Shaohua; Sun, Bo; Jiao, Yang

    2016-12-01

    Collagen networks play an important role in coordinating and regulating collective cellular dynamics via a number of signaling pathways. Here, we investigate the transmission of forces generated by contractile cells in 3D collagen-I networks. Specifically, the graph (bond-node) representations of collagen networks with collagen concentrations of 1, 2 and 4 mg ml-1 are derived from confocal microscopy data and used to model the network microstructure. Cell contraction is modeled by applying correlated displacements at specific nodes of the network, representing the focal adhesion sites. A nonlinear elastic model is employed to characterize the mechanical behavior of individual fiber bundles including strain hardening during stretching and buckling under compression. A force-based relaxation method is employed to obtain equilibrium network configurations under cell contraction. We find that for all collagen concentrations, the majority of the forces are carried by a small number of heterogeneous force chains emitted from the contracting cells, which is qualitatively consistent with our experimental observations. The force chains consist of fiber segments that either possess a high degree of alignment before cell contraction or are aligned due to fiber reorientation induced by cell contraction. 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 can support long-range force transmission. The force chains emerge even at very small cell contractions, and the number of force chains increases with increasing cell contraction. At large cell contractions, the fibers close to the cell surface are in the nonlinear regime, and the nonlinear region is localized in a small neighborhood of the cell. In addition, the number of force chains increases with increasing collagen concentration, due to the larger number of focal adhesion sites

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. An entropic characterization of protein interaction networks and cellular robustness.

    PubMed

    Manke, Thomas; Demetrius, Lloyd; Vingron, Martin

    2006-12-22

    The structure of molecular networks is believed to determine important aspects of their cellular function, such as the organismal resilience against random perturbations. Ultimately, however, cellular behaviour is determined by the dynamical processes, which are constrained by network topology. The present work is based on a fundamental relation from dynamical systems theory, which states that the macroscopic resilience of a steady state is correlated with the uncertainty in the underlying microscopic processes, a property that can be measured by entropy. Here, we use recent network data from large-scale protein interaction screens to characterize the diversity of possible pathways in terms of network entropy. This measure has its origin in statistical mechanics and amounts to a global characterization of both structural and dynamical resilience in terms of microscopic elements. We demonstrate how this approach can be used to rank network elements according to their contribution to network entropy and also investigate how this suggested ranking reflects on the functional data provided by gene knockouts and RNAi experiments in yeast and Caenorhabditis elegans. Our analysis shows that knockouts of proteins with large contribution to network entropy are preferentially lethal. This observation is robust with respect to several possible errors and biases in the experimental data. It underscores the significance of entropy as a fundamental invariant of the dynamical system, and as a measure of structural and dynamical properties of networks. Our analytical approach goes beyond the phenomenological studies of cellular robustness based on local network observables, such as connectivity. One of its principal achievements is to provide a rationale to study proxies of cellular resilience and rank proteins according to their importance within the global network context.

  17. Widrow-cellular neural network and optoelectronic implementation

    NASA Astrophysics Data System (ADS)

    Bal, Abdullah

    A new type of optoelectronic cellular neural network has been developed by providing the capability of coefficients adjusment of cellular neural network (CNN) using Widrow based perceptron learning algorithm. The new supervised cellular neural network is called Widrow-CNN. Despite the unsupervised CNN, the proposed learning algorithm allows to use the Widrow-CNN for various image processing applications easily. Also, the capability of CNN for image processing and feature extraction has been improved using basic joint transform correlation architecture. This hardware application presents high speed processing capability compared to digital applications. The optoelectronic Widrow-CNN has been tested for classic CNN feature extraction problems. It yields the best results even in case of hard feature extraction problems such as diagonal line detection and vertical line determination.

  18. Cellular and network mechanisms of electrographic seizures

    PubMed Central

    Bazhenov, Maxim; Timofeev, Igor; Fröhlich, Flavio; Sejnowski, Terrence J.

    2008-01-01

    Epileptic seizures constitute a complex multiscale phenomenon that is characterized by synchronized hyperexcitation of neurons in neuronal networks. Recent progress in understanding pathological seizure dynamics provides crucial insights into underlying mechanisms and possible new avenues for the development of novel treatment modalities. Here we review some recent work that combines in vivo experiments and computational modeling to unravel the pathophysiology of seizures of cortical origin. We particularly focus on how activity-dependent changes in extracellular potassium concentration affects the intrinsic dynamics of neurons involved in cortical seizures characterized by spike/wave complexes and fast runs. PMID:19190736

  19. TRANSWESD: inferring cellular networks with transitive reduction

    PubMed Central

    Klamt, Steffen; Flassig, Robert J.; Sundmacher, Kai

    2010-01-01

    Motivation: Distinguishing direct from indirect influences is a central issue in reverse engineering of biological networks because it facilitates detection and removal of false positive edges. Transitive reduction is one approach for eliminating edges reflecting indirect effects but its use in reconstructing cyclic interaction graphs with true redundant structures is problematic. Results: We present TRANSWESD, an elaborated variant of TRANSitive reduction for WEighted Signed Digraphs that overcomes conceptual problems of existing versions. Major changes and improvements concern: (i) new statistical approaches for generating high-quality perturbation graphs from systematic perturbation experiments; (ii) the use of edge weights (association strengths) for recognizing true redundant structures; (iii) causal interpretation of cycles; (iv) relaxed definition of transitive reduction; and (v) approximation algorithms for large networks. Using standardized benchmark tests, we demonstrate that our method outperforms existing variants of transitive reduction and is, despite its conceptual simplicity, highly competitive with other reverse engineering methods. Contact: klamt@mpi-magdeburg.mpg.de Supplementary information: Supplementary data are available at Bioinformatics online. PMID:20605927

  20. Modeling Integrated Cellular Machinery Using Hybrid Petri-Boolean Networks

    PubMed Central

    Berestovsky, Natalie; Zhou, Wanding; Nagrath, Deepak; Nakhleh, Luay

    2013-01-01

    The behavior and phenotypic changes of cells are governed by a cellular circuitry that represents a set of biochemical reactions. Based on biological functions, this circuitry is divided into three types of networks, each encoding for a major biological process: signal transduction, transcription regulation, and metabolism. This division has generally enabled taming computational complexity dealing with the entire system, allowed for using modeling techniques that are specific to each of the components, and achieved separation of the different time scales at which reactions in each of the three networks occur. Nonetheless, with this division comes loss of information and power needed to elucidate certain cellular phenomena. Within the cell, these three types of networks work in tandem, and each produces signals and/or substances that are used by the others to process information and operate normally. Therefore, computational techniques for modeling integrated cellular machinery are needed. In this work, we propose an integrated hybrid model (IHM) that combines Petri nets and Boolean networks to model integrated cellular networks. Coupled with a stochastic simulation mechanism, the model simulates the dynamics of the integrated network, and can be perturbed to generate testable hypotheses. Our model is qualitative and is mostly built upon knowledge from the literature and requires fine-tuning of very few parameters. We validated our model on two systems: the transcriptional regulation of glucose metabolism in human cells, and cellular osmoregulation in S. cerevisiae. The model produced results that are in very good agreement with experimental data, and produces valid hypotheses. The abstract nature of our model and the ease of its construction makes it a very good candidate for modeling integrated networks from qualitative data. The results it produces can guide the practitioner to zoom into components and interconnections and investigate them using such more

  1. Modeling integrated cellular machinery using hybrid Petri-Boolean networks.

    PubMed

    Berestovsky, Natalie; Zhou, Wanding; Nagrath, Deepak; Nakhleh, Luay

    2013-01-01

    The behavior and phenotypic changes of cells are governed by a cellular circuitry that represents a set of biochemical reactions. Based on biological functions, this circuitry is divided into three types of networks, each encoding for a major biological process: signal transduction, transcription regulation, and metabolism. This division has generally enabled taming computational complexity dealing with the entire system, allowed for using modeling techniques that are specific to each of the components, and achieved separation of the different time scales at which reactions in each of the three networks occur. Nonetheless, with this division comes loss of information and power needed to elucidate certain cellular phenomena. Within the cell, these three types of networks work in tandem, and each produces signals and/or substances that are used by the others to process information and operate normally. Therefore, computational techniques for modeling integrated cellular machinery are needed. In this work, we propose an integrated hybrid model (IHM) that combines Petri nets and Boolean networks to model integrated cellular networks. Coupled with a stochastic simulation mechanism, the model simulates the dynamics of the integrated network, and can be perturbed to generate testable hypotheses. Our model is qualitative and is mostly built upon knowledge from the literature and requires fine-tuning of very few parameters. We validated our model on two systems: the transcriptional regulation of glucose metabolism in human cells, and cellular osmoregulation in S. cerevisiae. The model produced results that are in very good agreement with experimental data, and produces valid hypotheses. The abstract nature of our model and the ease of its construction makes it a very good candidate for modeling integrated networks from qualitative data. The results it produces can guide the practitioner to zoom into components and interconnections and investigate them using such more

  2. Designed Proteins To Modulate Cellular Networks

    PubMed Central

    Cortajarena, Aitziber L.; Liu, Tina Y.; Hochstrasser, Mark; Regan, Lynne

    2012-01-01

    A major challenge of protein design is to create useful new proteins that interact specifically with biological targets in living cells. Such binding modules have many potential applications, including the targeted perturbation of protein networks. As a general approach to create such modules, we designed a library with approximately 109 different binding specificities based on a small 3-tetratricopeptide repeat (TPR) motif framework. We employed a novel strategy, based on split GFP reassembly, to screen the library for modules with the desired binding specificity. Using this approach, we identified modules that bind tightly and specifically to Dss1, a small human protein that interacts with the tumor suppressor protein BRCA2. We showed that these modules also bind the yeast homologue of Dss1, Sem1. Furthermore, we demonstrated that these modules inhibit Sem1 activity in yeast. This strategy will be generally applicable to make novel genetically encoded tools for systems/synthetic biology applications. PMID:20020775

  3. The community structure of human cellular signaling network.

    PubMed

    Diao, Yuanbo; Li, Menglong; Feng, Zinan; Yin, Jiajian; Pan, Yi

    2007-08-21

    Living cell is highly responsive to specific chemicals in its environment, such as hormones and molecules in food or aromas. The reason is ascribed to the existence of widespread and diverse signal transduction pathways, between which crosstalks usually exist, thus constitute a complex signaling network. Evidently, knowledge of topology characteristic of this network could contribute a lot to the understanding of diverse cellular behaviors and life phenomena thus come into being. In this presentation, signal transduction data is extracted from KEGG to construct a cellular signaling network of Homo sapiens, which has 931 nodes and 6798 links in total. Computing the degree distribution, we find it is not a random network, but a scale-free network following a power-law of P(K) approximately K(-gamma), with gamma approximately equal to 2.2. Among three graph partition algorithms, the Guimera's simulated annealing method is chosen to study the details of topology structure and other properties of this cellular signaling network, as it shows the best performance. To reveal the underlying biological implications, further investigation is conducted on ad hoc community and sketch map of individual community is drawn accordingly. The involved experiment data can be found in the supplementary material.

  4. From molecules to cellular networks: past and future outlook.

    PubMed

    Fang, Xiaona; Wang, Jin

    2017-02-16

    Cellular networks have been the focus of studies in modern systems biology. They are crucial in understanding cell functions and related diseases. We review some past progress in both the theory and experiments, and we also provide several future perspectives for the field.

  5. From molecules to cellular networks: past and future outlook

    NASA Astrophysics Data System (ADS)

    Fang, Xiaona; Wang, Jin

    2017-02-01

    Cellular networks have been the focus of studies in modern systems biology. They are crucial in understanding cell functions and related diseases. We review some past progress in both the theory and experiments, and we also provide several future perspectives for the field.

  6. 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.

  7. 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.

  8. A competitive layer model for cellular neural networks.

    PubMed

    Zhou, Wei; Zurada, Jacek M

    2012-09-01

    This paper discusses a Competitive Layer Model (CLM) for a class of recurrent Cellular Neural Networks (CNNs) from continuous-time type to discrete-time type. The objective of the CLM is to partition a set of input features into salient groups. The complete convergence of such networks in continuous-time type has been discussed first. We give a necessary condition, and a necessary and sufficient condition, which allow the CLM performance existence in our networks. We also discuss the properties of such networks of discrete-time type, and propose a novel CLM iteration method. Such method shows similar performance and storage allocation but faster convergence compared with the previous CLM iteration method (Wersing, Steil, & Ritter, 2001a). Especially for a large scale network with many features and layers, it can significantly reduce the computing time. Examples and simulation results are used to illustrate the developed theory, the comparison between two CLM iteration methods, and the application in image segmentation.

  9. 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

  10. Cellular-based modeling of oscillatory dynamics in brain networks.

    PubMed

    Skinner, Frances K

    2012-08-01

    Oscillatory, population activities have long been known to occur in our brains during different behavioral states. We know that many different cell types exist and that they contribute in distinct ways to the generation of these activities. I review recent papers that involve cellular-based models of brain networks, most of which include theta, gamma and sharp wave-ripple activities. To help organize the modeling work, I present it from a perspective of three different types of cellular-based modeling: 'Generic', 'Biophysical' and 'Linking'. Cellular-based modeling is taken to encompass the four features of experiment, model development, theory/analyses, and model usage/computation. The three modeling types are shown to include these features and interactions in different ways.

  11. 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.

  12. Protein Kinase CK2: Intricate Relationships within Regulatory Cellular Networks.

    PubMed

    Nuñez de Villavicencio-Diaz, Teresa; Rabalski, Adam J; Litchfield, David W

    2017-03-05

    Protein kinase CK2 is a small family of protein kinases that has been implicated in an expanding array of biological processes. While it is widely accepted that CK2 is a regulatory participant in a multitude of fundamental cellular processes, CK2 is often considered to be a constitutively active enzyme which raises questions about how it can be a regulatory participant in intricately controlled cellular processes. To resolve this apparent paradox, we have performed a systematic analysis of the published literature using text mining as well as mining of proteomic databases together with computational assembly of networks that involve CK2. These analyses reinforce the notion that CK2 is involved in a broad variety of biological processes and also reveal an extensive interplay between CK2 phosphorylation and other post-translational modifications. The interplay between CK2 and other post-translational modifications suggests that CK2 does have intricate roles in orchestrating cellular events. In this respect, phosphorylation of specific substrates by CK2 could be regulated by other post-translational modifications and CK2 could also have roles in modulating other post-translational modifications. Collectively, these observations suggest that the actions of CK2 are precisely coordinated with other constituents of regulatory cellular networks.

  13. Protein Kinase CK2: Intricate Relationships within Regulatory Cellular Networks

    PubMed Central

    Nuñez de Villavicencio-Diaz, Teresa; Rabalski, Adam J.; Litchfield, David W.

    2017-01-01

    Protein kinase CK2 is a small family of protein kinases that has been implicated in an expanding array of biological processes. While it is widely accepted that CK2 is a regulatory participant in a multitude of fundamental cellular processes, CK2 is often considered to be a constitutively active enzyme which raises questions about how it can be a regulatory participant in intricately controlled cellular processes. To resolve this apparent paradox, we have performed a systematic analysis of the published literature using text mining as well as mining of proteomic databases together with computational assembly of networks that involve CK2. These analyses reinforce the notion that CK2 is involved in a broad variety of biological processes and also reveal an extensive interplay between CK2 phosphorylation and other post-translational modifications. The interplay between CK2 and other post-translational modifications suggests that CK2 does have intricate roles in orchestrating cellular events. In this respect, phosphorylation of specific substrates by CK2 could be regulated by other post-translational modifications and CK2 could also have roles in modulating other post-translational modifications. Collectively, these observations suggest that the actions of CK2 are precisely coordinated with other constituents of regulatory cellular networks. PMID:28273877

  14. Digital implementation of shunting-inhibitory cellular neural network

    NASA Astrophysics Data System (ADS)

    Hammadou, Tarik; Bouzerdoum, Abdesselam; Bermak, Amine

    2000-05-01

    Shunting inhibition is a model of early visual processing which can provide contrast and edge enhancement, and dynamic range compression. An architecture of digital Shunting Inhibitory Cellular Neural Network for real time image processing is presented. The proposed architecture is intended to be used in a complete vision system for edge detection and image enhancement. The present hardware architecture, is modeled and simulated in VHDL. Simulation results show the functional validity of the proposed architecture.

  15. 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.

  16. 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.

  17. 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.

  18. Reverse Engineering Cellular Networks with Information Theoretic Methods

    PubMed Central

    Villaverde, Alejandro F.; Ross, John; Banga, Julio R.

    2013-01-01

    Building mathematical models of cellular networks lies at the core of systems biology. It involves, among other tasks, the reconstruction of the structure of interactions between molecular components, which is known as network inference or reverse engineering. Information theory can help in the goal of extracting as much information as possible from the available data. A large number of methods founded on these concepts have been proposed in the literature, not only in biology journals, but in a wide range of areas. Their critical comparison is difficult due to the different focuses and the adoption of different terminologies. Here we attempt to review some of the existing information theoretic methodologies for network inference, and clarify their differences. While some of these methods have achieved notable success, many challenges remain, among which we can mention dealing with incomplete measurements, noisy data, counterintuitive behaviour emerging from nonlinear relations or feedback loops, and computational burden of dealing with large data sets. PMID:24709703

  19. 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.

  20. 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.

  1. 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

  2. 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

  3. 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.

  4. 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.

  5. 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.

  6. Perturbation biology: inferring signaling networks in cellular systems.

    PubMed

    Molinelli, Evan J; Korkut, Anil; Wang, Weiqing; Miller, Martin L; Gauthier, Nicholas P; Jing, Xiaohong; Kaushik, Poorvi; He, Qin; Mills, Gordon; Solit, David B; Pratilas, Christine A; Weigt, Martin; Braunstein, Alfredo; Pagnani, Andrea; Zecchina, Riccardo; Sander, Chris

    2013-01-01

    We present a powerful experimental-computational technology for inferring network models that predict the response of cells to perturbations, and that may be useful in the design of combinatorial therapy against cancer. The experiments are systematic series of perturbations of cancer cell lines by targeted drugs, singly or in combination. The response to perturbation is quantified in terms of relative changes in the measured levels of proteins, phospho-proteins and cellular phenotypes such as viability. Computational network models are derived de novo, i.e., without prior knowledge of signaling pathways, and are based on simple non-linear differential equations. The prohibitively large solution space of all possible network models is explored efficiently using a probabilistic algorithm, Belief Propagation (BP), which is three orders of magnitude faster than standard Monte Carlo methods. Explicit executable models are derived for a set of perturbation experiments in SKMEL-133 melanoma cell lines, which are resistant to the therapeutically important inhibitor of RAF kinase. The resulting network models reproduce and extend known pathway biology. They empower potential discoveries of new molecular interactions and predict efficacious novel drug perturbations, such as the inhibition of PLK1, which is verified experimentally. This technology is suitable for application to larger systems in diverse areas of molecular biology.

  7. 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

  8. Multi-casting approach for vascular networks in cellularized hydrogels.

    PubMed

    Justin, Alexander W; Brooks, Roger A; Markaki, Athina E

    2016-12-01

    Vascularization is essential for living tissue and remains a major challenge in the field of tissue engineering. A lack of a perfusable channel network within a large and densely populated tissue engineered construct leads to necrotic core formation, preventing fabrication of functional tissues and organs. We report a new method for producing a hierarchical, three-dimensional (3D) and perfusable vasculature in a large, cellularized fibrin hydrogel. Bifurcating channels, varying in size from 1 mm to 200-250 µm, are formed using a novel process in which we convert a 3D printed thermoplastic material into a gelatin network template, by way of an intermediate alginate hydrogel. This enables a CAD-based model design, which is highly customizable, reproducible, and which can yield highly complex architectures, to be made into a removable material, which can be used in cellular environments. Our approach yields constructs with a uniform and high density of cells in the bulk, made from bioactive collagen and fibrin hydrogels. Using standard cell staining and immuno-histochemistry techniques, we showed good cell seeding and the presence of tight junctions between channel endothelial cells, and high cell viability and cell spreading in the bulk hydrogel.

  9. Multi-casting approach for vascular networks in cellularized hydrogels

    PubMed Central

    Justin, Alexander W.; Brooks, Roger A.

    2016-01-01

    Vascularization is essential for living tissue and remains a major challenge in the field of tissue engineering. A lack of a perfusable channel network within a large and densely populated tissue engineered construct leads to necrotic core formation, preventing fabrication of functional tissues and organs. We report a new method for producing a hierarchical, three-dimensional (3D) and perfusable vasculature in a large, cellularized fibrin hydrogel. Bifurcating channels, varying in size from 1 mm to 200–250 µm, are formed using a novel process in which we convert a 3D printed thermoplastic material into a gelatin network template, by way of an intermediate alginate hydrogel. This enables a CAD-based model design, which is highly customizable, reproducible, and which can yield highly complex architectures, to be made into a removable material, which can be used in cellular environments. Our approach yields constructs with a uniform and high density of cells in the bulk, made from bioactive collagen and fibrin hydrogels. Using standard cell staining and immuno-histochemistry techniques, we showed good cell seeding and the presence of tight junctions between channel endothelial cells, and high cell viability and cell spreading in the bulk hydrogel. PMID:27928031

  10. Countrywide rainfall maps from a commercial cellular telecommunication network

    NASA Astrophysics Data System (ADS)

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

    2012-12-01

    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. Many countries do not have continuously operating weather radars, and have no or few rain gauges. A new development is rainfall estimation from microwave links of commercial cellular telecommunication networks. Such networks cover large parts of the land surface of the earth and have a high density, especially in urban areas. The estimation of rainfall using commercial microwave links could therefore become a valuable source of information. The data produced by microwave links is essentially a by-product of the communication between mobile telephones. 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. A dataset from a commercial microwave link network over the Netherlands is analyzed, containing data from an unprecedented number of links (1500) 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 calibration and validation are done using gauge-adjusted radar data

  11. Myosin lever arm directs collective motion on cellular actin network.

    PubMed

    Hariadi, Rizal F; Cale, Mario; Sivaramakrishnan, Sivaraj

    2014-03-18

    The molecular motor myosin teams up to drive muscle contraction, membrane traffic, and cell division in biological cells. Myosin function in cells emerges from the interaction of multiple motors tethered to a scaffold, with surrounding actin filaments organized into 3D networks. Despite the importance of myosin function, the influence of intermotor interactions on collective motion remains poorly understood. In this study, we used precisely engineered myosin assemblies to examine emergence in collective myosin movement. We report that tethering multiple myosin VI motors, but not myosin V motors, modifies their movement trajectories on keratocyte actin networks. Single myosin V and VI dimers display similar skewed trajectories, albeit in opposite directions, when traversing the keratocyte actin network. In contrast, tethering myosin VI motors, but not myosin V motors, progressively straightens the trajectories with increasing myosin number. Trajectory shape of multimotor scaffolds positively correlates with the stiffness of the myosin lever arm. Swapping the flexible myosin VI lever arm for the relatively rigid myosin V lever increases trajectory skewness, and vice versa. A simplified model of coupled motor movement demonstrates that the differences in flexural rigidity of the two myosin lever arms is sufficient to account for the differences in observed behavior of groups of myosin V and VI motors. In accordance with this model trajectory, shapes for scaffolds containing both myosin V and VI are dominated by the myosin with a stiffer lever arm. Our findings suggest that structural features unique to each myosin type may confer selective advantages in cellular functions.

  12. A rigorous framework for multiscale simulation of stochastic cellular networks

    PubMed Central

    Chevalier, Michael W.; El-Samad, Hana

    2009-01-01

    Noise and stochasticity are fundamental to biology and derive from the very nature of biochemical reactions where thermal motion of molecules translates into randomness in the sequence and timing of reactions. This randomness leads to cell-cell variability even in clonal populations. Stochastic biochemical networks are modeled as continuous time discrete state Markov processes whose probability density functions evolve according to a chemical master equation (CME). The CME is not solvable but for the simplest cases, and one has to resort to kinetic Monte Carlo techniques to simulate the stochastic trajectories of the biochemical network under study. A commonly used such algorithm is the stochastic simulation algorithm (SSA). Because it tracks every biochemical reaction that occurs in a given system, the SSA presents computational difficulties especially when there is a vast disparity in the timescales of the reactions or in the number of molecules involved in these reactions. This is common in cellular networks, and many approximation algorithms have evolved to alleviate the computational burdens of the SSA. Here, we present a rigorously derived modified CME framework based on the partition of a biochemically reacting system into restricted and unrestricted reactions. Although this modified CME decomposition is as analytically difficult as the original CME, it can be naturally used to generate a hierarchy of approximations at different levels of accuracy. Most importantly, some previously derived algorithms are demonstrated to be limiting cases of our formulation. We apply our methods to biologically relevant test systems to demonstrate their accuracy and efficiency. PMID:19673546

  13. Cellular Neural Network for Real Time Image Processing

    SciTech Connect

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

    2008-03-12

    Since their introduction in 1988, Cellular Nonlinear Networks (CNNs) have found a key role as image processing instruments. Thanks to their structure they are able of processing individual pixels in a parallel way providing fast image processing capabilities that has been applied to a wide range of field among which nuclear fusion. In the last years, indeed, visible and infrared video cameras have become more and more important in tokamak fusion experiments for the twofold aim of understanding the physics and monitoring the safety of the operation. Examining the output of these cameras in real-time can provide significant information for plasma control and safety of the machines. The potentiality of CNNs can be exploited to this aim. To demonstrate the feasibility of the approach, CNN image processing has been applied to several tasks both at the Frascati Tokamak Upgrade (FTU) and the Joint European Torus (JET)

  14. Cellular Neural Network for Real Time Image Processing

    NASA Astrophysics Data System (ADS)

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

    2008-03-01

    Since their introduction in 1988, Cellular Nonlinear Networks (CNNs) have found a key role as image processing instruments. Thanks to their structure they are able of processing individual pixels in a parallel way providing fast image processing capabilities that has been applied to a wide range of field among which nuclear fusion. In the last years, indeed, visible and infrared video cameras have become more and more important in tokamak fusion experiments for the twofold aim of understanding the physics and monitoring the safety of the operation. Examining the output of these cameras in real-time can provide significant information for plasma control and safety of the machines. The potentiality of CNNs can be exploited to this aim. To demonstrate the feasibility of the approach, CNN image processing has been applied to several tasks both at the Frascati Tokamak Upgrade (FTU) and the Joint European Torus (JET).

  15. Separation of Bouguer anomaly map using cellular neural network

    NASA Astrophysics Data System (ADS)

    Albora, A. Muhittin; Ucan, Osman N.; Ozmen, Atilla; Ozkan, Tulay

    2001-02-01

    In this paper, a modern image-processing technique, the Cellular Neural Network (CNN) has been firstly applied to Bouguer anomaly map of synthetic examples and then to data from the Sivas-Divrigi Akdag region. CNN is an analog parallel computing paradigm defined in space and characterized by the locality of connections between processing neurons. The behaviour of the CNN is defined by two template matrices and a template vector. We have optimised the weight coefficients of these templates using the Recurrent Perceptron Learning Algorithm (RPLA). After testing CNN performance on synthetic examples, the CNN approach has been applied to the Bouguer anomaly of Sivas-Divrigi Akdag region and the results match drilling logs done by Mineral Research and Exploration (MTA).

  16. Coexistence of 3G repeaters with LTE base stations.

    PubMed

    Yeo, Woon-Young; Lee, Sang-Min; Hwang, Gyung-Ho; Kim, Jae-Hoon

    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.

  17. 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.

  18. 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.

  19. Using cellular network diagrams to interpret large-scale datasets: past progress and future challenges

    NASA Astrophysics Data System (ADS)

    Karp, Peter D.; Latendresse, Mario; Paley, Suzanne

    2011-03-01

    Cellular networks are graphs of molecular interactions within the cell. Thanks to the confluence of genome sequencing and bioinformatics, scientists are now able to reconstruct cellular network models for more than 1,000 organisms. A variety of bioinformatics tools have been developed to support the visualization and navigation of cellular network data. Another important application is the use of cellular network diagrams to visualize and interpret large-scale datasets, such as gene-expression data. We present the Cellular Overview, a network visualization tool developed at SRI International (SRI) to support visualization, navigation, and interpretation of large-scale datasets on metabolic networks. Different variations of the diagram have been generated algorithmically for more than 1,000 organisms. We discuss the graphical design of the diagram and its interactive capabilities.

  20. 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.

  1. 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.

  2. Hierarchical Interference Mitigation for Massive MIMO Cellular Networks

    NASA Astrophysics Data System (ADS)

    Liu, An; Lau, Vincent

    2014-09-01

    We propose a hierarchical interference mitigation scheme for massive MIMO cellular networks. The MIMO precoder at each base station (BS) is partitioned into an inner precoder and an outer precoder. The inner precoder controls the intra-cell interference and is adaptive to local channel state information (CSI) at each BS (CSIT). The outer precoder controls the inter-cell interference and is adaptive to channel statistics. Such hierarchical precoding structure reduces the number of pilot symbols required for CSI estimation in massive MIMO downlink and is robust to the backhaul latency. We study joint optimization of the outer precoders, the user selection, and the power allocation to maximize a general concave utility which has no closed-form expression. We first apply random matrix theory to obtain an approximated problem with closed-form objective. We show that the solution of the approximated problem is asymptotically optimal with respect to the original problem as the number of antennas per BS grows large. Then using the hidden convexity of the problem, we propose an iterative algorithm to find the optimal solution for the approximated problem. We also obtain a low complexity algorithm with provable convergence. Simulations show that the proposed design has significant gain over various state-of-the-art baselines.

  3. 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.

  4. Network motifs in integrated cellular networks of transcription-regulation and protein-protein interaction

    NASA Astrophysics Data System (ADS)

    Yeger-Lotem, Esti; Sattath, Shmuel; Kashtan, Nadav; Itzkovitz, Shalev; Milo, Ron; Pinter, Ron Y.; Alon, Uri; Margalit, Hanah

    2004-04-01

    Genes and proteins generate molecular circuitry that enables the cell to process information and respond to stimuli. A major challenge is to identify characteristic patterns in this network of interactions that may shed light on basic cellular mechanisms. Previous studies have analyzed aspects of this network, concentrating on either transcription-regulation or protein-protein interactions. Here we search for composite network motifs: characteristic network patterns consisting of both transcription-regulation and protein-protein interactions that recur significantly more often than in random networks. To this end we developed algorithms for detecting motifs in networks with two or more types of interactions and applied them to an integrated data set of protein-protein interactions and transcription regulation in Saccharomyces cerevisiae. We found a two-protein mixed-feedback loop motif, five types of three-protein motifs exhibiting coregulation and complex formation, and many motifs involving four proteins. Virtually all four-protein motifs consisted of combinations of smaller motifs. This study presents a basic framework for detecting the building blocks of networks with multiple types of interactions.

  5. 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.

  6. 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

  7. 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

    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, and

  8. 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.

  9. 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…

  10. 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.

  11. 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

  12. A metabolic-transcriptional network links sleep and cellular energetics in the brain.

    PubMed

    Wisor, Jonathan P

    2012-01-01

    This review proposes a mechanistic link between cellular metabolic status, transcriptional regulatory changes and sleep. Sleep loss is associated with changes in cellular metabolic status in the brain. Metabolic sensors responsive to cellular metabolic status regulate the circadian clock transcriptional network. Modifications of the transcriptional activity of circadian clock genes affect sleep/wake state changes. Changes in sleep state reverse sleep loss-induced changes in cellular metabolic status. It is thus proposed that the regulation of circadian clock genes by cellular metabolic sensors is a critical intermediate step in the link between cellular metabolic status and sleep. Studies of this regulatory relationship may offer insights into the function of sleep at the cellular level.

  13. 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...

  14. 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

  15. Caenorhabditis elegans metabolic gene regulatory networks govern the cellular economy.

    PubMed

    Watson, Emma; Walhout, Albertha J M

    2014-10-01

    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 (NHRs) in responding to dietary conditions, regulation of metabolic genes and metabolic regulators by miRNAs, and feedback between metabolic genes and their regulators.

  16. Almost automorphic solutions for shunting inhibitory cellular neural networks with time-varying delays.

    PubMed

    Xu, Changjin; Liao, Maoxin

    2015-01-01

    This paper is concerned with the shunting inhibitory cellular neural networks with time-varying delays. Under some suitable conditions, we establish some criteria on the existence and global exponential stability of the almost automorphic solutions of the networks. Numerical simulations are given to support the theoretical findings.

  17. Networking with noise at the molecular, cellular, and population level

    NASA Astrophysics Data System (ADS)

    Vilar, Jose

    2002-03-01

    The intrinsic stochastic nature of biochemical reactions affects enzymatic and transcriptional networks at different levels. Yet, cells are able to function effectively and consistently amidst such random fluctuations. I will discuss some molecular mechanisms that are able to reduce the intrinsic noise of chemical reactions, how suitable designs can make networks resistant to noise, and what strategies can be used by populations to achieve precise functions.

  18. 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.

  19. 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.

  20. Channel modeling for fifth generation cellular networks and wireless sensor networks

    NASA Astrophysics Data System (ADS)

    Torabi, Amir

    In view of exponential growth in data traffic demand, the wireless communications industry has aimed to increase the capacity of existing networks by 1000 times over the next 20 years. A combination of extreme cell densification, more bandwidth, and higher spectral efficiency is needed to support the data traffic requirements for fifth generation (5G) cellular communications. In this research, the potential improvements achieved by using three major 5G enabling technologies (i.e., small cells, millimeter-wave spectrum, and massive MIMO) in rural and urban environments are investigated. This work develops SPM and KA-based ray models to investigate the impact of geometrical parameters on terrain-based multiuser MIMO channel characteristic. Moreover, a new directional 3D channel model is developed for urban millimeter-wave (mmW) small cells. Path-loss, spatial correlation, coverage distance, and coherence length are studied in urban areas. Exploiting physical optics (PO) and geometric optics (GO) solutions, closed form expressions are derived for spatial correlation. Achievable spatial diversity is evaluated using horizontal and vertical linear arrays as well as planar 2D arrays. In another study, a versatile near-ground field prediction model is proposed to facilitate accurate wireless sensor network (WSN) simulations. Monte Carlo simulations are used to investigate the effects of antenna height, frequency of operation, polarization, and terrain dielectric and roughness properties on WSNs performance.

  1. 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…

  2. 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…

  3. 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.

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

    PubMed

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

    2013-10-24

    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.

  5. 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

  6. 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.

  7. Molecular Signaling Network Motifs Provide a Mechanistic Basis for Cellular Threshold Responses

    PubMed Central

    Bhattacharya, Sudin; Conolly, Rory B.; Clewell, Harvey J.; Kaminski, Norbert E.; Andersen, Melvin E.

    2014-01-01

    Background: Increasingly, there is a move toward using in vitro toxicity testing to assess human health risk due to chemical exposure. As with in vivo toxicity testing, an important question for in vitro results is whether there are thresholds for adverse cellular responses. Empirical evaluations may show consistency with thresholds, but the main evidence has to come from mechanistic considerations. Objectives: Cellular response behaviors depend on the molecular pathway and circuitry in the cell and the manner in which chemicals perturb these circuits. Understanding circuit structures that are inherently capable of resisting small perturbations and producing threshold responses is an important step towards mechanistically interpreting in vitro testing data. Methods: Here we have examined dose–response characteristics for several biochemical network motifs. These network motifs are basic building blocks of molecular circuits underpinning a variety of cellular functions, including adaptation, homeostasis, proliferation, differentiation, and apoptosis. For each motif, we present biological examples and models to illustrate how thresholds arise from specific network structures. Discussion and Conclusion: Integral feedback, feedforward, and transcritical bifurcation motifs can generate thresholds. Other motifs (e.g., proportional feedback and ultrasensitivity)produce responses where the slope in the low-dose region is small and stays close to the baseline. Feedforward control may lead to nonmonotonic or hormetic responses. We conclude that network motifs provide a basis for understanding thresholds for cellular responses. Computational pathway modeling of these motifs and their combinations occurring in molecular signaling networks will be a key element in new risk assessment approaches based on in vitro cellular assays. Citation: Zhang Q, Bhattacharya S, Conolly RB, Clewell HJ III, Kaminski NE, Andersen ME. 2014. Molecular signaling network motifs provide a

  8. A new cellular automaton model for urban two-way road networks.

    PubMed

    Shi, Junqing; Cheng, Lin; Long, Jiancheng; Liu, Yuanlin

    2014-01-01

    A new cellular automaton (CA) model is proposed to simulate traffic dynamics in urban two-way road network systems. The NaSch rule is adopted to represent vehicle movements on road sections. Two novel rules are proposed to move the vehicles in intersection areas, and an additional rule is developed to avoid the "gridlock" phenomenon. Simulation results show that the network fundamental diagram is very similar to that of road traffic flow. We found that the randomization probability and the maximum vehicle speed have significant impact on network traffic mobility for free-flow state. Their effect may be weak when the network is congested.

