Science.gov

Sample records for layered niche networks

  1. Youth as Content Producers in a Niche Social Network Site

    ERIC Educational Resources Information Center

    Greenhow, Christine

    2010-01-01

    Most U.S. teenagers participate in online social network sites, devoting hours to these networks, often at the expense of other leisure-time activities. This article describes young people's activities within one topic-focused niche network, outlining its unique features and the role of young people as content producers within and beyond the…

  2. Youth as content producers in a niche social network site.

    PubMed

    Greenhow, Christine

    2010-01-01

    Most U.S. teenagers participate in online social network sites, devoting hours to these networks, often at the expense of other leisure-time activities. This article describes young people's activities within one topic-focused niche network, outlining its unique features and the role of young people as content producers within and beyond the space. Links between youth's online contributions and their interest, self-expression, social connections, and civic involvement are discussed. PMID:21240953

  3. The outer mucus layer hosts a distinct intestinal microbial niche

    PubMed Central

    Li, Hai; Limenitakis, Julien P.; Fuhrer, Tobias; Geuking, Markus B.; Lawson, Melissa A.; Wyss, Madeleine; Brugiroux, Sandrine; Keller, Irene; Macpherson, Jamie A.; Rupp, Sandra; Stolp, Bettina; Stein, Jens V.; Stecher, Bärbel; Sauer, Uwe; McCoy, Kathy D.; Macpherson, Andrew J.

    2015-01-01

    The overall composition of the mammalian intestinal microbiota varies between individuals: within each individual there are differences along the length of the intestinal tract related to host nutrition, intestinal motility and secretions. Mucus is a highly regenerative protective lubricant glycoprotein sheet secreted by host intestinal goblet cells; the inner mucus layer is nearly sterile. Here we show that the outer mucus of the large intestine forms a unique microbial niche with distinct communities, including bacteria without specialized mucolytic capability. Bacterial species present in the mucus show differential proliferation and resource utilization compared with the same species in the intestinal lumen, with high recovery of bioavailable iron and consumption of epithelial-derived carbon sources according to their genome-encoded metabolic repertoire. Functional competition for existence in this intimate layer is likely to be a major determinant of microbiota composition and microbial molecular exchange with the host. PMID:26392213

  4. Microcosms metacommunities in river network: niche effects and biodiversity

    NASA Astrophysics Data System (ADS)

    Giometto, A.; Carrara, F.; Altermatt, F.; Rinaldo, A.

    2012-04-01

    Many highly diverse landscapes exhibit hierarchical spatial structures that are shaped by geomorphological processes. Riverine ecosystems, among the most diverse habitats on Earth, represent an outstanding example of such mechanisms. In these landscapes, in which connectivity directly influences metacommunity processes, habitat capacity contributes to control biodiversity at several levels. A previous study has already highlighted the effect of connectivity on species distribution at local and regional scales, but habitat capacity was kept uniform. We studied the interaction of connectivity and habitat capacity in an aquatic microcosm experiment, in which microbial communities were grown in 36-well culture plates connected by dispersal. Dispersal occurred by periodic transfer of culture medium among connected local communities, following river network topology. The effect of habitat capacity in these landscapes was investigated by comparing three different spatial configurations of local community volumes: 1. Power law distributed volumes, according to drainage area. 2. Spatial random permutation of the volumes in the above configuration. 3. Equal distribution of volumes (preserving the total volume with respect to the above configurations). The net effect of habitat capacity on community composition was isolated in a control treatment in which communities were kept isolated for the whole duration of the experiment. In all treatments we observed that varying volumes induced niche effects: some protozoan species preferentially occupied larger nodes (systematically in isolation). Nevertheless, there is evidence that position along the network played a significant role in shaping biodiversity patterns. Size distribution measurements for each community were taken with a CASY cell counter, and species abundances data on log scale precision were collected by direct microscope observation.

  5. Multi-user cognitive radio network resource allocation based on the adaptive niche immune genetic algorithm

    NASA Astrophysics Data System (ADS)

    Zu, Yun-Xiao; Zhou, Jie

    2012-01-01

    Multi-user cognitive radio network resource allocation based on the adaptive niche immune genetic algorithm is proposed, and a fitness function is provided. Simulations are conducted using the adaptive niche immune genetic algorithm, the simulated annealing algorithm, the quantum genetic algorithm and the simple genetic algorithm, respectively. The results show that the adaptive niche immune genetic algorithm performs better than the other three algorithms in terms of the multi-user cognitive radio network resource allocation, and has quick convergence speed and strong global searching capability, which effectively reduces the system power consumption and bit error rate.

  6. Engineering interpenetrating network hydrogels as biomimetic cell niche with independently tunable biochemical and mechanical properties.

    PubMed

    Tong, Xinming; Yang, Fan

    2014-02-01

    Hydrogels have been widely used as artificial cell niche to mimic extracellular matrix with tunable properties. However, changing biochemical cues in hydrogels developed-to-date would often induce simultaneous changes in mechanical properties, which do not support mechanistic studies on stem cell-niche interactions. Here we report the development of a PEG-based interpenetrating network (IPN), which is composed of two polymer networks that can independently and simultaneously crosslink to form hydrogels in a cell-friendly manner. The resulting IPN hydrogel allows independently tunable biochemical and mechanical properties, as well as stable and more homogeneous presentation of biochemical ligands in 3D than currently available methods. We demonstrate the potential of our IPN platform for elucidating stem cell-niche interactions by modulating osteogenic differentiation of human adipose-derived stem cells. The versatility of such IPN hydrogels is further demonstrated using three distinct and widely used polymers to form the mechanical network while keeping the biochemical network constant.

  7. Extended evolution: A conceptual framework for integrating regulatory networks and niche construction.

    PubMed

    Laubichler, Manfred D; Renn, Jürgen

    2015-11-01

    This paper introduces a conceptual framework for the evolution of complex systems based on the integration of regulatory network and niche construction theories. It is designed to apply equally to cases of biological, social and cultural evolution. Within the conceptual framework we focus especially on the transformation of complex networks through the linked processes of externalization and internalization of causal factors between regulatory networks and their corresponding niches and argue that these are an important part of evolutionary explanations. This conceptual framework extends previous evolutionary models and focuses on several challenges, such as the path-dependent nature of evolutionary change, the dynamics of evolutionary innovation and the expansion of inheritance systems.

  8. Gene regulatory networks controlling hematopoietic progenitor niche cell production and differentiation in the Drosophila lymph gland.

    PubMed

    Tokusumi, Yumiko; Tokusumi, Tsuyoshi; Shoue, Douglas A; Schulz, Robert A

    2012-01-01

    Hematopoiesis occurs in two phases in Drosophila, with the first completed during embryogenesis and the second accomplished during larval development. The lymph gland serves as the venue for the final hematopoietic program, with this larval tissue well-studied as to its cellular organization and genetic regulation. While the medullary zone contains stem-like hematopoietic progenitors, the posterior signaling center (PSC) functions as a niche microenvironment essential for controlling the decision between progenitor maintenance versus cellular differentiation. In this report, we utilize a PSC-specific GAL4 driver and UAS-gene RNAi strains, to selectively knockdown individual gene functions in PSC cells. We assessed the effect of abrogating the function of 820 genes as to their requirement for niche cell production and differentiation. 100 genes were shown to be essential for normal niche development, with various loci placed into sub-groups based on the functions of their encoded protein products and known genetic interactions. For members of three of these groups, we characterized loss- and gain-of-function phenotypes. Gene function knockdown of members of the BAP chromatin-remodeling complex resulted in niche cells that do not express the hedgehog (hh) gene and fail to differentiate filopodia believed important for Hh signaling from the niche to progenitors. Abrogating gene function of various members of the insulin-like growth factor and TOR signaling pathways resulted in anomalous PSC cell production, leading to a defective niche organization. Further analysis of the Pten, TSC1, and TSC2 tumor suppressor genes demonstrated their loss-of-function condition resulted in severely altered blood cell homeostasis, including the abundant production of lamellocytes, specialized hemocytes involved in innate immune responses. Together, this cell-specific RNAi knockdown survey and mutant phenotype analyses identified multiple genes and their regulatory networks required for

  9. Extended evolution: A conceptual framework for integrating regulatory networks and niche construction

    PubMed Central

    Renn, Jürgen

    2015-01-01

    ABSTRACT This paper introduces a conceptual framework for the evolution of complex systems based on the integration of regulatory network and niche construction theories. It is designed to apply equally to cases of biological, social and cultural evolution. Within the conceptual framework we focus especially on the transformation of complex networks through the linked processes of externalization and internalization of causal factors between regulatory networks and their corresponding niches and argue that these are an important part of evolutionary explanations. This conceptual framework extends previous evolutionary models and focuses on several challenges, such as the path‐dependent nature of evolutionary change, the dynamics of evolutionary innovation and the expansion of inheritance systems. J. Exp. Zool. (Mol. Dev. Evol.) 324B: 565–577, 2015. © 2015 The Authors. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution published by Wiley Periodicals, Inc. PMID:26097188

  10. Niche partitioning due to adaptive foraging reverses effects of nestedness and connectance on pollination network stability.

    PubMed

    Valdovinos, Fernanda S; Brosi, Berry J; Briggs, Heather M; Moisset de Espanés, Pablo; Ramos-Jiliberto, Rodrigo; Martinez, Neo D

    2016-10-01

    Much research debates whether properties of ecological networks such as nestedness and connectance stabilise biological communities while ignoring key behavioural aspects of organisms within these networks. Here, we computationally assess how adaptive foraging (AF) behaviour interacts with network architecture to determine the stability of plant-pollinator networks. We find that AF reverses negative effects of nestedness and positive effects of connectance on the stability of the networks by partitioning the niches among species within guilds. This behaviour enables generalist pollinators to preferentially forage on the most specialised of their plant partners which increases the pollination services to specialist plants and cedes the resources of generalist plants to specialist pollinators. We corroborate these behavioural preferences with intensive field observations of bee foraging. Our results show that incorporating key organismal behaviours with well-known biological mechanisms such as consumer-resource interactions into the analysis of ecological networks may greatly improve our understanding of complex ecosystems. PMID:27600659

  11. Niche partitioning due to adaptive foraging reverses effects of nestedness and connectance on pollination network stability.

    PubMed

    Valdovinos, Fernanda S; Brosi, Berry J; Briggs, Heather M; Moisset de Espanés, Pablo; Ramos-Jiliberto, Rodrigo; Martinez, Neo D

    2016-10-01

    Much research debates whether properties of ecological networks such as nestedness and connectance stabilise biological communities while ignoring key behavioural aspects of organisms within these networks. Here, we computationally assess how adaptive foraging (AF) behaviour interacts with network architecture to determine the stability of plant-pollinator networks. We find that AF reverses negative effects of nestedness and positive effects of connectance on the stability of the networks by partitioning the niches among species within guilds. This behaviour enables generalist pollinators to preferentially forage on the most specialised of their plant partners which increases the pollination services to specialist plants and cedes the resources of generalist plants to specialist pollinators. We corroborate these behavioural preferences with intensive field observations of bee foraging. Our results show that incorporating key organismal behaviours with well-known biological mechanisms such as consumer-resource interactions into the analysis of ecological networks may greatly improve our understanding of complex ecosystems.

  12. Sparse coding for layered neural networks

    NASA Astrophysics Data System (ADS)

    Katayama, Katsuki; Sakata, Yasuo; Horiguchi, Tsuyoshi

    2002-07-01

    We investigate storage capacity of two types of fully connected layered neural networks with sparse coding when binary patterns are embedded into the networks by a Hebbian learning rule. One of them is a layered network, in which a transfer function of even layers is different from that of odd layers. The other is a layered network with intra-layer connections, in which the transfer function of inter-layer is different from that of intra-layer, and inter-layered neurons and intra-layered neurons are updated alternately. We derive recursion relations for order parameters by means of the signal-to-noise ratio method, and then apply the self-control threshold method proposed by Dominguez and Bollé to both layered networks with monotonic transfer functions. We find that a critical value αC of storage capacity is about 0.11|a ln a| -1 ( a≪1) for both layered networks, where a is a neuronal activity. It turns out that the basin of attraction is larger for both layered networks when the self-control threshold method is applied.

  13. Inter-layer synchronization in multiplex networks of identical layers.

    PubMed

    Sevilla-Escoboza, R; Sendiña-Nadal, I; Leyva, I; Gutiérrez, R; Buldú, J M; Boccaletti, S

    2016-06-01

    Inter-layer synchronization is a distinctive process of multiplex networks whereby each node in a given layer evolves synchronously with all its replicas in other layers, irrespective of whether or not it is synchronized with the other units of the same layer. We analytically derive the necessary conditions for the existence and stability of such a state, and verify numerically the analytical predictions in several cases where such a state emerges. We further inspect its robustness against a progressive de-multiplexing of the network, and provide experimental evidence by means of multiplexes of nonlinear electronic circuits affected by intrinsic noise and parameter mismatch. PMID:27368794

  14. Quantum key distribution networks layer model

    NASA Astrophysics Data System (ADS)

    Wen, Hao; Han, Zheng-fu; Hong, Pei-lin; Guo, Guang-can

    2008-03-01

    Quantum Key Distribution (QKD) networks allow multiple users to generate and share secret quantum keys with unconditional security. Although many schemes of QKD networks have been presented, they are only concentrated on the system realization and physical implementations. For the complete practical quantum network, a succinct theoretic model that systematically describes the working processes from physical schemes to key process protocols, from network topology to key management, and from quantum communication to classical communication is still absent. One would hope that research and experience have shown that there are certain succinct model in the design of communication network. With demonstration of the different QKD links and the four primary types of quantum networks including probability multiplexing, wavelength multiplexing, time multiplexing and quantum multiplexing, we suggest a layer model for QKD networks which will be compatible with different implementations and protocols. We divide it into four main layers by their functional independency while defining each layer's services and responsibilities in detail, orderly named quantum links layer, quantum networks layer, quantum key distribution protocols process layer, and keys management layer. It will be helpful for the systematic design and construction of real QKD networks.

  15. Concise Review: Breast Cancer Stem Cells: Regulatory Networks, Stem Cell Niches, and Disease Relevance

    PubMed Central

    2014-01-01

    Accumulating evidence has shown that cancer stem cells (CSCs), the cancer cells that have long-term proliferative potential and the ability to regenerate tumors with phenotypically heterogeneous cell types, are important mediators of tumor metastasis and cancer relapse. In breast cancer, these cells often possess attributes of cells that have undergone an epithelial-mesenchymal transition (EMT). Signaling networks mediated by microRNAs and EMT-inducing transcription factors connect the EMT program with the core stem cell regulatory machineries. These signaling networks are also regulated by extrinsic niche signals that induce and maintain CSCs, contributing to metastatic colonization and promoting the reactivation of dormant tumor cells. Targeting these CSC pathways is likely to improve the efficacy of conventional chemo- and radiotherapies. PMID:24904174

  16. Finding Missing Interactions of the Arabidopsis thaliana Root Stem Cell Niche Gene Regulatory Network

    PubMed Central

    Azpeitia, Eugenio; Weinstein, Nathan; Benítez, Mariana; Mendoza, Luis; Alvarez-Buylla, Elena R.

    2013-01-01

    Over the last few decades, the Arabidopsis thaliana root stem cell niche (RSCN) has become a model system for the study of plant development and stem cell niche dynamics. Currently, many of the molecular mechanisms involved in RSCN maintenance and development have been described. A few years ago, we published a gene regulatory network (GRN) model integrating this information. This model suggested that there were missing components or interactions. Upon updating the model, the observed stable gene configurations of the RSCN could not be recovered, indicating that there are additional missing components or interactions in the model. In fact, due to the lack of experimental data, GRNs inferred from published data are usually incomplete. However, predicting the location and nature of the missing data is a not trivial task. Here, we propose a set of procedures for detecting and predicting missing interactions in Boolean networks. We used these procedures to predict putative missing interactions in the A. thaliana RSCN network model. Using our approach, we identified three necessary interactions to recover the reported gene activation configurations that have been experimentally uncovered for the different cell types within the RSCN: (1) a regulation of PHABULOSA to restrict its expression domain to the vascular cells, (2) a self-regulation of WOX5, possibly by an indirect mechanism through the auxin signaling pathway, and (3) a positive regulation of JACKDAW by MAGPIE. The procedures proposed here greatly reduce the number of possible Boolean functions that are biologically meaningful and experimentally testable and that do not contradict previous data. We believe that these procedures can be used on any Boolean network. However, because the procedures were designed for the specific case of the RSCN, formal demonstrations of the procedures should be shown in future efforts. PMID:23658556

  17. Underwater acoustic wireless sensor networks: advances and future trends in physical, MAC and routing layers.

    PubMed

    Climent, Salvador; Sanchez, Antonio; Capella, Juan Vicente; Meratnia, Nirvana; Serrano, Juan Jose

    2014-01-01

    This survey aims to provide a comprehensive overview of the current research on underwater wireless sensor networks, focusing on the lower layers of the communication stack, and envisions future trends and challenges. It analyzes the current state-of-the-art on the physical, medium access control and routing layers. It summarizes their security threads and surveys the currently proposed studies. Current envisioned niches for further advances in underwater networks research range from efficient, low-power algorithms and modulations to intelligent, energy-aware routing and medium access control protocols. PMID:24399155

  18. Underwater acoustic wireless sensor networks: advances and future trends in physical, MAC and routing layers.

    PubMed

    Climent, Salvador; Sanchez, Antonio; Capella, Juan Vicente; Meratnia, Nirvana; Serrano, Juan Jose

    2014-01-01

    This survey aims to provide a comprehensive overview of the current research on underwater wireless sensor networks, focusing on the lower layers of the communication stack, and envisions future trends and challenges. It analyzes the current state-of-the-art on the physical, medium access control and routing layers. It summarizes their security threads and surveys the currently proposed studies. Current envisioned niches for further advances in underwater networks research range from efficient, low-power algorithms and modulations to intelligent, energy-aware routing and medium access control protocols.

  19. Underwater Acoustic Wireless Sensor Networks: Advances and Future Trends in Physical, MAC and Routing Layers

    PubMed Central

    Climent, Salvador; Sanchez, Antonio; Capella, Juan Vicente; Meratnia, Nirvana; Serrano, Juan Jose

    2014-01-01

    This survey aims to provide a comprehensive overview of the current research on underwater wireless sensor networks, focusing on the lower layers of the communication stack, and envisions future trends and challenges. It analyzes the current state-of-the-art on the physical, medium access control and routing layers. It summarizes their security threads and surveys the currently proposed studies. Current envisioned niches for further advances in underwater networks research range from efficient, low-power algorithms and modulations to intelligent, energy-aware routing and medium access control protocols. PMID:24399155

  20. Interactions between Niche and Regime: An Analysis of Learning and Innovation Networks for Sustainable Agriculture across Europe

    ERIC Educational Resources Information Center

    Ingram, Julie; Maye, Damian; Kirwan, James; Curry, Nigel; Kubinakova, Katarina

    2015-01-01

    Purpose: This paper aims to reveal, and contribute to an understanding of, the processes that connect learning and innovation networks in sustainable agriculture to elements of the mainstream agricultural regime. Drawing on the innovations and transition literature, the paper frames the analysis around niche-regime interaction using the notion of…

  1. Layer-layer competition in multiplex complex networks.

    PubMed

    Gómez-Gardeñes, J; de Domenico, M; Gutiérrez, G; Arenas, A; Gómez, S

    2015-12-13

    The coexistence of multiple types of interactions within social, technological and biological networks has moved the focus of the physics of complex systems towards a multiplex description of the interactions between their constituents. This novel approach has unveiled that the multiplex nature of complex systems has strong influence in the emergence of collective states and their critical properties. Here we address an important issue that is intrinsic to the coexistence of multiple means of interactions within a network: their competition. To this aim, we study a two-layer multiplex in which the activity of users can be localized in each of the layers or shared between them, favouring that neighbouring nodes within a layer focus their activity on the same layer. This framework mimics the coexistence and competition of multiple communication channels, in a way that the prevalence of a particular communication platform emerges as a result of the localization of user activity in one single interaction layer. Our results indicate that there is a transition from localization (use of a preferred layer) to delocalization (combined usage of both layers) and that the prevalence of a particular layer (in the localized state) depends on the structural properties.

  2. Layer-layer competition in multiplex complex networks.

    PubMed

    Gómez-Gardeñes, J; de Domenico, M; Gutiérrez, G; Arenas, A; Gómez, S

    2015-12-13

    The coexistence of multiple types of interactions within social, technological and biological networks has moved the focus of the physics of complex systems towards a multiplex description of the interactions between their constituents. This novel approach has unveiled that the multiplex nature of complex systems has strong influence in the emergence of collective states and their critical properties. Here we address an important issue that is intrinsic to the coexistence of multiple means of interactions within a network: their competition. To this aim, we study a two-layer multiplex in which the activity of users can be localized in each of the layers or shared between them, favouring that neighbouring nodes within a layer focus their activity on the same layer. This framework mimics the coexistence and competition of multiple communication channels, in a way that the prevalence of a particular communication platform emerges as a result of the localization of user activity in one single interaction layer. Our results indicate that there is a transition from localization (use of a preferred layer) to delocalization (combined usage of both layers) and that the prevalence of a particular layer (in the localized state) depends on the structural properties. PMID:26527811

  3. Modeling MAC layer for powerline communications networks

    NASA Astrophysics Data System (ADS)

    Hrasnica, Halid; Haidine, Abdelfatteh

    2001-02-01

    The usage of electrical power distribution networks for voice and data transmission, called Powerline Communications, becomes nowadays more and more attractive, particularly in the telecommunication access area. The most important reasons for that are the deregulation of the telecommunication market and a fact that the access networks are still property of former monopolistic companies. In this work, first we analyze a PLC network and system structure as well as a disturbance scenario in powerline networks. After that, we define a logical structure of the powerline MAC layer and propose the reservation MAC protocols for the usage in the PLC network which provides collision free data transmission. This makes possible better network utilization and realization of QoS guarantees which can make PLC networks competitive to other access technologies.

  4. Genetic basis for developmental homeostasis of germline stem cell niche number: a network of Tramtrack-Group nuclear BTB factors.

    PubMed

    Bartoletti, Mathieu; Rubin, Thomas; Chalvet, Fabienne; Netter, Sophie; Dos Santos, Nicolas; Poisot, Emilie; Paces-Fessy, Mélanie; Cumenal, Delphine; Peronnet, Frédérique; Pret, Anne-Marie; Théodore, Laurent

    2012-01-01

    The potential to produce new cells during adult life depends on the number of stem cell niches and the capacity of stem cells to divide, and is therefore under the control of programs ensuring developmental homeostasis. However, it remains generally unknown how the number of stem cell niches is controlled. In the insect ovary, each germline stem cell (GSC) niche is embedded in a functional unit called an ovariole. The number of ovarioles, and thus the number of GSC niches, varies widely among species. In Drosophila, morphogenesis of ovarioles starts in larvae with the formation of terminal filaments (TFs), each made of 8-10 cells that pile up and sort in stacks. TFs constitute organizers of individual germline stem cell niches during larval and early pupal development. In the Drosophila melanogaster subgroup, the number of ovarioles varies interspecifically from 8 to 20. Here we show that pipsqueak, Trithorax-like, batman and the bric-à-brac (bab) locus, all encoding nuclear BTB/POZ factors of the Tramtrack Group, are involved in limiting the number of ovarioles in D. melanogaster. At least two different processes are differentially perturbed by reducing the function of these genes. We found that when the bab dose is reduced, sorting of TF cells into TFs was affected such that each TF contains fewer cells and more TFs are formed. In contrast, psq mutants exhibited a greater number of TF cells per ovary, with a normal number of cells per TF, thereby leading to formation of more TFs per ovary than in the wild type. Our results indicate that two parallel genetic pathways under the control of a network of nuclear BTB factors are combined in order to negatively control the number of germline stem cell niches.

  5. A Layered Approach To Pacs Network Architecture

    NASA Astrophysics Data System (ADS)

    Hegde, Shankar S.; Prewitt, Judith M.

    1984-08-01

    Although the functions performed by the different nodes on the PACS network are many, it is possible to formulate a minimum set of service primitives such that the application software residing at the nodes can utilize those primitives to perform the functions. These primitives define the framework for the communication interface. The question of how these primitives fit into the concept of a layered network architecture is explored in this paper. The OSI model as applicable to the PACS network is described, the areas that need standardization are briefly mentioned, and the ongoing standardization efforts are addressed from the OSI perspective.

  6. Intra-layer synchronization in multiplex networks

    NASA Astrophysics Data System (ADS)

    Gambuzza, L. V.; Frasca, M.; Gómez-Gardeñes, J.

    2015-04-01

    We study synchronization of N oscillators indirectly coupled through a medium which is inhomogeneous and has its own dynamics. The system is formalized in terms of a multilayer network, where the top layer is made of disconnected oscillators and the bottom one, modeling the medium, consists of oscillators coupled according to a given topology. The different dynamics of the medium and the top layer is accounted for by including a frequency mismatch between them. We show a novel regime of synchronization as intra-layer coherence does not necessarily require inter-layer coherence. This regime appears under mild conditions on the bottom layer: arbitrary topologies may be considered, provided that they support synchronization of the oscillators of the medium. The existence of a density-dependent threshold as in quorum-sensing phenomena is also demonstrated.

  7. Signaling Networks among Stem Cell Precursors, Transit-Amplifying Progenitors, and their Niche in Developing Hair Follicles.

    PubMed

    Rezza, Amélie; Wang, Zichen; Sennett, Rachel; Qiao, Wenlian; Wang, Dongmei; Heitman, Nicholas; Mok, Ka Wai; Clavel, Carlos; Yi, Rui; Zandstra, Peter; Ma'ayan, Avi; Rendl, Michael

    2016-03-29

    The hair follicle (HF) is a complex miniorgan that serves as an ideal model system to study stem cell (SC) interactions with the niche during growth and regeneration. Dermal papilla (DP) cells are required for SC activation during the adult hair cycle, but signal exchange between niche and SC precursors/transit-amplifying cell (TAC) progenitors that regulates HF morphogenetic growth is largely unknown. Here we use six transgenic reporters to isolate 14 major skin and HF cell populations. With next-generation RNA sequencing, we characterize their transcriptomes and define unique molecular signatures. SC precursors, TACs, and the DP niche express a plethora of ligands and receptors. Signaling interaction network analysis reveals a bird's-eye view of pathways implicated in epithelial-mesenchymal interactions. Using a systematic tissue-wide approach, this work provides a comprehensive platform, linked to an interactive online database, to identify and further explore the SC/TAC/niche crosstalk regulating HF growth. PMID:27009580

  8. Layer I as a putative neurogenic niche in young adult guinea pig cerebrum.

    PubMed

    Xiong, Kun; Cai, Yan; Zhang, Xue-Mei; Huang, Ju-Fang; Liu, Zhong-Yu; Fu, Guang-Ming; Feng, Jia-Chun; Clough, Richard W; Patrylo, Peter R; Luo, Xue-Gang; Hu, Chun-Hong; Yan, Xiao-Xin

    2010-10-01

    A considerable number of cells expressing typical immature neuronal markers including doublecortin (DCX+) are present around layer II in the cerebral cortex of young and adult guinea pigs and other larger mammals, and their origin and biological implication await further characterization. We show here in young adult guinea pigs that these DCX+ cells are accompanied by in situ cell division around the superficial cortical layers mostly in layer I, but they co-express proliferating cell nuclear antigen (PCNA) and an early neuronal fate determining factor, PAX6. A small number of these DCX+ cells also colocalize with BrdU following administration of this mitotic indicator. Cranial X-ray irradiation causes a decline of DCX+ cells around layer II, and novel environmental exploration induces c-Fos expression among these cells in several neocortical areas. Together, these data are compatible with a notion that DCX+ cortical neurons around layer II might derive from proliferable neuronal precursors around layer I in young adult guinea pig cerebrum, and that these cells might be modulated by experience under physiological conditions.

  9. Ecological-niche modeling and prioritization of conservation-area networks for Mexican herpetofauna.

    PubMed

    Urbina-Cardona, J Nicolás; Flores-Villela, Oscar

    2010-08-01

    One of the most important tools in conservation biology is information on the geographic distribution of species and the variables determining those patterns. We used maximum-entropy niche modeling to run distribution models for 222 amphibian and 371 reptile species (49% endemics and 27% threatened) for which we had 34,619 single geographic records. The planning region is in southeastern Mexico, is 20% of the country's area, includes 80% of the country's herpetofauna, and lacks an adequate protected-area system. We used probabilistic data to build distribution models of herpetofauna for use in prioritizing conservation areas for three target groups (all species and threatened and endemic species). The accuracy of species-distribution models was better for endemic and threatened species than it was for all species. Forty-seven percent of the region has been deforested and additional conservation areas with 13.7% to 88.6% more native vegetation (76% to 96% of the areas are outside the current protected-area system) are needed. There was overlap in 26 of the main selected areas in the conservation-area network prioritized to preserve the target groups, and for all three target groups the proportion of vegetation types needed for their conservation was constant: 30% pine and oak forests, 22% tropical evergreen forest, 17% low deciduous forest, and 8% montane cloud forests. The fact that different groups of species require the same proportion of habitat types suggests that the pine and oak forests support the highest proportion of endemic and threatened species and should therefore be given priority over other types of vegetation for inclusion in the protected areas of southeastern Mexico.

  10. Cascading processes on multiplex networks: Impact of weak layers

    NASA Astrophysics Data System (ADS)

    Lee, Kyu-Min; Goh, Kwang-Il

    Many real-world complex systems such as biological and socio-technological systems consist of manifold layers in multiplex networks. The multiple network layers give rise to the nonlinear effect for the emergent dynamics of systems. Especially, the weak layers plays the significant role in nonlinearity of multiplex networks, which can be neglected in single-layer network framework overlaying all layers. Here we present a simple model of cascades on multiplex networks of heterogeneous layers. The model is simulated on the multiplex network of international trades. We found that the multiplex model produces more catastrophic cascading failures which were the result of collective behaviors from coupling layers rather than the simple summation effect. Therefore risks can be systematically underestimated in simply overlaid network system because the impact of weak layers is overlooked. Our simple theoretical model would have some implications to investigate and design optimal real-world complex systems.

  11. BMP-SHH signaling network controls epithelial stem cell fate via regulation of its niche in the developing tooth.

    PubMed

    Li, Jingyuan; Feng, Jifan; Liu, Yang; Ho, Thach-Vu; Grimes, Weston; Ho, Hoang Anh; Park, Shery; Wang, Songlin; Chai, Yang

    2015-04-20

    During embryogenesis, ectodermal stem cells adopt different fates and form diverse ectodermal organs, such as teeth, hair follicles, mammary glands, and salivary glands. Interestingly, these ectodermal organs differ in their tissue homeostasis, which leads to differential abilities for continuous growth postnatally. Mouse molars lose the ability to grow continuously, whereas incisors retain this ability. In this study, we found that a BMP-Smad4-SHH-Gli1 signaling network may provide a niche supporting transient Sox2+ dental epithelial stem cells in mouse molars. This mechanism also plays a role in continuously growing mouse incisors. The differential fate of epithelial stem cells in mouse molars and incisors is controlled by this BMP/SHH signaling network, which partially accounts for the different postnatal growth potential of molars and incisors. Collectively, our study highlights the importance of crosstalk between two signaling pathways, BMP and SHH, in regulating the fate of epithelial stem cells during organogenesis.

  12. Ecological niche

    SciTech Connect

    Shugart, H.H.

    1980-01-01

    The ecological niche of an organism is the set of environmental conditions under which the particular functions of the organism could be expected to assure its survival. It comprises both the set of conditions where the organism lives (often termed the habitat of the organism) and the functional role of the organism in the ecosystem. Recent works in niche theory have enabled ecologists to develop predictions and actual applications. The history of the niche concept, applications of niche theory, and ecological differences between similar species are discussed.

  13. Artificial Stem Cell Niches

    PubMed Central

    Lutolf, Matthias P.; Blau, Helen M.

    2011-01-01

    Stem cells are characterized by their dual ability to reproduce themselves (self-renew) and specialize (differentiate), yielding a plethora of daughter cells that maintain and regenerate tissues. In contrast to their embryonic counterparts, adult stem cells retain their unique functions only if they are in intimate contact with an instructive microenvironment, termed stem cell niche. In these niches, stem cells integrate a complex array of molecular signals that, in concert with induced cell-intrinsic regulatory networks, control their function and balance their numbers in response to physiologic demands. This progress report provides a perspective on how advanced materials technologies could be used (i) to engineer and systematically analyze specific aspects of functional stem cells niches in a controlled fashion in vitro and (ii) to target stem cell niches in vivo. Such “artificial niches” constitute potent tools for elucidating stem cell regulatory mechanisms with the capacity to directly impact the development of novel therapeutic strategies for tissue regeneration. PMID:20882496

  14. Realization problem of multi-layer cellular neural networks.

    PubMed

    Ban, Jung-Chao; Chang, Chih-Hung

    2015-10-01

    This paper investigates whether the output space of a multi-layer cellular neural network can be realized via a single layer cellular neural network in the sense of the existence of finite-to-one map from one output space to the other. Whenever such realization exists, the phenomena exhibited in the output space of the revealed single layer cellular neural network is at most a constant multiple of the phenomena exhibited in the output space of the original multi-layer cellular neural network. Meanwhile, the computation complexity of a single layer system is much less than the complexity of a multi-layer system. Namely, one can trade the precision of the results for the execution time. We remark that a routine extension of the proposed methodology in this paper can be applied to the substitution of hidden spaces although the detailed illustration is omitted.

  15. Improved efficient routing strategy on two-layer complex networks

    NASA Astrophysics Data System (ADS)

    Ma, Jinlong; Han, Weizhan; Guo, Qing; Zhang, Shuai; Wang, Junfang; Wang, Zhihao

    2016-10-01

    The traffic dynamics of multi-layer networks has become a hot research topic since many networks are comprised of two or more layers of subnetworks. Due to its low traffic capacity, the traditional shortest path routing (SPR) protocol is susceptible to congestion on two-layer complex networks. In this paper, we propose an efficient routing strategy named improved global awareness routing (IGAR) strategy which is based on the betweenness centrality of nodes in the two layers. With the proposed strategy, the routing paths can bypass hub nodes of both layers to enhance the transport efficiency. Simulation results show that the IGAR strategy can bring much better traffic capacity than the SPR and the global awareness routing (GAR) strategies. Because of the significantly improved traffic performance, this study is helpful to alleviate congestion of the two-layer complex networks.

  16. Plant stem cell niches.

    PubMed

    Aichinger, Ernst; Kornet, Noortje; Friedrich, Thomas; Laux, Thomas

    2012-01-01

    Multicellular organisms possess pluripotent stem cells to form new organs, replenish the daily loss of cells, or regenerate organs after injury. Stem cells are maintained in specific environments, the stem cell niches, that provide signals to block differentiation. In plants, stem cell niches are situated in the shoot, root, and vascular meristems-self-perpetuating units of organ formation. Plants' lifelong activity-which, as in the case of trees, can extend over more than a thousand years-requires that a robust regulatory network keep the balance between pluripotent stem cells and differentiating descendants. In this review, we focus on current models in plant stem cell research elaborated during the past two decades, mainly in the model plant Arabidopsis thaliana. We address the roles of mobile signals on transcriptional modules involved in balancing cell fates. In addition, we discuss shared features of and differences between the distinct stem cell niches of Arabidopsis.

  17. MAC layer security issues in wireless mesh networks

    NASA Astrophysics Data System (ADS)

    Reddy, K. Ganesh; Thilagam, P. Santhi

    2016-03-01

    Wireless Mesh Networks (WMNs) have emerged as a promising technology for a broad range of applications due to their self-organizing, self-configuring and self-healing capability, in addition to their low cost and easy maintenance. Securing WMNs is more challenging and complex issue due to their inherent characteristics such as shared wireless medium, multi-hop and inter-network communication, highly dynamic network topology and decentralized architecture. These vulnerable features expose the WMNs to several types of attacks in MAC layer. The existing MAC layer standards and implementations are inadequate to secure these features and fail to provide comprehensive security solutions to protect both backbone and client mesh. Hence, there is a need for developing efficient, scalable and integrated security solutions for WMNs. In this paper, we classify the MAC layer attacks and analyze the existing countermeasures. Based on attacks classification and countermeasures analysis, we derive the research directions to enhance the MAC layer security for WMNs.

  18. Strength of weak layers in cascading failures on multiplex networks: case of the international trade network.

    PubMed

    Lee, Kyu-Min; Goh, K-I

    2016-01-01

    Many real-world complex systems across natural, social, and economical domains consist of manifold layers to form multiplex networks. The multiple network layers give rise to nonlinear effect for the emergent dynamics of systems. Especially, weak layers that can potentially play significant role in amplifying the vulnerability of multiplex networks might be shadowed in the aggregated single-layer network framework which indiscriminately accumulates all layers. Here we present a simple model of cascading failure on multiplex networks of weight-heterogeneous layers. By simulating the model on the multiplex network of international trades, we found that the multiplex model produces more catastrophic cascading failures which are the result of emergent collective effect of coupling layers, rather than the simple sum thereof. Therefore risks can be systematically underestimated in single-layer network analyses because the impact of weak layers can be overlooked. We anticipate that our simple theoretical study can contribute to further investigation and design of optimal risk-averse real-world complex systems. PMID:27211291

  19. Strength of weak layers in cascading failures on multiplex networks: case of the international trade network

    PubMed Central

    Lee, Kyu-Min; Goh, K.-I.

    2016-01-01

    Many real-world complex systems across natural, social, and economical domains consist of manifold layers to form multiplex networks. The multiple network layers give rise to nonlinear effect for the emergent dynamics of systems. Especially, weak layers that can potentially play significant role in amplifying the vulnerability of multiplex networks might be shadowed in the aggregated single-layer network framework which indiscriminately accumulates all layers. Here we present a simple model of cascading failure on multiplex networks of weight-heterogeneous layers. By simulating the model on the multiplex network of international trades, we found that the multiplex model produces more catastrophic cascading failures which are the result of emergent collective effect of coupling layers, rather than the simple sum thereof. Therefore risks can be systematically underestimated in single-layer network analyses because the impact of weak layers can be overlooked. We anticipate that our simple theoretical study can contribute to further investigation and design of optimal risk-averse real-world complex systems. PMID:27211291

  20. Strength of weak layers in cascading failures on multiplex networks: case of the international trade network

    NASA Astrophysics Data System (ADS)

    Lee, Kyu-Min; Goh, K.-I.

    2016-05-01

    Many real-world complex systems across natural, social, and economical domains consist of manifold layers to form multiplex networks. The multiple network layers give rise to nonlinear effect for the emergent dynamics of systems. Especially, weak layers that can potentially play significant role in amplifying the vulnerability of multiplex networks might be shadowed in the aggregated single-layer network framework which indiscriminately accumulates all layers. Here we present a simple model of cascading failure on multiplex networks of weight-heterogeneous layers. By simulating the model on the multiplex network of international trades, we found that the multiplex model produces more catastrophic cascading failures which are the result of emergent collective effect of coupling layers, rather than the simple sum thereof. Therefore risks can be systematically underestimated in single-layer network analyses because the impact of weak layers can be overlooked. We anticipate that our simple theoretical study can contribute to further investigation and design of optimal risk-averse real-world complex systems.

  1. Asymmetrically interacting spreading dynamics on complex layered networks

    PubMed Central

    Wang, Wei; Tang, Ming; Yang, Hui; Younghae Do; Lai, Ying-Cheng; Lee, GyuWon

    2014-01-01

    The spread of disease through a physical-contact network and the spread of information about the disease on a communication network are two intimately related dynamical processes. We investigate the asymmetrical interplay between the two types of spreading dynamics, each occurring on its own layer, by focusing on the two fundamental quantities underlying any spreading process: epidemic threshold and the final infection ratio. We find that an epidemic outbreak on the contact layer can induce an outbreak on the communication layer, and information spreading can effectively raise the epidemic threshold. When structural correlation exists between the two layers, the information threshold remains unchanged but the epidemic threshold can be enhanced, making the contact layer more resilient to epidemic outbreak. We develop a physical theory to understand the intricate interplay between the two types of spreading dynamics. PMID:24872257

  2. A Cross-Layer PEP for DVB-RCS Networks

    NASA Astrophysics Data System (ADS)

    Giambene, Giovanni; Hadzic, Snezana

    The aim of this paper is to consider the problems of TCP performance in broadband GEO satellite networks and to propose a cross-layer approach for a transport-layer PEP that makes spoofing actions on ACKs to modify them in case the satellite network is congested. This approach is investigated here from the signaling standpoint with a special attention to the BSM reference model and considering a specific GEO satellite network architecture based on the DVB-S2/-RCS standards. The proposed PEP can prevent congestion in the satellite network, thus allowing a better TCP performance. This work has been carried out within the framework of the EU SatNEx II FP6 Network of Excellence.

  3. A layered network model of sensory cortex

    SciTech Connect

    Travis, B.J.

    1986-01-01

    An integrated computational approach to modeling sensory systems which couples realistic layered neural models of sensory cortex and midbrain nuclei to detailed models of the sense organs (e.g., retina or cochlea) is described. The approach is applied to the auditory system. Through an exercise of the model, it is shown that spatial location of sounds may be a natural consequence of the way cochlear response is mapped onto the cortex. 31 refs., 23 figs., 3 tabs.

  4. Layered Social Network Analysis Reveals Complex Relationships in Kindergarteners.

    PubMed

    Golemiec, Mireille; Schneider, Jonathan; Boyce, W Thomas; Bush, Nicole R; Adler, Nancy; Levine, Joel D

    2016-01-01

    The interplay between individuals forms building blocks for social structure. Here, we examine the structure of behavioral interactions among kindergarten classroom with a hierarchy-neutral approach to examine all possible underlying patterns in the formation of layered networks of "reciprocal" interactions. To understand how these layers are coordinated, we used a layered motif approach. Our dual layered motif analysis can therefore be thought of as the dynamics of smaller groups that tile to create the group structure, or alternatively they provide information on what the average child would do in a given local social environment. When we examine the regulated motifs in layered networks, we find that transitivity is at least partially involved in the formation of these layered network structures. We also found complex combinations of the expected reciprocal interactions. The mechanisms used to understand social networks of kindergarten children here are also applicable on a more general scale to any group of individuals where interactions and identities can be readily observed and scored. PMID:26973572

  5. Layered Social Network Analysis Reveals Complex Relationships in Kindergarteners

    PubMed Central

    Golemiec, Mireille; Schneider, Jonathan; Boyce, W. Thomas; Bush, Nicole R.; Adler, Nancy; Levine, Joel D.

    2016-01-01

    The interplay between individuals forms building blocks for social structure. Here, we examine the structure of behavioral interactions among kindergarten classroom with a hierarchy-neutral approach to examine all possible underlying patterns in the formation of layered networks of “reciprocal” interactions. To understand how these layers are coordinated, we used a layered motif approach. Our dual layered motif analysis can therefore be thought of as the dynamics of smaller groups that tile to create the group structure, or alternatively they provide information on what the average child would do in a given local social environment. When we examine the regulated motifs in layered networks, we find that transitivity is at least partially involved in the formation of these layered network structures. We also found complex combinations of the expected reciprocal interactions. The mechanisms used to understand social networks of kindergarten children here are also applicable on a more general scale to any group of individuals where interactions and identities can be readily observed and scored. PMID:26973572

  6. Growing multiplex networks with arbitrary number of layers

    NASA Astrophysics Data System (ADS)

    Momeni, Naghmeh; Fotouhi, Babak

    2015-12-01

    This paper focuses on the problem of growing multiplex networks. Currently, the results on the joint degree distribution of growing multiplex networks present in the literature pertain to the case of two layers and are confined to the special case of homogeneous growth and are limited to the state state (that is, the limit of infinite size). In the present paper, we first obtain closed-form solutions for the joint degree distribution of heterogeneously growing multiplex networks with arbitrary number of layers in the steady state. Heterogeneous growth means that each incoming node establishes different numbers of links in different layers. We consider both uniform and preferential growth. We then extend the analysis of the uniform growth mechanism to arbitrary times. We obtain a closed-form solution for the time-dependent joint degree distribution of a growing multiplex network with arbitrary initial conditions. Throughout, theoretical findings are corroborated with Monte Carlo simulations. The results shed light on the effects of the initial network on the transient dynamics of growing multiplex networks and takes a step towards characterizing the temporal variations of the connectivity of growing multiplex networks, as well as predicting their future structural properties.

  7. Multichannel MAC Layer In Mobile Ad—Hoc Network

    NASA Astrophysics Data System (ADS)

    Logesh, K.; Rao, Samba Siva

    2010-11-01

    This paper we presented the design objectives and technical challenges in Multichannel MAC protocols in Mobile Ad-hoc Network. In IEEE 802.11 a/b/g standards allow use of multiple channels, only a single channel is popularly used, due to the lack of efficient protocols that enable use of Multiple Channels. Even though complex environments in ad hoc networks require a combined control of physical (PHY) and medium access control (MAC) layers resources in order to optimize performance. And also we discuss the characteristics of cross-layer frame and give a multichannel MAC approach.

  8. Layer-by-layer micromolding of natural biopolymer scaffolds with intrinsic microfluidic networks.

    PubMed

    He, Jiankang; Wang, Ye; Liu, Yaxiong; Li, Dichen; Jin, Zhongmin

    2013-06-01

    A three-dimensional (3D) microfluidic network plays an important role in engineering thick organs. However, most of the existing methods are limited to mechanically robust synthetic biomaterials and only planar or simple microfluidic networks have been incorporated into soft natural biopolymers. Here we presented an automatic layer-by-layer micromolding strategy to reproducibly fabricate 3D microfluidic porous scaffolds directly from the aqueous solution of soft natural biopolymers. Process parameters such as the liquid volume for each layer and contact displacement were investigated to produce a structurally stable 3D microfluidic scaffold. Microscopic characterization demonstrated that the microfluidic channels were interconnected in 3D and successfully functioned as a convective pathway to transport a polymer solution. Endothelial cells grew relatively well in the porous microfluidic channels. It is envisioned that this method could provide an alternative way to reproducibly build complex 3D microfluidic networks into extracellular matrix-like scaffolds for the fabrication of soft vascularized organs. PMID:23443621

  9. Niche explosion.

    PubMed

    Normark, Benjamin B; Johnson, Norman A

    2011-05-01

    The following syndrome of features occurs in several groups of phytophagous insects: (1) wingless females, (2) dispersal by larvae, (3) woody hosts, (4) extreme polyphagy, (5) high abundance, resulting in status as economic pests, (6) invasiveness, and (7) obligate parthenogenesis in some populations. If extreme polyphagy is defined as feeding on 20 or more families of hostplants, this syndrome is found convergently in several species of bagworm moths, tussock moths, root weevils, and 5 families of scale insects. We hypothesize that extreme polyphagy in these taxa results from "niche explosion", a positive feedback loop connecting large population size to broad host range. The niche explosion has a demographic component (sometimes called the "amplification effect" in studies of pathogens) as well as a population-genetic component, due mainly to the increased effectiveness of natural selection in larger populations. The frequent origins of parthenogenesis in extreme polyphages are, in our interpretation, a consequence of this increased effectiveness of natural selection and consequent reduced importance of sexuality. The niche explosion hypothesis makes detailed predictions about the comparative genomics and population genetics of extreme polyphages and related specialists. It has a number of potentially important implications, including an explanation for the lack of observed trade-offs between generalists and specialists, a re-interpretation of the ecological correlates of parthenogenesis, and a general expectation that Malthusian population explosions may be amplified by Darwinian effects.

  10. Competitive dynamics of lexical innovations in multi-layer networks

    NASA Astrophysics Data System (ADS)

    Javarone, Marco Alberto

    2014-04-01

    We study the introduction of lexical innovations into a community of language users. Lexical innovations, i.e. new term added to people's vocabulary, plays an important role in the process of language evolution. Nowadays, information is spread through a variety of networks, including, among others, online and offline social networks and the World Wide Web. The entire system, comprising networks of different nature, can be represented as a multi-layer network. In this context, lexical innovations diffusion occurs in a peculiar fashion. In particular, a lexical innovation can undergo three different processes: its original meaning is accepted; its meaning can be changed or misunderstood (e.g. when not properly explained), hence more than one meaning can emerge in the population. Lastly, in the case of a loan word, it can be translated into the population language (i.e. defining a new lexical innovation or using a synonym) or into a dialect spoken by part of the population. Therefore, lexical innovations cannot be considered simply as information. We develop a model for analyzing this scenario using a multi-layer network comprising a social network and a media network. The latter represents the set of all information systems of a society, e.g. television, the World Wide Web and radio. Furthermore, we identify temporal directed edges between the nodes of these two networks. In particular, at each time-step, nodes of the media network can be connected to randomly chosen nodes of the social network and vice versa. In doing so, information spreads through the whole system and people can share a lexical innovation with their neighbors or, in the event they work as reporters, by using media nodes. Lastly, we use the concept of "linguistic sign" to model lexical innovations, showing its fundamental role in the study of these dynamics. Many numerical simulations have been performed to analyze the proposed model and its outcomes.

  11. Event-driven approach of layered multicast to network adaptation in RED-based IP networks

    NASA Astrophysics Data System (ADS)

    Nahm, Kitae; Li, Qing; Kuo, C.-C. J.

    2003-11-01

    In this work, we investigate the congestion control problem for layered video multicast in IP networks of active queue management (AQM) using a simple random early detection (RED) queue model. AQM support from networks improves the visual quality of video streaming but makes network adaptation more di+/-cult for existing layered video multicast proticols that use the event-driven timer-based approach. We perform a simplified analysis on the response of the RED algorithm to burst traffic. The analysis shows that the primary problem lies in the weak correlation between the network feedback and the actual network congestion status when the RED queue is driven by burst traffic. Finally, a design guideline of the layered multicast protocol is proposed to overcome this problem.

  12. TCP flow control using link layer information in mobile networks

    NASA Astrophysics Data System (ADS)

    Koga, Hiroyuki; Kawahara, Kenji; Oie, Yuji

    2002-07-01

    Mobile Networks have been expanding and IMT-2000 further increases their available bandwidth over wireless links. However, TCP, which is a reliable end-to-end transport protocol, is tuned to perform well in wired networks where bit error rates are very low and packet loss occurs mostly because of congestion. Although a TCP sender can execute flow control to utilize as much available bandwidth as possible in wired networks, it cannot work well in wireless networks characterized by high bit error rates. In the next generation mobile systems, sophisticated error recovery technologies of FEC and ARQ are indeed employed over wireless links, i.e., over Layer 2, to avoid performance degradation of upper layers. However, multiple retransmissions by Layer 2 ARQ can adversely increase transmission delay of TCP segments, which will further make TCP unnecessarily increase RTO (Retransmission TimeOut). Furthermore, a link bandwidth assigned to TCP flows can change in response to changing air conditions to use wireless links efficiently. TCP thus has to adapt its transmission rate according to the changing available bandwidth. The major goal of this study is to develop a receiver-based effective TCP flow control without any modification on TCP senders, which are probably connected with wired networks. For this end, we propose a TCP flow control employing some Layer 2 information on a wireless link at the mobile station. Our performance evaluation of the proposed TCP shows that the receiver-based TCP flow control can moderate the performance degradation very well even if FER on Layer 2 is high.

  13. A multi-layer network approach to MEG connectivity analysis.

    PubMed

    Brookes, Matthew J; Tewarie, Prejaas K; Hunt, Benjamin A E; Robson, Sian E; Gascoyne, Lauren E; Liddle, Elizabeth B; Liddle, Peter F; Morris, Peter G

    2016-05-15

    Recent years have shown the critical importance of inter-regional neural network connectivity in supporting healthy brain function. Such connectivity is measurable using neuroimaging techniques such as MEG, however the richness of the electrophysiological signal makes gaining a complete picture challenging. Specifically, connectivity can be calculated as statistical interdependencies between neural oscillations within a large range of different frequency bands. Further, connectivity can be computed between frequency bands. This pan-spectral network hierarchy likely helps to mediate simultaneous formation of multiple brain networks, which support ongoing task demand. However, to date it has been largely overlooked, with many electrophysiological functional connectivity studies treating individual frequency bands in isolation. Here, we combine oscillatory envelope based functional connectivity metrics with a multi-layer network framework in order to derive a more complete picture of connectivity within and between frequencies. We test this methodology using MEG data recorded during a visuomotor task, highlighting simultaneous and transient formation of motor networks in the beta band, visual networks in the gamma band and a beta to gamma interaction. Having tested our method, we use it to demonstrate differences in occipital alpha band connectivity in patients with schizophrenia compared to healthy controls. We further show that these connectivity differences are predictive of the severity of persistent symptoms of the disease, highlighting their clinical relevance. Our findings demonstrate the unique potential of MEG to characterise neural network formation and dissolution. Further, we add weight to the argument that dysconnectivity is a core feature of the neuropathology underlying schizophrenia. PMID:26908313

  14. A multi-layer network approach to MEG connectivity analysis

    PubMed Central

    Brookes, Matthew J.; Tewarie, Prejaas K.; Hunt, Benjamin A.E.; Robson, Sian E.; Gascoyne, Lauren E.; Liddle, Elizabeth B.; Liddle, Peter F.; Morris, Peter G.

    2016-01-01

    Recent years have shown the critical importance of inter-regional neural network connectivity in supporting healthy brain function. Such connectivity is measurable using neuroimaging techniques such as MEG, however the richness of the electrophysiological signal makes gaining a complete picture challenging. Specifically, connectivity can be calculated as statistical interdependencies between neural oscillations within a large range of different frequency bands. Further, connectivity can be computed between frequency bands. This pan-spectral network hierarchy likely helps to mediate simultaneous formation of multiple brain networks, which support ongoing task demand. However, to date it has been largely overlooked, with many electrophysiological functional connectivity studies treating individual frequency bands in isolation. Here, we combine oscillatory envelope based functional connectivity metrics with a multi-layer network framework in order to derive a more complete picture of connectivity within and between frequencies. We test this methodology using MEG data recorded during a visuomotor task, highlighting simultaneous and transient formation of motor networks in the beta band, visual networks in the gamma band and a beta to gamma interaction. Having tested our method, we use it to demonstrate differences in occipital alpha band connectivity in patients with schizophrenia compared to healthy controls. We further show that these connectivity differences are predictive of the severity of persistent symptoms of the disease, highlighting their clinical relevance. Our findings demonstrate the unique potential of MEG to characterise neural network formation and dissolution. Further, we add weight to the argument that dysconnectivity is a core feature of the neuropathology underlying schizophrenia. PMID:26908313

  15. A multi-layer network approach to MEG connectivity analysis.

    PubMed

    Brookes, Matthew J; Tewarie, Prejaas K; Hunt, Benjamin A E; Robson, Sian E; Gascoyne, Lauren E; Liddle, Elizabeth B; Liddle, Peter F; Morris, Peter G

    2016-05-15

    Recent years have shown the critical importance of inter-regional neural network connectivity in supporting healthy brain function. Such connectivity is measurable using neuroimaging techniques such as MEG, however the richness of the electrophysiological signal makes gaining a complete picture challenging. Specifically, connectivity can be calculated as statistical interdependencies between neural oscillations within a large range of different frequency bands. Further, connectivity can be computed between frequency bands. This pan-spectral network hierarchy likely helps to mediate simultaneous formation of multiple brain networks, which support ongoing task demand. However, to date it has been largely overlooked, with many electrophysiological functional connectivity studies treating individual frequency bands in isolation. Here, we combine oscillatory envelope based functional connectivity metrics with a multi-layer network framework in order to derive a more complete picture of connectivity within and between frequencies. We test this methodology using MEG data recorded during a visuomotor task, highlighting simultaneous and transient formation of motor networks in the beta band, visual networks in the gamma band and a beta to gamma interaction. Having tested our method, we use it to demonstrate differences in occipital alpha band connectivity in patients with schizophrenia compared to healthy controls. We further show that these connectivity differences are predictive of the severity of persistent symptoms of the disease, highlighting their clinical relevance. Our findings demonstrate the unique potential of MEG to characterise neural network formation and dissolution. Further, we add weight to the argument that dysconnectivity is a core feature of the neuropathology underlying schizophrenia.

  16. A network of tufted layer 5 pyramidal neurons.

    PubMed

    Markram, H

    1997-09-01

    Tufted layer 5 (TL5) pyramidal neurons are important projection neurons from the cerebral cortex to subcortical areas. Recent and ongoing experiments aimed at understanding the computational analysis performed by a network of synaptically connected TL5 neurons are reviewed here. The experiments employed dual and triple whole-cell patch clamp recordings from visually identified and preselected neurons in brain slices of somatosensory cortex of young (14- to 16-day-old) rats. These studies suggest that a local network of TL5 neurons within a cortical module of diameter 300 microns consists of a few hundred neurons that are extensively inter-connected with reciprocal feedback from at least first-, second- and third-order target neurons. A statistical analysis of synaptic innervation suggests that this recurrent network is not randomly arranged and hence each neuron could be functionally unique. Synaptic transmission between these neurons is characterized by use-dependent synaptic depression which confers novel properties to this recurrent network of neurons. First, a range of rates of depression for different synaptic connections enable each TL5 neuron to receive a unique mixture of information about the average firing rates and the temporally correlated action potential (AP) activity in the population of presynaptic TL5 neurons. Second, each AP generated by any neuron in the network induces a change (defined as an iteration step) in the functional coupling of the neurons in the network (defined as network configuration). It is proposed that the network configuration is iterated during a stimulus to achieve an optimally orchestrated network response. Hebbian, anti-Hebbian and neuromodulatory-induced modifications of neurotransmitter release probability change the rates of synaptic depression and thereby alter the iteration step size. These data may be important to understand the dynamics of electrical activity within the network.

  17. Rationality Validation of a Layered Decision Model for Network Defense

    SciTech Connect

    Wei, Huaqiang; Alves-Foss, James; Zhang, Du; Frincke, Deb

    2007-08-31

    We propose a cost-effective network defense strategy built on three key: three decision layers: security policies, defense strategies, and real-time defense tactics for countering immediate threats. A layered decision model (LDM) can be used to capture this decision process. The LDM helps decision-makers gain insight into the hierarchical relationships among inter-connected entities and decision types, and supports the selection of cost-effective defense mechanisms to safeguard computer networks. To be effective as a business tool, it is first necessary to validate the rationality of model before applying it to real-world business cases. This paper describes our efforts in validating the LDM rationality through simulation.

  18. Multi-area layered multicast scheme for MPLS networks

    NASA Astrophysics Data System (ADS)

    Ma, Yajie; Yang, Zongkai; Wang, Yuming; Chen, Jingwen

    2005-02-01

    Multi-protocol label switching (MPLS) is multiprotocols both at layer 2 and layer 3. It is suggested to overcome the shortcomings of performing complex longest prefix matching in layer 3 routing by using short, fixed length labels. The MPLS community has put more effort into the label switching of unicast IP traffic, but less in the MPLS multicast mechanism. The reasons are the higher label consumption, the dynamical mapping of L3 multicast tree to L2 LSPs and the 20-bit shim header which is much fewer than the IPv4 IP header. On the other hand, heterogeneity of node capability degrades total performance of a multicast group. In order to achieve the scalability as well as the heterogeneity in MPLS networks, a novel scheme of MPLS-based Multi-area Layered Multicast Scheme (MALM) is proposed. Unlike the existing schemes which focus on aggregating the multicast stream, we construct the multicast tree based on the virtual topology aggregation. The MPLS area is divided into different sub-areas to form the hierarchical virtual topology and the multicast group is reconstructed into multiple layers according to the node capability. At the same time, the label stack is used to save the label space. For stability of the MALM protocol, a multi-layer protection scheme is also discussed. The experiment results show that the proposed scheme saves label space and decrease the Multicast Forwarding Table in much degree.

  19. Energy management and multi-layer control of networked microgrids

    NASA Astrophysics Data System (ADS)

    Zamora, Ramon

    Networked microgrids is a group of neighboring microgrids that has ability to interchange power when required in order to increase reliability and resiliency. Networked microgrid can operate in different possible configurations including: islanded microgrid, a grid-connected microgrid without a tie-line converter, a grid-connected microgrid with a tie-line converter, and networked microgrids. These possible configurations and specific characteristics of renewable energy offer challenges in designing control and management algorithms for voltage, frequency and power in all possible operating scenarios. In this work, control algorithm is designed based on large-signal model that enables microgrid to operate in wide range of operating points. A combination between PI controller and feed-forward measured system responses will compensate for the changes in operating points. The control architecture developed in this work has multi-layers and the outer layer is slower than the inner layer in time response. The main responsibility of the designed controls are to regulate voltage magnitude and frequency, as well as output power of the DG(s). These local controls also integrate with a microgrid level energy management system or microgrid central controller (MGCC) for power and energy balance for. the entire microgrid in islanded, grid-connected, or networked microgid mode. The MGCC is responsible to coordinate the lower level controls to have reliable and resilient operation. In case of communication network failure, the decentralized energy management will operate locally and will activate droop control. Simulation results indicate the superiority of designed control algorithms compared to existing ones.

  20. Cross-layer restoration with software defined networking based on IP over optical transport networks

    NASA Astrophysics Data System (ADS)

    Yang, Hui; Cheng, Lei; Deng, Junni; Zhao, Yongli; Zhang, Jie; Lee, Young

    2015-10-01

    The IP over optical transport network is a very promising networking architecture applied to the interconnection of geographically distributed data centers due to the performance guarantee of low delay, huge bandwidth and high reliability at a low cost. It can enable efficient resource utilization and support heterogeneous bandwidth demands in highly-available, cost-effective and energy-effective manner. In case of cross-layer link failure, to ensure a high-level quality of service (QoS) for user request after the failure becomes a research focus. In this paper, we propose a novel cross-layer restoration scheme for data center services with software defined networking based on IP over optical network. The cross-layer restoration scheme can enable joint optimization of IP network and optical network resources, and enhance the data center service restoration responsiveness to the dynamic end-to-end service demands. We quantitatively evaluate the feasibility and performances through the simulation under heavy traffic load scenario in terms of path blocking probability and path restoration latency. Numeric results show that the cross-layer restoration scheme improves the recovery success rate and minimizes the overall recovery time.

  1. Desert shrub responses to experimental modification of precipitation seasonality and soil depth: relationship to the two-layer model and ecohydrological niche

    USGS Publications Warehouse

    Germino, Matthew J.; Reinhardt, Keith

    2013-01-01

    1. Ecohydrological niches are important for understanding plant community responses to climate shifts, particularly in dry lands. According to the two-layer hypothesis, selective use of deep-soil water increases growth or persistence of woody species during warm and dry summer periods and thereby contributes to their coexistence with shallow-rooted herbs in dry ecosystems. The resource-pool hypothesis further suggests that shallow-soil water benefits growth of all plants while deep-soil water primarily enhances physiological maintenance and survival of woody species. Few studies have directly tested these by manipulating deep-soil water availability and observing the long-term outcomes. 2. We predicted that factors promoting infiltration and storage of water in deep soils, specifically greater winter precipitation and soil depth, would enhance Artemisia tridentata (big sagebrush) in cold, winter-wet/summer-dry desert. Sagebrush responses to 20 years of winter irrigation were compared to summer- or no irrigation, on plots having relatively deep or shallow soils (2 m vs. 1 m depths). 3. Winter irrigation increased sagebrush cover, and crown and canopy volumes, but not density (individuals/plot) compared to summer or no irrigation, on deep-soil plots. On shallow-soil plots, winter irrigation surprisingly decreased shrub cover and size, and summer irrigation had no effect. Furthermore, multiple regression suggested that the variations in growth were related (i) firstly to water in shallow soils (0-0.2 m) and secondly to deeper soils (> 1 m deep) and (ii) more by springtime than by midsummer soil water. Water-use efficiency increased considerably on shallow soils without irrigation and was lowest with winter irrigation. 4. Synthesis. Sagebrush was more responsive to the seasonal timing of precipitation than to total annual precipitation. Factors that enhanced deep-water storage (deeper soils plus more winter precipitation) led to increases in Artemisia tridentata that

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

    PubMed

    Ban, Jung-Chao; Chang, Chih-Hung

    2016-07-01

    This paper aims to characterize whether a multi-layer cellular neural network is of deep architecture; namely, when can an n-layer cellular neural network be replaced by an m-layer cellular neural network for mlayers is conjugate. A decision procedure that addresses the necessary and sufficient condition for the topological conjugacy between two layers in a network is revealed.

  3. Re-examining "temporal niche".

    PubMed

    Smarr, Benjamin L; Schwartz, Michael D; Wotus, Cheryl; de la Iglesia, Horacio O

    2013-07-01

    The circadian system temporally organizes physiology and behavior throughout the 24-h day. At the core of this organization lies a network of multiple circadian oscillators located within the central nervous system as well as in virtually every peripheral organ. These oscillators define a 24-h temporal landscape of mutually interacting circadian rhythms that is known as the temporal niche of a species. This temporal niche is constituted by the collective phases of all biological rhythms emerging from this multi-oscillatory system. We review evidence showing that under different environmental conditions, this system can adopt different harmonic configurations. Thus, the classic chronobiological approach of searching for "the" circadian phase of an animal-typically by studying circadian rhythms of locomotor activity-represents a narrow look into the circadian system of an animal. We propose that the study of hormonal rhythms may lead to a more insightful assessment of a species' temporal niche.

  4. A physical layer perspective on access network sharing

    NASA Astrophysics Data System (ADS)

    Pfeiffer, Thomas

    2015-12-01

    Unlike in copper or wireless networks, there is no sharing of resources in fiber access networks yet, other than bit stream access or cable sharing, in which the fibers of a cable are let to one or multiple operators. Sharing optical resources on a single fiber among multiple operators or different services has not yet been applied. While this would allow for a better exploitation of installed infrastructures, there are operational issues which still need to be resolved, before this sharing model can be implemented in networks. Operating multiple optical systems and services over a common fiber plant, autonomously and independently from each other, can result in mutual distortions on the physical layer. These distortions will degrade the performance of the involved systems, unless precautions are taken in the infrastructure hardware to eliminate or to reduce them to an acceptable level. Moreover, the infrastructure needs to be designed such as to support different system technologies and to ensure a guaranteed quality of the end-to-end connections. In this paper, suitable means are proposed to be introduced in fiber access infrastructures that will allow for shared utilization of the fibers while safeguarding the operational needs and business interests of the involved parties.

  5. The probabilistic niche model reveals substantial variation in the niche structure of empirical food webs.

    PubMed

    Williams, Richard J; Purves, Drew W

    2011-09-01

    The structure of food webs, complex networks of interspecies feeding interactions, plays a crucial role in ecosystem resilience and function, and understanding food web structure remains a central problem in ecology. Previous studies have shown that key features of empirical food webs can be reproduced by low-dimensional "niche" models. Here we examine the form and variability of food web niche structure by fitting a probabilistic niche model to 37 empirical food webs, a much larger number of food webs than used in previous studies. The model relaxes previous assumptions about parameter distributions and hierarchy and returns parameter estimates for each species in each web. The model significantly outperforms previous niche model variants and also performs well for several webs where a body-size-based niche model performs poorly, implying that traits other than body size are important in structuring these webs' niche space. Parameter estimates frequently violate previous models' assumptions: in 19 of 37 webs, parameter values are not significantly hierarchical, 32 of 37 webs have nonuniform niche value distributions, and 15 of 37 webs lack a correlation between niche width and niche position. Extending the model to a two-dimensional niche space yields networks with a mixture of one- and two-dimensional niches and provides a significantly better fit for webs with a large number of species and links. These results confirm that food webs are strongly niche-structured but reveal substantial variation in the form of the niche structuring, a result with fundamental implications for ecosystem resilience and function.

  6. Mutational activation of niche-specific genes provides insight into regulatory networks and bacterial function in a complex environment

    PubMed Central

    Giddens, Stephen R.; Jackson, Robert W.; Moon, Christina D.; Jacobs, Michael A.; Zhang, Xue-Xian; Gehrig, Stefanie M.; Rainey, Paul B.

    2007-01-01

    The genome of the plant-colonizing bacterium Pseudomonas fluorescens SBW25 harbors a subset of genes that are expressed specifically on plant surfaces. The function of these genes is central to the ecological success of SBW25, but their study poses significant challenges because no phenotype is discernable in vitro. Here, we describe a genetic strategy with general utility that combines suppressor analysis with IVET (SPyVET) and provides a means of identifying regulators of niche-specific genes. Central to this strategy are strains carrying operon fusions between plant environment-induced loci (EIL) and promoterless ′dapB. These strains are prototrophic in the plant environment but auxotrophic on laboratory minimal medium. Regulatory elements were identified by transposon mutagenesis and selection for prototrophs on minimal medium. Approximately 106 mutants were screened for each of 27 strains carrying ′dapB fusions to plant EIL and the insertion point for the transposon determined in approximately 2,000 putative regulator mutants. Regulators were functionally characterized and used to provide insight into EIL phenotypes. For one strain carrying a fusion to the cellulose-encoding wss operon, five different regulators were identified including a diguanylate cyclase, the flagella activator, FleQ, and alginate activator, AmrZ (AlgZ). Further rounds of suppressor analysis, possible by virtue of the SPyVET strategy, revealed an additional two regulators including the activator AlgR, and allowed the regulatory connections to be determined. PMID:17989226

  7. The neuron network forecasting dynamics of the ozone layer

    NASA Astrophysics Data System (ADS)

    Lankin, J.; Sakash, I.

    One of the major tasks today is preserving the Earth's ozonosphere, - because the ozone layer serves as a screen, filtering a part of harmful solar ultraviolet radiation. During the recent decades, some scientists of different countries have paid their attention to significant decrease of ozone density in the atmosphere above certain points of the Earth's surface. If the average ozone concentration in the atmosphere is about 300-350 D. u., its annual drop above the Antarctic continent follows to the values of concentration even of 90 D. u. Such -- and similar -- publications have triggered widespread public interest (tied to the global environmental crisis); the phenomenon has been named "an ozone hole" and followed by an explosion of scientific interest to ozonospheric studies. In order to simulate hourly TOC oscillations, the ground observation data (City of Tomsk, Russia - 56 N and 84 E) has been used. The following models of ÒÎÑ have been designed: hourly (hourly CCO values are been forecasted for March 30 and 31, 1996-99), diurnal (June 14 -- October 31, 1998), monthly (September 1975 -- August 1977) and annual (1975-1982) ones. The study performed has proven a high degree of effectiveness of using neuron networks for simulating the dynamics of the Earth's ozonosphere. A real opportunity to design local prognostic models using neuronets is revealed. In future, some three-dimentional global models of ozonosphere and atmosphere may be established. However, there a number of cases of significant variations of the ozone concentration time rows for different seasons and time spans. Studying and predicting such changes is of the great interest in terms of better understanding the specifics of developing the atmospheric processes and improving the technology of the forecast. The study is focused upon revealing the precursors of the spontaneous "ozone hole" (areas of the lowered concentration of ozone) formation in the stratosphere and based on neuron network

  8. Why do niches develop in Caesarean uterine scars? Hypotheses on the aetiology of niche development.

    PubMed

    Vervoort, A J M W; Uittenbogaard, L B; Hehenkamp, W J K; Brölmann, H A M; Mol, B W J; Huirne, J A F

    2015-12-01

    Caesarean section (CS) results in the occurrence of the phenomenon 'niche'. A 'niche' describes the presence of a hypoechoic area within the myometrium of the lower uterine segment, reflecting a discontinuation of the myometrium at the site of a previous CS. Using gel or saline instillation sonohysterography, a niche is identified in the scar in more than half of the women who had had a CS, most with the uterus closed in one single layer, without closure of the peritoneum. An incompletely healed scar is a long-term complication of the CS and is associated with more gynaecological symptoms than is commonly acknowledged. Approximately 30% of women with a niche report spotting at 6-12 months after their CS. Other reported symptoms in women with a niche are dysmenorrhoea, chronic pelvic pain and dyspareunia. Given the association between a niche and gynaecological symptoms, obstetric complications and potentially with subfertility, it is important to elucidate the aetiology of niche development after CS in order to develop preventive strategies. Based on current published data and our observations during sonographic, hysteroscopic and laparoscopic evaluations of niches we postulate some hypotheses on niche development. Possible factors that could play a role in niche development include a very low incision through cervical tissue, inadequate suturing technique during closure of the uterine scar, surgical interventions that increase adhesion formation or patient-related factors that impair wound healing or increase inflammation or adhesion formation.

  9. A multiobjective two-layer transportation network design model

    SciTech Connect

    Figlali, A.; Koc, T.

    1994-12-31

    In this paper, a two-layer transportation network design model with three objectives is presented. The objectives are: (1) to minimize the primary path length (or travelling time) from a predetermined starting node to a predetermined terminus node; (2) to minimize the total distance traversed by the demand to reach the primary path; (3) to minimize the total road construction cost. The problem is formulated as an integer linear programming model and solved as relaxed continuous linear programming model. If fractional values for the variables occur, then a branch and bound algorithm may be employed to obtain 0 or 1 variable values. In the model, three different solution procedure is suggested which depends on the preference position of the decision maker. Such problems are encountered in the applications of the construction of a new rail line between two major cities of a developing country; in the construction of networks of highways and unimproved roads; in the design of airline routes and in the design of energy distribution systems.

  10. Criteria for Evaluating Alternative Network and Link Layer Protocols for the NASA Constellation Program Communication Architecture

    NASA Technical Reports Server (NTRS)

    Benbenek, Daniel; Soloff, Jason; Lieb, Erica

    2010-01-01

    Selecting a communications and network architecture for future manned space flight requires an evaluation of the varying goals and objectives of the program, development of communications and network architecture evaluation criteria, and assessment of critical architecture trades. This paper uses Cx Program proposed exploration activities as a guideline; lunar sortie, outpost, Mars, and flexible path options are described. A set of proposed communications network architecture criteria are proposed and described. They include: interoperability, security, reliability, and ease of automating topology changes. Finally a key set of architecture options are traded including (1) multiplexing data at a common network layer vs. at the data link layer, (2) implementing multiple network layers vs. a single network layer, and (3) the use of a particular network layer protocol, primarily IPv6 vs. Delay Tolerant Networking (DTN). In summary, the protocol options are evaluated against the proposed exploration activities and their relative performance with respect to the criteria are assessed. An architectural approach which includes (a) the capability of multiplexing at both the network layer and the data link layer and (b) a single network layer for operations at each program phase, as these solutions are best suited to respond to the widest array of program needs and meet each of the evaluation criteria.

  11. Self-Organized Information Processing in Neuronal Networks: Replacing Layers in Deep Networks by Dynamics

    NASA Astrophysics Data System (ADS)

    Kirst, Christoph

    It is astonishing how the sub-parts of a brain co-act to produce coherent behavior. What are mechanism that coordinate information processing and communication and how can those be changed flexibly in order to cope with variable contexts? Here we show that when information is encoded in the deviations around a collective dynamical reference state of a recurrent network the propagation of these fluctuations is strongly dependent on precisely this underlying reference. Information here 'surfs' on top of the collective dynamics and switching between states enables fast and flexible rerouting of information. This in turn affects local processing and consequently changes in the global reference dynamics that re-regulate the distribution of information. This provides a generic mechanism for self-organized information processing as we demonstrate with an oscillatory Hopfield network that performs contextual pattern recognition. Deep neural networks have proven to be very successful recently. Here we show that generating information channels via collective reference dynamics can effectively compress a deep multi-layer architecture into a single layer making this mechanism a promising candidate for the organization of information processing in biological neuronal networks.

  12. Mesoscopic structures reveal the network between the layers of multiplex data sets

    NASA Astrophysics Data System (ADS)

    Iacovacci, Jacopo; Wu, Zhihao; Bianconi, Ginestra

    2015-10-01

    Multiplex networks describe a large variety of complex systems, whose elements (nodes) can be connected by different types of interactions forming different layers (networks) of the multiplex. Multiplex networks include social networks, transportation networks, or biological networks in the cell or in the brain. Extracting relevant information from these networks is of crucial importance for solving challenging inference problems and for characterizing the multiplex networks microscopic and mesoscopic structure. Here we propose an information theory method to extract the network between the layers of multiplex data sets, forming a "network of networks." We build an indicator function, based on the entropy of network ensembles, to characterize the mesoscopic similarities between the layers of a multiplex network, and we use clustering techniques to characterize the communities present in this network of networks. We apply the proposed method to study the Multiplex Collaboration Network formed by scientists collaborating on different subjects and publishing in the American Physical Society journals. The analysis of this data set reveals the interplay between the collaboration networks and the organization of knowledge in physics.

  13. Mesoscopic structures reveal the network between the layers of multiplex data sets.

    PubMed

    Iacovacci, Jacopo; Wu, Zhihao; Bianconi, Ginestra

    2015-10-01

    Multiplex networks describe a large variety of complex systems, whose elements (nodes) can be connected by different types of interactions forming different layers (networks) of the multiplex. Multiplex networks include social networks, transportation networks, or biological networks in the cell or in the brain. Extracting relevant information from these networks is of crucial importance for solving challenging inference problems and for characterizing the multiplex networks microscopic and mesoscopic structure. Here we propose an information theory method to extract the network between the layers of multiplex data sets, forming a "network of networks." We build an indicator function, based on the entropy of network ensembles, to characterize the mesoscopic similarities between the layers of a multiplex network, and we use clustering techniques to characterize the communities present in this network of networks. We apply the proposed method to study the Multiplex Collaboration Network formed by scientists collaborating on different subjects and publishing in the American Physical Society journals. The analysis of this data set reveals the interplay between the collaboration networks and the organization of knowledge in physics.

  14. The robustness of multiplex networks under layer node-based attack

    NASA Astrophysics Data System (ADS)

    Zhao, Da-Wei; Wang, Lian-Hai; Zhi, Yong-Feng; Zhang, Jun; Wang, Zhen

    2016-04-01

    From transportation networks to complex infrastructures, and to social and economic networks, a large variety of systems can be described in terms of multiplex networks formed by a set of nodes interacting through different network layers. Network robustness, as one of the most successful application areas of complex networks, has attracted great interest in a myriad of research realms. In this regard, how multiplex networks respond to potential attack is still an open issue. Here we study the robustness of multiplex networks under layer node-based random or targeted attack, which means that nodes just suffer attacks in a given layer yet no additional influence to their connections beyond this layer. A theoretical analysis framework is proposed to calculate the critical threshold and the size of giant component of multiplex networks when nodes are removed randomly or intentionally. Via numerous simulations, it is unveiled that the theoretical method can accurately predict the threshold and the size of giant component, irrespective of attack strategies. Moreover, we also compare the robustness of multiplex networks under multiplex node-based attack and layer node-based attack, and find that layer node-based attack makes multiplex networks more vulnerable, regardless of average degree and underlying topology.

  15. The robustness of multiplex networks under layer node-based attack.

    PubMed

    Zhao, Da-wei; Wang, Lian-hai; Zhi, Yong-feng; Zhang, Jun; Wang, Zhen

    2016-04-14

    From transportation networks to complex infrastructures, and to social and economic networks, a large variety of systems can be described in terms of multiplex networks formed by a set of nodes interacting through different network layers. Network robustness, as one of the most successful application areas of complex networks, has attracted great interest in a myriad of research realms. In this regard, how multiplex networks respond to potential attack is still an open issue. Here we study the robustness of multiplex networks under layer node-based random or targeted attack, which means that nodes just suffer attacks in a given layer yet no additional influence to their connections beyond this layer. A theoretical analysis framework is proposed to calculate the critical threshold and the size of giant component of multiplex networks when nodes are removed randomly or intentionally. Via numerous simulations, it is unveiled that the theoretical method can accurately predict the threshold and the size of giant component, irrespective of attack strategies. Moreover, we also compare the robustness of multiplex networks under multiplex node-based attack and layer node-based attack, and find that layer node-based attack makes multiplex networks more vulnerable, regardless of average degree and underlying topology.

  16. Generalized single-hidden layer feedforward networks for regression problems.

    PubMed

    Wang, Ning; Er, Meng Joo; Han, Min

    2015-06-01

    In this paper, traditional single-hidden layer feedforward network (SLFN) is extended to novel generalized SLFN (GSLFN) by employing polynomial functions of inputs as output weights connecting randomly generated hidden units with corresponding output nodes. The significant contributions of this paper are as follows: 1) a primal GSLFN (P-GSLFN) is implemented using randomly generated hidden nodes and polynomial output weights whereby the regression matrix is augmented by full or partial input variables and only polynomial coefficients are to be estimated; 2) a simplified GSLFN (S-GSLFN) is realized by decomposing the polynomial output weights of the P-GSLFN into randomly generated polynomial nodes and tunable output weights; 3) both P- and S-GSLFN are able to achieve universal approximation if the output weights are tuned by ridge regression estimators; and 4) by virtue of the developed batch and online sequential ridge ELM (BR-ELM and OSR-ELM) learning algorithms, high performance of the proposed GSLFNs in terms of generalization and learning speed is guaranteed. Comprehensive simulation studies and comparisons with standard SLFNs are carried out on real-world regression benchmark data sets. Simulation results demonstrate that the innovative GSLFNs using BR-ELM and OSR-ELM are superior to standard SLFNs in terms of accuracy, training speed, and structure compactness.

  17. Persona: Network Layer Anonymity and Accountability for Next Generation Internet

    NASA Astrophysics Data System (ADS)

    Mallios, Yannis; Modi, Sudeep; Agarwala, Aditya; Johns, Christina

    Individual privacy has become a major concern, due to the intrusive nature of the services and websites that collect increasing amounts of private information. One of the notions that can lead towards privacy protection is that of anonymity. Unfortunately, anonymity can also be maliciously exploited by attackers to hide their actions and identity. Thus some sort of accountability is also required. The current Internet has failed to provide both properties, as anonymity techniques are difficult to fully deploy and thus are easily attacked, while the Internet provides limited level of accountability. The Next Generation Internet (NGI) provides us with the opportunity to examine how these conflicting properties could be efficiently applied and thus protect users’ privacy while holding malicious users accountable. In this paper we present the design of a scheme, called Persona that can provide anonymity and accountability in the network layer of NGI. More specifically, our design requirements are to combine these two conflicting desires in a stateless manner within routers. Persona allows users to choose different levels of anonymity, while it allows the discovery of malicious nodes.

  18. Performance Impacts of Lower-Layer Cryptographic Methods in Mobile Wireless Ad Hoc Networks

    SciTech Connect

    VAN LEEUWEN, BRIAN P.; TORGERSON, MARK D.

    2002-10-01

    In high consequence systems, all layers of the protocol stack need security features. If network and data-link layer control messages are not secured, a network may be open to adversarial manipulation. The open nature of the wireless channel makes mobile wireless mobile ad hoc networks (MANETs) especially vulnerable to control plane manipulation. The objective of this research is to investigate MANET performance issues when cryptographic processing delays are applied at the data-link layer. The results of analysis are combined with modeling and simulation experiments to show that network performance in MANETs is highly sensitive to the cryptographic overhead.

  19. Can we neglect the multi-layer structure of functional networks?

    NASA Astrophysics Data System (ADS)

    Zanin, Massimiliano

    2015-07-01

    Functional networks, i.e. networks representing dynamic relationships between the components of a complex system, have been instrumental for our understanding of, among others, the human brain. Due to limited data availability, the multi-layer nature of numerous functional networks has hitherto been neglected, and nodes are endowed with a single type of links even when multiple relationships coexist at different physical levels. A relevant problem is the assessment of the benefits yielded by studying a multi-layer functional network, against the simplicity guaranteed by the reconstruction and use of the corresponding single layer projection. Here, I tackle this issue by using as a test case, the functional network representing the dynamics of delay propagation through European airports. Neglecting the multi-layer structure of a functional network has dramatic consequences on our understanding of the underlying system, a fact to be taken into account when a projection is the only available information.

  20. Cultural niche construction in a metapopulation.

    PubMed

    Borenstein, Elhanan; Kendal, Jeremy; Feldman, Marcus

    2006-08-01

    Cultural niche construction is the process by which certain evolving cultural traits form a cultural niche that affects the evolution of other genetic and cultural traits [Laland, K., et al., 2001. Cultural niche construction and human evolution. J. Evol. Biol. 14, 22-33; Ihara, Y., Feldman, M., 2004. Cultural niche construction and the evolution of small family size. Theor. Popul. Biol. 65, 105-111]. In this study we focus on cultural niche construction in a metapopulation (a population of populations), where the frequency of one cultural trait (e.g. the level of education) determines the transmission rate of a second trait (e.g. the adoption of fertility reduction preferences) within and between populations. We formulate the Metapopulation Cultural Niche Construction (MPCNC) model by defining the cultural niche induced by the first trait as the construction of a social interaction network on which the second trait may percolate. Analysis of the model reveals dynamics that are markedly different from those observed in a single population, allowing, for example, different (or even opposing) dynamics in each population. In particular, this model can account for the puzzling phenomenon reported in previous studies [Bongaarts, J., Watkins, S., 1996. Social interactions and contemporary fertility transitions. Popul. Dev. Rev. 22 (4), 639-682] that the onset of the demographic transition in different countries occurred at ever lower levels of development.

  1. Combining multi-layered bitmap files using network specific hardware

    DOEpatents

    DuBois, David H.; DuBois, Andrew J.; Davenport, Carolyn Connor

    2012-02-28

    Images and video can be produced by compositing or alpha blending a group of image layers or video layers. Increasing resolution or the number of layers results in increased computational demands. As such, the available computational resources limit the images and videos that can be produced. A computational architecture in which the image layers are packetized and streamed through processors can be easily scaled so to handle many image layers and high resolutions. The image layers are packetized to produce packet streams. The packets in the streams are received, placed in queues, and processed. For alpha blending, ingress queues receive the packetized image layers which are then z sorted and sent to egress queues. The egress queue packets are alpha blended to produce an output image or video.

  2. Ambient Intelligence Context-Based Cross-Layer Design in Wireless Sensor Networks

    PubMed Central

    Liu, Yang; Seet, Boon-Chong; Al-Anbuky, Adnan

    2014-01-01

    By exchanging information directly between non-adjacent protocol layers, cross-layer (CL) interaction can significantly improve and optimize network performances such as energy efficiency and delay. This is particularly important for wireless sensor networks (WSNs) where sensor devices are energy-constrained and deployed for real-time monitoring applications. Existing CL schemes mainly exploit information exchange between physical, medium access control (MAC), and routing layers, with only a handful involving application layer. For the first time, we proposed a framework for CL optimization based on user context of ambient intelligence (AmI) application and an ontology-based context modeling and reasoning mechanism. We applied the proposed framework to jointly optimize MAC and network (NET) layer protocols for WSNs. Extensive evaluations show that the resulting optimization through context awareness and CL interaction for both MAC and NET layer protocols can yield substantial improvements in terms of throughput, packet delivery, delay, and energy performances. PMID:25317760

  3. Collaborative-Hybrid Multi-Layer Network Control for Emerging Cyber-Infrastructures

    SciTech Connect

    Lehman, Tom; Ghani, Nasir; Boyd, Eric

    2010-08-31

    At a high level, there were four basic task areas identified for the Hybrid-MLN project. They are: o Multi-Layer, Multi-Domain, Control Plane Architecture and Implementation, including OSCARS layer2 and InterDomain Adaptation, Integration of LambdaStation and Terapaths with Layer2 dynamic provisioning, Control plane software release, Scheduling, AAA, security architecture, Network Virtualization architecture, Multi-Layer Network Architecture Framework Definition; o Heterogeneous DataPlane Testing; o Simulation; o Project Publications, Reports, and Presentations.

  4. The United States pork niche market phenomenon.

    PubMed

    Honeyman, M S; Pirog, R S; Huber, G H; Lammers, P J; Hermann, J R

    2006-08-01

    After the broad industrialization of the US pork industry, there has been a development of niche markets for export and domestic pork; that is, there is a pork niche market phenomenon. The US pork niche market phenomenon is characterized, and 2 of the major markets are explained in detail. With the Midwest's tradition of a diversified family-based agriculture and record low hog prices of the late 1990s, the conditions were conducive for this phenomenon to develop. Pork niche markets utilize various sales methods including Internet sales, local abattoir sales, direct marketing, farmer networks, and targeting to organized groups. In 2003, there were approximately 35 to 40 active pork niche marketing efforts in Iowa. The Berkshire breed is an example of a swine breed that has had a recent resurgence because of niche markets. Berkshire pork is known for tenderness and excellent quality. Berkshire registrations have increased 4-fold in the last 10 yr. One of the larger niche marketers of "natural pork" is Niman Ranch Pork, which has more than 400 farmer-producers and processes about 2,500 pigs weekly. Many US consumers of pork are interested in issues concerning the environment, food safety, pig welfare, and pig farm ownership and structure. These consumers may be willing to pay more for pork from farmers who are also concerned about these issues. Small- and medium-sized swine farmers are active in pork niche markets. Niche markets claim product differentiation by superior or unique product quality and social attributes. Quality attributes include certain swine breeds, and meat quality, freshness, taste or flavor, and tenderness. Social or credence attributes often are claimed and include freedom from antibiotics and growth promotants; local family farm production; natural, organic, outdoor, or bedded rearing; humane rearing; known origin; environmentally friendly production; and the absence of animal by-products in the feed. Niche pork markets and alternative swine

  5. The United States pork niche market phenomenon.

    PubMed

    Honeyman, M S; Pirog, R S; Huber, G H; Lammers, P J; Hermann, J R

    2006-08-01

    After the broad industrialization of the US pork industry, there has been a development of niche markets for export and domestic pork; that is, there is a pork niche market phenomenon. The US pork niche market phenomenon is characterized, and 2 of the major markets are explained in detail. With the Midwest's tradition of a diversified family-based agriculture and record low hog prices of the late 1990s, the conditions were conducive for this phenomenon to develop. Pork niche markets utilize various sales methods including Internet sales, local abattoir sales, direct marketing, farmer networks, and targeting to organized groups. In 2003, there were approximately 35 to 40 active pork niche marketing efforts in Iowa. The Berkshire breed is an example of a swine breed that has had a recent resurgence because of niche markets. Berkshire pork is known for tenderness and excellent quality. Berkshire registrations have increased 4-fold in the last 10 yr. One of the larger niche marketers of "natural pork" is Niman Ranch Pork, which has more than 400 farmer-producers and processes about 2,500 pigs weekly. Many US consumers of pork are interested in issues concerning the environment, food safety, pig welfare, and pig farm ownership and structure. These consumers may be willing to pay more for pork from farmers who are also concerned about these issues. Small- and medium-sized swine farmers are active in pork niche markets. Niche markets claim product differentiation by superior or unique product quality and social attributes. Quality attributes include certain swine breeds, and meat quality, freshness, taste or flavor, and tenderness. Social or credence attributes often are claimed and include freedom from antibiotics and growth promotants; local family farm production; natural, organic, outdoor, or bedded rearing; humane rearing; known origin; environmentally friendly production; and the absence of animal by-products in the feed. Niche pork markets and alternative swine

  6. Optical/electronical hybrid three-layer neural network for pattern recognition

    NASA Astrophysics Data System (ADS)

    Zhang, YanXin; Shen, Jinyuan

    1991-08-01

    A three-layer neural network implemented by optical and electronical techniques for pattern recognition is described in this paper. The principles, architecture, and the experimental results of the hardware system for pattern recognition are presented.

  7. A new backpropagation learning algorithm for layered neural networks with nondifferentiable units.

    PubMed

    Oohori, Takahumi; Naganuma, Hidenori; Watanabe, Kazuhisa

    2007-05-01

    We propose a digital version of the backpropagation algorithm (DBP) for three-layered neural networks with nondifferentiable binary units. This approach feeds teacher signals to both the middle and output layers, whereas with a simple perceptron, they are given only to the output layer. The additional teacher signals enable the DBP to update the coupling weights not only between the middle and output layers but also between the input and middle layers. A neural network based on DBP learning is fast and easy to implement in hardware. Simulation results for several linearly nonseparable problems such as XOR demonstrate that the DBP performs favorably when compared to the conventional approaches. Furthermore, in large-scale networks, simulation results indicate that the DBP provides high performance. PMID:17381272

  8. A new backpropagation learning algorithm for layered neural networks with nondifferentiable units.

    PubMed

    Oohori, Takahumi; Naganuma, Hidenori; Watanabe, Kazuhisa

    2007-05-01

    We propose a digital version of the backpropagation algorithm (DBP) for three-layered neural networks with nondifferentiable binary units. This approach feeds teacher signals to both the middle and output layers, whereas with a simple perceptron, they are given only to the output layer. The additional teacher signals enable the DBP to update the coupling weights not only between the middle and output layers but also between the input and middle layers. A neural network based on DBP learning is fast and easy to implement in hardware. Simulation results for several linearly nonseparable problems such as XOR demonstrate that the DBP performs favorably when compared to the conventional approaches. Furthermore, in large-scale networks, simulation results indicate that the DBP provides high performance.

  9. Enhanced Detectability of Community Structure in Multilayer Networks through Layer Aggregation.

    PubMed

    Taylor, Dane; Shai, Saray; Stanley, Natalie; Mucha, Peter J

    2016-06-01

    Many systems are naturally represented by a multilayer network in which edges exist in multiple layers that encode different, but potentially related, types of interactions, and it is important to understand limitations on the detectability of community structure in these networks. Using random matrix theory, we analyze detectability limitations for multilayer (specifically, multiplex) stochastic block models (SBMs) in which L layers are derived from a common SBM. We study the effect of layer aggregation on detectability for several aggregation methods, including summation of the layers' adjacency matrices for which we show the detectability limit vanishes as O(L^{-1/2}) with increasing number of layers, L. Importantly, we find a similar scaling behavior when the summation is thresholded at an optimal value, providing insight into the common-but not well understood-practice of thresholding pairwise-interaction data to obtain sparse network representations. PMID:27314740

  10. Improved efficient static weighted routing strategy on two-layer complex networks

    NASA Astrophysics Data System (ADS)

    Zhang, Shuai; Liang, Man-Gui; Jiang, Zhong-Yuan; Li, Hui-Jia

    2015-05-01

    Global static routing is one kind of important routing algorithms for complex networks, especially in large communication networks. In this paper, we propose a heuristic global static routing algorithm to mitigate traffic congestion on two-layer complex networks. The proposed routing algorithm extends the relevant static weighted routing algorithm in the literature [Y. Zhou, Y. F. Peng, X. L. Yang and K. P. Long, Phys. Sci. 84, 055802 (2011)]. Our routing path is constructed from a proper assignment of edge weights by considering the static information of both layers and an adjustable parameter α. When this routing algorithm is adopted on BA-BA two-layer networks with an appropriate parameter α, it can achieve the maximum network traffic capacity compared with the shortest path (SP) routing algorithm and the static weighted routing algorithm.

  11. Physical and Cross-Layer Security Enhancement and Resource Allocation for Wireless Networks

    ERIC Educational Resources Information Center

    Bashar, Muhammad Shafi Al

    2011-01-01

    In this dissertation, we present novel physical (PHY) and cross-layer design guidelines and resource adaptation algorithms to improve the security and user experience in the future wireless networks. Physical and cross-layer wireless security measures can provide stronger overall security with high efficiency and can also provide better…

  12. A new one-layer neural network for linear and quadratic programming.

    PubMed

    Gao, Xingbao; Liao, Li-Zhi

    2010-06-01

    In this paper, we present a new neural network for solving linear and quadratic programming problems in real time by introducing some new vectors. The proposed neural network is stable in the sense of Lyapunov and can converge to an exact optimal solution of the original problem when the objective function is convex on the set defined by equality constraints. Compared with existing one-layer neural networks for quadratic programming problems, the proposed neural network has the least neurons and requires weak stability conditions. The validity and transient behavior of the proposed neural network are demonstrated by some simulation results.

  13. Reciprocity in spatial evolutionary public goods game on double-layered network.

    PubMed

    Kim, Jinho; Yook, Soon-Hyung; Kim, Yup

    2016-08-09

    Spatial evolutionary games have mainly been studied on a single, isolated network. However, in real world systems, many interaction topologies are not isolated but many different types of networks are inter-connected to each other. In this study, we investigate the spatial evolutionary public goods game (SEPGG) on double-layered random networks (DRN). Based on the mean-field type arguments and numerical simulations, we find that SEPGG on DRN shows very rich interesting phenomena, especially, depending on the size of each layer, intra-connectivity, and inter-connected couplings, the network reciprocity of SEPGG on DRN can be drastically enhanced through the inter-connected coupling. Furthermore, SEPGG on DRN can provide a more general framework which includes the evolutionary dynamics on multiplex networks and inter-connected networks at the same time.

  14. Reciprocity in spatial evolutionary public goods game on double-layered network

    PubMed Central

    Kim, Jinho; Yook, Soon-Hyung; Kim, Yup

    2016-01-01

    Spatial evolutionary games have mainly been studied on a single, isolated network. However, in real world systems, many interaction topologies are not isolated but many different types of networks are inter-connected to each other. In this study, we investigate the spatial evolutionary public goods game (SEPGG) on double-layered random networks (DRN). Based on the mean-field type arguments and numerical simulations, we find that SEPGG on DRN shows very rich interesting phenomena, especially, depending on the size of each layer, intra-connectivity, and inter-connected couplings, the network reciprocity of SEPGG on DRN can be drastically enhanced through the inter-connected coupling. Furthermore, SEPGG on DRN can provide a more general framework which includes the evolutionary dynamics on multiplex networks and inter-connected networks at the same time. PMID:27503801

  15. Reciprocity in spatial evolutionary public goods game on double-layered network

    NASA Astrophysics Data System (ADS)

    Kim, Jinho; Yook, Soon-Hyung; Kim, Yup

    2016-08-01

    Spatial evolutionary games have mainly been studied on a single, isolated network. However, in real world systems, many interaction topologies are not isolated but many different types of networks are inter-connected to each other. In this study, we investigate the spatial evolutionary public goods game (SEPGG) on double-layered random networks (DRN). Based on the mean-field type arguments and numerical simulations, we find that SEPGG on DRN shows very rich interesting phenomena, especially, depending on the size of each layer, intra-connectivity, and inter-connected couplings, the network reciprocity of SEPGG on DRN can be drastically enhanced through the inter-connected coupling. Furthermore, SEPGG on DRN can provide a more general framework which includes the evolutionary dynamics on multiplex networks and inter-connected networks at the same time.

  16. Layer-switching cost and optimality in information spreading on multiplex networks

    NASA Astrophysics Data System (ADS)

    Min, Byungjoon; Gwak, Sang-Hwan; Lee, Nanoom; Goh, K.-I.

    2016-02-01

    We study a model of information spreading on multiplex networks, in which agents interact through multiple interaction channels (layers), say online vs. offline communication layers, subject to layer-switching cost for transmissions across different interaction layers. The model is characterized by the layer-wise path-dependent transmissibility over a contact, that is dynamically determined dependently on both incoming and outgoing transmission layers. We formulate an analytical framework to deal with such path-dependent transmissibility and demonstrate the nontrivial interplay between the multiplexity and spreading dynamics, including optimality. It is shown that the epidemic threshold and prevalence respond to the layer-switching cost non-monotonically and that the optimal conditions can change in abrupt non-analytic ways, depending also on the densities of network layers and the type of seed infections. Our results elucidate the essential role of multiplexity that its explicit consideration should be crucial for realistic modeling and prediction of spreading phenomena on multiplex social networks in an era of ever-diversifying social interaction layers.

  17. Layer-switching cost and optimality in information spreading on multiplex networks

    PubMed Central

    Min, Byungjoon; Gwak, Sang-Hwan; Lee, Nanoom; Goh, K. -I.

    2016-01-01

    We study a model of information spreading on multiplex networks, in which agents interact through multiple interaction channels (layers), say online vs. offline communication layers, subject to layer-switching cost for transmissions across different interaction layers. The model is characterized by the layer-wise path-dependent transmissibility over a contact, that is dynamically determined dependently on both incoming and outgoing transmission layers. We formulate an analytical framework to deal with such path-dependent transmissibility and demonstrate the nontrivial interplay between the multiplexity and spreading dynamics, including optimality. It is shown that the epidemic threshold and prevalence respond to the layer-switching cost non-monotonically and that the optimal conditions can change in abrupt non-analytic ways, depending also on the densities of network layers and the type of seed infections. Our results elucidate the essential role of multiplexity that its explicit consideration should be crucial for realistic modeling and prediction of spreading phenomena on multiplex social networks in an era of ever-diversifying social interaction layers. PMID:26887527

  18. Evolution of pollination niches in a generalist plant clade.

    PubMed

    Gómez, José María; Perfectti, Francisco; Abdelaziz, Mohamed; Lorite, Juan; Muñoz-Pajares, Antonio Jesús; Valverde, Javier

    2015-01-01

    It is widely assumed that floral diversification occurs by adaptive shifts between pollination niches. In contrast to specialized flowers, identifying pollination niches of generalist flowers is a challenge. Consequently, how generalist pollination niches evolve is largely unknown. We apply tools from network theory and comparative methods to investigate the evolution of pollination niches among generalist species belonging to the genus Erysimum. These species have similar flowers. We found that the studied species may be grouped in several multidimensional niches separated not by a shift of pollinators, but instead by quantitative variation in the relative abundance of pollinator functional groups. These pollination niches did not vary in generalization degree; we did not find any evolutionary trend toward specialization within the studied clade. Furthermore, the evolution of pollination niche fitted to a Brownian motion model without phylogenetic signal, and was characterized by frequent events of niche convergences and divergences. We presume that the evolution of Erysimum pollination niches has occurred mostly by recurrent shifts between slightly different generalized pollinator assemblages varying spatially as a mosaic and without any change in specialization degree. Most changes in pollination niches do not prompt floral divergence, a reason why adaptation to pollinators is uncommon in generalist plants.

  19. Inferring the mesoscale structure of layered, edge-valued, and time-varying networks.

    PubMed

    Peixoto, Tiago P

    2015-10-01

    Many network systems are composed of interdependent but distinct types of interactions, which cannot be fully understood in isolation. These different types of interactions are often represented as layers, attributes on the edges, or as a time dependence of the network structure. Although they are crucial for a more comprehensive scientific understanding, these representations offer substantial challenges. Namely, it is an open problem how to precisely characterize the large or mesoscale structure of network systems in relation to these additional aspects. Furthermore, the direct incorporation of these features invariably increases the effective dimension of the network description, and hence aggravates the problem of overfitting, i.e., the use of overly complex characterizations that mistake purely random fluctuations for actual structure. In this work, we propose a robust and principled method to tackle these problems, by constructing generative models of modular network structure, incorporating layered, attributed and time-varying properties, as well as a nonparametric Bayesian methodology to infer the parameters from data and select the most appropriate model according to statistical evidence. We show that the method is capable of revealing hidden structure in layered, edge-valued, and time-varying networks, and that the most appropriate level of granularity with respect to the additional dimensions can be reliably identified. We illustrate our approach on a variety of empirical systems, including a social network of physicians, the voting correlations of deputies in the Brazilian national congress, the global airport network, and a proximity network of high-school students.

  20. Inferring topologies via driving-based generalized synchronization of two-layer networks

    NASA Astrophysics Data System (ADS)

    Wang, Yingfei; Wu, Xiaoqun; Feng, Hui; Lu, Jun-an; Xu, Yuhua

    2016-05-01

    The interaction topology among the constituents of a complex network plays a crucial role in the network’s evolutionary mechanisms and functional behaviors. However, some network topologies are usually unknown or uncertain. Meanwhile, coupling delays are ubiquitous in various man-made and natural networks. Hence, it is necessary to gain knowledge of the whole or partial topology of a complex dynamical network by taking into consideration communication delay. In this paper, topology identification of complex dynamical networks is investigated via generalized synchronization of a two-layer network. Particularly, based on the LaSalle-type invariance principle of stochastic differential delay equations, an adaptive control technique is proposed by constructing an auxiliary layer and designing proper control input and updating laws so that the unknown topology can be recovered upon successful generalized synchronization. Numerical simulations are provided to illustrate the effectiveness of the proposed method. The technique provides a certain theoretical basis for topology inference of complex networks. In particular, when the considered network is composed of systems with high-dimension or complicated dynamics, a simpler response layer can be constructed, which is conducive to circuit design. Moreover, it is practical to take into consideration perturbations caused by control input. Finally, the method is applicable to infer topology of a subnetwork embedded within a complex system and locate hidden sources. We hope the results can provide basic insight into further research endeavors on understanding practical and economical topology inference of networks.

  1. Inferring the mesoscale structure of layered, edge-valued, and time-varying networks

    NASA Astrophysics Data System (ADS)

    Peixoto, Tiago P.

    2015-10-01

    Many network systems are composed of interdependent but distinct types of interactions, which cannot be fully understood in isolation. These different types of interactions are often represented as layers, attributes on the edges, or as a time dependence of the network structure. Although they are crucial for a more comprehensive scientific understanding, these representations offer substantial challenges. Namely, it is an open problem how to precisely characterize the large or mesoscale structure of network systems in relation to these additional aspects. Furthermore, the direct incorporation of these features invariably increases the effective dimension of the network description, and hence aggravates the problem of overfitting, i.e., the use of overly complex characterizations that mistake purely random fluctuations for actual structure. In this work, we propose a robust and principled method to tackle these problems, by constructing generative models of modular network structure, incorporating layered, attributed and time-varying properties, as well as a nonparametric Bayesian methodology to infer the parameters from data and select the most appropriate model according to statistical evidence. We show that the method is capable of revealing hidden structure in layered, edge-valued, and time-varying networks, and that the most appropriate level of granularity with respect to the additional dimensions can be reliably identified. We illustrate our approach on a variety of empirical systems, including a social network of physicians, the voting correlations of deputies in the Brazilian national congress, the global airport network, and a proximity network of high-school students.

  2. A proposed architecture for a satellite-based mobile communications network - The lowest three layers

    NASA Technical Reports Server (NTRS)

    Yan, T. Y.; Naderi, F. M.

    1986-01-01

    Architecture for a commercial mobile satellite network is proposed. The mobile satellite system (MSS) is composed of a network management center, mobile terminals, base stations, and gateways; the functions of each component are described. The satellite is a 'bent pipe' that performs frequency translations, and it has multiple UHF beams. The development of the MSS design based on the seven-layer open system interconnection model is examined. Consideration is given to the functions of the physical, data link, and network layers and the integrated adaptive mobile access protocol.