  9. A New Cellular Automaton Model for Urban Two-Way Road Networks

    PubMed Central

    Shi, Junqing; Cheng, Lin; Liu, Yuanlin

    2014-01-01

    A new cellular automaton (CA) model is proposed to simulate traffic dynamics in urban two-way road network systems. The NaSch rule is adopted to represent vehicle movements on road sections. Two novel rules are proposed to move the vehicles in intersection areas, and an additional rule is developed to avoid the “gridlock” phenomenon. Simulation results show that the network fundamental diagram is very similar to that of road traffic flow. We found that the randomization probability and the maximum vehicle speed have significant impact on network traffic mobility for free-flow state. Their effect may be weak when the network is congested. PMID:25435868

  10. Intrinsic Cellular Properties and Connectivity Density Determine Variable Clustering Patterns in Randomly Connected Inhibitory Neural Networks.

    PubMed

    Rich, Scott; Booth, Victoria; Zochowski, Michal

    2016-01-01

    The plethora of inhibitory interneurons in the hippocampus and cortex play a pivotal role in generating rhythmic activity by clustering and synchronizing cell firing. Results of our simulations demonstrate that both the intrinsic cellular properties of neurons and the degree of network connectivity affect the characteristics of clustered dynamics exhibited in randomly connected, heterogeneous inhibitory networks. We quantify intrinsic cellular properties by the neuron's current-frequency relation (IF curve) and Phase Response Curve (PRC), a measure of how perturbations given at various phases of a neurons firing cycle affect subsequent spike timing. We analyze network bursting properties of networks of neurons with Type I or Type II properties in both excitability and PRC profile; Type I PRCs strictly show phase advances and IF curves that exhibit frequencies arbitrarily close to zero at firing threshold while Type II PRCs display both phase advances and delays and IF curves that have a non-zero frequency at threshold. Type II neurons whose properties arise with or without an M-type adaptation current are considered. We analyze network dynamics under different levels of cellular heterogeneity and as intrinsic cellular firing frequency and the time scale of decay of synaptic inhibition are varied. Many of the dynamics exhibited by these networks diverge from the predictions of the interneuron network gamma (ING) mechanism, as well as from results in all-to-all connected networks. Our results show that randomly connected networks of Type I neurons synchronize into a single cluster of active neurons while networks of Type II neurons organize into two mutually exclusive clusters segregated by the cells' intrinsic firing frequencies. Networks of Type II neurons containing the adaptation current behave similarly to networks of either Type I or Type II neurons depending on network parameters; however, the adaptation current creates differences in the cluster dynamics

  11. Intrinsic Cellular Properties and Connectivity Density Determine Variable Clustering Patterns in Randomly Connected Inhibitory Neural Networks

    PubMed Central

    Rich, Scott; Booth, Victoria; Zochowski, Michal

    2016-01-01

    The plethora of inhibitory interneurons in the hippocampus and cortex play a pivotal role in generating rhythmic activity by clustering and synchronizing cell firing. Results of our simulations demonstrate that both the intrinsic cellular properties of neurons and the degree of network connectivity affect the characteristics of clustered dynamics exhibited in randomly connected, heterogeneous inhibitory networks. We quantify intrinsic cellular properties by the neuron's current-frequency relation (IF curve) and Phase Response Curve (PRC), a measure of how perturbations given at various phases of a neurons firing cycle affect subsequent spike timing. We analyze network bursting properties of networks of neurons with Type I or Type II properties in both excitability and PRC profile; Type I PRCs strictly show phase advances and IF curves that exhibit frequencies arbitrarily close to zero at firing threshold while Type II PRCs display both phase advances and delays and IF curves that have a non-zero frequency at threshold. Type II neurons whose properties arise with or without an M-type adaptation current are considered. We analyze network dynamics under different levels of cellular heterogeneity and as intrinsic cellular firing frequency and the time scale of decay of synaptic inhibition are varied. Many of the dynamics exhibited by these networks diverge from the predictions of the interneuron network gamma (ING) mechanism, as well as from results in all-to-all connected networks. Our results show that randomly connected networks of Type I neurons synchronize into a single cluster of active neurons while networks of Type II neurons organize into two mutually exclusive clusters segregated by the cells' intrinsic firing frequencies. Networks of Type II neurons containing the adaptation current behave similarly to networks of either Type I or Type II neurons depending on network parameters; however, the adaptation current creates differences in the cluster dynamics

  12. [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.

  13. Exploring Spatio-temporal Dynamics of Cellular Automata for Pattern Recognition in Networks.

    PubMed

    Miranda, Gisele Helena Barboni; Machicao, Jeaneth; Bruno, Odemir Martinez

    2016-11-22

    Network science is an interdisciplinary field which provides an integrative approach for the study of complex systems. In recent years, network modeling has been used for the study of emergent phenomena in many real-world applications. Pattern recognition in networks has been drawing attention to the importance of network characterization, which may lead to understanding the topological properties that are related to the network model. In this paper, the Life-Like Network Automata (LLNA) method is introduced, which was designed for pattern recognition in networks. LLNA uses the network topology as a tessellation of Cellular Automata (CA), whose dynamics produces a spatio-temporal pattern used to extract the feature vector for network characterization. The method was evaluated using synthetic and real-world networks. In the latter, three pattern recognition applications were used: (i) identifying organisms from distinct domains of life through their metabolic networks, (ii) identifying online social networks and (iii) classifying stomata distribution patterns varying according to different lighting conditions. LLNA was compared to structural measurements and surpasses them in real-world applications, achieving improvement in the classification rate as high as 23%, 4% and 7% respectively. Therefore, the proposed method is a good choice for pattern recognition applications using networks and demonstrates potential for general applicability.

  14. Exploring Spatio-temporal Dynamics of Cellular Automata for Pattern Recognition in Networks

    NASA Astrophysics Data System (ADS)

    Miranda, Gisele Helena Barboni; Machicao, Jeaneth; Bruno, Odemir Martinez

    2016-11-01

    Network science is an interdisciplinary field which provides an integrative approach for the study of complex systems. In recent years, network modeling has been used for the study of emergent phenomena in many real-world applications. Pattern recognition in networks has been drawing attention to the importance of network characterization, which may lead to understanding the topological properties that are related to the network model. In this paper, the Life-Like Network Automata (LLNA) method is introduced, which was designed for pattern recognition in networks. LLNA uses the network topology as a tessellation of Cellular Automata (CA), whose dynamics produces a spatio-temporal pattern used to extract the feature vector for network characterization. The method was evaluated using synthetic and real-world networks. In the latter, three pattern recognition applications were used: (i) identifying organisms from distinct domains of life through their metabolic networks, (ii) identifying online social networks and (iii) classifying stomata distribution patterns varying according to different lighting conditions. LLNA was compared to structural measurements and surpasses them in real-world applications, achieving improvement in the classification rate as high as 23%, 4% and 7% respectively. Therefore, the proposed method is a good choice for pattern recognition applications using networks and demonstrates potential for general applicability.

  15. Exploring Spatio-temporal Dynamics of Cellular Automata for Pattern Recognition in Networks

    PubMed Central

    Miranda, Gisele Helena Barboni; Machicao, Jeaneth; Bruno, Odemir Martinez

    2016-01-01

    Network science is an interdisciplinary field which provides an integrative approach for the study of complex systems. In recent years, network modeling has been used for the study of emergent phenomena in many real-world applications. Pattern recognition in networks has been drawing attention to the importance of network characterization, which may lead to understanding the topological properties that are related to the network model. In this paper, the Life-Like Network Automata (LLNA) method is introduced, which was designed for pattern recognition in networks. LLNA uses the network topology as a tessellation of Cellular Automata (CA), whose dynamics produces a spatio-temporal pattern used to extract the feature vector for network characterization. The method was evaluated using synthetic and real-world networks. In the latter, three pattern recognition applications were used: (i) identifying organisms from distinct domains of life through their metabolic networks, (ii) identifying online social networks and (iii) classifying stomata distribution patterns varying according to different lighting conditions. LLNA was compared to structural measurements and surpasses them in real-world applications, achieving improvement in the classification rate as high as 23%, 4% and 7% respectively. Therefore, the proposed method is a good choice for pattern recognition applications using networks and demonstrates potential for general applicability. PMID:27874024

  16. Modeling psychiatric disorders at the cellular and network levels.

    PubMed

    Brennand, K J; Simone, A; Tran, N; Gage, F H

    2012-12-01

    Although psychiatric disorders such as autism spectrum disorders, schizophrenia and bipolar disorder affect a number of brain regions and produce a complex array of clinical symptoms, basic phenotypes likely exist at the level of single neurons and simple networks. Being highly heritable, it is hypothesized that these disorders are amenable to cell-based studies in vitro. Using induced pluripotent stem cell-derived neurons and/or induced neurons from fibroblasts, limitless numbers of live human neurons can now be generated from patients with a genetic background permissive to the disease state. We predict that cell-based studies will ultimately contribute to our understanding of the initiation, progression and treatment of these psychiatric disorders.

  17. Characterization of one-dimensional cellular automata rules through topological network features

    NASA Astrophysics Data System (ADS)

    D'Alotto, Lou; Pizzuti, Clara

    2016-10-01

    The paper investigates the relationship between the classification schemes, defined by Wolfram and Gilman, of one-dimensional cellular automata through concepts coming from network theory. An automaton is represented with a network, generated from the elementary rule defining its behavior. Characteristic features of this graph are computed and machine learning classification models are built. Such models allow to classify automaton rules and to compare Wolfram's and Gilman's classes by comparing the classes predicted by these models.

  18. A mathematical model to study the dynamics of epithelial cellular networks.

    PubMed

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

    2012-01-01

    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).

  19. Multi-Cell Cooperation with Fairness Constraint in the Downlink OFDMA Cellular Networks

    NASA Astrophysics Data System (ADS)

    Li, Hongxing; Luo, Hanwen; Chen, Wen; Guo, Jia

    In this letter, we study cell cooperation in the downlink OFDMA cellular networks. The proposed cooperation scheme is based on fractional frequency reuse (FFR), where a cooperation group consists of three sector antennas from three adjacent cells and the subchannels of each cooperation group are allocated coordinately to users. Simulation results demonstrate the effectiveness of the proposed schemes in terms of throughput and fairness.

  20. 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.

  1. Cooperative Game-Based Energy Efficiency Management over Ultra-Dense Wireless Cellular Networks

    PubMed Central

    Li, Ming; Chen, Pengpeng; Gao, Shouwan

    2016-01-01

    Ultra-dense wireless cellular networks have been envisioned as a promising technique for handling the explosive increase of wireless traffic volume. With the extensive deployment of small cells in wireless cellular networks, the network spectral efficiency (SE) is improved with the use of limited frequency. However, the mutual inter-tier and intra-tier interference between or among small cells and macro cells becomes serious. On the other hand, more chances for potential cooperation among different cells are introduced. Energy efficiency (EE) has become one of the most important problems for future wireless networks. This paper proposes a cooperative bargaining game-based method for comprehensive EE management in an ultra-dense wireless cellular network, which highlights the complicated interference influence on energy-saving challenges and the power-coordination process among small cells and macro cells. Especially, a unified EE utility with the consideration of the interference mitigation is proposed to jointly address the SE, the deployment efficiency (DE), and the EE. In particular, closed-form power-coordination solutions for the optimal EE are derived to show the convergence property of the algorithm. Moreover, a simplified algorithm is presented to reduce the complexity of the signaling overhead, which is significant for ultra-dense small cells. Finally, numerical simulations are provided to illustrate the efficiency of the proposed cooperative bargaining game-based and simplified schemes. PMID:27649170

  2. Cooperative Game-Based Energy Efficiency Management over Ultra-Dense Wireless Cellular Networks.

    PubMed

    Li, Ming; Chen, Pengpeng; Gao, Shouwan

    2016-09-13

    Ultra-dense wireless cellular networks have been envisioned as a promising technique for handling the explosive increase of wireless traffic volume. With the extensive deployment of small cells in wireless cellular networks, the network spectral efficiency (SE) is improved with the use of limited frequency. However, the mutual inter-tier and intra-tier interference between or among small cells and macro cells becomes serious. On the other hand, more chances for potential cooperation among different cells are introduced. Energy efficiency (EE) has become one of the most important problems for future wireless networks. This paper proposes a cooperative bargaining game-based method for comprehensive EE management in an ultra-dense wireless cellular network, which highlights the complicated interference influence on energy-saving challenges and the power-coordination process among small cells and macro cells. Especially, a unified EE utility with the consideration of the interference mitigation is proposed to jointly address the SE, the deployment efficiency (DE), and the EE. In particular, closed-form power-coordination solutions for the optimal EE are derived to show the convergence property of the algorithm. Moreover, a simplified algorithm is presented to reduce the complexity of the signaling overhead, which is significant for ultra-dense small cells. Finally, numerical simulations are provided to illustrate the efficiency of the proposed cooperative bargaining game-based and simplified schemes.

  3. 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.

  4. 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.

  5. Almost Periodic Dynamics for Memristor-Based Shunting Inhibitory Cellular Neural Networks with Leakage Delays

    PubMed Central

    Lu, Lin

    2016-01-01

    We investigate a class of memristor-based shunting inhibitory cellular neural networks with leakage delays. By applying a new Lyapunov function method, we prove that the neural network which has a unique almost periodic solution is globally exponentially stable. Moreover, the theoretical findings of this paper on the almost periodic solution are applied to prove the existence and stability of periodic solution for memristor-based shunting inhibitory cellular neural networks with leakage delays and periodic coefficients. An example is given to illustrate the effectiveness of the theoretical results. The results obtained in this paper are completely new and complement the previously known studies of Wu (2011) and Chen and Cao (2002). PMID:27840634

  6. Hardware Implementation of a Desktop Supercomputer for High Performance Image Processing. Color Image Processing Using Cellular Neural Networks

    DTIC Science & Technology

    1994-11-01

    This report addresses the functional behavior of Cellular Neural Networks (CNN). The impact of variable convergence times on the proper operation of...The report discusses the new fault model, presents the algorithmic procedures and shows simulated testing results. Cellular neural Networks , Testing.

  7. Quantum complexity: Quantum mutual information, complex networks, and emergent phenomena in quantum cellular automata

    NASA Astrophysics Data System (ADS)

    Vargas, David L.

    Emerging quantum simulator technologies provide a new challenge to quantum many body theory. Quantifying the emergent order in and predicting the dynamics of such complex quantum systems requires a new approach. We develop such an approach based on complex network analysis of quantum mutual information. First, we establish the usefulness of quantum mutual information complex networks by reproducing the phase diagrams of transverse Ising and Bose-Hubbard models. By quantifying the complexity of quantum cellular automata we then demonstrate the applicability of complex network theory to non-equilibrium quantum dynamics. We conclude with a study of student collaboration networks, correlating a student's role in a collaboration network with their grades. This work thus initiates a quantitative theory of quantum complexity and provides a new tool for physics education research. (Abstract shortened by ProQuest.).

  8. 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.

  9. The role of field coupling in nano-scale cellular nonlinear networks.

    PubMed

    Porod, Wolfgang; Csaba, Gyorgy; Csurgay, Arpad

    2003-12-01

    We review some of our previous work on field-coupling in nano-scale cellular arrays. Electronic devices based on metallic and magnetic nanoscale dots and molecular structures have been suggested, however, no technologically viable architecture for nanoelectronic circuit integration has emerged so far. A natural architecture on the nanoscale appears to be near-neighbor cellular networking, and we explore promising alternative ways of integrating nanodevices by direct physical field coupling, i.e. either by Coulomb or by magnetic interactions. We review new architectures for such field-coupled nanocircuits.

  10. Cellular and Network Contributions to Excitability of Layer 5 Neocortical Pyramidal Neurons in the Rat

    PubMed Central

    Bar-Yehuda, Dan; Korngreen, Alon

    2007-01-01

    There is a considerable gap between investigating the dynamics of single neurons and the computational aspects of neural networks. A growing number of studies have attempted to overcome this gap using the excitation in brain slices elicited by various chemical manipulations of the bath solution. However, there has been no quantitative study on the effects of these manipulations on the cellular and network factors controlling excitability. Using the whole-cell configuration of the patch-clamp technique we recorded the membrane potential from the soma of layer 5 pyramidal neurons in acute brain slices from the somatosensory cortex of young rats at 22°C and 35°C. Using blockers of synaptic transmission, we show distinct changes in cellular properties following modification of the ionic composition of the artificial cerebrospinal fluid (ACSF). Thus both cellular and network changes may contribute to the observed effects of slice excitation solutions on the physiology of single neurons. Furthermore, our data suggest that the difference in the ionic composition of current standard ACSF from that of CSF measured in vivo cause ACSF to depress network activity in acute brain slices. This may affect outcomes of experiments investigating biophysical and physiological properties of neurons in such preparations. Our results strongly advocate the necessity of redesigning experiments routinely carried out in the quiescent acute brain slice preparation. PMID:18030343

  11. Joint Mode Selection and Resource Allocation for Cellular Controlled Short-Range Communication in OFDMA Networks

    NASA Astrophysics Data System (ADS)

    Deng, Hui; Tao, Xiaoming; Ge, Ning; Lu, Jianhua

    This letter studies cellular controlled short-range communication in OFDMA networks. The network needs to decide when to allow direct communication between a closely located device-to-device (D2D) pair instead of conveying data from one device to the other via the base station and when not to, in addition to subchannel and power allocation. Our goal is to maximize the total network throughput while guaranteeing the rate requirements of all users. For that purpose, we formulate an optimization problem subject to subchannel and power constraints. A scheme which combines a joint mode selection and subchannel allocation algorithm based on equal power allocation with a power reallocation scheme is proposed. Simulation results show that our proposed scheme can improve the network throughput and outage probability compared with other schemes.

  12. Adding learning to cellular genetic algorithms for training recurrent neural networks.

    PubMed

    Ku, K W; Mak, M W; Siu, W C

    1999-01-01

    This paper proposes a hybrid optimization algorithm which combines the efforts of local search (individual learning) and cellular genetic algorithms (GA's) for training recurrent neural networks (RNN's). Each weight of an RNN is encoded as a floating point number, and a concatenation of the numbers forms a chromosome. Reproduction takes place locally in a square grid with each grid point representing a chromosome. Two approaches, Lamarckian and Baldwinian mechanisms, for combining cellular GA's and learning have been compared. Different hill-climbing algorithms are incorporated into the cellular GA's as learning methods. These include the real-time recurrent learning (RTRL) and its simplified versions, and the delta rule. The RTRL algorithm has been successively simplified by freezing some of the weights to form simplified versions. The delta rule, which is the simplest form of learning, has been implemented by considering the RNN's as feedforward networks during learning. The hybrid algorithms are used to train the RNN's to solve a long-term dependency problem. The results show that Baldwinian learning is inefficient in assisting the cellular GA. It is conjectured that the more difficult it is for genetic operations to produce the genotypic changes that match the phenotypic changes due to learning, the poorer is the convergence of Baldwinian learning. Most of the combinations using the Lamarckian mechanism show an improvement in reducing the number of generations required for an optimum network; however, only a few can reduce the actual time taken. Embedding the delta rule in the cellular GA's has been found to be the fastest method. It is also concluded that learning should not be too extensive if the hybrid algorithm is to be benefit from learning.

  13. Sensitivity analysis of FBMC-based multi-cellular networks to synchronization errors and HPA nonlinearities

    NASA Astrophysics Data System (ADS)

    Elmaroud, Brahim; Faqihi, Ahmed; Aboutajdine, Driss

    2017-01-01

    In this paper, we study the performance of asynchronous and nonlinear FBMC-based multi-cellular networks. The considered system includes a reference mobile perfectly synchronized with its reference base station (BS) and K interfering BSs. Both synchronization errors and high-power amplifier (HPA) distortions will be considered and a theoretical analysis of the interference signal will be conducted. On the basis of this analysis, we will derive an accurate expression of signal-to-noise-plus-interference ratio (SINR) and bit error rate (BER) in the presence of a frequency-selective channel. In order to reduce the computational complexity of the BER expression, we applied an interesting lemma based on the moment generating function of the interference power. Finally, the proposed model is evaluated through computer simulations which show a high sensitivity of the asynchronous FBMC-based multi-cellular network to HPA nonlinear distortions.

  14. Complete stability of cellular neural networks with unbounded time-varying delays.

    PubMed

    Wang, Lili; Chen, Tianping

    2012-12-01

    In this paper, we are concerned with the delayed cellular neural networks (DCNNs) in the case that the time-varying delays are unbounded. Under some conditions, it shows that the DCNNs can exhibit 3(n) equilibrium points. Then, we track the dynamics of u(t)(t>0) in two cases with respect to different types of subset regions in which u(0) is located. It concludes that every solution trajectory u(t) would converge to one of the equilibrium points despite the time-varying delays, that is, the delayed cellular neural networks are completely stable. The method is novel and the results obtained extend the existing ones. In addition, two illustrative examples are presented to verify the effectiveness of our results.

  15. 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

    2014-12-07

    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.

  16. 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

  17. Cellular neural network implementation using a phase-only joint transform correlator

    NASA Astrophysics Data System (ADS)

    Zhang, Shuqun; Karim, Mohammad A.

    1999-04-01

    A phase-only joint transform correlator (JTC) is used to realize cellular neural networks (CNNs). The operation of summing cross-correlations of bipolar data in CNNs can be realized in parallel by phase-encoding bipolar data. Compared to other optical systems for implementing CNNs, the proposed method offers the advantages of easier implementation and robustness in terms of system alignment, and requires neither electronic precalculation nor data rearrangement. Simulation results of the proposed optical CNNs for edge detection are provided.

  18. Exponential stability of delayed and impulsive cellular neural networks with partially Lipschitz continuous activation functions.

    PubMed

    Song, Xueli; Xin, Xing; Huang, Wenpo

    2012-05-01

    The paper discusses exponential stability of distributed delayed and impulsive cellular neural networks with partially Lipschitz continuous activation functions. By relative nonlinear measure method, some novel criteria are obtained for the uniqueness and exponential stability of the equilibrium point. Our method abandons usual assumptions on global Lipschitz continuity, boundedness and monotonicity of activation functions. Our results are generalization and improvement of some existing ones. Finally, two examples and their simulations are presented to illustrate the correctness of our analysis.

  19. 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.

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

    PubMed

    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.

  1. 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

  2. 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.

  3. 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

    2016-06-14

    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.

  4. 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

  5. Hybrid RF and Digital Beamformer for Cellular Networks: Algorithms, Microwave Architectures, and Measurements

    NASA Astrophysics Data System (ADS)

    Venkateswaran, Vijay; Pivit, Florian; Guan, Lei

    2016-07-01

    Modern wireless communication networks, particularly cellular networks utilize multiple antennas to improve the capacity and signal coverage. In these systems, typically an active transceiver is connected to each antenna. However, this one-to-one mapping between transceivers and antennas will dramatically increase the cost and complexity of a large phased antenna array system. In this paper, firstly we propose a \\emph{partially adaptive} beamformer architecture where a reduced number of transceivers with a digital beamformer (DBF) is connected to an increased number of antennas through an RF beamforming network (RFBN). Then, based on the proposed architecture, we present a methodology to derive the minimum number of transceivers that are required for marco-cell and small-cell base stations, respectively. Subsequently, in order to achieve optimal beampatterns with given cellular standard requirements and RF operational constraints, we propose efficient algorithms to jointly design DBF and RFBN. Starting from the proposed algorithms, we specify generic microwave RFBNs for optimal marco-cell and small-cell networks. In order to verify the proposed approaches, we compare the performance of RFBN using simulations and anechoic chamber measurements. Experimental measurement results confirm the robustness and performance of the proposed hybrid DBF-RFBN concept eventually ensuring that theoretical multi-antenna capacity and coverage are achieved at a little incremental cost.

  6. 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.

  7. 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

  8. 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.

  9. Prototype Foamy Virus Bet Impairs the Dimerization and Cytosolic Solubility of Human APOBEC3G

    PubMed Central

    Jaguva Vasudevan, Ananda Ayyappan; Perković, Mario; Bulliard, Yannick; Cichutek, Klaus; Trono, Didier; Häussinger, Dieter

    2013-01-01

    Cellular cytidine deaminases from the APOBEC3 family are potent restriction factors that are able to block the replication of retroviruses. Consequently, retroviruses have evolved a variety of different mechanisms to counteract inhibition by APOBEC3 proteins. Lentiviruses such as human immunodeficiency virus (HIV) express Vif, which interferes with APOBEC3 proteins by targeting these restriction factors for proteasomal degradation, hence blocking their ability to access the reverse transcriptase complex in the virions. Other retroviruses use less-well-characterized mechanisms to escape the APOBEC3-mediated cellular defense. Here we show that the prototype foamy virus Bet protein can protect foamy viruses and an unrelated simian immunodeficiency virus against human APOBEC3G (A3G). In our system, Bet binds to A3G and prevents its encapsidation without inducing its degradation. Bet failed to coimmunoprecipitate with A3G mutants unable to form homodimers and dramatically reduced the recovery of A3G proteins from soluble cytoplasmic cell fractions. The Bet-A3G interaction is probably a direct binding interaction and seems to be independent of RNA. Together, these data suggest a novel model whereby Bet uses two possibly complementary mechanisms to counteract A3G: (i) Bet prevents encapsidation of A3G by blocking A3G dimerization, and (ii) Bet sequesters A3G in immobile complexes, impairing its ability to interact with nascent virions. PMID:23760237

  10. A Memristive Multilayer Cellular Neural Network With Applications to Image Processing.

    PubMed

    Hu, Xiaofang; Feng, Gang; Duan, Shukai; Liu, Lu

    2016-05-13

    The memristor has been extensively studied in electrical engineering and biological sciences as a means to compactly implement the synaptic function in neural networks. The cellular neural network (CNN) is one of the most implementable artificial neural network models and capable of massively parallel analog processing. In this paper, a novel memristive multilayer CNN (Mm-CNN) model is presented along with its performance analysis and applications. In this new CNN design, the memristor crossbar circuit acts as the synapse, which realizes one signed synaptic weight with a pair of memristors and performs the synaptic weighting compactly and linearly. Moreover, the complex weighted summation is executed in an efficient way with a proper design of Mm-CNN cell circuits. The proposed Mm-CNN has several merits, such as compactness, nonvolatility, versatility, and programmability of synaptic weights. Its performance in several image processing applications is illustrated through simulations.

  11. Micro-connectomics: probing the organization of neuronal networks at the cellular scale.

    PubMed

    Schröter, Manuel; Paulsen, Ole; Bullmore, Edward T

    2017-03-01

    Defining the organizational principles of neuronal networks at the cellular scale, or micro-connectomics, is a key challenge of modern neuroscience. In this Review, we focus on graph theoretical parameters of micro-connectome topology, often informed by economical principles that conceptually originated with Ramón y Cajal's conservation laws. First, we summarize results from studies in intact small organisms and in samples from larger nervous systems. We then evaluate the evidence for an economical trade-off between biological cost and functional value in the organization of neuronal networks. Various results suggest that many aspects of neuronal network organization are indeed the outcome of competition between these two fundamental selection pressures.

  12. The translational machinery is an optimized molecular network that affects cellular homoeostasis and disease.

    PubMed

    Kazana, Eleanna; von der Haar, Tobias

    2014-02-01

    Translation involves interactions between mRNAs, ribosomes, tRNAs and a host of translation factors. Emerging evidence on the eukaryotic translational machinery indicates that these factors are organized in a highly optimized network, in which the levels of the different factors are finely matched to each other. This optimal factor network is essential for producing proteomes that result in optimal fitness, and perturbations to the optimal network that significantly affect translational activity therefore result in non-optimal proteomes, fitness losses and disease. On the other hand, experimental evidence indicates that translation and cell growth are relatively robust to perturbations, and viability can be maintained even upon significant damage to individual translation factors. How the eukaryotic translational machinery is optimized, and how it can maintain optimization in the face of changing internal parameters, are open questions relevant to the interaction between translation and cellular disease states.

  13. 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.

  14. A global genetic interaction network maps a wiring diagram of cellular function.

    PubMed

    Costanzo, Michael; VanderSluis, Benjamin; Koch, Elizabeth N; Baryshnikova, Anastasia; Pons, Carles; Tan, Guihong; Wang, Wen; Usaj, Matej; Hanchard, Julia; Lee, Susan D; Pelechano, Vicent; Styles, Erin B; Billmann, Maximilian; van Leeuwen, Jolanda; van Dyk, Nydia; Lin, Zhen-Yuan; Kuzmin, Elena; Nelson, Justin; Piotrowski, Jeff S; Srikumar, Tharan; Bahr, Sondra; Chen, Yiqun; Deshpande, Raamesh; Kurat, Christoph F; Li, Sheena C; Li, Zhijian; Usaj, Mojca Mattiazzi; Okada, Hiroki; Pascoe, Natasha; San Luis, Bryan-Joseph; Sharifpoor, Sara; Shuteriqi, Emira; Simpkins, Scott W; Snider, Jamie; Suresh, Harsha Garadi; Tan, Yizhao; Zhu, Hongwei; Malod-Dognin, Noel; Janjic, Vuk; Przulj, Natasa; Troyanskaya, Olga G; Stagljar, Igor; Xia, Tian; Ohya, Yoshikazu; Gingras, Anne-Claude; Raught, Brian; Boutros, Michael; Steinmetz, Lars M; Moore, Claire L; Rosebrock, Adam P; Caudy, Amy A; Myers, Chad L; Andrews, Brenda; Boone, Charles

    2016-09-23

    We generated a global genetic interaction network for Saccharomyces cerevisiae, constructing more than 23 million double mutants, identifying about 550,000 negative and about 350,000 positive genetic interactions. This comprehensive network maps genetic interactions for essential gene pairs, highlighting essential genes as densely connected hubs. Genetic interaction profiles enabled assembly of a hierarchical model of cell function, including modules corresponding to protein complexes and pathways, biological processes, and cellular compartments. Negative interactions connected functionally related genes, mapped core bioprocesses, and identified pleiotropic genes, whereas positive interactions often mapped general regulatory connections among gene pairs, rather than shared functionality. The global network illustrates how coherent sets of genetic interactions connect protein complex and pathway modules to map a functional wiring diagram of the cell.

  15. Issues for the integration of satellite and terrestrial cellular networks for mobile communications

    NASA Astrophysics Data System (ADS)

    Delre, Enrico; Mistretta, Ignazio; Dellipriscoli, Francesco; Settimo, Franco

    1991-09-01

    Satellite and terrestrial cellular systems naturally complement each other for land mobile communications, even though present systems have been developed independently. The main advantages of the integrated system are a faster wide area coverage, a better management of overloading traffic conditions, an extension to geographical areas not covered by the terrestrial network and, in perspective, the provision of only one integrated system for all mobile communications (land, aeronautical, and maritime). To achieve these goals, as far as possible the same protocols of the terrestrial network should be used also for the satellite network. Discussed here are the main issues arising from the requirements of the main integrated system. Some results are illustrated, and possible future improvements due to technical solutions are presented.

  16. Cellular pulse-coupled neural network with adaptive weights for image segmentation and its VLSI implementation

    NASA Astrophysics Data System (ADS)

    Schreiter, Juerg; Ramacher, Ulrich; Heittmann, Arne; Matolin, Daniel; Schuffny, Rene

    2004-05-01

    We present a cellular pulse coupled neural network with adaptive weights and its analog VLSI implementation. The neural network operates on a scalar image feature, such as grey scale or the output of a spatial filter. It detects segments and marks them with synchronous pulses of the corresponding neurons. The network consists of integrate-and-fire neurons, which are coupled to their nearest neighbors via adaptive synaptic weights. Adaptation follows either one of two empirical rules. Both rules lead to spike grouping in wave like patterns. This synchronous activity binds groups of neurons and labels the corresponding image segments. Applications of the network also include feature preserving noise removal, image smoothing, and detection of bright and dark spots. The adaptation rules are insensitive for parameter deviations, mismatch and non-ideal approximation of the implied functions. That makes an analog VLSI implementation feasible. Simulations showed no significant differences in the synchronization properties between networks using the ideal adaptation rules and networks resembling implementation properties such as randomly distributed parameters and roughly implemented adaptation functions. A prototype is currently being designed and fabricated using an Infineon 130nm technology. It comprises a 128 × 128 neuron array, analog image memory, and an address event representation pulse output.

  17. Multifunctional Superelastic Foam-Like Boron Nitride Nanotubular Cellular-Network Architectures.

    PubMed

    Xue, Yanming; Dai, Pengcheng; Zhou, Min; Wang, Xi; Pakdel, Amir; Zhang, Chao; Weng, Qunhong; Takei, Toshiaki; Fu, Xiuwei; Popov, Zakhar I; Sorokin, Pavel B; Tang, Chengchun; Shimamura, Kiyoshi; Bando, Yoshio; Golberg, Dmitri

    2017-01-24

    Construction of cellular architectures has been expected to enhance materials' mechanical tolerance and to stimulate and broaden their efficient utilizations in many potential fields. However, hitherto, there have been rather scarce developments in boron nitride (BN)-type cellular architectures because of well-known difficulties in the syntheses of BN-based structures. Herein, cellular-network multifunctional foams made of interconnective nanotubular hexagonal BN (h-BN) architectures are developed using carbothermal reduction-assisted in situ chemical vapor deposition conversion from N-doped tubular graphitic cellular foams. These ultralight, chemically inert, thermally stable, and robust-integrity (supporting about 25,000 times of their own weight) three-dimensional-BN foams exhibit a 98.5% porosity, remarkable shape recovery (even after cycling compressions with 90% deformations), excellent resistance to water intrusion, thermal diffusion stability, and high strength and stiffness. They remarkably reduce the coefficient of thermal expansion and dielectric constant of polymeric poly(methyl methacrylate) composites, greatly contribute to their thermal conductivity improvement, and effectively limit polymeric composite softening at elevated temperatures. The foams also demonstrate high-capacity adsorption-separation and removal ability for a wide range of oils and organic chemicals in oil/water systems and reliable recovery under their cycling usage as organic adsorbers. These created multifunctional foams should be valuable in many high-end practical applications.

  18. 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.

  19. 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.

  20. Three Years of Country-Wide Rainfall Maps from Cellular Communication Networks

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

    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 communication networks may be used 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 estimation 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, which can be converted to average rainfall intensities over the length of a link. This is particularly interesting for those countries where few surface rainfall observations are available. A data set from a commercial microwave link network over the Netherlands is analyzed. The data set runs from January 2011 - January 2014 and consists of roughly 2000 links covering the land surface of the Netherlands (35,500 square kilometers). From this 3-year data set country-wide rainfall maps are retrieved, which are compared to a gauge-adjusted radar data set. The ability of cellular communication networks to estimate rainfall is studied for different temporal and spatial scales, as well as for several air temperature classes. Case studies are presented to investigate the performance of the algorithm during snow and sleet and to show the influence of dew formation on the antennas on the received signal levels. To summarize, the results further confirm the potential of these networks for rainfall monitoring.

  1. High-resolution CMOS MEA platform to study neurons at subcellular, cellular, and network levels.

    PubMed

    Müller, Jan; Ballini, Marco; Livi, Paolo; Chen, Yihui; Radivojevic, Milos; Shadmani, Amir; Viswam, Vijay; Jones, Ian L; Fiscella, Michele; Diggelmann, Roland; Stettler, Alexander; Frey, Urs; Bakkum, Douglas J; Hierlemann, Andreas

    2015-07-07

    Studies on information processing and learning properties of neuronal networks would benefit from simultaneous and parallel access to the activity of a large fraction of all neurons in such networks. Here, we present a CMOS-based device, capable of simultaneously recording the electrical activity of over a thousand cells in in vitro neuronal networks. The device provides sufficiently high spatiotemporal resolution to enable, at the same time, access to neuronal preparations on subcellular, cellular, and network level. The key feature is a rapidly reconfigurable array of 26 400 microelectrodes arranged at low pitch (17.5 μm) within a large overall sensing area (3.85 × 2.10 mm(2)). An arbitrary subset of the electrodes can be simultaneously connected to 1024 low-noise readout channels as well as 32 stimulation units. Each electrode or electrode subset can be used to electrically stimulate or record the signals of virtually any neuron on the array. We demonstrate the applicability and potential of this device for various different experimental paradigms: large-scale recordings from whole networks of neurons as well as investigations of axonal properties of individual neurons.