  3. Traffic dynamics on two-layer complex networks with limited delivering capacity

    NASA Astrophysics Data System (ADS)

    Ma, Jinlong; Han, Weizhan; Guo, Qing; Wang, Zhenyong

    2016-08-01

    The traffic dynamics of multi-layer networks has attracted a great deal of interest since many real networks are comprised of two or more layers of subnetworks. Due to its low traffic capacity, the average delivery capacity allocation strategy is susceptible to congestion with the wildly used shortest path routing protocol on two-layer complex networks. In this paper, we introduce a delivery capacity allocation strategy into the traffic dynamics on two-layer complex networks and focus on its effect on the traffic capacity measured by the critical point Rc of phase transition from free flow to congestion. When the total nodes delivering capacity is fixed, the delivering capacity of each node in physical layer is assigned to the degree distributions of both the physical and logical layers. Simulation results show that the proposed strategy can bring much better traffic capacity than that with the average delivery capacity allocation strategy. Because of the significantly improved traffic performance, this work may be useful for optimal design of networked traffic dynamics.

  4. Dynamics of learning near singularities in layered networks.

    PubMed

    Wei, Haikun; Zhang, Jun; Cousseau, Florent; Ozeki, Tomoko; Amari, Shun-Ichi

    2008-03-01

    We explicitly analyze the trajectories of learning near singularities in hierarchical networks, such as multilayer perceptrons and radial basis function networks, which include permutation symmetry of hidden nodes, and show their general properties. Such symmetry induces singularities in their parameter space, where the Fisher information matrix degenerates and odd learning behaviors, especially the existence of plateaus in gradient descent learning, arise due to the geometric structure of singularity. We plot dynamic vector fields to demonstrate the universal trajectories of learning near singularities. The singularity induces two types of plateaus, the on-singularity plateau and the near-singularity plateau, depending on the stability of the singularity and the initial parameters of learning. The results presented in this letter are universally applicable to a wide class of hierarchical models. Detailed stability analysis of the dynamics of learning in radial basis function networks and multilayer perceptrons will be presented in separate work.

  5. Layer-crossing overhead and information spreading in multiplex social networks

    NASA Astrophysics Data System (ADS)

    Min, Byungjoon; Goh, K.-I.

    2014-03-01

    Many real-world systems consist of multiple different layers of networks and interplay between them. Taking such multiplexity into account is important to a complete understanding of the structure and dynamics of complex systems. In this respect, we propose and study a model of information or disease spreading on multiplex social networks, in which agents interact or communicate through multiple channels (layers), and there exists a layer-switching overhead for transmission across the interaction layers. The model is characterized by the path-dependent transmissibility over a contact, which is dynamically determined, dependent on both incoming and outgoing transmission layers due to the switching overhead. We formulate a generalized theory with a mapping to deal with such a path-dependent transmissibility, and demonstrate dependency of epidemic threshold and epidemic outbreak size with respect to multiplexity characteristics such as the densities of network layers, layer-crossing costs, and type of seed infections. Our results suggest that explicit consideration of multiplexity can be crucial in realistic modeling of spreading processes on social networks.

  6. Runaway cultural niche construction.

    PubMed

    Rendell, Luke; Fogarty, Laurel; Laland, Kevin N

    2011-03-27

    Cultural niche construction is a uniquely potent source of selection on human populations, and a major cause of recent human evolution. Previous theoretical analyses have not, however, explored the local effects of cultural niche construction. Here, we use spatially explicit coevolutionary models to investigate how cultural processes could drive selection on human genes by modifying local resources. We show that cultural learning, expressed in local niche construction, can trigger a process with dynamics that resemble runaway sexual selection. Under a broad range of conditions, cultural niche-constructing practices generate selection for gene-based traits and hitchhike to fixation through the build up of statistical associations between practice and trait. This process can occur even when the cultural practice is costly, or is subject to counteracting transmission biases, or the genetic trait is selected against. Under some conditions a secondary hitchhiking occurs, through which genetic variants that enhance the capability for cultural learning are also favoured by similar dynamics. We suggest that runaway cultural niche construction could have played an important role in human evolution, helping to explain why humans are simultaneously the species with the largest relative brain size, the most potent capacity for niche construction and the greatest reliance on culture.

  7. Multilayer in-place learning networks for modeling functional layers in the laminar cortex.

    PubMed

    Weng, Juyang; Luwang, Tianyu; Lu, Hong; Xue, Xiangyang

    2008-01-01

    Currently, there is a lack of general-purpose in-place learning networks that model feature layers in the cortex. By "general-purpose" we mean a general yet adaptive high-dimensional function approximator. In-place learning is a biological concept rooted in the genomic equivalence principle, meaning that each neuron is fully responsible for its own learning in its environment and there is no need for an external learner. Presented in this paper is the Multilayer In-place Learning Network (MILN) for this ambitious goal. Computationally, in-place learning provides unusually efficient learning algorithms whose simplicity, low computational complexity, and generality are set apart from typical conventional learning algorithms. Based on the neuroscience literature, we model the layer 4 and layer 2/3 as the feature layers in the 6-layer laminar cortex, with layer 4 using unsupervised learning and layer 2/3 using supervised learning. As a necessary requirement for autonomous mental development, MILN generates invariant neurons in different layers, with increasing invariance from earlier to later layers and the total invariance in the last motor layer. Such self-generated invariant representation is enabled mainly by descending (top-down) connections. The self-generated invariant representation is used as intermediate representations for learning later tasks in open-ended development. PMID:18314307

  8. Niche construction in the light of niche theory.

    PubMed

    Kylafis, Grigoris; Loreau, Michel

    2011-02-01

    Ecological niche construction, the process whereby an organism improves its environment to enhance its growth and persistence, is an important missing element of niche theory. Niche theory has mainly focused on niche-deteriorating processes, such as resource consumption, predation and competition, which have negative effects on population growth. Here, we integrate niche construction explicitly into modern niche theory. We use a graphical approach to analyse how a species' niche-improving impacts interplay with niche-deteriorating impacts to modify its response to the environment. In a model of two consumers that compete for one limiting resource and one predator, we show how niche construction modifies the traditional niche-deteriorating impacts of its agent or of competing species, and hence the potential for species coexistence. By altering the balance between intraspecific and interspecific competitive effects, niche construction can either generate net interspecific facilitation or strengthen interspecific competition. The adaptive benefit derived from niche construction also strongly affects the realized niche of a niche-constructing species.

  9. Usage of Neural Network to Predict Aluminium Oxide Layer Thickness

    PubMed Central

    Michal, Peter; Vagaská, Alena; Gombár, Miroslav; Kmec, Ján; Spišák, Emil; Kučerka, Daniel

    2015-01-01

    This paper shows an influence of chemical composition of used electrolyte, such as amount of sulphuric acid in electrolyte, amount of aluminium cations in electrolyte and amount of oxalic acid in electrolyte, and operating parameters of process of anodic oxidation of aluminium such as the temperature of electrolyte, anodizing time, and voltage applied during anodizing process. The paper shows the influence of those parameters on the resulting thickness of aluminium oxide layer. The impact of these variables is shown by using central composite design of experiment for six factors (amount of sulphuric acid, amount of oxalic acid, amount of aluminium cations, electrolyte temperature, anodizing time, and applied voltage) and by usage of the cubic neural unit with Levenberg-Marquardt algorithm during the results evaluation. The paper also deals with current densities of 1 A·dm−2 and 3 A·dm−2 for creating aluminium oxide layer. PMID:25922850

  10. Physical-Layer Network Coding for VPN in TDM-PON

    NASA Astrophysics Data System (ADS)

    Wang, Qike; Tse, Kam-Hon; Chen, Lian-Kuan; Liew, Soung-Chang

    2012-12-01

    We experimentally demonstrate a novel optical physical-layer network coding (PNC) scheme over time-division multiplexing (TDM) passive optical network (PON). Full-duplex error-free communications between optical network units (ONUs) at 2.5 Gb/s are shown for all-optical virtual private network (VPN) applications. Compared to the conventional half-duplex communications set-up, our scheme can increase the capacity by 100% with power penalty smaller than 3 dB. Synchronization of two ONUs is not required for the proposed VPN scheme

  11. Cross-layer design for prompt and reliable transmissions over body area networks.

    PubMed

    Torabi, Narjes; Leung, Victor C M

    2014-07-01

    In this paper, we propose a cross-layer design to make ambulatory health monitoring via body area networks (BAN) more reliable and robust. The proposed design builds on our centralized body area network access scheme (CBAS), a receiver-initiated medium access control (MAC) scheme that improves the visibility of a BAN in a coexistent environment, where diverse networks with various physical and MAC protocols share the radio spectrum. The design enhances CBAS by incorporating a network layer scheme that improves the packet delivery ratio (PDR), while minimizing the need for multihop cooperative transmissions; thus, packet delay is less compromised to achieve higher PDRs. The MAC layer provides the network layer with local information about the quality of on-body links to enable the BAN to identify the most reliable links in a distributed manner. Extensive experimental results are presented, which give insights on how the proposed cross-layer design improves PDR and packet delay. Results show the effectiveness of the proposed design which takes advantage of dynamic scheduling and multihop relays as warranted by the link conditions. PMID:24132027

  12. Cross-layer design for prompt and reliable transmissions over body area networks.

    PubMed

    Torabi, Narjes; Leung, Victor C M

    2014-07-01

    In this paper, we propose a cross-layer design to make ambulatory health monitoring via body area networks (BAN) more reliable and robust. The proposed design builds on our centralized body area network access scheme (CBAS), a receiver-initiated medium access control (MAC) scheme that improves the visibility of a BAN in a coexistent environment, where diverse networks with various physical and MAC protocols share the radio spectrum. The design enhances CBAS by incorporating a network layer scheme that improves the packet delivery ratio (PDR), while minimizing the need for multihop cooperative transmissions; thus, packet delay is less compromised to achieve higher PDRs. The MAC layer provides the network layer with local information about the quality of on-body links to enable the BAN to identify the most reliable links in a distributed manner. Extensive experimental results are presented, which give insights on how the proposed cross-layer design improves PDR and packet delay. Results show the effectiveness of the proposed design which takes advantage of dynamic scheduling and multihop relays as warranted by the link conditions.

  13. A Framework for Supporting Survivability, Network Planning and Cross-Layer Optimization in Future Multi-Domain Terabit Networks

    SciTech Connect

    Baldin, Ilya; Huang, Shu; Gopidi, Rajesh

    2015-01-28

    This final project report describes the accomplishments, products and publications from the award. It includes the overview of the project goals to devise a framework for managing resources in multi-domain, multi-layer networks, as well the details of the mathematical problem formulation and the description of the prototype built to prove the concept.

  14. Visual cortical mechanisms of perceptual grouping: interacting layers, networks, columns, and maps.

    PubMed

    Ross, W D; Grossberg, S; Mingolla, E

    2000-07-01

    The visual cortex has a laminar organization whose circuits form functional columns in cortical maps. How this laminar architecture supports visual percepts is not well understood. A neural model proposes how the laminar circuits of V1 and V2 generate perceptual groupings that maintain sensitivity to the contrasts and spatial organization of scenic cues. The model can decisively choose which groupings cohere and survive, even while balanced excitatory and inhibitory interactions preserve contrast-sensitive measures of local boundary likelihood or strength. In the model, excitatory inputs from lateral geniculate nucleus (LGN) activate layers 4 and 6 of V1. Layer 6 activates an on-center off-surround network of inputs to layer 4. Together these layer 4 inputs preserve analog sensitivity to LGN input contrasts. Layer 4 cells excite pyramidal cells in layer 2/3, which activate monosynaptic long-range horizontal excitatory connections between layer 2/3 pyramidal cells, and short-range disynaptic inhibitory connections mediated by smooth stellate cells. These interactions support inward perceptual grouping between two or more boundary inducers, but not outward grouping from a single inducer. These boundary signals feed back to layer 4 via the layer 6-to-4 on-center off-surround network. This folded feedback joins cells in different layers into functional columns while selecting winning groupings. Layer 6 in V1 also sends top-down signals to LGN using an on-center off-surround network, which suppresses LGN cells that do not receive feedback, while selecting, enhancing, and synchronizing activity of those that do. The model is used to simulate psychophysical and neurophysiological data about perceptual grouping, including various Gestalt grouping laws.

  15. OSI Network-layer Abstraction: Analysis of Simulation Dynamics and Performance Indicators

    NASA Astrophysics Data System (ADS)

    Lawniczak, Anna T.; Gerisch, Alf; Di Stefano, Bruno

    2005-06-01

    The Open Systems Interconnection (OSI) reference model provides a conceptual framework for communication among computers in a data communication network. The Network Layer of this model is responsible for the routing and forwarding of packets of data. We investigate the OSI Network Layer and develop an abstraction suitable for the study of various network performance indicators, e.g. throughput, average packet delay, average packet speed, average packet path-length, etc. We investigate how the network dynamics and the network performance indicators are affected by various routing algorithms and by the addition of randomly generated links into a regular network connection topology of fixed size. We observe that the network dynamics is not simply the sum of effects resulting from adding individual links to the connection topology but rather is governed nonlinearly by the complex interactions caused by the existence of all randomly added and already existing links in the network. Data for our study was gathered using Netzwerk-1, a C++ simulation tool that we developed for our abstraction.

  16. Atomic layer deposition of aluminum oxide films for carbon nanotube network transistor passivation.

    PubMed

    Grigoras, Kestutis; Zavodchikova, Marina Y; Nasibulin, Albert G; Kauppinen, Esko I; Ermolov, Vladimir; Franssila, Sami

    2011-10-01

    Ultra-thin (2-5 nm thick) aluminum oxide layers were grown on non-functionalized individual single walled carbon nanotubes (SWCNT) and their bundles by atomic layer deposition (ALD) technique in order to investigate the mechanism of the coating process. Transmission electron microscopy (TEM) was used to examine the uniformity and conformality of the coatings grown at different temperatures (80 degrees C or 220 degrees C) and with different precursors for oxidation (water and ozone). We found that bundles of SWCNTs were coated continuously, but at the same time, bare individual nanotubes remained uncoated. The successful coating of bundles was explained by the formation of interstitial pores between the individual SWCNTs constituting the bundle, where the precursor molecules can adhere, initiating the layer growth. Thicker alumina layers (20-35 nm thick) were used for the coating of bottom-gated SWCNT-network based field effect transistors (FETs). ALD layers, grown at different conditions, were found to influence the performance of the SWCNT-network FETs: low temperature ALD layers caused the ambipolarity of the channel and pronounced n-type conduction, whereas high temperature ALD processes resulted in hysteresis suppression in the transfer characteristics of the SWCNT transistors and preserved p-type conduction. Fixed charges in the ALD layer have been considered as the main factor influencing the conduction change of the SWCNT network based transistors.

  17. The Hematopoietic Niche in Myeloproliferative Neoplasms

    PubMed Central

    Schmitt-Graeff, Annette H.; Nitschke, Roland; Zeiser, Robert

    2015-01-01

    Specialized microanatomical areas of the bone marrow provide the signals that are mandatory for the maintenance and regulation of hematopoietic stem cells (HSCs) and progenitor cells. A complex microenvironment adjacent to the marrow vasculature (vascular niche) and close to the endosteum (endosteal niche) harbors multiple cell types including mesenchymal stromal cells and their derivatives such as CAR cells expressing high levels of chemokines C-X-C motif ligand 12 and early osteoblastic lineage cells, endothelial cells, and megakaryocytes. The characterization of the cellular and molecular networks operating in the HSC niche has opened new perspectives for the understanding of the bidirectional cross-talk between HSCs and stromal cell populations in normal and malignant conditions. A structural and functional remodeling of the niche may contribute to the development of myeloproliferative neoplasms (MPN). Malignant HSCs may alter the function and survival of MSCs that do not belong to the neoplastic clone. For example, a regression of nestin+ MSCs by apoptosis has been attributed to neuroglial damage in MPN. Nonneoplastic MSCs in turn can promote aggressiveness and drug resistance of malignant cells. In the future, strategies to counteract the pathological interaction between the niche and neoplastic HSCs may offer additional treatment strategies for MPN patients. PMID:26696752

  18. A two-layer team-assembly model for invention networks

    NASA Astrophysics Data System (ADS)

    Inoue, Hiroyasu

    2014-12-01

    Companies are exposed to rigid competition, so they seek how best to improve the capabilities of their innovations. One strategy is to collaborate with other companies in order to speed up their own innovations. Such inter-company collaborations are conducted by inventors belonging to the companies. At the same time, the inventors also seem to be affected by past collaborations between companies. Therefore, interdependency of two networks, namely inventor and company networks, exists. This paper discusses a model that replicates two-layer networks extracted from patent data of Japan and the United States in terms of degree distributions. The model replicates two-layer networks with the interdependency. Moreover it is the only model that uses local information, while other models have to use overall information, which is unrealistic. In addition, the proposed model replicates empirical data better than other models.

  19. Two-layer competitive based Hopfield neural network for medical image edge detection

    NASA Astrophysics Data System (ADS)

    Chang, Chuan Y.; Chung, Pau-Choo

    2000-03-01

    In medical applications, the detection and outlining of boundaries of organs and tumors in computed tomography (CT) and magnetic resonance imaging (MRI) images are prerequisite. A two-layer Hopfield neural network called the competitive Hopfield edge-finding neural network (CHEFNN) is presented for finding the edges of CT and MRI images. Different from conventional 2D Hopfield neural networks, the CHEFNN extends the one-layer 2D Hopfield network at the original image plane a two-layer 3D Hopfield network with edge detection to be implemented on its third dimension. With the extended 3D architecture, the network is capable of incorporating a pixel's contextual information into a pixel- labeling procedure. As a result, the effect of tiny details or noises will be effectively removed by the CHEFNN and the drawback of disconnected fractions can be overcome. Furthermore, by making use of the competitive learning rule to update the neuron states, the problem of satisfying strong constraints can be alleviated and results in a fast convergence. Our experimental results show that the CHEFNN can obtain more appropriate, more continued edge points than the Laplacian-based, Marr-Hildreth, Canny, and wavelet-based methods.

  20. The Balanced Cross-Layer Design Routing Algorithm in Wireless Sensor Networks Using Fuzzy Logic.

    PubMed

    Li, Ning; Martínez, José-Fernán; Hernández Díaz, Vicente

    2015-08-10

    Recently, the cross-layer design for the wireless sensor network communication protocol has become more and more important and popular. Considering the disadvantages of the traditional cross-layer routing algorithms, in this paper we propose a new fuzzy logic-based routing algorithm, named the Balanced Cross-layer Fuzzy Logic (BCFL) routing algorithm. In BCFL, we use the cross-layer parameters' dispersion as the fuzzy logic inference system inputs. Moreover, we give each cross-layer parameter a dynamic weight according the value of the dispersion. For getting a balanced solution, the parameter whose dispersion is large will have small weight, and vice versa. In order to compare it with the traditional cross-layer routing algorithms, BCFL is evaluated through extensive simulations. The simulation results show that the new routing algorithm can handle the multiple constraints without increasing the complexity of the algorithm and can achieve the most balanced performance on selecting the next hop relay node. Moreover, the Balanced Cross-layer Fuzzy Logic routing algorithm can adapt to the dynamic changing of the network conditions and topology effectively.

  1. The Balanced Cross-Layer Design Routing Algorithm in Wireless Sensor Networks Using Fuzzy Logic.

    PubMed

    Li, Ning; Martínez, José-Fernán; Hernández Díaz, Vicente

    2015-01-01

    Recently, the cross-layer design for the wireless sensor network communication protocol has become more and more important and popular. Considering the disadvantages of the traditional cross-layer routing algorithms, in this paper we propose a new fuzzy logic-based routing algorithm, named the Balanced Cross-layer Fuzzy Logic (BCFL) routing algorithm. In BCFL, we use the cross-layer parameters' dispersion as the fuzzy logic inference system inputs. Moreover, we give each cross-layer parameter a dynamic weight according the value of the dispersion. For getting a balanced solution, the parameter whose dispersion is large will have small weight, and vice versa. In order to compare it with the traditional cross-layer routing algorithms, BCFL is evaluated through extensive simulations. The simulation results show that the new routing algorithm can handle the multiple constraints without increasing the complexity of the algorithm and can achieve the most balanced performance on selecting the next hop relay node. Moreover, the Balanced Cross-layer Fuzzy Logic routing algorithm can adapt to the dynamic changing of the network conditions and topology effectively. PMID:26266412

  2. The Balanced Cross-Layer Design Routing Algorithm in Wireless Sensor Networks Using Fuzzy Logic

    PubMed Central

    Li, Ning; Martínez, José-Fernán; Díaz, Vicente Hernández

    2015-01-01

    Recently, the cross-layer design for the wireless sensor network communication protocol has become more and more important and popular. Considering the disadvantages of the traditional cross-layer routing algorithms, in this paper we propose a new fuzzy logic-based routing algorithm, named the Balanced Cross-layer Fuzzy Logic (BCFL) routing algorithm. In BCFL, we use the cross-layer parameters’ dispersion as the fuzzy logic inference system inputs. Moreover, we give each cross-layer parameter a dynamic weight according the value of the dispersion. For getting a balanced solution, the parameter whose dispersion is large will have small weight, and vice versa. In order to compare it with the traditional cross-layer routing algorithms, BCFL is evaluated through extensive simulations. The simulation results show that the new routing algorithm can handle the multiple constraints without increasing the complexity of the algorithm and can achieve the most balanced performance on selecting the next hop relay node. Moreover, the Balanced Cross-layer Fuzzy Logic routing algorithm can adapt to the dynamic changing of the network conditions and topology effectively. PMID:26266412

  3. [Research on Early Identification of Bipolar Disorder Based on Multi-layer Perceptron Neural Network].

    PubMed

    Zhang, Haowei; Gao, Yanni; Yuan, Chengmei; Liu, Ying; Ding, Yuqing

    2015-06-01

    Multi-layer perceptron (MLP) neural network belongs to multi-layer feedforward neural network, and has the ability and characteristics of high intelligence. It can realize the complex nonlinear mapping by its own learning through the network. Bipolar disorder is a serious mental illness with high recurrence rate, high self-harm rate and high suicide rate. Most of the onset of the bipolar disorder starts with depressive episode, which can be easily misdiagnosed as unipolar depression and lead to a delayed treatment so as to influence the prognosis. The early identifica- tion of bipolar disorder is of great importance for patients with bipolar disorder. Due to the fact that the process of early identification of bipolar disorder is nonlinear, we in this paper discuss the MLP neural network application in early identification of bipolar disorder. This study covered 250 cases, including 143 cases with recurrent depression and 107 cases with bipolar disorder, and clinical features were statistically analyzed between the two groups. A total of 42 variables with significant differences were screened as the input variables of the neural network. Part of the samples were randomly selected as the learning sample, and the other as the test sample. By choosing different neu- ral network structures, all results of the identification of bipolar disorder were relatively good, which showed that MLP neural network could be used in the early identification of bipolar disorder. PMID:26485974

  4. [Research on Early Identification of Bipolar Disorder Based on Multi-layer Perceptron Neural Network].

    PubMed

    Zhang, Haowei; Gao, Yanni; Yuan, Chengmei; Liu, Ying; Ding, Yuqing

    2015-06-01

    Multi-layer perceptron (MLP) neural network belongs to multi-layer feedforward neural network, and has the ability and characteristics of high intelligence. It can realize the complex nonlinear mapping by its own learning through the network. Bipolar disorder is a serious mental illness with high recurrence rate, high self-harm rate and high suicide rate. Most of the onset of the bipolar disorder starts with depressive episode, which can be easily misdiagnosed as unipolar depression and lead to a delayed treatment so as to influence the prognosis. The early identifica- tion of bipolar disorder is of great importance for patients with bipolar disorder. Due to the fact that the process of early identification of bipolar disorder is nonlinear, we in this paper discuss the MLP neural network application in early identification of bipolar disorder. This study covered 250 cases, including 143 cases with recurrent depression and 107 cases with bipolar disorder, and clinical features were statistically analyzed between the two groups. A total of 42 variables with significant differences were screened as the input variables of the neural network. Part of the samples were randomly selected as the learning sample, and the other as the test sample. By choosing different neu- ral network structures, all results of the identification of bipolar disorder were relatively good, which showed that MLP neural network could be used in the early identification of bipolar disorder.

  5. A One-Layer Recurrent Neural Network for Real-Time Portfolio Optimization With Probability Criterion.

    PubMed

    Liu, Qingshan; Dang, Chuangyin; Huang, Tingwen

    2013-02-01

    This paper presents a decision-making model described by a recurrent neural network for dynamic portfolio optimization. The portfolio-optimization problem is first converted into a constrained fractional programming problem. Since the objective function in the programming problem is not convex, the traditional optimization techniques are no longer applicable for solving this problem. Fortunately, the objective function in the fractional programming is pseudoconvex on the feasible region. It leads to a one-layer recurrent neural network modeled by means of a discontinuous dynamic system. To ensure the optimal solutions for portfolio optimization, the convergence of the proposed neural network is analyzed and proved. In fact, the neural network guarantees to get the optimal solutions for portfolio-investment advice if some mild conditions are satisfied. A numerical example with simulation results substantiates the effectiveness and illustrates the characteristics of the proposed neural network.

  6. Dynamic Graph Analytic Framework (DYGRAF): greater situation awareness through layered multi-modal network analysis

    NASA Astrophysics Data System (ADS)

    Margitus, Michael R.; Tagliaferri, William A., Jr.; Sudit, Moises; LaMonica, Peter M.

    2012-06-01

    Understanding the structure and dynamics of networks are of vital importance to winning the global war on terror. To fully comprehend the network environment, analysts must be able to investigate interconnected relationships of many diverse network types simultaneously as they evolve both spatially and temporally. To remove the burden from the analyst of making mental correlations of observations and conclusions from multiple domains, we introduce the Dynamic Graph Analytic Framework (DYGRAF). DYGRAF provides the infrastructure which facilitates a layered multi-modal network analysis (LMMNA) approach that enables analysts to assemble previously disconnected, yet related, networks in a common battle space picture. In doing so, DYGRAF provides the analyst with timely situation awareness, understanding and anticipation of threats, and support for effective decision-making in diverse environments.

  7. Single-Layer Graphene as a Barrier Layer for Intense UV Laser-Induced Damages for Silver Nanowire Network.

    PubMed

    Das, Suprem R; Nian, Qiong; Saei, Mojib; Jin, Shengyu; Back, Doosan; Kumar, Prashant; Janes, David B; Alam, Muhammad A; Cheng, Gary J

    2015-11-24

    Single-layer graphene (SLG) has been proposed as the thinnest protective/barrier layer for wide applications involving resistance to oxidation, corrosion, atomic/molecular diffusion, electromagnetic interference, and bacterial contamination. Functional metallic nanostructures have lower thermal stability than their bulk forms and are therefore susceptible to high energy photons. Here, we demonstrate that SLG can shield metallic nanostructures from intense laser radiation that would otherwise ablate them. By irradiation via a UV laser beam with nanosecond pulse width and a range of laser intensities (in millions of watt per cm(2)) onto a silver nanowire network, and conformally wrapping SLG on top of the nanowire network, we demonstrate that graphene "extracts and spreads" most of the thermal energy away from nanowire, thereby keeping it damage-free. Without graphene wrapping, the radiation would fragment the wires into smaller pieces and even decompose them into droplets. A systematic molecular dynamics simulation confirms the mechanism of SLG shielding. Consequently, particular damage-free and ablation-free laser-based nanomanufacturing of hybrid nanostructures might be sparked off by application of SLG on functional surfaces and nanofeatures. PMID:26447828

  8. A Survey on Multimedia-Based Cross-Layer Optimization in Visual Sensor Networks

    PubMed Central

    Costa, Daniel G.; Guedes, Luiz Affonso

    2011-01-01

    Visual sensor networks (VSNs) comprised of battery-operated electronic devices endowed with low-resolution cameras have expanded the applicability of a series of monitoring applications. Those types of sensors are interconnected by ad hoc error-prone wireless links, imposing stringent restrictions on available bandwidth, end-to-end delay and packet error rates. In such context, multimedia coding is required for data compression and error-resilience, also ensuring energy preservation over the path(s) toward the sink and improving the end-to-end perceptual quality of the received media. Cross-layer optimization may enhance the expected efficiency of VSNs applications, disrupting the conventional information flow of the protocol layers. When the inner characteristics of the multimedia coding techniques are exploited by cross-layer protocols and architectures, higher efficiency may be obtained in visual sensor networks. This paper surveys recent research on multimedia-based cross-layer optimization, presenting the proposed strategies and mechanisms for transmission rate adjustment, congestion control, multipath selection, energy preservation and error recovery. We note that many multimedia-based cross-layer optimization solutions have been proposed in recent years, each one bringing a wealth of contributions to visual sensor networks. PMID:22163908

  9. Cross-Layer Algorithms for QoS Enhancement in Wireless Multimedia Sensor Networks

    NASA Astrophysics Data System (ADS)

    Saxena, Navrati; Roy, Abhishek; Shin, Jitae

    A lot of emerging applications like advanced telemedicine and surveillance systems, demand sensors to deliver multimedia content with precise level of QoS enhancement. Minimizing energy in sensor networks has been a much explored research area but guaranteeing QoS over sensor networks still remains an open issue. In this letter we propose a cross-layer approach combining Network and MAC layers, for QoS enhancement in wireless multimedia sensor networks. In the network layer a statistical estimate of sensory QoS parameters is performed and a nearoptimal genetic algorithmic solution is proposed to solve the NP-complete QoS-routing problem. On the other hand the objective of the proposed MAC algorithm is to perform the QoS-based packet classification and automatic adaptation of the contention window. Simulation results demonstrate that the proposed protocol is capable of providing lower delay and better throughput, at the cost of reasonable energy consumption, in comparison with other existing sensory QoS protocols.

  10. Constraints of nonresponding flows based on cross layers in the networks

    NASA Astrophysics Data System (ADS)

    Zhou, Zhi-Chao; Xiao, Yang; Wang, Dong

    2016-02-01

    In the active queue management (AQM) scheme, core routers cannot manage and constrain user datagram protocol (UDP) data flows by the sliding window control mechanism in the transport layer due to the nonresponsive nature of such traffic flows. However, the UDP traffics occupy a large part of the network service nowadays which brings a great challenge to the stability of the more and more complex networks. To solve the uncontrollable problem, this paper proposes a cross layers random early detection (CLRED) scheme, which can control the nonresponding UDP-like flows rate effectively when congestion occurs in the access point (AP). The CLRED makes use of the MAC frame acknowledgement (ACK) transmitting congestion information to the sources nodes and utilizes the back-off windows of the MAC layer throttling data rate. Consequently, the UDP-like flows data rate can be restrained timely by the sources nodes in order to alleviate congestion in the complex networks. The proposed CLRED can constrain the nonresponsive flows availably and make the communication expedite, so that the network can sustain stable. The simulation results of network simulator-2 (NS2) verify the proposed CLRED scheme.

  11. Unraveling the impacts of IXP in internet ecosystem using bi-layered network

    NASA Astrophysics Data System (ADS)

    Fan, Zhongyan; Tang, Wallace K. S.

    2016-08-01

    The Internet is a huge complex network, consisting of tens thousands of Autonomous Systems (ASes). Being a logical fabric of the Internet, the AS-level topology serves as a manageable and useful vehicle for the study of Internet characteristics. However, Internet exchange points (IXPs) have been ignored in previous studies despite of being one of the primary mechanisms for AS interconnections and playing an important role for improving data traffic. In this paper, a novel bi-layered network model is proposed to present an IXP-AS topology. The bi-layered network is built based on the actual architecture, from which a comprehensive study of current AS ecosystem and the impacts of IXP can be made. As revealed by network metrics applied onto the bi-layered network, IXP is always of higher centrality as compared with ASes, well matching its role. By comparing the results in 2009 and 2014, rapid growth in IXP number, membership and impacts are noticed. There are over 98% source-destination pairs routes (with shortest path routing protocol) affected by IXP in 2014. Our results also show that, being an IXP member is more favorable than being a non-member, hence it attracts many ASes, especially those with low centrality, in recent years.

  12. Effect of externality in multiplex networks on one-layer synchronization

    NASA Astrophysics Data System (ADS)

    Jiang, Xin; Li, Meng; Zheng, Zhiming; Ma, Yifang; Ma, Lili

    2015-06-01

    Synchronization phenomenon plays an important role in the dynamic process on complex networks. In this letter, we consider synchronization under multiplex structures and explore the effect of external parts on the multilayered Kuramoto model with positive correlation between frequencies and degree. We show that large and strong mixing parts of the external layer may put off synchronization while the coupling strength of external layers has an accelerating, but limited, influence on synchronization. In particular, an explosive synchronization can be obtained by weakening the co-evolution coupling strength. The transition tends to be smooth when the co-evolution coupling strength increases. Our findings indicate that externality from multiplex networks, especially the mixing parts, and the co-evolution coupling strength should be of importance for synchronization on one certain layer.

  13. Explicit synchronisation of heterogeneous dynamics networks via three-layer communication framework

    NASA Astrophysics Data System (ADS)

    Wang, Bohui; Wang, Jingcheng; Zhang, Langwen; Zhang, Bin

    2016-06-01

    This paper addresses the explicit synchronisation of heterogeneous dynamics networks via three-layer communication framework. The main contribution is to propose an explicit synchronisation algorithm, in which the synchronisation errors of all the agents are decoupled. By constructing a three-layer node model, the proposed algorithm removes the assumptions that the topology is fixed and the synchronisation process is coupled. By introducing appropriate assumptions, the algorithm leads to a class of explicit synchronisation protocols based on the states of agents in different layers. It is proved in the sense of Lyapunov that, if the dwell time is larger than a threshold, the explicit synchronisation can be achieved for closed-loop heterogeneous dynamics networks under switching topologies. The results are further extended to the cases in which the switching topologies are only frequently but not always connected. Simulation results are presented with four single-link manipulators to verify the theoretical analysis.

  14. The Study of Cross-layer Optimization for Wireless Rechargeable Sensor Networks Implemented in Coal Mines.

    PubMed

    Ding, Xu; Shi, Lei; Han, Jianghong; Lu, Jingting

    2016-01-28

    Wireless sensor networks deployed in coal mines could help companies provide workers working in coal mines with more qualified working conditions. With the underground information collected by sensor nodes at hand, the underground working conditions could be evaluated more precisely. However, sensor nodes may tend to malfunction due to their limited energy supply. In this paper, we study the cross-layer optimization problem for wireless rechargeable sensor networks implemented in coal mines, of which the energy could be replenished through the newly-brewed wireless energy transfer technique. The main results of this article are two-fold: firstly, we obtain the optimal relay nodes' placement according to the minimum overall energy consumption criterion through the Lagrange dual problem and KKT conditions; secondly, the optimal strategies for recharging locomotives and wireless sensor networks are acquired by solving a cross-layer optimization problem. The cyclic nature of these strategies is also manifested through simulations in this paper.

  15. Ensemble learning in fixed expansion layer networks for mitigating catastrophic forgetting.

    PubMed

    Coop, Robert; Mishtal, Aaron; Arel, Itamar

    2013-10-01

    Catastrophic forgetting is a well-studied attribute of most parameterized supervised learning systems. A variation of this phenomenon, in the context of feedforward neural networks, arises when nonstationary inputs lead to loss of previously learned mappings. The majority of the schemes proposed in the literature for mitigating catastrophic forgetting were not data driven and did not scale well. We introduce the fixed expansion layer (FEL) feedforward neural network, which embeds a sparsely encoding hidden layer to help mitigate forgetting of prior learned representations. In addition, we investigate a novel framework for training ensembles of FEL networks, based on exploiting an information-theoretic measure of diversity between FEL learners, to further control undesired plasticity. The proposed methodology is demonstrated on a basic classification task, clearly emphasizing its advantages over existing techniques. The architecture proposed can be enhanced to address a range of computational intelligence tasks, such as regression problems and system control. PMID:24808599

  16. The Study of Cross-layer Optimization for Wireless Rechargeable Sensor Networks Implemented in Coal Mines

    PubMed Central

    Ding, Xu; Shi, Lei; Han, Jianghong; Lu, Jingting

    2016-01-01

    Wireless sensor networks deployed in coal mines could help companies provide workers working in coal mines with more qualified working conditions. With the underground information collected by sensor nodes at hand, the underground working conditions could be evaluated more precisely. However, sensor nodes may tend to malfunction due to their limited energy supply. In this paper, we study the cross-layer optimization problem for wireless rechargeable sensor networks implemented in coal mines, of which the energy could be replenished through the newly-brewed wireless energy transfer technique. The main results of this article are two-fold: firstly, we obtain the optimal relay nodes’ placement according to the minimum overall energy consumption criterion through the Lagrange dual problem and KKT conditions; secondly, the optimal strategies for recharging locomotives and wireless sensor networks are acquired by solving a cross-layer optimization problem. The cyclic nature of these strategies is also manifested through simulations in this paper. PMID:26828500

  17. Predicting Anticancer Drug Responses Using a Dual-Layer Integrated Cell Line-Drug Network Model

    PubMed Central

    Fang, Yun; Wang, Jun; Zheng, Xiaoqi; Liu, X. Shirley

    2015-01-01

    The ability to predict the response of a cancer patient to a therapeutic agent is a major goal in modern oncology that should ultimately lead to personalized treatment. Existing approaches to predicting drug sensitivity rely primarily on profiling of cancer cell line panels that have been treated with different drugs and selecting genomic or functional genomic features to regress or classify the drug response. Here, we propose a dual-layer integrated cell line-drug network model, which uses both cell line similarity network (CSN) data and drug similarity network (DSN) data to predict the drug response of a given cell line using a weighted model. Using the Cancer Cell Line Encyclopedia (CCLE) and Cancer Genome Project (CGP) studies as benchmark datasets, our single-layer model with CSN or DSN and only a single parameter achieved a prediction performance comparable to the previously generated elastic net model. When using the dual-layer model integrating both CSN and DSN, our predicted response reached a 0.6 Pearson correlation coefficient with observed responses for most drugs, which is significantly better than the previous results using the elastic net model. We have also applied the dual-layer cell line-drug integrated network model to fill in the missing drug response values in the CGP dataset. Even though the dual-layer integrated cell line-drug network model does not specifically model mutation information, it correctly predicted that BRAF mutant cell lines would be more sensitive than BRAF wild-type cell lines to three MEK1/2 inhibitors tested. PMID:26418249

  18. A two-layer recurrent neural network for nonsmooth convex optimization problems.

    PubMed

    Qin, Sitian; Xue, Xiaoping

    2015-06-01

    In this paper, a two-layer recurrent neural network is proposed to solve the nonsmooth convex optimization problem subject to convex inequality and linear equality constraints. Compared with existing neural network models, the proposed neural network has a low model complexity and avoids penalty parameters. It is proved that from any initial point, the state of the proposed neural network reaches the equality feasible region in finite time and stays there thereafter. Moreover, the state is unique if the initial point lies in the equality feasible region. The equilibrium point set of the proposed neural network is proved to be equivalent to the Karush-Kuhn-Tucker optimality set of the original optimization problem. It is further proved that the equilibrium point of the proposed neural network is stable in the sense of Lyapunov. Moreover, from any initial point, the state is proved to be convergent to an equilibrium point of the proposed neural network. Finally, as applications, the proposed neural network is used to solve nonlinear convex programming with linear constraints and L1 -norm minimization problems.

  19. The Multidimensional Nutritional Niche.

    PubMed

    Machovsky-Capuska, Gabriel E; Senior, Alistair M; Simpson, Stephen J; Raubenheimer, David

    2016-05-01

    The dietary generalist-specialist distinction plays a pivotal role in theoretical and applied ecology, conservation, invasion biology, and evolution and yet the concept remains poorly characterised. Diets, which are commonly used to define niche breadth, are almost exclusively considered in terms of foods, with little regard for the mixtures of nutrients and other compounds they contain. We use nutritional geometry (NG) to integrate nutrition with food-level approaches to the dietary niche and illustrate the application of our framework in the important context of invasion biology. We use an example that involves a model with four hypothetical nonexclusive scenarios. We additionally show how this approach can provide fresh theoretical insight into the ways nutrition and food choices impact trait evolution and trophic interactions.

  20. Trans-Omics: How To Reconstruct Biochemical Networks Across Multiple 'Omic' Layers.

    PubMed

    Yugi, Katsuyuki; Kubota, Hiroyuki; Hatano, Atsushi; Kuroda, Shinya

    2016-04-01

    We propose 'trans-omic' analysis for reconstructing global biochemical networks across multiple omic layers by use of both multi-omic measurements and computational data integration. We introduce technologies for connecting multi-omic data based on prior knowledge of biochemical interactions and characterize a biochemical trans-omic network by concepts of a static and dynamic nature. We introduce case studies of metabolism-centric trans-omic studies to show how to reconstruct a biochemical trans-omic network by connecting multi-omic data and how to analyze it in terms of the static and dynamic nature. We propose a trans-ome-wide association study (trans-OWAS) connecting phenotypes with trans-omic networks that reflect both genetic and environmental factors, which can characterize several complex lifestyle diseases as breakdowns in the trans-omic system.

  1. Artificial vision by multi-layered neural networks: neocognitron and its advances.

    PubMed

    Fukushima, Kunihiko

    2013-01-01

    The neocognitron is a neural network model proposed by Fukushima (1980). Its architecture was suggested by neurophysiological findings on the visual systems of mammals. It is a hierarchical multi-layered network. It acquires the ability to robustly recognize visual patterns through learning. Although the neocognitron has a long history, modifications of the network to improve its performance are still going on. For example, a recent neocognitron uses a new learning rule, named add-if-silent, which makes the learning process much simpler and more stable. Nevertheless, a high recognition rate can be kept with a smaller scale of the network. Referring to the history of the neocognitron, this paper discusses recent advances in the neocognitron. We also show that various new functions can be realized by, for example, introducing top-down connections to the neocognitron: mechanism of selective attention, recognition and completion of partly occluded patterns, restoring occluded contours, and so on.

  2. A one-layer recurrent neural network for constrained nonconvex optimization.

    PubMed

    Li, Guocheng; Yan, Zheng; Wang, Jun

    2015-01-01

    In this paper, a one-layer recurrent neural network is proposed for solving nonconvex optimization problems subject to general inequality constraints, designed based on an exact penalty function method. It is proved herein that any neuron state of the proposed neural network is convergent to the feasible region in finite time and stays there thereafter, provided that the penalty parameter is sufficiently large. The lower bounds of the penalty parameter and convergence time are also estimated. In addition, any neural state of the proposed neural network is convergent to its equilibrium point set which satisfies the Karush-Kuhn-Tucker conditions of the optimization problem. Moreover, the equilibrium point set is equivalent to the optimal solution to the nonconvex optimization problem if the objective function and constraints satisfy given conditions. Four numerical examples are provided to illustrate the performances of the proposed neural network.

  3. Availability Improvement of Layer 2 Seamless Networks Using OpenFlow

    PubMed Central

    Molina, Elias; Jacob, Eduardo; Matias, Jon; Moreira, Naiara; Astarloa, Armando

    2015-01-01

    The network robustness and reliability are strongly influenced by the implementation of redundancy and its ability of reacting to changes. In situations where packet loss or maximum latency requirements are critical, replication of resources and information may become the optimal technique. To this end, the IEC 62439-3 Parallel Redundancy Protocol (PRP) provides seamless recovery in layer 2 networks by delegating the redundancy management to the end-nodes. In this paper, we present a combination of the Software-Defined Networking (SDN) approach and PRP topologies to establish a higher level of redundancy and thereby, through several active paths provisioned via the OpenFlow protocol, the global reliability is increased, as well as data flows are managed efficiently. Hence, the experiments with multiple failure scenarios, which have been run over the Mininet network emulator, show the improvement in the availability and responsiveness over other traditional technologies based on a single active path. PMID:25759861

  4. A cross-layer duty cycle MAC protocol supporting a pipeline feature for wireless sensor networks.

    PubMed

    Tong, Fei; Xie, Rong; Shu, Lei; Kim, Young-Chon

    2011-01-01

    Although the conventional duty cycle MAC protocols for Wireless Sensor Networks (WSNs) such as RMAC perform well in terms of saving energy and reducing end-to-end delivery latency, they were designed independently and require an extra routing protocol in the network layer to provide path information for the MAC layer. In this paper, we propose a new cross-layer duty cycle MAC protocol with data forwarding supporting a pipeline feature (P-MAC) for WSNs. P-MAC first divides the whole network into many grades around the sink. Each node identifies its grade according to its logical hop distance to the sink and simultaneously establishes a sleep/wakeup schedule using the grade information. Those nodes in the same grade keep the same schedule, which is staggered with the schedule of the nodes in the adjacent grade. Then a variation of the RTS/CTS handshake mechanism is used to forward data continuously in a pipeline fashion from the higher grade to the lower grade nodes and finally to the sink. No extra routing overhead is needed, thus increasing the network scalability while maintaining the superiority of duty-cycling. The simulation results in OPNET show that P-MAC has better performance than S-MAC and RMAC in terms of packet delivery latency and energy efficiency.

  5. Non-coding RNAs and a layered architecture of genetic networks

    NASA Astrophysics Data System (ADS)

    Zhdanov, Vladimir P.

    2010-12-01

    In eukaryotic cells, protein-coding sequences constitute a relatively small part of the genome. The rest of the genome is transcribed to non-coding RNAs (ncRNAs). Such RNAs form the cornerstone of a regulatory network that operates in parallel with the protein network. Their biological functions are based primarily on the ability to pair with and deactivate target messenger RNAs (mRNAs). To clarify the likely role of ncRNAs in complex genetic networks, we present and comprehensively analyze a kinetic model of one of the key counterparts of the network architectures. Specifically, the genes transcribed to ncRNAs are considered to interplay with a hierarchical two-layer set of genes transcribed to mRNAs. The genes forming the bottom layer are regulated from the top and negatively self-regulated. If the former regulation is positive, the dependence of the RNA populations on the governing parameters is found to be often non-monotonous. Specifically, the model predicts bistability. If the regulation is negative, the dependence of the RNA populations on the governing parameters is monotonous. In particular, the population of the mRNAs, corresponding to the genes forming the bottom layer, is nearly constant.

  6. A Cross-Layer Duty Cycle MAC Protocol Supporting a Pipeline Feature for Wireless Sensor Networks

    PubMed Central

    Tong, Fei; Xie, Rong; Shu, Lei; Kim, Young-Chon

    2011-01-01

    Although the conventional duty cycle MAC protocols for Wireless Sensor Networks (WSNs) such as RMAC perform well in terms of saving energy and reducing end-to-end delivery latency, they were designed independently and require an extra routing protocol in the network layer to provide path information for the MAC layer. In this paper, we propose a new cross-layer duty cycle MAC protocol with data forwarding supporting a pipeline feature (P-MAC) for WSNs. P-MAC first divides the whole network into many grades around the sink. Each node identifies its grade according to its logical hop distance to the sink and simultaneously establishes a sleep/wakeup schedule using the grade information. Those nodes in the same grade keep the same schedule, which is staggered with the schedule of the nodes in the adjacent grade. Then a variation of the RTS/CTS handshake mechanism is used to forward data continuously in a pipeline fashion from the higher grade to the lower grade nodes and finally to the sink. No extra routing overhead is needed, thus increasing the network scalability while maintaining the superiority of duty-cycling. The simulation results in OPNET show that P-MAC has better performance than S-MAC and RMAC in terms of packet delivery latency and energy efficiency. PMID:22163895

  7. Layered vanadyl (IV) nitroprusside: Magnetic interaction through a network of hydrogen bonds

    NASA Astrophysics Data System (ADS)

    Gil, D. M.; Osiry, H.; Pomiro, F.; Varetti, E. L.; Carbonio, R. E.; Alejandro, R. R.; Ben Altabef, A.; Reguera, E.

    2016-07-01

    The hydrogen bond and π-π stacking are two non-covalent interactions able to support cooperative magnetic ordering between paramagnetic centers. This contribution reports the crystal structure and related magnetic properties for VO[Fe(CN)5NO]·2H2O, which has a layered structure. This solid crystallizes with an orthorhombic unit cell, in the Pna21 space group, with cell parameters a=14.1804(2), b=10.4935(1), c=7.1722(8) Å and four molecules per unit cell (Z=4). Its crystal structure was solved and refined from powder X-ray diffraction data. Neighboring layers remain linked through a network of hydrogen bonds involving a water molecule coordinated to the axial position for the V atom and the unbridged axial NO and CN ligands. An uncoordinated water molecule is found forming a triple bridge between these last two ligands and the coordinated water molecule. The magnetic measurements, recorded down to 2 K, shows a ferromagnetic interaction between V atoms located at neighboring layers, with a Curie-Weiss constant of 3.14 K. Such ferromagnetic behavior was interpreted as resulting from a superexchange interaction through the network of strong OH····OH2O, OH····NCN, and OH····ONO hydrogen bonds that connects neighboring layers. The interaction within the layer must be of antiferromagnetic nature and it was detected close to 2 K.

  8. Reverse-feeding effect of epidemic by propagators in two-layered networks

    NASA Astrophysics Data System (ADS)

    Dayu, Wu; Yanping, Zhao; Muhua, Zheng; Jie, Zhou; Zonghua, Liu

    2016-02-01

    Epidemic spreading has been studied for a long time and is currently focused on the spreading of multiple pathogens, especially in multiplex networks. However, little attention has been paid to the case where the mutual influence between different pathogens comes from a fraction of epidemic propagators, such as bisexual people in two separated groups of heterosexual and homosexual people. We here study this topic by presenting a network model of two layers connected by impulsive links, in contrast to the persistent links in each layer. We let each layer have a distinct pathogen and their interactive infection is implemented by a fraction of propagators jumping between the corresponding pairs of nodes in the two layers. By this model we show that (i) the propagators take the key role to transmit pathogens from one layer to the other, which significantly influences the stabilized epidemics; (ii) the epidemic thresholds will be changed by the propagators; and (iii) a reverse-feeding effect can be expected when the infective rate is smaller than its threshold of isolated spreading. A theoretical analysis is presented to explain the numerical results. Project supported by the National Natural Science Foundation of China (Grant Nos. 11135001, 11375066, and 11405059) and the National Basic Key Program of China (Grant No. 2013CB834100).

  9. Two-layer wireless distributed sensor/control network based on RF

    NASA Astrophysics Data System (ADS)

    Feng, Li; Lin, Yuchi; Zhou, Jingjing; Dong, Guimei; Xia, Guisuo

    2006-11-01

    A project of embedded Wireless Distributed Sensor/Control Network (WDSCN) based on RF is presented after analyzing the disadvantages of traditional measure and control system. Because of high-cost and complexity, such wireless techniques as Bluetooth and WiFi can't meet the needs of WDSCN. The two-layer WDSCN is designed based on RF technique, which operates in the ISM free frequency channel with low power and high transmission speed. Also the network is low cost, portable and moveable, integrated with the technologies of computer network, sensor, microprocessor and wireless communications. The two-layer network topology is selected in the system; a simple but efficient self-organization net protocol is designed to fit the periodic data collection, event-driven and store-and-forward. Furthermore, adaptive frequency hopping technique is adopted for anti-jamming apparently. The problems about power reduction and synchronization of data in wireless system are solved efficiently. Based on the discussion above, a measure and control network is set up to control such typical instruments and sensors as temperature sensor and signal converter, collect data, and monitor environmental parameters around. This system works well in different rooms. Experiment results show that the system provides an efficient solution to WDSCN through wireless links, with high efficiency, low power, high stability, flexibility and wide working range.

  10. Reactivity surveillance in a nuclear reactor by using a layered artificial neural network

    SciTech Connect

    Arul, A.J. . Reactor Physics Div.)

    1994-07-01

    Layered neural networks, which are a class of models based on neuronal computation in biological systems, are applied to the task of reactivity monitoring in a nuclear reactor to improve the safety and the reliability of the operating plant. Training is done with a maximum likelihood method, which is suitable for on-line training. Operational data from the Fast Breeder Test Reactor are used to study its performance. The adaptability of the network to slow variations in the system parameters and its ability to learn in a noisy environment are studied.

  11. Energy Efficient, Cross-Layer Enabled, Dynamic Aggregation Networks for Next Generation Internet

    NASA Astrophysics Data System (ADS)

    Wang, Michael S.

    Today, the Internet traffic is growing at a near exponential rate, driven predominately by data center-based applications and Internet-of-Things services. This fast-paced growth in Internet traffic calls into question the ability of the existing optical network infrastructure to support this continued growth. The overall optical networking equipment efficiency has not been able to keep up with the traffic growth, creating a energy gap that makes energy and cost expenditures scale linearly with the traffic growth. The implication of this energy gap is that it is infeasible to continue using existing networking equipment to meet the growing bandwidth demand. A redesign of the optical networking platform is needed. The focus of this dissertation is on the design and implementation of energy efficient, cross-layer enabled, dynamic optical networking platforms, which is a promising approach to address the exponentially growing Internet bandwidth demand. Chapter 1 explains the motivation for this work by detailing the huge Internet traffic growth and the unsustainable energy growth of today's networking equipment. Chapter 2 describes the challenges and objectives of enabling agile, dynamic optical networking platforms and the vision of the Center for Integrated Access Networks (CIAN) to realize these objectives; the research objectives of this dissertation and the large body of related work in this field is also summarized. Chapter 3 details the design and implementation of dynamic networking platforms that support wavelength switching granularity. The main contribution of this work involves the experimental validation of deep cross-layer communication across the optical performance monitoring (OPM), data, and control planes. The first experiment shows QoS-aware video streaming over a metro-scale test-bed through optical power monitoring of the transmission wavelength and cross-layer feedback control of the power level. The second experiment extends the performance

  12. Adaptive nonlinear polynomial neural networks for control of boundary layer/structural interaction

    NASA Technical Reports Server (NTRS)

    Parker, B. Eugene, Jr.; Cellucci, Richard L.; Abbott, Dean W.; Barron, Roger L.; Jordan, Paul R., III; Poor, H. Vincent

    1993-01-01

    The acoustic pressures developed in a boundary layer can interact with an aircraft panel to induce significant vibration in the panel. Such vibration is undesirable due to the aerodynamic drag and structure-borne cabin noises that result. The overall objective of this work is to develop effective and practical feedback control strategies for actively reducing this flow-induced structural vibration. This report describes the results of initial evaluations using polynomial, neural network-based, feedback control to reduce flow induced vibration in aircraft panels due to turbulent boundary layer/structural interaction. Computer simulations are used to develop and analyze feedback control strategies to reduce vibration in a beam as a first step. The key differences between this work and that going on elsewhere are as follows: that turbulent and transitional boundary layers represent broadband excitation and thus present a more complex stochastic control scenario than that of narrow band (e.g., laminar boundary layer) excitation; and secondly, that the proposed controller structures are adaptive nonlinear infinite impulse response (IIR) polynomial neural network, as opposed to the traditional adaptive linear finite impulse response (FIR) filters used in most studies to date. The controllers implemented in this study achieved vibration attenuation of 27 to 60 dB depending on the type of boundary layer established by laminar, turbulent, and intermittent laminar-to-turbulent transitional flows. Application of multi-input, multi-output, adaptive, nonlinear feedback control of vibration in aircraft panels based on polynomial neural networks appears to be feasible today. Plans are outlined for Phase 2 of this study, which will include extending the theoretical investigation conducted in Phase 2 and verifying the results in a series of laboratory experiments involving both bum and plate models.

  13. Adaptive nonlinear polynomial neural networks for control of boundary layer/structural interaction

    NASA Astrophysics Data System (ADS)

    Parker, B. Eugene, Jr.; Cellucci, Richard L.; Abbott, Dean W.; Barron, Roger L.; Jordan, Paul R., III; Poor, H. Vincent

    1993-12-01

    The acoustic pressures developed in a boundary layer can interact with an aircraft panel to induce significant vibration in the panel. Such vibration is undesirable due to the aerodynamic drag and structure-borne cabin noises that result. The overall objective of this work is to develop effective and practical feedback control strategies for actively reducing this flow-induced structural vibration. This report describes the results of initial evaluations using polynomial, neural network-based, feedback control to reduce flow induced vibration in aircraft panels due to turbulent boundary layer/structural interaction. Computer simulations are used to develop and analyze feedback control strategies to reduce vibration in a beam as a first step. The key differences between this work and that going on elsewhere are as follows: that turbulent and transitional boundary layers represent broadband excitation and thus present a more complex stochastic control scenario than that of narrow band (e.g., laminar boundary layer) excitation; and secondly, that the proposed controller structures are adaptive nonlinear infinite impulse response (IIR) polynomial neural network, as opposed to the traditional adaptive linear finite impulse response (FIR) filters used in most studies to date. The controllers implemented in this study achieved vibration attenuation of 27 to 60 dB depending on the type of boundary layer established by laminar, turbulent, and intermittent laminar-to-turbulent transitional flows. Application of multi-input, multi-output, adaptive, nonlinear feedback control of vibration in aircraft panels based on polynomial neural networks appears to be feasible today. Plans are outlined for Phase 2 of this study, which will include extending the theoretical investigation conducted in Phase 2 and verifying the results in a series of laboratory experiments involving both bum and plate models.

  14. Experimental validation of optical layer performance monitoring using an all-optical network testbed

    NASA Astrophysics Data System (ADS)

    Vukovic, Alex; Savoie, Michel J.; Hua, Heng

    2004-11-01

    Communication transmission systems continue to evolve towards higher data rates, increased wavelength densities, longer transmission distances and more intelligence. Further development of dense wavelength division multiplexing (DWDM) and all-optical networks (AONs) will demand ever-tighter monitoring to assure a specified quality of service (QoS). Traditional monitoring methods have been proven to be insufficient. Higher degree of self-control, intelligence and optimization for functions within next generation networks require new monitoring schemes to be developed and deployed. Both perspective and challenges of performance monitoring, its techniques, requirements and drivers are discussed. It is pointed out that optical layer monitoring is a key enabler for self-control of next generation optical networks. Aside from its real-time feedback and the safeguarding of neighbouring channels, optical performance monitoring ensures the ability to build and control complex network topologies while maintaining an efficiently high QoS. Within an all-optical network testbed environment, key performance monitoring parameters are identified, assessed through real-time proof-of-concept, and proposed for network applications for the safeguarding of neighbouring channels in WDM systems.

  15. Finding a Niche

    PubMed Central

    2010-01-01

    Although I always knew I wanted to be a scientist, I didn't know I would become a cell biologist. Events in life that you would never have predicted can greatly impact your career trajectory. I have learned to let those events take me in new directions. Following a desire to investigate an understudied area of cell biology, I have found a niche. In this area, my lab is poised to contribute significantly toward understanding the fundamental molecular mechanisms underlying polarized plant cell growth. PMID:21079002

  16. Cross-layer ultrasound video streaming over mobile WiMAX and HSUPA networks.

    PubMed

    Alinejad, Ali; Philip, Nada Y; Istepanian, Robert S H

    2012-01-01

    It is well known that the evolution of 4G-based mobile multimedia network systems will contribute significantly to future mobile healthcare (m-health) applications that require high bandwidth and fast data rates. Central to the success of such emerging applications is the compatibility of broadband networks, such as mobile Worldwide Interoperability For Microwave Access (WiMAX) and High-Speed Uplink Packet Access (HSUPA), and especially their rate adaption issues combined with the acceptable real-time medical quality of service requirements. In this paper, we address the relevant challenges of cross-layer design requirements for real-time rate adaptation of ultrasound video streaming in mobile WiMAX and HSUPA networks. A comparative performance analysis of such approach is validated in two experimental m-health test bed systems for both mobile WiMAX and HSUPA networks. The experimental results have shown an improved performance of mobile WiMAX compared to the HSUPA using the same cross-layer optimization approach. PMID:21571613

  17. Cross-layer ultrasound video streaming over mobile WiMAX and HSUPA networks.

    PubMed

    Alinejad, Ali; Philip, Nada Y; Istepanian, Robert S H

    2012-01-01

    It is well known that the evolution of 4G-based mobile multimedia network systems will contribute significantly to future mobile healthcare (m-health) applications that require high bandwidth and fast data rates. Central to the success of such emerging applications is the compatibility of broadband networks, such as mobile Worldwide Interoperability For Microwave Access (WiMAX) and High-Speed Uplink Packet Access (HSUPA), and especially their rate adaption issues combined with the acceptable real-time medical quality of service requirements. In this paper, we address the relevant challenges of cross-layer design requirements for real-time rate adaptation of ultrasound video streaming in mobile WiMAX and HSUPA networks. A comparative performance analysis of such approach is validated in two experimental m-health test bed systems for both mobile WiMAX and HSUPA networks. The experimental results have shown an improved performance of mobile WiMAX compared to the HSUPA using the same cross-layer optimization approach.

  18. Layer 1 VPN services in distributed next-generation SONET/SDH networks with inverse multiplexing

    NASA Astrophysics Data System (ADS)

    Ghani, N.; Muthalaly, M. V.; Benhaddou, D.; Alanqar, W.

    2006-05-01

    Advances in next-generation SONET/SDH along with GMPLS control architectures have enabled many new service provisioning capabilities. In particular, a key services paradigm is the emergent Layer 1 virtual private network (L1 VPN) framework, which allows multiple clients to utilize a common physical infrastructure and provision their own 'virtualized' circuit-switched networks. This precludes expensive infrastructure builds and increases resource utilization for carriers. Along these lines, a novel L1 VPN services resource management scheme for next-generation SONET/SDH networks is proposed that fully leverages advanced virtual concatenation and inverse multiplexing features. Additionally, both centralized and distributed GMPLS-based implementations are also tabled to support the proposed L1 VPN services model. Detailed performance analysis results are presented along with avenues for future research.

  19. A one-layer recurrent neural network for constrained nonsmooth invex optimization.

    PubMed

    Li, Guocheng; Yan, Zheng; Wang, Jun

    2014-02-01

    Invexity is an important notion in nonconvex optimization. In this paper, a one-layer recurrent neural network is proposed for solving constrained nonsmooth invex optimization problems, designed based on an exact penalty function method. It is proved herein that any state of the proposed neural network is globally convergent to the optimal solution set of constrained invex optimization problems, with a sufficiently large penalty parameter. In addition, any neural state is globally convergent to the unique optimal solution, provided that the objective function and constraint functions are pseudoconvex. Moreover, any neural state is globally convergent to the feasible region in finite time and stays there thereafter. The lower bounds of the penalty parameter and convergence time are also estimated. Two numerical examples are provided to illustrate the performances of the proposed neural network.

  20. Feedback linearisation control of an induction machine augmented by single-hidden layer neural networks

    NASA Astrophysics Data System (ADS)

    Ait Abbas, Hamou; Belkheiri, Mohammed; Zegnini, Boubakeur

    2016-01-01

    We consider adaptive output feedback control methodology of highly uncertain nonlinear systems with both parametric uncertainties and unmodelled dynamics. The approach is also applicable to systems of unknown, but bounded dimension. However, the relative degree of the regulated output is assumed to be known. This new control strategy is proposed to address the tracking problem of an induction motor based on a modified field-oriented control method. The obtained controller is then augmented by an online neural network that serves as an approximator for the neglected dynamics and modelling errors. The network weight adaptation rule is derived from the Lyapunov stability analysis, that guarantees boundedness of all the error signals of the closed-loop system. Computer simulations of an output feedback controlled induction machine, augmented via single-hidden-layer neural networks, demonstrate the practical potential of the proposed control algorithm.

  1. Creating a two-layered augmented artificial immune system for application to computer network intrusion detection

    NASA Astrophysics Data System (ADS)

    Judge, Matthew G.; Lamont, Gary B.

    2009-05-01

    Computer network security has become a very serious concern of commercial, industrial, and military organizations due to the increasing number of network threats such as outsider intrusions and insider covert activities. An important security element of course is network intrusion detection which is a difficult real world problem that has been addressed through many different solution attempts. Using an artificial immune system has been shown to be one of the most promising results. By enhancing jREMISA, a multi-objective evolutionary algorithm inspired artificial immune system, with a secondary defense layer; we produce improved accuracy of intrusion classification and a flexibility in responsiveness. This responsiveness can be leveraged to provide a much more powerful and accurate system, through the use of increased processing time and dedicated hardware which has the flexibility of being located out of band.

  2. Cross-layer design for intrusion detection and data security in wireless ad hoc sensor networks

    NASA Astrophysics Data System (ADS)

    Hortos, William S.

    2007-09-01

    A wireless ad hoc sensor network is a configuration for area surveillance that affords rapid, flexible deployment in arbitrary threat environments. There is no infrastructure support and sensor nodes communicate with each other only when they are in transmission range. The nodes are severely resource-constrained, with limited processing, memory and power capacities and must operate cooperatively to fulfill a common mission in typically unattended modes. In a wireless sensor network (WSN), each sensor at a node can observe locally some underlying physical phenomenon and sends a quantized version of the observation to sink (destination) nodes via wireless links. Since the wireless medium can be easily eavesdropped, links can be compromised by intrusion attacks from nodes that may mount denial-of-service attacks or insert spurious information into routing packets, leading to routing loops, long timeouts, impersonation, and node exhaustion. A cross-layer design based on protocol-layer interactions is proposed for detection and identification of various intrusion attacks on WSN operation. A feature set is formed from selected cross-layer parameters of the WSN protocol to detect and identify security threats due to intrusion attacks. A separate protocol is not constructed from the cross-layer design; instead, security attributes and quantified trust levels at and among nodes established during data exchanges complement customary WSN metrics of energy usage, reliability, route availability, and end-to-end quality-of-service (QoS) provisioning. Statistical pattern recognition algorithms are applied that use observed feature-set patterns observed during network operations, viewed as security audit logs. These algorithms provide the "best" network global performance in the presence of various intrusion attacks. A set of mobile (software) agents distributed at the nodes implement the algorithms, by moving among the layers involved in the network response at each active node

  3. In defense of 'niche modeling'.

    PubMed

    Warren, Dan L

    2012-09-01

    There is a growing awareness of problems with the estimation of the ecological tolerances of species through correlative modeling approaches. These problems have led some investigators to argue for abandoning terms such as 'ecological niche model' and 'environmental niche model' in favor of the ostensibly more value-neutral 'species distribution model', as the models are thought to frequently be poor estimators of the niche. Here, I argue that most applications to which these models are put require the assumption that they do estimate the niche, however imperfectly, and that obscuring this inescapable and potentially flawed assumption in the terminology may only serve to hinder the development of the field.

  4. Global forward-predicting dynamic routing for traffic concurrency space stereo multi-layer scale-free network

    NASA Astrophysics Data System (ADS)

    Xie, Wei-Hao; Zhou, Bin; Liu, En-Xiao; Lu, Wei-Dang; Zhou, Ting

    2015-09-01

    Many real communication networks, such as oceanic monitoring network and land environment observation network, can be described as space stereo multi-layer structure, and the traffic in these networks is concurrent. Understanding how traffic dynamics depend on these real communication networks and finding an effective routing strategy that can fit the circumstance of traffic concurrency and enhance the network performance are necessary. In this light, we propose a traffic model for space stereo multi-layer complex network and introduce two kinds of global forward-predicting dynamic routing strategies, global forward-predicting hybrid minimum queue (HMQ) routing strategy and global forward-predicting hybrid minimum degree and queue (HMDQ) routing strategy, for traffic concurrency space stereo multi-layer scale-free networks. By applying forward-predicting strategy, the proposed routing strategies achieve better performances in traffic concurrency space stereo multi-layer scale-free networks. Compared with the efficient routing strategy and global dynamic routing strategy, HMDQ and HMQ routing strategies can optimize the traffic distribution, alleviate the number of congested packets effectively and reach much higher network capacity. Project supported by the Youth Science Funds of Shandong Academy of Sciences, China (Grant No. 2014QN032).

  5. Cooperation influenced by the correlation degree of two-layered complex networks in evolutionary prisoner's dilemma games

    NASA Astrophysics Data System (ADS)

    Guan, Jian-Yue; Wu, Zhi-Xi; Huang, Zi-Gang; Wang, Ying-Hai

    2010-02-01

    An evolutionary prisoner's dilemma game is investigated on two-layered complex networks respectively representing interaction and learning networks in one and two dimensions. A parameter q is introduced to denote the correlation degree between the two-layered networks. Using Monte Carlo simulations we studied the effects of the correlation degree on cooperative behaviour and found that the cooperator density nontrivially changes with q for different payoff parameter values depending on the detailed strategy updating and network dimension. An explanation for the obtained results is provided.

  6. Heat freezes niche evolution.

    PubMed

    Araújo, Miguel B; Ferri-Yáñez, Francisco; Bozinovic, Francisco; Marquet, Pablo A; Valladares, Fernando; Chown, Steven L

    2013-09-01

    Climate change is altering phenology and distributions of many species and further changes are projected. Can species physiologically adapt to climate warming? We analyse thermal tolerances of a large number of terrestrial ectotherm (n = 697), endotherm (n = 227) and plant (n = 1816) species worldwide, and show that tolerance to heat is largely conserved across lineages, while tolerance to cold varies between and within species. This pattern, previously documented for ectotherms, is apparent for this group and for endotherms and plants, challenging the longstanding view that physiological tolerances of species change continuously across climatic gradients. An alternative view is proposed in which the thermal component of climatic niches would overlap across species more than expected. We argue that hard physiological boundaries exist that constrain evolution of tolerances of terrestrial organisms to high temperatures. In contrast, evolution of tolerances to cold should be more frequent. One consequence of conservatism of upper thermal tolerances is that estimated niches for cold-adapted species will tend to underestimate their upper thermal limits, thereby potentially inflating assessments of risk from climate change. In contrast, species whose climatic preferences are close to their upper thermal limits will unlikely evolve physiological tolerances to increased heat, thereby being predictably more affected by warming.

  7. Latitudinal gradients in biotic niche breadth vary across ecosystem types.

    PubMed

    Cirtwill, Alyssa R; Stouffer, Daniel B; Romanuk, Tamara N

    2015-11-22

    Several properties of food webs-the networks of feeding links between species-are known to vary systematically with the species richness of the underlying community. Under the 'latitude-niche breadth hypothesis', which predicts that species in the tropics will tend to evolve narrower niches, one might expect that these scaling relationships could also be affected by latitude. To test this hypothesis, we analysed the scaling relationships between species richness and average generality, vulnerability and links per species across a set of 196 empirical food webs. In estuarine, marine and terrestrial food webs there was no effect of latitude on any scaling relationship, suggesting constant niche breadth in these habitats. In freshwater communities, on the other hand, there were strong effects of latitude on scaling relationships, supporting the latitude-niche breadth hypothesis. These contrasting findings indicate that it may be more important to account for habitat than latitude when exploring gradients in food-web structure.

  8. Layered Location-Based Security Mechanism for Mobile Sensor Networks: Moving Security Areas

    PubMed Central

    Wang, Ze; Zhang, Haijuan; Wu, Luqiang; Zhou, Chang

    2015-01-01

    Network security is one of the most important issues in mobile sensor networks (MSNs). Networks are particularly vulnerable in hostile environments because of many factors, such as uncertain mobility, limitations on computation, and the need for storage in mobile nodes. Though some location-based security mechanisms can resist some malicious attacks, they are only suitable for static networks and may sometimes require large amounts of storage. To solve these problems, using location information, which is one of the most important properties in outdoor wireless networks, a security mechanism called a moving security area (MSA) is proposed to resist malicious attacks by using mobile nodes’ dynamic location-based keys. The security mechanism is layered by performing different detection schemes inside or outside the MSA. The location-based private keys will be updated only at the appropriate moments, considering the balance of cost and security performance. By transferring parts of the detection tasks from ordinary nodes to the sink node, the memory requirements are distributed to different entities to save limited energy. PMID:26404278

  9. Security risk assessment of the primary layer of wavelength division multiplexing passive optical network

    NASA Astrophysics Data System (ADS)

    Koudelka, Petr; Siska, Petr; Latal, Jan; Poboril, Radek; Hajek, Lukas; Kepak, Stanislav; Vasinek, Vladimir

    2015-01-01

    Next-generation passive optical access networks come to the fore nowadays. These optical next-generation networks are the response to the increasing qualitative requirements from end users. Technologies using Time Division Multiplexing include NG-PON (XG-PON 1 and XG-PON 2) and 10GEPON. Their advantage is the applicability to older topologies, which are operated by the original technology of passive optical access networks. Wavelength Division Multiplexing Passive Optical Network (WDM-PON) is an alternative also belonging to next-generation networks. Time Division Multiplexing is in this case replaced by Wavelength Division Multiplexing. Certain variants of WDM-PON use a combination of broadband light source, optical circulator, optical phased array and tunable FP laser. Construction of the terminal units (ONU) is advantageous because it can always tune in to the appropriate wavelength in the given optical DWDM channel (100 GHz). The disadvantage is the increased security risk on the primary layer due to channel crosstalk in an optical phased array (AWG). The aim of this paper is to assess the degree of security risk in real conditions. The article includes both simulation and real measurements in C + L bands with 100 GHz DWDM spacing.

  10. Layered Location-Based Security Mechanism for Mobile Sensor Networks: Moving Security Areas.

    PubMed

    Wang, Ze; Zhang, Haijuan; Wu, Luqiang; Zhou, Chang

    2015-09-25

    Network security is one of the most important issues in mobile sensor networks (MSNs). Networks are particularly vulnerable in hostile environments because of many factors, such as uncertain mobility, limitations on computation, and the need for storage in mobile nodes. Though some location-based security mechanisms can resist some malicious attacks, they are only suitable for static networks and may sometimes require large amounts of storage. To solve these problems, using location information, which is one of the most important properties in outdoor wireless networks, a security mechanism called a moving security area (MSA) is proposed to resist malicious attacks by using mobile nodes' dynamic location-based keys. The security mechanism is layered by performing different detection schemes inside or outside the MSA. The location-based private keys will be updated only at the appropriate moments, considering the balance of cost and security performance. By transferring parts of the detection tasks from ordinary nodes to the sink node, the memory requirements are distributed to different entities to save limited energy.

  11. Cross-layer cluster-based energy-efficient protocol for wireless sensor networks.

    PubMed

    Mammu, Aboobeker Sidhik Koyamparambil; Hernandez-Jayo, Unai; Sainz, Nekane; de la Iglesia, Idoia

    2015-01-01

    Recent developments in electronics and wireless communications have enabled the improvement of low-power and low-cost wireless sensors networks (WSNs). One of the most important challenges in WSNs is to increase the network lifetime due to the limited energy capacity of the network nodes. Another major challenge in WSNs is the hot spots that emerge as locations under heavy traffic load. Nodes in such areas quickly drain energy resources, leading to disconnection in network services. In such an environment, cross-layer cluster-based energy-efficient algorithms (CCBE) can prolong the network lifetime and energy efficiency. CCBE is based on clustering the nodes to different hexagonal structures. A hexagonal cluster consists of cluster members (CMs) and a cluster head (CH). The CHs are selected from the CMs based on nodes near the optimal CH distance and the residual energy of the nodes. Additionally, the optimal CH distance that links to optimal energy consumption is derived. To balance the energy consumption and the traffic load in the network, the CHs are rotated among all CMs. In WSNs, energy is mostly consumed during transmission and reception. Transmission collisions can further decrease the energy efficiency. These collisions can be avoided by using a contention-free protocol during the transmission period. Additionally, the CH allocates slots to the CMs based on their residual energy to increase sleep time. Furthermore, the energy consumption of CH can be further reduced by data aggregation. In this paper, we propose a data aggregation level based on the residual energy of CH and a cost-aware decision scheme for the fusion of data. Performance results show that the CCBE scheme performs better in terms of network lifetime, energy consumption and throughput compared to low-energy adaptive clustering hierarchy (LEACH) and hybrid energy-efficient distributed clustering (HEED).

  12. Cross-Layer Cluster-Based Energy-Efficient Protocol for Wireless Sensor Networks

    PubMed Central

    Mammu, Aboobeker Sidhik Koyamparambil; Hernandez-Jayo, Unai; Sainz, Nekane; de la Iglesia, Idoia

    2015-01-01

    Recent developments in electronics and wireless communications have enabled the improvement of low-power and low-cost wireless sensors networks (WSNs). One of the most important challenges in WSNs is to increase the network lifetime due to the limited energy capacity of the network nodes. Another major challenge in WSNs is the hot spots that emerge as locations under heavy traffic load. Nodes in such areas quickly drain energy resources, leading to disconnection in network services. In such an environment, cross-layer cluster-based energy-efficient algorithms (CCBE) can prolong the network lifetime and energy efficiency. CCBE is based on clustering the nodes to different hexagonal structures. A hexagonal cluster consists of cluster members (CMs) and a cluster head (CH). The CHs are selected from the CMs based on nodes near the optimal CH distance and the residual energy of the nodes. Additionally, the optimal CH distance that links to optimal energy consumption is derived. To balance the energy consumption and the traffic load in the network, the CHs are rotated among all CMs. In WSNs, energy is mostly consumed during transmission and reception. Transmission collisions can further decrease the energy efficiency. These collisions can be avoided by using a contention-free protocol during the transmission period. Additionally, the CH allocates slots to the CMs based on their residual energy to increase sleep time. Furthermore, the energy consumption of CH can be further reduced by data aggregation. In this paper, we propose a data aggregation level based on the residual energy of CH and a cost-aware decision scheme for the fusion of data. Performance results show that the CCBE scheme performs better in terms of network lifetime, energy consumption and throughput compared to low-energy adaptive clustering hierarchy (LEACH) and hybrid energy-efficient distributed clustering (HEED). PMID:25860073

  13. A Hybrid Constructive Algorithm for Single-Layer Feedforward Networks Learning.

    PubMed

    Wu, Xing; Rózycki, Paweł; Wilamowski, Bogdan M

    2015-08-01

    Single-layer feedforward networks (SLFNs) have been proven to be a universal approximator when all the parameters are allowed to be adjustable. It is widely used in classification and regression problems. The SLFN learning involves two tasks: determining network size and training the parameters. Most current algorithms could not be satisfactory to both sides. Some algorithms focused on construction and only tuned part of the parameters, which may not be able to achieve a compact network. Other gradient-based optimization algorithms focused on parameters tuning while the network size has to be preset by the user. Therefore, trial-and-error approach has to be used to search the optimal network size. Because results of each trial cannot be reused in another trial, it costs much computation. In this paper, a hybrid constructive (HC)algorithm is proposed for SLFN learning, which can train all the parameters and determine the network size simultaneously. At first, by combining Levenberg-Marquardt algorithm and least-square method, a hybrid algorithm is presented for training SLFN with fixed network size. Then,with the hybrid algorithm, an incremental constructive scheme is proposed. A new randomly initialized neuron is added each time when the training entrapped into local minima. Because the training continued on previous results after adding new neurons, the proposed HC algorithm works efficiently. Several practical problems were given for comparison with other popular algorithms. The experimental results demonstrated that the HC algorithm worked more efficiently than those optimization methods with trial and error, and could achieve much more compact SLFN than those construction algorithms.

  14. Two-layer tree-connected feed-forward neural network model for neural cryptography

    NASA Astrophysics Data System (ADS)

    Lei, Xinyu; Liao, Xiaofeng; Chen, Fei; Huang, Tingwen

    2013-03-01

    Neural synchronization by means of mutual learning provides an avenue to design public key exchange protocols, bringing about what is known as neural cryptography. Two identically structured neural networks learn from each other and reach full synchronization eventually. The full synchronization enables two networks to have the same weight, which can be used as a secret key for many subsequent cryptographic purposes. It is striking to observe that after the first decade of neural cryptography, the tree parity machine (TPM) network with hidden unit K=3 appears to be the sole network that is suitable for a neural protocol. No convincingly secure neural protocol is well designed by using other network structures despite considerable research efforts. With the goal of overcoming the limitations of a suitable network structure, in this paper we develop a two-layer tree-connected feed-forward neural network (TTFNN) model for a neural protocol. The TTFNN model captures the notion that two partners are capable of exchanging a vector with multiple bits in each time step. An in-depth study of the dynamic process of TTFNN-based protocols is then undertaken, based upon which a feasible condition is theoretically obtained to seek applicable protocols. Afterward, according to two analytically derived heuristic rules, a complete methodology for designing feasible TTFNN-based protocols is elaborated. A variety of feasible neural protocols are constructed, which exhibit the effectiveness and benefits of the proposed model. With another look from the perspective of application, TTFNN-based instances, which can outperform the conventional TPM-based protocol with respect to synchronization speed, are also experimentally confirmed.

  15. Collision avoidance in TV white spaces: a cross-layer design approach for cognitive radio networks

    NASA Astrophysics Data System (ADS)

    Foukalas, Fotis; Karetsos, George T.

    2015-07-01

    One of the most promising applications of cognitive radio networks (CRNs) is the efficient exploitation of TV white spaces (TVWSs) for enhancing the performance of wireless networks. In this paper, we propose a cross-layer design (CLD) of carrier sense multiple access with collision avoidance (CSMA/CA) mechanism at the medium access control (MAC) layer with spectrum sensing (SpSe) at the physical layer, for identifying the occupancy status of TV bands. The proposed CLD relies on a Markov chain model with a state pair containing both the SpSe and the CSMA/CA from which we derive the collision probability and the achievable throughput. Analytical and simulation results are obtained for different collision avoidance and SpSe implementation scenarios by varying the contention window, back off stage and probability of detection. The obtained results depict the achievable throughput under different collision avoidance and SpSe implementation scenarios indicating thereby the performance of collision avoidance in TVWSs-based CRNs.

  16. A no-go theorem for one-layer feedforward networks.

    PubMed

    Giusti, Chad; Itskov, Vladimir

    2014-11-01

    It is often hypothesized that a crucial role for recurrent connections in the brain is to constrain the set of possible response patterns, thereby shaping the neural code. This implies the existence of neural codes that cannot arise solely from feedforward processing. We set out to find such codes in the context of one-layer feedforward networks and identified a large class of combinatorial codes that indeed cannot be shaped by the feedforward architecture alone. However, these codes are difficult to distinguish from codes that share the same sets of maximal activity patterns in the presence of subtractive noise. When we coarsened the notion of combinatorial neural code to keep track of only maximal patterns, we found the surprising result that all such codes can in fact be realized by one-layer feedforward networks. This suggests that recurrent or many-layer feedforward architectures are not necessary for shaping the (coarse) combinatorial features of neural codes. In particular, it is not possible to infer a computational role for recurrent connections from the combinatorics of neural response patterns alone. Our proofs use mathematical tools from classical combinatorial topology, such as the nerve lemma and the existence of an inverse nerve. An unexpected corollary of our main result is that any prescribed (finite) homotopy type can be realized by a subset of the form [Formula: see text], where Ρ is a polyhedron.

  17. A no-go theorem for one-layer feedforward networks.

    PubMed

    Giusti, Chad; Itskov, Vladimir

    2014-11-01

    It is often hypothesized that a crucial role for recurrent connections in the brain is to constrain the set of possible response patterns, thereby shaping the neural code. This implies the existence of neural codes that cannot arise solely from feedforward processing. We set out to find such codes in the context of one-layer feedforward networks and identified a large class of combinatorial codes that indeed cannot be shaped by the feedforward architecture alone. However, these codes are difficult to distinguish from codes that share the same sets of maximal activity patterns in the presence of subtractive noise. When we coarsened the notion of combinatorial neural code to keep track of only maximal patterns, we found the surprising result that all such codes can in fact be realized by one-layer feedforward networks. This suggests that recurrent or many-layer feedforward architectures are not necessary for shaping the (coarse) combinatorial features of neural codes. In particular, it is not possible to infer a computational role for recurrent connections from the combinatorics of neural response patterns alone. Our proofs use mathematical tools from classical combinatorial topology, such as the nerve lemma and the existence of an inverse nerve. An unexpected corollary of our main result is that any prescribed (finite) homotopy type can be realized by a subset of the form [Formula: see text], where Ρ is a polyhedron. PMID:25149704

  18. Linking two distinct layered networks of nanosized {Ln18} and {Cu24} wheels through isonicotinate ligands.

    PubMed

    Cheng, Jian-Wen; Zhang, Jie; Zheng, Shou-Tian; Yang, Guo-Yu

    2008-01-01

    A new series of heterolanthanide(III)-copper(I) wheel-cluster complexes [Ln6(micro3-O)2](IN)18-[Cu8(micro4-I)2(micro2-I)3].H3O (IN=isonicotinate; Ln=Y 1, Nd 2, Dy 3, Gd 4, Sm 5, Eu 6, Tb 7) were prepared by hydrothermal reaction at low pH. X-ray crystallographic studies reveal that two unusual trinuclear [Ln3(micro3-O)] and tetranuclear [Cu4(micro4-I)] cores are successfully used as secondary building units to make two different nanosized wheels [Ln18(micro3-O)6(CO2)48](6-), {Ln18}, and [Cu24(micro4-I)6(micro2-I)12]6+, {Cu24}, with 12-rings and a diameter of 26.7 and 26.4 A, respectively. The wheels are further assembled into two-dimensional (2D) {Ln18} and {Cu24} networks, the linkages between two distinct layered networks of {Ln18} and {Cu24} wheels by IN pillars along the c axis giving a series of unprecedented three-dimensional (3D) sandwich frameworks. To our knowledge, compounds 1-7 are the first examples containing two different layered networks of nanosized Ln and transition metal (TM) wheels in wheel-cluster chemistry. The IR, UV/Vis, thermogravimetric analysis (TGA), luminescent, and magnetic properties of these complexes were also studied.

  19. A robust cross-layer metric for routing protocol in mobile wireless ad hoc networks

    NASA Astrophysics Data System (ADS)

    Mucchi, Lorenzo; Chisci, Luigi; Fabbrini, Luca; Giovannetti, Giulio

    2012-12-01

    In a mobile ad-hoc network (MANET) where Mobile Nodes (MNs) self-organize to ensure the communication over radio links, routing protocols clearly play a significant role. In future MANETs, protocols should provide routing under full mobility, power constraints, fast time-varying channels, and nodes subject to high loading. In this article, a novel robust routing protocol, named distributed X-layer fastest path (DXFP), is proposed. The protocol is based on a cross-layer metric which is robust against the time-variations of the network as far as topology (mobility), congestion of the nodes and channel quality (fading, power constraints) are concerned. All these features are integrated in a single physical cost, i.e., the network crossing time, which has to be minimized. Furthermore, several routes from source to destination are stored for a given data flow to efficiently face the disconnections which frequently occur in MANETs. It is shown that the DXFP protocol, though locally operating in a fully distributed way within the MNs, provides, for each data flow, the optimum routes according to the considered metric. The DXFP protocol has been compared with two of the most commonly used routing protocols for MANETs, i.e., dynamic source routing and ad hoc on-demand distance vector, showing significant improvements in performance and robustness.

  20. Combined bio-inspired/evolutionary computational methods in cross-layer protocol optimization for wireless ad hoc sensor networks

    NASA Astrophysics Data System (ADS)

    Hortos, William S.

    2011-06-01

    Published studies have focused on the application of one bio-inspired or evolutionary computational method to the functions of a single protocol layer in a wireless ad hoc sensor network (WSN). For example, swarm intelligence in the form of ant colony optimization (ACO), has been repeatedly considered for the routing of data/information among nodes, a network-layer function, while genetic algorithms (GAs) have been used to select transmission frequencies and power levels, physical-layer functions. Similarly, artificial immune systems (AISs) as well as trust models of quantized data reputation have been invoked for detection of network intrusions that cause anomalies in data and information; these act on the application and presentation layers. Most recently, a self-organizing scheduling scheme inspired by frog-calling behavior for reliable data transmission in wireless sensor networks, termed anti-phase synchronization, has been applied to realize collision-free transmissions between neighboring nodes, a function of the MAC layer. In a novel departure from previous work, the cross-layer approach to WSN protocol design suggests applying more than one evolutionary computational method to the functions of the appropriate layers to improve the QoS performance of the cross-layer design beyond that of one method applied to a single layer's functions. A baseline WSN protocol design, embedding GAs, anti-phase synchronization, ACO, and a trust model based on quantized data reputation at the physical, MAC, network, and application layers, respectively, is constructed. Simulation results demonstrate the synergies among the bioinspired/ evolutionary methods of the proposed baseline design improve the overall QoS performance of networks over that of a single computational method.

  1. Fabrication of chalcopyrite light-absorbing layers based on nanoparticle and nanowire networks

    NASA Astrophysics Data System (ADS)

    Ren, Yuhang; Luo, Paifeng; Gao, Bo; Cevher, Zehra; Sun, Chivin

    2013-03-01

    We report on a method of preparing chalcopyrite, CuInGaSe2 (CIGS) light-absorbing layers using low cost air stable ink based on semiconductor nanoparticle and nanowires. The nanoparticles and nanowires are prepared from metal salts such as metal chloride and acetate at room temperature without inert gas protection. A uniform and non-aggregation CIGS precursor layer is fabricated with the formation of nanoparticle and nanowire networks utilizing ultrasonic spaying technique. We obtain a high quality CIGS absorber by cleaning the residue salts and carbon agents at an increased temperature and through selenizing the pretreated CIGS precursors. Our results offer an opportunity for the low-cost deposition of chalcopyrite absorber materials at large scale with high throughput. This work was partially sponsored by Sun Harmonics Ltd. and by NYSTAR through the Photonics Center for Applied Technology at the City University of New York.

  2. Interfacial and Network Characteristics of Silicon Nanoparticle Layers Used in Printed Electronics

    NASA Astrophysics Data System (ADS)

    Männl, Ulrich; Chuvilin, Andrey; Magunje, Batsirai; Ohieku Jonah, Emmanuel; Härting, Margit; Britton, David Thomas

    2013-05-01

    In printed electronics the use of semiconducting silicon nanoparticles allows more than the simple printing of conductive materials. It gives the possibility of fabricating robust and inexpensive, active and reactive components like temperature sensors which are shown as an example. In our approach high quality silicon nanoparticles with stable, essentially oxide-free surfaces are used to replace the pigment in water-based graphic inks, which on curing have unique semiconducting properties, arising from the transport of charge through a percolation network of crystalline silicon nanoparticles. In this study scanning electron microscopy (SEM) and high-resolution transmission electron microscopy (HRTEM) were employed to investigate the mesoscale structure of the particle network and, more importantly the structure of the interface between particles. An intimate contact between lattice planes of different particles was observed, without the presence of an intervening oxide layer.

  3. Toward a complete in silico, multi-layered embryonic stem cell regulatory network

    PubMed Central

    Xu, Huilei; Schaniel, Christoph; Lemischka, Ihor R.; Ma’ayan, Avi

    2010-01-01

    Recent efforts in systematically profiling embryonic stem (ES) cells have yielded a wealth of high-throughput data. Complementarily, emerging databases and computational tools facilitate ES cell studies and further pave the way toward the in silico reconstruction of regulatory networks encompassing multiple molecular layers. Here, we briefly survey databases, algorithms, and software tools used to organize and analyze high-throughput experimental data collected to study mammalian cellular systems with a focus on ES cells. The vision of using heterogeneous data to reconstruct a complete multilayered ES cell regulatory network is discussed. This review also provides an accompanying manually extracted dataset of different types of regulatory interactions from low-throughput experimental ES cell studies available at http://amp.pharm.mssm.edu/iscmid/literature. PMID:20890967

  4. K-complex detection using multi-layer perceptrons and recurrent networks.

    PubMed

    Jansen, B H; Desai, P R

    1994-01-01

    The feasibility of using a multi-layer perceptron and Elman's recurrent network for the detection of specific waveforms (K-complexes) in electroencephalograms (EEGs), regardless of their location in the signal segment, is explored. Experiments with simulated and actual EEG data were performed. In case of the perceptron, the input consisted of the magnitude and/or phase values obtained from 10-s signal intervals, whereas the recurrent net operated on the digitized data samples directly. It was found that both nets performed well on the simulated data, but not on the actual EEG data. The reasons for the failure of both nets are discussed.

  5. Coordinated Multi-layer Multi-domain Optical Network (COMMON) for Large-Scale Science Applications (COMMON)

    SciTech Connect

    Vokkarane, Vinod

    2013-09-01

    We intend to implement a Coordinated Multi-layer Multi-domain Optical Network (COMMON) Framework for Large-scale Science Applications. In the COMMON project, specific problems to be addressed include 1) anycast/multicast/manycast request provisioning, 2) deployable OSCARS enhancements, 3) multi-layer, multi-domain quality of service (QoS), and 4) multi-layer, multidomain path survivability. In what follows, we outline the progress in the above categories (Year 1, 2, and 3 deliverables).

  6. Multi-Domain VLAN Path Signaling Method Having Tag Swapping Function for GMPLS Controlled Wide Area Layer-2 Network

    NASA Astrophysics Data System (ADS)

    Kikuta, Kou; Nishida, Masahiro; Ishii, Daisuke; Okamoto, Satoru; Yamanaka, Naoaki

    A multi-domain GMPLS layer-2 switch capable network with VLAN tag swapping is demonstrated for the first time. In this demonstration, we verify three new features, establishing path with designating VLAN IDs, swapping VLAN ID on prototype switch, and management of VLAN IDs per domain. Using those three features, carrier-class Ethernet backbone networks which supports path route designation in multi-domain network can be established.

  7. Deep Learning and Developmental Learning: Emergence of Fine-to-Coarse Conceptual Categories at Layers of Deep Belief Network.

    PubMed

    Sadeghi, Zahra

    2016-09-01

    In this paper, I investigate conceptual categories derived from developmental processing in a deep neural network. The similarity matrices of deep representation at each layer of neural network are computed and compared with their raw representation. While the clusters generated by raw representation stand at the basic level of abstraction, conceptual categories obtained from deep representation shows a bottom-up transition procedure. Results demonstrate a developmental course of learning from specific to general level of abstraction through learned layers of representations in a deep belief network. PMID:27251165

  8. Deep Learning and Developmental Learning: Emergence of Fine-to-Coarse Conceptual Categories at Layers of Deep Belief Network.

    PubMed

    Sadeghi, Zahra

    2016-09-01

    In this paper, I investigate conceptual categories derived from developmental processing in a deep neural network. The similarity matrices of deep representation at each layer of neural network are computed and compared with their raw representation. While the clusters generated by raw representation stand at the basic level of abstraction, conceptual categories obtained from deep representation shows a bottom-up transition procedure. Results demonstrate a developmental course of learning from specific to general level of abstraction through learned layers of representations in a deep belief network.

  9. Reaction Network of Layer-to-Tunnel Transition of MnO2.

    PubMed

    Li, Ye-Fei; Zhu, Sheng-Cai; Liu, Zhi-Pan

    2016-04-27

    As a model system of 2-D oxide material, layered δ-MnO2 has important applications in Li ion battery systems. δ-MnO2 is also widely utilized as a precursor to synthesize other stable structure variants in the MnO2 family, such as α-, β-, R-, and γ-phases, which are 3-D interlinked structures with different tunnels. By utilizing the stochastic surface walking (SSW) pathway sampling method, we here for the first time resolve the atomistic mechanism and the kinetics of the layer-to-tunnel transition of MnO2, that is, from δ-MnO2 to the α-, β-, and R-phases. The SSW sampling determines the lowest-energy pathway from thousands of likely pathways that connects different phases. The reaction barriers of layer-to-tunnel phase transitions are found to be low, being 0.2-0.3 eV per formula unit, which suggests a complex competing reaction network toward different tunnel phases. All the transitions initiate via a common shearing and buckling movement of the MnO2 layer that leads to the breaking of the Mn-O framework and the formation of Mn(3+) at the transition state. Important hints are thus gleaned from these lowest-energy pathways: (i) the large pore size product is unfavorable for the entropic reason; (ii) cations are effective dopants to control the kinetics and selectivity in layer-to-tunnel transitions, which in general lowers the phase transition barrier and facilitates the creation of larger tunnel size; (iii) the phase transition not only changes the electronic structure but also induces the macroscopic morphology changes due to the interfacial strain. PMID:27054525

  10. Networked Thermodynamic Boundary Layer Profiling with AERIs during the PECAN Field Campaign

    NASA Astrophysics Data System (ADS)

    Gero, P. J.; Turner, D. D.; Hackel, D.; Phillips, C.; Smith, N.; Wagner, T.

    2015-12-01

    The Plains Elevated Convection at Night (PECAN) campaign was a large-scale field experiment in the Great Plains region of the U.S. that was conducted in June-July 2015. Nocturnal storms provide the majority of the precipitation in the Great Plains, yet the initiation and evolution of nocturnal convection is not understood to the same level as daytime surface-based convection, and thus provides significant challenges for operational weather forecasters. PECAN's objectives were to study elevated nocturnal convection initiation and the lifecycle of nocturnal convection. Specific research areas that were studied were the evolution of mesoscale convective systems, the structure and evolution of nocturnal low-level jets, atmospheric bores, and elevated convection initiation. A broad range of fixed and mobile observing systems were deployed by several agencies and organizations in a domain centered around Kansas. The Atmospheric Emitted Radiance Interferometer (AERI) is a ground-based instrument that measures downwelling infrared radiance from the atmosphere. AERI observations can be used to obtain vertical profiles of tropospheric temperature and water vapor in the lowest 3 km of the troposphere, as well as measurements of the concentration of various trace gases and microphysical and optical properties of clouds and aerosols. A network of eight AERIs was deployed in the domain during PECAN, with six at fixed sites and two in mobile facilities. One of the goals of the campaign was a demonstration of the use of real-time high-temporal-resolution boundary layer profiles from the network of AERIs for characterizing the mesoscale environment and its evolution during the weather events sampled during PECAN. If successful, a future network could be implemented across CONUS and thermodynamic profiles in the boundary layer data assimilated to help improve numerical weather prediction. We present an overview of the AERI deployments, a summary of the technique used to retrieve

  11. A novel approach to ECG classification based upon two-layered HMMs in body sensor networks.

    PubMed

    Liang, Wei; Zhang, Yinlong; Tan, Jindong; Li, Yang

    2014-03-27

    This paper presents a novel approach to ECG signal filtering and classification. Unlike the traditional techniques which aim at collecting and processing the ECG signals with the patient being still, lying in bed in hospitals, our proposed algorithm is intentionally designed for monitoring and classifying the patient's ECG signals in the free-living environment. The patients are equipped with wearable ambulatory devices the whole day, which facilitates the real-time heart attack detection. In ECG preprocessing, an integral-coefficient-band-stop (ICBS) filter is applied, which omits time-consuming floating-point computations. In addition, two-layered Hidden Markov Models (HMMs) are applied to achieve ECG feature extraction and classification. The periodic ECG waveforms are segmented into ISO intervals, P subwave, QRS complex and T subwave respectively in the first HMM layer where expert-annotation assisted Baum-Welch algorithm is utilized in HMM modeling. Then the corresponding interval features are selected and applied to categorize the ECG into normal type or abnormal type (PVC, APC) in the second HMM layer. For verifying the effectiveness of our algorithm on abnormal signal detection, we have developed an ECG body sensor network (BSN) platform, whereby real-time ECG signals are collected, transmitted, displayed and the corresponding classification outcomes are deduced and shown on the BSN screen.

  12. Layer-specific potentiation of network GABAergic inhibition in the CA1 area of the hippocampus

    PubMed Central

    Colavita, Michelangelo; Terral, Geoffrey; Lemercier, Clement E.; Drago, Filippo; Marsicano, Giovanni; Massa, Federico

    2016-01-01

    One of the most important functions of GABAergic inhibition in cortical regions is the tight control of spatiotemporal activity of principal neuronal ensembles. However, electrophysiological recordings do not provide sufficient spatial information to determine the spatiotemporal properties of inhibitory plasticity. Using Voltage Sensitive Dye Imaging (VSDI) in mouse hippocampal slices, we demonstrate that GABAA-mediated field inhibitory postsynaptic potentials undergo layer-specific potentiation upon activation of metabotropic glutamate receptors (mGlu). VSDI recordings allowed detection of pharmacologically isolated GABAA-dependent hyperpolarization signals. Bath-application of the selective group-I mGlu receptor agonist, (S)-3,5-Dihydroxyphenylglycine (DHPG), induces an enhancement of the GABAergic VSDI-recorded signal, which is more or less pronounced in different hippocampal layers. This potentiation is mediated by mGlu5 and downstream activation of IP3 receptors. Our results depict network GABAergic activity in the hippocampal CA1 region and its sub-layers, showing also a novel form of inhibitory synaptic plasticity tightly coupled to glutamatergic activity. PMID:27345695

  13. A new Jacobian matrix for optimal learning of single-layer neural networks.

    PubMed

    Peng, Jian Xun; Li, Kang; Irwin, George W

    2008-01-01

    This paper investigates the learning of a wide class of single-hidden-layer feedforward neural networks (SLFNs) with two sets of adjustable parameters, i.e., the nonlinear parameters in the hidden nodes and the linear output weights. The main objective is to both speed up the convergence of second-order learning algorithms such as Levenberg-Marquardt (LM), as well as to improve the network performance. This is achieved here by reducing the dimension of the solution space and by introducing a new Jacobian matrix. Unlike conventional supervised learning methods which optimize these two sets of parameters simultaneously, the linear output weights are first converted into dependent parameters, thereby removing the need for their explicit computation. Consequently, the neural network (NN) learning is performed over a solution space of reduced dimension. A new Jacobian matrix is then proposed for use with the popular second-order learning methods in order to achieve a more accurate approximation of the cost function. The efficacy of the proposed method is shown through an analysis of the computational complexity and by presenting simulation results from four different examples. PMID:18269943

  14. Growth of high quality GaN layer on carbon nanotube-graphene network structure as intermediate layer

    NASA Astrophysics Data System (ADS)

    Seo, Taeo Hoon; Park, Ah Hyun; Park, Sungchan; Kim, Myung Jong; Suh, Eun-Kyung

    2015-03-01

    In general, high-quality GaN layers are synthesized on low-temperature (LT) GaN buffer layer on a single crystal sapphire substrate. However, large differences in fundamental properties such as lattice constants and thermal expansion coefficients between GaN layer and sapphire substrate generate high density of threading dislocation (TD) that leads to deterioration of optical and structural properties. Graphene has been attracting much attention due to its excellent physical properties However, direct epitaxial growth of GaN film onto graphene layer on substrates is not easily accessible due to the lack of chemical reactivity on graphene which consisted of C-C bond of sp2 hexagonally arranged carbon atoms with no dangling bonds. In this work, an intermediate layer for the GaN growth on sapphire substrate was constructed by inserting carbon nanotubes and graphene hybrid structure (CGH) Optical and structural properties of GaN layer grown on CGH were compared with those of GaN layer directly grown on sapphire CNTs act as nucleation sites and play a crucial role in the growth of single crystal high-quality GaN on graphene layer. Also, graphene film acts as a mask for epitaxial lateral overgrowth of GaN layer, which can effectively reduce TD density. A grant from the Korea Institute of Science and Technology (KIST) institutional program.

  15. Layers

    NASA Astrophysics Data System (ADS)

    Hong, K. J.; Jeong, T. S.; Youn, C. J.

    2014-09-01

    The temperature-dependent photoresponse characteristics of MnAl2S4 layers have been investigated, for the first time, by use of photocurrent (PC) spectroscopy. Three peaks were observed at all temperatures. The electronic origin of these peaks was associated with band-to-band transitions from the valence-band states Γ4( z), Γ5( x), and Γ5( y) to the conduction-band state Γ1( s). On the basis of the relationship between PC-peak energy and temperature, the optical band gap could be well expressed by the expression E g( T) = E g(0) - 2.80 × 10-4 T 2/(287 + T), where E g(0) was estimated to be 3.7920 eV, 3.7955 eV, and 3.8354 eV for the valence-band states Γ4( z), Γ5( x), and Γ5( y), respectively. Results from PC spectroscopy revealed the crystal-field and spin-orbit splitting were 3.5 meV and 39.9 meV. The gradual decrease of PC intensity with decreasing temperature can be explained on the basis of trapping centers associated with native defects in the MnAl2S4 layers. Plots of log J ph, the PC current density, against 1/ T, revealed a dominant trap level in the high-temperature region. By comparing PC and the Hall effect results, we confirmed that this trap level is a shallow donor 18.9 meV below the conduction band.

  16. Cross-layer protocols optimized for real-time multimedia services in energy-constrained mobile ad hoc networks

    NASA Astrophysics Data System (ADS)

    Hortos, William S.

    2003-07-01

    Mobile ad hoc networking (MANET) supports self-organizing, mobile infrastructures and enables an autonomous network of mobile nodes that can operate without a wired backbone. Ad hoc networks are characterized by multihop, wireless connectivity via packet radios and by the need for efficient dynamic protocols. All routers are mobile and can establish connectivity with other nodes only when they are within transmission range. Importantly, ad hoc wireless nodes are resource-constrained, having limited processing, memory, and battery capacity. Delivery of high quality-ofservice (QoS), real-time multimedia services from Internet-based applications over a MANET is a challenge not yet achieved by proposed Internet Engineering Task Force (IETF) ad hoc network protocols in terms of standard performance metrics such as end-to-end throughput, packet error rate, and delay. In the distributed operations of route discovery and maintenance, strong interaction occurs across MANET protocol layers, in particular, the physical, media access control (MAC), network, and application layers. The QoS requirements are specified for the service classes by the application layer. The cross-layer design must also satisfy the battery-limited energy constraints, by minimizing the distributed power consumption at the nodes and of selected routes. Interactions across the layers are modeled in terms of the set of concatenated design parameters including associated energy costs. Functional dependencies of the QoS metrics are described in terms of the concatenated control parameters. New cross-layer designs are sought that optimize layer interdependencies to achieve the "best" QoS available in an energy-constrained, time-varying network. The protocol design, based on a reactive MANET protocol, adapts the provisioned QoS to dynamic network conditions and residual energy capacities. The cross-layer optimization is based on stochastic dynamic programming conditions derived from time-dependent models of

  17. Photonic layer security in fiber-optic networks and optical OFDM transmission

    NASA Astrophysics Data System (ADS)

    Wang, Zhenxing

    Currently the Internet is experiencing an explosive growth in the world. Such growth leads to an increased data transmission rate demand in fiber-optical networks. Optical orthogonal frequency multiplexing (OFDM) is considered as a promising solution to achieve data rate beyond 100Gb/s per wavelength channel. In the meanwhile, because of extensive data transmission and sharing, data security has become an important problem and receives considerable attention in current research literature. This thesis focuses on data security issues at the physical layer of optical networks involving code-division multiple access (CDMA) systems and steganography methods. The thesis also covers several implementation issues in optical OFDM transmission. Optical CDMA is regarded as a good candidate to provide photonic layer security in multi-access channels. In this thesis we provide a systematic analysis of the security performance of incoherent optical CDMA codes. Based on the analysis, we proposed and experimentally demonstrated several methods to improve the security performance of the optical CDMA systems, such as applying all-optical encryption, and code hopping using nonlinear wavelength conversion. Moreover, we demonstrate that the use of wireless CDMA codes in optical systems can enhance the security in one single-user end-to-end optical channel. Optical steganography is another method to provide photonic data security and involves hiding the existence of data transmissions. In the thesis, we demonstrate that an optical steganography channel can exist in phase modulated public channels as well as traditional on-off-keying (OOK) modulated channels, without data synchronization. We also demonstrate an optical steganography system with enhanced security by utilizing temporal phase modulation techniques. Additionally, as one type of an overlay channel, the optical steganography technology can carry the sensor data collected by wireless sensor network on top of public optical

  18. Scratching the Niche That Controls C. elegans Germline Stem Cells

    PubMed Central

    Byrd, Dana T.; Kimble, Judith

    2010-01-01

    The C. elegans gonad provides a well-defined model for a stem cell niche and its control of self-renewal and differentiation. The distal tip cell (DTC) forms a mesenchymal niche that controls germline stem cells (GSCs), both to generate the germline tissue during development and to maintain it during adulthood. The DTC uses GLP-1/Notch signaling to regulate GSCs; germ cells respond to Notch signaling with a network of RNA regulators to control the decision between self-renewal and entry into the meiotic cell cycle. PMID:19765664

  19. Adaptive MAC-layer protocol for multiservice digital access via tree and branch communication networks

    NASA Astrophysics Data System (ADS)

    Kotikalapudi, Sriram; Li, Chia-Chang; Magill, Peter D.; Whitaker, Norman A.; Dail, James E.; Dajer, Miguel A.; Siller, Curtis A., Jr.