  2. 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.

  3. A new method for the re-implementation of threshold logic functions with cellular neural networks.

    PubMed

    Bénédic, Y; Wira, P; Mercklé, J

    2008-08-01

    A new strategy is presented for the implementation of threshold logic functions with binary-output Cellular Neural Networks (CNNs). The objective is to optimize the CNNs weights to develop a robust implementation. Hence, the concept of generative set is introduced as a convenient representation of any linearly separable Boolean function. Our analysis of threshold logic functions leads to a complete algorithm that automatically provides an optimized generative set. New weights are deduced and a more robust CNN template assuming the same function can thus be implemented. The strategy is illustrated by a detailed example.

  4. Moving object segmentation algorithm based on cellular neural networks in the H.264 compressed domain

    NASA Astrophysics Data System (ADS)

    Feng, Jie; Chen, Yaowu; Tian, Xiang

    2009-07-01

    A cellular neural network (CNN)-based moving object segmentation algorithm in the H.264 compressed domain is proposed. This algorithm mainly utilizes motion vectors directly extracted from H.264 bitstreams. To improve the robustness of the motion vector information, the intramodes in I-frames are used for smooth and nonsmooth region classification, and the residual coefficient energy of P-frames is used to update the classification results first. Then, an adaptive motion vector filter is used according to interpartition modes. Finally, many CNN models are applied to implement moving object segmentation based on motion vector fields. Experiment results are presented to verify the efficiency and the robustness of this algorithm.

  5. 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.

  6. 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

  7. 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.

  8. Modeling Immune Network Through Cellular Automata:. a Unified Mechanism of Immunological Memory

    NASA Astrophysics Data System (ADS)

    Chowdhury, Debashish; Deshpande, Varsha; Stauffer, Dietrich

    The populations of the various types of immunocompetent cells in the immune system are described as cellular automata and the population dynamics of these cells are formulated in terms of dynamical maps in discrete time. Both intra-clonal interactions (i.e., interactions among the cell types belonging to the same clone) and inter-clonal interactions (i.e., interactions among the cell types belonging to different clones) are included in the models proposed here. While the intra-clonal interactions are shown to play a crucial role in the primary response of some clones and in the formation of the immunological memory, the inter-clonal interactions are responsible for retaining the memory through a dynamical process driven by the mutual stimulation of the clones. We present the results for two different types of connectivity, namely, a “necklace” network and a network in “shape space”.

  9. Modeling of Diffusion through a Network: A New Approach using Cellular Automata and Network Science Techniques

    DTIC Science & Technology

    2010-05-01

    to Professor Chris Arney and LTC Donovan Phillips for providing valuable feedback on this project. vii MODELING OF DIFFUSION THROUGH A...only does the study of networks afford the U.S. Army greater information sharing abilities, it could also give a better understanding of enemy...These models are named for the conditions by which a node changes state. The first model gives each node its own threshold which must be reached before

  10. The Influence of Cold Temperature on Cellular Excitability of Hippocampal Networks

    PubMed Central

    Vara, Hugo; Caires, Rebeca; Ballesta, Juan J.; Belmonte, Carlos; Viana, Felix

    2012-01-01

    The hippocampus plays an important role in short term memory, learning and spatial navigation. A characteristic feature of the hippocampal region is its expression of different electrical population rhythms and activities during different brain states. Physiological fluctuations in brain temperature affect the activity patterns in hippocampus, but the underlying cellular mechanisms are poorly understood. In this work, we investigated the thermal modulation of hippocampal activity at the cellular network level. Primary cell cultures of mouse E17 hippocampus displayed robust network activation upon light cooling of the extracellular solution from baseline physiological temperatures. The activity generated was dependent on action potential firing and excitatory glutamatergic synaptic transmission. Involvement of thermosensitive channels from the transient receptor potential (TRP) family in network activation by temperature changes was ruled out, whereas pharmacological and immunochemical experiments strongly pointed towards the involvement of temperature-sensitive two-pore-domain potassium channels (K2P), TREK/TRAAK family. In hippocampal slices we could show an increase in evoked and spontaneous synaptic activity produced by mild cooling in the physiological range that was prevented by chloroform, a K2P channel opener. We propose that cold-induced closure of background TREK/TRAAK family channels increases the excitability of some hippocampal neurons, acting as a temperature-sensitive gate of network activation. Our findings in the hippocampus open the possibility that small temperature variations in the brain in vivo, associated with metabolism or blood flow oscillations, act as a switch mechanism of neuronal activity and determination of firing patterns through regulation of thermosensitive background potassium channel activity. PMID:23300680

  11. 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.

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

    PubMed

    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.

  13. 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

  14. Country-wide rainfall maps from a commercial cellular telephone network

    NASA Astrophysics Data System (ADS)

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

    2012-04-01

    Accurate rainfall observations with high spatial and temporal resolutions are needed for many applications, for instance, as input for hydrological models. Weather radars often provide data with sufficient spatial and temporal resolution, but usually need adjustment. In general, only few rain gauge measurements are available to adjust the radar data in real-time, for example, each hour. Physically based methods, such as a VPR correction, can be valuable and hold a promise. However, they are not always performed in real-time yet and can be difficult to implement. The estimation of rainfall using microwave links from commercial cellular telephone networks is a new and potentially valuable source of information. Such networks cover large parts of the land surface of the earth and have a high density. The data produced by the microwave links in such networks is essentially a by-product of the communication between mobile telephones. 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. A recent study of us shows that urban rainfall can be estimated from commercial microwave link data for the Rotterdam region, a densely-populated delta city in the Netherlands. A data set from a commercial microwave link network over the Netherlands is analyzed, containing approximately 1500 links covering the land surface of the Netherlands (35500 km2). This data set consists of several days with extreme rainfall in June, July and August 2011. A methodology is presented to derive rainfall intensities and daily rainfall depths from the microwave link data, which have a temporal resolution of 15 min. The magnitude and dynamics of these rainfall intensities

  15. Knowledge-guided fuzzy logic modeling to infer cellular signaling networks from proteomic data

    PubMed Central

    Liu, Hui; Zhang, Fan; Mishra, Shital Kumar; Zhou, Shuigeng; Zheng, Jie

    2016-01-01

    Modeling of signaling pathways is crucial for understanding and predicting cellular responses to drug treatments. However, canonical signaling pathways curated from literature are seldom context-specific and thus can hardly predict cell type-specific response to external perturbations; purely data-driven methods also have drawbacks such as limited biological interpretability. Therefore, hybrid methods that can integrate prior knowledge and real data for network inference are highly desirable. In this paper, we propose a knowledge-guided fuzzy logic network model to infer signaling pathways by exploiting both prior knowledge and time-series data. In particular, the dynamic time warping algorithm is employed to measure the goodness of fit between experimental and predicted data, so that our method can model temporally-ordered experimental observations. We evaluated the proposed method on a synthetic dataset and two real phosphoproteomic datasets. The experimental results demonstrate that our model can uncover drug-induced alterations in signaling pathways in cancer cells. Compared with existing hybrid models, our method can model feedback loops so that the dynamical mechanisms of signaling networks can be uncovered from time-series data. By calibrating generic models of signaling pathways against real data, our method supports precise predictions of context-specific anticancer drug effects, which is an important step towards precision medicine. PMID:27774993

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

    PubMed Central

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

    2014-01-01

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

  17. 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

    2016-08-25

    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.

  18. Knowledge-guided fuzzy logic modeling to infer cellular signaling networks from proteomic data

    NASA Astrophysics Data System (ADS)

    Liu, Hui; Zhang, Fan; Mishra, Shital Kumar; Zhou, Shuigeng; Zheng, Jie

    2016-10-01

    Modeling of signaling pathways is crucial for understanding and predicting cellular responses to drug treatments. However, canonical signaling pathways curated from literature are seldom context-specific and thus can hardly predict cell type-specific response to external perturbations; purely data-driven methods also have drawbacks such as limited biological interpretability. Therefore, hybrid methods that can integrate prior knowledge and real data for network inference are highly desirable. In this paper, we propose a knowledge-guided fuzzy logic network model to infer signaling pathways by exploiting both prior knowledge and time-series data. In particular, the dynamic time warping algorithm is employed to measure the goodness of fit between experimental and predicted data, so that our method can model temporally-ordered experimental observations. We evaluated the proposed method on a synthetic dataset and two real phosphoproteomic datasets. The experimental results demonstrate that our model can uncover drug-induced alterations in signaling pathways in cancer cells. Compared with existing hybrid models, our method can model feedback loops so that the dynamical mechanisms of signaling networks can be uncovered from time-series data. By calibrating generic models of signaling pathways against real data, our method supports precise predictions of context-specific anticancer drug effects, which is an important step towards precision medicine.

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

    PubMed Central

    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

  20. 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.

  1. 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

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. Spike integration and cellular memory in a rhythmic network from Na+/K+ pump current dynamics

    PubMed Central

    Pulver, Stefan R.

    2009-01-01

    The output of a neural circuit results from an interaction between the intrinsic properties of neurons within the circuit and the features of the synaptic connections between them. The plasticity of intrinsic properties has been primarily attributed to modification of ion channel function and/or number. In this study, we demonstrate a mechanism for intrinsic plasticity in rhythmically active Drosophila neurons that is not conductance-based. Larval motor neurons show a long lasting sodium-dependent afterhyperpolarization (AHP) following bursts of action potentials that is mediated by the electrogenic activity of Na+/K+ ATPase. This AHP persists for multiple seconds following volleys of action potentials and is able to function as a pattern-insensitive integrator of spike number that is independent of external calcium. This current also interacts with endogenous Shal K+ conductances to modulate spike timing for multiple seconds following rhythmic activity, providing a cellular memory of network activity on a behaviorally relevant time scale. PMID:19966842

  7. Adaptive call admission control and resource allocation in multi server wireless/cellular network

    NASA Astrophysics Data System (ADS)

    Jain, Madhu; Mittal, Ragini

    2016-11-01

    The ever increasing demand of the subscribers has put pressure on the capacity of wireless networks around the world. To utilize the scare resources, in the present paper we propose an optimal allocation scheme for an integrated wireless/cellular model with handoff priority and handoff guarantee services. The suggested algorithm optimally allocates the resources in each cell and dynamically adjust threshold to control the admission. To give the priority to handoff calls over the new calls, the provision of guard channels and subrating scheme is taken into consideration. The handoff voice call may balk and renege from the system while waiting in the buffer. An iterative algorithm is implemented to generate the arrival rate of the handoff calls in each cell. Various performance indices are established in term of steady state probabilities. The sensitivity analysis has also been carried out to examine the tractability of algorithms and to explore the effects of system descriptors on the performance indices.

  8. 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.

  9. 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

  10. Roadmap to cellular reprogramming--manipulating transcriptional networks with DNA, RNA, proteins and small molecules.

    PubMed

    Wörsdörfer, P; Thier, M; Kadari, A; Edenhofer, F

    2013-06-01

    Recent reports demonstrate that the plasticity of mammalian somatic cells is much higher than previously assumed and that ectopic expression of transcription factors may have the potential to induce the conversion of any cell type into another. Fibroblast cells can be converted into embryonic stem cell-like cells, neural cells, cardiomyocytes, macrophage-like cells as well as blood progenitors. Additionally, the conversion of astrocytes into neurons or neural stem cells into monocytes has been demonstrated. Nowadays, in the era of systems biology, continuously growing holistic data sets are providing increasing insights into core transcriptional networks and cellular signaling pathways. This knowledge enables cell biologists to understand how cellular fate is determined and how it could be manipulated. As a consequence for biomedical applications, it might be soon possible to convert patient specific somatic cells directly into desired transplantable other cell types. The clinical value, however, of such reprogrammed cells is currently limited due to the invasiveness of methods applied to induce reprogramming factor activity. This review will focus on experimental strategies to ectopically induce cell fate modulators. We will emphasize those strategies that enable efficient and robust overexpression of transcription factors by minimal genetic alterations of the host genome. Furthermore, we will discuss procedures devoid of any genomic manipulation, such as the direct delivery of mRNA, proteins, or the use of small molecules. By this, we aim to give a comprehensive overview on state of the art techniques that harbor the potential to generate safe reprogrammed cells for clinical applications.

  11. 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.

  12. 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.

  13. Input-dependent wave propagations in asymmetric cellular automata: possible behaviors of feed-forward loop in biological reaction network.

    PubMed

    Awazu, Akinori

    2008-07-01

    Dynamical aspects of the asymmetric cellular automata were investigated to consider the signaling processes in biological systems. As a meta-model of the cascade of feed-forward loop type network motifs in biological reaction networks, we consider the one dimensional asymmetric cellular automata where the state of each cell is controlled by a trio of cells, the cell itself, the nearest upstream cell and the next nearest upstream cell. Through the systematic simulations, some novel input-dependent wave propagations were found in certain asymmetric CA, which may be useful for the signaling processes like the distinction, the filtering and the memory of external stimuli.

  14. 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

  15. Inter-cellular signaling network reveals a mechanistic transition in tumor microenvironment

    PubMed Central

    Wu, Yu; Garmire, Lana X.; Fan, Rong

    2012-01-01

    We conducted inter-cellular cytokine correlation and network analysis based upon a stochastic population dynamics model that comprises five cell types and fifteen signaling molecules inter-connected through a large number of cell-cell communication pathways. We observed that the signaling molecules are tightly correlated even at very early stages (e.g. the first month) of human glioma, but such correlation rapidly diminishes when tumor grows to a size that can be clinically detected. Further analysis suggests that paracrine is shown to be the dominant force during tumor initiation and priming, while autocrine supersedes it and supports a robust tumor expansion. In correspondence, the cytokine correlation network evolves through an increasing to decreasing complexity. This study indicates a possible mechanistic transition from the microenvironment-controlled, paracrine-based regulatory mechanism to self-sustained rapid progression to fetal malignancy. It also reveals key nodes that are responsible for such transition and can be potentially harnessed for the design of new anti-cancer therapies. PMID:23080410

  16. Trans-species learning of cellular signaling systems with bimodal deep belief networks

    PubMed Central

    Chen, Lujia; Cai, Chunhui; Chen, Vicky; Lu, Xinghua

    2015-01-01

    Motivation: Model organisms play critical roles in biomedical research of human diseases and drug development. An imperative task is to translate information/knowledge acquired from model organisms to humans. In this study, we address a trans-species learning problem: predicting human cell responses to diverse stimuli, based on the responses of rat cells treated with the same stimuli. Results: We hypothesized that rat and human cells share a common signal-encoding mechanism but employ different proteins to transmit signals, and we developed a bimodal deep belief network and a semi-restricted bimodal deep belief network to represent the common encoding mechanism and perform trans-species learning. These ‘deep learning’ models include hierarchically organized latent variables capable of capturing the statistical structures in the observed proteomic data in a distributed fashion. The results show that the models significantly outperform two current state-of-the-art classification algorithms. Our study demonstrated the potential of using deep hierarchical models to simulate cellular signaling systems. Availability and implementation: The software is available at the following URL: http://pubreview.dbmi.pitt.edu/TransSpeciesDeepLearning/. The data are available through SBV IMPROVER website, https://www.sbvimprover.com/challenge-2/overview, upon publication of the report by the organizers. Contact: xinghua@pitt.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25995230

  17. 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.

  18. 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

  19. 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.

  20. Examining the limits of cellular adaptation bursting mechanisms in biologically-based excitatory networks of the hippocampus.

    PubMed

    Ferguson, K A; Njap, F; Nicola, W; Skinner, F K; Campbell, S A

    2015-12-01

    Determining the biological details and mechanisms that are essential for the generation of population rhythms in the mammalian brain is a challenging problem. This problem cannot be addressed either by experimental or computational studies in isolation. Here we show that computational models that are carefully linked with experiment provide insight into this problem. Using the experimental context of a whole hippocampus preparation in vitro that spontaneously expresses theta frequency (3-12 Hz) population bursts in the CA1 region, we create excitatory network models to examine whether cellular adaptation bursting mechanisms could critically contribute to the generation of this rhythm. We use biologically-based cellular models of CA1 pyramidal cells and network sizes and connectivities that correspond to the experimental context. By expanding our mean field analyses to networks with heterogeneity and non all-to-all coupling, we allow closer correspondence with experiment, and use these analyses to greatly extend the range of parameter values that are explored. We find that our model excitatory networks can produce theta frequency population bursts in a robust fashion.Thus, even though our networks are limited by not including inhibition at present, our results indicate that cellular adaptation in pyramidal cells could be an important aspect for the occurrence of theta frequency population bursting in the hippocampus. These models serve as a starting framework for the inclusion of inhibitory cells and for the consideration of additional experimental features not captured in our present network models.

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

    PubMed

    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.

  2. Anisotropic cellular network formation in engineered muscle tissue through the self-organization of neurons and endothelial cells.

    PubMed

    Takahashi, Hironobu; Shimizu, Tatsuya; Nakayama, Masamichi; Yamato, Masayuki; Okano, Teruo

    2015-02-18

    Tissue anisotropy directed by cell sheets: Aligned myoblasts can be harvested as an anisotropic cell sheet using a micropatterned thermoresponsive substrate. Neurons and endothelial cells sandwiched between multiple anisotropic cell sheets self-organize oriented cellular networks in the tissue construct. This simple tissue engineering technique is useful for the creation of biomimetic microstructures in complex tissue, required for future advances in regenerative medicine.

  3. Nanoscale Characterization of Interaction of APOBEC3G with RNA.

    PubMed

    Pan, Yangang; Sun, Zhiqiang; Maiti, Atanu; Kanai, Tapan; Matsuo, Hiroshi; Li, Ming; Harris, Reuben S; Shlyakhtenko, Luda S; Lyubchenko, Yuri L

    2017-03-14

    The human cytidine deaminase APOBEC3G (A3G) is a potent inhibitor of the HIV-1 virus in the absence of viral infectivity factor (Vif). The molecular mechanism of A3G antiviral activity is primarily attributed to deamination of single-stranded DNA (ssDNA); however, the nondeamination mechanism also contributes to HIV-1 restriction. The interaction of A3G with ssDNA and RNA is required for its antiviral activity. Here we used atomic force microscopy to directly visualize A3G-RNA and A3G-ssDNA complexes and compare them to each other. Our results showed that A3G in A3G-RNA complexes exists primarily in monomeric-dimeric states, similar to its stoichiometry in complexes with ssDNA. New A3G-RNA complexes in which A3G binds to two RNA molecules were identified. These data suggest the existence of two separate RNA binding sites on A3G. Such complexes were not observed with ssDNA substrates. Time-lapse high-speed atomic force microscopy was applied to characterize the dynamics of the complexes. The data revealed that the two RNA binding sites have different affinities for A3G. On the basis of the obtained results, a model for the interaction of A3G with RNA is proposed.

  4. DNA-damage response network at the crossroads of cell-cycle checkpoints, cellular senescence and apoptosis.

    PubMed

    Schmitt, Estelle; Paquet, Claudie; Beauchemin, Myriam; Bertrand, Richard

    2007-06-01

    Tissue homeostasis requires a carefully-orchestrated balance between cell proliferation, cellular senescence and cell death. Cells proliferate through a cell cycle that is tightly regulated by cyclin-dependent kinase activities. Cellular senescence is a safeguard program limiting the proliferative competence of cells in living organisms. Apoptosis eliminates unwanted cells by the coordinated activity of gene products that regulate and effect cell death. The intimate link between the cell cycle, cellular senescence, apoptosis regulation, cancer development and tumor responses to cancer treatment has become eminently apparent. Extensive research on tumor suppressor genes, oncogenes, the cell cycle and apoptosis regulatory genes has revealed how the DNA damage-sensing and -signaling pathways, referred to as the DNA-damage response network, are tied to cell proliferation, cell-cycle arrest, cellular senescence and apoptosis. DNA-damage responses are complex, involving "sensor" proteins that sense the damage, and transmit signals to "transducer" proteins, which, in turn, convey the signals to numerous "effector" proteins implicated in specific cellular pathways, including DNA repair mechanisms, cell-cycle checkpoints, cellular senescence and apoptosis. The Bcl-2 family of proteins stands among the most crucial regulators of apoptosis and performs vital functions in deciding whether a cell will live or die after cancer chemotherapy and irradiation. In addition, several studies have now revealed that members of the Bcl-2 family also interface with the cell cycle, DNA repair/recombination and cellular senescence, effects that are generally distinct from their function in apoptosis. In this review, we report progress in understanding the molecular networks that regulate cell-cycle checkpoints, cellular senescence and apoptosis after DNA damage, and discuss the influence of some Bcl-2 family members on cell-cycle checkpoint regulation.

  5. 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

  6. 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.

  7. Image-based quantitative analysis of gold immunochromatographic strip via cellular neural network approach.

    PubMed

    Zeng, Nianyin; Wang, Zidong; Zineddin, Bachar; Li, Yurong; Du, Min; Xiao, Liang; Liu, Xiaohui; Young, Terry

    2014-05-01

    Gold immunochromatographic strip assay provides a rapid, simple, single-copy and on-site way to detect the presence or absence of the target analyte. This paper aims to develop a method for accurately segmenting the test line and control line of the gold immunochromatographic strip (GICS) image for quantitatively determining the trace concentrations in the specimen, which can lead to more functional information than the traditional qualitative or semi-quantitative strip assay. The canny operator as well as the mathematical morphology method is used to detect and extract the GICS reading-window. Then, the test line and control line of the GICS reading-window are segmented by the cellular neural network (CNN) algorithm, where the template parameters of the CNN are designed by the switching particle swarm optimization (SPSO) algorithm for improving the performance of the CNN. It is shown that the SPSO-based CNN offers a robust method for accurately segmenting the test and control lines, and therefore serves as a novel image methodology for the interpretation of GICS. Furthermore, quantitative comparison is carried out among four algorithms in terms of the peak signal-to-noise ratio. It is concluded that the proposed CNN algorithm gives higher accuracy and the CNN is capable of parallelism and analog very-large-scale integration implementation within a remarkably efficient time.

  8. Cellular neural networks, the Navier-Stokes equation, and microarray image reconstruction.

    PubMed

    Zineddin, Bachar; Wang, Zidong; Liu, Xiaohui

    2011-11-01

    Although the last decade has witnessed a great deal of improvements achieved for the microarray technology, many major developments in all the main stages of this technology, including image processing, are still needed. Some hardware implementations of microarray image processing have been proposed in the literature and proved to be promising alternatives to the currently available software systems. However, the main drawback of those proposed approaches is the unsuitable addressing of the quantification of the gene spot in a realistic way without any assumption about the image surface. Our aim in this paper is to present a new image-reconstruction algorithm using the cellular neural network that solves the Navier-Stokes equation. This algorithm offers a robust method for estimating the background signal within the gene-spot region. The MATCNN toolbox for Matlab is used to test the proposed method. Quantitative comparisons are carried out, i.e., in terms of objective criteria, between our approach and some other available methods. It is shown that the proposed algorithm gives highly accurate and realistic measurements in a fully automated manner within a remarkably efficient time.

  9. 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.

  10. Early warning of illegal development for protected areas by integrating cellular automata with neural networks.

    PubMed

    Li, Xia; Lao, Chunhua; Liu, Yilun; Liu, Xiaoping; Chen, Yimin; Li, Shaoying; Ai, Bing; He, Zijian

    2013-11-30

    Ecological security has become a major issue under fast urbanization in China. As the first two cities in this country, Shenzhen and Dongguan issued the ordinance of Eco-designated Line of Control (ELC) to "wire" ecologically important areas for strict protection in 2005 and 2009 respectively. Early warning systems (EWS) are a useful tool for assisting the implementation ELC. In this study, a multi-model approach is proposed for the early warning of illegal development by integrating cellular automata (CA) and artificial neural networks (ANN). The objective is to prevent the ecological risks or catastrophe caused by such development at an early stage. The integrated model is calibrated by using the empirical information from both remote sensing and handheld GPS (global positioning systems). The MAR indicator which is the ratio of missing alarms to all the warnings is proposed for better assessment of the model performance. It is found that the fast urban development has caused significant threats to natural-area protection in the study area. The integration of CA, ANN and GPS provides a powerful tool for describing and predicting illegal development which is in highly non-linear and fragmented forms. The comparison shows that this multi-model approach has much better performances than the single-model approach for the early warning. Compared with the single models of CA and ANN, this integrated multi-model can improve the value of MAR by 65.48% and 5.17% respectively.

  11. Adiponectin fine-tuning of liver regeneration dynamics revealed through cellular network modeling.

    PubMed

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

    2014-11-10

    Following partial hepatectomy, the liver initiates a regenerative program involving hepatocyte priming and replication driven by coordinated cytokine and growth factor actions. 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 IL-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. This article is protected by copyright. All rights reserved.

  12. 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.

  13. 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.

  14. Interaction of cellular and network mechanisms for efficient pheromone coding in moths

    PubMed Central

    Belmabrouk, Hana; Nowotny, Thomas; Rospars, Jean-Pierre; Martinez, Dominique

    2011-01-01

    Sensory systems, both in the living and in machines, have to be optimized with respect to their environmental conditions. The pheromone subsystem of the olfactory system of moths is a particularly well-defined example in which rapid variations of odor content in turbulent plumes require fast, concentration-invariant neural representations. It is not clear how cellular and network mechanisms in the moth antennal lobe contribute to coding efficiency. Using computational modeling, we show that intrinsic potassium currents (IA and ISK) in projection neurons may combine with extrinsic inhibition from local interneurons to implement a dual latency code for both pheromone identity and intensity. The mean latency reflects stimulus intensity, whereas latency differences carry concentration-invariant information about stimulus identity. In accordance with physiological results, the projection neurons exhibit a multiphasic response of inhibition–excitation–inhibition. Together with synaptic inhibition, intrinsic currents IA and ISK account for the first and second inhibitory phases and contribute to a rapid encoding of pheromone information. The first inhibition plays the role of a reset to limit variability in the time to first spike. The second inhibition prevents responses of excessive duration to allow tracking of intermittent stimuli. PMID:22109556

  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. 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

  17. 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

  18. Impedance Matching Network for High Frequency Ultrasonic Transducer for Cellular Applications

    PubMed Central

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

    2015-01-01

    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 2.6 mm (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

  19. 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.

  20. Assessment of General Public Exposure to LTE signals compared to other Cellular Networks Present in Thessaloniki, Greece.

    PubMed

    Gkonis, Fotios; Boursianis, Achilles; Samaras, Theodoros

    2016-12-15

    To assess general public exposure to electromagnetic fields from Long Term Evolution (LTE) base stations, measurements at 10 sites in Thessaloniki, Greece were performed. Results are compared with other mobile cellular networks currently in use. All exposure values satisfy the guidelines for general public exposure of the International Commission on Non-Ionizing Radiation Protection (ICNIRP), as well as the reference levels by the Greek legislation at all sites. LTE electric field measurements were recorded up to 0.645 V/m. By applying the ICNIRP guidelines, the exposure ratio for all LTE signals is between 2.9 × 10(-5) and 2.8 × 10(-2) From the measurements results it is concluded that the average and maximum power density contribution of LTE downlink signals to the overall cellular networks signals are 7.8% and 36.7%, respectively.

  1. 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.

  2. 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.

  3. 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

  4. 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.

  5. AID and Apobec3G haphazard deamination and mutational diversity

    PubMed Central

    Jaszczur, Malgorzata; Bertram, Jeffrey G.; Pham, Phuong; Scharff, Matthew D.

    2012-01-01

    Activation-induced deoxycytidine deaminase (AID) and Apobec 3G (Apo3G) cause mutational diversity by initiating mutations on regions of single-stranded (ss) DNA. Expressed in B cells, AID deaminates C → U in actively transcribed immunoglobulin (Ig) variable and switch regions to initiate the somatic hypermutation (SHM) and class switch recombination (CSR) that are essential for antibody diversity. Apo3G expressed in T cells catalyzes C deaminations on reverse transcribed cDNA causing HIV-1 retroviral inactivation. When operating properly, AID- and Apo3G-initiated mutations boost human fitness. Yet, both enzymes are potentially powerful somatic cell “mutators”. Loss of regulated expression and proper genome targeting can cause human cancer. Here, we review well-established biological roles of AID and Apo3G. We provide a synopsis of AID partnering proteins during SHM and CSR, and describe how an Apo2 crystal structure provides “surrogate” insight for AID and Apo3G biochemical behavior. However, large gaps remain in our understanding of how dC deaminases search ssDNA to identify trinucleotide motifs to deaminate. We discuss two recent methods to analyze ssDNA scanning and deamination. Apo3G scanning and deamination is visualized in real-time using single-molecule FRET, and AID deamination efficiencies are determined with a random walk analysis. AID and Apo3G encounter many candidate deamination sites while scanning ssDNA. Generating mutational diversity is a principal aim of AID and an important ancillary property of Apo3G. Success seems likely to involve hit and miss deamination motif targeting, biased strongly toward miss. PMID:23178850

  6. 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.

  7. Systematic reverse engineering of network topologies: a case study of resettable bistable cellular responses.

    PubMed

    Mondal, Debasish; Dougherty, Edward; Mukhopadhyay, Abhishek; Carbo, Adria; Yao, Guang; Xing, Jianhua

    2014-01-01

    A focused theme in systems biology is to uncover design principles of biological networks, that is, how specific network structures yield specific systems properties. For this purpose, we have previously developed a reverse engineering procedure to identify network topologies with high likelihood in generating desired systems properties. Our method searches the continuous parameter space of an assembly of network topologies, without enumerating individual network topologies separately as traditionally done in other reverse engineering procedures. Here we tested this CPSS (continuous parameter space search) method on a previously studied problem: the resettable bistability of an Rb-E2F gene network in regulating the quiescence-to-proliferation transition of mammalian cells. From a simplified Rb-E2F gene network, we identified network topologies responsible for generating resettable bistability. The CPSS-identified topologies are consistent with those reported in the previous study based on individual topology search (ITS), demonstrating the effectiveness of the CPSS approach. Since the CPSS and ITS searches are based on different mathematical formulations and different algorithms, the consistency of the results also helps cross-validate both approaches. A unique advantage of the CPSS approach lies in its applicability to biological networks with large numbers of nodes. To aid the application of the CPSS approach to the study of other biological systems, we have developed a computer package that is available in Information S1.

  8. 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.

  9. 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

  10. 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

  11. A novel spatter detection algorithm based on typical cellular neural network operations for laser beam welding processes

    NASA Astrophysics Data System (ADS)

    Nicolosi, L.; Abt, F.; Blug, A.; Heider, A.; Tetzlaff, R.; Höfler, H.

    2012-01-01

    Real-time monitoring of laser beam welding (LBW) has increasingly gained importance in several manufacturing processes ranging from automobile production to precision mechanics. In the latter, a novel algorithm for the real-time detection of spatters was implemented in a camera based on cellular neural networks. The latter can be connected to the optics of commercially available laser machines leading to real-time monitoring of LBW processes at rates up to 15 kHz. Such high monitoring rates allow the integration of other image evaluation tasks such as the detection of the full penetration hole for real-time control of process parameters.

  12. 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.

  13. EIF3G is associated with narcolepsy across ethnicities

    PubMed Central

    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

    2015-01-01

    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

  14. Impact of Network Structure and Cellular Response on Spike Time Correlations

    PubMed Central

    Trousdale, James; Hu, Yu; Shea-Brown, Eric; Josić, Krešimir

    2012-01-01

    Novel experimental techniques reveal the simultaneous activity of larger and larger numbers of neurons. As a result there is increasing interest in the structure of cooperative – or correlated – activity in neural populations, and in the possible impact of such correlations on the neural code. A fundamental theoretical challenge is to understand how the architecture of network connectivity along with the dynamical properties of single cells shape the magnitude and timescale of correlations. We provide a general approach to this problem by extending prior techniques based on linear response theory. We consider networks of general integrate-and-fire cells with arbitrary architecture, and provide explicit expressions for the approximate cross-correlation between constituent cells. These correlations depend strongly on the operating point (input mean and variance) of the neurons, even when connectivity is fixed. Moreover, the approximations admit an expansion in powers of the matrices that describe the network architecture. This expansion can be readily interpreted in terms of paths between different cells. We apply our results to large excitatory-inhibitory networks, and demonstrate first how precise balance – or lack thereof – between the strengths and timescales of excitatory and inhibitory synapses is reflected in the overall correlation structure of the network. We then derive explicit expressions for the average correlation structure in randomly connected networks. These expressions help to identify the important factors that shape coordinated neural activity in such networks. PMID:22457608

  15. A double herd krill based algorithm for location area optimization in mobile wireless cellular network.

    PubMed

    Vincylloyd, F; Anand, B

    2015-01-01

    In wireless communication systems, mobility tracking deals with determining a mobile subscriber (MS) covering the area serviced by the wireless network. Tracking a mobile subscriber is governed by the two fundamental components called location updating (LU) and paging. This paper presents a novel hybrid method using a krill herd algorithm designed to optimize the location area (LA) within available spectrum such that total network cost, comprising location update (LU) cost and cost for paging, is minimized without compromise. Based on various mobility patterns of users and network architecture, the design of the LR area is formulated as a combinatorial optimization problem. Numerical results indicate that the proposed model provides a more accurate update boundary in real environment than that derived from a hexagonal cell configuration with a random walk movement pattern. The proposed model allows the network to maintain a better balance between the processing incurred due to location update and the radio bandwidth utilized for paging between call arrivals.

  16. 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.

  17. Discrimination of liver cancer in cellular level based on backscatter micro-spectrum with PCA algorithm and BP neural network

    NASA Astrophysics Data System (ADS)

    Yang, Jing; Wang, Cheng; Cai, Gan; Dong, Xiaona

    2016-10-01

    The incidence and mortality rate of the primary liver cancer are very high and its postoperative metastasis and recurrence have become important factors to the prognosis of patients. Circulating tumor cells (CTC), as a new tumor marker, play important roles in the early diagnosis and individualized treatment. This paper presents an effective method to distinguish liver cancer based on the cellular scattering spectrum, which is a non-fluorescence technique based on the fiber confocal microscopic spectrometer. Combining the principal component analysis (PCA) with back propagation (BP) neural network were utilized to establish an automatic recognition model for backscatter spectrum of the liver cancer cells from blood cell. PCA was applied to reduce the dimension of the scattering spectral data which obtained by the fiber confocal microscopic spectrometer. After dimensionality reduction by PCA, a neural network pattern recognition model with 2 input layer nodes, 11 hidden layer nodes, 3 output nodes was established. We trained the network with 66 samples and also tested it. Results showed that the recognition rate of the three types of cells is more than 90%, the relative standard deviation is only 2.36%. The experimental results showed that the fiber confocal microscopic spectrometer combining with the algorithm of PCA and BP neural network can automatically identify the liver cancer cell from the blood cells. This will provide a better tool for investigating the metastasis of liver cancers in vivo, the biology metabolic characteristics of liver cancers and drug transportation. Additionally, it is obviously referential in practical application.

  18. 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.

  19. 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.

  20. Coverage extension and balancing the transmitted power of the moving relay node at LTE-A cellular network.

    PubMed

    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.

  1. Design, Surface Treatment, Cellular Plating, and Culturing of Modular Neuronal Networks Composed of Functionally Inter-connected Circuits.

    PubMed

    Kanner, Sivan; Bisio, Marta; Cohen, Gilad; Goldin, Miri; Tedesco, Marieteresa; Hanein, Yael; Ben-Jacob, Eshel; Barzilai, Ari; Chiappalone, Michela; Bonifazi, Paolo

    2015-04-15

    The brain operates through the coordinated activation and the dynamic communication of neuronal assemblies. A major open question is how a vast repertoire of dynamical motifs, which underlie most diverse brain functions, can emerge out of a fixed topological and modular organization of brain circuits. Compared to in vivo studies of neuronal circuits which present intrinsic experimental difficulties, in vitro preparations offer a much larger possibility to manipulate and probe the structural, dynamical and chemical properties of experimental neuronal systems. This work describes an in vitro experimental methodology which allows growing of modular networks composed by spatially distinct, functionally interconnected neuronal assemblies. The protocol allows controlling the two-dimensional (2D) architecture of the neuronal network at different levels of topological complexity. A desired network patterning can be achieved both on regular cover slips and substrate embedded micro electrode arrays. Micromachined structures are embossed on a silicon wafer and used to create biocompatible polymeric stencils, which incorporate the negative features of the desired network architecture. The stencils are placed on the culturing substrates during the surface coating procedure with a molecular layer for promoting cellular adhesion. After removal of the stencils, neurons are plated and they spontaneously redirected to the coated areas. By decreasing the inter-compartment distance, it is possible to obtain either isolated or interconnected neuronal circuits. To promote cell survival, cells are co-cultured with a supporting neuronal network which is located at the periphery of the culture dish. Electrophysiological and optical recordings of the activity of modular networks obtained respectively by using substrate embedded micro electrode arrays and calcium imaging are presented. While each module shows spontaneous global synchronizations, the occurrence of inter-module synchronization

  2. 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.