    1995-11-01

    Described here is an adaptive MAC-layer protocol that supports multiservice (STM and ATM) applications in the context of subscriber access to tree and branch (e.g., fiber-coaxial cable) networks. The protocol adapts to changing demands for a mix of circuit and cell mode applications, and efficiently allocates upstream and downstream bandwidth to a variety of bursty and isochronous traffic sources. In the case of a hybrid fiber-coaxial (HFC) network the protocol resides in customer premises equipment and a common head-end controller. A medium-access control (MAC) processor provides for dividing the time domain for a given digital bitstream into successive frames, each with multiple STM and ATM time slots. Within the STM region of a frame, variable length time slots are allocated to calls (e.g., telephony, video telephony) requiring different amounts of bandwidth. A contention access signaling channel is also provided in this region for call control and set-up requests. Within the ATM region fixed-length time slots accommodate one individual ATM cell. These ATM time slots may be reserved for a user for the duration of a call or burst of successive ATM cells, or shared via a contention process. At least one contention time slot is available for signaling messages related to ATM call control and set-up requests. Further, the fixed-length ATM time slots may be reserved by a user for the duration of a call, or shared through a contention process. This paper describes the MAC-layer protocol, its relation to circuit- and ATM- amenable applications, and its performance with respect to signaling throughput and latency, and bandwidth efficiency for several service scenarios.

  20. Layered decomposition for the model order reduction of timescale separated biochemical reaction networks.

    PubMed

    Prescott, Thomas P; Papachristodoulou, Antonis

    2014-09-01

    Biochemical reaction networks tend to exhibit behaviour on more than one timescale and they are inevitably modelled by stiff systems of ordinary differential equations. Singular perturbation is a well-established method for approximating stiff systems at a given timescale. Standard applications of singular perturbation partition the state variable into fast and slow modules and assume a quasi-steady state behaviour in the fast module. In biochemical reaction networks, many reactants may take part in both fast and slow reactions; it is not necessarily the case that the reactants themselves are fast or slow. Transformations of the state space are often required in order to create fast and slow modules, which thus no longer model the original species concentrations. This paper introduces a layered decomposition, which is a natural choice when reaction speeds are separated in scale. The new framework ensures that model reduction can be carried out without seeking state space transformations, and that the effect of the fast dynamics on the slow timescale can be described directly in terms of the original species.

  1. Fuzzy Logic based Handoff Latency Reduction Mechanism in Layer 2 of Heterogeneous Mobile IPv6 Networks

    NASA Astrophysics Data System (ADS)

    Anwar, Farhat; Masud, Mosharrof H.; Latif, Suhaimi A.

    2013-12-01

    Mobile IPv6 (MIPv6) is one of the pioneer standards that support mobility in IPv6 environment. It has been designed to support different types of technologies for providing seamless communications in next generation network. However, MIPv6 and subsequent standards have some limitations due to its handoff latency. In this paper, a fuzzy logic based mechanism is proposed to reduce the handoff latency of MIPv6 for Layer 2 (L2) by scanning the Access Points (APs) while the Mobile Node (MN) is moving among different APs. Handoff latency occurs when the MN switches from one AP to another in L2. Heterogeneous network is considered in this research in order to reduce the delays in L2. Received Signal Strength Indicator (RSSI) and velocity of the MN are considered as the input of fuzzy logic technique. This technique helps the MN to measure optimum signal quality from APs for the speedy mobile node based on fuzzy logic input rules and makes a list of interfaces. A suitable interface from the list of available interfaces can be selected like WiFi, WiMAX or GSM. Simulation results show 55% handoff latency reduction and 50% packet loss improvement in L2 compared to standard to MIPv6.

  2. A design philosophy for multi-layer neural networks with applications to robot control

    NASA Technical Reports Server (NTRS)

    Vadiee, Nader; Jamshidi, MO

    1989-01-01

    A system is proposed which receives input information from many sensors that may have diverse scaling, dimension, and data representations. The proposed system tolerates sensory information with faults. The proposed self-adaptive processing technique has great promise in integrating the techniques of artificial intelligence and neural networks in an attempt to build a more intelligent computing environment. The proposed architecture can provide a detailed decision tree based on the input information, information stored in a long-term memory, and the adapted rule-based knowledge. A mathematical model for analysis will be obtained to validate the cited hypotheses. An extensive software program will be developed to simulate a typical example of pattern recognition problem. It is shown that the proposed model displays attention, expectation, spatio-temporal, and predictory behavior which are specific to the human brain. The anticipated results of this research project are: (1) creation of a new dynamic neural network structure, and (2) applications to and comparison with conventional multi-layer neural network structures. The anticipated benefits from this research are vast. The model can be used in a neuro-computer architecture as a building block which can perform complicated, nonlinear, time-varying mapping from a multitude of input excitory classes to an output or decision environment. It can be used for coordinating different sensory inputs and past experience of a dynamic system and actuating signals. The commercial applications of this project can be the creation of a special-purpose neuro-computer hardware which can be used in spatio-temporal pattern recognitions in such areas as air defense systems, e.g., target tracking, and recognition. Potential robotics-related applications are trajectory planning, inverse dynamics computations, hierarchical control, task-oriented control, and collision avoidance.

  3. Mimicking Neural Stem Cell Niche by Biocompatible Substrates

    PubMed Central

    Regalado-Santiago, Citlalli; Juárez-Aguilar, Enrique; Olivares-Hernández, Juan David; Tamariz, Elisa

    2016-01-01

    Neural stem cells (NSCs) participate in the maintenance, repair, and regeneration of the central nervous system. During development, the primary NSCs are distributed along the ventricular zone of the neural tube, while, in adults, NSCs are mainly restricted to the subependymal layer of the subventricular zone of the lateral ventricles and the subgranular zone of the dentate gyrus in the hippocampus. The circumscribed areas where the NSCs are located contain the secreted proteins and extracellular matrix components that conform their niche. The interplay among the niche elements and NSCs determines the balance between stemness and differentiation, quiescence, and proliferation. The understanding of niche characteristics and how they regulate NSCs activity is critical to building in vitro models that include the relevant components of the in vivo niche and to developing neuroregenerative approaches that consider the extracellular environment of NSCs. This review aims to examine both the current knowledge on neurogenic niche and how it is being used to develop biocompatible substrates for the in vitro and in vivo mimicking of extracellular NSCs conditions. PMID:26880934

  4. Ecological niche of Legionella pneumophila

    SciTech Connect

    Fliermans, C.B.

    1983-01-01

    This paper discusses the ecological niches, relationships and controls of Legionella derived from environmental sources. Only as clinical cases and studies relate directly to the ecological understanding of the bacterium will they be discussed. This review seeks to separate the ecological parameters associated with Legionella that are often incorporated into the medical literature as well as to highlight specific ecological studies. A series of ecological studies demonstrates the niches of Legionella, the ecological parameters that allow the bacterium to survive, grow and to be disseminated. Relationships among given habitats are explored along with biological relationships within a given habitat.

  5. A one-layer recurrent neural network with a discontinuous hard-limiting activation function for quadratic programming.

    PubMed

    Liu, Q; Wang, J

    2008-04-01

    In this paper, a one-layer recurrent neural network with a discontinuous hard-limiting activation function is proposed for quadratic programming. This neural network is capable of solving a large class of quadratic programming problems. The state variables of the neural network are proven to be globally stable and the output variables are proven to be convergent to optimal solutions as long as the objective function is strictly convex on a set defined by the equality constraints. In addition, a sequential quadratic programming approach based on the proposed recurrent neural network is developed for general nonlinear programming. Simulation results on numerical examples and support vector machine (SVM) learning show the effectiveness and performance of the neural network.

  6. Latitudinal Variations Of The F3 Layer Observed From The SEALION Ionosonde Network

    NASA Astrophysics Data System (ADS)

    Uemoto, J.; Ono, T.; Maruyama, T.; Saito, S.; Iizima, M.; Kumamoto, A.

    2006-12-01

    [INTRODUCTION] The occurrence probability, local time, solar and magnetic activity dependences of the F3 layer have been clarified experimentally from ionosonde observations as well as model calculation, whereas some unexplained problems have remained; It has been reported that the F3 layer was frequently obrved in June solstice season at Fortaleza in Brazil (geographic latitude -4 deg, geographic longitude 322 deg, and dip latitude -5.4 deg) though in this season (local winter season), frequently occurrences of the F3 layer were not predicted from the model calculation with normal values of the E x B drift and meridional neutral wind and seasonal dependence of occurrences at Waltair (17.7 deg, 83.3 deg, 11.5 deg) shows a different tendency from that at Fortaleza. The latter problem seems to result from geographic control or differences of dip latitude between two observation locations, however, its physical mechanism has not been clarified. Then conjugate observations in a magnetic meridional plane are needed. For the purpose of clarifying the mechanism of the F3 layer in more detail, we are analyzing the ionosonde data of the South East Asian Low-latitude IOnosonde Network [SEALION] mainly provided by NiCT which consists of 4 ionosonde stations. In this study, we analyzed ionosonde data observed at Chiang Mai (CMU [18.8 deg, 98.9 deg, 13.0 deg]), Chumphon(CPN [10.7 deg, 99.4 deg, 3.3 deg]) and Kototabang (KTB [-0.2 deg, 100.3 deg, -10.0 deg]). [ANALYSIS] As a result from analyzing ionosonde data on 31st March, 2005, following dip latitudinal differences have been found; At CPN, in the vicinity of the dip equator, the F3 layer moved upward rapidly and disappeared in earlier local time, while at CMU and KTB, in the low dip latitude region, the F3 layer stayed at almost the same altitude and remained to be detectable with longer time duration. [CONCLUSION] From comparing between observation results and the model calculation, it is suggested that such a dip

  7. Exosomes as Novel Regulators of Adult Neurogenic Niches.

    PubMed

    Bátiz, Luis Federico; Castro, Maite A; Burgos, Patricia V; Velásquez, Zahady D; Muñoz, Rosa I; Lafourcade, Carlos A; Troncoso-Escudero, Paulina; Wyneken, Ursula

    2015-01-01

    Adult neurogenesis has been convincingly demonstrated in two regions of the mammalian brain: the sub-granular zone (SGZ) of the dentate gyrus (DG) in the hippocampus, and the sub-ventricular zone (SVZ) of the lateral ventricles (LV). SGZ newborn neurons are destined to the granular cell layer (GCL) of the DG, while new neurons from the SVZ neurons migrate rostrally into the olfactory bulb (OB). The process of adult neurogenesis persists throughout life and is supported by a pool of neural stem cells (NSCs), which reside in a unique and specialized microenvironment known as "neurogenic niche". Neurogenic niches are structured by a complex organization of different cell types, including the NSC-neuron lineage, glial cells and vascular cells. Thus, cell-to-cell communication plays a key role in the dynamic modulation of homeostasis and plasticity of the adult neurogenic process. Specific cell-cell contacts and extracellular signals originated locally provide the necessary support and regulate the balance between self-renewal and differentiation of NSCs. Furthermore, extracellular signals originated at distant locations, including other brain regions or systemic organs, may reach the niche through the cerebrospinal fluid (CSF) or the vasculature and influence its nature. The role of several secreted molecules, such as cytokines, growth factors, neurotransmitters, and hormones, in the biology of adult NSCs, has been systematically addressed. Interestingly, in addition to these well-recognized signals, a novel type of intercellular messengers has been identified recently: the extracellular vesicles (EVs). EVs, and particularly exosomes, are implicated in the transfer of mRNAs, microRNAs (miRNAs), proteins and lipids between cells and thus are able to modify the function of recipient cells. Exosomes appear to play a significant role in different stem cell niches such as the mesenchymal stem cell niche, cancer stem cell niche and pre-metastatic niche; however, their roles

  8. Magnitude-recurrence statistics for stratabound fracture networks in layered media

    NASA Astrophysics Data System (ADS)

    Eaton, David; Davidsen, Joern

    2014-05-01

    Variants of the Gutenberg-Richter (G-R) relation, which express scale-independent behavior of earthquakes over a range of values, are almost universally used to describe magnitude-recurrence statistics for microseismic observations. The b value, which is the slope derived from classic G-R plots, is a particularly important parameter that effectively measures the abundance of large-magnitude events relative to small events. Hydraulic fracture monitoring programs often yield apparent b values of 2.0 or greater. These values are exceptionally high compared to earthquake fault sysems, which typically exhibit b values close to 1.0. In some reports, a sudden reduction in b value during treatment has been attributed to unintended activation of a pre-existing fault. An alternative model is developed here to describe magnitude statistics of microseismic events that occur on steeply dipping to vertical fracture surfaces in horizontally layered media. Termination of fractures at mechanical layer boundaries imposes a size-dependent scaling relationship and results in a stratabound fracture networks, which are well described in a number of field studies. In the case of constant stress drop, microseismic magnitude distributions will mimic bed-thickness distributions under these circumstances. A lognormal distribution of mechanical bed thickness, which provides a good fit for three examples considered here from various parts of North America, leads asymptotically to a Gaussian distribution of microseismic magnitudes that readily explains apparent observed b values of close to 2.0. This model is consistent with a sudden reduction in b value arising from uninended triggering of a pre-existing fault, and also implies that subtle changes in b value during a treatment program may be indicative of spatial variations in reservoir facies.

  9. Foundations of implementing the competitive layer model by Lotka-Volterra recurrent neural networks.

    PubMed

    Yi, Zhang

    2010-03-01

    The competitive layer model (CLM) can be described by an optimization problem. The problem can be further formulated by an energy function, called the CLM energy function, in the subspace of nonnegative orthant. The set of minimum points of the CLM energy function forms the set of solutions of the CLM problem. Solving the CLM problem means to find out such solutions. Recurrent neural networks (RNNs) can be used to implement the CLM to solve the CLM problem. The key point is to make the set of minimum points of the CLM energy function just correspond to the set of stable attractors of the recurrent neural networks. This paper proposes to use Lotka-Volterra RNNs (LV RNNs) to implement the CLM. The contribution of this paper is to establish foundations of implementing the CLM by LV RNNs. The contribution mainly contains three parts. The first part is on the CLM energy function. Necessary and sufficient conditions for minimum points of the CLM energy function are established by detailed study. The second part is on the convergence of the proposed model of the LV RNNs. It is proven that interesting trajectories are convergent. The third part is the most important. It proves that the set of stable attractors of the proposed LV RNN just equals the set of minimum points of the CLM energy function in the nonnegative orthant. Thus, the LV RNNs can be used to solve the problem of the CLM. It is believed that by establishing such basic rigorous theories, more and interesting applications of the CLM can be found.

  10. A NICHE FOR ISOTOPIC ECOLOGY

    EPA Science Inventory

    Fifty years ago, GE Hutchinson defined the ecological niche as a hypervolume in n-dimensional space with environmental variables as axes. Ecologists have recently developed renewed interest in the concept, and technological advances now allow us to use stable isotope analyses to ...

  11. Storage capacity and learning algorithms for two-layer neural networks

    NASA Astrophysics Data System (ADS)

    Engel, A.; Köhler, H. M.; Tschepke, F.; Vollmayr, H.; Zippelius, A.

    1992-05-01

    A two-layer feedforward network of McCulloch-Pitts neurons with N inputs and K hidden units is analyzed for N-->∞ and K finite with respect to its ability to implement p=αN random input-output relations. Special emphasis is put on the case where all hidden units are coupled to the output with the same strength (committee machine) and the receptive fields of the hidden units either enclose all input units (fully connected) or are nonoverlapping (tree structure). The storage capacity is determined generalizing Gardner's treatment [J. Phys. A 21, 257 (1988); Europhys. Lett. 4, 481 (1987)] of the single-layer perceptron. For the treelike architecture, a replica-symmetric calculation yields αc~ √K for a large number K of hidden units. This result violates an upper bound derived by Mitchison and Durbin [Biol. Cybern. 60, 345 (1989)]. One-step replica-symmetry breaking gives lower values of αc. In the fully connected committee machine there are in general correlations among different hidden units. As the limit of capacity is approached, the hidden units are anticorrelated: One hidden unit attempts to learn those patterns which have not been learned by the others. These correlations decrease as 1/K, so that for K-->∞ the capacity per synapse is the same as for the tree architecture, whereas for small K we find a considerable enhancement for the storage per synapse. Numerical simulations were performed to explicitly construct solutions for the tree as well as the fully connected architecture. A learning algorithm is suggested. It is based on the least-action algorithm, which is modified to take advantage of the two-layer structure. The numerical simulations yield capacities p that are slightly more than twice the number of degrees of freedom, while the fully connected net can store relatively more patterns than the tree. Various generalizations are discussed. Variable weights from hidden to output give the same results for the storage capacity as does the committee

  12. Cross-layer protocol design for QoS optimization in real-time wireless sensor networks

    NASA Astrophysics Data System (ADS)

    Hortos, William S.

    2010-04-01

    The metrics of quality of service (QoS) for each sensor type in a wireless sensor network can be associated with metrics for multimedia that describe the quality of fused information, e.g., throughput, delay, jitter, packet error rate, information correlation, etc. These QoS metrics are typically set at the highest, or application, layer of the protocol stack to ensure that performance requirements for each type of sensor data are satisfied. Application-layer metrics, in turn, depend on the support of the lower protocol layers: session, transport, network, data link (MAC), and physical. The dependencies of the QoS metrics on the performance of the higher layers of the Open System Interconnection (OSI) reference model of the WSN protocol, together with that of the lower three layers, are the basis for a comprehensive approach to QoS optimization for multiple sensor types in a general WSN model. The cross-layer design accounts for the distributed power consumption along energy-constrained routes and their constituent nodes. Following the author's previous work, the cross-layer interactions in the WSN protocol are represented by a set of concatenated protocol parameters and enabling resource levels. The "best" cross-layer designs to achieve optimal QoS are established by applying the general theory of martingale representations to the parameterized multivariate point processes (MVPPs) for discrete random events occurring in the WSN. Adaptive control of network behavior through the cross-layer design is realized through the parametric factorization of the stochastic conditional rates of the MVPPs. The cross-layer protocol parameters for optimal QoS are determined in terms of solutions to stochastic dynamic programming conditions derived from models of transient flows for heterogeneous sensor data and aggregate information over a finite time horizon. Markov state processes, embedded within the complex combinatorial history of WSN events, are more computationally

  13. Additive Routes to Action Learning: Layering Experience Shapes Engagement of the Action Observation Network

    PubMed Central

    Kirsch, Louise P.; Cross, Emily S.

    2015-01-01

    The way in which we perceive others in action is biased by one's prior experience with an observed action. For example, we can have auditory, visual, or motor experience with actions we observe others perform. How action experience via 1, 2, or all 3 of these modalities shapes action perception remains unclear. Here, we combine pre- and post-training functional magnetic resonance imaging measures with a dance training manipulation to address how building experience (from auditory to audiovisual to audiovisual plus motor) with a complex action shapes subsequent action perception. Results indicate that layering experience across these 3 modalities activates a number of sensorimotor cortical regions associated with the action observation network (AON) in such a way that the more modalities through which one experiences an action, the greater the response is within these AON regions during action perception. Moreover, a correlation between left premotor activity and participants' scores for reproducing an action suggests that the better an observer can perform an observed action, the stronger the neural response is. The findings suggest that the number of modalities through which an observer experiences an action impacts AON activity additively, and that premotor cortical activity might serve as an index of embodiment during action observation. PMID:26209850

  14. A single-layer network unsupervised feature learning method for white matter hyperintensity segmentation

    NASA Astrophysics Data System (ADS)

    Vijverberg, Koen; Ghafoorian, Mohsen; van Uden, Inge W. M.; de Leeuw, Frank-Erik; Platel, Bram; Heskes, Tom

    2016-03-01

    Cerebral small vessel disease (SVD) is a disorder frequently found among the old people and is associated with deterioration in cognitive performance, parkinsonism, motor and mood impairments. White matter hyperintensities (WMH) as well as lacunes, microbleeds and subcortical brain atrophy are part of the spectrum of image findings, related to SVD. Accurate segmentation of WMHs is important for prognosis and diagnosis of multiple neurological disorders such as MS and SVD. Almost all of the published (semi-)automated WMH detection models employ multiple complex hand-crafted features, which require in-depth domain knowledge. In this paper we propose to apply a single-layer network unsupervised feature learning (USFL) method to avoid hand-crafted features, but rather to automatically learn a more efficient set of features. Experimental results show that a computer aided detection system with a USFL system outperforms a hand-crafted approach. Moreover, since the two feature sets have complementary properties, a hybrid system that makes use of both hand-crafted and unsupervised learned features, shows a significant performance boost compared to each system separately, getting close to the performance of an independent human expert.

  15. Estimating Planetary Boundary Layer Heights from NOAA Profiler Network Wind Profiler Data

    NASA Technical Reports Server (NTRS)

    Molod, Andrea M.; Salmun, H.; Dempsey, M

    2015-01-01

    An algorithm was developed to estimate planetary boundary layer (PBL) heights from hourly archived wind profiler data from the NOAA Profiler Network (NPN) sites located throughout the central United States. Unlike previous studies, the present algorithm has been applied to a long record of publicly available wind profiler signal backscatter data. Under clear conditions, summertime averaged hourly time series of PBL heights compare well with Richardson-number based estimates at the few NPN stations with hourly temperature measurements. Comparisons with clear sky reanalysis based estimates show that the wind profiler PBL heights are lower by approximately 250-500 m. The geographical distribution of daily maximum PBL heights corresponds well with the expected distribution based on patterns of surface temperature and soil moisture. Wind profiler PBL heights were also estimated under mostly cloudy conditions, and are generally higher than both the Richardson number based and reanalysis PBL heights, resulting in a smaller clear-cloudy condition difference. The algorithm presented here was shown to provide a reliable summertime climatology of daytime hourly PBL heights throughout the central United States.

  16. A polarization-independent liquid crystal phase modulation using polymer-network liquid crystal with orthogonal alignment layers

    NASA Astrophysics Data System (ADS)

    Chen, Ming-Syuan; Lin, Wei-Chih; Tsou, Yu-Shih; Lin, Yi-Hsin

    2012-10-01

    A polarization-independent liquid crystal (LC) phase modulation using polymer-network liquid crystals with orthogonal alignments layers (T-PNLC) is demonstrated. T-PNLC consists of three layers. LC directors in the two layers near glass substrates are orthogonal to each other. In the middle layer, LC directors are perpendicular to the glass substrate. The advantages of such T-PNLC include polarizer-free, larger phase shift (~0.4π rad) than the residual phase type (<0.05π rad), and low operating voltage (< 30Vrms). It does not require bias voltage for avoiding scattering because the refractive index of liquid crystals matches that of polymers. The phase shift of T-PNLC is affected by the cell gap and the curing voltages. The potential applications are laser beam steering, spatial light modulators and electrically tunable micro-lens arrays.

  17. Self-assembled Ag nanoparticle network passivated by a nano-sized ZnO layer for transparent and flexible film heaters

    SciTech Connect

    Seo, Ki-Won; Kim, Han-Ki; Kim, Min-Yi; Chang, Hyo-Sik

    2015-12-15

    We investigated a self-assembled Ag nanoparticle network electrode passivated by a nano-sized ZnO layer for use in high-performance transparent and flexible film heaters (TFFHs). The low temperature atomic layer deposition of a nano-sized ZnO layer effectively filled the uncovered area of Ag network and improved the current spreading in the self-assembled Ag network without a change in the sheet resistance and optical transmittance as well as mechanical flexibility. The time-temperature profiles and heat distribution analysis demonstrate that the performance of the TFTH with the ZnO/Ag network is superior to that of a TFFH with Ag nanowire electrodes. In addition, the TFTHs with ZnO/Ag network exhibited better stability than the TFFH with a bare Ag network due to the effective current spreading through the nano-sized ZnO layer.

  18. Regulatory System for Stem/Progenitor Cell Niches in the Adult Rodent Pituitary

    PubMed Central

    Yoshida, Saishu; Kato, Takako; Kato, Yukio

    2016-01-01

    The anterior lobe of the pituitary gland is a master endocrine tissue composed of five types of endocrine cells. Although the turnover rate of pituitary endocrine cells is as low as about 1.6% per day, recent studies have demonstrated that Sex-determining region Y-box 2 (SOX2)+-cells exist as pituitary stem/progenitor cells in the adult anterior lobe and contribute to cell regeneration. Notably, SOX2+-pituitary stem/progenitor cells form two types of niches in this tissue: the marginal cell layer (MCL-niche) and the dense cell clusters scattering in the parenchyma (parenchymal-niche). However, little is known about the mechanisms and factors for regulating the pituitary stem/progenitor cell niches, as well as the functional differences between the two types of niches. Elucidation of the regulatory mechanisms in the niches might enable us to understand the cell regeneration system that acts in accordance with physiological demands in the adult pituitary. In this review, so as to reveal the regulatory mechanisms of the two types of niche, we summarize the regulatory factors and their roles in the adult rodent pituitary niches by focusing on three components: soluble factors, cell surface proteins and extracellular matrixes. PMID:26761002

  19. Evolution of climate niches in European mammals?

    PubMed Central

    Dormann, Carsten F.; Gruber, Bernd; Winter, Marten; Herrmann, Dirk

    2010-01-01

    Our ability to predict consequences of climate change is severely impaired by the lack of knowledge on the ability of species to adapt to changing environmental conditions. We used distribution data for 140 mammal species in Europe, together with data on climate, land cover and topography, to derive a statistical description of their realized climate niche. We then compared climate niche overlap of pairs of species, selected on the basis of phylogenetic information. In contrast to expectations, related species were not similar in their climate niche. Rather, even species pairs that had a common ancestor less than 1 Ma already display very high climate niche distances. We interpret our finding as a strong interspecific competitive constraint on the realized niche, rather than a rapid evolution of the fundamental niche. If correct, our results imply a very limited usefulness of climate niche models for the prediction of future mammal distributions. PMID:19828492

  20. Evolution of climate niches in European mammals?

    PubMed

    Dormann, Carsten F; Gruber, Bernd; Winter, Marten; Herrmann, Dirk

    2010-04-23

    Our ability to predict consequences of climate change is severely impaired by the lack of knowledge on the ability of species to adapt to changing environmental conditions. We used distribution data for 140 mammal species in Europe, together with data on climate, land cover and topography, to derive a statistical description of their realized climate niche. We then compared climate niche overlap of pairs of species, selected on the basis of phylogenetic information. In contrast to expectations, related species were not similar in their climate niche. Rather, even species pairs that had a common ancestor less than 1 Ma already display very high climate niche distances. We interpret our finding as a strong interspecific competitive constraint on the realized niche, rather than a rapid evolution of the fundamental niche. If correct, our results imply a very limited usefulness of climate niche models for the prediction of future mammal distributions.

  1. Morphological and niche divergence of pinyon pines.

    PubMed

    Ortiz-Medrano, Alejandra; Scantlebury, Daniel Patrick; Vázquez-Lobo, Alejandra; Mastretta-Yanes, Alicia; Piñero, Daniel

    2016-05-01

    The environmental variables that define a species ecological niche should be associated with the evolutionary patterns present in the adaptations that resulted from living in these conditions. Thus, when comparing across species, we can expect to find an association between phylogenetically independent phenotypic characters and ecological niche evolution. Few studies have evaluated how organismal phenotypes might mirror patterns of niche evolution if these phenotypes reflect adaptations. Doing so could contribute on the understanding of the origin and maintenance of phenotypic diversity observed in nature. Here, we show the pattern of niche evolution of the pinyon pine lineage (Pinus subsection Cembroides); then, we suggest morphological adaptations possibly related to niche divergence, and finally, we test for correlation between ecological niche and morphology. We demonstrate that niche divergence is the general pattern within the clade and that it is positively correlated with adaptation. PMID:27092235

  2. Exosomes as Novel Regulators of Adult Neurogenic Niches

    PubMed Central

    Bátiz, Luis Federico; Castro, Maite A.; Burgos, Patricia V.; Velásquez, Zahady D.; Muñoz, Rosa I.; Lafourcade, Carlos A.; Troncoso-Escudero, Paulina; Wyneken, Ursula

    2016-01-01

    Adult neurogenesis has been convincingly demonstrated in two regions of the mammalian brain: the sub-granular zone (SGZ) of the dentate gyrus (DG) in the hippocampus, and the sub-ventricular zone (SVZ) of the lateral ventricles (LV). SGZ newborn neurons are destined to the granular cell layer (GCL) of the DG, while new neurons from the SVZ neurons migrate rostrally into the olfactory bulb (OB). The process of adult neurogenesis persists throughout life and is supported by a pool of neural stem cells (NSCs), which reside in a unique and specialized microenvironment known as “neurogenic niche”. Neurogenic niches are structured by a complex organization of different cell types, including the NSC-neuron lineage, glial cells and vascular cells. Thus, cell-to-cell communication plays a key role in the dynamic modulation of homeostasis and plasticity of the adult neurogenic process. Specific cell-cell contacts and extracellular signals originated locally provide the necessary support and regulate the balance between self-renewal and differentiation of NSCs. Furthermore, extracellular signals originated at distant locations, including other brain regions or systemic organs, may reach the niche through the cerebrospinal fluid (CSF) or the vasculature and influence its nature. The role of several secreted molecules, such as cytokines, growth factors, neurotransmitters, and hormones, in the biology of adult NSCs, has been systematically addressed. Interestingly, in addition to these well-recognized signals, a novel type of intercellular messengers has been identified recently: the extracellular vesicles (EVs). EVs, and particularly exosomes, are implicated in the transfer of mRNAs, microRNAs (miRNAs), proteins and lipids between cells and thus are able to modify the function of recipient cells. Exosomes appear to play a significant role in different stem cell niches such as the mesenchymal stem cell niche, cancer stem cell niche and pre-metastatic niche; however, their

  3. Human Niche Construction and Hydrology

    NASA Astrophysics Data System (ADS)

    Ertsen, Maurits

    2014-05-01

    The poster will introduce Human Niche Construction Theory to clarify the capacity of organisms to modify their environment and thereby influence their own and other species' evolution. HNC allows building a recursive relationship between long-term human actions and landscape modification. Discussing the concept will also allow studying why we should understand societal collapse in new ways and whether policies towards sustainability will have a potential for success.

  4. Using Hybrid Algorithm to Improve Intrusion Detection in Multi Layer Feed Forward Neural Networks

    ERIC Educational Resources Information Center

    Ray, Loye Lynn

    2014-01-01

    The need for detecting malicious behavior on a computer networks continued to be important to maintaining a safe and secure environment. The purpose of this study was to determine the relationship of multilayer feed forward neural network architecture to the ability of detecting abnormal behavior in networks. This involved building, training, and…

  5. CROSS-DISCIPLINARY PHYSICS AND RELATED AREAS OF SCIENCE AND TECHNOLOGY: Mechanism for propagation of rate signals through a 10-layer feedforward neuronal network

    NASA Astrophysics Data System (ADS)

    Li, Jie; Yu, Wan-Qing; Xu, Ding; Liu, Feng; Wang, Wei

    2009-12-01

    Using numerical simulations, we explore the mechanism for propagation of rate signals through a 10-layer feedforward network composed of Hodgkin-Huxley (HH) neurons with sparse connectivity. When white noise is afferent to the input layer, neuronal firing becomes progressively more synchronous in successive layers and synchrony is well developed in deeper layers owing to the feedforward connections between neighboring layers. The synchrony ensures the successful propagation of rate signals through the network when the synaptic conductance is weak. As the synaptic time constant τsyn varies, coherence resonance is observed in the network activity due to the intrinsic property of HH neurons. This makes the output firing rate single-peaked as a function of τsyn, suggesting that the signal propagation can be modulated by the synaptic time constant. These results are consistent with experimental results and advance our understanding of how information is processed in feedforward networks.

  6. At the Edge of Chaos: How Cerebellar Granular Layer Network Dynamics Can Provide the Basis for Temporal Filters.

    PubMed

    Rössert, Christian; Dean, Paul; Porrill, John

    2015-10-01

    Models of the cerebellar microcircuit often assume that input signals from the mossy-fibers are expanded and recoded to provide a foundation from which the Purkinje cells can synthesize output filters to implement specific input-signal transformations. Details of this process are however unclear. While previous work has shown that recurrent granule cell inhibition could in principle generate a wide variety of random outputs suitable for coding signal onsets, the more general application for temporally varying signals has yet to be demonstrated. Here we show for the first time that using a mechanism very similar to reservoir computing enables random neuronal networks in the granule cell layer to provide the necessary signal separation and extension from which Purkinje cells could construct basis filters of various time-constants. The main requirement for this is that the network operates in a state of criticality close to the edge of random chaotic behavior. We further show that the lack of recurrent excitation in the granular layer as commonly required in traditional reservoir networks can be circumvented by considering other inherent granular layer features such as inverted input signals or mGluR2 inhibition of Golgi cells. Other properties that facilitate filter construction are direct mossy fiber excitation of Golgi cells, variability of synaptic weights or input signals and output-feedback via the nucleocortical pathway. Our findings are well supported by previous experimental and theoretical work and will help to bridge the gap between system-level models and detailed models of the granular layer network.

  7. How is the rate of climatic-niche evolution related to climatic-niche breadth?

    PubMed

    Fisher-Reid, M Caitlin; Kozak, Kenneth H; Wiens, John J

    2012-12-01

    The rate of climatic-niche evolution is important to many research areas in ecology, evolution, and conservation biology, including responses of species to global climate change, spread of invasive species, speciation, biogeography, and patterns of species richness. Previous studies have implied that clades with higher rates of climatic-niche evolution among species should have species with narrower niche breadths, but there is also evidence suggesting the opposite pattern. However, the relationships between rate and breadth have not been explicitly analyzed. Here, we examine the relationships between the rate of climatic-niche evolution and climatic-niche breadth using phylogenetic and climatic data for 250 species in the salamander family Plethodontidae, a group showing considerable variation in both rates of climatic-niche evolution and climatic-niche breadths. Contrary to some expectations, we find no general relationship between climatic-niche breadth and the rate of climatic-niche evolution. Climatic-niche breadths for some ecologically important climatic variables considered separately (temperature seasonality and annual precipitation) do show significant relationships with the rate of climatic-niche evolution, but rates are faster in clades in which species have broader (not narrower) niche breadths. In summary, our results show that narrower niche breadths are not necessarily associated with faster rates of niche evolution.

  8. A Performance Evaluation of NACK-Oriented Protocols as the Foundation of Reliable Delay- Tolerant Networking Convergence Layers

    NASA Technical Reports Server (NTRS)

    Iannicca, Dennis; Hylton, Alan; Ishac, Joseph

    2012-01-01

    Delay-Tolerant Networking (DTN) is an active area of research in the space communications community. DTN uses a standard layered approach with the Bundle Protocol operating on top of transport layer protocols known as convergence layers that actually transmit the data between nodes. Several different common transport layer protocols have been implemented as convergence layers in DTN implementations including User Datagram Protocol (UDP), Transmission Control Protocol (TCP), and Licklider Transmission Protocol (LTP). The purpose of this paper is to evaluate several stand-alone implementations of negative-acknowledgment based transport layer protocols to determine how they perform in a variety of different link conditions. The transport protocols chosen for this evaluation include Consultative Committee for Space Data Systems (CCSDS) File Delivery Protocol (CFDP), Licklider Transmission Protocol (LTP), NACK-Oriented Reliable Multicast (NORM), and Saratoga. The test parameters that the protocols were subjected to are characteristic of common communications links ranging from terrestrial to cis-lunar and apply different levels of delay, line rate, and error.

  9. Performance evaluation of transport layer protocols for transmitting real-time data over DiffServ networks

    NASA Astrophysics Data System (ADS)

    Noda, Yoko; Sakai, Tatsuhiko; Shigeno, Hiroshi; Matsushita, Yutaka

    2001-07-01

    In this paper, we discuss transport layer protocols to support real-time data transmission overnetworks using Differentiated Services (Diffserv) where bandwidth is guaranteed. Assuming that an application transmits streaming video data over a Diffserv network, we have performed simulation experiments to evaluate performance of real-time transmission using standard internet protocols, UDP and TCP as a transport layer protocol. The application is designed to buffer a portion of the data on the receiver before starting the playback and to operate in a streaming mode. Consequently, when packets are lost over Diffserv networks, TCP shows better performance than UDP. Simulation results show that employment of SACK option for TCP can recover lost packets efficiently and improve performance of real-time transmission. Currently, a growing number of real-time media applications over Internet are being implemented using UDP, because reliable delivery mechanism of TCP can obstruct real-time data transmission that is timing critical. However, in our experimental environment, retransmission and congestion control mechanism of TCP make use of bandwidth guaranteed by Diffserv, and help to provide more reliable delivery of real-time data than UDP without serious impacts on time-sensitive delivery. Therefore, despite of the general belief that TCP is not suitable for time-sensitive delivery, in our experiment, we show that TCP is a transport layer protocol suitable for real-time data transmission over Diffserv networks.

  10. Competition at the Wireless Sensor Network MAC Layer: Low Power Probing interfering with X-MAC

    NASA Astrophysics Data System (ADS)

    Zacharias, Sven; Newe, Thomas

    2011-08-01

    Wireless Sensor Networks (WSNs) combine sensors with computer networks and enable very dense, in-situ and live measurements of data over a large area. Since this emerging technology has the potential to be embedded almost everywhere for numberless applications, interference between different networks can become a serious issue. For most WSNs, it is assumed today that the network medium access is non-competitive. On the basis of X-MAC interfered by Low Power Probing, this paper shows the danger and the effects of different sensor networks communicating on a single wireless channel of the 2.4 GHz band, which is used by the IEEE 802.15.4 standard.

  11. Evolution of niche width and adaptive diversification.

    PubMed

    Ackermann, Martin; Doebeli, Michael

    2004-12-01

    Theoretical models suggest that resource competition can lead to the adaptive splitting of consumer populations into diverging lineages, that is, to adaptive diversification. In general, diversification is likely if consumers use only a narrow range of resources and thus have a small niche width. Here we use analytical and numerical methods to study the consequences for diversification if the niche width itself evolves. We found that the evolutionary outcome depends on the inherent costs or benefits of widening the niche. If widening the niche did not have costs in terms of overall resource uptake, then the consumer evolved a niche that was wide enough for disruptive selection on the niche position to vanish; adaptive diversification was no longer observed. However, if widening the niche was costly, then the niche widths remained relatively narrow, allowing for adaptive diversification in niche position. Adaptive diversification and speciation resulting from competition for a broadly distributed resource is thus likely if the niche width is fixed and relatively narrow or free to evolve but subject to costs. These results refine the conditions for adaptive diversification due to competition and formulate them in a way that might be more amenable for experimental investigations. PMID:15696740

  12. Diversity, dilemmas, and monopolies of niche construction.

    PubMed

    Krakauer, David C; Page, Karen M; Erwin, Douglas H

    2009-01-01

    The behavior of organisms can contribute to the transformation of their environments. When organismal impacts on the environment feed back to influence organismal density, viability, fertility, or persistence, the environment can be construed as an extension of the organism. This process of fitness-enhancing environmental transformation has been called niche construction. We focus on the relationship of niche construction with species or strain diversity and on the variability of investment in niche construction versus reproduction. We demonstrate a fundamental dilemma of niche construction, whereby the construction of a shared resource leads to a tragedy of the commons, with competition tending to eliminate niche construction strategies. The ability to monopolize a niche, either through spatial proximity or through preferential exploitation, can stabilize niche construction and promote ecological coexistence among polymorphic constructors. We consider both sympatric and allopatric origins of niche construction. Under a variety of different construction mechanisms, variability in the investment in niche construction versus reproduction suggests reproductive altruism but is fully consistent with selfish behavior. We discuss the implications of niche-construction theory on the evolution of life cycles and development, behavioral plasticity, the division of labor, and long-term macroevolutionary trends.

  13. Phylogenetic conservatism of environmental niches in mammals.

    PubMed

    Cooper, Natalie; Freckleton, Rob P; Jetz, Walter

    2011-08-01

    Phylogenetic niche conservatism is the pattern where close relatives occupy similar niches, whereas distant relatives are more dissimilar. We suggest that niche conservatism will vary across clades in relation to their characteristics. Specifically, we investigate how conservatism of environmental niches varies among mammals according to their latitude, range size, body size and specialization. We use the Brownian rate parameter, σ(2), to measure the rate of evolution in key variables related to the ecological niche and define the more conserved group as the one with the slower rate of evolution. We find that tropical, small-ranged and specialized mammals have more conserved thermal niches than temperate, large-ranged or generalized mammals. Partitioning niche conservatism into its spatial and phylogenetic components, we find that spatial effects on niche variables are generally greater than phylogenetic effects. This suggests that recent evolution and dispersal have more influence on species' niches than more distant evolutionary events. These results have implications for our understanding of the role of niche conservatism in species richness patterns and for gauging the potential for species to adapt to global change.

  14. Introducing MERGANSER: A Flexible Framework for Ecological Niche Modeling

    NASA Astrophysics Data System (ADS)

    Klawonn, M.; Dow, E. M.

    2015-12-01

    Ecological Niche Modeling (ENM) is a collection of techniques to find a "fundamental niche", the range of environmental conditions suitable for a species' survival in the absence of inter-species interactions, given a set of environmental parameters. Traditional approaches to ENM face a number of obstacles including limited data accessibility, data management problems, computational costs, interface usability, and model validation. The MERGANSER system, which stands for Modeling Ecological Residency Given A Normalized Set of Environmental Records, addresses these issues through powerful data persistence and flexible data access, coupled with a clear presentation of results and fine-tuned control over model parameters. MERGANSER leverages data measuring 72 weather related phenomena, land cover, soil type, population, species occurrence, general species information, and elevation, totaling over 1.5 TB of data. To the best of the authors' knowledge, MERGANSER uses higher-resolution spatial data sets than previously published models. Since MERGANSER stores data in an instance of Apache SOLR, layers generated in support of niche models are accessible to users via simplified Apache Lucene queries. This is made even simpler via an HTTP front end that generates Lucene queries automatically. Specifically, a user need only enter the name of a place and a species to run a model. Using this approach to synthesizing model layers, the MERGANSER system has successfully reproduced previously published niche model results with a simplified user experience. Input layers for the model are generated dynamically using OpenStreetMap and SOLR's spatial search functionality. Models are then run using either user-specified or automatically determined parameters after normalizing them into a common grid. Finally, results are visualized in the web interface, which allows for quick validation. Model results and all surrounding metadata are also accessible to the user for further study.

  15. Evolution of pollination niches and floral divergence in the generalist plant Erysimum mediohispanicum

    PubMed Central

    Gómez, J. M.; Muñoz-Pajares, A. J.; Abdelaziz, M.; Lorite, J.; Perfectti, F.

    2014-01-01

    Background and Aims How generalist plants diverge in response to pollinator selection without becoming specialized is still unknown. This study explores this question, focusing on the evolution of the pollination system in the pollination generalist Erysimum mediohispanicum (Brassicaceae). Methods Pollinator assemblages were surveyed from 2001 to 2010 in 48 geo-referenced populations covering the entire geographic distribution of E. mediohispanicum. Bipartite modularity, a complex network tool, was used to find the pollination niche of each population. Evolution of the pollination niches and the correlated evolution of floral traits and pollination niches were explored using within-species comparative analyses. Key Results Despite being generalists, the E. mediohispanicum populations studied can be classified into five pollination niches. The boundaries between niches were not sharp, the niches differing among them in the relative frequencies of the floral visitor functional groups. The absence of spatial autocorrelation and phylogenetic signal indicates that the niches were distributed in a phylogeographic mosaic. The ancestral E. mediohispanicum populations presumably belonged to the niche defined by a high number of beetle and ant visits. A correlated evolution was found between pollination niches and some floral traits, suggesting the existence of generalist pollination ecotypes. Conclusions It is conjectured that the geographic variation in pollination niches has contributed to the observed floral divergence in E. mediohispanicum. The process mediating this floral divergence presumably has been adaptive wandering, but the adaptation to the local pollinator faunas has been not universal. The outcome is a landscape where a few populations locally adapted to their pollination environment (generalist pollination ecotypes) coexist with many populations where this local adaptation has failed and where the plant phenotype is not primarily shaped by pollinators. PMID

  16. The regulatory niche of intestinal stem cells.

    PubMed

    Sailaja, Badi Sri; He, Xi C; Li, Linheng

    2016-09-01

    The niche constitutes a unique category of cells that support the microenvironment for the maintenance and self-renewal of stem cells. Intestinal stem cells reside at the base of the crypt, which contains adjacent epithelial cells, stromal cells and smooth muscle cells, and soluble and cell-associated growth and differentiation factors. We summarize here recent advances in our understanding of the crucial role of the niche in regulating stem cells. The stem cell niche maintains a balance among quiescence, proliferation and regeneration of intestinal stem cells after injury. Mesenchymal cells, Paneth cells, immune cells, endothelial cells and neural cells are important regulatory components that secrete niche ligands, growth factors and cytokines. Intestinal homeostasis is regulated by niche signalling pathways, specifically Wnt, bone morphogenetic protein, Notch and epidermal growth factor. These insights into the regulatory stem cell niche during homeostasis and post-injury regeneration offer the potential to accelerate development of therapies for intestine-related disorders.

  17. The regulatory niche of intestinal stem cells.

    PubMed

    Sailaja, Badi Sri; He, Xi C; Li, Linheng

    2016-09-01

    The niche constitutes a unique category of cells that support the microenvironment for the maintenance and self-renewal of stem cells. Intestinal stem cells reside at the base of the crypt, which contains adjacent epithelial cells, stromal cells and smooth muscle cells, and soluble and cell-associated growth and differentiation factors. We summarize here recent advances in our understanding of the crucial role of the niche in regulating stem cells. The stem cell niche maintains a balance among quiescence, proliferation and regeneration of intestinal stem cells after injury. Mesenchymal cells, Paneth cells, immune cells, endothelial cells and neural cells are important regulatory components that secrete niche ligands, growth factors and cytokines. Intestinal homeostasis is regulated by niche signalling pathways, specifically Wnt, bone morphogenetic protein, Notch and epidermal growth factor. These insights into the regulatory stem cell niche during homeostasis and post-injury regeneration offer the potential to accelerate development of therapies for intestine-related disorders. PMID:27060879

  18. Interactions between structural and chemical biomimetism in synthetic stem cell niches.

    PubMed

    Nava, Michele M; Raimondi, Manuela T; Credi, Caterina; De Marco, Carmela; Turri, Stefano; Cerullo, Giulio; Osellame, Roberto

    2015-02-01

    Advancements in understanding stem cell functions and differentiation are of key importance for the clinical success of stem-cell-based therapies. 3D structural niches fabricated by two-photon polymerization are a powerful platform for controlling stem cell growth and differentiation. In this paper, we investigate the possibility of further controlling stem cell fate by tuning the mechanical properties of such niches through coating with thin layers of biomimetic hyaluronan-based and gelatin-based hydrogels. We first assess the biocompatibility of chemical coatings and then study the interactions between structural and chemical biomimetism on the response of MSCs in terms of proliferation and differentiation. We observed a clear effect of the hydrogel coating on otherwise identical 3D scaffolds. In particular, in gelatin-coated niches we observed a stronger metabolic activity and commitment toward the osteo-chondral lineage with respect to hyaluronan-coated niches. Conversely, a reduction in the homing effect was observed in all the coated niches, especially in gelatin-coated niches. This study demonstrates the feasibility of controlling independently different mechanical cues, in bioengineered stem cell niches, i.e. the 3D scaffold geometry and the surface stiffness. This will allow, on the one hand, understanding their specific role in stem cell proliferation and differentiation and, on the other hand, finely tuning their synergistic effect. PMID:25594262

  19. Niche Applications of Irreversible Electroporation.

    PubMed

    Bhatia, Shivank S; Arya, Rahul; Narayanan, Govindarajan

    2015-09-01

    Irreversible electroporation (IRE) induces cell death by exposing it to high-voltage, low-energy DC current pulses. The mechanism of cell death and healing is a departure from the other existing technologies such as radiofrequency ablation, microwave ablation, and cryoablation. These thermal ablative technologies have several applications in oncology but have limitations that have also been established. IRE has shown promise to overcome some of these limitations and has enabled the use of an ablative technology in treating lesions close to the bile ducts and vasculature and in organs such as the pancreas. This review highlights some of the niche applications of IRE and the data so far.

  20. Niche-tracking migrants and niche-switching residents: evolution of climatic niches in New World warblers (Parulidae).

    PubMed

    Gómez, Camila; Tenorio, Elkin A; Montoya, Paola; Cadena, Carlos Daniel

    2016-02-10

    Differences in life-history traits between tropical and temperate lineages are often attributed to differences in their climatic niche dynamics. For example, the more frequent appearance of migratory behaviour in temperate-breeding species than in species originally breeding in the tropics is believed to have resulted partly from tropical climatic stability and niche conservatism constraining tropical species from shifting their ranges. However, little is known about the patterns and processes underlying climatic niche evolution in migrant and resident animals. We evaluated the evolution of overlap in climatic niches between seasons and its relationship to migratory behaviour in the Parulidae, a family of New World passerine birds. We used ordination methods to measure seasonal niche overlap and niche breadth of 54 resident and 49 migrant species and used phylogenetic comparative methods to assess patterns of climatic niche evolution. We found that despite travelling thousands of kilometres, migrants tracked climatic conditions across the year to a greater extent than tropical residents. Migrant species had wider niches than resident species, although residents as a group occupied a wider climatic space and niches of migrants and residents overlapped extensively. Neither breeding latitude nor migratory distance explained variation among species in climatic niche overlap between seasons. Our findings support the notion that tropical species have narrower niches than temperate-breeders, but does not necessarily constrain their ability to shift or expand their geographical ranges and become migratory. Overall, the tropics may have been historically less likely to experience the suite of components that generate strong selection pressures for the evolution of migratory behaviour.

  1. Niche-tracking migrants and niche-switching residents: evolution of climatic niches in New World warblers (Parulidae).

    PubMed

    Gómez, Camila; Tenorio, Elkin A; Montoya, Paola; Cadena, Carlos Daniel

    2016-02-10

    Differences in life-history traits between tropical and temperate lineages are often attributed to differences in their climatic niche dynamics. For example, the more frequent appearance of migratory behaviour in temperate-breeding species than in species originally breeding in the tropics is believed to have resulted partly from tropical climatic stability and niche conservatism constraining tropical species from shifting their ranges. However, little is known about the patterns and processes underlying climatic niche evolution in migrant and resident animals. We evaluated the evolution of overlap in climatic niches between seasons and its relationship to migratory behaviour in the Parulidae, a family of New World passerine birds. We used ordination methods to measure seasonal niche overlap and niche breadth of 54 resident and 49 migrant species and used phylogenetic comparative methods to assess patterns of climatic niche evolution. We found that despite travelling thousands of kilometres, migrants tracked climatic conditions across the year to a greater extent than tropical residents. Migrant species had wider niches than resident species, although residents as a group occupied a wider climatic space and niches of migrants and residents overlapped extensively. Neither breeding latitude nor migratory distance explained variation among species in climatic niche overlap between seasons. Our findings support the notion that tropical species have narrower niches than temperate-breeders, but does not necessarily constrain their ability to shift or expand their geographical ranges and become migratory. Overall, the tropics may have been historically less likely to experience the suite of components that generate strong selection pressures for the evolution of migratory behaviour. PMID:26865303

  2. Assessment of planetary boundary layer and residual layer heights in the Northeastern U.S. using Lidar, a network of surface observations, and the WRF-STILT model

    NASA Astrophysics Data System (ADS)

    Barrera, Y.; Nehrkorn, T.; Hegarty, J. D.; Wofsy, S. C.; Gottlieb, E.; Sargent, M. R.; Decola, P.; Jones, T.