  3. 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.

  4. Cellular and network-level adaptations to in utero methadone exposure along the ventral respiratory column in the neonate rat.

    PubMed

    Gourévitch, Boris; Cai, Jun; Mellen, Nicholas

    2016-03-20

    Neonatal abstinence syndrome (NAS) occurs in babies chronically exposed to opioids during pregnancy. NAS shares features with opioid withdrawal symptoms seen in adults, including autonomic dysregulation. Here, the effect of low-dose in utero methadone (MTD) exposure on respiration-modulated networks along the ventral respiratory column (VRC) in ventrolateral medulla was investigated in the neonate Sprague-Dawley rat. MTD was administered via drinking water (3mg/kg/day in drinking water of the mother E7-E21). Lower expression levels of myelin-associated proteins phosphorylated axonal neurofilament subunit H (pNFH), 2',3'-Cyclicnucleotide 3'-phosphodiesterase (CNPase) and myelin basic protein (MBP), in MTD-exposed pups compared to controls at P3, P6 and P10 indicated MTD transport across the placenta. We investigated whether in utero MTD exposure led to network-level excitability changes consistent with tolerance, and also probed for changes in endogenous opioid modulation of respiratory networks. To this end, high-speed (45.5Hz) optical recordings of respiratory network activity in control and MTD-exposed neonate (P0-P2) pups before and during administration of the μ-opioid receptor antagonist naloxone (NAL; 10μM) were carried out. Spike rate was estimated from optical traces via deconvolution, and coupling between all neuron pairs in recorded networks was quantified using the normalized transfer entropy (NTE). Recordings of local networks along the VRC, together with recordings of respiratory output from ventral root C1 did not reveal changes in respiratory activity at the system level, but cellular and network changes in MTD-exposed pups were consistent with the development of opioid tolerance. MTD-exposed pups were found to have i. higher neuronal firing rates; ii. higher covariance between neuronal activity and motor output; iii. more bidirectionally and unidirectionally coupled neurons, and fewer uncoupled neurons; iv. stronger coupling and shorter

  5. Reconstruction of cellular signal transduction networks using perturbation assays and linear programming.

    PubMed

    Knapp, Bettina; Kaderali, Lars

    2013-01-01

    Perturbation experiments for example using RNA interference (RNAi) offer an attractive way to elucidate gene function in a high throughput fashion. The placement of hit genes in their functional context and the inference of underlying networks from such data, however, are challenging tasks. One of the problems in network inference is the exponential number of possible network topologies for a given number of genes. Here, we introduce a novel mathematical approach to address this question. We formulate network inference as a linear optimization problem, which can be solved efficiently even for large-scale systems. We use simulated data to evaluate our approach, and show improved performance in particular on larger networks over state-of-the art methods. We achieve increased sensitivity and specificity, as well as a significant reduction in computing time. Furthermore, we show superior performance on noisy data. We then apply our approach to study the intracellular signaling of human primary nave CD4(+) T-cells, as well as ErbB signaling in trastuzumab resistant breast cancer cells. In both cases, our approach recovers known interactions and points to additional relevant processes. In ErbB signaling, our results predict an important role of negative and positive feedback in controlling the cell cycle progression.

  6. 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.

  7. 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

  8. 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.

  9. 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

  10. 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.

  11. Cell Edge Capacity Improvement by Using Adaptive Base Station Cooperation in Cellular Networks with Fractional Frequency Reuse

    NASA Astrophysics Data System (ADS)

    Xu, Liang; Yamamoto, Koji; Murata, Hidekazu; Yoshida, Susumu

    The present paper focuses on the application of the base station cooperation (BSC) technique in fractional frequency reuse (FFR) networks. Fractional frequency reuse is considered to be a promising scheme for avoiding the inter-cell interference problem in OFDMA cellular systems, such as WiMAX, in which the edge mobile stations (MSs) of adjacent cells use different subchannels for separate transmission. However, the problem of FFR is that the cell edge spectral efficiency (SE) is much lower than that of the cell center. The BSC technique, in which adjacent BSs perform cooperative transmission for one cell edge MS with the same channel, may improve the cell edge SE. However, since more BSs transmit signals for one cell edge MS, the use of BSC can also increase the inter-cell interference, which might degrade the network performance. In this paper, with a focus on this tradeoff, we propose an adaptive BSC scheme in which BSC is only performed for the cell edge MSs that can achieve a significant capacity increase with only a slight increase in inter-cell interference. Moreover, a channel reallocation scheme is proposed in order to further improve the performance of the adaptive BSC scheme. The simulation results reveal that, compared to the conventional FFR scheme, the proposed schemes are effective for improving the performance of FFR networks.

  12. The potential of cellular technology to mediate social networks for support of chronic disease self-management.

    PubMed

    Roblin, Douglas W

    2011-01-01

    Productive interactions among patients, friends/family, and health care providers, as outlined by the Chronic Care Model, are important for promoting adherence to recommended care and good health outcomes among adults with a chronic illness. Characteristics of these interactions--active participation, collaboration, and data sharing among constituents--are the same as those of social networks organized around Web 2.0 principles and technology. Thus, the Web 2.0 framework can be used to configure social networks without the inherent spatiotemporal constraints of face-to-face interactions that remain prevalent in health care delivery. In this article, the author outlines various design principles and decisions for a pilot study in which cellular technology was used to mediate interactions between adults with Type 2 diabetes and supporters (i.e., family members or friends selected by the patients who agree provide support) to motivate regular self-monitoring of blood glucose (among the diabetes participants). Participants generally found the network to be relatively easy to use. Some diabetes patients reported improved attention to self-monitoring; and, patient-selected supporters indicated improvements in emotional and instrumental support that should benefit diabetes patients' lifestyle and health.

  13. Inhibition of LINE-1 and Alu retrotransposition by exosomes encapsidating APOBEC3G and APOBEC3F.

    PubMed

    Khatua, Atanu K; Taylor, Harry E; Hildreth, James E K; Popik, Waldemar

    2010-04-25

    Human cytidine deaminases, including APOBEC3G (A3G) and A3F, are part of a cellular defense system against retroviruses and retroelements including non-LTR retrotransposons LINE-1 (L1) and Alu. Expression of cellular A3 proteins is sufficient for inhibition of L1 and Alu retrotransposition, but the effect of A3 proteins transferred in exosomes on retroelement mobilization is unknown. Here, we demonstrate for the first time that exosomes secreted by CD4(+)H9 T cells and mature monocyte-derived dendritic cells encapsidate A3G and A3F and inhibit L1 and Alu retrotransposition. A3G is the major contributor to the inhibitory activity of exosomes, however, the contribution of A3F in H9 exosomes cannot be excluded. Additionally, we show that exosomes encapsidate mRNAs coding for A3 proteins. A3G mRNA, and less so A3F, was enriched in exosomes secreted by H9 cells. Exosomal A3G mRNA was functional in vitro. Whether exosomes inhibit retrotransposons in vivo requires further investigation.

  14. 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

  15. Hierarchical random cellular neural networks for system-level brain-like signal processing.

    PubMed

    Kozma, Robert; Puljic, Marko

    2013-09-01

    Sensory information processing and cognition in brains are modeled using dynamic systems theory. The brain's dynamic state is described by a trajectory evolving in a high-dimensional state space. We introduce a hierarchy of random cellular automata as the mathematical tools to describe the spatio-temporal dynamics of the cortex. The corresponding brain model is called neuropercolation which has distinct advantages compared to traditional models using differential equations, especially in describing spatio-temporal discontinuities in the form of phase transitions. Phase transitions demarcate singularities in brain operations at critical conditions, which are viewed as hallmarks of higher cognition and awareness experience. The introduced Monte-Carlo simulations obtained by parallel computing point to the importance of computer implementations using very large-scale integration (VLSI) and analog platforms.

  16. An asymmetric image cryptosystem based on the adaptive synchronization of an uncertain unified chaotic system and a cellular neural network

    NASA Astrophysics Data System (ADS)

    Cheng, Chao-Jung; Cheng, Chi-Bin

    2013-10-01

    Chaotic dynamics provide a fast and simple means to create an excellent image cryptosystem, because it is extremely sensitive to initial conditions and system parameters, pseudorandomness, and non-periodicity. However, most chaos-based image encryption schemes are symmetric cryptographic techniques, which have been proven to be more vulnerable, compared to an asymmetric cryptosystem. This paper develops an asymmetric image cryptosystem, based on the adaptive synchronization of two different chaotic systems, namely a unified chaotic system and a cellular neural network. An adaptive controller with parameter update laws is formulated, using the Lyapunov stability theory, to asymptotically synchronize the two chaotic systems. The synchronization controller is embedded in the image cryptosystem and generates a pair of asymmetric keys, for image encryption and decryption. Using numerical simulations, three sets of experiments are conducted to evaluate the feasibility and reliability of the proposed chaos-based image cryptosystem.

  17. An Integrative Model of the Cardiovascular System Coupling Heart Cellular Mechanics with Arterial Network Hemodynamics

    PubMed Central

    Kim, Young-Tae; Lee, Jeong Sang; Youn, Chan-Hyun; Choi, Jae-Sung

    2013-01-01

    The current study proposes a model of the cardiovascular system that couples heart cell mechanics with arterial hemodynamics to examine the physiological role of arterial blood pressure (BP) in left ventricular hypertrophy (LVH). We developed a comprehensive multiphysics and multiscale cardiovascular model of the cardiovascular system that simulates physiological events, from membrane excitation and the contraction of a cardiac cell to heart mechanics and arterial blood hemodynamics. Using this model, we delineated the relationship between arterial BP or pulse wave velocity and LVH. Computed results were compared with existing clinical and experimental observations. To investigate the relationship between arterial hemodynamics and LVH, we performed a parametric study based on arterial wall stiffness, which was obtained in the model. Peak cellular stress of the left ventricle and systolic blood pressure (SBP) in the brachial and central arteries also increased; however, further increases were limited for higher arterial stiffness values. Interestingly, when we doubled the value of arterial stiffness from the baseline value, the percentage increase of SBP in the central artery was about 6.7% whereas that of the brachial artery was about 3.4%. It is suggested that SBP in the central artery is more critical for predicting LVH as compared with other blood pressure measurements. PMID:23960442

  18. Translational regulation of APOBEC3G mRNA by Vif requires its 5'UTR and contributes to restoring HIV-1 infectivity.

    PubMed

    Guerrero, Santiago; Libre, Camille; Batisse, Julien; Mercenne, Gaëlle; Richer, Delphine; Laumond, Géraldine; Decoville, Thomas; Moog, Christiane; Marquet, Roland; Paillart, Jean-Christophe

    2016-12-20

    The essential HIV-1 viral infectivity factor (Vif) allows productive infection of non-permissive cells expressing cytidine deaminases APOBEC3G (A3G) and A3F by decreasing their cellular level, and preventing their incorporation into virions. Unlike the Vif-induced degradation of A3G, the functional role of the inhibition of A3G translation by Vif remained unclear. Here, we show that two stem-loop structures within the 5'-untranslated region of A3G mRNA are crucial for translation inhibition by Vif in cells, and most Vif alleles neutralize A3G translation efficiently. Interestingly, K26R mutation in Vif abolishes degradation of A3G by the proteasome but has no effect at the translational level, indicating these two pathways are independent. These two mechanisms, proteasomal degradation and translational inhibition, similarly contribute to decrease the cellular level of A3G by Vif and to prevent its incorporation into virions. Importantly, inhibition of A3G translation is sufficient to partially restore viral infectivity in the absence of proteosomal degradation. These findings demonstrate that HIV-1 has evolved redundant mechanisms to specifically inhibit the potent antiviral activity of A3G.

  19. Translational regulation of APOBEC3G mRNA by Vif requires its 5′UTR and contributes to restoring HIV-1 infectivity

    PubMed Central

    Guerrero, Santiago; Libre, Camille; Batisse, Julien; Mercenne, Gaëlle; Richer, Delphine; Laumond, Géraldine; Decoville, Thomas; Moog, Christiane; Marquet, Roland; Paillart, Jean-Christophe

    2016-01-01

    The essential HIV-1 viral infectivity factor (Vif) allows productive infection of non-permissive cells expressing cytidine deaminases APOBEC3G (A3G) and A3F by decreasing their cellular level, and preventing their incorporation into virions. Unlike the Vif-induced degradation of A3G, the functional role of the inhibition of A3G translation by Vif remained unclear. Here, we show that two stem-loop structures within the 5′-untranslated region of A3G mRNA are crucial for translation inhibition by Vif in cells, and most Vif alleles neutralize A3G translation efficiently. Interestingly, K26R mutation in Vif abolishes degradation of A3G by the proteasome but has no effect at the translational level, indicating these two pathways are independent. These two mechanisms, proteasomal degradation and translational inhibition, similarly contribute to decrease the cellular level of A3G by Vif and to prevent its incorporation into virions. Importantly, inhibition of A3G translation is sufficient to partially restore viral infectivity in the absence of proteosomal degradation. These findings demonstrate that HIV-1 has evolved redundant mechanisms to specifically inhibit the potent antiviral activity of A3G. PMID:27996044

  20. Cellular and neurochemical basis of sleep stages in the thalamocortical network.

    PubMed

    Krishnan, Giri P; Chauvette, Sylvain; Shamie, Isaac; Soltani, Sara; Timofeev, Igor; Cash, Sydney S; Halgren, Eric; Bazhenov, Maxim

    2016-11-16

    The link between the combined action of neuromodulators in the brain and global brain states remains a mystery. In this study, using biophysically realistic models of the thalamocortical network, we identified the critical intrinsic and synaptic mechanisms, associated with the putative action of acetylcholine (ACh), GABA and monoamines, which lead to transitions between primary brain vigilance states (waking, non-rapid eye movement sleep [NREM] and REM sleep) within an ultradian cycle. Using ECoG recordings from humans and LFP recordings from cats and mice, we found that during NREM sleep the power of spindle and delta oscillations is negatively correlated in humans and positively correlated in animal recordings. We explained this discrepancy by the differences in the relative level of ACh. Overall, our study revealed the critical intrinsic and synaptic mechanisms through which different neuromodulators acting in combination result in characteristic brain EEG rhythms and transitions between sleep stages.

  1. Transcriptional regulatory networks in cellular responses and tolerance to dehydration and cold stresses.

    PubMed

    Yamaguchi-Shinozaki, Kazuko; Shinozaki, Kazuo

    2006-01-01

    Plant growth and productivity are greatly affected by environmental stresses such as drought, high salinity, and low temperature. Expression of a variety of genes is induced by these stresses in various plants. The products of these genes function not only in stress tolerance but also in stress response. In the signal transduction network from perception of stress signals to stress-responsive gene expression, various transcription factors and cis-acting elements in the stress-responsive promoters function for plant adaptation to environmental stresses. Recent progress has been made in analyzing the complex cascades of gene expression in drought and cold stress responses, especially in identifying specificity and cross talk in stress signaling. In this review article, we highlight transcriptional regulation of gene expression in response to drought and cold stresses, with particular emphasis on the role of transcription factors and cis-acting elements in stress-inducible promoters.

  2. Multimode fibers in millimeter-wave evolution for 5G cellular networks

    NASA Astrophysics Data System (ADS)

    Vázquez, C.; Montero, D. S.; Ponce, W.; Lallana, P. C.; Larrabeiti, D.; Montalvo, J.; Tapetado, A.; Pinzón, P. J.

    2016-02-01

    Small-cell and cloud-RAN systems along with the use of the millimeter-wave band have been considered as promising solutions to meet the capacity demand of the future wireless access networks. Radio over Multimode fibers (RoMMF) can play a role in the integrated optical-wireless access systems for next-generation wireless communications, mainly in within-building environments. The numerical results show the effectiveness of MMF to transmit at 60 GHz band with 7- GHz bandwidth for different link lengths and refractive index profiles under restricted mode launching and using narrow linewidth sources. The integration with optically powered remote antenna units is also proposed based on the large core effective area of MMF. Temperature impairments and graded index plastic optical fiber transmission are also discussed.

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

    PubMed

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

    2015-01-01

    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 and their localized patterning leading to remarkably different cell types aggregated into variably sized parts of the central nervous system have begun to emerge. Insights at the cellular and molecular level have begun 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, which were 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.

  4. 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

  5. Connecting Land-Based Networks to Ships

    DTIC Science & Technology

    2012-09-01

    Broadband Global Area Network ( BGAN ) ....................43 5. Client and Server Laptops...43 Figure 24. Hughes 9450 BGAN Mobile Satellite Terminal...Figure 33. 2G/3G cellular connection speed test result on land ........................................67 Figure 34. Hughes 9450 INMARSAT BGAN

  6. Mapping the cellular network of the circadian clock in two cockroach species.

    PubMed

    Wen, Chih-Jen; Lee, How-Jing

    2008-08-01

    The German cockroach, Blattella germanica, and the double-striped cockroach, B. bisignata, are sibling species with a similar period sequence but a distinctive circadian rhythm in locomotion. The cell distribution of immunoreactivity (ir) against three clock-related proteins, Period (PER), Pigment Dispersing Factor (PDF), and Corazonin (CRZ), was compared between the species. The PER-ir cells tend to form clusters and are sprayed out in the central nervous system. Three major PER-ir cells are located in the optic lobes, which are the sites of the major circadian clock. They are interconnected with PER-ir axon bundles. Interestingly, the potential output signal of the circadian clock, PDF, is co-localized with PER in all three groups of cells. However, only two CRZ-ir cells and their axons are found in the optic lobes and they are not co-localized with PER-ir or PDF-ir cells and axons. Since only one circadian rhythm is expressed in locomotion, the time signals from both major clocks in optic lobes are coupled by connection with PDF-ir axons. A group of 3-4 PER-ir cells in the protocerebrum display typical characteristics of neurosecretary cells. In addition, there are numerous, small PER-ir and PDF-ir co-localized cells in the pars intercerebralis (PI), which have direct connections with the neurohemoorgan, corpora cardiaca, through PER-ir and PDF-ir axons. Based on these findings, the cellular connection shows a circadian control through the endocrine route. For the rest of central nervous system, only a few PER-ir and PDF-ir cells or axons are detected. This finding implies the circadian clock for locomotion is not located in subesophageal ganglion, thoracic or abdominal ganglia, but may use other neural messengers to pass on circadian signals. Since the overall distribution pattern of the clock cells are the same for B. germanica and B. bisignata, the possible explanation for the different expressions of locomotion between the species depends on genes downstream

  7. 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.

  8. 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

  9. Mapping global sensitivity of cellular network dynamics: sensitivity heat maps and a global summation law.

    PubMed

    Rand, D A

    2008-08-06

    The dynamical systems arising from gene regulatory, signalling and metabolic networks are strongly nonlinear, have high-dimensional state spaces and depend on large numbers of parameters. Understanding the relation between the structure and the function for such systems is a considerable challenge. We need tools to identify key points of regulation, illuminate such issues as robustness and control and aid in the design of experiments. Here, I tackle this by developing new techniques for sensitivity analysis. In particular, I show how to globally analyse the sensitivity of a complex system by means of two new graphical objects: the sensitivity heat map and the parameter sensitivity spectrum. The approach to sensitivity analysis is global in the sense that it studies the variation in the whole of the model's solution rather than focusing on output variables one at a time, as in classical sensitivity analysis. This viewpoint relies on the discovery of local geometric rigidity for such systems, the mathematical insight that makes a practicable approach to such problems feasible for highly complex systems. In addition, we demonstrate a new summation theorem that substantially generalizes previous results for oscillatory and other dynamical phenomena. This theorem can be interpreted as a mathematical law stating the need for a balance between fragility and robustness in such systems.

  10. Cellular and neurochemical basis of sleep stages in the thalamocortical network

    PubMed Central

    Krishnan, Giri P; Chauvette, Sylvain; Shamie, Isaac; Soltani, Sara; Timofeev, Igor; Cash, Sydney S; Halgren, Eric; Bazhenov, Maxim

    2016-01-01

    The link between the combined action of neuromodulators in the brain and global brain states remains a mystery. In this study, using biophysically realistic models of the thalamocortical network, we identified the critical intrinsic and synaptic mechanisms, associated with the putative action of acetylcholine (ACh), GABA and monoamines, which lead to transitions between primary brain vigilance states (waking, non-rapid eye movement sleep [NREM] and REM sleep) within an ultradian cycle. Using ECoG recordings from humans and LFP recordings from cats and mice, we found that during NREM sleep the power of spindle and delta oscillations is negatively correlated in humans and positively correlated in animal recordings. We explained this discrepancy by the differences in the relative level of ACh. Overall, our study revealed the critical intrinsic and synaptic mechanisms through which different neuromodulators acting in combination result in characteristic brain EEG rhythms and transitions between sleep stages. DOI: http://dx.doi.org/10.7554/eLife.18607.001 PMID:27849520

  11. 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.

  12. Uplink performance investigations of the service area based beyond 3G system JOINT

    NASA Astrophysics Data System (ADS)

    Liu, Y.; Weber, T.; Zirwas, W.

    2005-05-01

    The joint transmission and detection integrated network (JOINT) is a novel OFDM-based vNP00 air interface solution for beyond 3G (B3G) mobile radio communications systems WMSL02. JOINT aims at eliminating the multiple access interference (MAI) and improving the system capacity by the application of MIMO techniques applied in the service area (SA) based system architecture. In a SA based structure the intra-SA multiple access interference (MAI) can be easily combated by algorithms like, e.g., joint detection (JD) Kle96,Ver98 in the uplink. The parameters like, e.g., the SA size, the system load and reuse factor show great impacts on the system performances, in terms of the average bit error rate (BER) and the BER statistics. Spectrum efficiency of JOINT is also investigated based on the simulation results.

  13. APOBEC3G-Mediated G-to-A Hypermutation of the HIV-1 Genome: The Missing Link in Antiviral Molecular Mechanisms

    PubMed Central

    Okada, Ayaka; Iwatani, Yasumasa

    2016-01-01

    APOBEC3G (A3G) is a member of the cellular polynucleotide cytidine deaminases, which catalyze the deamination of cytosine (dC) to uracil (dU) in single-stranded DNA. These enzymes potently inhibit the replication of a variety of retroviruses and retrotransposons, including HIV-1. A3G is incorporated into vif-deficient HIV-1 virions and targets viral reverse transcripts, particularly minus-stranded DNA products, in newly infected cells. It is well established that the enzymatic activity of A3G is closely correlated with the potential to greatly inhibit HIV-1 replication in the absence of Vif. However, the details of the underlying molecular mechanisms are not fully understood. One potential mechanism of A3G antiviral activity is that the A3G-dependent deamination may trigger degradation of the dU-containing reverse transcripts by cellular uracil DNA glycosylases (UDGs). More recently, another mechanism has been suggested, in which the virion-incorporated A3G generates lethal levels of the G-to-A hypermutation in the viral DNA genome, thus potentially driving the viruses into “error catastrophe” mode. In this mini review article, we summarize the deaminase-dependent and deaminase-independent molecular mechanisms of A3G and discuss how A3G-mediated deamination is linked to antiviral mechanisms. PMID:28066353

  14. 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

    2015-09-04

    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.

  15. 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.

  16. 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.

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

    PubMed

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

    2016-02-23

    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.

  18. A wireless video monitoring system based on 3G communication technology

    NASA Astrophysics Data System (ADS)

    Xia, Zhen-Hua; Wang, Xiao-Shuang

    2011-11-01

    With the rapid development of the electronic technology, multimedia technology and mobile communication technology, video monitoring system is going to the embedded, digital and wireless direction. In this paper, a solution of wireless video monitoring system based on WCDMA is proposed. This solution makes full use of the advantages of 3G, which have Extensive coverage network and wide bandwidth. It can capture the video streaming from the chip's video port, real-time encode the image data by the high speed DSP, and have enough bandwidth to transmit the monitoring image through WCDMA wireless network. The experiments demonstrate that the system has the advantages of high stability, good image quality, good transmission performance, and in addition, the system has been widely used, not be restricted by geographical position since it adopts wireless transmission. So, it is suitable used in sparsely populated, harsh environment scenario.

  19. 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.

  20. Two and a half years of country-wide rainfall maps using radio links from commercial cellular telecommunication networks

    NASA Astrophysics Data System (ADS)

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

    2016-10-01

    Although rainfall estimation employing microwave links from cellular telecommunication networks is recognized as a new promising measurement technique, its potential for long-term large-scale operational rainfall monitoring remains to be demonstrated. This study contributes to this endeavor by deriving a continuous series of rainfall maps from a large 2.5 year microwave link data set of, on average, 3383 links (2044 link paths) covering Netherlands (˜3.5 × 104 km2), a midlatitude country (˜5°E, ˜52°N) with a temperate climate. Maps are extensively verified against an independent gauge-adjusted radar rainfall data set for different temporal (15 min, 1 h, 1 day, 1 month) and spatial (0.9, 74 km2) scales. The usefulness of different steps in the rainfall retrieval algorithm, i.e., a wet-dry classification method and a filter to remove outliers, is systematically assessed. A novel dew filter is developed to correct for dew-induced wet antenna attenuation, which, although a relative underestimation of 6% to 9% is found, generally yields good results. The microwave link rainfall estimation technique performs well for the summer months (June, July, August), even outperforming interpolation of automatic rain gauge data (with a density of ˜1 gauge per 1000 km2), but large deviations are found for the winter months (December, January, February). These deviations are generally expected to be related to frozen or melting precipitation. Hence, our results show the potential of commercial microwave links for long-term large-scale operational rainfall monitoring.

  1. Murine Hyperglycemic Vasculopathy and Cardiomyopathy: Whole-Genome Gene Expression Analysis Predicts Cellular Targets and Regulatory Networks Influenced by Mannose Binding Lectin

    PubMed Central

    Zou, Chenhui; La Bonte, Laura R.; Pavlov, Vasile I.; Stahl, Gregory L.

    2012-01-01

    Hyperglycemia, in the absence of type 1 or 2 diabetes, is an independent risk factor for cardiovascular disease. We have previously demonstrated a central role for mannose binding lectin (MBL)-mediated cardiac dysfunction in acute hyperglycemic mice. In this study, we applied whole-genome microarray data analysis to investigate MBL’s role in systematic gene expression changes. The data predict possible intracellular events taking place in multiple cellular compartments such as enhanced insulin signaling pathway sensitivity, promoted mitochondrial respiratory function, improved cellular energy expenditure and protein quality control, improved cytoskeleton structure, and facilitated intracellular trafficking, all of which may contribute to the organismal health of MBL null mice against acute hyperglycemia. Our data show a tight association between gene expression profile and tissue function which might be a very useful tool in predicting cellular targets and regulatory networks connected with in vivo observations, providing clues for further mechanistic studies. PMID:22375142

  2. Proceedings of International Workshop on Cellular Neural Networks and their Applications (2nd) held in Munich, Germany, October 14 -16, 1992.

    DTIC Science & Technology

    1992-10-16

    Galias, Univ. of Mining and Metallurgy , Krakow, Poland 23 12.10 Template Synthesis of Cellular Neural Networks for Information Coding and Decoding M...Laboratory and Department of Electrical Engineering and Computer Science, University of California at Berkeley, Berkeley CA 94720 and the + Dual and...with continuous Signals Stephan Schwarz and Wolfgang Mathis University of Wuppertal Department of Electrical Engineering Institute for Computer Aided

  3. Existence and stability of pseudo almost periodic solutions for shunting inhibitory cellular neural networks with neutral type delays and time-varying leakage delays.

    PubMed

    Xu, Changjin; Zhang, Qiming; Wu, Yusen

    2014-01-01

    In this paper, shunting inhibitory cellular neural networks(SICNNs) with neutral type delays and time-varying leakage delays are investigated. By applying Lyapunov functional method and differential inequality techniques, a set of sufficient conditions are obtained for the existence and exponential stability of pseudo almost periodic solutions of the model. An example is given to support the theoretical findings. Our results improve and generalize those of the previous studies.

  4. Modelling of Pico Satellite Network Applications to Maritime Interdiction Operations

    DTIC Science & Technology

    2011-06-01

    Orbiting (LEO) satellite links (such as Iridium, GlobalStar), cellular GSM 3G/4G networking to feed a tag’s GPS location (or similar methods in GPS ... denied areas) to a C2 center’s situational awareness systems. Such methods have multiple limitations due to their high dependency on access to the LEO

  5. 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

  6. System-level insights into the cellular interactome of a non-model organism: inferring, modelling and analysing functional gene network of soybean (Glycine max).

    PubMed

    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

  7. Based on 3G and RFID logistic delivery management system application and practice analysis

    NASA Astrophysics Data System (ADS)

    Li, Xiaojun; Peng, Longjun; Zhong, Kaiwen; Huang, Jianming

    2008-10-01

    This article in view of the Logistic Delivery Management characteristic, analysis the logistic delivery management cannot satisfy requests rapid reaction and conformity transportation at present and so on. This article elaborated based on 3G (GIS, GPS, and GPRS) and RFID technology logistic delivery contents and so on management system, system design and architecture design, and its effective integration. The system design mentality uses the systems engineering method, follows the humanist idea, and embarks from user's demand, according to the user demand and the network request, divides according to the laminated structure into the decision-making strata, the service level, the management maintenance level and the technical support level 4 levels. The overall structural design including the system function structural design and the software system design, and take some province logistic delivery management system in management service as an example, introduced the design mentality and the application way.

  8. Nuclear Exclusion of the HIV-1 host defense factor APOBEC3G requires a novel cytoplasmic retention signal and is not dependent on RNA binding.

    PubMed

    Bennett, Ryan P; Presnyak, Vladimir; Wedekind, Joseph E; Smith, Harold C

    2008-03-21

    Human APOBEC3G (hA3G) is a host factor that defends against HIV-1 as well as other exogenous retroviruses and endogenous retroelements. To this end, hA3G is restricted to the cytoplasm of T lymphocytes where it interacts with viral RNA and proteins to assemble with viral particles causing a post-entry block during reverse transcription. hA3G also exhibits a mechanism to inhibit the reverse transcription of retroelements by RNA binding and sequestration into mRNA processing centers in the cytoplasm. We have determined that the molecular basis for this specialized property of hA3G is a novel cytoplasmic retention signal (CRS) that is necessary and sufficient to restrict wild-type hA3G and chimeric constructs to the cytoplasm. The CRS resides within amino acids 113-128 and is embedded within a basic flanking sequence and does not require RNA binding to retain hA3G in the cytoplasm. Paralogs of hA3G that have nuclear or cytoplasmic distributions differ from hA3G within the region encompassing the CRS motif with respect to charge and amino acid composition. We propose that the CRS enables hA3G to interact with cytoplasmic factors, and thereby enables hA3G to serve in host cell defense by restricting an antiviral sentinel to the cytoplasm. The CRS lies in a region involved in both Gag and Vif interactions; therefore, identification of this motif has important implications for the design of therapeutics that target HIV-1 while maintaining antiviral and cellular functions.

  9. DNA Mutagenic Activity and Capacity for HIV-1 Restriction of the Cytidine Deaminase APOBEC3G Depends on Whether DNA or RNA Binds to Tyrosine 315.

    PubMed

    Polevoda, Bogdan; Joseph, Rebecca; Friedman, Alan E; Bennett, Ryan P; Greiner, Rebecca; De Zoysa, Thareendra; Stewart, Ryan A; Smith, Harold C

    2017-04-05

    APOBEC3G (A3G) belongs to the AID/APOBEC protein family of cytidine deaminases (CDA) that bind to nucleic acids. A3G mutates the HIV genome by deamination of dC to dU, leading to accumulation of virus-inactivating mutations. Binding to cellular RNAs inhibits A3G binding to substrate single-stranded (ss) DNA and CDA activity. RNA and ssDNA bind to the same three A3G tryptic peptides (amino acids 181-194, 314-320, and 345-374) that form parts of a continuously exposed protein surface extending from the catalytic domain in the C-terminus of A3G to its N-terminus. We show here that the A3G tyrosines 181 and 315 directly cross-link ssDNA. Binding experiments showed that a Y315A mutation alone significantly reduced A3G binding to both ssDNA and RNA, whereas Y181A and Y182A mutations only moderately affected A3G nucleic acid binding. Consistent with these findings, the Y315A mutant exhibited little to no deaminase activity in an E. coli DNA mutator reporter, while Y181A and Y182A mutants retained ~50% of wild-type A3G activity. The Y315A mutant also showed a markedly reduced ability to assemble into viral particles and had reduced antiviral activity. In uninfected cells, the impaired RNA-binding capacity of Y315A was evident by a shift of A3G from high-molecular-mass ribonucleoprotein complexes to low-molecular-mass complexes. We conclude that Y315 is essential for coordinating ssDNA interaction with or entry to the deaminase domain and hypothesize that RNA bound to Y315 may be sufficient to competitively inhibit ssDNA deaminase-dependent antiviral activity.

  10. APOBEC3G polymorphism as a selective barrier to cross-species transmission and emergence of pathogenic SIV and AIDS in a primate host.

    PubMed

    Krupp, Annabel; McCarthy, Kevin R; Ooms, Marcel; Letko, Michael; Morgan, Jennifer S; Simon, Viviana; Johnson, Welkin E

    2013-01-01

    Cellular restriction factors, which render cells intrinsically resistant to viruses, potentially impose genetic barriers to cross-species transmission and emergence of viral pathogens in nature. One such factor is APOBEC3G. To overcome APOBEC3G-mediated restriction, many lentiviruses encode Vif, a protein that targets APOBEC3G for degradation. As with many restriction factor genes, primate APOBEC3G displays strong signatures of positive selection. This is interpreted as evidence that the primate APOBEC3G locus reflects a long-term evolutionary "arms-race" between retroviruses and their primate hosts. Here, we provide direct evidence that APOBEC3G has functioned as a barrier to cross-species transmission, selecting for viral resistance during emergence of the AIDS-causing pathogen SIVmac in captive colonies of Asian macaques in the 1970s. Specifically, we found that rhesus macaques have multiple, functionally distinct APOBEC3G alleles, and that emergence of SIVmac and simian AIDS required adaptation of the virus to evade APOBEC3G-mediated restriction. Our evidence includes the first comparative analysis of APOBEC3G polymorphism and function in both a reservoir and recipient host species (sooty mangabeys and rhesus macaques, respectively), and identification of adaptations unique to Vif proteins of the SIVmac lineage that specifically antagonize rhesus APOBEC3G alleles. By demonstrating that interspecies variation in a known restriction factor selected for viral counter-adaptations in the context of a documented case of cross-species transmission, our results lend strong support to the evolutionary "arms-race" hypothesis. Importantly, our study confirms that APOBEC3G divergence can be a critical determinant of interspecies transmission and emergence of primate lentiviruses, including viruses with the potential to infect and spread in human populations.

  11. 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.

  12. 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

  13. 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

  14. Existence and global exponential stability of almost periodic solution for cellular neural networks with variable coefficients and time-varying delays.

    PubMed

    Jiang, Haijun; Zhang, Long; Teng, Zhidong

    2005-11-01

    In this paper, we study cellular neural networks with almost periodic variable coefficients and time-varying delays. By using the existence theorem of almost periodic solution for general functional differential equations, introducing many real parameters and applying the Lyapunov functional method and the technique of Young inequality, we obtain some sufficient conditions to ensure the existence, uniqueness, and global exponential stability of almost periodic solution. The results obtained in this paper are new, useful, and extend and improve the existing ones in previous literature.

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

    PubMed

    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.

  16. 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

  17. 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.

  18. Cellular and network properties in the functioning of the nervous system: from central pattern generators to cognition.

    PubMed

    Arshavsky, Yuri I

    2003-03-01

    The relation between individual neurons and neuronal networks in performing brain functions is one of the central questions in modern neuroscience. Most of the current literature suggests that the role of individual neurons is negligible and neural networks play a dominant role in the functioning of the nervous system. Individual neurons are usually viewed as network elements whose functions are limited to generating electrical signals and releasing neurotransmitters. Here I summarize experimental evidence that challenges this concept and argue that the unique, intrinsic properties of highly specialized individual neurons are as important for the functioning of the brain as the network properties. I first discuss the studies of relatively 'simple' functions of the nervous system, such as the control of rhythmic 'automatic' movements and generation of circadian rhythm, which indicate that individual neurons may continue performing their functions after being separated from corresponding networks. I then argue that the complex cognitive functions, such as declarative memory, language processing, and face recognition, are likely to be underlain by the properties of groups of highly specialized neurons. These neurons appear to be genetically predisposed to perform cognitive functions and their dysfunctions cannot be compensated by other elements of the nervous system. Under this concept, the electrical signals circulating within and between neural networks are considered to be a means of forming coordinated dynamic ensembles of neurons involved in performing specific functions. While still speculative, this hypothesis may provoke new approaches to studies of neural mechanisms underpinning cognitive functions of the brain.

  19. Probing Cellular and Molecular Mechanisms of Cigarette Smoke-Induced Immune Response in the Progression of Chronic Obstructive Pulmonary Disease Using Multiscale Network Modeling.

    PubMed

    Pan, Zhichao; Yu, Haishan; Liao, Jie-Lou

    Chronic obstructive pulmonary disease (COPD) is a chronic inflammatory disorder characterized by progressive destruction of lung tissues and airway obstruction. COPD is currently the third leading cause of death worldwide and there is no curative treatment available so far. Cigarette smoke (CS) is the major risk factor for COPD. Yet, only a relatively small percentage of smokers develop the disease, showing that disease susceptibility varies significantly among smokers. As smoking cessation can prevent the disease in some smokers, quitting smoking cannot halt the progression of COPD in others. Despite extensive research efforts, cellular and molecular mechanisms of COPD remain elusive. In particular, the disease susceptibility and smoking cessation effects are poorly understood. To address these issues in this work, we develop a multiscale network model that consists of nodes, which represent molecular mediators, immune cells and lung tissues, and edges describing the interactions between the nodes. Our model study identifies several positive feedback loops and network elements playing a determinant role in the CS-induced immune response and COPD progression. The results are in agreement with clinic and laboratory measurements, offering novel insight into the cellular and molecular mechanisms of COPD. The study in this work also provides a rationale for targeted therapy and personalized medicine for the disease in future.

  20. Probing Cellular and Molecular Mechanisms of Cigarette Smoke-Induced Immune Response in the Progression of Chronic Obstructive Pulmonary Disease Using Multiscale Network Modeling

    PubMed Central

    Pan, Zhichao; Yu, Haishan; Liao, Jie-Lou

    2016-01-01

    Chronic obstructive pulmonary disease (COPD) is a chronic inflammatory disorder characterized by progressive destruction of lung tissues and airway obstruction. COPD is currently the third leading cause of death worldwide and there is no curative treatment available so far. Cigarette smoke (CS) is the major risk factor for COPD. Yet, only a relatively small percentage of smokers develop the disease, showing that disease susceptibility varies significantly among smokers. As smoking cessation can prevent the disease in some smokers, quitting smoking cannot halt the progression of COPD in others. Despite extensive research efforts, cellular and molecular mechanisms of COPD remain elusive. In particular, the disease susceptibility and smoking cessation effects are poorly understood. To address these issues in this work, we develop a multiscale network model that consists of nodes, which represent molecular mediators, immune cells and lung tissues, and edges describing the interactions between the nodes. Our model study identifies several positive feedback loops and network elements playing a determinant role in the CS-induced immune response and COPD progression. The results are in agreement with clinic and laboratory measurements, offering novel insight into the cellular and molecular mechanisms of COPD. The study in this work also provides a rationale for targeted therapy and personalized medicine for the disease in future. PMID:27669518

  1. 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

  2. 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.

  3. APOBEC3G expression is correlated with poor prognosis in colon carcinoma patients with hepatic metastasis.

    PubMed

    Lan, Huanrong; Jin, Ketao; Gan, Meifu; Wen, Shouxiang; Bi, Tienan; Zhou, Shenkang; Zhu, Naibiao; Teng, Lisong; Yu, Wenjie

    2014-01-01

    Increased expression of apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3G (APOBEC3G) in human primary colorectal tumors and hepatic metastasis has been detected. However, the clinical relevance of APOBEC3G in colon carcinoma hepatic metastasis remains uncertain. The aim of this study was to assess the prognostic value of APOBEC3G in colon carcinoma patients with hepatic metastasis after hepatic resection. APOBEC3G expression was evaluated by immunohistochemistry in paraffin-embedded primary colon carcinoma and paired hepatic metastasis tissues from 136 patients with liver metastasis from colon carcinoma that underwent hepatic resection. The relation between APOBEC3G expression and clinicopathologic factors and long-term prognosis in these 136 patients was retrospectively examined. The prognostic significance of negative or positive APOBEC3G expression in colon carcinoma hepatic metastasis was assessed using Kaplan-Meier survival analysis and log-rank tests. Positive expression of APOBEC3G was correlated with liver metastasis of colon cancer. Univariate analysis indicated significantly worse overall survival (OS) for patients with a positive APOBEC3G expression in colon carcinoma hepatic metastasis than for patients with a negative APOBEC3G expression. Multivariate analysis showed positive-APOBEC3G in colon carcinoma hepatic metastasis to be an independent prognostic factor for OS after hepatic resection (P = 0.000). Positive expression of APOBEC3G was statistically significantly associated with poor prognosis of colon carcinoma patients with hepatic metastasis. APOBEC3G could be a novel predictor for poor prognosis of colon carcinoma patients with hepatic metastasis after hepatic resection.

  4. Cancer stem cells display extremely large evolvability: alternating plastic and rigid networks as a potential Mechanism: network models, novel therapeutic target strategies, and the contributions of hypoxia, inflammation and cellular senescence.

    PubMed

    Csermely, Peter; Hódsági, János; Korcsmáros, Tamás; Módos, Dezső; Perez-Lopez, Áron R; Szalay, Kristóf; Veres, Dániel V; Lenti, Katalin; Wu, Ling-Yun; Zhang, Xiang-Sun

    2015-02-01

    Cancer is increasingly perceived as a systems-level, network phenomenon. The major trend of malignant transformation can be described as a two-phase process, where an initial increase of network plasticity is followed by a decrease of plasticity at late stages of tumor development. The fluctuating intensity of stress factors, like hypoxia, inflammation and the either cooperative or hostile interactions of tumor inter-cellular networks, all increase the adaptation potential of cancer cells. This may lead to the bypass of cellular senescence, and to the development of cancer stem cells. We propose that the central tenet of cancer stem cell definition lies exactly in the indefinability of cancer stem cells. Actual properties of cancer stem cells depend on the individual "stress-history" of the given tumor. Cancer stem cells are characterized by an extremely large evolvability (i.e. a capacity to generate heritable phenotypic variation), which corresponds well with the defining hallmarks of cancer stem cells: the possession of the capacity to self-renew and to repeatedly re-build the heterogeneous lineages of cancer cells that comprise a tumor in new environments. Cancer stem cells represent a cell population, which is adapted to adapt. We argue that the high evolvability of cancer stem cells is helped by their repeated transitions between plastic (proliferative, symmetrically dividing) and rigid (quiescent, asymmetrically dividing, often more invasive) phenotypes having plastic and rigid networks. Thus, cancer stem cells reverse and replay cancer development multiple times. We describe network models potentially explaining cancer stem cell-like behavior. Finally, we propose novel strategies including combination therapies and multi-target drugs to overcome the Nietzschean dilemma of cancer stem cell targeting: "what does not kill me makes me stronger".

  5. Elucidation of the time course of adenosine deaminase APOBEC3G and viral infectivity factor vif in HIV-2287-infected infant macaques

    PubMed Central

    Endsley, Aaron N.; Ho, Rodney J.Y.

    2012-01-01

    Background Although the interactions of cellular cytidine deaminase A3G and viral infection factor (vif) of human immunodeficiency virus (HIV) were reported, regulation of A3G after in vivo HIV infection and disease progression is not known. Methods Time courses of plasma virus, CD4+ T lymphocyte Macaca levels, and concentrations of A3G and vif transcripts were determined in infant macaques infected with HIV-2287. These in vivo results were compared with those collected in vitro in HIV-2-infected T cells. Results Human immunodeficiency virus-infected macaques exhibited plasma viremia (≥108 copies/ml) followed by a precipitous CD4+ T-cell (from 40–70 to ≤5%) decline. An initial increase in A3G transcripts coincides with early increases in virus and vif RNA. As virus load continues to increase, A3G RNA decreases but recovers at a later phase as virus level stabilizes. Pearson correlation analysis revealed strong interactions of A3G–CD4, vif–CD4, and A3G–vif. Conclusions There is a time-dependent A3G and vif RNA interaction throughout the course of HIV infection. PMID:22017399

  6. 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.

  7. Stochastic asymptotical synchronization of chaotic Markovian jumping fuzzy cellular neural networks with mixed delays and the Wiener process based on sampled-data control

    NASA Astrophysics Data System (ADS)

    Kalpana, M.; Balasubramaniam, P.

    2013-07-01

    We investigate the stochastic asymptotical synchronization of chaotic Markovian jumping fuzzy cellular neural networks (MJFCNNs) with discrete, unbounded distributed delays, and the Wiener process based on sampled-data control using the linear matrix inequality (LMI) approach. The Lyapunov—Krasovskii functional combined with the input delay approach as well as the free-weighting matrix approach is employed to derive several sufficient criteria in terms of LMIs to ensure that the delayed MJFCNNs with the Wiener process is stochastic asymptotical synchronous. Restrictions (e.g., time derivative is smaller than one) are removed to obtain a proposed sampled-data controller. Finally, a numerical example is provided to demonstrate the reliability of the derived results.

  8. Examining the process of de novo gene birth: an educational primer on "integration of new genes into cellular networks, and their structural maturation".

    PubMed

    Frietze, Seth; Leatherman, Judith

    2014-03-01

    New genes that arise from modification of the noncoding portion of a genome rather than being duplicated from parent genes are called de novo genes. These genes, identified by their brief evolution and lack of parent genes, provide an opportunity to study the timeframe in which emerging genes integrate into cellular networks, and how the characteristics of these genes change as they mature into bona fide genes. An article by G. Abrusán provides an opportunity to introduce students to fundamental concepts in evolutionary and comparative genetics and to provide a technical background by which to discuss systems biology approaches when studying the evolutionary process of gene birth. Basic background needed to understand the Abrusán study and details on comparative genomic concepts tailored for a classroom discussion are provided, including discussion questions and a supplemental exercise on navigating a genome database.

  9. Examining the Process of de Novo Gene Birth: An Educational Primer on “Integration of New Genes into Cellular Networks, and Their Structural Maturation”

    PubMed Central

    Frietze, Seth; Leatherman, Judith

    2014-01-01

    SUMMARY New genes that arise from modification of the noncoding portion of a genome rather than being duplicated from parent genes are called de novo genes. These genes, identified by their brief evolution and lack of parent genes, provide an opportunity to study the timeframe in which emerging genes integrate into cellular networks, and how the characteristics of these genes change as they mature into bona fide genes. An article by G. Abrusán provides an opportunity to introduce students to fundamental concepts in evolutionary and comparative genetics and to provide a technical background by which to discuss systems biology approaches when studying the evolutionary process of gene birth. Basic background needed to understand the Abrusán study and details on comparative genomic concepts tailored for a classroom discussion are provided, including discussion questions and a supplemental exercise on navigating a genome database. PMID:24653207

  10. Smokeless Tobacco Extract (STE)-Induced Toxicity in Mammalian Cells is Mediated by the Disruption of Cellular Microtubule Network: A Key Mechanism of Cytotoxicity

    PubMed Central

    Chakrabarty, Subhendu; Ganguli, Arnab; Chakrabarti, Gopal

    2013-01-01

    Smokeless tobacco usage is a growing public health problem worldwide. The molecular mechanism(s) underlying smokeless tobacco associated tissue damage remain largely unidentified. In the present study we have tried to explore the effects of aqueous extract of smokeless tobacco (STE) on tubulin-microtubule, the major cytoskeleton protein that maintains cells morphology and participates in cell division. Exposure to STE resulted in dose-dependent cytotoxicity in a variety of mammalian transformed cell lines such as human lung epithelial cells A549, human liver epithelial cells HepG2, and mouse squamous epithelial cells HCC7, as well as non-tumorogenic human peripheral blood mononuclear cells PBMC. Cellular morphology of STE-treated cells was altered and the associated disruption of microtubule network indicates that STE targets tubulin-microtubule system in both cell lines. Furthermore it was also observed that STE-treatment resulted in the selective degradation of cellular tubulin, whereas actin remains unaltered. In vitro, polymerization of purified tubulin was inhibited by STE with the IC50 value∼150 µg/ml and this is associated with the loss of reactive cysteine residues of tubulin. Application of thiol-based antioxidant N-acetyl cysteine (NAC) significantly abrogates STE-mediated microtubule damage and associated cytotoxicity in both A549 and HepG2 cells. These results suggest that microtubule damage is one of the key mechanisms of STE-induced cytotoxity in mammalian cells. PMID:23874548

  11. Smokeless tobacco extract (STE)-induced toxicity in mammalian cells is mediated by the disruption of cellular microtubule network: a key mechanism of cytotoxicity.

    PubMed

    Das, Amlan; Bhattacharya, Abhijit; Chakrabarty, Subhendu; Ganguli, Arnab; Chakrabarti, Gopal

    2013-01-01

    Smokeless tobacco usage is a growing public health problem worldwide. The molecular mechanism(s) underlying smokeless tobacco associated tissue damage remain largely unidentified. In the present study we have tried to explore the effects of aqueous extract of smokeless tobacco (STE) on tubulin-microtubule, the major cytoskeleton protein that maintains cells morphology and participates in cell division. Exposure to STE resulted in dose-dependent cytotoxicity in a variety of mammalian transformed cell lines such as human lung epithelial cells A549, human liver epithelial cells HepG2, and mouse squamous epithelial cells SCC7, [corrected] as well as non-tumorogenic human peripheral blood mononuclear cells PBMC. Cellular morphology of STE-treated cells was altered and the associated disruption of microtubule network indicates that STE targets tubulin-microtubule system in both cell lines. Furthermore it was also observed that STE-treatment resulted in the selective degradation of cellular tubulin, whereas actin remains unaltered. In vitro, polymerization of purified tubulin was inhibited by STE with the IC50 value∼150 µg/ml and this is associated with the loss of reactive cysteine residues of tubulin. Application of thiol-based antioxidant N-acetyl cysteine (NAC) significantly abrogates STE-mediated microtubule damage and associated cytotoxicity in both A549 and HepG2 cells. These results suggest that microtubule damage is one of the key mechanisms of STE-induced cytotoxity in mammalian cells.

  12. Meta-analysis of retrograde signaling in Arabidopsis thaliana reveals a core module of genes embedded in complex cellular signaling networks.

    PubMed

    Gläßer, Christine; Haberer, Georg; Finkemeier, Iris; Pfannschmidt, Thomas; Kleine, Tatjana; Leister, Dario; Dietz, Karl-Josef; Häusler, Rainer Erich; Grimm, Bernhard; Mayer, Klaus Franz Xaver

    2014-07-01

    Plastid-to-nucleus signaling is essential for the coordination and adjustment of cellular metabolism in response to environmental and developmental cues of plant cells. A variety of operational retrograde signaling pathways have been described that are thought to be triggered by reactive oxygen species, photosynthesis redox imbalance, tetrapyrrole intermediates, and other metabolic traits. Here we report a meta-analysis based on transcriptome and protein interaction data. Comparing the output of these pathways reveals the commonalities and peculiarities stimulated by six different sources impinging on operational retrograde signaling. Our study provides novel insights into the interplay of these pathways, supporting the existence of an as-yet unknown core response module of genes being regulated under all conditions tested. Our analysis further highlights affiliated regulatory cis-elements and classifies abscisic acid and auxin-based signaling as secondary components involved in the response cascades following a plastidial signal. Our study provides a global analysis of structure and interfaces of different pathways involved in plastid-to-nucleus signaling and a new view on this complex cellular communication network.

  13. 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.

  14. Development of benzimidazole derivatives to inhibit HIV-1 replication through protecting APOBEC3G protein.

    PubMed

    Pan, Ting; He, Xin; Chen, Bing; Chen, Hui; Geng, Guannan; Luo, Haihua; Zhang, Hui; Bai, Chuan

    2015-05-05

    Human APOBEC3G (apolipoprotein B mRNA-editing enzyme, catalytic polypeptide-like 3G, A3G) is a potent restriction factor against human immunodeficiency virus type 1 (HIV-1) by inducing hypermutation of G to A in viral genome after its incorporation into virions. HIV-1 Vif (Virion Infectivity Factor) counteracts A3G by inducing ubiquitination and proteasomal degradation of A3G protein. Vif-A3G axis therefore is a promising therapeutic target of HIV-1. Here we report the screening, synthesis and SAR studies of benzimidazole derivatives as potent inhibitors against HIV-1 replication via protecting A3G protein. Based on the steep SAR of the benzimidazole scaffold, we identified compound 14 and 26 which provided the best potency, with IC50 values of 3.45 nM and 58.03 nM respectively in the anti-HIV-1 replication assay in H9 cells. Compound 14 and 26 also afforded protective effects on A3G protein level. Both compounds have been proved to be safe in acute toxicological studies. Taken together, we suggest that these two benzimidazole derivatives can be further developed as a new category of anti-HIV-1 leads.

  15. 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.

  16. Practical demonstration of spectrally efficient FDM millimeter-wave radio over fiber systems for 5G cellular networking

    NASA Astrophysics Data System (ADS)

    Mikroulis, Spiros; Xu, Tongyang; Darwazeh, Izzat

    2016-02-01

    This work reports the first demonstration of spectrally efficient frequency division multiplexed (SEFDM) signal transmission based on mm-wave radio over fiber (RoF) technology. Such systems aim to satisfy the beyond 4G (5G) demands of low cost, low energy, millimeter-wave carrier frequencies and high spectral efficiency. The proposed radio over fiber topology, using passive optical network (PON) infrastructure and low-cost multimode fiber (MMF), is analyzed and a proof-of-concept SEFDM radio over 250m OM-1 MMF transmission with a 3m 60GHz wireless link is successfully demonstrated. Different systems are demonstrated, at raw data rates up to 3.7 Gb/s, showing SEFDM spectrum saving up to 40% relative to OFDM.

  17. 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.

  18. APOBEC3G-Augmented Stem Cell Therapy to Modulate HIV Replication: A Computational Study.

    PubMed

    Hosseini, Iraj; Mac Gabhann, Feilim

    2013-01-01

    The interplay between the innate immune system restriction factor APOBEC3G and the HIV protein Vif is a key host-retrovirus interaction. APOBEC3G can counteract HIV infection in at least two ways: by inducing lethal mutations on the viral cDNA; and by blocking steps in reverse transcription and viral integration into the host genome. HIV-Vif blocks these antiviral functions of APOBEC3G by impeding its encapsulation. Nonetheless, it has been shown that overexpression of APOBEC3G, or interfering with APOBEC3G-Vif binding, can efficiently block in vitro HIV replication. Some clinical studies have also suggested that high levels of APOBEC3G expression in HIV patients are correlated with increased CD4+ T cell count and low levels of viral load; however, other studies have reported contradictory results and challenged this observation. Stem cell therapy to replace a patient's immune cells with cells that are more HIV-resistant is a promising approach. Pre-implantation gene transfection of these stem cells can augment the HIV-resistance of progeny CD4+ T cells. As a protein, APOBEC3G has the advantage that it can be genetically encoded, while small molecules cannot. We have developed a mathematical model to quantitatively study the effects on in vivo HIV replication of therapeutic delivery of CD34+ stem cells transfected to overexpress APOBEC3G. Our model suggests that stem cell therapy resulting in a high fraction of APOBEC3G-overexpressing CD4+ T cells can effectively inhibit in vivo HIV replication. We extended our model to simulate the combination of APOBEC3G therapy with other biological activities, to estimate the likelihood of improved outcomes.

  19. Determinants of Sequence-Specificity within Human AID and APOBEC3G

    PubMed Central

    Carpenter, Michael A.; Rajagurubandara, Erandi; Wijesinghe, Priyanga; Bhagwat, Ashok S.

    2010-01-01

    Human APOBEC3G (A3G) and activation-induced deaminase (AID) belong to a family of DNA-cytosine deaminases. While A3G targets the last C in a run of C’s, AID targets C in the consensus sequence WRC (W is A or T and R is a purine). Guided by the structures of the A3G carboxyl-terminal catalytic domain (A3G-CTD), we identified two potential regions (region 1 and region 2) that may interact with DNA and swapped the corresponding regions between a variant of A3G-CTD and AID. The resulting hybrids were expressed in Escherichia coli and two different genetic assays and a biochemical assay were used to determine the sequence selectivity of the hybrids in promoting C to T mutations. The results show that while the 10 amino acid region 2 of A3G was its principal sequence-specificity determinant, region 1 of A3G enhanced the target cytosine preference conferred by region 2. In contrast, neither of the two regions in AID individually or in combination were sufficient to confer the DNA sequence preference of this protein upon A3G. Instead, introduction of AID sequences in A3G relaxed the sequence-specificity of the latter protein. Our results show that the sequence-selectivity of APOBEC family of enzymes is determined by at least two separate sequence segments and there may be additional regions of the protein involved in DNA sequence recognition. PMID:20338830

  20. Processing the Bouguer anomaly map of Biga and the surrounding area by the cellular neural network: application to the southwestern Marmara region

    NASA Astrophysics Data System (ADS)

    Aydogan, D.

    2007-04-01

    An image processing technique called the cellular neural network (CNN) approach is used in this study to locate geological features giving rise to gravity anomalies such as faults or the boundary of two geologic zones. CNN is a stochastic image processing technique based on template optimization using the neighborhood relationships of cells. These cells can be characterized by a functional block diagram that is typical of neural network theory. The functionality of CNN is described in its entirety by a number of small matrices (A, B and I) called the cloning template. CNN can also be considered to be a nonlinear convolution of these matrices. This template describes the strength of the nearest neighbor interconnections in the network. The recurrent perceptron learning algorithm (RPLA) is used in optimization of cloning template. The CNN and standard Canny algorithms were first tested on two sets of synthetic gravity data with the aim of checking the reliability of the proposed approach. The CNN method was compared with classical derivative techniques by applying the cross-correlation method (CC) to the same anomaly map as this latter approach can detect some features that are difficult to identify on the Bouguer anomaly maps. This approach was then applied to the Bouguer anomaly map of Biga and its surrounding area, in Turkey. Structural features in the area between Bandirma, Biga, Yenice and Gonen in the southwest Marmara region are investigated by applying the CNN and CC to the Bouguer anomaly map. Faults identified by these algorithms are generally in accordance with previously mapped surface faults. These examples show that the geologic boundaries can be detected from Bouguer anomaly maps using the cloning template approach. A visual evaluation of the outputs of the CNN and CC approaches is carried out, and the results are compared with each other. This approach provides quantitative solutions based on just a few assumptions, which makes the method more

  1. Analysis of a Proposed Third Generation (3G) Mobile Communication Standard, Time Division - Synchronous Code Division Multiple Access (TD-SCDMA)

    DTIC Science & Technology

    2002-06-01

    provider for cellular communications, dominating 62% of the market with currently over 600 million subscribers. By being backward compatible with this...network, TD-SCDMA will have a great marketing advantage over non-GSM based technology. Currently in the U.S., the cellular service providers AT&T and

  2. The corticotropin-releasing hormone network and the hypothalamic-pituitary-adrenal axis: molecular and cellular mechanisms involved.

    PubMed

    Bonfiglio, Juan José; Inda, Carolina; Refojo, Damián; Holsboer, Florian; Arzt, Eduardo; Silberstein, Susana

    2011-01-01

    Corticotropin-releasing hormone (CRH) plays a key role in adjusting the basal and stress-activated hypothalamic-pituitary-adrenal axis (HPA). CRH is also widely distributed in extrahypothalamic circuits, where it acts as a neuroregulator to integrate the complex neuroendocrine, autonomic, and behavioral adaptive response to stress. Hyperactive and/or dysregulated CRH circuits are involved in neuroendocrinological disturbances and stress-related mood disorders such as anxiety and depression. This review describes the main physiological features of the CRH network and summarizes recent relevant information concerning the molecular mechanism of CRH action obtained from signal transduction studies using cells and wild-type and transgenic mice lines. Special focus is placed on the MAPK signaling pathways triggered by CRH through the CRH receptor 1 that plays an essential role in CRH action in pituitary corticotrophs and in specific brain structures. Recent findings underpin the concept of specific CRH-signaling pathways restricted to specific anatomical areas. Understanding CRH action at molecular levels will not only provide insight into the precise CRH mechanism of action, but will also be instrumental in identifying novel targets for pharmacological intervention in neuroendocrine tissues and specific brain areas involved in CRH-related disorders.

  3. 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.

  4. 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.

  5. 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.

  6. An Investigation into the Use of 3G Mobile Communications to Provide Telehealth Services in Rural KwaZulu-Natal

    PubMed Central

    Mars, Maurice

    2015-01-01

    Abstract Background: We investigated the use of third-generation (3G) mobile communications to provide telehealth services in remote health clinics in rural KwaZulu-Natal, South Africa. Materials and Methods: We specified a minimal set of services as our use case that would be representative of typical activity and to provide a baseline for analysis of network performance. Services included database access to manage chronic disease, local support and management of patients (to reduce unnecessary travel to the hospital), emergency care (up to 8 h for an ambulance to arrive), e-mail, access to up-to-date information (Web), and teleclinics. We made site measurements at a representative set of health clinics to determine the type of coverage (general packet radio service [GPRS]/3G), its capabilities to support videoconferencing (H323 and Skype™ [Microsoft, Redmond, WA]) and audio (Skype), and throughput for transmission control protocol (TCP) to gain a measure of application performance. Results: We found that none of the remote health clinics had 3G service. The GPRS service provided typical upload speed of 44 kilobits per second (Kbps) and download speed of 64 Kbps. This was not sufficient to support any form of videoconferencing. We also observed that GPRS had significant round trip time (RTT), in some cases in excess of 750 ms, and this led to slow start-up for TCP applications. Conclusions: We found audio was always so broken as to be unusable and further observed that many applications such as Web access would fail under conditions of very high RTT. We found some health clinics were so remote that they had no mobile service. 3G, where available, had measured upload speed of 331 Kbps and download speed of 446 Kbps and supported videoconferencing and audio at all sites, but we frequently experienced 3G changing to GPRS. We conclude that mobile communications currently provide insufficient coverage and capability to provide reliable clinical services and

  7. 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

  8. 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.

  9. 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

  10. Design of cryptographically secure AES like S-Box using second-order reversible cellular automata for wireless body area network applications.

    PubMed

    Gangadari, Bhoopal Rao; Rafi Ahamed, Shaik

    2016-09-01

    In biomedical, data security is the most expensive resource for wireless body area network applications. Cryptographic algorithms are used in order to protect the information against unauthorised access. Advanced encryption standard (AES) cryptographic algorithm plays a vital role in telemedicine applications. The authors propose a novel approach for design of substitution bytes (S-Box) using second-order reversible one-dimensional cellular automata (RCA(2)) as a replacement to the classical look-up-table (LUT) based S-Box used in AES algorithm. The performance of proposed RCA(2) based S-Box and conventional LUT based S-Box is evaluated in terms of security using the cryptographic properties such as the nonlinearity, correlation immunity bias, strict avalanche criteria and entropy. Moreover, it is also shown that RCA(2) based S-Boxes are dynamic in nature, invertible and provide high level of security. Further, it is also found that the RCA(2) based S-Box have comparatively better performance than that of conventional LUT based S-Box.

  11. MARK4 is a novel microtubule-associated proteins/microtubule affinity-regulating kinase that binds to the cellular microtubule network and to centrosomes.

    PubMed

    Trinczek, Bernhard; Brajenovic, Miro; Ebneth, Andreas; Drewes, Gerard

    2004-02-13

    The MARK protein kinases were originally identified by their ability to phosphorylate a serine motif in the microtubule-binding domain of tau that is critical for microtubule binding. Here, we report the cloning and expression of a novel human paralog, MARK4, which shares 75% overall homology with MARK1-3 and is predominantly expressed in brain. Homology is most pronounced in the catalytic domain (90%), and MARK4 readily phosphorylates tau and the related microtubule-associated protein 2 (MAP2) and MAP4. In contrast to the three paralogs that all exhibit uniform cytoplasmic localization, MARK4 colocalizes with the centrosome and with microtubules in cultured cells. Overexpression of MARK4 causes thinning out of the microtubule network, concomitant with a reorganization of microtubules into bundles. In line with these findings, we show that a tandem affinity-purified MARK4 protein complex contains alpha-, beta-, and gamma-tubulin. In differentiated neuroblastoma cells, MARK4 is localized prominently at the tips of neurite-like processes. We suggest that although the four MARK/PAR-1 kinases might play multiple cellular roles in concert with different targets, MARK4 is likely to be directly involved in microtubule organization in neuronal cells and may contribute to the pathological phosphorylation of tau in Alzheimer's disease.

  12. iCDI-PseFpt: identify the channel-drug interaction in cellular networking with PseAAC and molecular fingerprints.

    PubMed

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

    2013-11-21

    Many crucial functions in life, such as heartbeat, sensory transduction and central nervous system response, are controlled by cell signalings via various ion channels. Therefore, ion channels have become an excellent drug target, and study of ion channel-drug interaction networks is an important topic for drug development. However, it is both time-consuming and costly to determine whether a drug and a protein ion channel are interacting with each other in a cellular network by means of experimental techniques. Although some computational methods were developed in this regard based on the knowledge of the 3D (three-dimensional) structure of protein, unfortunately their usage is quite limited because the 3D structures for most protein ion channels are still unknown. With the avalanche of protein sequences generated in the post-genomic age, it is highly desirable to develop the sequence-based computational method to address this problem. To take up the challenge, we developed a new predictor called iCDI-PseFpt, in which the protein ion-channel sample is formulated by the PseAAC (pseudo amino acid composition) generated with the gray model theory, the drug compound by the 2D molecular fingerprint, and the operation engine is the fuzzy K-nearest neighbor algorithm. The overall success rate achieved by iCDI-PseFpt via the jackknife cross-validation was 87.27%, which is remarkably higher than that by any of the existing predictors in this area. As a user-friendly web-server, iCDI-PseFpt is freely accessible to the public at the website http://www.jci-bioinfo.cn/iCDI-PseFpt/. Furthermore, for the convenience of most experimental scientists, a step-by-step guide is provided on how to use the web-server to get the desired results without the need to follow the complicated math equations presented in the paper just for its integrity. It has not escaped our notice that the current approach can also be used to study other drug-target interaction networks.

  13. Toxicological study of a new maintenance fluid, Veen 3G, in rats.

    PubMed

    Kamei, J; Onodera, K; Kawaguchi, M; Shibata, M; Kagawa, M; Wachi, M; Kojima, J

    2002-10-01

    A study of the different volume and infusion rates of a new maintenance fluid, Veen 3G, on the general conditions of rats was investigated during the 14 days after infusion. In Experiment I, 100 ml/kg and 200 ml/kg of Veen 3G were infused at a rate of 300 ml/kg/h in male and female rats. Results were compared with those for Gurunon Ringer solution (GRS) in male and female rats. We observed only transient polyuria in animals administered by each dose of Veen 3G and GRS for 0-15 min after infusion. Necropsy was not observed in any of the animals tested 14 days after infusion. In Experiment II, 200 ml/kg of Veen 3G was infused at rates of 200, 400, 800 and 1600 ml/kg/h in male rats. At 800 and 1600 ml/kg/h, irregular respiration and decrease in movement were observed concomitantly with polyuria. Three out of 4 rats died immediately after the infusion of Veen 3G at a rate of 1600 ml/kg/h, and one rat was still alive 14 days after the infusion. In this experiment, 200 ml/kg Veen 3G was safe when we infused at a rate of less than 400 ml/kg/h in male rats. Since this rate is about 27-80 times higher than that used clinically in maintenance treatment, Veen 3G is suggested to be safe, with the exception of polyuria, in clinical situations at the standard infusion rate (5-15 ml/kg/h).

  14. Integrated performance of a frequency domain multiplexing readout in the SPT-3G receiver

    NASA Astrophysics Data System (ADS)

    Bender, A. N.; Ade, P. A. R.; Anderson, A. J.; Avva, J.; Ahmed, Z.; Arnold, K.; Austermann, J. E.; Basu Thakur, R.; Benson, B. A.; Bleem, L. E.; Byrum, K.; Carlstrom, J. E.; Carter, F. W.; Chang, C. L.; Cho, H. M.; Cliche, J. F.; Crawford, T. M.; Cukierman, A.; Czaplewski, D. A.; Ding, J.; Divan, R.; de Haan, T.; Dobbs, M. A.; Dutcher, D.; Everett, W.; Gilbert, A.; Groh, J. C.; Guyser, R.; Halverson, N. W.; Harke-Hosemann, A.; Harrington, N. L.; Hattori, K.; Henning, J. W.; Hilton, G. C.; Holzapfel, W. L.; Huang, N.; Irwin, K. D.; Jeong, O.; Khaire, T.; Korman, M.; Kubik, D.; Kuo, C. L.; Lee, A. T.; Leitch, E. M.; Lendinez, S.; Meyer, S. S.; Miller, C. S.; Montgomery, J.; Nadolski, A.; Natoli, T.; Nguyen, H.; Novosad, V.; Padin, S.; Pan, Z.; Pearson, J.; Posada, C. M.; Rahlin, A.; Reichardt, C. L.; Ruhl, J. E.; Saliwanchik, B. R.; Sayre, J. T.; Shariff, J. A.; Shirley, Ian; Shirokoff, E.; Smecher, G.; Sobrin, J.; Stan, L.; Stark, A. A.; Story, K.; Suzuki, A.; Tang, Q. Y.; Thompson, K. L.; Tucker, C.; Vanderlinde, K.; Vieira, J. D.; Wang, G.; Whitehorn, N.; Yefremenko, V.; Yoon, K. W.

    2016-07-01

    The third generation receiver for the South Pole Telescope, SPT-3G, will make extremely deep, arcminuteresolution maps of the temperature and polarization of the cosmic microwave background. The SPT-3G maps will enable studies of the B-mode polarization signature, constraining primordial gravitational waves as well as the effect of massive neutrinos on structure formation in the late universe. The SPT-3G receiver will achieve exceptional sensitivity through a focal plane of 16,000 transition-edge sensor bolometers, an order of magnitude more than the current SPTpol receiver. SPT-3G uses a frequency domain multiplexing (fMux) scheme to read out the focal plane, combining the signals from 64 bolometers onto a single pair of wires. The fMux readout facilitates the large number of detectors in the SPT-3G focal plane by limiting the thermal load due to readout wiring on the 250 millikelvin cryogenic stage. A second advantage of the fMux system is that the operation of each bolometer can be optimized. In addition to these benefits, the fMux readout introduces new challenges into the design and operation of the receiver. The bolometers are operated at a range of frequencies up to 5 MHz, requiring control of stray reactances over a large bandwidth. Additionally, crosstalk between multiplexed detectors will inject large false signals into the data if not adequately mitigated. SPT-3G is scheduled to deploy to the South Pole Telescope in late 2016. Here, we present the pre-deployment performance of the fMux readout system with the SPT-3G focal plane.

  15. 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.