    2015-12-01

    Simulation of the planetary boundary layer (PBL) and residual layer (RL) are key requirements for forecasting air quality in cities and detecting transboundary air pollution events. This study combines information from a network of Mini Micropulse Lidar (MPL) instruments, the CALIOP satellite, meteorological and air pollution measuring sensors, and a particle-transport model to critically test mesoscale transport models at the regional level. Aerosol backscattering measurements were continuously taken with MPL units in various locations within the Northeastern U.S., between September 2012 to August 2015. Data is analyzed using wavelet covariance transforms and image processing techniques. Initial results for the city of Boston show a PBL growth rate between approx. 150 and 300 meters per hour, in the morning to early afternoon (~12-19 UTC). The RL was present throughout the night and day at approx. 1.3 to 2.0 km. Transboundary air pollution events were detected and quantified, and variations in concentrations of greenhouse gases and aerosols were also evaluated. Results were compared to information retrieved from Weather and Research Forecasting (WRF) model and the Stochastic Time-Inverted Lagrangian Transport (STILT) model.

  3. Polymer network/carbon layer on monolith support and monolith catalytic reactor

    DOEpatents

    Nordquist, Andrew Francis; Wilhelm, Frederick Carl; Waller, Francis Joseph; Machado, Reinaldo Mario

    2003-08-26

    The present invention relates to an improved monolith catalytic reactor and a monolith support. The improvement in the support resides in a polymer network/carbon coating applied to the surface of a porous substrate and a catalytic metal, preferably a transition metal catalyst applied to the surface of the polymer network/carbon coating. The monolith support has from 100 to 800 cells per square inch and a polymer network/carbon coating with surface area of from 0.1 to 15 m.sup.2 /gram as measured by adsorption of N.sub.2 or Kr using the BET method.

  4. Robust, Multi-layered Plan Execution and Revision for Operation of a Network of Communication Antennas

    NASA Technical Reports Server (NTRS)

    Chien, S. A.; Hill, R. W., Jr.; Govindjee, A.; Wang, X.; Estlin, T.; Griesel, M. A.; Lam, R.; Fayyad, K. V.

    1996-01-01

    This paper describes a hierarchical scheduling, planning, control, and execution monitoring architecture for automating operations of a worldwide network of communications antennas. The purpose of this paper is to describe an architecture for automating the process of capturing spacecraft data.

  5. Cross layer optimization for cloud-based radio over optical fiber networks

    NASA Astrophysics Data System (ADS)

    Shao, Sujie; Guo, Shaoyong; Qiu, Xuesong; Yang, Hui; Meng, Luoming

    2016-07-01

    To adapt the 5G communication, the cloud radio access network is a paradigm introduced by operators which aggregates all base stations computational resources into a cloud BBU pool. The interaction between RRH and BBU or resource schedule among BBUs in cloud have become more frequent and complex with the development of system scale and user requirement. It can promote the networking demand among RRHs and BBUs, and force to form elastic optical fiber switching and networking. In such network, multiple stratum resources of radio, optical and BBU processing unit have interweaved with each other. In this paper, we propose a novel multiple stratum optimization (MSO) architecture for cloud-based radio over optical fiber networks (C-RoFN) with software defined networking. Additionally, a global evaluation strategy (GES) is introduced in the proposed architecture. MSO can enhance the responsiveness to end-to-end user demands and globally optimize radio frequency, optical spectrum and BBU processing resources effectively to maximize radio coverage. The feasibility and efficiency of the proposed architecture with GES strategy are experimentally verified on OpenFlow-enabled testbed in terms of resource occupation and path provisioning latency.

  6. Distributed beamforming designs to improve physical layer security in wireless relay networks

    NASA Astrophysics Data System (ADS)

    Qian, Mujun; Liu, Chen; Fu, Youhua

    2014-12-01

    This paper investigates security-oriented beamforming designs in a relay network composed of a source-destination pair, multiple relays, and a passive eavesdropper. Unlike most of the earlier works, we assume that only statistical information of the relay-eavesdropper channels is known to the relays. We propose beamforming solutions for amplify-and-forward (AF) and decode-and-forward (DF) relay networks to improve secrecy capacity. In an AF network, the beamforming design is obtained by approximating a product of two correlated Rayleigh quotients to a single Rayleigh quotient using the Taylor series expansion. Our study reveals that in an AF network, the secrecy capacity does not always grow as the eavesdropper moves away from the relays or as total relay transmit power increases. Moreover, if the destination is nearer to the relays than the eavesdropper is, a suboptimal power is derived in closed form through monotonicity analysis of secrecy capacity. While in a DF network, secrecy capacity is a single Rayleigh quotient problem which can be easily solved. We also found that if the relay-eavesdropper distances are about the same, it is unnecessary to consider the eavesdropper in a DF network. Numerical results show that for either AF or DF relaying protocol, the proposed beamforming scheme provides higher secrecy capacity than traditional approaches.

  7. Using an artificial neural network approach to estimate surface-layer optical turbulence at Mauna Loa, Hawaii.

    PubMed

    Wang, Yao; Basu, Sukanta

    2016-05-15

    In this Letter, an artificial neural network (ANN) approach is proposed for the estimation of optical turbulence (Cn2) in the atmospheric surface layer. Five routinely available meteorological variables are used as the inputs. Observed Cn2 data near the Mauna Loa Observatory, Hawaii are utilized for validation. The proposed approach has demonstrated its prowess by capturing the temporal evolution of Cn2 remarkably well. More interestingly, this ANN approach is found to outperform a widely used similarity theory-based conventional formulation for all the prevalent atmospheric conditions (including strongly stratified conditions).

  8. Using an artificial neural network approach to estimate surface-layer optical turbulence at Mauna Loa, Hawaii.

    PubMed

    Wang, Yao; Basu, Sukanta

    2016-05-15

    In this Letter, an artificial neural network (ANN) approach is proposed for the estimation of optical turbulence (Cn2) in the atmospheric surface layer. Five routinely available meteorological variables are used as the inputs. Observed Cn2 data near the Mauna Loa Observatory, Hawaii are utilized for validation. The proposed approach has demonstrated its prowess by capturing the temporal evolution of Cn2 remarkably well. More interestingly, this ANN approach is found to outperform a widely used similarity theory-based conventional formulation for all the prevalent atmospheric conditions (including strongly stratified conditions). PMID:27176996

  9. Forecasting of the critical frequency of the ionosphere F2 layer by the method of artificial neural networks

    NASA Astrophysics Data System (ADS)

    Barkhatov, N. A.; Revunov, S. E.; Uryadov, V. P.

    2004-12-01

    An algorithm of forecasting of the ionosphere F2 layer critical frequency for time intervals: 1, 2, 3, 12, and 24 hours was developed on the basis of the technology of artificial neural networks (ANN). The experimental search for a valid training array and architecture of ANN was performed. The solar wind parameters, interplanetary magnetic field, and geomagnetic disturbance indexes were additionally used in the forecasting. This made it possible to improve its effectiveness. The practical importance of the performed work is in the application of its results for efficient correction of the ionosphere model for an improvement of the ionosphere shortwave radio communication.

  10. An Adaptive Niching Genetic Algorithm using a niche size equalization mechanism

    NASA Astrophysics Data System (ADS)

    Nagata, Yuichi

    Niching GAs have been widely investigated to apply genetic algorithms (GAs) to multimodal function optimization problems. In this paper, we suggest a new niching GA that attempts to form niches, each consisting of an equal number of individuals. The proposed GA can be applied also to combinatorial optimization problems by defining a distance metric in the search space. We apply the proposed GA to the job-shop scheduling problem (JSP) and demonstrate that the proposed niching method enhances the ability to maintain niches and improve the performance of GAs.

  11. Target Article with Commentaries: Developmental Niche Construction

    ERIC Educational Resources Information Center

    Flynn, Emma G.; Laland, Kevin N.; Kendal, Rachel L.; Kendal, Jeremy R.

    2013-01-01

    Niche construction is the modification of components of the environment through an organism's activities. Humans modify their environments mainly through ontogenetic and cultural processes, and it is this reliance on learning, plasticity and culture that lends human niche construction a special potency. In this paper we aim to facilitate…

  12. The stem cell niches in bone

    PubMed Central

    Yin, Tong; Li, Linheng

    2006-01-01

    The stem cell niche is composed of a specialized population of cells that plays an essential role in regulating adult stem cell self-renewal and differentiation. In adults, osteoblasts, responsible for osteogenesis, and hematopoietic cells, responsible for hematopoiesis, are closely associated in the bone marrow, suggesting a reciprocal relationship between the two. It was recently discovered that a subset of osteoblasts functions as a key component of the HSC niche (namely, the osteoblastic niche), controlling HSC numbers. HSCs interact not only with osteoblasts but also with other stromal cells, including endothelial cells. Sinusoidal endothelial cells in bone marrow have been revealed as an alternative HSC niche called the vascular niche. In this Review we compare the architecture of these 2 HSC niches in bone marrow. We also highlight the function of osteoblasts in maintaining a quiescent HSC microenvironment and the likely role of the vascular niche in regulating stem cell proliferation, differentiation, and mobilization. In addition, we focus on studies of animal models and in vitro assays that have provided direct insights into the actions of these osteoblastic and vascular niches, revealing central roles for numerous signaling and adhesion molecules. Many of the discoveries described herein may contribute to future clinical treatments for hematopoietic and bone-related disorders, including cancer. PMID:16670760

  13. Hutchinson's duality: the once and future niche.

    PubMed

    Colwell, Robert K; Rangel, Thiago F

    2009-11-17

    The duality between "niche" and "biotope" proposed by G. Evelyn Hutchinson provides a powerful way to conceptualize and analyze biogeographical distributions in relation to spatial environmental patterns. Both Joseph Grinnell and Charles Elton had attributed niches to environments. Attributing niches, instead, to species, allowed Hutchinson's key innovation: the formal severing of physical place from environment that is expressed by the duality. In biogeography, the physical world (a spatial extension of what Hutchinson called the biotope) is conceived as a map, each point (or cell) of which is characterized by its geographical coordinates and the local values of n environmental attributes at a given time. Exactly the same n environmental attributes define the corresponding niche space, as niche axes, allowing reciprocal projections between the geographic distribution of a species, actual or potential, past or future, and its niche. In biogeographical terms, the realized niche has come to express not only the effects of species interactions (as Hutchinson intended), but also constraints of dispersal limitation and the lack of contemporary environments corresponding to parts of the fundamental niche. Hutchinson's duality has been used to classify and map environments; model potential species distributions under past, present, and future climates; study the distributions of invasive species; discover new species; and simulate increasingly more realistic worlds, leading to spatially explicit, stochastic models that encompass speciation, extinction, range expansion, and evolutionary adaptation to changing environments. PMID:19805163

  14. Layers of epistasis: genome-wide regulatory networks and network approaches to genome-wide association studies

    PubMed Central

    Cowper-Sal·lari, Richard; Cole, Michael D.; Karagas, Margaret R.; Lupien, Mathieu; Moore, Jason H.

    2010-01-01

    The conceptual foundation of the genome-wide association study (GWAS) has advanced unchecked since its conception. A revision might seem premature as the potential of GWAS has not been fully realized. Multiple technical and practical limitations need to be overcome before GWAS can be fairly criticized. But with the completion of hundreds of studies and a deeper understanding of the genetic architecture of disease, warnings are being raised. The results compiled to date indicate that risk-associated variants lie predominantly in non-coding regions of the genome. Additionally, alternative methodologies are uncovering large and heterogeneous sets of rare variants underlying disease. The fear is that, even in its fulfilment, the current GWAS paradigm might be incapable of dissecting all kinds of phenotypes. In the following text we review several initiatives that aim to overcome these limitations. The overarching theme of these studies is the inclusion of biological knowledge to both the analysis and interpretation of genotyping data. GWAS is uninformed of biology by design and although there is some virtue in its simplicity it is also its most conspicuous deficiency. We propose a framework in which to integrate these novel approaches, both empirical and theoretical, in the form of a genome-wide regulatory network (GWRN). By processing experimental data into networks, emerging data types based on chromatin-immunoprecipitation are made computationally tractable. This will give GWAS re-analysis efforts the most current and relevant substrates, and root them firmly on our knowledge of human disease. PMID:21197657

  15. Meta-food-chains as a many-layer epidemic process on networks

    NASA Astrophysics Data System (ADS)

    Barter, Edmund; Gross, Thilo

    2016-02-01

    Notable recent works have focused on the multilayer properties of coevolving diseases. We point out that very similar systems play an important role in population ecology. Specifically we study a meta-food-web model that was recently proposed by Pillai et al. [Theor. Ecol. 3, 223 (2009), 10.1007/s12080-009-0065-1]. This model describes a network of species connected by feeding interactions, which spread over a network of spatial patches. Focusing on the essential case, where the network of feeding interactions is a chain, we develop an analytical approach for the computation of the degree distributions of colonized spatial patches for the different species in the chain. This framework allows us to address ecologically relevant questions. Considering configuration model ensembles of spatial networks, we find that there is an upper bound for the fraction of patches that a given species can occupy, which depends only on the networks mean degree. For a given mean degree there is then an optimal degree distribution that comes closest to the upper bound. Notably scale-free degree distributions perform worse than more homogeneous degree distributions if the mean degree is sufficiently high. Because species experience the underlying network differently the optimal degree distribution for one particular species is generally not the optimal distribution for the other species in the same food web. These results are of interest for conservation ecology, where, for instance, the task of selecting areas of old-growth forest to preserve in an agricultural landscape, amounts to the design of a patch network.

  16. The Cell as the First Niche Construction.

    PubMed

    Torday, John S

    2016-01-01

    Niche construction nominally describes how organisms can form their own environments, increasing their capacity to adapt to their surroundings. It is hypothesized that the formation of the first cell as 'internal' Niche Construction was the foundation for life, and that subsequent niche constructions were iterative exaptations of that event. The first instantation of niche construction has been faithfully adhered to by returning to the unicellular state, suggesting that the life cycle is zygote to zygote, not adult to adult as is commonly held. The consequent interactions between niche construction and epigenetic inheritance provide a highly robust, interactive, mechanistic way of thinking about evolution being determined by initial conditions rather than merely by chance mutation and selection. This novel perspective offers an opportunity to reappraise the processes involved in evolution mechanistically, allowing for scientifically testable hypotheses rather than relying on metaphors, dogma, teleology and tautology. PMID:27136594

  17. The Cell as the First Niche Construction

    PubMed Central

    Torday, John S.

    2016-01-01

    Niche construction nominally describes how organisms can form their own environments, increasing their capacity to adapt to their surroundings. It is hypothesized that the formation of the first cell as ‘internal’ Niche Construction was the foundation for life, and that subsequent niche constructions were iterative exaptations of that event. The first instantation of niche construction has been faithfully adhered to by returning to the unicellular state, suggesting that the life cycle is zygote to zygote, not adult to adult as is commonly held. The consequent interactions between niche construction and epigenetic inheritance provide a highly robust, interactive, mechanistic way of thinking about evolution being determined by initial conditions rather than merely by chance mutation and selection. This novel perspective offers an opportunity to reappraise the processes involved in evolution mechanistically, allowing for scientifically testable hypotheses rather than relying on metaphors, dogma, teleology and tautology. PMID:27136594

  18. Making sense of hematopoietic stem cell niches

    PubMed Central

    Boulais, Philip E.

    2015-01-01

    The hematopoietic stem cell (HSC) niche commonly refers to the pairing of hematopoietic and mesenchymal cell populations that regulate HSC self-renewal, differentiation, and proliferation. Anatomic localization of the niche is a dynamic unit from the developmental stage that allows proliferating HSCs to expand before they reach the bone marrow where they adopt a quiescent phenotype that protects their integrity and functions. Recent studies have sought to clarify the complexity behind the HSC niche by assessing the contributions of specific cell populations to HSC maintenance. In particular, perivascular microenvironments in the bone marrow confer distinct vascular niches that regulate HSC quiescence and the supply of lineage-committed progenitors. Here, we review recent data on the cellular constituents and molecular mechanisms involved in the communication between HSCs and putative niches. PMID:25762174

  19. The Cell as the First Niche Construction.

    PubMed

    Torday, John S

    2016-04-28

    Niche construction nominally describes how organisms can form their own environments, increasing their capacity to adapt to their surroundings. It is hypothesized that the formation of the first cell as 'internal' Niche Construction was the foundation for life, and that subsequent niche constructions were iterative exaptations of that event. The first instantation of niche construction has been faithfully adhered to by returning to the unicellular state, suggesting that the life cycle is zygote to zygote, not adult to adult as is commonly held. The consequent interactions between niche construction and epigenetic inheritance provide a highly robust, interactive, mechanistic way of thinking about evolution being determined by initial conditions rather than merely by chance mutation and selection. This novel perspective offers an opportunity to reappraise the processes involved in evolution mechanistically, allowing for scientifically testable hypotheses rather than relying on metaphors, dogma, teleology and tautology.

  20. Cross-Layer Service Discovery Mechanism for OLSRv2 Mobile Ad Hoc Networks

    PubMed Central

    Vara, M. Isabel; Campo, Celeste

    2015-01-01

    Service discovery plays an important role in mobile ad hoc networks (MANETs). The lack of central infrastructure, limited resources and high mobility make service discovery a challenging issue for this kind of network. This article proposes a new service discovery mechanism for discovering and advertising services integrated into the Optimized Link State Routing Protocol Version 2 (OLSRv2). In previous studies, we demonstrated the validity of a similar service discovery mechanism integrated into the previous version of OLSR (OLSRv1). In order to advertise services, we have added a new type-length-value structure (TLV) to the OLSRv2 protocol, called service discovery message (SDM), according to the Generalized MANET Packet/Message Format defined in Request For Comments (RFC) 5444. Each node in the ad hoc network only advertises its own services. The advertisement frequency is a user-configurable parameter, so that it can be modified depending on the user requirements. Each node maintains two service tables, one to store information about its own services and another one to store information about the services it discovers in the network. We present simulation results, that compare our service discovery integrated into OLSRv2 with the one defined for OLSRv1 and with the integration of service discovery in Ad hoc On-demand Distance Vector (AODV) protocol, in terms of service discovery ratio, service latency and network overhead. PMID:26205272

  1. Cross-Layer Service Discovery Mechanism for OLSRv2 Mobile Ad Hoc Networks.

    PubMed

    Vara, M Isabel; Campo, Celeste

    2015-01-01

    Service discovery plays an important role in mobile ad hoc networks (MANETs). The lack of central infrastructure, limited resources and high mobility make service discovery a challenging issue for this kind of network. This article proposes a new service discovery mechanism for discovering and advertising services integrated into the Optimized Link State Routing Protocol Version 2 (OLSRv2). In previous studies, we demonstrated the validity of a similar service discovery mechanism integrated into the previous version of OLSR (OLSRv1). In order to advertise services, we have added a new type-length-value structure (TLV) to the OLSRv2 protocol, called service discovery message (SDM), according to the Generalized MANET Packet/Message Format defined in Request For Comments (RFC) 5444. Each node in the ad hoc network only advertises its own services. The advertisement frequency is a user-configurable parameter, so that it can be modified depending on the user requirements. Each node maintains two service tables, one to store information about its own services and another one to store information about the services it discovers in the network. We present simulation results, that compare our service discovery integrated into OLSRv2 with the one defined for OLSRv1 and with the integration of service discovery in Ad hoc On-demand Distance Vector (AODV) protocol, in terms of service discovery ratio, service latency and network overhead. PMID:26205272

  2. Cross-Layer Service Discovery Mechanism for OLSRv2 Mobile Ad Hoc Networks.

    PubMed

    Vara, M Isabel; Campo, Celeste

    2015-07-20

    Service discovery plays an important role in mobile ad hoc networks (MANETs). The lack of central infrastructure, limited resources and high mobility make service discovery a challenging issue for this kind of network. This article proposes a new service discovery mechanism for discovering and advertising services integrated into the Optimized Link State Routing Protocol Version 2 (OLSRv2). In previous studies, we demonstrated the validity of a similar service discovery mechanism integrated into the previous version of OLSR (OLSRv1). In order to advertise services, we have added a new type-length-value structure (TLV) to the OLSRv2 protocol, called service discovery message (SDM), according to the Generalized MANET Packet/Message Format defined in Request For Comments (RFC) 5444. Each node in the ad hoc network only advertises its own services. The advertisement frequency is a user-configurable parameter, so that it can be modified depending on the user requirements. Each node maintains two service tables, one to store information about its own services and another one to store information about the services it discovers in the network. We present simulation results, that compare our service discovery integrated into OLSRv2 with the one defined for OLSRv1 and with the integration of service discovery in Ad hoc On-demand Distance Vector (AODV) protocol, in terms of service discovery ratio, service latency and network overhead.

  3. Stress and displacement around a crack in layered network systems mimicking nacre

    NASA Astrophysics Data System (ADS)

    Aoyanagi, Yuko; Okumura, Ko

    2009-06-01

    Nacre is a natural composite material which has been studied because of its remarkable structure and its strength. In this paper, we revisit a layered model of nacre proposed previously [K. Okumura and P. G. de Gennes, Eur. Phys. J. E 4, 121 (2001)] in order to understand the physical reasons for the toughening via numerical simulation. We construct a two-dimensional lattice model which reflects the layered structure and perform a numerical study. This grid model reproduces the essential features predicted by the analytical solutions to the previous model and the results elucidate the reasons why the tip-stress concentration is reduced and tip displacement is enhanced in the layered system.

  4. Vascular niches: endothelial cells as tissue- and site-specific multifunctional team players in health and disease.

    PubMed

    Géraud, Cyrill; Koch, Philipp-S; Goerdt, Sergij

    2014-08-01

    The cardiovascular system is a circulatory system that transports the blood and reaches out to almost every site of the body. Endothelial cells (EC) as the innermost cell layer of blood vessels constitute a huge interface between the blood and nearly all other tissues and cells. Although blood vessels and their EC were considered as rather inert and passive conduits early in the history of vascular discoveries, progress in vascular research now suggests that EC are actively involved in a plethora of physiological or pathophysiological processes. Endothelial heterogeneity and the concept of vascular niches are in the spotlight of current research in vascular biology. Endothelial heterogeneity comprises morphologic, molecular and functional features. It allows EC to adapt to the organ- and site-specific requirements exhibited by different segments of the vascular tree. In organ-specific vascular niches, EC mutually interact with neighboring cells. EC-derived cytokines, called angiokines, acting in a paracrine (angiocrine) fashion have been shown to be decisively involved in various biological processes ranging from stem cell maintenance to organ regeneration as well as cancer progression and metastasis. In summary, EC should always be considered as teammates in the maintenance and regulation of complex multicellular network interactions in health and disease.

  5. Conformal organic-inorganic hybrid network polymer thin films by molecular layer deposition using trimethylaluminum and glycidol.

    PubMed

    Gong, Bo; Peng, Qing; Parsons, Gregory N

    2011-05-19

    Growing interest in nanoscale organic-inorganic hybrid network polymer materials is driving exploration of new bulk and thin film synthesis reaction mechanisms. Molecular layer deposition (MLD) is a vapor-phase deposition process, based on atomic layer deposition (ALD) which proceeds by exposing a surface to an alternating sequence of two or more reactant species, where each surface half-reaction goes to completion before the next reactant exposure. This work describes film growth using trimethyl aluminum and heterobifunctional glycidol at moderate temperatures (90-150 °C), producing a relatively stable organic-inorganic network polymer of the form (-Al-O-(C(4)H(8))-O-)(n). Film growth rate and in situ reaction analysis indicate that film growth does not initially follow a steady-state rate, but increases rapidly during early film growth. The mechanism is consistent with subsurface species transport and trapping, previously documented during MLD and ALD on polymers. A water exposure step after the TMA produces a more linear growth rate, likely by blocking TMA subsurface diffusion. Uniform and conformal films are formed on complex nonplanar substrates. Upon postdeposition annealing, films transform into microporous metal oxides with ∼5 Å pore size and surface area as high as ∼327 m(2)/g, and the resulting structures duplicate the shape of the original substrate. These hybrid films and porous materials could find uses in several research fields including gas separations and diffusion barriers, biomedical scaffolds, high surface area coatings, and others.

  6. Cross Layer Adaptation of Check Intervals in Low Power Listening MAC Protocols for Lifetime Improvement in Wireless Sensor Networks

    PubMed Central

    Escolar, Soledad; Chessa, Stefano; Carretero, Jesús; Marinescu, Maria-Cristina

    2012-01-01

    Preamble sampling-based MAC protocols designed for Wireless Sensor Networks (WSN) are aimed at prolonging the lifetime of the nodes by scheduling their times of activity. This scheduling exploits node synchronization to find the right trade-off between energy consumption and delay. In this paper we consider the problem of node synchronization in preamble sampling protocols. We propose Cross Layer Adaptation of Check intervals (CLAC), a novel protocol intended to reduce the energy consumption of the nodes without significantly increasing the delay. Our protocol modifies the scheduling of the nodes based on estimating the delay experienced by a packet that travels along a multi-hop path. CLAC uses routing and MAC layer information to compute a delay that matches the packet arrival time. We have implemented CLAC on top of well-known routing and MAC protocols for WSN, and we have evaluated our implementation using the Avrora simulator. The simulation results confirm that CLAC improves the network lifetime at no additional packet loss and without affecting the end-to-end delay. PMID:23112613

  7. A Review of Protocol Implementations and Energy Efficient Cross-Layer Design for Wireless Body Area Networks

    PubMed Central

    Hughes, Laurie; Wang, Xinheng; Chen, Tao

    2012-01-01

    The issues inherent in caring for an ever-increasing aged population has been the subject of endless debate and continues to be a hot topic for political discussion. The use of hospital-based facilities for the monitoring of chronic physiological conditions is expensive and ties up key healthcare professionals. The introduction of wireless sensor devices as part of a Wireless Body Area Network (WBAN) integrated within an overall eHealth solution could bring a step change in the remote management of patient healthcare. Sensor devices small enough to be placed either inside or on the human body can form a vital part of an overall health monitoring network. An effectively designed energy efficient WBAN should have a minimal impact on the mobility and lifestyle of the patient. WBAN technology can be deployed within a hospital, care home environment or in the patient's own home. This study is a review of the existing research in the area of WBAN technology and in particular protocol adaptation and energy efficient cross-layer design. The research reviews the work carried out across various layers of the protocol stack and highlights how the latest research proposes to resolve the various challenges inherent in remote continual healthcare monitoring. PMID:23202185

  8. Hybrid Multi-Layer Network Control for Emerging Cyber-Infrastructures

    SciTech Connect

    Summerhill, Richard

    2009-08-14

    There were four basic task areas identified for the Hybrid-MLN project. They are: o Multi-Layer, Multi-Domain, Control Plane Architecture and Implementation, o Heterogeneous DataPlane Testing, o Simulation, o Project Publications, Reports, and Presentations.

  9. The layered sensing operations center: a modeling and simulation approach to developing complex ISR networks

    NASA Astrophysics Data System (ADS)

    Curtis, Christopher; Lenzo, Matthew; McClure, Matthew; Preiss, Bruce

    2010-04-01

    In order to anticipate the constantly changing landscape of global warfare, the United States Air Force must acquire new capabilities in the field of Intelligence, Surveillance, and Reconnaissance (ISR). To meet this challenge, the Air Force Research Laboratory (AFRL) is developing a unifying construct of "Layered Sensing" which will provide military decision-makers at all levels with the timely, actionable, and trusted information necessary for complete battlespace awareness. Layered Sensing is characterized by the appropriate combination of sensors and platforms (including those for persistent sensing), infrastructure, and exploitation capabilities to enable this synergistic awareness. To achieve the Layered Sensing vision, AFRL is pursuing a Modeling & Simulation (M&S) strategy through the Layered Sensing Operations Center (LSOC). An experimental ISR system-of-systems test-bed, the LSOC integrates DoD standard simulation tools with commercial, off-the-shelf video game technology for rapid scenario development and visualization. These tools will help facilitate sensor management performance characterization, system development, and operator behavioral analysis. Flexible and cost-effective, the LSOC will implement a non-proprietary, open-architecture framework with well-defined interfaces. This framework will incentivize the transition of current ISR performance models to service-oriented software design for maximum re-use and consistency. This paper will present the LSOC's development and implementation thus far as well as a summary of lessons learned and future plans for the LSOC.

  10. Current and Future Niche of North and Central American Sand Flies (Diptera: Psychodidae) in Climate Change Scenarios

    PubMed Central

    Moo-Llanes, David; Ibarra-Cerdeña, Carlos N.; Rebollar-Téllez, Eduardo A.; Ibáñez-Bernal, Sergio; González, Camila; Ramsey, Janine M.

    2013-01-01

    Ecological niche models are useful tools to infer potential spatial and temporal distributions in vector species and to measure epidemiological risk for infectious diseases such as the Leishmaniases. The ecological niche of 28 North and Central American sand fly species, including those with epidemiological relevance, can be used to analyze the vector's ecology and its association with transmission risk, and plan integrated regional vector surveillance and control programs. In this study, we model the environmental requirements of the principal North and Central American phlebotomine species and analyze three niche characteristics over future climate change scenarios: i) potential change in niche breadth, ii) direction and magnitude of niche centroid shifts, iii) shifts in elevation range. Niche identity between confirmed or incriminated Leishmania vector sand flies in Mexico, and human cases were analyzed. Niche models were constructed using sand fly occurrence datapoints from Canada, USA, Mexico, Guatemala and Belize. Nine non-correlated bioclimatic and four topographic data layers were used as niche components using GARP in OpenModeller. Both B2 and A2 climate change scenarios were used with two general circulation models for each scenario (CSIRO and HadCM3), for 2020, 2050 and 2080. There was an increase in niche breadth to 2080 in both scenarios for all species with the exception of Lutzomyia vexator. The principal direction of niche centroid displacement was to the northwest (64%), while the elevation range decreased greatest for tropical, and least for broad-range species. Lutzomyia cruciata is the only epidemiologically important species with high niche identity with that of Leishmania spp. in Mexico. Continued landscape modification in future climate change will provide an increased opportunity for the geographic expansion of NCA sand flys' ENM and human exposure to vectors of Leishmaniases. PMID:24069478

  11. Current and future niche of North and Central American sand flies (Diptera: psychodidae) in climate change scenarios.

    PubMed

    Moo-Llanes, David; Ibarra-Cerdeña, Carlos N; Rebollar-Téllez, Eduardo A; Ibáñez-Bernal, Sergio; González, Camila; Ramsey, Janine M

    2013-01-01

    Ecological niche models are useful tools to infer potential spatial and temporal distributions in vector species and to measure epidemiological risk for infectious diseases such as the Leishmaniases. The ecological niche of 28 North and Central American sand fly species, including those with epidemiological relevance, can be used to analyze the vector's ecology and its association with transmission risk, and plan integrated regional vector surveillance and control programs. In this study, we model the environmental requirements of the principal North and Central American phlebotomine species and analyze three niche characteristics over future climate change scenarios: i) potential change in niche breadth, ii) direction and magnitude of niche centroid shifts, iii) shifts in elevation range. Niche identity between confirmed or incriminated Leishmania vector sand flies in Mexico, and human cases were analyzed. Niche models were constructed using sand fly occurrence datapoints from Canada, USA, Mexico, Guatemala and Belize. Nine non-correlated bioclimatic and four topographic data layers were used as niche components using GARP in OpenModeller. Both B2 and A2 climate change scenarios were used with two general circulation models for each scenario (CSIRO and HadCM3), for 2020, 2050 and 2080. There was an increase in niche breadth to 2080 in both scenarios for all species with the exception of Lutzomyia vexator. The principal direction of niche centroid displacement was to the northwest (64%), while the elevation range decreased greatest for tropical, and least for broad-range species. Lutzomyia cruciata is the only epidemiologically important species with high niche identity with that of Leishmania spp. in Mexico. Continued landscape modification in future climate change will provide an increased opportunity for the geographic expansion of NCA sand flys' ENM and human exposure to vectors of Leishmaniases.

  12. Current and future niche of North and Central American sand flies (Diptera: psychodidae) in climate change scenarios.

    PubMed

    Moo-Llanes, David; Ibarra-Cerdeña, Carlos N; Rebollar-Téllez, Eduardo A; Ibáñez-Bernal, Sergio; González, Camila; Ramsey, Janine M

    2013-01-01

    Ecological niche models are useful tools to infer potential spatial and temporal distributions in vector species and to measure epidemiological risk for infectious diseases such as the Leishmaniases. The ecological niche of 28 North and Central American sand fly species, including those with epidemiological relevance, can be used to analyze the vector's ecology and its association with transmission risk, and plan integrated regional vector surveillance and control programs. In this study, we model the environmental requirements of the principal North and Central American phlebotomine species and analyze three niche characteristics over future climate change scenarios: i) potential change in niche breadth, ii) direction and magnitude of niche centroid shifts, iii) shifts in elevation range. Niche identity between confirmed or incriminated Leishmania vector sand flies in Mexico, and human cases were analyzed. Niche models were constructed using sand fly occurrence datapoints from Canada, USA, Mexico, Guatemala and Belize. Nine non-correlated bioclimatic and four topographic data layers were used as niche components using GARP in OpenModeller. Both B2 and A2 climate change scenarios were used with two general circulation models for each scenario (CSIRO and HadCM3), for 2020, 2050 and 2080. There was an increase in niche breadth to 2080 in both scenarios for all species with the exception of Lutzomyia vexator. The principal direction of niche centroid displacement was to the northwest (64%), while the elevation range decreased greatest for tropical, and least for broad-range species. Lutzomyia cruciata is the only epidemiologically important species with high niche identity with that of Leishmania spp. in Mexico. Continued landscape modification in future climate change will provide an increased opportunity for the geographic expansion of NCA sand flys' ENM and human exposure to vectors of Leishmaniases. PMID:24069478

  13. Bottom-up GGM algorithm for constructing multiple layered hierarchical gene regulatory networks

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Multilayered hierarchical gene regulatory networks (ML-hGRNs) are very important for understanding genetics regulation of biological pathways. However, there are currently no computational algorithms available for directly building ML-hGRNs that regulate biological pathways. A bottom-up graphic Gaus...

  14. THE NICHE CONSTRUCTION PERSPECTIVE: A CRITICAL APPRAISAL*

    PubMed Central

    Scott-Phillips, Thomas C; Laland, Kevin N; Shuker, David M; Dickins, Thomas E; West, Stuart A

    2014-01-01

    Niche construction refers to the activities of organisms that bring about changes in their environments, many of which are evolutionarily and ecologically consequential. Advocates of niche construction theory (NCT) believe that standard evolutionary theory fails to recognize the full importance of niche construction, and consequently propose a novel view of evolution, in which niche construction and its legacy over time (ecological inheritance) are described as evolutionary processes, equivalent in importance to natural selection. Here, we subject NCT to critical evaluation, in the form of a collaboration between one prominent advocate of NCT, and a team of skeptics. We discuss whether niche construction is an evolutionary process, whether NCT obscures or clarifies how natural selection leads to organismal adaptation, and whether niche construction and natural selection are of equivalent explanatory importance. We also consider whether the literature that promotes NCT overstates the significance of niche construction, whether it is internally coherent, and whether it accurately portrays standard evolutionary theory. Our disagreements reflect a wider dispute within evolutionary theory over whether the neo-Darwinian synthesis is in need of reformulation, as well as different usages of some key terms (e.g., evolutionary process). PMID:24325256

  15. Niche construction game cancer cells play

    NASA Astrophysics Data System (ADS)

    Bergman, Aviv; Gligorijevic, Bojana

    2015-10-01

    Niche construction concept was originally defined in evolutionary biology as the continuous interplay between natural selection via environmental conditions and the modification of these conditions by the organism itself. Processes unraveling during cancer metastasis include construction of niches, which cancer cells use towards more efficient survival, transport into new environments and preparation of the remote sites for their arrival. Many elegant experiments were done lately illustrating, for example, the premetastatic niche construction, but there is practically no mathematical modeling done which would apply the niche construction framework. To create models useful for understanding niche construction role in cancer progression, we argue that a) genetic, b) phenotypic and c) ecological levels are to be included. While the model proposed here is phenomenological in its current form, it can be converted into a predictive outcome model via experimental measurement of the model parameters. Here we give an overview of an experimentally formulated problem in cancer metastasis and propose how niche construction framework can be utilized and broadened to model it. Other life science disciplines, such as host-parasite coevolution, may also benefit from niche construction framework adaptation, to satisfy growing need for theoretical considerations of data collected by experimental biology.

  16. Hutchinson's duality: The once and future niche

    PubMed Central

    Colwell, Robert K.; Rangel, Thiago F.

    2009-01-01

    The duality between “niche” and “biotope” proposed by G. Evelyn Hutchinson provides a powerful way to conceptualize and analyze biogeographical distributions in relation to spatial environmental patterns. Both Joseph Grinnell and Charles Elton had attributed niches to environments. Attributing niches, instead, to species, allowed Hutchinson's key innovation: the formal severing of physical place from environment that is expressed by the duality. In biogeography, the physical world (a spatial extension of what Hutchinson called the biotope) is conceived as a map, each point (or cell) of which is characterized by its geographical coordinates and the local values of n environmental attributes at a given time. Exactly the same n environmental attributes define the corresponding niche space, as niche axes, allowing reciprocal projections between the geographic distribution of a species, actual or potential, past or future, and its niche. In biogeographical terms, the realized niche has come to express not only the effects of species interactions (as Hutchinson intended), but also constraints of dispersal limitation and the lack of contemporary environments corresponding to parts of the fundamental niche. Hutchinson's duality has been used to classify and map environments; model potential species distributions under past, present, and future climates; study the distributions of invasive species; discover new species; and simulate increasingly more realistic worlds, leading to spatially explicit, stochastic models that encompass speciation, extinction, range expansion, and evolutionary adaptation to changing environments. PMID:19805163

  17. Rethinking adaptation: the niche-construction perspective.

    PubMed

    Day, Rachel L; Laland, Kevin N; Odling-Smee, F John

    2003-01-01

    Niche construction refers to the capacity of organisms to construct, modify, and select important components of their local environments, such as nests, burrows, pupal cases, chemicals, and nutrients. A small but increasing number of evolutionary biologists regard niche construction as an evolutionary process in its own right, rather than as a mere product of natural selection. Through niche construction organisms not only influence the nature of their world, but also in part determine the selection pressures to which they and their descendants are exposed, and they do so in a non-random manner. Mathematical population genetics analyses have revealed that niche construction is likely to be evolutionarily consequential because of the feedback that it generates in the evolutionary process. A parallel movement has emerged in ecosystem ecology, where researchers stress the utility of regarding organisms as ecosystem engineers, who partly control energy and matter flows. From the niche construction standpoint, the evolving complementary match between organisms and environments is the product of reciprocal interacting processes of natural selection and niche construction. This essay reviews the arguments put forward in favor of the niche-construction perspective.

  18. The niche construction perspective: a critical appraisal.

    PubMed

    Scott-Phillips, Thomas C; Laland, Kevin N; Shuker, David M; Dickins, Thomas E; West, Stuart A

    2014-05-01

    Niche construction refers to the activities of organisms that bring about changes in their environments, many of which are evolutionarily and ecologically consequential. Advocates of niche construction theory (NCT) believe that standard evolutionary theory fails to recognize the full importance of niche construction, and consequently propose a novel view of evolution, in which niche construction and its legacy over time (ecological inheritance) are described as evolutionary processes, equivalent in importance to natural selection. Here, we subject NCT to critical evaluation, in the form of a collaboration between one prominent advocate of NCT, and a team of skeptics. We discuss whether niche construction is an evolutionary process, whether NCT obscures or clarifies how natural selection leads to organismal adaptation, and whether niche construction and natural selection are of equivalent explanatory importance. We also consider whether the literature that promotes NCT overstates the significance of niche construction, whether it is internally coherent, and whether it accurately portrays standard evolutionary theory. Our disagreements reflect a wider dispute within evolutionary theory over whether the neo-Darwinian synthesis is in need of reformulation, as well as different usages of some key terms (e.g., evolutionary process).

  19. Niche construction game cancer cells play*

    PubMed Central

    Bergman, Aviv; Gligorijevic, Bojana

    2016-01-01

    Niche construction concept was originally defined in evolutionary biology as the continuous interplay between natural selection via environmental conditions and the modification of these conditions by the organism itself. Processes unraveling during cancer metastasis include construction of niches, which cancer cells use towards more efficient survival, transport into new environments and preparation of the remote sites for their arrival. Many elegant experiments were done lately illustrating, for example, the premetastatic niche construction, but there is practically no mathematical modeling done which would apply the niche construction framework. To create models useful for understanding niche construction role in cancer progression, we argue that a) genetic, b) phenotypic and c) ecological levels are to be included. While the model proposed here is phenomenological in its current form, it can be converted into a predictive outcome model via experimental measurement of the model parameters. Here we give an overview of an experimentally formulated problem in cancer metastasis and propose how niche construction framework can be utilized and broadened to model it. Other life science disciplines, such as host-parasite coevolution, may also benefit from niche construction framework adaptation, to satisfy growing need for theoretical considerations of data collected by experimental biology. PMID:27656339

  20. The niche construction perspective: a critical appraisal.

    PubMed

    Scott-Phillips, Thomas C; Laland, Kevin N; Shuker, David M; Dickins, Thomas E; West, Stuart A

    2014-05-01

    Niche construction refers to the activities of organisms that bring about changes in their environments, many of which are evolutionarily and ecologically consequential. Advocates of niche construction theory (NCT) believe that standard evolutionary theory fails to recognize the full importance of niche construction, and consequently propose a novel view of evolution, in which niche construction and its legacy over time (ecological inheritance) are described as evolutionary processes, equivalent in importance to natural selection. Here, we subject NCT to critical evaluation, in the form of a collaboration between one prominent advocate of NCT, and a team of skeptics. We discuss whether niche construction is an evolutionary process, whether NCT obscures or clarifies how natural selection leads to organismal adaptation, and whether niche construction and natural selection are of equivalent explanatory importance. We also consider whether the literature that promotes NCT overstates the significance of niche construction, whether it is internally coherent, and whether it accurately portrays standard evolutionary theory. Our disagreements reflect a wider dispute within evolutionary theory over whether the neo-Darwinian synthesis is in need of reformulation, as well as different usages of some key terms (e.g., evolutionary process). PMID:24325256

  1. Quantitative imaging of microvascular blood flow networks in deep cortical layers by 1310 nm µODT

    PubMed Central

    You, Jiang; Zhang, Qiujia; Park, Kicheon; Du, Congwu

    2016-01-01

    There is growing interest in new neuroimage techniques that permit not only high-resolution quantification of cerebral blood flow velocity (CBFv) in capillaries, but also a large field of view to map the CBFv network dynamics. Such image capabilities are of great importance for decoding the functional difference across multiple cortical layers under stimuli. To tackle the limitation of optical penetration depth, we present a new ultrahigh-resolution optical coherence Doppler tomography (µODT) system at 1310 nm and compare it with a prior 800 nm µODT system for mouse brain 3D CBFv imaging. We show that the new 1310 nm µODT allows for dramatically increased depth (~4 times) of quantitative CBFv imaging to 1.4 mm, thus covering the full thickness of the mouse cortex (i.e., layers I–VI). Interestingly, we show that such a unique 3D CBFv imaging capability allows identification of microcirculatory redistribution across different cortical layers resulting from repeated cocaine exposures. PMID:26371919

  2. A Multi-layered Protein Network Stabilizes the Escherichia coli FtsZ-ring and Modulates Constriction Dynamics

    PubMed Central

    Buss, Jackson; Coltharp, Carla; Shtengel, Gleb; Yang, Xinxing; Hess, Harald; Xiao, Jie

    2015-01-01

    The prokaryotic tubulin homolog, FtsZ, forms a ring-like structure (FtsZ-ring) at midcell. The FtsZ-ring establishes the division plane and enables the assembly of the macromolecular division machinery (divisome). Although many molecular components of the divisome have been identified and their interactions extensively characterized, the spatial organization of these proteins within the divisome is unclear. Consequently, the physical mechanisms that drive divisome assembly, maintenance, and constriction remain elusive. Here we applied single-molecule based superresolution imaging, combined with genetic and biophysical investigations, to reveal the spatial organization of cellular structures formed by four important divisome proteins in E. coli: FtsZ, ZapA, ZapB and MatP. We show that these interacting proteins are arranged into a multi-layered protein network extending from the cell membrane to the chromosome, each with unique structural and dynamic properties. Further, we find that this protein network stabilizes the FtsZ-ring, and unexpectedly, slows down cell constriction, suggesting a new, unrecognized role for this network in bacterial cell division. Our results provide new insight into the structure and function of the divisome, and highlight the importance of coordinated cell constriction and chromosome segregation. PMID:25848771

  3. [Relation between fundamental and realized ecological niche].

    PubMed

    Severtsov, A S

    2012-01-01

    Since species are formed in course of evolutionary process, their ecological niches are formed in the evolutionary process, too. Species exist in a state of evolutionary stasis diring hundreds of thousands and millions years. Stasis in sustained mainly by counterbalance of vectors of directional selection. Niche can be viewed as a multidimensional structure. Multitude of environmental factors acts upon every population, which cause elimination and, by that, selection for adaptation to each eliminating factor. Different directions of these vectors of selection lead to their counteractions; selection in one direction is interfered by selection in an opposite direction. The counterbalance of vectors of selection interferes with progressive evolution thus supporting stasis. During species existence in a stasis condition it endures a whole set of various deterioration of environment. Such deteriorations lead to imbalance of selective processes. Unbalanced vectors of selection form adaptations to extreme conditions of existence. Such adaptations are superfluous as for usual conditions; but they define fitness borders and, by that, borders of a fundamental niche. Realized niche, as well as fundamental one, is a multidimensional structure. Each population occupies a subniche of the specific realized niche. Thus, it occupies habitats where conditions are as close to an ecological optimum as can be admitted by the conditions in the given part of the areal. The sum of all subniches of populations--the specific realized niche--coincides with a part of fundamental niche because only the part of adaptive possibilities of a species sufficient for existence in the given environment is used. Interspecific competition, even when it is capable to restrict consumption of limiting resources, is not the reason of the realized niche limitation. Restriction of one or two of niche parameters does not influece all others parameters of its multidimensional space.

  4. Phylogeny and niche conservatism in North and Central American triatomine bugs (Hemiptera: Reduviidae: Triatominae), vectors of Chagas' disease.

    PubMed

    Ibarra-Cerdeña, Carlos N; Zaldívar-Riverón, Alejandro; Peterson, A Townsend; Sánchez-Cordero, Víctor; Ramsey, Janine M

    2014-10-01

    The niche conservatism hypothesis states that related species diverge in niche characteristics at lower rates than expected, given their lineage divergence. Here we analyze whether niche conservatism is a common pattern among vector species (Hemiptera: Reduviidae: Triatominae) of Trypanosoma cruzi that inhabit North and Central America, a highly heterogeneous landmass in terms of environmental gradients. Mitochondrial and nuclear loci were used in a multi-locus phylogenetic framework to reconstruct phylogenetic relationships among species and estimate time of divergence of selected clades to draw biogeographic inferences. Then, we estimated similarity between the ecological niche of sister species and tested the niche conservatism hypothesis using our best estimate of phylogeny. Triatoma is not monophyletic. A primary clade with all North and Central American (NCA) triatomine species from the genera Triatoma, Dipetalogaster, and Panstrongylus, was consistently recovered. Nearctic species within the NCA clade (T. p. protracta, T. r. rubida) diverged during the Pliocene, whereas the Neotropical species (T. phyllosoma, T. longipennis, T. dimidiata complex) are estimated to have diverged more recently, during the Pleistocene. The hypothesis of niche conservatism could not be rejected for any of six sister species pairs. Niche similarity between sister species best fits a retention model. While this framework is used here to infer niche evolution, it has a direct impact on spatial vector dynamics driven by human population movements, expansion of transportation networks and climate change scenarios. PMID:25356550

  5. Phylogeny and niche conservatism in North and Central American triatomine bugs (Hemiptera: Reduviidae: Triatominae), vectors of Chagas' disease.

    PubMed

    Ibarra-Cerdeña, Carlos N; Zaldívar-Riverón, Alejandro; Peterson, A Townsend; Sánchez-Cordero, Víctor; Ramsey, Janine M

    2014-10-01

    The niche conservatism hypothesis states that related species diverge in niche characteristics at lower rates than expected, given their lineage divergence. Here we analyze whether niche conservatism is a common pattern among vector species (Hemiptera: Reduviidae: Triatominae) of Trypanosoma cruzi that inhabit North and Central America, a highly heterogeneous landmass in terms of environmental gradients. Mitochondrial and nuclear loci were used in a multi-locus phylogenetic framework to reconstruct phylogenetic relationships among species and estimate time of divergence of selected clades to draw biogeographic inferences. Then, we estimated similarity between the ecological niche of sister species and tested the niche conservatism hypothesis using our best estimate of phylogeny. Triatoma is not monophyletic. A primary clade with all North and Central American (NCA) triatomine species from the genera Triatoma, Dipetalogaster, and Panstrongylus, was consistently recovered. Nearctic species within the NCA clade (T. p. protracta, T. r. rubida) diverged during the Pliocene, whereas the Neotropical species (T. phyllosoma, T. longipennis, T. dimidiata complex) are estimated to have diverged more recently, during the Pleistocene. The hypothesis of niche conservatism could not be rejected for any of six sister species pairs. Niche similarity between sister species best fits a retention model. While this framework is used here to infer niche evolution, it has a direct impact on spatial vector dynamics driven by human population movements, expansion of transportation networks and climate change scenarios.

  6. Phylogeny and Niche Conservatism in North and Central American Triatomine Bugs (Hemiptera: Reduviidae: Triatominae), Vectors of Chagas' Disease

    PubMed Central

    Ibarra-Cerdeña, Carlos N.; Zaldívar-Riverón, Alejandro; Peterson, A. Townsend; Sánchez-Cordero, Víctor; Ramsey, Janine M.

    2014-01-01

    The niche conservatism hypothesis states that related species diverge in niche characteristics at lower rates than expected, given their lineage divergence. Here we analyze whether niche conservatism is a common pattern among vector species (Hemiptera: Reduviidae: Triatominae) of Trypanosoma cruzi that inhabit North and Central America, a highly heterogeneous landmass in terms of environmental gradients. Mitochondrial and nuclear loci were used in a multi-locus phylogenetic framework to reconstruct phylogenetic relationships among species and estimate time of divergence of selected clades to draw biogeographic inferences. Then, we estimated similarity between the ecological niche of sister species and tested the niche conservatism hypothesis using our best estimate of phylogeny. Triatoma is not monophyletic. A primary clade with all North and Central American (NCA) triatomine species from the genera Triatoma, Dipetalogaster, and Panstrongylus, was consistently recovered. Nearctic species within the NCA clade (T. p. protracta, T. r. rubida) diverged during the Pliocene, whereas the Neotropical species (T. phyllosoma, T. longipennis, T. dimidiata complex) are estimated to have diverged more recently, during the Pleistocene. The hypothesis of niche conservatism could not be rejected for any of six sister species pairs. Niche similarity between sister species best fits a retention model. While this framework is used here to infer niche evolution, it has a direct impact on spatial vector dynamics driven by human population movements, expansion of transportation networks and climate change scenarios. PMID:25356550

  7. Multi-layer holographic bifurcative neural network system for real-time adaptive EOS data analysis

    NASA Technical Reports Server (NTRS)

    Liu, Hua-Kuang; Huang, K. S.; Diep, J.

    1993-01-01

    Optical data processing techniques have the inherent advantage of high data throughout, low weight and low power requirements. These features are particularly desirable for onboard spacecraft in-situ real-time data analysis and data compression applications. the proposed multi-layer optical holographic neural net pattern recognition technique will utilize the nonlinear photorefractive devices for real-time adaptive learning to classify input data content and recognize unexpected features. Information can be stored either in analog or digital form in a nonlinear photofractive device. The recording can be accomplished in time scales ranging from milliseconds to microseconds. When a system consisting of these devices is organized in a multi-layer structure, a feedforward neural net with bifurcating data classification capability is formed. The interdisciplinary research will involve the collaboration with top digital computer architecture experts at the University of Southern California.

  8. Physical layer one-time-pad data encryption through synchronized semiconductor laser networks

    NASA Astrophysics Data System (ADS)

    Argyris, Apostolos; Pikasis, Evangelos; Syvridis, Dimitris

    2016-02-01

    Semiconductor lasers (SL) have been proven to be a key device in the generation of ultrafast true random bit streams. Their potential to emit chaotic signals under conditions with desirable statistics, establish them as a low cost solution to cover various needs, from large volume key generation to real-time encrypted communications. Usually, only undemanding post-processing is needed to convert the acquired analog timeseries to digital sequences that pass all established tests of randomness. A novel architecture that can generate and exploit these true random sequences is through a fiber network in which the nodes are semiconductor lasers that are coupled and synchronized to central hub laser. In this work we show experimentally that laser nodes in such a star network topology can synchronize with each other through complex broadband signals that are the seed to true random bit sequences (TRBS) generated at several Gb/s. The potential for each node to access real-time generated and synchronized with the rest of the nodes random bit streams, through the fiber optic network, allows to implement an one-time-pad encryption protocol that mixes the synchronized true random bit sequence with real data at Gb/s rates. Forward-error correction methods are used to reduce the errors in the TRBS and the final error rate at the data decoding level. An appropriate selection in the sampling methodology and properties, as well as in the physical properties of the chaotic seed signal through which network locks in synchronization, allows an error free performance.