  16. Inhibition of hepatitis B virus replication by APOBEC3G in vitro and in vivo

    PubMed Central

    Lei, Yan-Chang; Hao, You-Hua; Zhang, Zheng-Mao; Tian, Yong-Jun; Wang, Bao-Ju; Yang, Yan; Zhao, Xi-Ping; Lu, Meng-Ji; Gong, Fei-Li; Yang, Dong-Liang

    2006-01-01

    AIM: To investigate the effect of APOBEC3G mediated antiviral activity against hepatitis B virus (HBV) in cell cultures and replication competent HBV vector-based mouse model. METHODS: The mammalian hepatoma cells Huh7 and HepG2 were cotransfected with various amounts of CMV-driven expression vector encoding APOBEC3G and replication competent 1.3 fold over-length HBV. Levels of HBsAg and HBeAg in the media of the transfected cells were determined by ELISA. The expression of HBcAg in transfected cells was detected by western blot. HBV DNA and RNA from intracellular core particles were examined by Northern and Southern blot analyses. To assess activity of the APOBEC3G in vivo, an HBV vector-based model was used in which APOBEC3G and the HBV vector were co-delivered via high-volume tail vein injection. Levels of HBsAg and HBV DNA in the sera of mice as well as HBV core-associated RNA in the liver of mice were determined by ELISA and quantitative PCR analysis respectively. RESULTS: There was a dose dependent decrease in the levels of intracellular core-associated HBV DNA and extracellular production of HBsAg and HBeAg. The levels of intracellular core-associated viral RNA also decreased, but the expression of HBcAg in transfected cells showed almost no change. Consistent with in vitro results, levels of HBsAg in the sera of mice were dramatically decreased. More than 1.5 log10 decrease in levels of serum HBV DNA and liver HBV RNA were observed in the APOBEC3G-treated groups compared with the control groups. CONCLUSION: These findings indicate that APOBEC3G could suppress HBV replication and antigen expression both in vivo and in vitro, promising an advance in treatment of HBV infection. PMID:16874860

  17. Nodule Detection in a Lung Region that's Segmented with Using Genetic Cellular Neural Networks and 3D Template Matching with Fuzzy Rule Based Thresholding

    PubMed Central

    Osman, Onur; Ucan, Osman N.

    2008-01-01

    Objective The purpose of this study was to develop a new method for automated lung nodule detection in serial section CT images with using the characteristics of the 3D appearance of the nodules that distinguish themselves from the vessels. Materials and Methods Lung nodules were detected in four steps. First, to reduce the number of region of interests (ROIs) and the computation time, the lung regions of the CTs were segmented using Genetic Cellular Neural Networks (G-CNN). Then, for each lung region, ROIs were specified with using the 8 directional search; +1 or -1 values were assigned to each voxel. The 3D ROI image was obtained by combining all the 2-Dimensional (2D) ROI images. A 3D template was created to find the nodule-like structures on the 3D ROI image. Convolution of the 3D ROI image with the proposed template strengthens the shapes that are similar to those of the template and it weakens the other ones. Finally, fuzzy rule based thresholding was applied and the ROI's were found. To test the system's efficiency, we used 16 cases with a total of 425 slices, which were taken from the Lung Image Database Consortium (LIDC) dataset. Results The computer aided diagnosis (CAD) system achieved 100% sensitivity with 13.375 FPs per case when the nodule thickness was greater than or equal to 5.625 mm. Conclusion Our results indicate that the detection performance of our algorithm is satisfactory, and this may well improve the performance of computer-aided detection of lung nodules. PMID:18253070

  18. iDrug-Target: predicting the interactions between drug compounds and target proteins in cellular networking via benchmark dataset optimization approach.

    PubMed

    Xiao, Xuan; Min, Jian-Liang; Lin, Wei-Zhong; Liu, Zi; Cheng, Xiang; Chou, Kuo-Chen

    2015-01-01

    Information about the interactions of drug compounds with proteins in cellular networking is very important for drug development. Unfortunately, all the existing predictors for identifying drug-protein interactions were trained by a skewed benchmark data-set where the number of non-interactive drug-protein pairs is overwhelmingly larger than that of the interactive ones. Using this kind of highly unbalanced benchmark data-set to train predictors would lead to the outcome that many interactive drug-protein pairs might be mispredicted as non-interactive. Since the minority interactive pairs often contain the most important information for drug design, it is necessary to minimize this kind of misprediction. In this study, we adopted the neighborhood cleaning rule and synthetic minority over-sampling technique to treat the skewed benchmark datasets and balance the positive and negative subsets. The new benchmark datasets thus obtained are called the optimized benchmark datasets, based on which a new predictor called iDrug-Target was developed that contains four sub-predictors: iDrug-GPCR, iDrug-Chl, iDrug-Ezy, and iDrug-NR, specialized for identifying the interactions of drug compounds with GPCRs (G-protein-coupled receptors), ion channels, enzymes, and NR (nuclear receptors), respectively. Rigorous cross-validations on a set of experiment-confirmed datasets have indicated that these new predictors remarkably outperformed the existing ones for the same purpose. To maximize users' convenience, a public accessible Web server for iDrug-Target has been established at http://www.jci-bioinfo.cn/iDrug-Target/ , by which users can easily get their desired results. It has not escaped our notice that the aforementioned strategy can be widely used in many other areas as well.

  19. APOBEC3G and APOBEC3F Act in Concert To Extinguish HIV-1 Replication

    PubMed Central

    Krisko, John F.; Begum, Nurjahan; Baker, Caroline E.

    2016-01-01

    ABSTRACT The multifunctional HIV-1 accessory protein Vif counters the antiviral activities of APOBEC3G (A3G) and APOBEC3F (A3F), and some Vifs counter stable alleles of APOBEC3H (A3H). Studies in humanized mice have shown that HIV-1 lacking Vif expression is not viable. Here, we look at the relative contributions of the three APOBEC3s to viral extinction. Inoculation of bone marrow/liver/thymus (BLT) mice with CCR5-tropic HIV-1JRCSF (JRCSF) expressing a vif gene inactive for A3G but not A3F degradation activity (JRCSFvifH42/43D) displayed either no or delayed replication. JRCSF expressing a vif gene mutated to inactivate A3F degradation but not A3G degradation (JRCSFvifW79S) always replicated to high viral loads with variable delays. JRCSF with vif mutated to lack both A3G and A3F degradation activities (JRCSFvifH42/43DW79S) failed to replicate, mimicking JRCSF without Vif expression (JRCSFΔvif). JRCSF and JRCSFvifH42/43D, but not JRCSFvifW79S or JRCSFvifH42/43DW79S, degraded APOBEC3D. With one exception, JRCSFs expressing mutant Vifs that replicated acquired enforced vif mutations. These mutations partially restored A3G or A3F degradation activity and fully replaced JRCSFvifH42/43D or JRCSFvifW79S by 10 weeks. Surprisingly, induced mutations temporally lagged behind high levels of virus in blood. In the exceptional case, JRCSFvifH42/43D replicated after a prolonged delay with no mutations in vif but instead a V27I mutation in the RNase H coding sequence. JRCSFvifH42/43D infections exhibited massive GG/AG mutations in pol viral DNA, but in viral RNA, there were no fixed mutations in the Gag or reverse transcriptase coding sequence. A3H did not contribute to viral extinction but, in combination with A3F, could delay JRCSF replication. A3H was also found to hypermutate viral DNA. IMPORTANCE Vif degradation of A3G and A3F enhances viral fitness, as virus with even a partially restored capacity for degradation outgrows JRCSFvifH42/43D and JRCSFvifW79S. Unexpectedly

  20. SPT-3G: The third generation camera and survey for the South Pole Telescope

    NASA Astrophysics Data System (ADS)

    Henning, Jason; SPT-3G Collaboration

    2015-01-01

    We discuss the design and status of the third generation camera, SPT-3G, for the South Pole Telescope (SPT), and the scientific goals of the resultant SPT-3G survey. The SPT is a 10-m telescope located at the NSF Amundsen-Scott South Pole station optimized for low-noise and high-resolution imaging of the cosmic microwave background (CMB). The camera will consist of 16,200 polarization-sensitive transition-edge sensors (TES), contained within 2,700 multichroic pixels with observing bands centered at 95, 150, and 220 GHz. The SPT-3G survey will observe for four years starting in 2016. It will map 2500 square degrees to a depth of approximately 2 μK·arcmin in temperature: an order of magnitude lower noise than current state-of-the-art arcminute-scale surveys over comparable areas. This unprecedented map depth will enable high signal-to-noise imaging of B-modes due to gravitational lensing of the CMB. These measurements will place constraints on the sum of the neutrino masses and the shape and amplitude of an inflationary B-mode signal at larger angular scales. The SPT-3G survey will also detect several thousand clusters, in particular significantly expanding the number of known high-redshift massive clusters, enabling new constraints on gravity and cosmology.

  1. 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.

  2. 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

  3. Restraint hypothermia in cold-exposed rats at 3 G and 1 G

    NASA Technical Reports Server (NTRS)

    Monson, C. B.; Horowitz, J. M.; Horwitz, B. A.

    1982-01-01

    The relationship between heat loss, heat production, and hypothermia was investigated in experiments with rats which determined if hypergravity affects heat production by altering oxygen consumption and if restraint modifies the ability of the rats to activate thermogenic mechanisms after cold exposure in a hypergravic field. Restrained and unrestrained rats were exposed for 1 hr periods to 1 G and 3 G at ambient temperatures of 24 C or 10 C, and the rate of oxygen consumption, the core temperatures, and the tail temperatures were measured. Results show that thermoregulatory mechanisms are impaired when rats are exposed to 3 G fields, and at 24 C as well as at 10 C this impairment leads to an inappropriate increase in heat loss.

  4. Anti-APOBEC3G Activity of HIV-1 Vif Protein Is Attenuated in Elite Controllers

    PubMed Central

    Kikuchi, Tadashi; Iwabu, Yukie; Tada, Takuya; Kawana-Tachikawa, Ai; Koga, Michiko; Hosoya, Noriaki; Nomura, Shigeru; Brumme, Zabrina L.; Jessen, Heiko; Pereyra, Florencia; Trocha, Alicja; Walker, Bruce D.; Iwamoto, Aikichi

    2015-01-01

    ABSTRACT HIV-1-infected individuals who control viremia to below the limit of detection without antiviral therapy have been termed elite controllers (EC). Functional attenuation of some HIV-1 proteins has been reported in EC. The HIV-1 accessory protein Vif (virion infectivity factor) enhances viral infectivity through anti-retroviral factor apolipoprotein B mRNA editing enzyme catalytic polypeptide-like 3G (APOBEC3G) degradation; however, little is known regarding Vif function in EC. Here, the anti-APOBEC3G activities of clonal, plasma HIV RNA-derived Vif sequences from 46 EC, 46 noncontrollers (NC), and 44 individuals with acute infection (AI) were compared. Vesicular stomatitis virus glycoprotein (VSV-G)-pseudotyped viruses were generated by cotransfecting 293T cells with expression plasmids encoding patient-derived Vif, human APOBEC3G, VSV-G, and a vif/env-deficient luciferase-reporter HIV-1 proviral DNA clone. Viral stocks were used to infect 293T cells, and Vif anti-APOBEC3G activity was quantified in terms of luciferase signal. On average, the anti-APOBEC3G activities of EC-derived Vif sequences (median log10 relative light units [RLU], 4.54 [interquartile range {IQR}, 4.30 to 4.66]) were significantly lower than those of sequences derived from NC (4.75 [4.60 to 4.92], P < 0.0001) and AI (4.74 [4.62 to 4.94], P < 0.0001). Reduced Vif activities were not associated with particular HLA class I alleles expressed by the host. Vif functional motifs were highly conserved in all patient groups. No single viral polymorphism could explain the reduced anti-APOBEC3G activity of EC-derived Vif, suggesting that various combinations of minor polymorphisms may underlie these effects. These results further support the idea of relative attenuation of viral protein function in EC-derived HIV sequences. IMPORTANCE HIV-1 elite controllers (EC) are rare individuals who are able to control plasma viremia to undetectable levels without antiretroviral therapy. Understanding the

  5. Wildlife hazards from Furadan 3G applications to rice in Texas

    USGS Publications Warehouse

    Flickinger, Edward L.; King, K.A.; Stout, W.F.; Mohn, M.M.

    1980-01-01

    Mortality of birds, fish, frogs, crayfish, earthworms, and nontarget insects occurred in rice fields after treatments of Furadan 3G granules in 3 Texas counties in 1970 and 1973-75. Three western sandpipers (Ereunetes mauri), 1 pectoral sandpiper (Erolia melanotos), and 2 red-winged blackbirds (Agelaius phoeniceus) were found dead or moribund between 17 and 24 hours after treatment. Cricket frogs (Acris crepitans blanchardi) were intoxicated 15 minutes post-treatment, and mosquito fish (Gambusia affinis) showed effects 1 hour post-treatment. Mortality of mosquito fish, Gulf menhaden (Brevoortia patronus), Atlantic croaker (Micropogon undulatus), and European carp (Cyprinus carpio) usually occurred between 24 and 28 hours after treatment. Mortality of frogs, crayfish, and nontarget insects generally occurred in rice field water between 1 and 45 hours after treatment. Mortality of earthworms in soil persisted for 52 hours. As a replacement for aldrin in Texas rice fields, Furadan 3G appeared to cause Iess mortality of birds than aldrin, but Furadan 3G was toxic to birds, fish, and invertebrates.

  6. Human cellular restriction factors that target HIV-1 replication

    PubMed Central

    Strebel, Klaus; Luban, Jeremy; Jeang, Kuan-Teh

    2009-01-01

    Recent findings have highlighted roles played by innate cellular factors in restricting intracellular viral replication. In this review, we discuss in brief the activities of apolipoprotein B mRNA-editing enzyme 3G (APOBEC3G), bone marrow stromal cell antigen 2 (BST-2), cyclophilin A, tripartite motif protein 5 alpha (Trim5α), and cellular microRNAs as examples of host restriction factors that target HIV-1. We point to countermeasures encoded by HIV-1 for moderating the potency of these cellular restriction functions. PMID:19758442

  7. Hepatitis B virus X protein is capable of down-regulating protein level of host antiviral protein APOBEC3G

    PubMed Central

    Chen, Ruidong; Zhao, Xue; Wang, Yongxiang; Xie, Youhua; Liu, Jing

    2017-01-01

    The apolipoprotein B mRNA editing catalytic polypeptide-like (APOBEC) family proteins bind RNA and single-stranded DNA, and create C-to-U base modifications through cytidine deaminase activity. APOBEC3G restricts human immunodeficiency virus 1 (HIV-1) infection by creating hypermutations in proviral DNA, while HIV-1-encoded vif protein antagonizes such restriction by targeting APOBEC3G for degradation. APOBEC3G also inhibits hepatitis B virus (HBV): APOBEC3G co-expression inhibits HBV replication and evidences exist indicating APOBEC3G-mediated HBV hypermutations in patients. HBV encodes a small non-structural X protein (HBx) with a recognized activating effect on HBV life cycle. In this work, we report the discovery that HBx selectively and dose-dependently decreases the protein level of co-expressed APOBEC3G in transfected Huh-7 cells. The effect was shown to take place post-translationally, but does not rely on protein degradation via proteasome or lysosome. Further work demonstrated that intracellular APOBEC3G is normally exported via exosome secretion and inhibition of exosome biogenesis causes retention of intracellular APOBEC3G. Finally, HBx co-expression specifically enhanced externalization of APOBEC3G via exosomes, resulting in decrease of intracellular APOBEC3G protein level. These data suggest the possibility that in addition to other mechanisms, HBx-mediated activation of HBV might also involve antagonizing of intracellular restriction factor APOBEC3G through promotion of its export. PMID:28098260

  8. 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).

  9. APOBEC3G cytosine deamination hotspots are defined by both sequence context and single-stranded DNA secondary structure.

    PubMed

    Holtz, Colleen M; Sadler, Holly A; Mansky, Louis M

    2013-07-01

    Apolipoprotein B mRNA-editing, enzyme-catalytic, polypeptide-like 3G (i.e., APOBEC3G or A3G) is an evolutionarily conserved cytosine deaminase that potently restricts human immunodeficiency virus type 1 (HIV-1), retrotransposons and other viruses. A3G has a nucleotide target site specificity for cytosine dinucleotides, though only certain cytosine dinucleotides are 'hotspots' for cytosine deamination, and others experience little or no editing by A3G. The factors that define these critical A3G hotspots are not fully understood. To investigate how A3G hotspots are defined, we used an in vitro fluorescence resonance energy transfer-based oligonucleotide assay to probe the site specificity of A3G. Our findings strongly suggest that the target single-stranded DNA (ssDNA) secondary structure as well as the bases directly 3' and 5' of the cytosine dinucleotide are critically important A3G recognition. For instance, A3G cannot readily deaminate a cytosine dinucleotide in ssDNA stem structures or in nucleotide base loops composed of three bases. Single-stranded nucleotide loops up to seven bases in length were poor targets for A3G activity unless cytosine residues flanked the cytosine dinucleotide. Furthermore, we observed that A3G favors adenines, cytosines and thymines flanking the cytosine dinucleotide target in unstructured regions of ssDNA. Low cytosine deaminase activity was detected when guanines flanked the cytosine dinucleotide. Taken together, our findings provide the first demonstration that A3G cytosine deamination hotspots are defined by both the sequence context of the cytosine dinucleotide target as well as the ssDNA secondary structure. This knowledge can be used to better trace the origins of mutations to A3G activity, and illuminate its impact on processes such as HIV-1 genetic variation.

  10. A comparison of VLBI with the ICE-3G glacial rebound model

    NASA Technical Reports Server (NTRS)

    James, Thomas S.; Lambert, Anthony

    1993-01-01

    Crustal motion predicted by the ICE-3G glacial rebound model exhibits a pattern of tangential (horizontal) divergence away from the centers of uplift, which in North America and Europe are located around Hudson Bay and the Gulf of Bothnia. Tangential velocities reach peak magnitudes of 1-2 mm/yr, and must be included when predicting VLBI baseline length change rates due to postglacial rebound. Out of 18 observed VLBI baselines examined three are situated such that their predicted length rates are around their 2 sigma uncertainties or greater. It is encouraging that two of these baselines exhibit predicted length rates within 2 sigma of the observed rates.

  11. 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

  12. 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.

  13. 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)

  14. HOWRAN: An Hybrid Optical Wireless Radio Access Network for WiMAX Antennas Backhauling

    NASA Astrophysics Data System (ADS)

    Gagnaire, Maurice; Youssef, Tony

    In comparison to existing 3G or 3G+ wireless systems, fourth generation (4G), long-term evolution (LTE) or mobile Wimax are characterized by higher bit rates, highly fluctuant traffic matrices and higher antenna’s density. Current backhauling techniques federating radio antennas are not suited to these new characteristics. Several investigations are carried out for the design of new generation radio access networks (NG-RAN) in charge of concentrating radio cellular traffic from the base stations to the core network. In this paper, we propose an original approach based on an Hybrid Optical Wireless Radio Access Network (HOWRAN) exploiting the benefits of radio-over-fiber technologies and of recent advances in the field of optical devices and systems. As an illustration, we apply the HOWRAN concept to the backhauling of fixed or mobile WiMAX base stations. The two main innovative aspects of HOWRAN are depicted: its hardware architecture and its control plane.

  15. Energetic costs of cellular computation.

    PubMed

    Mehta, Pankaj; Schwab, David J

    2012-10-30

    Cells often perform computations in order to respond to environmental cues. A simple example is the classic problem, first considered by Berg and Purcell, of determining the concentration of a chemical ligand in the surrounding media. On general theoretical grounds, it is expected that such computations require cells to consume energy. In particular, Landauer's principle states that energy must be consumed in order to erase the memory of past observations. Here, we explicitly calculate the energetic cost of steady-state computation of ligand concentration for a simple two-component cellular network that implements a noisy version of the Berg-Purcell strategy. We show that learning about external concentrations necessitates the breaking of detailed balance and consumption of energy, with greater learning requiring more energy. Our calculations suggest that the energetic costs of cellular computation may be an important constraint on networks designed to function in resource poor environments, such as the spore germination networks of bacteria.

  16. Energetic costs of cellular computation

    PubMed Central

    Mehta, Pankaj; Schwab, David J.

    2012-01-01

    Cells often perform computations in order to respond to environmental cues. A simple example is the classic problem, first considered by Berg and Purcell, of determining the concentration of a chemical ligand in the surrounding media. On general theoretical grounds, it is expected that such computations require cells to consume energy. In particular, Landauer’s principle states that energy must be consumed in order to erase the memory of past observations. Here, we explicitly calculate the energetic cost of steady-state computation of ligand concentration for a simple two-component cellular network that implements a noisy version of the Berg–Purcell strategy. We show that learning about external concentrations necessitates the breaking of detailed balance and consumption of energy, with greater learning requiring more energy. Our calculations suggest that the energetic costs of cellular computation may be an important constraint on networks designed to function in resource poor environments, such as the spore germination networks of bacteria. PMID:23045633

  17. Metadata Standard and Data Exchange Specifications to Describe, Model, and Integrate Complex and Diverse High-Throughput Screening Data from the Library of Integrated Network-based Cellular Signatures (LINCS).

    PubMed

    Vempati, Uma D; Chung, Caty; Mader, Chris; Koleti, Amar; Datar, Nakul; Vidović, Dušica; Wrobel, David; Erickson, Sean; Muhlich, Jeremy L; Berriz, Gabriel; Benes, Cyril H; Subramanian, Aravind; Pillai, Ajay; Shamu, Caroline E; Schürer, Stephan C

    2014-06-01

    The National Institutes of Health Library of Integrated Network-based Cellular Signatures (LINCS) program is generating extensive multidimensional data sets, including biochemical, genome-wide transcriptional, and phenotypic cellular response signatures to a variety of small-molecule and genetic perturbations with the goal of creating a sustainable, widely applicable, and readily accessible systems biology knowledge resource. Integration and analysis of diverse LINCS data sets depend on the availability of sufficient metadata to describe the assays and screening results and on their syntactic, structural, and semantic consistency. Here we report metadata specifications for the most important molecular and cellular components and recommend them for adoption beyond the LINCS project. We focus on the minimum required information to model LINCS assays and results based on a number of use cases, and we recommend controlled terminologies and ontologies to annotate assays with syntactic consistency and semantic integrity. We also report specifications for a simple annotation format (SAF) to describe assays and screening results based on our metadata specifications with explicit controlled vocabularies. SAF specifically serves to programmatically access and exchange LINCS data as a prerequisite for a distributed information management infrastructure. We applied the metadata specifications to annotate large numbers of LINCS cell lines, proteins, and small molecules. The resources generated and presented here are freely available.

  18. The anti-viral factor APOBEC3G enhances natural killer cell recognition of HIV-infected primary T cells

    PubMed Central

    Norman, Jason M.; Mashiba, Michael; McNamara, Lucy A; Onafuwa-Nuga, Adewunmi; Chiari-Fort, Estelle; Shen, Wenwen; Collins, Kathleen L.

    2011-01-01

    APOBEC3G (A3G) is an intrinsic antiviral factor that inhibits HIV replication by deaminating cytidine residues to uridine. This causes G-to-A hypermutation in the opposite strand and results in viral inactivation. HIV counteracts A3G through the activity of viral infectivity factor (Vif), which promotes A3G degradation. We report that viral protein R (Vpr), which interacts with a uracil glycosylase, also counteracts A3G by reducing uridine incorporation. However, this process results in activation of the DNA damage response pathway and expression of NK cell activating ligands. Our results reveal that pathogen-induced cytidine deamination and the DNA damage response to viral-mediated repair of uridine incorporation enhance recognition of HIV-infected cells by NK cells. PMID:21874023

  19. 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.

  20. Coding region variant 186H/R in Exon 4 of APOBEC3G among individuals of Western India.

    PubMed

    Singh, Hariom; Marathe, Shruti; Nain, Sumitra; Nema, Vijay; Angadi, Mansa; Bapat, Shradha; Pawar, Jyoti; Ghate, Manisha; Sahay, Seema; Gangakhedkar, Raman R

    2016-05-01

    The allelic variations in the AIDS restriction genes have been associated with the acquisition of HIV-1 and its progression. The distribution of antiviral gene variants significantly differs between populations. Therefore, we aimed to evaluate the distribution of variant allele of 186H/R in exon4 of APOBEC3G between HIV infected individuals and healthy controls among western Indian.In the present cross-sectional study, we enrolled a total of 153 HIV-infected patients confirmed and 156 unrelated healthy individuals. Polymorphism for 186H/R in exon4 of APOBEC3G gene was genotyped by PCR-RFLP. With the frequency of 186HR heterozygous genotype of APOBEC3G was found to be 13% in healthy controls and none in HIV infected cases. The frequency of 186HH common genotype of APOBEC3G was observed higher in HIV infected individuals compared with healthy controls (100% vs 91.7%). The variant genotype 186RR in APOBEC3G was not found in both the groups. The frequency of 186R allele of APOBEC3G was found 4.16% in healthy controls and nil in HIV-infected cases. The frequency of 186H allele of APOBEC3G was found to be higher in HIV-infected cases compared with healthy controls (100% vs 95.83%). The frequency of 186R allele in exon4 of APOBEC3G was found to be 4.16% in healthy controls. This observation differs from the previous report published from North India stating the absence of 186R allele of APOBEC3G in the North Indian individuals. The variant 186H/R in exon4 of APOBEC3G was neither associated with risk of acquisition of HIV-1 nor its progression.

  1. Alterations of a Cellular Cholesterol Metabolism Network Are a Molecular Feature of Obesity-Related Type 2 Diabetes and Cardiovascular Disease

    PubMed Central

    Ding, Jingzhong; Reynolds, Lindsay M.; Zeller, Tanja; Müller, Christian; Lohman, Kurt; Nicklas, Barbara J.; Kritchevsky, Stephen B.; Huang, Zhiqing; de la Fuente, Alberto; Soranzo, Nicola; Settlage, Robert E.; Chuang, Chia-Chi; Howard, Timothy; Xu, Ning; Goodarzi, Mark O.; Chen, Y.-D. Ida; Rotter, Jerome I.; Siscovick, David S.; Parks, John S.; Murphy, Susan; Jacobs, David R.; Post, Wendy; Tracy, Russell P.; Wild, Philipp S.; Blankenberg, Stefan; Hoeschele, Ina; Herrington, David; McCall, Charles E.

    2015-01-01

    Obesity is linked to type 2 diabetes (T2D) and cardiovascular diseases; however, the underlying molecular mechanisms remain unclear. We aimed to identify obesity-associated molecular features that may contribute to obesity-related diseases. Using circulating monocytes from 1,264 Multi-Ethnic Study of Atherosclerosis (MESA) participants, we quantified the transcriptome and epigenome. We discovered that alterations in a network of coexpressed cholesterol metabolism genes are a signature feature of obesity and inflammatory stress. This network included 11 BMI-associated genes related to sterol uptake (↑LDLR, ↓MYLIP), synthesis (↑SCD, FADS1, HMGCS1, FDFT1, SQLE, CYP51A1, SC4MOL), and efflux (↓ABCA1, ABCG1), producing a molecular profile expected to increase intracellular cholesterol. Importantly, these alterations were associated with T2D and coronary artery calcium (CAC), independent from cardiometabolic factors, including serum lipid profiles. This network mediated the associations between obesity and T2D/CAC. Several genes in the network harbored C-phosphorus-G dinucleotides (e.g., ABCG1/cg06500161), which overlapped Encyclopedia of DNA Elements (ENCODE)-annotated regulatory regions and had methylation profiles that mediated the associations between BMI/inflammation and expression of their cognate genes. Taken together with several lines of previous experimental evidence, these data suggest that alterations of the cholesterol metabolism gene network represent a molecular link between obesity/inflammation and T2D/CAC. PMID:26153245

  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.

  3. 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…

  4. APOBEC3G is a single-stranded DNA cytidine deaminase and functions independently of HIV reverse transcriptase

    PubMed Central

    Suspène, Rodolphe; Sommer, Peter; Henry, Michel; Ferris, Stéphane; Guétard, Denise; Pochet, Sylvie; Chester, Ann; Navaratnam, Naveenan; Wain-Hobson, Simon; Vartanian, Jean-Pierre

    2004-01-01

    In the absence of the viral vif gene, human immunodeficiency virus (HIV) may be restricted by the APOBEC3G gene on chromosome 22. The role of the HIV Vif protein is to exclude host cell APOBEC3G from the budding virion. As APOBEC3G shows sequence homology to cytidine deaminases, it is presumed that in the absence of Vif, cytidine residues in the cDNA are deaminated yielding uracil. It is not known if additional proteins mediate APOBEC3G function or if deamination occurs in concert with reverse transcription. This report describes an in vitro assay showing that Baculovirus derived APOBEC3G alone extensively deaminates cDNA independently of reverse transcriptase. It reproduces the dinucleotide context typical of G → A hypermutants derived from a Δvif virus. By using an RNaseH– form of reverse transcriptase, it was shown that the cDNA has to be free of its RNA template to allow deamination. APOBEC3G deamination of dC or dCTP was not detected. In short, APOBEC3G is a single-stranded DNA cytidine deaminase capable of restricting retroviral replication. PMID:15121899

  5. 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.

  6. 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

  7. EEG Changes Due to Experimentally Induced 3G Mobile Phone Radiation.

    PubMed

    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.

  8. 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

  9. Multifunctional periodic cellular metals.

    PubMed

    Wadley, Haydn N G

    2006-01-15

    Periodic cellular metals with honeycomb and corrugated topologies are widely used for the cores of light weight sandwich panel structures. Honeycombs have closed cell pores and are well suited for thermal protection while also providing efficient load support. Corrugated core structures provide less efficient and highly anisotropic load support, but enable cross flow heat exchange opportunities because their pores are continuous in one direction. Recent advances in topology design and fabrication have led to the emergence of lattice truss structures with open cell structures. These three classes of periodic cellular metals can now be fabricated from a wide variety of structural alloys. Many topologies are found to provide adequate stiffness and strength for structural load support when configured as the cores of sandwich panels. Sandwich panels with core relative densities of 2-10% and cell sizes in the millimetre range are being assessed for use as multifunctional structures. The open, three-dimensional interconnected pore networks of lattice truss topologies provide opportunities for simultaneously supporting high stresses while also enabling cross flow heat exchange. These highly compressible structures also provide opportunities for the mitigation of high intensity dynamic loads created by impacts and shock waves in air or water. By filling the voids with polymers and hard ceramics, these structures have also been found to offer significant resistance to penetration by projectiles.

  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. 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.

  12. Optimal translation initiation enables Vif-deficient human immunodeficiency virus type 1 to escape restriction by APOBEC3G.

    PubMed

    Haché, Guylaine; Abbink, Truus E M; Berkhout, Ben; Harris, Reuben S

    2009-06-01

    APOBEC3G restricts Vif-deficient human immunodeficiency virus type 1 (HIV-1) by deaminating viral cDNA cytosines to uracils. This promutagenic activity is counteracted by HIV-1 Vif, which is a natural APOBEC3G antagonist. However, we previously reported that Vif-deficient HIV-1 could evolve resistance to APOBEC3G by a novel mechanism requiring an A200-to-C/T transition mutation and Vpr inactivation. A pyrimidine at nucleotide 200 in the untranslated leader region contributed to resistance by increasing virus particle production, which resulted in fewer APOBEC3G molecules per particle. Here we show that the A200-to-C/T mutation functions posttranscriptionally by inactivating an upstream start codon, which in turn enables optimal viral mRNA translation from canonical start codons.

  13. Random Mutagenesis MAPPIT Analysis Identifies Binding Sites for Vif and Gag in Both Cytidine Deaminase Domains of Apobec3G

    PubMed Central

    Uyttendaele, Isabel; Lavens, Delphine; Catteeuw, Dominiek; Lemmens, Irma; Bovijn, Celia

    2012-01-01

    The mammalian two-hybrid system MAPPIT allows the detection of protein-protein interactions in intact human cells. We developed a random mutagenesis screening strategy based on MAPPIT to detect mutations that disrupt the interaction of one protein with multiple protein interactors simultanously. The strategy was used to detect residues of the human cytidine deaminase Apobec3G that are important for its homodimerization and its interaction with the HIV-1 Gag and Vif proteins. The strategy is able to identify the previously described head-to-head homodimerization interface in the N-terminal domain of Apobec3G. Our analysis further detects two new potential interaction surfaces in the N-and C-terminal domain of Apobec3G for interaction with Vif and Gag or for Apobec3G dimerization. PMID:22970171

  14. 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

  15. Mechanism of Enhanced HIV Restriction by Virion Coencapsidated Cytidine Deaminases APOBEC3F and APOBEC3G.

    PubMed

    Ara, Anjuman; Love, Robin P; Follack, Tyson B; Ahmed, Khawaja A; Adolph, Madison B; Chelico, Linda

    2017-02-01

    The APOBEC3 (A3) enzymes, A3G and A3F, are coordinately expressed in CD4(+) T cells and can become coencapsidated into HIV-1 virions, primarily in the absence of the viral infectivity factor (Vif). A3F and A3G are deoxycytidine deaminases that inhibit HIV-1 replication by inducing guanine-to-adenine hypermutation through deamination of cytosine to form uracil in minus-strand DNA. The effect of the simultaneous presence of both A3G and A3F on HIV-1 restriction ability is not clear. Here, we used a single-cycle infectivity assay and biochemical analyses to determine if coencapsidated A3G and A3F differ in their restriction capacity from A3G or A3F alone. Proviral DNA sequencing demonstrated that compared to each A3 enzyme alone, A3G and A3F, when combined, had a coordinate effect on hypermutation. Using size exclusion chromatography, rotational anisotropy, and in vitro deamination assays, we demonstrate that A3F promotes A3G deamination activity by forming an A3F/G hetero-oligomer in the absence of RNA which is more efficient at deaminating cytosines. Further, A3F caused the accumulation of shorter reverse transcripts due to decreasing reverse transcriptase efficiency, which would leave single-stranded minus-strand DNA exposed for longer periods of time, enabling more deamination events to occur. Although A3G and A3F are known to function alongside each other, these data provide evidence for an A3F/G hetero-oligomeric A3 with unique properties compared to each individual counterpart.

  16. A high-linearity SiGe RF power amplifier for 3 G and 4 G small basestations

    NASA Astrophysics Data System (ADS)

    Johansson, Ted; Solati, Noora; Fritzin, Jonas

    2012-08-01

    This article presents the design and evaluation of a linear 3.3 V SiGe power amplifier for 3 G and 4 G femtocells with 18 dBm modulated output power at 2140 MHz. Different biasing schemes to achieve high linearity with low standby current were studied. The adjacent channel power ratio linearity performance with wide-band code division multiple access (3 G) and long term evolution (4 G) downlink signals were compared and differences analysed and explained.

  17. 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.

  18. First-In-Class Small Molecule Inhibitors of the Single-Strand DNA Cytosine Deaminase APOBEC3G

    PubMed Central

    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.

    2012-01-01

    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. 20/34 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 substrate DNA cytosines. PMID:22181350

  19. A Comparison of Two Single-Stranded DNA Binding Models by Mutational Analysis of APOBEC3G

    PubMed Central

    Shindo, Keisuke; Li, Ming; Gross, Phillip J.; Brown, William L.; Harjes, Elena; Lu, Yongjian; Matsuo, Hiroshi; Harris, Reuben S.

    2012-01-01

    APOBEC3G is the best known of several DNA cytosine deaminases that function to inhibit the replication of parasitic genetic elements including the lentivirus HIV. Several high-resolution structures of the APOBEC3G catalytic domain have been generated, but none reveal how this enzyme binds to substrate single-stranded DNA. Here, we constructed a panel of APOBEC3G amino acid substitution mutants and performed a series of biochemical, genetic, and structural assays to distinguish between “Brim” and “Kink” models for single-strand DNA binding. Each model predicts distinct sets of interactions between surface arginines and negatively charged phosphates in the DNA backbone. Concordant with both models, changing the conserved arginine at position 313 to glutamate abolished both catalytic and restriction activities. In support of the Brim model, arginine to glutamate substitutions at positions 213, 215, and 320 also compromised these APOBEC3G activities. Arginine to glutamate substitutions at Kink model residues 374 and 376 had smaller effects. These observations were supported by A3G catalytic domain-ssDNA chemical shift perturbation experiments. The overall data set is most consistent with the Brim model for single-stranded DNA binding by APOBEC3G. PMID:24832226

  20. First-in-class small molecule inhibitors of the single-strand DNA cytosine deaminase APOBEC3G.

    PubMed

    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

    2012-03-16

    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.

  1. 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.

  2. Protein N-glycosylation in oral cancer: dysregulated cellular networks among DPAGT1, E-cadherin adhesion and canonical Wnt signaling.

    PubMed

    Varelas, Xaralabos; Bouchie, Meghan P; Kukuruzinska, Maria A

    2014-07-01

    N-Linked glycosylation (N-glycosylation) of proteins has long been associated with oncogenesis, but not until recently have the molecular mechanisms underlying this relationship begun to be unraveled. Here, we review studies describing how dysregulation of the N-glycosylation-regulating gene, DPAGT1, drives oral cancer. DPAGT1 encodes the first and rate-limiting enzyme in the assembly of the lipid-linked oligosaccharide precursor in the endoplasmic reticulum and thus mediates N-glycosylation of many cancer-related proteins. DPAGT1 controls N-glycosylation of E-cadherin, the major epithelial cell-cell adhesion receptor and a tumor suppressor, thereby affecting intercellular adhesion and cytoskeletal dynamics. DPAGT1 also regulates and is regulated by Wnt/β-catenin signaling, impacting the balance between proliferation and adhesion in homeostatic tissues. Thus, aberrant induction of DPAGT1 promotes a positive feedback network with Wnt/β-catenin that represses E-cadherin-based adhesion and drives tumorigenic phenotypes. Further, modification of receptor tyrosine kinases (RTKs) with N-glycans is known to control their surface presentation via the galectin lattice, and thus increased DPAGT1 expression likely contributes to abnormal activation of RTKs in oral cancer. Collectively, these studies suggest that dysregulation of the DPAGT1/Wnt/E-cadherin network underlies the etiology and pathogenesis of oral cancer.

  3. Plastic alteration of vestibulo-cardiovascular reflex induced by 2 weeks of 3-G load in conscious rats.

    PubMed

    Abe, Chikara; Tanaka, Kunihiko; Awazu, Chihiro; Chen, Huayue; Morita, Hironobu

    2007-08-01

    Previous studies conducted in our laboratory have demonstrated that the vestibular system plays a significant role in controlling arterial pressure (AP) in conscious rats under conditions of transient microgravity. The vestibular system is known to be highly plastic, and on exposure to different gravitational environments, the sensitivity of the vestibular system-mediated AP response might be altered. In order to test this hypothesis, rats were maintained in a 3-G or a normal 1-G environment for 2 weeks, and the AP responses to free drop-induced microgravity were determined. In 1-G rats, the microgravity increased the AP by 37 +/- 3 mmHg; this pressor response was significantly attenuated by vestibular lesion (VL) (24 +/- 3 mmHg) or body stabilization (29 +/- 2 mmHg). Thus, the microgravity-induced pressor response was mediated by both the vestibular and nonvestibular systems; the input of the latter system was blocked by body stabilization. In the 3-G rats, the pressor responses were significantly suppressed compared to those in the corresponding 1-G rats; i.e., the AP increased by 24 +/- 2 mmHg in freely moving 3-G rats, by 10 +/- 4 mmHg in 3-G rats with VL, and by 13 +/- 4 mmHg in stabilized 3-G rats. Furthermore, there was no difference between the 1- and 3-G rats in terms of the pressor response induced by stressors such as a loud noise or an air jet. These results indicate that pre-exposure to 3-G for 2 weeks induces plasticity in both the vestibular- and nonvestibular-mediated AP responses to microgravity.

  4. 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.

  5. 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.

  6. SMAC: A soft MAC to reduce control overhead and latency in CDMA-based AMI networks

    DOE PAGES

    Garlapati, Shravan; Kuruganti, Teja; Buehrer, Michael R.; ...

    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

  7. 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.

  8. Effects of electromagnetic radiation from 3G mobile phone on heart rate, blood pressure and ECG parameters in rats.

    PubMed

    Colak, Cengiz; Parlakpinar, Hakan; Ermis, Necip; Tagluk, Mehmet Emin; Colak, Cemil; Sarihan, Ediz; Dilek, Omer Faruk; Turan, Bahadir; Bakir, Sevtap; Acet, Ahmet

    2012-08-01

    Effects of electromagnetic energy radiated from mobile phones (MPs) on heart is one of the research interests. The current study was designed to investigate the effects of electromagnetic radiation (EMR) from third-generation (3G) MP on the heart rate (HR), blood pressure (BP) and ECG parameters and also to investigate whether exogenous melatonin can exert any protective effect on these parameters. In this study 36 rats were randomized and evenly categorized into 4 groups: group 1 (3G-EMR exposed); group 2 (3G-EMR exposed + melatonin); group 3 (control) and group 4 (control + melatonin). The rats in groups 1 and 2 were exposed to 3G-specific MP's EMR for 20 days (40 min/day; 20 min active (speech position) and 20 min passive (listening position)). Group 2 was also administered with melatonin for 20 days (5 mg/kg daily during the experimental period). ECG signals were recorded from cannulated carotid artery both before and after the experiment, and BP and HR were calculated on 1st, 3rd and 5th min of recordings. ECG signals were processed and statistically evaluated. In our experience, the obtained results did not show significant differences in the BP, HR and ECG parameters among the groups both before and after the experiment. Melatonin, also, did not exhibit any additional effects, neither beneficial nor hazardous, on the heart hemodynamics of rats. Therefore, the strategy (noncontact) of using a 3G MP could be the reason for ineffectiveness; and use of 3G MP, in this perspective, seems to be safer compared to the ones used in close contact with the head. However, further study is needed for standardization of such an assumption.

  9. The murine Nck SH2/SH3 adaptors are important for the development of mesoderm-derived embryonic structures and for regulating the cellular actin network.

    PubMed

    Bladt, Friedhelm; Aippersbach, Elke; Gelkop, Sigal; Strasser, Geraldine A; Nash, Piers; Tafuri, Anna; Gertler, Frank B; Pawson, Tony

    2003-07-01

    Mammalian Nck1 and Nck2 are closely related adaptor proteins that possess three SH3 domains, followed by an SH2 domain, and are implicated in coupling phosphotyrosine signals to polypeptides that regulate the actin cytoskeleton. However, the in vivo functions of Nck1 and Nck2 have not been defined. We have mutated the murine Nck1 and Nck2 genes and incorporated beta-galactosidase reporters into the mutant loci. In mouse embryos, the two Nck genes have broad and overlapping expression patterns. They are functionally redundant in the sense that mice deficient for either Nck1 or Nck2 are viable, whereas inactivation of both Nck1 and Nck2 results in profound defects in mesoderm-derived notochord and embryonic lethality at embryonic day 9.5. Fibroblast cell lines derived from Nck1(-/-) Nck2(-/-) embryos have defects in cell motility and in the organization of the lamellipodial actin network. These data suggest that the Nck SH2/SH3 adaptors have important functions in the development of mesodermal structures during embryogenesis, potentially linked to a role in cell movement and cytoskeletal organization.

  10. RADStation3G: a platform for cardiovascular image analysis integrating PACS, 3D+t visualization and grid computing.

    PubMed

    Perez, F; Huguet, J; Aguilar, R; Lara, L; Larrabide, I; Villa-Uriol, M C; López, J; Macho, J M; Rigo, A; Rosselló, J; Vera, S; Vivas, E; Fernàndez, J; Arbona, A; Frangi, A F; Herrero Jover, J; González Ballester, M A

    2013-06-01

    RADStation3G is a software platform for cardiovascular image analysis and surgery planning. It provides image visualization and management in 2D, 3D and 3D+t; data storage (images or operational results) in a PACS (using DICOM); and exploitation of patients' data such as images and pathologies. Further, it provides support for computationally expensive processes with grid technology. In this article we first introduce the platform and present a comparison with existing systems, according to the platform's modules (for cardiology, angiology, PACS archived enriched searching and grid computing), and then RADStation3G is described in detail.

  11. 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.

  12. 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

  13. 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.

  14. 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.

  15. 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.

  16. Hydrothermal synthesis of In2S3/g-C3N4 heterojunctions with enhanced photocatalytic activity.

    PubMed

    Xing, Chaosheng; Wu, Zhudong; Jiang, Deli; Chen, Min

    2014-11-01

    Graphitic carbon nitride (g-C3N4) was hybridized by In2S3 to form a novel In2S3/g-C3N4 heterojunction photocatalyst via a hydrothermal method. TEM and HRTEM results reveal that In2S3 nanoparticles and g-C3N4 closely contact with each other to form an intimate interface. The as-obtained In2S3/g-C3N4 heterojunctions exhibit higher photocatalytic activity than those of pure g-C3N4 and In2S3 for the photodegradation of rhodamine B (RhB) under visible light irradiation. The enhanced photocatalytic performance of In2S3/g-C3N4 heterojunctions could be attributed to its wide absorption in the visible region and efficient electron-hole separation. On the basis of radical scavenger experiments, superoxide radicals and holes are suggested to play a critical role in RhB degradation over In2S3/g-C3N4 heterojunctions.

  17. 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.

  18. N-terminal and C-terminal cytosine deaminase domain of APOBEC3G inhibit hepatitis B virus replication

    PubMed Central

    Lei, Yan-Chang; Tian, Yong-Jun; Ding, Hong-Hui; Wang, Bao-Ju; Yang, Yan; Hao, You-Hua; Zhao, Xi-Ping; Lu, Meng-Ji; Gong, Fei-Li; Yang, Dong-Liang

    2006-01-01

    AIM: To investigate the effect of human apolipoprotein B mRNA-editing enzyme catalytic-polypeptide 3G (APOBEC3G) and its N-terminal or C-terminal cytosine deaminase domain-mediated antiviral activity against hepatitis B virus (HBV) in vitro and in vivo. METHODS: The mammalian hepatoma cells HepG2 and HuH7 were cotransfected with APOBEC3G and its N-terminal or C-terminal cytosine deaminase domain expression vector and 1.3-fold-overlength HBV DNA as well as the linear monomeric HBV of genotype B and C. For in vivo study, an HBV vector-based mouse model was used in which APOBEC3G and its N-terminal or C-terminal cytosine deaminase domain expression vectors were co-delivered with 1.3-fold-overlength HBV DNA via high-volume tail vein injection. Levels of hepatitis B virus surface antigen (HBsAg) and hepatitis B virus e antigen (HBeAg) in the media of the transfected cells and in the sera of mice were determined by ELISA. The expression of hepatitis B virus core antigen (HBcAg) in the transfected cells was determined by Western blot analysis. Core-associated HBV DNA was examined by Southern blot analysis. Levels of HBV DNA in the sera of mice as well as HBV core-associated RNA in the liver of mice were determined by quantitative PCR and quantitative RT-PCR analysis, respectively. RESULTS: Human APOBEC3G exerted an anti-HBV activity in a dose-dependent manner in HepG2 cells, and comparable suppressive effects were observed on genotype B and C as that of genotype A. Interestingly, the N-terminal or C-terminal cytosine deaminase domain alone could also inhibit HBV replication in HepG2 cells as well as Huh7 cells. Consistent with in vitro results, the levels of HBsAg in the sera of mice were dramatically decreased, with more than 50 times decrease in the levels of serum HBV DNA and core-associated RNA in the liver of mice treated with APOBEC3G and its N-terminal or C-terminal cytosine deaminase domain as compared to the controls. CONCLUSION: Our findings provide probably the

  19. 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.

  20. 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

  1. Possible Footprints of APOBEC3F and/or Other APOBEC3 Deaminases, but Not APOBEC3G, on HIV-1 from Patients with Acute/Early and Chronic Infections

    PubMed Central

    Armitage, Andrew E.; Deforche, Koen; Welch, John J.; Van Laethem, Kristel; Camacho, Ricardo; Rambaut, Andrew

    2014-01-01

    ABSTRACT Members of the apolipoprotein B mRNA-editing enzyme-catalytic polypeptide-like-3 (APOBEC3) innate cellular cytidine deaminase family, particularly APOBEC3F and APOBEC3G, can cause extensive and lethal G-to-A mutations in HIV-1 plus-strand DNA (termed hypermutation). It is unclear if APOBEC3-induced mutations in vivo are always lethal or can occur at sublethal levels that increase HIV-1 diversification and viral adaptation to the host. The viral accessory protein Vif counteracts APOBEC3 activity by binding to APOBEC3 and promoting proteasome degradation; however, the efficiency of this interaction varies, since a range of hypermutation frequencies are observed in HIV-1 patient DNA. Therefore, we examined “footprints” of APOBEC3G and APOBEC3F activity in longitudinal HIV-1 RNA pol sequences from approximately 3,000 chronically infected patients by determining whether G-to-A mutations occurred in motifs that were favored or disfavored by these deaminases. G-to-A mutations were more frequent in APOBEC3G-disfavored than in APOBEC3G-favored contexts. In contrast, mutations in APOBEC3F-disfavored contexts were relatively rare, whereas mutations in contexts favoring APOBEC3F (and possibly other deaminases) occurred 16% more often than average G-to-A mutations. These results were supported by analyses of >500 HIV-1 env sequences from acute/early infection. IMPORTANCE Collectively, our results suggest that APOBEC3G-induced mutagenesis is lethal to HIV-1, whereas mutagenesis caused by APOBEC3F and/or other deaminases may result in sublethal mutations that might facilitate viral diversification. Therefore, Vif-specific cytotoxic T lymphocyte (CTL) responses and drugs that manipulate the interplay between Vif and APOBEC3 may have beneficial or detrimental clinical effects depending on how they affect the binding of Vif to various members of the APOBEC3 family. PMID:25165112

  2. 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.

  3. 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

  4. Large arrays of dual-polarized multichroic TES detectors for CMB measurements with the SPT-3G receiver

    NASA Astrophysics Data System (ADS)

    Posada, Chrystian M.; Ade, Peter A. R.; Anderson, Adam J.; Avva, Jessica; Ahmed, Zeeshan; Arnold, Kam S.; Austermann, Jason; Bender, Amy N.; Benson, Bradford A.; Bleem, Lindsey; Byrum, Karen; Carlstrom, John E.; Carter, Faustin W.; Chang, Clarence; Cho, Hsiao-Mei; Cukierman, Ari; Czaplewski, David A.; Ding, Junjia; Divan, Ralu N. S.; de Haan, Tijmen; Dobbs, Matt; Dutcher, Daniel; Everett, Wenderline; Gannon, Renae N.; Guyser, Robert J.; Halverson, Nils W.; Harrington, Nicholas L.; Hattori, Kaori; Henning, Jason W.; Hilton, Gene C.; Holzapfel, William L.; Huang, Nicholas; Irwin, Kent D.; Jeong, Oliver; Khaire, Trupti; Korman, Milo; Kubik, Donna L.; Kuo, Chao-Lin; Lee, Adrian T.; Leitch, Erik M.; Lendinez Escudero, Sergi; Meyer, Stephan S.; Miller, Christina S.; Montgomery, Joshua; Nadolski, Andrew; Natoli, Tyler J.; Nguyen, Hogan; Novosad, Valentyn; Padin, Stephen; Pan, Zhaodi; Pearson, John E.; Rahlin, Alexandra; Reichardt, Christian L.; Ruhl, John E.; Saliwanchik, Benjamin; Shirley, Ian; Sayre, James T.; Shariff, Jamil A.; Shirokoff, Erik D.; Stan, Liliana; Stark, Antony A.; Sobrin, Joshua; Story, Kyle; Suzuki, Aritoki; Tang, Qing Yang; Thakur, Ritoban B.; Thompson, Keith L.; Tucker, Carole E.; Vanderlinde, Keith; Vieira, Joaquin D.; Wang, Gensheng; Whitehorn, Nathan; Yefremenko, Volodymyr; Yoon, Ki Won

    2016-07-01

    Detectors for cosmic microwave background (CMB) experiments are now essentially background limited, so a straightforward alternative to improve sensitivity is to increase the number of detectors. Large arrays of multichroic pixels constitute an economical approach to increasing the number of detectors within a given focal plane area. Here, we present the fabrication of large arrays of dual-polarized multichroic transition-edge-sensor (TES) bolometers for the South Pole Telescope third-generation CMB receiver (SPT-3G). The complete SPT-3G receiver will have 2690 pixels, each with six detectors, allowing for individual measurement of three spectral bands (centered at 95 GHz, 150 GHz and 220 GHz) in two orthogonal polarizations. In total, the SPT-3G focal plane will have 16140 detectors. Each pixel is comprised of a broad-band sinuous antenna coupled to a niobium microstrip transmission line. In-line filters are used to define the different band-passes before the millimeter-wavelength signal is fed to the respective Ti/Au TES sensors. Detectors are read out using a 64x frequency domain multiplexing (fMux) scheme. The microfabrication of the SPT-3G detector arrays involves a total of 18 processes, including 13 lithography steps. Together with the fabrication process, the effect of processing on the Ti/Au TES's Tc is discussed. In addition, detectors fabricated with Ti/Au TES films with Tc between 400 mK 560 mK are presented and their thermal characteristics are evaluated. Optical characterization of the arrays is presented as well, indicating that the response of the detectors is in good agreement with the design values for all three spectral bands (95 GHz, 150 GHz, and 220 GHz). The measured optical efficiency of the detectors is between 0.3 and 0.8. Results discussed here are extracted from a batch of research of development wafers used to develop the baseline process for the fabrication of the arrays of detectors to be deployed with the SPT-3G receiver. Results from

  5. A synthetic snRNA m3G-CAP enhances nuclear delivery of exogenous proteins and nucleic acids.

    PubMed

    Moreno, Pedro M D; Wenska, Malgorzata; Lundin, Karin E; Wrange, Orjan; Strömberg, Roger; Smith, C I Edvard

    2009-04-01

    Accessing the nucleus through the surrounding membrane poses one of the major obstacles for therapeutic molecules large enough to be excluded due to nuclear pore size limits. In some therapeutic applications the large size of some nucleic acids, like plasmid DNA, hampers their access to the nuclear compartment. However, also for small oligonucleotides, achieving higher nuclear concentrations could be of great benefit. We report on the synthesis and possible applications of a natural RNA 5'-end nuclear localization signal composed of a 2,2,7-trimethylguanosine cap (m(3)G-CAP). The cap is found in the small nuclear RNAs that are constitutive part of the small nuclear ribonucleoprotein complexes involved in nuclear splicing. We demonstrate the use of the m(3)G signal as an adaptor that can be attached to different oligonucleotides, thereby conferring nuclear targeting capabilities with capacity to transport large-size cargo molecules. The synthetic capping of oligos interfering with splicing may have immediate clinical applications.

  6. Preparation of WO3/g-C3N4 composites and their application in oxidative desulfurization

    NASA Astrophysics Data System (ADS)

    Zhao, Rongxiang; Li, Xiuping; Su, Jianxun; Gao, Xiaohan

    2017-01-01

    WO3/graphitic carbon nitride (g-C3N4) composites were successfully synthesized through direct calcining of a mixture of WO3 and g-C3N4 at 400 °C for 2 h. The WO3 was prepared by calcination of phosphotungstic acid at 550 °C for 4 h, and the g-C3N4 was obtained by calcination of melamine at 520 °C for 4 h. The WO3/g-C3N4 composites were characterized by X-ray diffraction (XRD), Scanning electron microscopy (SEM), Fourier-transform infrared spectroscopy (FT-IR), and Brunner-Emmett-Teller analysis (BET). The WO3/g-C3N4 composites exhibited stronger XRD peaks of WO3 and g-C3N4 than the WO3 and pure g-C3N4. In addition, two WO3 peaks at 25.7° and 26.6° emerged for the 36% -WO3/g-C3N4 composite. This finding indicated that WO3 was highly dispersed on the surface of the g-C3N4 nanosheets and interacted with the nanosheets, which resulted in the appearance of (012) and (022) planes of WO3. The WO3/g-C3N4 composite also exhibited a larger specific surface area and higher degree of crystallization than WO3 or pure g-C3N4, which resulted in high catalytic activity of the catalyst. Desulfurization experiments demonstrated that the desulfurization rate of dibenzothiophene (DBT) in model oil reached 91.2% under optimal conditions. Moreover, the activity of the catalyst was not significantly decreased after five recycles.

  7. A Cellular Biophysics Textbook

    NASA Astrophysics Data System (ADS)

    Wilder, Alan Joseph

    2011-12-01

    In the past two decades, great advances have been made in understanding of the biophysical mechanisms of the protein machines that carry out the fundamental processes of the cell. It is now known that all major eukaryotic cellular processes require a complicated assemblage of proteins acting via a series of concerted motions. In order to grasp current understanding of cellular mechanisms, the new generation of cell biologists needs to be trained in the general characteristics of these cellular properties and the methods with which to study them. This cellular biophysics textbook, to be used in conjunction with the cellular biophysics course (MCB143) at UC-Davis, provides a great tool in the instruction of the new generation of cellular biologists. It provides a hierarchical view of the cell, from atoms to protein machines and explains in depth the mechanisms of cytoskeletal force generators as an example of these principles.

  8. 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

  9. Developing a Resilient Green Cellular Network

    DTIC Science & Technology

    2013-12-01

    labor , and planning to deploy that subsequently detracts from conducting immediate response and recovery. This research is intended to propose a path...This mitigating strategy requires substantial time, labor , and planning to deploy that subsequently detracts from conducting immediate response and...29 A. KATRINA .......................................................................................................29 B. DERECHO

  10. 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.

  11. Plasmonic Nanostructured Cellular Automata

    NASA Astrophysics Data System (ADS)

    Alkhazraji, Emad; Ghalib, A.; Manzoor, K.; Alsunaidi, M. A.

    2017-03-01

    In this work, we have investigated the scattering plasmonic resonance characteristics of silver nanospheres with a geometrical distribution that is modelled by Cellular Automata using time-domain numerical analysis. Cellular Automata are discrete mathematical structures that model different natural phenomena. Two binary one-dimensional Cellular Automata rules are considered to model the nanostructure, namely rule 30 and rule 33. The analysis produces three-dimensional scattering profiles of the entire plasmonic nanostructure. For the Cellular Automaton rule 33, the introduction of more Cellular Automata generations resulted only in slight red and blue shifts in the plasmonic modes with respect to the first generation. On the other hand, while rule 30 introduced significant red shifts in the resonance peaks at early generations, at later generations however, a peculiar effect is witnessed in the scattering profile as new peaks emerge as a feature of the overall Cellular Automata structure rather than the sum of the smaller parts that compose it. We strongly believe that these features that emerge as a result adopting the different 256 Cellular Automata rules as configuration models of nanostructures in different applications and systems might possess a great potential in enhancing their capability, sensitivity, efficiency, and power utilization.

  12. Effect of 3G cell phone exposure with computer controlled 2-D stepper motor on non-thermal activation of the hsp27/p38MAPK stress pathway in rat brain.

    PubMed

    Kesari, Kavindra Kumar; Meena, Ramovatar; Nirala, Jayprakash; Kumar, Jitender; Verma, H N

    2014-03-01

    Cell phone radiation exposure and its biological interaction is the present concern of debate. Present study aimed to investigate the effect of 3G cell phone exposure with computer controlled 2-D stepper motor on 45-day-old male Wistar rat brain. Animals were exposed for 2 h a day for 60 days by using mobile phone with angular movement up to zero to 30°. The variation of the motor is restricted to 90° with respect to the horizontal plane, moving at a pre-determined rate of 2° per minute. Immediately after 60 days of exposure, animals were scarified and numbers of parameters (DNA double-strand break, micronuclei, caspase 3, apoptosis, DNA fragmentation, expression of stress-responsive genes) were performed. Result shows that microwave radiation emitted from 3G mobile phone significantly induced DNA strand breaks in brain. Meanwhile a significant increase in micronuclei, caspase 3 and apoptosis were also observed in exposed group (P < 0.05). Western blotting result shows that 3G mobile phone exposure causes a transient increase in phosphorylation of hsp27, hsp70, and p38 mitogen-activated protein kinase (p38MAPK), which leads to mitochondrial dysfunction-mediated cytochrome c release and subsequent activation of caspases, involved in the process of radiation-induced apoptotic cell death. Study shows that the oxidative stress is the main factor which activates a variety of cellular signal transduction pathways, among them the hsp27/p38MAPK is the pathway of principle stress response. Results conclude that 3G mobile phone radiations affect the brain function and cause several neurological disorders.

  13. 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.

  14. Identification of dominant negative human immunodeficiency virus type 1 Vif mutants that interfere with the functional inactivation of APOBEC3G by virus-encoded Vif.

    PubMed

    Walker, Robert C; Khan, Mohammad A; Kao, Sandra; Goila-Gaur, Ritu; Miyagi, Eri; Strebel, Klaus

    2010-05-01

    APOBEC3G (A3G) is a host cytidine deaminase that serves as a potent intrinsic inhibitor of retroviral replication. A3G is packaged into human immunodeficiency virus type 1 virions and deaminates deoxycytidine to deoxyuridine on nascent minus-strand retroviral cDNA, leading to hyper-deoxyguanine-to-deoxyadenine mutations on positive-strand cDNA and inhibition of viral replication. The antiviral activity of A3G is suppressed by Vif, a lentiviral accessory protein that prevents encapsidation of A3G. In this study, we identified dominant negative mutants of Vif that interfered with the ability of wild-type Vif to inhibit the encapsidation and antiviral activity of A3G. These mutants were nonfunctional due to mutations in the highly conserved HCCH and/or SOCS box motifs, which are required for assembly of a functional Cul5-E3 ubiquitin ligase complex. Similarly, mutation or deletion of a PPLP motif, which was previously reported to be important for Vif dimerization, induced a dominant negative phenotype. Expression of dominant negative Vif counteracted the Vif-induced reduction of intracellular A3G levels, presumably by preventing Vif-induced A3G degradation. Consequently, dominant negative Vif interfered with wild-type Vif's ability to exclude A3G from viral particles and reduced viral infectivity despite the presence of wild-type Vif. The identification of dominant negative mutants of Vif presents exciting possibilities for the design of novel antiviral strategies.

  15. Cellular aging and cancer

    PubMed Central

    Hornsby, Peter J.

    2010-01-01

    Aging is manifest in a variety of changes over time, including changes at the cellular level. Cellular aging acts primarily as a tumor suppressor mechanism, but also may enhance cancer development under certain circumstances. One important process of cellular aging is oncogene-induced senescence, which acts as an important anti-cancer mechanism. Cellular senescence resulting from damage caused by activated oncogenes prevents the growth or potentially neoplastic cells. Moreover, cells that have entered senescence appear to be targets for elimination by the innnate immune system. In another aspect of cellular aging, the absence of telomerase activity in normal tissues results in such cells lacking a telomere maintenance mechanism. One consequence is that in aging there is an increase in cells with shortened telomeres. In the presence of active oncogenes that cause expansion of a neoplastic clone, shortening of telomeres leading to telomere dysfunction prevents the indefinite expansion of the clone because the cells enter crisis. Crisis results from fusions and other defects caused by dysfunctional telomeres and is a terminal state of the neoplastic clone. In this way the absence of telomerase in human cells, while one cause of cellular aging, also acts as an anti-cancer mechanism. PMID:20705476

  16. Transient inter-cellular polymeric linker.

    PubMed

    Ong, Siew-Min; He, Lijuan; Thuy Linh, Nguyen Thi; Tee, Yee-Han; Arooz, Talha; Tang, Guping; Tan, Choon-Hong; Yu, Hanry

    2007-09-01

    Three-dimensional (3D) tissue-engineered constructs with bio-mimicry cell-cell and cell-matrix interactions are useful in regenerative medicine. In cell-dense and matrix-poor tissues of the internal organs, cells support one another via cell-cell interactions, supplemented by small amount of the extra-cellular matrices (ECM) secreted by the cells. Here we connect HepG2 cells directly but transiently with inter-cellular polymeric linker to facilitate cell-cell interaction and aggregation. The linker consists of a non-toxic low molecular-weight polyethyleneimine (PEI) backbone conjugated with multiple hydrazide groups that can aggregate cells within 30 min by reacting with the aldehyde handles on the chemically modified cell-surface glycoproteins. The cells in the cellular aggregates proliferated; and maintained the cortical actin distribution of the 3D cell morphology while non-aggregated cells died over 7 days of suspension culture. The aggregates lost distinguishable cell-cell boundaries within 3 days; and the ECM fibers became visible around cells from day 3 onwards while the inter-cellular polymeric linker disappeared from the cell surfaces over time. The transient inter-cellular polymeric linker can be useful for forming 3D cellular and tissue constructs without bulk biomaterials or extensive network of engineered ECM for various applications.

  17. Wound Documentation by Using 3G Mobile as Acquisition Terminal: An Appropriate Proposal for Community Wound Care.

    PubMed

    Ge, Kui; Wu, Minjie; Liu, Hu; Gong, Jiahong; Zhang, Yi; Hu, Qiang; Fang, Min; Tao, Yanping; Cai, Minqiang; Chen, Hua; Wang, Jianbo; Xie, Ting; Lu, Shuliang

    2015-06-01

    The increasing numbers of cases of wound disease are now posing a big challenge in China. For more convenience of wound patients, wound management in community health care centers under the supervision of a specialist at general hospitals is an ideal solution. To ensure an accurate diagnosis in community health clinics, it is important that "the same language" for wound description, which may be composed of unified format description, including wound image, must be achieved. We developed a wound information management system that was built up by acquisition terminal, wound description, data bank, and related software. In this system, a 3G mobile phone was applied as acquisition terminal, which could be used to access to the data bank. This documentation system was thought to be an appropriate proposal for community wound care because of its objectivity, uniformity, and facilitation. It also provides possibility for epidemiological study in the future.

  18. Small-molecule APOBEC3G DNA cytosine deaminase inhibitors based on a 4-amino-1,2,4-triazole-3-thiol scaffold.

    PubMed

    Olson, Margaret E; Li, Ming; Harris, Reuben S; Harki, Daniel A

    2013-01-01

    APOBEC3G (A3G) is a single-stranded DNA cytosine deaminase that functions in innate immunity against retroviruses and retrotransposons. Although A3G can potently restrict Vif-deficient HIV-1 replication by catalyzing excessive levels of G→A hypermutation, sublethal levels of A3G-catalyzed mutation may contribute to the high level of HIV-1 fitness and its incurable prognosis. To chemically modulate A3G catalytic activity with the goal of decreasing the HIV-1 genomic mutation rate, we synthesized and biochemically evaluated a class of 4-amino-1,2,4-triazole-3-thiol small-molecule inhibitors identified by high-throughput screening. This class of compounds exhibits low-micromolar (3.9-8.2 μM) inhibitory potency and remarkable specificity for A3G versus the related cytosine deaminase, APOBEC3A. Chemical modification of inhibitors, A3G mutational screening, and thiol reactivity studies implicate C321, a residue proximal to the active site, as the critical A3G target for this class of molecules.

  19. NIa-Pro of Papaya ringspot virus interacts with Carica papaya eukaryotic translation initiation factor 3 subunit G (CpeIF3G).

    PubMed

    Gao, Le; Tuo, Decai; Shen, Wentao; Yan, Pu; Li, Xiaoying; Zhou, Peng

    2015-02-01

    The interaction of papaya eukaryotic translation initiation factor 3 subunit G (CpeIF3G) with Papaya ringspot virus (PRSV) NIa-Pro was validated using a bimolecular fluorescence complementation assay in papaya protoplasts based on the previous yeast two-hybrid assay results. The C-terminal (residues 133-239) fragment of PRSV NIa-Pro and the central domain (residues 59-167) of CpeIF3G were required for effective interaction between NIa-Pro and CpeIF3G as shown by a Sos recruitment yeast two-hybrid system with several deletion mutants of NIa-Pro and CpeIF3G. The central domain of CpeIF3G, which contains a C2HC-type zinc finger motif, is required to bind to other eIFs of the translational machinery. In addition, quantitative real-time reverse transcription PCR assay confirmed that PRSV infection leads to a 2- to 4.5-fold up-regulation of CpeIF3G mRNA in papaya. Plant eIF3G is involved in various stress response by enhancing the translation of resistance-related proteins. It is proposed that the NIa-Pro-CpeIF3G interaction may impair translation preinitiation complex assembly of defense proteins and interfere with host defense.

  20. A hydrodynamic analysis of APOBEC3G reveals a monomer-dimer-tetramer self-association that has implications for anti-HIV function.

    PubMed

    Salter, Jason D; Krucinska, Jolanta; Raina, Jay; Smith, Harold C; Wedekind, Joseph E

    2009-11-17

    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.

  1. Triangles bridge the scales: Quantifying cellular contributions to tissue deformation

    NASA Astrophysics Data System (ADS)

    Merkel, Matthias; Etournay, Raphaël; Popović, Marko; Salbreux, Guillaume; Eaton, Suzanne; Jülicher, Frank

    2017-03-01

    In this article, we propose a general framework to study the dynamics and topology of cellular networks that capture the geometry of cell packings in two-dimensional tissues. Such epithelia undergo large-scale deformation during morphogenesis of a multicellular organism. Large-scale deformations emerge from many individual cellular events such as cell shape changes, cell rearrangements, cell divisions, and cell extrusions. Using a triangle-based representation of cellular network geometry, we obtain an exact decomposition of large-scale material deformation. Interestingly, our approach reveals contributions of correlations between cellular rotations and elongation as well as cellular growth and elongation to tissue deformation. Using this triangle method, we discuss tissue remodeling in the developing pupal wing of the fly Drosophila melanogaster.

  2. Fatigue of cellular materials

    SciTech Connect

    Huang, J.S.; Lin, J.Y.

    1996-01-01

    The fatigue of cellular materials is analyzed using dimensional arguments. When the first unbroken cell wall ahead of the macrocrack tip fails after some cycles of loading, the macrocrack advances one cell diameter, giving the macrocrack growth rate of cellular materials. Paris law for microcrack propagation, Basquin law for high cycle fatigue and Coffin-Manson law for low cycle fatigue are employed in calculating the number of cycles to failure of the first unbroken cell wall ahead of the macrocrack tip. It is found that fatigue of cellular materials depends on cyclic stress intensity range, cell size, relative density and the fatigue parameters of the solid from which they are made. Theoretical modelling of fatigue of foams is compared to data in polymer foams; agreement is good.

  3. Epigenetics and Cellular Metabolism

    PubMed Central

    Xu, Wenyi; Wang, Fengzhong; Yu, Zhongsheng; Xin, Fengjiao

    2016-01-01

    Living eukaryotic systems evolve delicate cellular mechanisms for responding to various environmental signals. Among them, epigenetic machinery (DNA methylation, histone modifications, microRNAs, etc.) is the hub in transducing external stimuli into transcriptional response. Emerging evidence reveals the concept that epigenetic signatures are essential for the proper maintenance of cellular metabolism. On the other hand, the metabolite, a main environmental input, can also influence the processing of epigenetic memory. Here, we summarize the recent research progress in the epigenetic regulation of cellular metabolism and discuss how the dysfunction of epigenetic machineries influences the development of metabolic disorders such as diabetes and obesity; then, we focus on discussing the notion that manipulating metabolites, the fuel of cell metabolism, can function as a strategy for interfering epigenetic machinery and its related disease progression as well. PMID:27695375

  4. Origins of cellular geometry

    PubMed Central

    2011-01-01

    Cells are highly complex and orderly machines, with defined shapes and a startling variety of internal organizations. Complex geometry is a feature of both free-living unicellular organisms and cells inside multicellular animals. Where does the geometry of a cell come from? Many of the same questions that arise in developmental biology can also be asked of cells, but in most cases we do not know the answers. How much of cellular organization is dictated by global cell polarity cues as opposed to local interactions between cellular components? Does cellular structure persist across cell generations? What is the relationship between cell geometry and tissue organization? What ensures that intracellular structures are scaled to the overall size of the cell? Cell biology is only now beginning to come to grips with these questions. PMID:21880160

  5. Reduction of lipid peroxidation products and advanced glycation end-product precursors by cyanobacterial aldo-keto reductase AKR3G1—a founding member of the AKR3G subfamily.

    PubMed

    Hintzpeter, Jan; Martin, Hans-Joerg; Maser, Edmund

    2015-01-01

    The purpose of this study was to investigate the origin and function of the aldo-keto reductase (AKR) superfamily as enzymes involved in the detoxification of xenobiotics. We used the cyanobacterium Synechocystis sp. PCC 6803 as a model organism and sequence alignments to find bacterial AKRs with highest identity to human enzymes. Disappearance of NADPH was monitored spectrophotometrically to calculate enzymatic activity. The molecular weight of the native protein was determined by size exclusion chromatography. Substrate docking was performed by SwissDock. Sequence alignments identified the NADPH-dependent AKR3G1 having 41.5 and 40% identity with the human enzymes AKR1B1 and AKR1B10, respectively. Highest enzymatic efficiency was observed with 4-oxonon-2-enal (4-ONE; k(cat)/K(m), 561 s(-1) mM(-1)) and 4-hydroxynonenal (k(cat)/K(m), 26.5 s(-1) mM(-1)), respectively. P74308 is the most efficient enzyme for 4-ONE discovered until now. Cooperativity of this monomeric enzyme was observed with some substrates. Enzyme inactivation or oligomerization as possible explanations for nonhyperbolic enzyme kinetics were ruled out by Selwyn's test and gel filtration. The role of the little investigated carbonyl-reducing enzymes in detoxification seems to be in fact a very old process with rarely observed nonhyperbolic enzyme kinetics as an adaptation mechanism to higher concentrations of reactive oxygen species.