  9. Regional application of multi-layer artificial neural networks in 3-D ionosphere tomography

    NASA Astrophysics Data System (ADS)

    Ghaffari Razin, Mir Reza; Voosoghi, Behzad

    2016-08-01

    Tomography is a very cost-effective method to study physical properties of the ionosphere. In this paper, residual minimization training neural network (RMTNN) is used in voxel-based tomography to reconstruct of 3-D ionosphere electron density with high spatial resolution. For numerical experiments, observations collected at 37 GPS stations from Iranian permanent GPS network (IPGN) are used. A smoothed TEC approach was used for absolute STEC recovery. To improve the vertical resolution, empirical orthogonal functions (EOFs) obtained from international reference ionosphere 2012 (IRI-2012) used as object function in training neural network. Ionosonde observations is used for validate reliability of the proposed method. Minimum relative error for RMTNN is 1.64% and maximum relative error is 15.61%. Also root mean square error (RMSE) of 0.17 × 1011 (electrons/m3) is computed for RMTNN which is less than RMSE of IRI2012. The results show that RMTNN has higher accuracy and compiles speed than other ionosphere reconstruction methods.

  10. Retinal pathways influence temporal niche

    PubMed Central

    Doyle, Susan E.; Yoshikawa, Tomoko; Hillson, Holly; Menaker, Michael

    2008-01-01

    In mammals, light input from the retina entrains central circadian oscillators located in the suprachiasmatic nuclei (SCN). The phase of circadian activity rhythms with respect to the external light:dark cycle is reversed in diurnal and nocturnal species, although the phase of SCN rhythms relative to the light cycle remains unchanged. Neural mechanisms downstream from the SCN are therefore believed to determine diurnality or nocturnality. Here, we report a switch from nocturnal to diurnal entrainment of circadian activity rhythms in double-knockout mice lacking the inner-retinal photopigment melanopsin (OPN4) and RPE65, a key protein used in retinal chromophore recycling. These mice retained only a small amount of rod function. The change in entrainment phase of Rpe65−/−;Opn4−/− mice was accompanied by a reversal of the rhythm of clock gene expression in the SCN and a reversal in acute masking effects of both light and darkness on activity, suggesting that the nocturnal to diurnal switch is due to a change in the neural response to light upstream from the SCN. A switch from nocturnal to diurnal activity rhythms was also found in wild-type mice transferred from standard intensity light:dark cycles to light:dark cycles in which the intensity of the light phase was reduced to scotopic levels. These results reveal a novel mechanism by which changes in retinal input can mediate acute temporal-niche switching. PMID:18695249

  11. Human niche construction in interdisciplinary focus

    PubMed Central

    Kendal, Jeremy; Tehrani, Jamshid J.; Odling-Smee, John

    2011-01-01

    Niche construction is an endogenous causal process in evolution, reciprocal to the causal process of natural selection. It works by adding ecological inheritance, comprising the inheritance of natural selection pressures previously modified by niche construction, to genetic inheritance in evolution. Human niche construction modifies selection pressures in environments in ways that affect both human evolution, and the evolution of other species. Human ecological inheritance is exceptionally potent because it includes the social transmission and inheritance of cultural knowledge, and material culture. Human genetic inheritance in combination with human cultural inheritance thus provides a basis for gene–culture coevolution, and multivariate dynamics in cultural evolution. Niche construction theory potentially integrates the biological and social aspects of the human sciences. We elaborate on these processes, and provide brief introductions to each of the papers published in this theme issue. PMID:21320894

  12. Stem cell niche engineering through droplet microfluidics.

    PubMed

    Allazetta, Simone; Lutolf, Matthias P

    2015-12-01

    Stem cells reside in complex niches in which their behaviour is tightly regulated by various biochemical and biophysical signals. In order to unveil some of the crucial stem cell-niche interactions and expedite the implementation of stem cells in clinical and pharmaceutical applications, in vitro methodologies are being developed to reconstruct key features of stem cell niches. Recently, droplet-based microfluidics has emerged as a promising strategy to build stem cell niche models in a miniaturized and highly precise fashion. This review highlights current advances in using droplet microfluidics in stem cell biology. We also discuss recent efforts in which microgel technology has been interfaced with high-throughput analyses to engender screening paradigms with an unparalleled potential for basic and applied biological studies.

  13. CROSS DRIFT ALCOVE/NICHE UTILITIES ANALYSIS

    SciTech Connect

    S. Goodin

    1999-07-08

    The purpose of this analysis is to provide the design basis and general arrangement requirements of the non-potable water, waste water, compressed air and ventilation (post excavation) utilities required in support of the Cross Drift alcoves and niches.

  14. Human niche construction in interdisciplinary focus.

    PubMed

    Kendal, Jeremy; Tehrani, Jamshid J; Odling-Smee, John

    2011-03-27

    Niche construction is an endogenous causal process in evolution, reciprocal to the causal process of natural selection. It works by adding ecological inheritance, comprising the inheritance of natural selection pressures previously modified by niche construction, to genetic inheritance in evolution. Human niche construction modifies selection pressures in environments in ways that affect both human evolution, and the evolution of other species. Human ecological inheritance is exceptionally potent because it includes the social transmission and inheritance of cultural knowledge, and material culture. Human genetic inheritance in combination with human cultural inheritance thus provides a basis for gene-culture coevolution, and multivariate dynamics in cultural evolution. Niche construction theory potentially integrates the biological and social aspects of the human sciences. We elaborate on these processes, and provide brief introductions to each of the papers published in this theme issue.

  15. Niche construction, genetic evolution and cultural change.

    PubMed

    Odling-Smee, F J

    1995-12-01

    In evolution, adaptation is traditionally viewed as a process by which natural selection moulds organisms to fit pre-established environmental templates. The changes organisms cause in environments are seldom thought evolutionarily significant. However, organisms partly create their own environments by 'niche construction'. A formal model of niche construction is discussed. It focusses on two genetic loci, E and A. It assumes: This model produces some surprising results. For example, timelags occur between the spread of niche construction and the response to the selection it generates. Niche construction also enhances the role of phenotypes in evolution. Organisms not only carry and propagate genes, but they also modify the selection pressures that select those genes. This dual role changes the relationship between genetic evolution; individual development; learning; and cultural processes in human beings.

  16. Mathematics of small stochastic reaction networks: A boundary layer theory for eigenstate analysis

    NASA Astrophysics Data System (ADS)

    Mjolsness, Eric; Prasad, Upendra

    2013-03-01

    We study and analyze the stochastic dynamics of a reversible bimolecular reaction A + B ↔ C called the "trivalent reaction." This reaction is of a fundamental nature and is part of many biochemical reaction networks. The stochastic dynamics is given by the stochastic master equation, which is difficult to solve except when the equilibrium state solution is desired. We present a novel way of finding the eigenstates of this system of difference-differential equations, using perturbation analysis of ordinary differential equations arising from approximation of the difference equations. The time evolution of the state probabilities can then be expressed in terms of the eigenvalues and the eigenvectors.

  17. The cancer stem cell niche: how essential is the niche in regulating stemness of tumor cells?

    PubMed

    Plaks, Vicki; Kong, Niwen; Werb, Zena

    2015-03-01

    Cancer stem cells (CSCs) are tumor cells that have the principal properties of self-renewal, clonal tumor initiation capacity, and clonal long-term repopulation potential. CSCs reside in niches, which are anatomically distinct regions within the tumor microenvironment. These niches maintain the principle properties of CSCs, preserve their phenotypic plasticity, protect them from the immune system, and facilitate their metastatic potential. In this perspective, we focus on the CSC niche and discuss its contribution to tumor initiation and progression. Since CSCs survive many commonly employed cancer therapies, we examine the prospects of targeting the niche components as preferable therapeutic targets. PMID:25748930

  18. The Cancer Stem Cell Niche: How Essential is the Niche in Regulating Stemness of Tumor Cells?

    PubMed Central

    Plaks, Vicki; Kong, Niwen; Werb, Zena

    2015-01-01

    Cancer stem cells (CSCs) are tumor cells that have the principal properties of self-renewal, clonal tumor initiation capacity and clonal long-term repopulation potential. CSCs reside in niches, which are anatomically distinct regions within the tumor microenvironment. These niches maintain the principle properties of CSCs, preserve their phenotypic plasticity, protect them from the immune system and facilitate their metastatic potential. In this perspective, we focus on the CSC niche and discuss its contribution to tumor initiation and progression. Since CSCs survive many commonly employed cancer therapies, we examine the prospects of targeting the niche components as preferable therapeutic targets. PMID:25748930

  19. Brain tumor detection using scalp eeg with modified Wavelet-ICA and multi layer feed forward neural network.

    PubMed

    Selvam, V Salai; Shenbagadevi, S

    2011-01-01

    Use of scalp EEG for the diagnosis of various cerebral disorders is progressively increasing. Though the advanced neuroimaging techniques such as MRI and CT-SCAN still stay as principal confirmative methods for detecting and localizing brain tumors, the development of automated systems for the detection of brain tumors using the scalp EEG has started attracting the researchers all over the world notably since 2000. This is because of two important facts: (i) cheapness and easiness of methods of recording and analyzing the scalp EEG and (ii) lower risk and possible early detection. This paper presents a method of detecting the brain tumor using the first, second and third order statistics of the scalp EEG with a Modified Wavelet-Independent Component Analysis (MwICA) technique and a multi-layer feed-forward neural network. PMID:22255732

  20. Using a Network of Boundary Layer Profilers to Characterize the Atmosphere at a Major Spaceport

    NASA Technical Reports Server (NTRS)

    Case, Jonathan L.; Lambert, Winifred; Merceret, Francis; Ward, Jennifer

    2006-01-01

    Space launch, landing, and ground operations at the Kennedy Space Center (KSC) and Cape Canaveral Air Force Station (CCAFS) in east-central Florida are highly sensitive to mesoscale weather conditions throughout the year. Due to the complex land-water interfaces and the important role of mesoscale circulations, a high-resolution network of five 915-MHz Doppler Radar Wind Profilers (DRWP) and 44 wind towers was installed over the KSC/CCAFS area. By using quality-controlled 915-MHz DRAT data along with the near-surface tower observations, the Applied Meteorology Unit and KSC Weather Office have studied the development and evolution of various mesoscale phenomena across KSC/CCAFS such as sea and land breezes, low-level jets, and frontal passages. This paper will present some examples of mesoscale phenomena that can impact space operations at KSC/CCAFS, focusing on the utility of the 915-MHz DRWP network in identifying important characteristics of sea/land breezes and low-level jets.

  1. [Multi-layer perceptron neural network based algorithm for simultaneous retrieving temperature and emissivity from hyperspectral FTIR data].

    PubMed

    Cheng, Jie; Xiao, Qing; Li, Xiao-Wen; Liu, Qin-Huo; Du, Yong-Ming

    2008-04-01

    The present paper firstly points out the defect of typical temperature and emissivity separation algorithms when dealing with hyperspectral FTIR data: the conventional temperature and emissivity algorithms can not reproduce correct emissivity value when the difference between the ground-leaving radiance and object's blackbody radiation at its true temperature and the instrument random noise are on the same order, and this phenomenon is very prone to occur rence near 714 and 1 250 cm(-1) in the field measurements. In order to settle this defect, a three-layer perceptron neural network has been introduced into the simultaneous inversion of temperature and emissivity from hyperspectral FTIR data. The soil emissivity spectra from the ASTER spectral library were used to produce the training data, the soil emissivity spectra from the MODIS spectral library were used to produce the test data, and the result of network test shows the MLP is robust. Meanwhile, the ISSTES algorithm was used to retrieve the temperature and emissivity form the test data. By comparing the results of MLP and ISSTES, we found the MLP can overcome the disadvantage of typical temperature and emisivity separation, although the rmse of derived emissivity using MLP is lower than the ISSTES as a whole. Hence, the MLP can be regarded as a beneficial complementarity of the typical temperature and emissivity separation.

  2. Niche-modulated and niche-modulating genes in bone marrow cells

    PubMed Central

    Cohen, Y; Garach-Jehoshua, O; Bar-Chaim, A; Kornberg, A

    2012-01-01

    Bone marrow (BM) cells depend on their niche for growth and survival. However, the genes modulated by niche stimuli have not been discriminated yet. For this purpose, we investigated BM aspirations from patients with various hematological malignancies. Each aspirate was fractionated, and the various samples were fixed at different time points and analyzed by microarray. Identification of niche-modulated genes relied on sustained change in expression following loss of niche regulation. Compared with the reference (‘authentic') samples, which were fixed immediately following aspiration, the BM samples fixed after longer stay out-of-niche acquired numerous changes in gene-expression profile (GEP). The overall genes modulated included a common subset of functionally diverse genes displaying prompt and sustained ‘switch' in expression irrespective of the tumor type. Interestingly, the ‘switch' in GEP was reversible and turned ‘off-and-on' again in culture conditions, resuming cell–cell–matrix contact versus respread into suspension, respectively. Moreover, the resuming of contact prolonged the survival of tumor cells out-of-niche, and the regression of the ‘contactless switch' was followed by induction of a new set of genes, this time mainly encoding extracellular proteins including angiogenic factors and extracellular matrix proteins. Our data set, being unique in authentic expression design, uncovered niche-modulated and niche-modulating genes capable of controlling homing, expansion and angiogenesis. PMID:23241658

  3. Macro-Climatic Distribution Limits Show Both Niche Expansion and Niche Specialization among C4 Panicoids

    PubMed Central

    Aagesen, Lone; Biganzoli, Fernando; Bena, Julia; Godoy-Bürki, Ana C.; Reinheimer, Renata; Zuloaga, Fernando O.

    2016-01-01

    Grasses are ancestrally tropical understory species whose current dominance in warm open habitats is linked to the evolution of C4 photosynthesis. C4 grasses maintain high rates of photosynthesis in warm and water stressed environments, and the syndrome is considered to induce niche shifts into these habitats while adaptation to cold ones may be compromised. Global biogeographic analyses of C4 grasses have, however, concentrated on diversity patterns, while paying little attention to distributional limits. Using phylogenetic contrast analyses, we compared macro-climatic distribution limits among ~1300 grasses from the subfamily Panicoideae, which includes 4/5 of the known photosynthetic transitions in grasses. We explored whether evolution of C4 photosynthesis correlates with niche expansions, niche changes, or stasis at subfamily level and within the two tribes Paniceae and Paspaleae. We compared the climatic extremes of growing season temperatures, aridity, and mean temperatures of the coldest months. We found support for all the known biogeographic distribution patterns of C4 species, these patterns were, however, formed both by niche expansion and niche changes. The only ubiquitous response to a change in the photosynthetic pathway within Panicoideae was a niche expansion of the C4 species into regions with higher growing season temperatures, but without a withdrawal from the inherited climate niche. Other patterns varied among the tribes, as macro-climatic niche evolution in the American tribe Paspaleae differed from the pattern supported in the globally distributed tribe Paniceae and at family level. PMID:26950074

  4. Macro-Climatic Distribution Limits Show Both Niche Expansion and Niche Specialization among C4 Panicoids.

    PubMed

    Aagesen, Lone; Biganzoli, Fernando; Bena, Julia; Godoy-Bürki, Ana C; Reinheimer, Renata; Zuloaga, Fernando O

    2016-01-01

    Grasses are ancestrally tropical understory species whose current dominance in warm open habitats is linked to the evolution of C4 photosynthesis. C4 grasses maintain high rates of photosynthesis in warm and water stressed environments, and the syndrome is considered to induce niche shifts into these habitats while adaptation to cold ones may be compromised. Global biogeographic analyses of C4 grasses have, however, concentrated on diversity patterns, while paying little attention to distributional limits. Using phylogenetic contrast analyses, we compared macro-climatic distribution limits among ~1300 grasses from the subfamily Panicoideae, which includes 4/5 of the known photosynthetic transitions in grasses. We explored whether evolution of C4 photosynthesis correlates with niche expansions, niche changes, or stasis at subfamily level and within the two tribes Paniceae and Paspaleae. We compared the climatic extremes of growing season temperatures, aridity, and mean temperatures of the coldest months. We found support for all the known biogeographic distribution patterns of C4 species, these patterns were, however, formed both by niche expansion and niche changes. The only ubiquitous response to a change in the photosynthetic pathway within Panicoideae was a niche expansion of the C4 species into regions with higher growing season temperatures, but without a withdrawal from the inherited climate niche. Other patterns varied among the tribes, as macro-climatic niche evolution in the American tribe Paspaleae differed from the pattern supported in the globally distributed tribe Paniceae and at family level.

  5. Macro-Climatic Distribution Limits Show Both Niche Expansion and Niche Specialization among C4 Panicoids.

    PubMed

    Aagesen, Lone; Biganzoli, Fernando; Bena, Julia; Godoy-Bürki, Ana C; Reinheimer, Renata; Zuloaga, Fernando O

    2016-01-01

    Grasses are ancestrally tropical understory species whose current dominance in warm open habitats is linked to the evolution of C4 photosynthesis. C4 grasses maintain high rates of photosynthesis in warm and water stressed environments, and the syndrome is considered to induce niche shifts into these habitats while adaptation to cold ones may be compromised. Global biogeographic analyses of C4 grasses have, however, concentrated on diversity patterns, while paying little attention to distributional limits. Using phylogenetic contrast analyses, we compared macro-climatic distribution limits among ~1300 grasses from the subfamily Panicoideae, which includes 4/5 of the known photosynthetic transitions in grasses. We explored whether evolution of C4 photosynthesis correlates with niche expansions, niche changes, or stasis at subfamily level and within the two tribes Paniceae and Paspaleae. We compared the climatic extremes of growing season temperatures, aridity, and mean temperatures of the coldest months. We found support for all the known biogeographic distribution patterns of C4 species, these patterns were, however, formed both by niche expansion and niche changes. The only ubiquitous response to a change in the photosynthetic pathway within Panicoideae was a niche expansion of the C4 species into regions with higher growing season temperatures, but without a withdrawal from the inherited climate niche. Other patterns varied among the tribes, as macro-climatic niche evolution in the American tribe Paspaleae differed from the pattern supported in the globally distributed tribe Paniceae and at family level. PMID:26950074

  6. Conditional Disease Development extracted from Longitudinal Health Care Cohort Data using Layered Network Construction

    PubMed Central

    Kannan, Venkateshan; Swartz, Fredrik; Kiani, Narsis A.; Silberberg, Gilad; Tsipras, Giorgos; Gomez-Cabrero, David; Alexanderson, Kristina; Tegnèr, Jesper

    2016-01-01

    Health care data holds great promise to be used in clinical decision support systems. However, frequent near-synonymous diagnoses recorded separately, as well as the sheer magnitude and complexity of the disease data makes it challenging to extract non-trivial conclusions beyond confirmatory associations from such a web of interactions. Here we present a systematic methodology to derive statistically valid conditional development of diseases. To this end we utilize a cohort of 5,512,469 individuals followed over 13 years at inpatient care, including data on disability pension and cause of death. By introducing a causal information fraction measure and taking advantage of the composite structure in the ICD codes, we extract an effective directed lower dimensional network representation (100 nodes and 130 edges) of our cohort. Unpacking composite nodes into bipartite graphs retrieves, for example, that individuals with behavioral disorders are more likely to be followed by prescription drug poisoning episodes, whereas women with leiomyoma were more likely to subsequently experience endometriosis. The conditional disease development represent putative causal relations, indicating possible novel clinical relationships and pathophysiological associations that have not been explored yet. PMID:27211115

  7. Aircraft optical cable plant: the physical layer for fly-by-light control networks

    NASA Astrophysics Data System (ADS)

    Weaver, Thomas L.

    1996-10-01

    A program was completed with joint industry and government funding to apply fiber optic technologies to aircraft. The technology offers many potential benefits. Among them are increased electromagnetic interference immunity and the possibility of reduced weight, increased reliability, and enlarged capability by redesigning architectures to use the large bandwidth of fiber optics. Those benefits can be realized if fiber optics meets the unique requirements of aircraft networks. Many independent efforts have been made in the development of the systems, known as cable plants, to link opto-electronic components. The FLASH program built on that work. Over the last two years, FLASH expanded on the cable plant efforts by building components based on a cohesive aircraft plant system concept. The concept was rooted in not just optical performance, but also cost, manufacturing, installation, maintenance, and support. To do that, the FLASH team evaluated requirements, delineated environmental and use conditions, designed, built, and tested components, such as cables, connectors, splices and backplanes for transport aircraft, tactical aircraft, and helicopters. In addition, the FLASH team developed installation and test methods, and support equipment for aircraft optical cable plants. The results of that design, development, and test effort are reported here.

  8. Conditional Disease Development extracted from Longitudinal Health Care Cohort Data using Layered Network Construction.

    PubMed

    Kannan, Venkateshan; Swartz, Fredrik; Kiani, Narsis A; Silberberg, Gilad; Tsipras, Giorgos; Gomez-Cabrero, David; Alexanderson, Kristina; Tegnèr, Jesper

    2016-01-01

    Health care data holds great promise to be used in clinical decision support systems. However, frequent near-synonymous diagnoses recorded separately, as well as the sheer magnitude and complexity of the disease data makes it challenging to extract non-trivial conclusions beyond confirmatory associations from such a web of interactions. Here we present a systematic methodology to derive statistically valid conditional development of diseases. To this end we utilize a cohort of 5,512,469 individuals followed over 13 years at inpatient care, including data on disability pension and cause of death. By introducing a causal information fraction measure and taking advantage of the composite structure in the ICD codes, we extract an effective directed lower dimensional network representation (100 nodes and 130 edges) of our cohort. Unpacking composite nodes into bipartite graphs retrieves, for example, that individuals with behavioral disorders are more likely to be followed by prescription drug poisoning episodes, whereas women with leiomyoma were more likely to subsequently experience endometriosis. The conditional disease development represent putative causal relations, indicating possible novel clinical relationships and pathophysiological associations that have not been explored yet. PMID:27211115

  9. Emergence of complexity in evolving niche-model food webs.

    PubMed

    Guill, Christian; Drossel, Barbara

    2008-03-01

    We have analysed mechanisms that promote the emergence of complex structures in evolving model food webs. The niche model is used to determine predator-prey relationships. Complexity is measured by species richness as well as trophic level structure and link density. Adaptive dynamics that allow predators to concentrate on the prey species they are best adapted to lead to a strong increase in species number but have only a small effect on the number and relative occupancy of trophic levels. The density of active links also remains small but a high number of potential links allows the network to adjust to changes in the species composition (emergence and extinction of species). Incorporating effects of body size on individual metabolism leads to a more complex trophic level structure: both the maximum and the average trophic level increase. So does the density of active links. Taking body size effects into consideration does not have a measurable influence on species richness. If species are allowed to adjust their foraging behaviour, the complexity of the evolving networks can also be influenced by the size of the external resources. The larger the resources, the larger and more complex is the food web it can sustain. Body size effects and increasing resources do not change size and the simple structure of the evolving networks if adaptive foraging is prohibited. This leads to the conclusion that in the framework of the niche model adaptive foraging is a necessary but not sufficient condition for the emergence of complex networks. It is found that despite the stabilising effect of foraging adaptation the system displays elements of self-organised critical behaviour.

  10. An epidermis-driven mechanism positions and scales stem cell niches in plants.

    PubMed

    Gruel, Jérémy; Landrein, Benoit; Tarr, Paul; Schuster, Christoph; Refahi, Yassin; Sampathkumar, Arun; Hamant, Olivier; Meyerowitz, Elliot M; Jönsson, Henrik

    2016-01-01

    How molecular patterning scales to organ size is highly debated in developmental biology. We explore this question for the characteristic gene expression domains of the plant stem cell niche residing in the shoot apical meristem. We show that a combination of signals originating from the epidermal cell layer can correctly pattern the key gene expression domains and notably leads to adaptive scaling of these domains to the size of the tissue. Using live imaging, we experimentally confirm this prediction. The identified mechanism is also sufficient to explain de novo stem cell niches in emerging flowers. Our findings suggest that the deformation of the tissue transposes meristem geometry into an instructive scaling and positional input for the apical plant stem cell niche. PMID:27152324

  11. An epidermis-driven mechanism positions and scales stem cell niches in plants

    PubMed Central

    Gruel, Jérémy; Landrein, Benoit; Tarr, Paul; Schuster, Christoph; Refahi, Yassin; Sampathkumar, Arun; Hamant, Olivier; Meyerowitz, Elliot M.; Jönsson, Henrik

    2016-01-01

    How molecular patterning scales to organ size is highly debated in developmental biology. We explore this question for the characteristic gene expression domains of the plant stem cell niche residing in the shoot apical meristem. We show that a combination of signals originating from the epidermal cell layer can correctly pattern the key gene expression domains and notably leads to adaptive scaling of these domains to the size of the tissue. Using live imaging, we experimentally confirm this prediction. The identified mechanism is also sufficient to explain de novo stem cell niches in emerging flowers. Our findings suggest that the deformation of the tissue transposes meristem geometry into an instructive scaling and positional input for the apical plant stem cell niche. PMID:27152324

  12. An epidermis-driven mechanism positions and scales stem cell niches in plants.

    PubMed

    Gruel, Jérémy; Landrein, Benoit; Tarr, Paul; Schuster, Christoph; Refahi, Yassin; Sampathkumar, Arun; Hamant, Olivier; Meyerowitz, Elliot M; Jönsson, Henrik

    2016-01-01

    How molecular patterning scales to organ size is highly debated in developmental biology. We explore this question for the characteristic gene expression domains of the plant stem cell niche residing in the shoot apical meristem. We show that a combination of signals originating from the epidermal cell layer can correctly pattern the key gene expression domains and notably leads to adaptive scaling of these domains to the size of the tissue. Using live imaging, we experimentally confirm this prediction. The identified mechanism is also sufficient to explain de novo stem cell niches in emerging flowers. Our findings suggest that the deformation of the tissue transposes meristem geometry into an instructive scaling and positional input for the apical plant stem cell niche.

  13. The niche, biogeography and species interactions

    PubMed Central

    Wiens, John J.

    2011-01-01

    In this paper, I review the relevance of the niche to biogeography, and what biogeography may tell us about the niche. The niche is defined as the combination of abiotic and biotic conditions where a species can persist. I argue that most biogeographic patterns are created by niche differences over space, and that even ‘geographic barriers’ must have an ecological basis. However, we know little about specific ecological factors underlying most biogeographic patterns. Some evidence supports the importance of abiotic factors, whereas few examples exist of large-scale patterns created by biotic interactions. I also show how incorporating biogeography may offer new perspectives on resource-related niches and species interactions. Several examples demonstrate that even after a major evolutionary radiation within a region, the region can still be invaded by ecologically similar species from another clade, countering the long-standing idea that communities and regions are generally ‘saturated’ with species. I also describe the somewhat paradoxical situation where competition seems to limit trait evolution in a group, but does not prevent co-occurrence of species with similar values for that trait (called here the ‘competition–divergence–co-occurrence conundrum’). In general, the interface of biogeography and ecology could be a major area for research in both fields. PMID:21768150

  14. Modelling the ecological niche from functional traits

    PubMed Central

    Kearney, Michael; Simpson, Stephen J.; Raubenheimer, David; Helmuth, Brian

    2010-01-01

    The niche concept is central to ecology but is often depicted descriptively through observing associations between organisms and habitats. Here, we argue for the importance of mechanistically modelling niches based on functional traits of organisms and explore the possibilities for achieving this through the integration of three theoretical frameworks: biophysical ecology (BE), the geometric framework for nutrition (GF) and dynamic energy budget (DEB) models. These three frameworks are fundamentally based on the conservation laws of thermodynamics, describing energy and mass balance at the level of the individual and capturing the prodigious predictive power of the concepts of ‘homeostasis’ and ‘evolutionary fitness’. BE and the GF provide mechanistic multi-dimensional depictions of climatic and nutritional niches, respectively, providing a foundation for linking organismal traits (morphology, physiology, behaviour) with habitat characteristics. In turn, they provide driving inputs and cost functions for mass/energy allocation within the individual as determined by DEB models. We show how integration of the three frameworks permits calculation of activity constraints, vital rates (survival, development, growth, reproduction) and ultimately population growth rates and species distributions. When integrated with contemporary niche theory, functional trait niche models hold great promise for tackling major questions in ecology and evolutionary biology. PMID:20921046

  15. Building stem cell niches from the molecule up through engineered peptide materials.

    PubMed

    Lampe, Kyle J; Heilshorn, Sarah C

    2012-06-25

    The native stem cell niche is a dynamic and complex microenvironment. Recapitulating this niche is a critical focus within the fields of stem cell biology, tissue engineering, and regenerative medicine and requires the development of well-defined, tunable materials. Recent biomaterial design strategies seek to create engineered matrices that interact with cells at the molecular scale and allow on-demand, cell-triggered matrix modifications. Peptide and protein engineering can accomplish these goals through the molecular-level design of bioinductive and bioresponsive materials. This brief review focuses on engineered peptide and protein materials suitable for use as in vitro neural stem cell niche mimics and in vivo central nervous system repair. A key hallmark of these materials is the immense design freedom to specify the exact amino acid sequence leading to multi-functional bulk materials with tunable properties. These advanced materials are engineered using rational design strategies to recapitulate key aspects of the native neural stem cell niche. The resulting materials often combine the advantages of biological matrices with the engineering control of synthetic polymers. Future design strategies are expected to endow these materials with multiple layers of bi-directional feedback between the cell and the matrix, which will lead to more advanced mimics of the highly dynamic neural stem cell niche.

  16. Engineering the niche for stem cells.

    PubMed

    Tan, Shawna; Barker, Nicholas

    2013-12-01

    Much has been made about the potential for stem cells in regenerative medicine but the reality is that the development of actual therapies has been slow. Adult stem cells rely heavily on the assortment of biochemical and biophysical elements that constitute the local microenvironment in which they exist. One goal of biomedicine is to create an artificial yet biofunctional niche to support multipotency, differentiation and proliferation. Such tools would facilitate more conclusive experimentation by biologists, pharmaceutical scientists and tissue engineers. While many bioengineering techniques and platforms are already in use, technological innovations now allow this to be done at a higher resolution and specificity. Ultimately, the multidisciplinary integration of engineering and biology will allow the niche to be generated at a scale that can be clinically exploited. Using the systems that constitute the intestinal, hematopoietic and epidermal tissues, this article summarizes the various approaches and tools currently employed to recreate stem cell niches and also explores recent advances in the field. PMID:24274105

  17. Engineering the niche for stem cells.

    PubMed

    Tan, Shawna; Barker, Nicholas

    2013-12-01

    Much has been made about the potential for stem cells in regenerative medicine but the reality is that the development of actual therapies has been slow. Adult stem cells rely heavily on the assortment of biochemical and biophysical elements that constitute the local microenvironment in which they exist. One goal of biomedicine is to create an artificial yet biofunctional niche to support multipotency, differentiation and proliferation. Such tools would facilitate more conclusive experimentation by biologists, pharmaceutical scientists and tissue engineers. While many bioengineering techniques and platforms are already in use, technological innovations now allow this to be done at a higher resolution and specificity. Ultimately, the multidisciplinary integration of engineering and biology will allow the niche to be generated at a scale that can be clinically exploited. Using the systems that constitute the intestinal, hematopoietic and epidermal tissues, this article summarizes the various approaches and tools currently employed to recreate stem cell niches and also explores recent advances in the field.

  18. The bone marrow niche for haematopoietic stem cells.

    PubMed

    Morrison, Sean J; Scadden, David T

    2014-01-16

    Niches are local tissue microenvironments that maintain and regulate stem cells. Haematopoiesis provides a model for understanding mammalian stem cells and their niches, but the haematopoietic stem cell (HSC) niche remains incompletely defined and beset by competing models. Recent progress has been made in elucidating the location and cellular components of the HSC niche in the bone marrow. The niche is perivascular, created partly by mesenchymal stromal cells and endothelial cells and often, but not always, located near trabecular bone. Outstanding questions concern the cellular complexity of the niche, the role of the endosteum and functional heterogeneity among perivascular microenvironments.

  19. The bone marrow niche for haematopoietic stem cells

    PubMed Central

    Morrison, Sean J.; Scadden, David T.

    2015-01-01

    Preface Niches are local tissue microenvironments that maintain and regulate stem cells. Haematopoiesis provides a paradigm for understanding mammalian stem cells and their niches, yet the haematopoietic stem cell (HSC) niche remains incompletely defined and beset by competing models. Here we review progress in elucidating the location and cellular components of the HSC niche in the bone marrow. The niche is perivascular, created partly by mesenchymal stromal cells and endothelial cells and often, but not always, located near trabecular bone. Outstanding questions concern the cellular complexity of the niche, the role of the endosteum, and functional heterogeneity among perivascular microenvironments. PMID:24429631

  20. Modeling renal progenitors - defining the niche.

    PubMed

    Tanigawa, Shunsuke; Perantoni, Alan O

    2016-01-01

    Significant recent advances in methodologies for the differentiation of pluripotent stem cells to renal progenitors as well as the definition of niche conditions for sustaining those progenitors have dramatically enhanced our understanding of their biology and developmental programing, prerequisites for establishing viable approaches to renal regeneration. In this article, we review the evolution of culture techniques and models for the study of metanephric development, describe the signaling mechanisms likely to be driving progenitor self-renewal, and discuss current efforts to generate de novo functional tissues, providing in depth protocols and niche conditions for the stabilization of the nephronic Six2+progenitor. PMID:26856661

  1. Stem cell maintenance in a different niche

    PubMed Central

    Ahn, Ji Yeon; Lee, Seung Tae

    2013-01-01

    To overcome the difficulty of controlling stem cell fate and function in applications to regenerative medicine, a number of alternative approaches have been made. Recent reports demonstrate that a non-cellular niche modulating the biophysical microenvironment with chemical factors can support stem cell self-renewal. In our previous studies, early establishment was executed to optimize biophysical factors and it was subsequently found that the microgeometry of the extracellular matrix made huge differences in stem cell behavior and phenotype. We review here a three-dimensional, non-cellular niche designed to support stem cell self-renewal. The characteristics of stem cells under the designed system are further discussed. PMID:23875159

  2. Pore Network Modeling and Synchrotron Imaging of Liquid Water in the Gas Diffusion Layer of Polymer Electrolyte Membrane Fuel Cells

    NASA Astrophysics Data System (ADS)

    Hinebaugh, James Thomas

    Polymer electrolyte membrane (PEM) fuel cells operate at levels of high humidity, leading to condensation throughout the cell components. The porous gas diffusion layer (GDL) must not become over-saturated with liquid water, due to its responsibility in providing diffusion pathways to and from the embedded catalyst sites. Due to the opaque and microscale nature of the GDL, a current challenge of the fuel cell industry is to identify the characteristics that make the GDL more or less robust against flooding. Modeling the system as a pore network is an attractive investigative strategy; however, for flooding simulations to provide meaningful material comparisons, accurate GDL topology and condensation distributions must be provided. The focus of this research is to provide the foundational tools with which to capture both of these requirements. The method of pore network modeling on topologically representative pore networks is demonstrated to describe flooding phenomena within GDL materials. A stochastic modeling algorithm is then developed to create pore spaces with the relevant features of GDL materials. Then, synchrotron based X-ray visualization experiments are developed and conducted to provide insight into condensation conditions. It was found that through-plane porosity distributions have significant effects on the GDL saturation levels. Some GDL manufacturing processes result in high porosity regions which are predicted to become heavily saturated with water if they are positioned between the condensation sites and the exhaust channels. Additionally, it was found that fiber diameter and the volume fraction of binding material applied to the GDL have significant impacts on the GDL heterogeneity and pore size distribution. Representative stochastic models must accurately describe these three material characteristics. In situ, dynamic liquid water behavior was visualized at the Canadian Light source, Inc. synchrotron using imaging and image processing

  3. Design of QoS-Aware Multi-Level MAC-Layer for Wireless Body Area Network.

    PubMed

    Hu, Long; Zhang, Yin; Feng, Dakui; Hassan, Mohammad Mehedi; Alelaiwi, Abdulhameed; Alamri, Atif

    2015-12-01

    With the advances in wearable computing and various wireless technologies, there is an increasing trend to outsource body signals from wireless body area network (WBAN) to outside world including cyber space, healthcare big data clouds, etc. Since the environmental and physiological data collected by multimodal sensors have different importance, the provisioning of quality of service (QoS) for the sensory data in WBAN is a critical issue. This paper proposes multiple level-based QoS design at WBAN media access control layer in terms of user level, data level and time level. In the proposed QoS provisioning scheme, different users have different priorities, various sensory data collected by different sensor nodes have different importance, while data priority for the same sensor node varies over time. The experimental results show that the proposed multi-level based QoS provisioning solution in WBAN yields better performance for meeting QoS requirements of personalized healthcare applications while achieving energy saving. PMID:26490150

  4. Design of QoS-Aware Multi-Level MAC-Layer for Wireless Body Area Network.

    PubMed

    Hu, Long; Zhang, Yin; Feng, Dakui; Hassan, Mohammad Mehedi; Alelaiwi, Abdulhameed; Alamri, Atif

    2015-12-01

    With the advances in wearable computing and various wireless technologies, there is an increasing trend to outsource body signals from wireless body area network (WBAN) to outside world including cyber space, healthcare big data clouds, etc. Since the environmental and physiological data collected by multimodal sensors have different importance, the provisioning of quality of service (QoS) for the sensory data in WBAN is a critical issue. This paper proposes multiple level-based QoS design at WBAN media access control layer in terms of user level, data level and time level. In the proposed QoS provisioning scheme, different users have different priorities, various sensory data collected by different sensor nodes have different importance, while data priority for the same sensor node varies over time. The experimental results show that the proposed multi-level based QoS provisioning solution in WBAN yields better performance for meeting QoS requirements of personalized healthcare applications while achieving energy saving.

  5. Liver Tumor Segmentation from MR Images Using 3D Fast Marching Algorithm and Single Hidden Layer Feedforward Neural Network.

    PubMed

    Le, Trong-Ngoc; Bao, Pham The; Huynh, Hieu Trung

    2016-01-01

    Objective. Our objective is to develop a computerized scheme for liver tumor segmentation in MR images. Materials and Methods. Our proposed scheme consists of four main stages. Firstly, the region of interest (ROI) image which contains the liver tumor region in the T1-weighted MR image series was extracted by using seed points. The noise in this ROI image was reduced and the boundaries were enhanced. A 3D fast marching algorithm was applied to generate the initial labeled regions which are considered as teacher regions. A single hidden layer feedforward neural network (SLFN), which was trained by a noniterative algorithm, was employed to classify the unlabeled voxels. Finally, the postprocessing stage was applied to extract and refine the liver tumor boundaries. The liver tumors determined by our scheme were compared with those manually traced by a radiologist, used as the "ground truth." Results. The study was evaluated on two datasets of 25 tumors from 16 patients. The proposed scheme obtained the mean volumetric overlap error of 27.43% and the mean percentage volume error of 15.73%. The mean of the average surface distance, the root mean square surface distance, and the maximal surface distance were 0.58 mm, 1.20 mm, and 6.29 mm, respectively. PMID:27597960

  6. Liver Tumor Segmentation from MR Images Using 3D Fast Marching Algorithm and Single Hidden Layer Feedforward Neural Network

    PubMed Central

    2016-01-01

    Objective. Our objective is to develop a computerized scheme for liver tumor segmentation in MR images. Materials and Methods. Our proposed scheme consists of four main stages. Firstly, the region of interest (ROI) image which contains the liver tumor region in the T1-weighted MR image series was extracted by using seed points. The noise in this ROI image was reduced and the boundaries were enhanced. A 3D fast marching algorithm was applied to generate the initial labeled regions which are considered as teacher regions. A single hidden layer feedforward neural network (SLFN), which was trained by a noniterative algorithm, was employed to classify the unlabeled voxels. Finally, the postprocessing stage was applied to extract and refine the liver tumor boundaries. The liver tumors determined by our scheme were compared with those manually traced by a radiologist, used as the “ground truth.” Results. The study was evaluated on two datasets of 25 tumors from 16 patients. The proposed scheme obtained the mean volumetric overlap error of 27.43% and the mean percentage volume error of 15.73%. The mean of the average surface distance, the root mean square surface distance, and the maximal surface distance were 0.58 mm, 1.20 mm, and 6.29 mm, respectively. PMID:27597960

  7. Nano-structural analysis of effective transport paths in fuel-cell catalyst layers by using stochastic material network methods

    NASA Astrophysics Data System (ADS)

    Shin, Seungho; Kim, Ah-Reum; Um, Sukkee

    2016-02-01

    A two-dimensional material network model has been developed to visualize the nano-structures of fuel-cell catalysts and to search for effective transport paths for the optimal performance of fuel cells in randomly-disordered composite catalysts. Stochastic random modeling based on the Monte Carlo method is developed using random number generation processes over a catalyst layer domain at a 95% confidence level. After the post-determination process of the effective connectivity, particularly for mass transport, the effective catalyst utilization factors are introduced to determine the extent of catalyst utilization in the fuel cells. The results show that the superficial pore volume fractions of 600 trials approximate a normal distribution curve with a mean of 0.5. In contrast, the estimated volume fraction of effectively inter-connected void clusters ranges from 0.097 to 0.420, which is much smaller than the superficial porosity of 0.5 before the percolation process. Furthermore, the effective catalyst utilization factor is determined to be linearly proportional to the effective porosity. More importantly, this study reveals that the average catalyst utilization is less affected by the variations of the catalyst's particle size and the absolute catalyst loading at a fixed volume fraction of void spaces.

  8. Validation of pore network simulations of ex-situ water distributions in a gas diffusion layer of proton exchange membrane fuel cells with X-ray tomographic images

    NASA Astrophysics Data System (ADS)

    Agaesse, Tristan; Lamibrac, Adrien; Büchi, Felix N.; Pauchet, Joel; Prat, Marc

    2016-11-01

    Understanding and modeling two-phase flows in the gas diffusion layer (GDL) of proton exchange membrane fuel cells are important in order to improve fuel cells performance. They are scientifically challenging because of the peculiarities of GDLs microstructures. In the present work, simulations on a pore network model are compared to X-ray tomographic images of water distributions during an ex-situ water invasion experiment. A method based on watershed segmentation was developed to extract a pore network from the 3D segmented image of the dry GDL. Pore network modeling and a full morphology model were then used to perform two-phase simulations and compared to the experimental data. The results show good agreement between experimental and simulated microscopic water distributions. Pore network extraction parameters were also benchmarked using the experimental data and results from full morphology simulations.

  9. Target article with commentaries: developmental niche construction.

    PubMed

    Flynn, Emma G; Laland, Kevin N; Kendal, Rachel L; Kendal, Jeremy R

    2013-03-01

    Niche construction is the modification of components of the environment through an organism's activities. Humans modify their environments mainly through ontogenetic and cultural processes, and it is this reliance on learning, plasticity and culture that lends human niche construction a special potency. In this paper we aim to facilitate discussion between researchers interested in niche construction and those interested in human cognitive development by highlighting some of the related processes. We discuss the transmission of culturally relevant information, how the human mind is a symbol-generating and artefact-devising system, and how these processes are bi-directional, with infants and children both being directed, and directing, their own development. We reflect on these in the light of four approaches: natural pedagogy, activity theory, distributed cognition and situated learning. Throughout, we highlight pertinent examples in non-humans that parallel or further explicate the processes discussed. Finally we offer three future directions; two involving the use of new techniques in the realms of neuroscience and modelling, and the third suggesting exploration of changes in the effects of niche construction across the lifespan.

  10. Bone metastasis and the metastatic niche.

    PubMed

    Ren, Guangwen; Esposito, Mark; Kang, Yibin

    2015-11-01

    The bone marrow has been long known to host a unique environment amenable to colonization by metastasizing tumor cells. Yet, the underlying molecular interactions within this specialized microenvironment which give rise to the high incidence of bone metastasis in breast and prostate cancer patients have long remained uncharacterized. With the recent description of the bone metastatic "niche," considerable focus has been placed on understanding how the bone stroma contributes to each step of metastasis. Discoveries within this field have demonstrated that when cancer cells home to the niche in which hematopoietic and mesenchymal stem/progenitor cells normally reside, a bidirectional crosstalk emerges between the tumor cells and the bone metastatic stroma. This communication modulates every step of cancer cell metastasis to the bone, including the initial homing and seeding, formation of micrometastases, outgrowth of macrometastases, and the maintenance of long-term dormancy of disseminated tumor cells in the bone. In clinical practice, targeting the bone metastatic niche is evolving into a promising avenue for the prevention of bone metastatic relapse, therapeutic resistance, and other aspects of cancer progression. Here, we review the current knowledge concerning the role of the bone metastatic niche in bone metastasis.

  11. ECRB ALCOVE AND NICHE GROUND SUPPORT ANALYSIS

    SciTech Connect

    J.W. Keifer

    1999-05-09

    The purpose of the analysis is to provide design bases for Enhanced Characterization of the Repository Block (ECRB) alcove and niche ground support drawings. The objective is to evaluate the ESF Alcove Ground Support Analysis (Ref 5.1) to determine if the calculations technically bound the ECRB alcoves and to address specific differences in the conditions and constraints.

  12. Relating habitat and climatic niches in birds.

    PubMed

    Barnagaud, Jean-Yves; Devictor, Vincent; Jiguet, Frédéric; Barbet-Massin, Morgane; Le Viol, Isabelle; Archaux, Frédéric

    2012-01-01

    Predicting species' responses to the combined effects of habitat and climate changes has become a major challenge in ecology and conservation biology. However, the effects of climatic and habitat gradients on species distributions have generally been considered separately. Here, we explore the relationships between the habitat and thermal dimensions of the ecological niche in European common birds. Using data from the French Breeding Bird Survey, a large-scale bird monitoring program, we correlated the habitat and thermal positions and breadths of 74 bird species, controlling for life history traits and phylogeny. We found that cold climate species tend to have niche positions in closed habitats, as expected by the conjunction of the biogeographic history of birds' habitats, and their current continent-scale gradients. We also report a positive correlation between thermal and habitat niche breadths, a pattern consistent with macroecological predictions concerning the processes shaping species' distributions. Our results suggest that the relationships between the climatic and habitat components of the niche have to be taken into account to understand and predict changes in species' distributions. PMID:22427891

  13. Relating Habitat and Climatic Niches in Birds

    PubMed Central

    Barnagaud, Jean-Yves; Devictor, Vincent; Jiguet, Frédéric; Barbet-Massin, Morgane; Le Viol, Isabelle; Archaux, Frédéric

    2012-01-01

    Predicting species' responses to the combined effects of habitat and climate changes has become a major challenge in ecology and conservation biology. However, the effects of climatic and habitat gradients on species distributions have generally been considered separately. Here, we explore the relationships between the habitat and thermal dimensions of the ecological niche in European common birds. Using data from the French Breeding Bird Survey, a large-scale bird monitoring program, we correlated the habitat and thermal positions and breadths of 74 bird species, controlling for life history traits and phylogeny. We found that cold climate species tend to have niche positions in closed habitats, as expected by the conjunction of the biogeographic history of birds' habitats, and their current continent-scale gradients. We also report a positive correlation between thermal and habitat niche breadths, a pattern consistent with macroecological predictions concerning the processes shaping species' distributions. Our results suggest that the relationships between the climatic and habitat components of the niche have to be taken into account to understand and predict changes in species' distributions. PMID:22427891

  14. microRNAs in Mitochondria: An Unexplored Niche.

    PubMed

    Borralho, Pedro M; Rodrigues, Cecília M P; Steer, Clifford J

    2015-01-01

    Mitochondria are pivotal organelles involved in the regulation of a myriad of crucial biological processes, including cell survival and cell death, rendering mitochondrial dysfunction a relevant step in numerous pathophysiological processes. MicroRNAs (miRNAs) are endogenous small noncoding RNAs that add a new layer of complexity to the control of gene expression. miRNAs function as master regulators and fine-tuners of gene expression, primarily via posttranscriptional mechanisms, and are increasingly demonstrated as a paramount class of endogenous molecules with relevant diagnostic, prognostic, and therapeutic applications. miRNAs and other RNA interference have recently been reported to be present in mitochondria from several species, and we are now beginning to unveil mitochondrial miRNA transport mechanisms, biological function and targets to ascertain their role in this unexplored niche. Here, we describe miRNA biogenesis and present key findings regarding miRNA localization to mitochondria, origin, putative biological function, and implications for human disease.

  15. Functional traits, convergent evolution, and periodic tables of niches.

    PubMed

    Winemiller, Kirk O; Fitzgerald, Daniel B; Bower, Luke M; Pianka, Eric R

    2015-08-01

    Ecology is often said to lack general theories sufficiently predictive for applications. Here, we examine the concept of a periodic table of niches and feasibility of niche classification schemes from functional trait and performance data. Niche differences and their influence on ecological patterns and processes could be revealed effectively by first performing data reduction/ordination analyses separately on matrices of trait and performance data compiled according to logical associations with five basic niche 'dimensions', or aspects: habitat, life history, trophic, defence and metabolic. Resultant patterns then are integrated to produce interpretable niche gradients, ordinations and classifications. Degree of scheme periodicity would depend on degrees of niche conservatism and convergence causing species clustering across multiple niche dimensions. We analysed a sample data set containing trait and performance data to contrast two approaches for producing niche schemes: species ordination within niche gradient space, and niche categorisation according to trait-value thresholds. Creation of niche schemes useful for advancing ecological knowledge and its applications will depend on research that produces functional trait and performance datasets directly related to niche dimensions along with criteria for data standardisation and quality. As larger databases are compiled, opportunities will emerge to explore new methods for data reduction, ordination and classification. PMID:26096695

  16. Realized niche shift during a global biological invasion

    PubMed Central

    Tingley, Reid; Vallinoto, Marcelo; Sequeira, Fernando; Kearney, Michael R.

    2014-01-01

    Accurate forecasts of biological invasions are crucial for managing invasion risk but are hampered by niche shifts resulting from evolved environmental tolerances (fundamental niche shifts) or the presence of novel biotic and abiotic conditions in the invaded range (realized niche shifts). Distinguishing between these kinds of niche shifts is impossible with traditional, correlative approaches to invasion forecasts, which exclusively consider the realized niche. Here we overcome this challenge by combining a physiologically mechanistic model of the fundamental niche with correlative models based on the realized niche to study the global invasion of the cane toad Rhinella marina. We find strong evidence that the success of R. marina in Australia reflects a shift in the species’ realized niche, as opposed to evolutionary shifts in range-limiting traits. Our results demonstrate that R. marina does not fill its fundamental niche in its native South American range and that areas of niche unfilling coincide with the presence of a closely related species with which R. marina hybridizes. Conversely, in Australia, where coevolved taxa are absent, R. marina largely fills its fundamental niche in areas behind the invasion front. The general approach taken here of contrasting fundamental and realized niche models provides key insights into the role of biotic interactions in shaping range limits and can inform effective management strategies not only for invasive species but also for assisted colonization under climate change. PMID:24982155

  17. Functional traits, convergent evolution, and periodic tables of niches.

    PubMed

    Winemiller, Kirk O; Fitzgerald, Daniel B; Bower, Luke M; Pianka, Eric R

    2015-08-01

    Ecology is often said to lack general theories sufficiently predictive for applications. Here, we examine the concept of a periodic table of niches and feasibility of niche classification schemes from functional trait and performance data. Niche differences and their influence on ecological patterns and processes could be revealed effectively by first performing data reduction/ordination analyses separately on matrices of trait and performance data compiled according to logical associations with five basic niche 'dimensions', or aspects: habitat, life history, trophic, defence and metabolic. Resultant patterns then are integrated to produce interpretable niche gradients, ordinations and classifications. Degree of scheme periodicity would depend on degrees of niche conservatism and convergence causing species clustering across multiple niche dimensions. We analysed a sample data set containing trait and performance data to contrast two approaches for producing niche schemes: species ordination within niche gradient space, and niche categorisation according to trait-value thresholds. Creation of niche schemes useful for advancing ecological knowledge and its applications will depend on research that produces functional trait and performance datasets directly related to niche dimensions along with criteria for data standardisation and quality. As larger databases are compiled, opportunities will emerge to explore new methods for data reduction, ordination and classification.

  18. Well-Constructed Single-Layer Molybdenum Disulfide Nanorose Cross-Linked by Three Dimensional-Reduced Graphene Oxide Network for Superior Water Splitting and Lithium Storage Property

    NASA Astrophysics Data System (ADS)

    Zhao, Yanyan; Kuai, Long; Liu, Yanguo; Wang, Pengpeng; Arandiyan, Hamidreza; Cao, Sufeng; Zhang, Jie; Li, Fengyun; Wang, Qing; Geng, Baoyou; Sun, Hongyu

    2015-03-01

    A facile one-step solution reaction route for growth of novel MoS2 nanorose cross-linked by 3D rGO network, in which the MoS2 nanorose is constructed by single-layered or few-layered MoS2 nanosheets, is presented. Due to the 3D assembled hierarchical architecture of the ultrathin MoS2 nanosheets and the interconnection of 3D rGO network, as well as the synergetic effects of MoS2 and rGO, the as-prepared MoS2-NR/rGO nanohybrids delivered high specific capacity, excellent cycling and good rate performance when evaluated as an anode material for lithium-ion batteries. Moreover, the nanohybrids also show excellent hydrogen-evolution catalytic activity and durability in an acidic medium, which is superior to MoS2 nanorose and their nanoparticles counterparts.