  6. 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

  7. Vehicular-networking- and road-weather-related research in Sodankylä

    NASA Astrophysics Data System (ADS)

    Sukuvaara, Timo; Mäenpää, Kari; Ylitalo, Riika

    2016-10-01

    Vehicular-networking- and especially safety-related wireless vehicular services have been under intensive research for almost a decade now. Only in recent years has road weather information also been acknowledged to play an important role when aiming to reduce traffic accidents and fatalities via intelligent transport systems (ITSs). Part of the progress can be seen as a result of the Finnish Meteorological Institute's (FMI) long-term research work in Sodankylä within the topic, originally started in 2006. Within multiple research projects, the FMI Arctic Research Centre has been developing wireless vehicular networking and road weather services, in co-operation with the FMI meteorological services team in Helsinki. At the beginning the wireless communication was conducted with traditional Wi-Fi type local area networking, but during the development the system has evolved into a hybrid communication system of a combined vehicular ad hoc networking (VANET) system with special IEEE 802.11p protocol and supporting cellular networking based on a commercial 3G network, not forgetting support for Wi-Fi-based devices also. For piloting purposes and further research, we have established a special combined road weather station (RWS) and roadside unit (RSU), to interact with vehicles as a service hotspot. In the RWS-RSU we have chosen to build support to all major approaches, IEEE 802.11, traditional Wi-Fi and cellular 3G. We employ road weather systems of FMI, along with RWS and vehicle data gathered from vehicles, in the up-to-date localized weather data delivered in real time. IEEE 802.11p vehicular networking is supported with Wi-Fi and 3G communications. This paper briefly introduces the research work related to vehicular networking and road weather services conducted in Sodankylä, as well as the research project involved in this work. The current status of instrumentation, available services and capabilities are presented in order to formulate a clear general view of

  8. Cytoskeletal Mechanisms for Breaking Cellular Symmetry

    PubMed Central

    Mullins, R. Dyche

    2010-01-01

    Cytoskeletal systems are networks of polymers found in all eukaryotic and many prokaryotic cells. Their purpose is to transmit and integrate information across cellular dimensions and help turn a disorderly mob of macromolecules into a spatially organized, living cell. Information, in this context, includes physical and chemical properties relevant to cellular physiology, including: the number and activity of macromolecules, cell shape, and mechanical force. Most animal cells are 10–50 microns in diameter, whereas the macromolecules that comprise them are 10,000-fold smaller (2–20 nm). To establish long-range order over cellular length scales, individual molecules must, therefore, self-assemble into larger polymers, with lengths (0.1–20 m) comparable to the size of a cell. These polymers must then be cross-linked into organized networks that fill the cytoplasm. Such cell-spanning polymer networks enable different parts of the cytoplasm to communicate directly with each other, either by transmitting forces or by carrying cargo from one spot to another. PMID:20182610

  9. 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)

  10. Cellular genetic therapy.

    PubMed

    Del Vecchio, F; Filareto, A; Spitalieri, P; Sangiuolo, F; Novelli, G

    2005-01-01

    Cellular genetic therapy is the ultimate frontier for those pathologies that are consequent to a specific nonfunctional cellular type. A viable cure for there kinds of diseases is the replacement of sick cells with healthy ones, which can be obtained from the same patient or a different donor. In fact, structures can be corrected and strengthened with the introduction of undifferentiated cells within specific target tissues, where they will specialize into the desired cellular types. Furthermore, consequent to the recent results obtained with the transdifferentiation experiments, a process that allows the in vitro differentiation of embryonic and adult stem cells, it has also became clear that many advantages may be obtained from the use of stem cells to produce drugs, vaccines, and therapeutic molecules. Since stem cells can sustain lineage potentials, the capacity for differentiation, and better tolerance for the introduction of exogenous genes, they are also considered as feasible therapeutic vehicles for gene therapy. In fact, it is strongly believed that the combination of cellular genetic and gene therapy approaches will definitely allow the development of new therapeutic strategies as well as the production of totipotent cell lines to be used as experimental models for the cure of genetic disorders.

  11. 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…

  12. Evolution of HIV-1 isolates that use a novel Vif-independent mechanism to resist restriction by human APOBEC3G.

    PubMed

    Haché, Guylaine; Shindo, Keisuke; Albin, John S; Harris, Reuben S

    2008-06-03

    The human APOBEC3G protein restricts the replication of Vif-deficient HIV-1 by deaminating nascent viral cDNA cytosines to uracils, leading to viral genomic strand G-to-A hypermutations. However, the HIV-1 Vif protein triggers APOBEC3G degradation, which helps to explain why this innate defense does not protect patients. The APOBEC3G-Vif interaction is a promising therapeutic target, but the benefit of the enabling of HIV-1 restriction in patients is unlikely to be known until Vif antagonists are developed. As a necessary prelude to such studies, cell-based HIV-1 evolution experiments were done to find out whether APOBEC3G can provide a long-term block to Vif-deficient virus replication and, if so, whether HIV-1 variants that resist restriction would emerge. APOBEC3G-expressing T cells were infected with Vif-deficient HIV-1. Virus infectivity was suppressed in 45/48 cultures for more than five weeks, but replication was eventually detected in three cultures. Virus-growth characteristics and sequencing demonstrated that these isolates were still Vif-deficient and that in fact, these viruses had acquired a promoter mutation and a Vpr null mutation. Resistance occurred by a novel tolerance mechanism in which the resistant viruses packaged less APOBEC3G and accumulated fewer hypermutations. These data support the development of antiretrovirals that antagonize Vif and thereby enable endogenous APOBEC3G to suppress HIV-1 replication.

  13. 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.

  14. 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.

  15. Biochemical basis of immunological and retroviral responses to DNA-targeted cytosine deamination by activation-induced cytidine deaminase and APOBEC3G.

    PubMed

    Chelico, Linda; Pham, Phuong; Petruska, John; Goodman, Myron F

    2009-10-09

    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.

  16. 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.

  17. 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.

  18. Endogenous factors enhance HIV infection of tissue naive CD4 T cells by stimulating high molecular mass APOBEC3G complex formation.

    PubMed

    Kreisberg, Jason F; Yonemoto, Wes; Greene, Warner C

    2006-04-17

    Human immunodeficiency virus (HIV) can infect resting CD4 T cells residing in lymphoid tissues but not those circulating in peripheral blood. The molecular mechanisms producing this difference remain unknown. We explored the potential role of the tissue microenvironment and its influence on the action of the antiviral factor APOBEC3G (A3G) in regulating permissivity to HIV infection. We found that endogenous IL-2 and -15 play a key role in rendering resident naive CD4 T cells susceptible to HIV infection. Infection of memory CD4 T cells also requires endogenous soluble factors, but not IL-2 or -15. A3G is found in a high molecular mass complex in HIV infection-permissive, tissue-resident naive CD4 T cells but resides in a low molecular mass form in nonpermissive, blood-derived naive CD4 T cells. Upon treatment with endogenous soluble factors, these cells become permissive for HIV infection, as low molecular mass A3G is induced to assemble into high molecular mass complexes. These findings suggest that in lymphoid tissues, endogenous soluble factors, likely including IL-2 and -15 and others, stimulate the formation of high molecular mass A3G complexes in tissue-resident naive CD4 T cells, thereby relieving the potent postentry restriction block for HIV infection conferred by low molecular mass A3G.

  19. The retroviral hypermutation specificity of APOBEC3F and APOBEC3G is governed by the C-terminal DNA cytosine deaminase domain.

    PubMed

    Haché, Guylaine; Liddament, Mark T; Harris, Reuben S

    2005-03-25

    The human proteins APOBEC3F and APOBEC3G restrict retroviral infection by deaminating cytosine residues in the first cDNA strand of a replicating virus. These proteins have two putative deaminase domains, and it is unclear whether one or both catalyze deamination, unlike their homologs, AID and APOBEC1, which are well characterized single domain deaminases. Here, we show that only the C-terminal cytosine deaminase domain of APOBEC3F and -3G governs retroviral hypermutation. A chimeric protein with the N-terminal cytosine deaminase domain from APOBEC3G and the C-terminal cytosine deaminase domain from APOBEC3F elicited a dinucleotide hypermutation preference nearly indistinguishable from that of APOBEC3F. This 5'-TC-->TT mutational specificity was confirmed in a heterologous Escherichia coli-based mutation assay, in which the 5'-CC-->CT dinucleotide hypermutation preference of APOBEC3G also mapped to the C-terminal deaminase domain. An N-terminal APOBEC3G deletion mutant displayed a preference indistinguishable from that of the full-length protein, and replacing the C-terminal deaminase domain of APOBEC3F with AID resulted in an AID-like mutational signature. Together, these data indicate that only the C-terminal domain of APOBEC3F and -3G dictates the retroviral minus strand 5'-TC and 5'-CC dinucleotide hypermutation preferences, respectively, leaving the N-terminal domain to perform other aspects of retroviral restriction.

  20. 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.

  1. Association of single nucleotide polymorphisms of APOBEC3G with susceptibility to HIV-1 infection and disease progression among men engaging in homosexual activity in northern China.

    PubMed

    Li, Qiuyan; Qiao, Yuandong; Zhang, Guangfa; He, Ning; Zhang, Xuelong; Jia, Xueyuan; Sun, Haiming; Wang, Chuntao; Xu, Lidan

    2017-01-01

    Men who have sex with men (MSM) are at high risk of HIV infection. The APOBEC3G (apolipoprotein B mRNA editing catalytic polypeptide 3G) protein is a component of innate antiviral immunity that inhibits HIV-1 replication. In the present study, a total of 483 HIV-1 seropositive men and 493 HIV-1 seronegative men were selected to investigate the association between single nucleotide polymorphisms (SNPs) of the APOBEC3G gene and susceptibility to HIV-1 infection and AIDS progression among MSM residing in northern China. Genotyping of four SNPs (rs5757465, rs3736685, rs8177832, and rs2899313) of the APOBEC3G was performed using the SNPscan™ Kit, while the rs2294367 polymorphism was genotyped using the SNaPshot multiplex system. Our results disclosed no association between the SNPs of APOBEC3G and susceptibility to HIV-1, or effects of these polymorphisms on the CD4(+) T cell count or clinical phase of disease. A meta-analysis of 1624 men with HIV-1 infection and 1523 controls suggested that the association between rs8177832 and susceptibility was not significant. However, we observed a trend towards association with HIV-1 infection for haplotype TTACA (p = 0.082). The potential role of variants of APOBEC3G in HIV-1/AIDS warrants further investigation.

  2. Convergence and Divergence in the Evolution of the APOBEC3G-Vif Interaction Reveal Ancient Origins of Simian Immunodeficiency Viruses

    PubMed Central

    Compton, Alex A.; Emerman, Michael

    2013-01-01

    Naturally circulating lentiviruses are abundant in African primate species today, yet their origins and history of transmitting between hosts remain obscure. As a means to better understand the age of primate lentiviruses, we analyzed primate genomes for signatures of lentivirus-driven evolution. Specifically, we studied the adaptive evolution of host restriction factor APOBEC3G (A3G) in Old World Monkey (OWM) species. We find recurrent mutation of A3G in multiple primate lineages at sites that determine susceptibility to antagonism by the lentiviral accessory protein Vif. Using a broad panel of SIV Vif isolates, we demonstrate that natural variation in OWM A3G confers resistance to Vif-mediated degradation, suggesting that adaptive variants of the host factor were selected upon exposure to pathogenic lentiviruses at least 5–6 million years ago (MYA). Furthermore, in members of the divergent Colobinae subfamily of OWM, a multi-residue insertion event in A3G that arose at least 12 MYA blocks the activity of Vif, suggesting an even more ancient origin of SIV. Moreover, analysis of the lentiviruses associated with Colobinae monkeys reveal that the interface of the A3G-Vif interaction has shifted and given rise to a second genetic conflict. Our analysis of virus-driven evolution describes an ancient yet ongoing genetic conflict between simian primates and lentiviruses on a million-year time scale. PMID:23359341

  3. Different Mutagenic Potential of HIV-1 Restriction Factors APOBEC3G and APOBEC3F Is Determined by Distinct Single-Stranded DNA Scanning Mechanisms

    PubMed Central

    Ara, Anjuman; Love, Robin P.; Chelico, Linda

    2014-01-01

    The APOBEC3 deoxycytidine deaminase family functions as host restriction factors that can block replication of Vif (virus infectivity factor) deficient HIV-1 virions to differing degrees by deaminating cytosines to uracils in single-stranded (−)HIV-1 DNA. Upon replication of the (−)DNA to (+)DNA, the HIV-1 reverse transcriptase incorporates adenines opposite the uracils, thereby inducing C/G→T/A mutations that can functionally inactivate HIV-1. Although both APOBEC3F and APOBEC3G are expressed in cell types HIV-1 infects and are suppressed by Vif, there has been no prior biochemical analysis of APOBEC3F, in contrast to APOBEC3G. Using synthetic DNA substrates, we characterized APOBEC3F and found that similar to APOBEC3G; it is a processive enzyme and can deaminate at least two cytosines in a single enzyme-substrate encounter. However, APOBEC3F scanning movement is distinct from APOBEC3G, and relies on jumping rather than both jumping and sliding. APOBEC3F jumping movements were also different from APOBEC3G. The lack of sliding movement from APOBEC3F is due to an 190NPM192 motif, since insertion of this motif into APOBEC3G decreases its sliding movements. The APOBEC3G NPM mutant induced significantly less mutations in comparison to wild-type APOBEC3G in an in vitro model HIV-1 replication assay and single-cycle infectivity assay, indicating that differences in DNA scanning were relevant to restriction of HIV-1. Conversely, mutation of the APOBEC3F 191Pro to 191Gly enables APOBEC3F sliding movements to occur. Although APOBEC3F 190NGM192 could slide, the enzyme did not induce more mutagenesis than wild-type APOBEC3F, demonstrating that the unique jumping mechanism of APOBEC3F abrogates the influence of sliding on mutagenesis. Overall, we demonstrate key differences in the impact of APOBEC3F- and APOBEC3G-induced mutagenesis on HIV-1 that supports a model in which both the processive DNA scanning mechanism and preferred deamination motif (APOBEC3F, 5

  4. 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

  5. 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

  6. [Cellular and molecular mechanisms of memory].

    PubMed

    Laroche, Serge

    2010-01-01

    A defining characteristic of the brain is its remarkable capacity to undergo activity-dependent functional and morphological remodelling via mechanisms of plasticity that form the basis of our capacity to encode and retain memories. Today, it is generally accepted that one key neurobiological mechanism underlying the formation of memories reside in activity-driven modifications of synaptic strength and structural remodelling of neural networks activated during learning. The discovery and detailed report of the phenomenon generally known as long-term potentiation, a long-lasting activity-dependent form of synaptic strengthening, opened a new chapter in the study of the neurobiological substrate of memory in the vertebrate brain, and this form of synaptic plasticity has now become the dominant model in the search for the cellular bases of learning and memory. To date, the key events in the cellular and molecular mechanisms underlying synaptic plasticity and memory formation are starting to be identified. They require the activation of specific receptors and of several molecular cascades to convert extracellular signals into persistent functional changes in neuronal connectivity. Accumulating evidence suggests that the rapid activation of neuronal gene programs is a key mechanism underlying the enduring modification of neural networks required for the laying down of memory. The recent developments in the search for the cellular and molecular mechanisms of memory storage are reviewed.

  7. [Cellular and molecular mechanisms of memory].

    PubMed

    Laroche, S

    2001-01-01

    There has been nearly a century of interest in the idea that information is encoded in the brain as specific spatio-temporal patterns of activity in distributed networks and stored as changes in the efficacy of synaptic connections on neurons that are activated during learning. The discovery and detailed report of the phenomenon generally known as long-term potentiation opened a new chapter in the study of synaptic plasticity in the vertebrate brain, and this form of synaptic plasticity has now become the dominant model in the search for the cellular bases of learning and memory. To date, the key events in the cellular and molecular mechanisms underlying synaptic plasticity are starting to be identified. They require the activation of specific receptors and of several molecular cascades to convert extracellular signals into persistent functional changes in neuronal connectivity. Accumulating evidence suggests that the rapid activation of the genetic machinery is a key mechanism underlying the enduring modification of neural networks required for the laying down of memory. The recent developments in the search for the cellular and molecular mechanisms of memory storage are reviewed.

  8. The Caveolin‐3 G56S sequence variant of unknown significance: Muscle biopsy findings and functional cell biological analysis

    PubMed Central

    Kollipara, Laxmikanth; Zahedi, René P.; Beckmann, Alf; Mohanadas, Nilane; Bauer, Hartmut; Häusler, Martin; Thoma, Stéphanie; Kress, Wolfram; Senderek, Jan; Weis, Joachim

    2016-01-01

    1 Purpose In the era of next‐generation sequencing, we are increasingly confronted with sequence variants of unknown significance. This phenomenon is also known for variations in Caveolin‐3 and can complicate the molecular diagnosis of the disease. Here, we aimed to study the ambiguous character of the G56S Caveolin‐3 variant. 2 Experimental design A comprehensive approach combining genetic and morphological studies of muscle derived from carriers of the G56S Caveolin‐3 variant were carried out and linked to biochemical assays (including phosphoblot studies and proteome profiling) and morphological investigations of cultured myoblasts. 3 Results Muscles showed moderate chronic myopathic changes in all carriers of the variant. Myogenic RCMH cells expressing the G56S Caveolin‐3 protein presented irregular Caveolin‐3 deposits within the Golgi in addition to a regular localization of the protein to the plasma membrane. This result was associated with abnormal findings on the ultra‐structural level. Phosphoblot studies revealed that G56S affects EGFR‐signaling. Proteomic profiling demonstrated alterations in levels of physiologically relevant proteins which are indicative for antagonization of G56S Caveolin‐3 expression. Remarkably, some proteomic alterations were enhanced by osmotic/mechanical stress. 4 Conclusions and clinical relevance Our studies suggest that G56S might influence the manifestation of myopathic changes upon the presence of additional cellular stress burden. Results of our studies moreover improve the current understanding of (genetic) causes of myopathic disorders classified as caveolinopathies. PMID:27739254

  9. A Comparative Analysis between GIMSS NDVIg and NDVI3g for Monitoring Vegetation Activity Change in the Northern Hemisphere during 1982-2008

    DOE PAGES

    Jiang, Nan; Zhu, Wenquan; Zheng, Zhoutao; ...

    2013-08-12

    The long-term Normalized Difference Vegetation Index (NDVI) time-series data set generated from the Advanced Very High Resolution Radiometers (AVHRR) has been widely used to monitor vegetation activity change. The third version of NDVI (NDVI3g) produced by the Global Inventory Modeling and Mapping Studies (GIMMS) group was released recently. The comparisons between the new and old versions should be conducted for linking existing studies with future applications of NDVI3g in monitoring vegetation activity change. Based on simple and piecewise linear regression methods, this research made a comparative analysis between NDVIg and NDVI3g for monitoring vegetation activity change and its responses tomore » climate change in the middle and high latitudes of the Northern Hemisphere during 1982–2008. Our results indicated that there were large differences between NDVIg and NDVI3g in the spatial patterns for both the overall changing trends and the timing of Turning Points (TP) in NDVI time series, which spread over almost the entire study region. The average NDVI trend from NDVI3g was almost twice as great as that from NDVIg and the detected average timing of TP from NDVI3g was about one year later. Although the general spatial patterns were consistent between two data sets for detecting the responses of growing-season NDVI to temperature and precipitation changes, there were large differences in the response magnitude, with a higher response magnitude to temperature in NDVI3g and an opposite response to precipitation change for the two data sets. Finally, these results demonstrated that the NDVIg data set may underestimate the vegetation activity change trend and its response to climate change in the middle and high latitudes of the Northern Hemisphere during the past three decades.« less

  10. A Comparative Analysis between GIMSS NDVIg and NDVI3g for Monitoring Vegetation Activity Change in the Northern Hemisphere during 1982-2008

    SciTech Connect

    Jiang, Nan; Zhu, Wenquan; Zheng, Zhoutao; Chen, Guangsheng; Fan, Deqin

    2013-08-12

    The long-term Normalized Difference Vegetation Index (NDVI) time-series data set generated from the Advanced Very High Resolution Radiometers (AVHRR) has been widely used to monitor vegetation activity change. The third version of NDVI (NDVI3g) produced by the Global Inventory Modeling and Mapping Studies (GIMMS) group was released recently. The comparisons between the new and old versions should be conducted for linking existing studies with future applications of NDVI3g in monitoring vegetation activity change. Based on simple and piecewise linear regression methods, this research made a comparative analysis between NDVIg and NDVI3g for monitoring vegetation activity change and its responses to climate change in the middle and high latitudes of the Northern Hemisphere during 1982–2008. Our results indicated that there were large differences between NDVIg and NDVI3g in the spatial patterns for both the overall changing trends and the timing of Turning Points (TP) in NDVI time series, which spread over almost the entire study region. The average NDVI trend from NDVI3g was almost twice as great as that from NDVIg and the detected average timing of TP from NDVI3g was about one year later. Although the general spatial patterns were consistent between two data sets for detecting the responses of growing-season NDVI to temperature and precipitation changes, there were large differences in the response magnitude, with a higher response magnitude to temperature in NDVI3g and an opposite response to precipitation change for the two data sets. Finally, these results demonstrated that the NDVIg data set may underestimate the vegetation activity change trend and its response to climate change in the middle and high latitudes of the Northern Hemisphere during the past three decades.

  11. 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…

  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. Oral Cellular Neurothekeoma

    PubMed Central

    Emami, Nader; Zawawi, Faisal; Ywakim, Rania; Daniel, Sam J.

    2013-01-01

    Cellular neurothekeoma is known as a cutaneous tumor with uncertain histogenesis. Very little involvement of mucosal membrane has been reported in the literature so far. This is a case report of an intraoral lesion in a 15-years-old girl. Histopathologic evaluation showed a tumor-consists of spindle to epitheloid cells forming micronodules in a concentric whorled shape pattern. Tumor cells were positive for CD63, vimentin, and NKI-C3. Total excision was performed and no recurrence happened after 16-month followup. PMID:23691398

  14. Cellular and molecular connections between sleep and synaptic plasticity.

    PubMed

    Benington, Joel H; Frank, Marcos G

    2003-02-01

    The hypothesis that sleep promotes learning and memory has long been a subject of active investigation. This hypothesis implies that sleep must facilitate synaptic plasticity in some way, and recent studies have provided evidence for such a function. Our knowledge of both the cellular neurophysiology of sleep states and of the cellular and molecular mechanisms underlying synaptic plasticity has expanded considerably in recent years. In this article, we review findings in these areas and discuss possible mechanisms whereby the neurophysiological processes characteristic of sleep states may serve to facilitate synaptic plasticity. We address this issue first on the cellular level, considering how activation of T-type Ca(2+) channels in nonREM sleep may promote either long-term depression or long-term potentiation, as well as how cellular events of REM sleep may influence these processes. We then consider how synchronization of neuronal activity in thalamocortical and hippocampal-neocortical networks in nonREM sleep and REM sleep could promote differential strengthening of synapses according to the degree to which activity in one neuron is synchronized with activity in other neurons in the network. Rather than advocating one specific cellular hypothesis, we have intentionally taken a broad approach, describing a range of possible mechanisms whereby sleep may facilitate synaptic plasticity on the cellular and/or network levels. We have also provided a general review of evidence for and against the hypothesis that sleep does indeed facilitate learning, memory, and synaptic plasticity.

  15. Revisiting Cardiac Cellular Composition

    PubMed Central

    Pinto, Alexander R.; Ilinykh, Alexei; Ivey, Malina J.; Kuwabara, Jill T.; D'Antoni, Michelle L.; Debuque, Ryan; Chandran, Anjana; Wang, Lina; Arora, Komal; Rosenthal, Nadia; Tallquist, Michelle D.

    2015-01-01

    Rationale Accurate knowledge of the cellular composition of the heart is essential to fully understand the changes that occur during pathogenesis and to devise strategies for tissue engineering and regeneration. Objective To examine the relative frequency of cardiac endothelial cells, hematopoietic-derived cells and fibroblasts in the mouse and human heart. Methods and Results Using a combination of genetic tools and cellular markers, we examined the occurrence of the most prominent cell types in the adult mouse heart. Immunohistochemistry revealed that endothelial cells constitute over 60%, hematopoietic-derived cells 5–10%, and fibroblasts under 20% of the non-myocytes in the heart. A refined cell isolation protocol and an improved flow cytometry approach provided an independent means of determining the relative abundance of non-myocytes. High dimensional analysis and unsupervised clustering of cell populations confirmed that endothelial cells are the most abundant cell population. Interestingly, fibroblast numbers are smaller than previously estimated, and two commonly assigned fibroblast markers, Sca-1 and CD90, underrepresent fibroblast numbers. We also describe an alternative fibroblast surface marker that more accurately identifies the resident cardiac fibroblast population. Conclusions This new perspective on the abundance of different cell types in the heart demonstrates that fibroblasts comprise a relatively minor population. By contrast, endothelial cells constitute the majority of non-cardiomyocytes and are likely to play a greater role in physiologic function and response to injury than previously appreciated. PMID:26635390

  16. Cellular Array Processing Simulation

    NASA Astrophysics Data System (ADS)

    Lee, Harry C.; Preston, Earl W.

    1981-11-01

    The Cellular Array Processing Simulation (CAPS) system is a high-level image language that runs on a multiprocessor configuration. CAPS is interpretively decoded on a conventional minicomputer with all image operation instructions executed on an array processor. The synergistic environment that exists between the minicomputer and the array processor gives CAPS its high-speed throughput, while maintaining a convenient conversational user language. CAPS was designed to be both modular and table driven so that it can be easily maintained and modified. CAPS uses the image convolution operator as one of its primitives and performs this cellular operation by decomposing it into parallel image steps that are scheduled to be executed on the array processor. Among its features is the ability to observe the imagery in real time as a user's algorithm is executed. This feature reduces the need for image storage space, since it is feasible to retain only original images and produce resultant images when needed. CAPS also contains a language processor that permits users to develop re-entrant image processing subroutines or algorithms.

  17. Facile preparation of Z-scheme WO3/g-C3N4 composite photocatalyst with enhanced photocatalytic performance under visible light

    NASA Astrophysics Data System (ADS)

    Cui, Lifeng; Ding, Xiang; Wang, Yangang; Shi, Huancong; Huang, Lihua; Zuo, Yuanhui; Kang, Shifei

    2017-01-01

    Visible-light-driven WO3/g-C3N4 composites photocatalysts were synthesized via a facile one-step simultaneously heating procedure with urea as the main precursor. These prepared catalyst samples were characterized by X-ray diffraction (XRD), thermogravimetric analysis (TG), transmission electron microscopy (TEM), N2 adsorption, ultraviolet-visible diffuse reflection spectroscopy (UV-vis), X-ray photoelectron spectroscopy (XPS), photoluminescence (PL) and electrochemical impedance spectroscopy (EIS). The photocatalytic activity of the WO3/g-C3N4 composites was evaluated by the photo-degradation of Rhodamine B (RhB) under visible light irradiation. The results indicated that the composites with 25 wt.% WO3 content exhibited highest photocatalytic activity compared to pure WO3, bare g-C3N4 and other WO3/g-C3N4 composites. The favorable photocatalytic activity of WO3/g-C3N4 composites was mainly attributed to the excellent surface properties, enhanced visible-light absorption and the desirable band positions. A possible Z-scheme photocatalytic mechanism was proposed based on structure and electrochemical characterizations results, which can well explain the enhanced migration rate of photogenerated electrons and holes in WO3/g-C3N4 heterojunctions.

  18. Interconnectivity of human cellular metabolism and disease prevalence

    NASA Astrophysics Data System (ADS)

    Lee, Deok-Sun

    2010-12-01

    Fluctuations of metabolic reaction fluxes may cause abnormal concentrations of toxic or essential metabolites, possibly leading to metabolic diseases. The mutual binding of enzymatic proteins and ones involving common metabolites enforces distinct coupled reactions, by which local perturbations may spread through the cellular network. Such network effects at the molecular interaction level in human cellular metabolism can reappear in the patterns of disease occurrence. Here we construct the enzyme-reaction network and the metabolite-reaction network, capturing the flux coupling of metabolic reactions caused by the interacting enzymes and the shared metabolites, respectively. Diseases potentially caused by the failure of individual metabolic reactions can be identified by using the known disease-gene association, which allows us to derive the probability of an inactivated reaction causing diseases from the disease records at the population level. We find that the greater the number of proteins that catalyze a reaction, the higher the mean prevalence of its associated diseases. Moreover, the number of connected reactions and the mean size of the avalanches in the networks constructed are also shown to be positively correlated with the disease prevalence. These findings illuminate the impact of the cellular network topology on disease development, suggesting that the global organization of the molecular interaction network should be understood to assist in disease diagnosis, treatment, and drug discovery.

  19. Real-time performance analysis of wireless multimedia networks based on partially observed multivariate point processes

    NASA Astrophysics Data System (ADS)

    Hortos, William S.

    2000-07-01

    Third-generation (3G) wireless networks will support integrated multimedia services based on a cellular extension of a packet-switched architecture using variants of the Internet protocol (IP). Services can be categorized as real- time and delay-sensitive, or non-real-time and delay- insensitive. Each call, arriving to or active within the network, carries demand for one or more services in parallel; each service type with a guaranteed quality of service (QoS). Admission of new calls to the wireless IP network (WIN) from the gateway of a wired network or from a mobile subscriber (MS) is allowed by call admission control procedures. Roaming of the MSs among the nodes of the WIN is controlled by handoff procedures between base stations (BSs), or BS controllers, and the MSs. Metrics such as the probabilities of call blocking and dropping, handoff transition time, processing latency of a call, throughput, and capacity are used to evaluate the performance of network control procedures. The metrics are directly related to the network resources required to provide the QoS for the integrated services.

  20. 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

  1. [Senescence and cellular immortality].

    PubMed

    Trentesaux, C; Riou, J-F

    2010-11-01

    Senescence was originally described from the observation of the limited ability of normal cells to grow in culture, and may be generated by telomere erosion, accumulation of DNA damages, oxidative stress and modulation of oncogenes or tumor suppressor genes. Senescence corresponds to a cellular response aiming to control tumor progression by limiting cell proliferation and thus constitutes an anticancer barrier. Senescence is observed in pre-malignant tumor stages and disappears from malignant tumors. Agents used in standard chemotherapy also have the potential to induce senescence, which may partly explain their therapeutic activities. It is possible to restore senescence in tumors using targeted therapies that triggers telomere dysfunction or reactivates suppressor genes functions, which are essential for the onset of senescence.

  2. 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

  3. Field efficacy of fipronil 3G, lambda-cyhalothrin 10%CS, and sumithion 50EC against the dengue vector Aedes albopictus in discarded tires.

    PubMed

    Sulaiman, S; Pawanchee, Z A; Wahab, A; Jamal, J; Sohadi, A R

    1999-12-01

    The efficacy of three insecticides, fipronil 3G, lambda-cyhalothrin 10%CS, and sumithion 50EC were evaluated against the dengue vector Aedes albopictus in discarded tires in Kuala Lumpur, Malaysia. The dosage given for each insecticide was 0.01 g of active ingredient/m2. Fipronil 3G was the most effective larvicide with a residual activity of up to two weeks, causing 88% mortality in Aedes albopictus. Lambda-cyhalothrin 10%CS was effective for one week causing 92% larval mortality and two weeks with 63% larval mortality. Sumithion 50EC had a residual efficacy of one week with 79% larval mortality.

  4. Scaling behavior in probabilistic neuronal cellular automata.

    PubMed

    Manchanda, Kaustubh; Yadav, Avinash Chand; Ramaswamy, Ramakrishna

    2013-01-01

    We study a neural network model of interacting stochastic discrete two-state cellular automata on a regular lattice. The system is externally tuned to a critical point which varies with the degree of stochasticity (or the effective temperature). There are avalanches of neuronal activity, namely, spatially and temporally contiguous sites of activity; a detailed numerical study of these activity avalanches is presented, and single, joint, and marginal probability distributions are computed. At the critical point, we find that the scaling exponents for the variables are in good agreement with a mean-field theory.

  5. Cellular circadian clocks in mood disorders.

    PubMed

    McCarthy, Michael J; Welsh, David K

    2012-10-01

    Bipolar disorder (BD) and major depressive disorder (MDD) are heritable neuropsychiatric disorders associated with disrupted circadian rhythms. The hypothesis that circadian clock dysfunction plays a causal role in these disorders has endured for decades but has been difficult to test and remains controversial. In the meantime, the discovery of clock genes and cellular clocks has revolutionized our understanding of circadian timing. Cellular circadian clocks are located in the suprachiasmatic nucleus (SCN), the brain's primary circadian pacemaker, but also throughout the brain and peripheral tissues. In BD and MDD patients, defects have been found in SCN-dependent rhythms of body temperature and melatonin release. However, these are imperfect and indirect indicators of SCN function. Moreover, the SCN may not be particularly relevant to mood regulation, whereas the lateral habenula, ventral tegmentum, and hippocampus, which also contain cellular clocks, have established roles in this regard. Dysfunction in these non-SCN clocks could contribute directly to the pathophysiology of BD/MDD. We hypothesize that circadian clock dysfunction in non-SCN clocks is a trait marker of mood disorders, encoded by pathological genetic variants. Because network features of the SCN render it uniquely resistant to perturbation, previous studies of SCN outputs in mood disorders patients may have failed to detect genetic defects affecting non-SCN clocks, which include not only mood-regulating neurons in the brain but also peripheral cells accessible in human subjects. Therefore, reporters of rhythmic clock gene expression in cells from patients or mouse models could provide a direct assay of the molecular gears of the clock, in cellular clocks that are likely to be more representative than the SCN of mood-regulating neurons in patients. This approach, informed by the new insights and tools of modern chronobiology, will allow a more definitive test of the role of cellular circadian clocks

  6. 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.

  7. 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.

  8. Agent-Based Modeling of Mitochondria Links Sub-Cellular Dynamics to Cellular Homeostasis and Heterogeneity.

    PubMed

    Dalmasso, Giovanni; Marin Zapata, Paula Andrea; Brady, Nathan Ryan; Hamacher-Brady, Anne

    2017-01-01

    Mitochondria are semi-autonomous organelles that supply energy for cellular biochemistry through oxidative phosphorylation. Within a cell, hundreds of mobile mitochondria undergo fusion and fission events to form a dynamic network. These morphological and mobility dynamics are essential for maintaining mitochondrial functional homeostasis, and alterations both impact and reflect cellular stress states. Mitochondrial homeostasis is further dependent on production (biogenesis) and the removal of damaged mitochondria by selective autophagy (mitophagy). While mitochondrial function, dynamics, biogenesis and mitophagy are highly-integrated processes, it is not fully understood how systemic control in the cell is established to maintain homeostasis, or respond to bioenergetic demands. Here we used agent-based modeling (ABM) to integrate molecular and imaging knowledge sets, and simulate population dynamics of mitochondria and their response to environmental energy demand. Using high-dimensional parameter searches we integrated experimentally-measured rates of mitochondrial biogenesis and mitophagy, and using sensitivity analysis we identified parameter influences on population homeostasis. By studying the dynamics of cellular subpopulations with distinct mitochondrial masses, our approach uncovered system properties of mitochondrial populations: (1) mitochondrial fusion and fission activities rapidly establish mitochondrial sub-population homeostasis, and total cellular levels of mitochondria alter fusion and fission activities and subpopulation distributions; (2) restricting the directionality of mitochondrial mobility does not alter morphology subpopulation distributions, but increases network transmission dynamics; and (3) maintaining mitochondrial mass homeostasis and responding to bioenergetic stress requires the integration of mitochondrial dynamics with the cellular bioenergetic state. Finally, (4) our model suggests sources of, and stress conditions amplifying

  9. Agent-Based Modeling of Mitochondria Links Sub-Cellular Dynamics to Cellular Homeostasis and Heterogeneity

    PubMed Central

    Dalmasso, Giovanni; Marin Zapata, Paula Andrea; Brady, Nathan Ryan; Hamacher-Brady, Anne

    2017-01-01

    Mitochondria are semi-autonomous organelles that supply energy for cellular biochemistry through oxidative phosphorylation. Within a cell, hundreds of mobile mitochondria undergo fusion and fission events to form a dynamic network. These morphological and mobility dynamics are essential for maintaining mitochondrial functional homeostasis, and alterations both impact and reflect cellular stress states. Mitochondrial homeostasis is further dependent on production (biogenesis) and the removal of damaged mitochondria by selective autophagy (mitophagy). While mitochondrial function, dynamics, biogenesis and mit