  19. Well-Constructed Single-Layer Molybdenum Disulfide Nanorose Cross-Linked by Three Dimensional-Reduced Graphene Oxide Network for Superior Water Splitting and Lithium Storage Property

    PubMed Central

    Zhao, Yanyan; Kuai, Long; Liu, Yanguo; Wang, Pengpeng; Arandiyan, Hamidreza; Cao, Sufeng; Zhang, Jie; Li, Fengyun; Wang, Qing; Geng, Baoyou; Sun, Hongyu

    2015-01-01

    A facile one-step solution reaction route for growth of novel MoS2 nanorose cross-linked by 3D rGO network, in which the MoS2 nanorose is constructed by single-layered or few-layered MoS2 nanosheets, is presented. Due to the 3D assembled hierarchical architecture of the ultrathin MoS2 nanosheets and the interconnection of 3D rGO network, as well as the synergetic effects of MoS2 and rGO, the as-prepared MoS2-NR/rGO nanohybrids delivered high specific capacity, excellent cycling and good rate performance when evaluated as an anode material for lithium-ion batteries. Moreover, the nanohybrids also show excellent hydrogen-evolution catalytic activity and durability in an acidic medium, which is superior to MoS2 nanorose and their nanoparticles counterparts. PMID:25735416

  20. The quiescent center and the stem cell niche in the adventitious roots of Arabidopsis thaliana

    PubMed Central

    Della Rovere, Federica; Fattorini, Laura; Ronzan, Marilena; Falasca, Giuseppina; Altamura, Maria Maddalena

    2016-01-01

    ABSTRACT Adventitious rooting is essential for the survival of numerous species from vascular cryptogams to monocots, and is required for successful micropropagation. The tissues involved in AR initiation may differ in planta and in in vitro systems. For example, in Arabidopsis thaliana, ARs originate from the hypocotyl pericycle in planta and the stem endodermis in in vitro cultured thin cell layers. The formation of adventitious roots (ARs) depends on numerous factors, among which the hormones, auxin, in particular. In both primary and lateral roots, growth depends on a functional stem cell niche in the apex, maintained by an active quiescent center (QC), and involving the expression of genes controlled by auxin and cytokinin. This review summarizes current knowledge about auxin and cytokinin control on genes involved in the definition and maintenance of QC, and stem cell niche, in the apex of Arabidopsis ARs in planta and in longitudinal thin cell layers. PMID:27089118

  1. The quiescent center and the stem cell niche in the adventitious roots of Arabidopsis thaliana.

    PubMed

    Rovere, Federica Della; Fattorini, Laura; Ronzan, Marilena; Falasca, Giuseppina; Altamura, Maria Maddalena

    2016-05-01

    Adventitious rooting is essential for the survival of numerous species from vascular cryptogams to monocots, and is required for successful micropropagation. The tissues involved in AR initiation may differ in planta and in in vitro systems. For example, in Arabidopsis thaliana, ARs originate from the hypocotyl pericycle in planta and the stem endodermis in in vitro cultured thin cell layers. The formation of adventitious roots (ARs) depends on numerous factors, among which the hormones, auxin, in particular. In both primary and lateral roots, growth depends on a functional stem cell niche in the apex, maintained by an active quiescent center (QC), and involving the expression of genes controlled by auxin and cytokinin. This review summarizes current knowledge about auxin and cytokinin control on genes involved in the definition and maintenance of QC, and stem cell niche, in the apex of Arabidopsis ARs in planta and in longitudinal thin cell layers. PMID:27089118

  2. Regulation of hematopoietic stem cells in the niche.

    PubMed

    Zhao, Meng; Li, LinHeng

    2015-12-01

    Hematopoiesis provides a suitable model for understanding adult stem cells and their niche. Hematopoietic stem cells (HSCs) continuously produce blood cells through orchestrated proliferation, self-renewal, and differentiation in the bone marrow (BM). Within the BM exists a highly organized microenvironment termed "niche" where stem cells reside and are maintained. HSC niche is the first evidence that a microenvironment contributes to protecting stem cell integrity and functionality in mammals. Although multiple models exist, recent progress has principally elucidated the cellular complexity of the HSC niche that maintains and regulates HSCs in BM. Here we introduce the development and summarize the achievements of HSC niche studies.

  3. Normal and Leukemic Stem Cell Niches: Insights and Therapeutic Opportunities

    PubMed Central

    Schepers, Koen; Campbell, Timothy B.; Passegué, Emmanuelle

    2015-01-01

    Hematopoietic stem cells (HSC) rely on instructive cues from the bone marrow (BM) niche to maintain their quiescence and adapt blood production to the organism’s needs. Alterations in the BM niche are commonly observed in blood malignancies and directly contribute to the aberrant function of disease-initiating leukemic stem cells (LSC). Here, we review recent insights into the cellular and molecular determinants of the normal HSC niche and describe how genetic changes in stromal cells and leukemia-induced BM niche remodeling contribute to blood malignancies. Moreover, we discuss how these findings can be applied to non cell-autonomous therapies targeting the LSC niche. PMID:25748932

  4. Improving the prediction accuracy of residue solvent accessibility and real-value backbone torsion angles of proteins by guided-learning through a two-layer neural network.

    PubMed

    Faraggi, Eshel; Xue, Bin; Zhou, Yaoqi

    2009-03-01

    This article attempts to increase the prediction accuracy of residue solvent accessibility and real-value backbone torsion angles of proteins through improved learning. Most methods developed for improving the backpropagation algorithm of artificial neural networks are limited to small neural networks. Here, we introduce a guided-learning method suitable for networks of any size. The method employs a part of the weights for guiding and the other part for training and optimization. We demonstrate this technique by predicting residue solvent accessibility and real-value backbone torsion angles of proteins. In this application, the guiding factor is designed to satisfy the intuitive condition that for most residues, the contribution of a residue to the structural properties of another residue is smaller for greater separation in the protein-sequence distance between the two residues. We show that the guided-learning method makes a 2-4% reduction in 10-fold cross-validated mean absolute errors (MAE) for predicting residue solvent accessibility and backbone torsion angles, regardless of the size of database, the number of hidden layers and the size of input windows. This together with introduction of two-layer neural network with a bipolar activation function leads to a new method that has a MAE of 0.11 for residue solvent accessibility, 36 degrees for psi, and 22 degrees for phi. The method is available as a Real-SPINE 3.0 server in http://sparks.informatics.iupui.edu.

  5. A synthetic niche for nephron progenitor cells.

    PubMed

    Brown, Aaron C; Muthukrishnan, Sree Deepthi; Oxburgh, Leif

    2015-07-27

    FGF, BMP, and WNT balance embryonic nephron progenitor cell (NPC) renewal and differentiation. By modulating these pathways, we have created an in vitro niche in which NPCs from embryonic kidneys or derived from human embryonic stem cells can be propagated. NPC cultures expanded up to one billion-fold in this environment can be induced to form tubules expressing nephron differentiation markers. Single-cell culture reveals phenotypic variability within the early CITED1-expressing NPC compartment, indicating that it is a mixture of cells with varying progenitor potential. Furthermore, we find that the developmental age of NPCs does not correlate with propagation capacity, indicating that cessation of nephrogenesis is related to factors other than an intrinsic clock. This in vitro nephron progenitor niche will have important applications for expansion of cells for engraftment and will facilitate investigation of mechanisms that determine the balance between renewal and differentiation in these cells. PMID:26190145

  6. Mammalian niche conservation through deep time.

    PubMed

    DeSantis, Larisa R G; Beavins Tracy, Rachel A; Koontz, Cassandra S; Roseberry, John C; Velasco, Matthew C

    2012-01-01

    Climate change alters species distributions, causing plants and animals to move north or to higher elevations with current warming. Bioclimatic models predict species distributions based on extant realized niches and assume niche conservation. Here, we evaluate if proxies for niches (i.e., range areas) are conserved at the family level through deep time, from the Eocene to the Pleistocene. We analyze the occurrence of all mammalian families in the continental USA, calculating range area, percent range area occupied, range area rank, and range polygon centroids during each epoch. Percent range area occupied significantly increases from the Oligocene to the Miocene and again from the Pliocene to the Pleistocene; however, mammalian families maintain statistical concordance between rank orders across time. Families with greater taxonomic diversity occupy a greater percent of available range area during each epoch and net changes in taxonomic diversity are significantly positively related to changes in percent range area occupied from the Eocene to the Pleistocene. Furthermore, gains and losses in generic and species diversity are remarkably consistent with ~2.3 species gained per generic increase. Centroids demonstrate southeastern shifts from the Eocene through the Pleistocene that may correspond to major environmental events and/or climate changes during the Cenozoic. These results demonstrate range conservation at the family level and support the idea that niche conservation at higher taxonomic levels operates over deep time and may be controlled by life history traits. Furthermore, families containing megafauna and/or terminal Pleistocene extinction victims do not incur significantly greater declines in range area rank than families containing only smaller taxa and/or only survivors, from the Pliocene to Pleistocene. Collectively, these data evince the resilience of families to climate and/or environmental change in deep time, the absence of terminal Pleistocene

  7. Drug addiction finds its own niche.

    PubMed

    Reid, Alastair

    2011-12-01

    The evolutionary framework suggested by Müller & Schumann (M&S) can be extended further by considering drug-taking in terms of Niche Construction Theory (NCT). It is suggested here that genetic and environmental components of addiction are modified by cultural acceptance of the advantages of non-addicted drug taking and the legitimate supply of performance-enhancing drugs. This may then reduce the prevalence of addiction.

  8. Layered Signaling Regulatory Networks Analysis of Gene Expression Involved in Malignant Tumorigenesis of Non-Resolving Ulcerative Colitis via Integration of Cross-Study Microarray Profiles

    PubMed Central

    Fan, Shengjun; Pan, Zhenyu; Geng, Qiang; Li, Xin; Wang, Yefan; An, Yu; Xu, Yan; Tie, Lu; Pan, Yan; Li, Xuejun

    2013-01-01

    Background Ulcerative colitis (UC) was the most frequently diagnosed inflammatory bowel disease (IBD) and closely linked to colorectal carcinogenesis. By far, the underlying mechanisms associated with the disease are still unclear. With the increasing accumulation of microarray gene expression profiles, it is profitable to gain a systematic perspective based on gene regulatory networks to better elucidate the roles of genes associated with disorders. However, a major challenge for microarray data analysis is the integration of multiple-studies generated by different groups. Methodology/Principal Findings In this study, firstly, we modeled a signaling regulatory network associated with colorectal cancer (CRC) initiation via integration of cross-study microarray expression data sets using Empirical Bayes (EB) algorithm. Secondly, a manually curated human cancer signaling map was established via comprehensive retrieval of the publicly available repositories. Finally, the co-differently-expressed genes were manually curated to portray the layered signaling regulatory networks. Results Overall, the remodeled signaling regulatory networks were separated into four major layers including extracellular, membrane, cytoplasm and nucleus, which led to the identification of five core biological processes and four signaling pathways associated with colorectal carcinogenesis. As a result, our biological interpretation highlighted the importance of EGF/EGFR signaling pathway, EPO signaling pathway, T cell signal transduction and members of the BCR signaling pathway, which were responsible for the malignant transition of CRC from the benign UC to the aggressive one. Conclusions The present study illustrated a standardized normalization approach for cross-study microarray expression data sets. Our model for signaling networks construction was based on the experimentally-supported interaction and microarray co-expression modeling. Pathway-based signaling regulatory networks analysis

  9. Making Blood: The Haematopoietic Niche throughout Ontogeny

    PubMed Central

    Al-Drees, Mohammad A.; Yeo, Jia Hao; Boumelhem, Badwi B.; Antas, Veronica I.; Brigden, Kurt W. L.; Colonne, Chanukya K.; Fraser, Stuart T.

    2015-01-01

    Approximately one-quarter of all cells in the adult human body are blood cells. The haematopoietic system is therefore massive in scale and requires exquisite regulation to be maintained under homeostatic conditions. It must also be able to respond when needed, such as during infection or following blood loss, to produce more blood cells. Supporting cells serve to maintain haematopoietic stem and progenitor cells during homeostatic and pathological conditions. This coalition of supportive cell types, organised in specific tissues, is termed the haematopoietic niche. Haematopoietic stem and progenitor cells are generated in a number of distinct locations during mammalian embryogenesis. These stem and progenitor cells migrate to a variety of anatomical locations through the conceptus until finally homing to the bone marrow shortly before birth. Under stress, extramedullary haematopoiesis can take place in regions that are typically lacking in blood-producing activity. Our aim in this review is to examine blood production throughout the embryo and adult, under normal and pathological conditions, to identify commonalities and distinctions between each niche. A clearer understanding of the mechanism underlying each haematopoietic niche can be applied to improving ex vivo cultures of haematopoietic stem cells and potentially lead to new directions for transplantation medicine. PMID:26113865

  10. Engineering stem cell niches in bioreactors

    PubMed Central

    Liu, Meimei; Liu, Ning; Zang, Ru; Li, Yan; Yang, Shang-Tian

    2013-01-01

    Stem cells, including embryonic stem cells, induced pluripotent stem cells, mesenchymal stem cells and amniotic fluid stem cells have the potential to be expanded and differentiated into various cell types in the body. Efficient differentiation of stem cells with the desired tissue-specific function is critical for stem cell-based cell therapy, tissue engineering, drug discovery and disease modeling. Bioreactors provide a great platform to regulate the stem cell microenvironment, known as “niches”, to impact stem cell fate decision. The niche factors include the regulatory factors such as oxygen, extracellular matrix (synthetic and decellularized), paracrine/autocrine signaling and physical forces (i.e., mechanical force, electrical force and flow shear). The use of novel bioreactors with precise control and recapitulation of niche factors through modulating reactor operation parameters can enable efficient stem cell expansion and differentiation. Recently, the development of microfluidic devices and microbioreactors also provides powerful tools to manipulate the stem cell microenvironment by adjusting flow rate and cytokine gradients. In general, bioreactor engineering can be used to better modulate stem cell niches critical for stem cell expansion, differentiation and applications as novel cell-based biomedicines. This paper reviews important factors that can be more precisely controlled in bioreactors and their effects on stem cell engineering. PMID:24179601

  11. PEDF & stem cells: niche vs. nurture.

    PubMed

    Fitchev, Philip; Chung, Chuhan; Plunkett, Beth A; Brendler, Charles B; Crawford, Susan E

    2014-01-01

    Anti-angiogenic pigment epithelium-derived factor (PEDF) is a multifunctional 50kD secreted glycoprotein emerging as a key factor in stem cell renewal. Characteristics of the stem cell niche can be highly dependent on location, access to the vasculature, oxygen tension and neighboring cells. In the neural stem cell (NSC) niche, specifically the subventricular zone, PEDF actively participates in the self renewal process and promotes stemness by upregulating Notch signaling effectors Hes1 and Hes5. The local vascular endothelial cells and ependymal cells are the likely sources of PEDF for the NSC while mesenchymal and retinal stem cells can actually produce PEDF. The opposing actions of PEDF and VEGF on various cells are recapitulated in the NSC niche. Intraventricular injection of PEDF promotes stem cell renewal, while injection of VEGF prompts differentiation and neurogenesis in the subventricular zone. Enhancing the expression of PEDF in stem cells has promising therapeutic implications. Bone marrow mesenchymal stem cells overexpressing PEDF effectively inhibited pathologic angiogenesis in the murine eye and these same cells suppressed hepatocellular carcinoma growth. As a protein with bioactivities in nearly all normal organ systems, it is likely that PEDF will continue to gain visibility as an essential component in the development and delivery of novel stem cell-based therapies to combat disease.

  12. Orexin-dependent activation of layer VIb enhances cortical network activity and integration of non-specific thalamocortical inputs.

    PubMed

    Hay, Y Audrey; Andjelic, Sofija; Badr, Sammy; Lambolez, Bertrand

    2015-11-01

    Neocortical layer VI is critically involved in thalamocortical activity changes during the sleep/wake cycle. It receives dense projections from thalamic nuclei sensitive to the wake-promoting neuropeptides orexins, and its deepest part, layer VIb, is the only cortical lamina reactive to orexins. This convergence of wake-promoting inputs prompted us to investigate how layer VIb can modulate cortical arousal, using patch-clamp recordings and optogenetics in rat brain slices. We found that the majority of layer VIb neurons were excited by nicotinic agonists and orexin through the activation of nicotinic receptors containing α4-α5-β2 subunits and OX2 receptor, respectively. Specific effects of orexin on layer VIb neurons were potentiated by low nicotine concentrations and we used this paradigm to explore their intracortical projections. Co-application of nicotine and orexin increased the frequency of excitatory post-synaptic currents in the ipsilateral cortex, with maximal effect in infragranular layers and minimal effect in layer IV, as well as in the contralateral cortex. The ability of layer VIb to relay thalamocortical inputs was tested using photostimulation of channelrhodopsin-expressing fibers from the orexin-sensitive rhomboid nucleus in the parietal cortex. Photostimulation induced robust excitatory currents in layer VIa neurons that were not pre-synaptically modulated by orexin, but exhibited a delayed, orexin-dependent, component. Activation of layer VIb by orexin enhanced the reliability and spike-timing precision of layer VIa responses to rhomboid inputs. These results indicate that layer VIb acts as an orexin-gated excitatory feedforward loop that potentiates thalamocortical arousal.

  13. Marble Algorithm: a solution to estimating ecological niches from presence-only records

    PubMed Central

    Qiao, Huijie; Lin, Congtian; Jiang, Zhigang; Ji, Liqiang

    2015-01-01

    We describe an algorithm that helps to predict potential distributional areas for species using presence-only records. The Marble Algorithm is a density-based clustering program based on Hutchinson’s concept of ecological niches as multidimensional hypervolumes in environmental space. The algorithm characterizes this niche space using the density-based spatial clustering of applications with noise (DBSCAN) algorithm. When MA is provided with a set of occurrence points in environmental space, the algorithm determines two parameters that allow the points to be grouped into several clusters. These clusters are used as reference sets describing the ecological niche, which can then be mapped onto geographic space and used as the potential distribution of the species. We used both virtual species and ten empirical datasets to compare MA with other distribution-modeling tools, including Bioclimate Analysis and Prediction System, Environmental Niche Factor Analysis, the Genetic Algorithm for Rule-set Production, Maximum Entropy Modeling, Artificial Neural Networks, Climate Space Models, Classification Tree Analysis, Generalised Additive Models, Generalised Boosted Models, Generalised Linear Models, Multivariate Adaptive Regression Splines and Random Forests. Results indicate that MA predicts potential distributional areas with high accuracy, moderate robustness, and above-average transferability on all datasets, particularly when dealing with small numbers of occurrences. PMID:26387771

  14. Single Layer Recurrent Neural Network for detection of swarm-like earthquakes in W-Bohemia/Vogtland-the method

    NASA Astrophysics Data System (ADS)

    Doubravová, Jana; Wiszniowski, Jan; Horálek, Josef

    2016-08-01

    In this paper, we present a new method of local event detection of swarm-like earthquakes based on neural networks. The proposed algorithm uses unique neural network architecture. It combines features used in other neural network concepts such as the Real Time Recurrent Network and Nonlinear Autoregressive Neural Network to achieve good performance of detection. We use the recurrence combined with various delays applied to recurrent inputs so the network remembers history of many samples. This method has been tested on data from a local seismic network in West Bohemia with promising results. We found that phases not picked in training data diminish the detection capability of the neural network and proper preparation of training data is therefore fundamental. To train the network we define a parameter called the learning importance weight of events and show that it affects the number of acceptable solutions achieved by many trials of the Back Propagation Through Time algorithm. We also compare the individual training of stations with training all of them simultaneously, and we conclude that results of joint training are better for some stations than training only one station.

  15. Ni foam supported three-dimensional vertically aligned and networked layered CoO nanosheet/graphene hybrid array as a high-performance oxygen evolution electrode

    NASA Astrophysics Data System (ADS)

    Yuan, Weiyong; Zhao, Ming; Yuan, Jia; Li, Chang Ming

    2016-07-01

    The sluggish oxygen evolution reaction (OER) represents a major kinetic bottleneck in water splitting. Herein we report the synthesis of a novel Ni foam (NF) supported 3-D vertically aligned and interconnected layered CoO nanosheet array with controlled density, layer thickness, and interlayer spacing, and the conformal self-assembly of graphene on this nanosheet array. The obtained CoO layered nanosheet/graphene hybrid nanoarray was directly used as an OER electrode, showing a current density of 10 mA cm-2 at an overpotential of 330 mV and a Tafel slope of 79 mV dec-1, both of which are much lower than pristine NF and the nanosheet array without graphene, and are among the lowest reported for Co-based OER catalysts and transition metal oxide-based ones measured under the same conditions. In addition, it can retain 92.4% of the current density after 66 h of chronoamperometry testing at a potential of 1.0 V vs. SCE, and 94.3% of the current density at 1.0 V vs. SCE after 200 cyclic voltammetry cycles (0-1.0 V vs. SCE). The excellent catalytic activity and stability toward OER are ascribed to the 3-D NF supported robustly grown networked layered nanosheet array structure and the synergistic effects between CoO layered nanosheets and graphene.

  16. Neutral biogeography and the evolution of climatic niches.

    PubMed

    Boucher, Florian C; Thuiller, Wilfried; Davies, T Jonathan; Lavergne, Sébastien

    2014-05-01

    Recent debate on whether climatic niches are conserved through time has focused on how phylogenetic niche conservatism can be measured by deviations from a Brownian motion model of evolutionary change. However, there has been no evaluation of this methodological approach. In particular, the fact that climatic niches are usually obtained from distribution data and are thus heavily influenced by biogeographic factors has largely been overlooked. Our main objective here was to test whether patterns of climatic niche evolution that are frequently observed might arise from neutral dynamics rather than from adaptive scenarios. We developed a model inspired by neutral biodiversity theory, where individuals disperse, compete, and undergo speciation independently of climate. We then sampled the climatic niches of species according to their geographic position and showed that even when species evolve independently of climate, their niches can nonetheless exhibit evolutionary patterns strongly differing from Brownian motion. Indeed, climatic niche evolution is better captured by a model of punctuated evolution with constraints due to landscape boundaries, two features that are traditionally interpreted as evidence for selective processes acting on the niche. We therefore suggest that deviation from Brownian motion alone should not be used as evidence for phylogenetic niche conservatism but that information on phenotypic traits directly linked to physiology is required to demonstrate that climatic niches have been conserved through time. PMID:24739191

  17. Neutral biogeography and the evolution of climatic niches

    PubMed Central

    Boucher, Florian C.; Thuiller, Wilfried; Davies, T. Jonathan; Lavergne, Sébastien

    2014-01-01

    Recent debate on whether climatic niches are conserved through time has focused on how phylogenetic niche conservatism can be measured by deviations from a Brownian motion model of evolutionary change. However, there has been no evaluation of this methodological approach. In particular, the fact that climatic niches are usually obtained from distribution data and are thus heavily influenced by biogeographic factors has largely been overlooked. Our main objective here was to test whether patterns of climatic niche evolution that are frequently observed might arise from neutral dynamics rather than adaptive scenarios. We develop a model inspired by Neutral Biodiversity Theory, where individuals disperse, compete, and undergo speciation independently of climate. We then sample the climatic niches of species according to their geographic position and show that even when species evolved independently of climate, their niches can nonetheless exhibit evolutionary patterns strongly differing from Brownian motion. Indeed, climatic niche evolution is better captured by a model of punctuated evolution with constraints due to landscape boundaries, two features that are traditionally interpreted as evidence for selective processes acting on the niche. We therefore suggest that deviation from Brownian motion alone should not be used as evidence for phylogenetic niche conservatism, but that information on phenotypic traits directly linked to physiology is required to demonstrate that climatic niches have been conserved through time. PMID:24739191

  18. Rapid evolution of adaptive niche construction in experimental microbial populations.

    PubMed

    Callahan, Benjamin J; Fukami, Tadashi; Fisher, Daniel S

    2014-11-01

    Many species engage in adaptive niche construction: modification of the local environment that increases the modifying organism's competitive fitness. Adaptive niche construction provides an alternative pathway to higher fitness, shaping the environment rather than conforming to it. Yet, experimental evidence for the evolutionary emergence of adaptive niche construction is lacking, leaving its role in evolution uncertain. Here we report a direct observation of the de novo evolution of adaptive niche construction in populations of the bacteria Pseudomonas fluorescens. In a laboratory experiment, we allowed several bacterial populations to adapt to a novel environment and assessed whether niche construction evolved over time. We found that adaptive niche construction emerged rapidly, within approximately 100 generations, and became ubiquitous after approximately 400 generations. The large fitness effect of this niche construction was dominated by the low fitness of evolved strains in the ancestrally modified environment: evolved niche constructors were highly dependent on their specific environmental modifications. Populations were subjected to frequent resetting of environmental conditions and severe reduction of spatial habitat structure, both of which are thought to make adaptive niche construction difficult to evolve. Our finding that adaptive niche construction nevertheless evolved repeatably suggests that it may play a more important role in evolution than generally thought.

  19. Ecological and evolutionary consequences of niche construction for its agent.

    PubMed

    Kylafis, Grigoris; Loreau, Michel

    2008-10-01

    Niche construction can generate ecological and evolutionary feedbacks that have been underinvestigated so far. We present an eco-evolutionary model that incorporates the process of niche construction to reveal its effects on the ecology and evolution of the niche-constructing agent. We consider a simple plant-soil nutrient ecosystem in which plants have the ability to increase the input of inorganic nutrient as an example of positive niche construction. On an ecological time scale, the model shows that niche construction allows the persistence of plants under infertile soil conditions that would otherwise lead to their extinction. This expansion of plants' niche, however, requires a high enough rate of niche construction and a high enough initial plant biomass to fuel the positive ecological feedback between plants and their soil environment. On an evolutionary time scale, we consider that the rates of niche construction and nutrient uptake coevolve in plants while a trade-off constrains their values. Different evolutionary outcomes are possible depending on the shape of the trade-off. We show that niche construction results in an evolutionary feedback between plants and their soil environment such that plants partially regulate soil nutrient content. The direct benefit accruing to plants, however, plays a crucial role in the evolutionary advantage of niche construction.

  20. Neutral biogeography and the evolution of climatic niches.

    PubMed

    Boucher, Florian C; Thuiller, Wilfried; Davies, T Jonathan; Lavergne, Sébastien

    2014-05-01

    Recent debate on whether climatic niches are conserved through time has focused on how phylogenetic niche conservatism can be measured by deviations from a Brownian motion model of evolutionary change. However, there has been no evaluation of this methodological approach. In particular, the fact that climatic niches are usually obtained from distribution data and are thus heavily influenced by biogeographic factors has largely been overlooked. Our main objective here was to test whether patterns of climatic niche evolution that are frequently observed might arise from neutral dynamics rather than from adaptive scenarios. We developed a model inspired by neutral biodiversity theory, where individuals disperse, compete, and undergo speciation independently of climate. We then sampled the climatic niches of species according to their geographic position and showed that even when species evolve independently of climate, their niches can nonetheless exhibit evolutionary patterns strongly differing from Brownian motion. Indeed, climatic niche evolution is better captured by a model of punctuated evolution with constraints due to landscape boundaries, two features that are traditionally interpreted as evidence for selective processes acting on the niche. We therefore suggest that deviation from Brownian motion alone should not be used as evidence for phylogenetic niche conservatism but that information on phenotypic traits directly linked to physiology is required to demonstrate that climatic niches have been conserved through time.

  1. Multi-layer electrode with nano-Li4Ti5O12 aggregates sandwiched between carbon nanotube and graphene networks for high power Li-ion batteries

    NASA Astrophysics Data System (ADS)

    Choi, Jin-Hoon; Ryu, Won-Hee; Park, Kyusung; Jo, Jeong-Dai; Jo, Sung-Moo; Lim, Dae-Soon; Kim, Il-Doo

    2014-12-01

    Self-aggregated Li4Ti5O12 particles sandwiched between graphene nanosheets (GNSs) and single-walled carbon nanotubes (SWCNTs) network are reported as new hybrid electrodes for high power Li-ion batteries. The multi-layer electrodes are fabricated by sequential process comprising air-spray coating of GNSs layer and the following electrostatic spray (E-spray) coating of well-dispersed colloidal Li4Ti5O12 nanoparticles, and subsequent air-spray coating of SWCNTs layer once again. In multi-stacked electrodes of GNSs/nanoporous Li4Ti5O12 aggregates/SWCNTs networks, GNSs and SWCNTs serve as conducting bridges, effectively interweaving the nanoporous Li4Ti5O12 aggregates, and help achieve superior rate capability as well as improved mechanical stability of the composite electrode by holding Li4Ti5O12 tightly without a binder. The multi-stacked electrodes deliver a specific capacity that maintains an impressively high capacity of 100 mA h g-1 at a high rate of 100C even after 1000 cycles.

  2. Multi-layer electrode with nano-Li4Ti5O12 aggregates sandwiched between carbon nanotube and graphene networks for high power Li-ion batteries.

    PubMed

    Choi, Jin-Hoon; Ryu, Won-Hee; Park, Kyusung; Jo, Jeong-Dai; Jo, Sung-Moo; Lim, Dae-Soon; Kim, Il-Doo

    2014-12-05

    Self-aggregated Li4Ti5O12 particles sandwiched between graphene nanosheets (GNSs) and single-walled carbon nanotubes (SWCNTs) network are reported as new hybrid electrodes for high power Li-ion batteries. The multi-layer electrodes are fabricated by sequential process comprising air-spray coating of GNSs layer and the following electrostatic spray (E-spray) coating of well-dispersed colloidal Li4Ti5O12 nanoparticles, and subsequent air-spray coating of SWCNTs layer once again. In multi-stacked electrodes of GNSs/nanoporous Li4Ti5O12 aggregates/SWCNTs networks, GNSs and SWCNTs serve as conducting bridges, effectively interweaving the nanoporous Li4Ti5O12 aggregates, and help achieve superior rate capability as well as improved mechanical stability of the composite electrode by holding Li4Ti5O12 tightly without a binder. The multi-stacked electrodes deliver a specific capacity that maintains an impressively high capacity of 100 mA h g(-1) at a high rate of 100C even after 1000 cycles.

  3. Evolutionary consequences of niche construction and their implications for ecology.

    PubMed

    Laland, K N; Odling-Smee, F J; Feldman, M W

    1999-08-31

    Organisms regularly modify local resource distributions, influencing both their ecosystems and the evolution of traits whose fitness depends on such alterable sources of natural selection in environments. We call these processes niche construction. We explore the evolutionary consequences of niche construction using a two-locus population genetic model, which extends earlier analyses by allowing resource distributions to be influenced both by niche construction and by independent processes of renewal and depletion. The analysis confirms that niche construction can be a potent evolutionary agent by generating selection that leads to the fixation of otherwise deleterious alleles, supporting stable polymorphisms where none are expected, eliminating what would otherwise be stable polymorphisms, and generating unusual evolutionary dynamics. Even small amounts of niche construction, or niche construction that only weakly affects resource dynamics, can significantly alter both ecological and evolutionary patterns.

  4. Niche differentiation of bacterial communities at a millimeter scale in Shark Bay microbial mats.

    PubMed

    Wong, Hon Lun; Smith, Daniela-Lee; Visscher, Pieter T; Burns, Brendan P

    2015-01-01

    Modern microbial mats can provide key insights into early Earth ecosystems, and Shark Bay, Australia, holds one of the best examples of these systems. Identifying the spatial distribution of microorganisms with mat depth facilitates a greater understanding of specific niches and potentially novel microbial interactions. High throughput sequencing coupled with elemental analyses and biogeochemical measurements of two distinct mat types (smooth and pustular) at a millimeter scale were undertaken in the present study. A total of 8,263,982 16S rRNA gene sequences were obtained, which were affiliated to 58 bacterial and candidate phyla. The surface of both mats were dominated by Cyanobacteria, accompanied with known or putative members of Alphaproteobacteria and Bacteroidetes. The deeper anoxic layers of smooth mats were dominated by Chloroflexi, while Alphaproteobacteria dominated the lower layers of pustular mats. In situ microelectrode measurements revealed smooth mats have a steeper profile of O2 and H2S concentrations, as well as higher oxygen production, consumption, and sulfate reduction rates. Specific elements (Mo, Mg, Mn, Fe, V, P) could be correlated with specific mat types and putative phylogenetic groups. Models are proposed for these systems suggesting putative surface anoxic niches, differential nitrogen fixing niches, and those coupled with methane metabolism.

  5. Niche differentiation of bacterial communities at a millimeter scale in Shark Bay microbial mats

    NASA Astrophysics Data System (ADS)

    Wong, Hon Lun; Smith, Daniela-Lee; Visscher, Pieter T.; Burns, Brendan P.

    2015-10-01

    Modern microbial mats can provide key insights into early Earth ecosystems, and Shark Bay, Australia, holds one of the best examples of these systems. Identifying the spatial distribution of microorganisms with mat depth facilitates a greater understanding of specific niches and potentially novel microbial interactions. High throughput sequencing coupled with elemental analyses and biogeochemical measurements of two distinct mat types (smooth and pustular) at a millimeter scale were undertaken in the present study. A total of 8,263,982 16S rRNA gene sequences were obtained, which were affiliated to 58 bacterial and candidate phyla. The surface of both mats were dominated by Cyanobacteria, accompanied with known or putative members of Alphaproteobacteria and Bacteroidetes. The deeper anoxic layers of smooth mats were dominated by Chloroflexi, while Alphaproteobacteria dominated the lower layers of pustular mats. In situ microelectrode measurements revealed smooth mats have a steeper profile of O2 and H2S concentrations, as well as higher oxygen production, consumption, and sulfate reduction rates. Specific elements (Mo, Mg, Mn, Fe, V, P) could be correlated with specific mat types and putative phylogenetic groups. Models are proposed for these systems suggesting putative surface anoxic niches, differential nitrogen fixing niches, and those coupled with methane metabolism.

  6. Niche differentiation of bacterial communities at a millimeter scale in Shark Bay microbial mats.

    PubMed

    Wong, Hon Lun; Smith, Daniela-Lee; Visscher, Pieter T; Burns, Brendan P

    2015-01-01

    Modern microbial mats can provide key insights into early Earth ecosystems, and Shark Bay, Australia, holds one of the best examples of these systems. Identifying the spatial distribution of microorganisms with mat depth facilitates a greater understanding of specific niches and potentially novel microbial interactions. High throughput sequencing coupled with elemental analyses and biogeochemical measurements of two distinct mat types (smooth and pustular) at a millimeter scale were undertaken in the present study. A total of 8,263,982 16S rRNA gene sequences were obtained, which were affiliated to 58 bacterial and candidate phyla. The surface of both mats were dominated by Cyanobacteria, accompanied with known or putative members of Alphaproteobacteria and Bacteroidetes. The deeper anoxic layers of smooth mats were dominated by Chloroflexi, while Alphaproteobacteria dominated the lower layers of pustular mats. In situ microelectrode measurements revealed smooth mats have a steeper profile of O2 and H2S concentrations, as well as higher oxygen production, consumption, and sulfate reduction rates. Specific elements (Mo, Mg, Mn, Fe, V, P) could be correlated with specific mat types and putative phylogenetic groups. Models are proposed for these systems suggesting putative surface anoxic niches, differential nitrogen fixing niches, and those coupled with methane metabolism. PMID:26499760

  7. Niche differentiation of bacterial communities at a millimeter scale in Shark Bay microbial mats

    PubMed Central

    Wong, Hon Lun; Smith, Daniela-Lee; Visscher, Pieter T.; Burns, Brendan P.

    2015-01-01

    Modern microbial mats can provide key insights into early Earth ecosystems, and Shark Bay, Australia, holds one of the best examples of these systems. Identifying the spatial distribution of microorganisms with mat depth facilitates a greater understanding of specific niches and potentially novel microbial interactions. High throughput sequencing coupled with elemental analyses and biogeochemical measurements of two distinct mat types (smooth and pustular) at a millimeter scale were undertaken in the present study. A total of 8,263,982 16S rRNA gene sequences were obtained, which were affiliated to 58 bacterial and candidate phyla. The surface of both mats were dominated by Cyanobacteria, accompanied with known or putative members of Alphaproteobacteria and Bacteroidetes. The deeper anoxic layers of smooth mats were dominated by Chloroflexi, while Alphaproteobacteria dominated the lower layers of pustular mats. In situ microelectrode measurements revealed smooth mats have a steeper profile of O2 and H2S concentrations, as well as higher oxygen production, consumption, and sulfate reduction rates. Specific elements (Mo, Mg, Mn, Fe, V, P) could be correlated with specific mat types and putative phylogenetic groups. Models are proposed for these systems suggesting putative surface anoxic niches, differential nitrogen fixing niches, and those coupled with methane metabolism. PMID:26499760

  8. Remote Sensing of Niches for Thermotropic Life.

    NASA Astrophysics Data System (ADS)

    Muller, A. W.

    2002-12-01

    The recognized biological energy sources are light and food. Mechanical systems can gain free energy from heat using a temperature difference or thermal cycling. Imagine that biological systems could also live on heat. Call the process `thermosynthesis' and let it occur in a thermal gradient or convection cell. Many candidate niches for thermosynthesizers then exist. Temperature differences are present across many interfaces: soil/air, rock/air, natural water (ocean, lake, river)/air, ice (also snow)/air, soil/snow, water (ocean,lake)/surface-ice. Within natural waters large temperature gradients are found; thermoclines separate the warm surface from the cold deep. Convection occurs in hot springs, in many other natural waters, and in the Earth's atmosphere. On Earth, organism presence is conspicuous in all these candidate niches. The Solar System contains many candidate niches as well. They should be detectable by IR methods. They can be categorized in five types: (1) Convection. Convecting oceans (Mars and Venus in the past) or atmospheres (Venus, Big Outer Planets). (2) Convecting Aquifer (Mars). (3) Surface-Ice Cover. Some of the Moons of the Outer Planets. (4) Shaded Crater Iterior. The poles of Mercury and The Moon. (5) Spinners. Small objects rotating in the sunlight: ice-covered meteorites, asteroids, comets. They could transport thermosynthesizers within the Solar System. How plausible is thermosynthesis? It can be shown that thermosynthesis (1) could be effected using parts of the contemporary photosynthetic machinery, and (2) may have supported early evolution. The standard biological energy carrier, ATP, would be synthesized during thermal cycling of a progenitor of the F1 moiety of the contemporary ATPsynthase enzyme; this progenitor is thermally folded/unfolded during the cycle. Contemporary ATPsynthase works according to the `binding change mechanism': substrates are bound in a local, dehydrated enzymatic cleft, where they condense to form a bound

  9. Ecological niche transferability using invasive species as a case study.

    PubMed

    Fernández, Miguel; Hamilton, Healy

    2015-01-01

    Species distribution modeling is widely applied to predict invasive species distributions and species range shifts under climate change. Accurate predictions depend upon meeting the assumption that ecological niches are conserved, i.e., spatially or temporally transferable. Here we present a multi-taxon comparative analysis of niche conservatism using biological invasion events well documented in natural history museum collections. Our goal is to assess spatial transferability of the climatic niche of a range of noxious terrestrial invasive species using two complementary approaches. First we compare species' native versus invasive ranges in environmental space using two distinct methods, Principal Components Analysis and Mahalanobis distance. Second we compare species' native versus invaded ranges in geographic space as estimated using the species distribution modeling technique Maxent and the comparative index Hellinger's I. We find that species exhibit a range of responses, from almost complete transferability, in which the invaded niches completely overlap with the native niches, to a complete dissociation between native and invaded ranges. Intermediate responses included expansion of dimension attributable to either temperature or precipitation derived variables, as well as niche expansion in multiple dimensions. We conclude that the ecological niche in the native range is generally a poor predictor of invaded range and, by analogy, the ecological niche may be a poor predictor of range shifts under climate change. We suggest that assessing dimensions of niche transferability prior to standard species distribution modeling may improve the understanding of species' dynamics in the invaded range.

  10. Evolution of climatic niche specialization: a phylogenetic analysis in amphibians.

    PubMed

    Bonetti, Maria Fernanda; Wiens, John J

    2014-11-22

    The evolution of climatic niche specialization has important implications for many topics in ecology, evolution and conservation. The climatic niche reflects the set of temperature and precipitation conditions where a species can occur. Thus, specialization to a limited set of climatic conditions can be important for understanding patterns of biogeography, species richness, community structure, allopatric speciation, spread of invasive species and responses to climate change. Nevertheless, the factors that determine climatic niche width (level of specialization) remain poorly explored. Here, we test whether species that occur in more extreme climates are more highly specialized for those conditions, and whether there are trade-offs between niche widths on different climatic niche axes (e.g. do species that tolerate a broad range of temperatures tolerate only a limited range of precipitation regimes?). We test these hypotheses in amphibians, using phylogenetic comparative methods and global-scale datasets, including 2712 species with both climatic and phylogenetic data. Our results do not support either hypothesis. Rather than finding narrower niches in more extreme environments, niches tend to be narrower on one end of a climatic gradient but wider on the other. We also find that temperature and precipitation niche breadths are positively related, rather than showing trade-offs. Finally, our results suggest that most amphibian species occur in relatively warm and dry environments and have relatively narrow climatic niche widths on both of these axes. Thus, they may be especially imperilled by anthropogenic climate change.

  11. Evolution of climatic niche specialization: a phylogenetic analysis in amphibians

    PubMed Central

    Bonetti, Maria Fernanda; Wiens, John J.

    2014-01-01

    The evolution of climatic niche specialization has important implications for many topics in ecology, evolution and conservation. The climatic niche reflects the set of temperature and precipitation conditions where a species can occur. Thus, specialization to a limited set of climatic conditions can be important for understanding patterns of biogeography, species richness, community structure, allopatric speciation, spread of invasive species and responses to climate change. Nevertheless, the factors that determine climatic niche width (level of specialization) remain poorly explored. Here, we test whether species that occur in more extreme climates are more highly specialized for those conditions, and whether there are trade-offs between niche widths on different climatic niche axes (e.g. do species that tolerate a broad range of temperatures tolerate only a limited range of precipitation regimes?). We test these hypotheses in amphibians, using phylogenetic comparative methods and global-scale datasets, including 2712 species with both climatic and phylogenetic data. Our results do not support either hypothesis. Rather than finding narrower niches in more extreme environments, niches tend to be narrower on one end of a climatic gradient but wider on the other. We also find that temperature and precipitation niche breadths are positively related, rather than showing trade-offs. Finally, our results suggest that most amphibian species occur in relatively warm and dry environments and have relatively narrow climatic niche widths on both of these axes. Thus, they may be especially imperilled by anthropogenic climate change. PMID:25274369

  12. Evolution of climatic niche specialization: a phylogenetic analysis in amphibians.

    PubMed

    Bonetti, Maria Fernanda; Wiens, John J

    2014-11-22

    The evolution of climatic niche specialization has important implications for many topics in ecology, evolution and conservation. The climatic niche reflects the set of temperature and precipitation conditions where a species can occur. Thus, specialization to a limited set of climatic conditions can be important for understanding patterns of biogeography, species richness, community structure, allopatric speciation, spread of invasive species and responses to climate change. Nevertheless, the factors that determine climatic niche width (level of specialization) remain poorly explored. Here, we test whether species that occur in more extreme climates are more highly specialized for those conditions, and whether there are trade-offs between niche widths on different climatic niche axes (e.g. do species that tolerate a broad range of temperatures tolerate only a limited range of precipitation regimes?). We test these hypotheses in amphibians, using phylogenetic comparative methods and global-scale datasets, including 2712 species with both climatic and phylogenetic data. Our results do not support either hypothesis. Rather than finding narrower niches in more extreme environments, niches tend to be narrower on one end of a climatic gradient but wider on the other. We also find that temperature and precipitation niche breadths are positively related, rather than showing trade-offs. Finally, our results suggest that most amphibian species occur in relatively warm and dry environments and have relatively narrow climatic niche widths on both of these axes. Thus, they may be especially imperilled by anthropogenic climate change. PMID:25274369

  13. Foraging and farming as niche construction: stable and unstable adaptations.

    PubMed

    Rowley-Conwy, Peter; Layton, Robert

    2011-03-27

    All forager (or hunter-gatherer) societies construct niches, many of them actively by the concentration of wild plants into useful stands, small-scale cultivation, burning of natural vegetation to encourage useful species, and various forms of hunting, collectively termed 'low-level food production'. Many such niches are stable and can continue indefinitely, because forager populations are usually stable. Some are unstable, but these usually transform into other foraging niches, not geographically expansive farming niches. The Epipalaeolithic (final hunter-gatherer) niche in the Near East was complex but stable, with a relatively high population density, until destabilized by an abrupt climatic change. The niche was unintentionally transformed into an agricultural one, due to chance genetic and behavioural attributes of some wild plant and animal species. The agricultural niche could be exported with modifications over much of the Old World. This was driven by massive population increase and had huge impacts on local people, animals and plants wherever the farming niche was carried. Farming niches in some areas may temporarily come close to stability, but the history of the last 11,000 years does not suggest that agriculture is an effective strategy for achieving demographic and political stability in the world's farming populations.

  14. Ecological Niche Transferability Using Invasive Species as a Case Study

    PubMed Central

    Fernández, Miguel; Hamilton, Healy

    2015-01-01

    Species distribution modeling is widely applied to predict invasive species distributions and species range shifts under climate change. Accurate predictions depend upon meeting the assumption that ecological niches are conserved, i.e., spatially or temporally transferable. Here we present a multi-taxon comparative analysis of niche conservatism using biological invasion events well documented in natural history museum collections. Our goal is to assess spatial transferability of the climatic niche of a range of noxious terrestrial invasive species using two complementary approaches. First we compare species’ native versus invasive ranges in environmental space using two distinct methods, Principal Components Analysis and Mahalanobis distance. Second we compare species’ native versus invaded ranges in geographic space as estimated using the species distribution modeling technique Maxent and the comparative index Hellinger’s I. We find that species exhibit a range of responses, from almost complete transferability, in which the invaded niches completely overlap with the native niches, to a complete dissociation between native and invaded ranges. Intermediate responses included expansion of dimension attributable to either temperature or precipitation derived variables, as well as niche expansion in multiple dimensions. We conclude that the ecological niche in the native range is generally a poor predictor of invaded range and, by analogy, the ecological niche may be a poor predictor of range shifts under climate change. We suggest that assessing dimensions of niche transferability prior to standard species distribution modeling may improve the understanding of species’ dynamics in the invaded range. PMID:25785858

  15. Foraging and farming as niche construction: stable and unstable adaptations

    PubMed Central

    Rowley-Conwy, Peter; Layton, Robert

    2011-01-01

    All forager (or hunter–gatherer) societies construct niches, many of them actively by the concentration of wild plants into useful stands, small-scale cultivation, burning of natural vegetation to encourage useful species, and various forms of hunting, collectively termed ‘low-level food production’. Many such niches are stable and can continue indefinitely, because forager populations are usually stable. Some are unstable, but these usually transform into other foraging niches, not geographically expansive farming niches. The Epipalaeolithic (final hunter–gatherer) niche in the Near East was complex but stable, with a relatively high population density, until destabilized by an abrupt climatic change. The niche was unintentionally transformed into an agricultural one, due to chance genetic and behavioural attributes of some wild plant and animal species. The agricultural niche could be exported with modifications over much of the Old World. This was driven by massive population increase and had huge impacts on local people, animals and plants wherever the farming niche was carried. Farming niches in some areas may temporarily come close to stability, but the history of the last 11 000 years does not suggest that agriculture is an effective strategy for achieving demographic and political stability in the world's farming populations. PMID:21320899

  16. Chemical stabilization and improved thermal resilience of molecular arrangements: possible formation of a surface network of bonds by multiple pulse atomic layer deposition.

    PubMed

    de Pauli, Muriel; Matos, Matheus J S; Siles, Pablo F; Prado, Mariana C; Neves, Bernardo R A; Ferreira, Sukarno O; Mazzoni, Mário S C; Malachias, Angelo

    2014-08-14

    In this work, we make use of an atomic layer deposition (ALD) surface reaction based on trimethyl-aluminum (TMA) and water to modify O-H terminated self-assembled layers of octadecylphosphonic acid (OPA). The structural modifications were investigated by X-ray reflectivity, X-ray diffraction, and atomic force microscopy. We observed a significant improvement in the thermal stability of ALD-modified molecules, with the existence of a supramolecular packing structure up to 500 °C. Following the experimental observations, density functional theory (DFT) calculations indicate the possibility of formation of a covalent network with aluminum atoms connecting OPA molecules at terrace surfaces. Chemical stability is also achieved on top of such a composite surface, inhibiting further ALD oxide deposition. On the other hand, in the terrace edges, where the covalent array is discontinued, the chemical conditions allow for oxide growth. Analysis of the DFT results on band structure and density of states of modified OPA molecules suggests that besides the observed thermal resilience, the dielectric character of OPA layers is preserved. This new ALD-modified OPA composite is potentially suitable for applications such as dielectric layers in organic devices, where better thermal performance is required.

  17. Chemical stabilization and improved thermal resilience of molecular arrangements: possible formation of a surface network of bonds by multiple pulse atomic layer deposition.

    PubMed

    de Pauli, Muriel; Matos, Matheus J S; Siles, Pablo F; Prado, Mariana C; Neves, Bernardo R A; Ferreira, Sukarno O; Mazzoni, Mário S C; Malachias, Angelo

    2014-08-14

    In this work, we make use of an atomic layer deposition (ALD) surface reaction based on trimethyl-aluminum (TMA) and water to modify O-H terminated self-assembled layers of octadecylphosphonic acid (OPA). The structural modifications were investigated by X-ray reflectivity, X-ray diffraction, and atomic force microscopy. We observed a significant improvement in the thermal stability of ALD-modified molecules, with the existence of a supramolecular packing structure up to 500 °C. Following the experimental observations, density functional theory (DFT) calculations indicate the possibility of formation of a covalent network with aluminum atoms connecting OPA molecules at terrace surfaces. Chemical stability is also achieved on top of such a composite surface, inhibiting further ALD oxide deposition. On the other hand, in the terrace edges, where the covalent array is discontinued, the chemical conditions allow for oxide growth. Analysis of the DFT results on band structure and density of states of modified OPA molecules suggests that besides the observed thermal resilience, the dielectric character of OPA layers is preserved. This new ALD-modified OPA composite is potentially suitable for applications such as dielectric layers in organic devices, where better thermal performance is required. PMID:25055162

  18. Physical-layer energy-efficient receiving method based on selective sampling in orthogonal frequency division multiplexing access passive optical network

    NASA Astrophysics Data System (ADS)

    Li, Jun; He, Hao; Bi, Meihua; Hu, Weisheng

    2014-05-01

    We propose a physical-layer energy-efficient receiving method based on selective sampling in an orthogonal frequency division multiplexing access passive optical network (OFDMA-PON). By using the special designed frame head, the receiver within an optical network unit (ONU) can identify the destination of the incoming frame. The receiver only samples at the time when the destination is in agreement with the ONU, while it stays in standby during the rest of the time. We clarify its feasibility through an experiment and analyze the downstream traffic delay by simulation. The results indicate that under limited delay conditions, ˜60% energy can be saved compared with the traditional receiving method in the OFDMA-PON system with 512 ONUs.

  19. Enhanced performance of polymer solar cell with ZnO nanoparticle electron transporting layer passivated by in situ cross-linked three-dimensional polymer network

    NASA Astrophysics Data System (ADS)

    Wu, Zhongwei; Song, Tao; Xia, Zhouhui; Wei, Huaixin; Sun, Baoquan

    2013-12-01

    An in situ cross-linked three-dimensional polymer network has been developed to passivate ZnO nanoparticles as an electron transporting layer (ETL) to improve the performance of inverted organic solar cells. The passivated ZnO ETL-based devices achieve efficiencies of 3.26% for poly(3-hexylthiophene) (P3HT):[6,6]-phenyl-C61-butyric acid methyl ester (PCBM) and 7.37% for poly[[4,8-bis[(2-ethylhexyl)oxy]benzo[1,2-b:4,5-b‧]dithiophene-2,6-diyl][3-fluoro-2-[(2-ethylhexyl)carbonyl]thieno[3,4-b]thiophenediyl

  20. Localization of juxtacrine factor ephrin-B2 in pituitary stem/progenitor cell niches throughout life.

    PubMed

    Yoshida, Saishu; Kato, Takako; Higuchi, Masashi; Chen, Mo; Ueharu, Hiroki; Nishimura, Naoto; Kato, Yukio

    2015-03-01

    We have recently reported that Sox2-expressing pituitary stem/progenitor cells contact each other via a tight-junction protein CAR to form stem/progenitor cell niches in the marginal cell layer facing the lumen and in the clusters scattered in the parenchyma of the anterior lobe. However, the microenvironment of the niche for the maintenance of stem cell function in the pituitary remains obscure. In this study of pituitary stem/progenitor cell niches, we have attempted to identify the expression of juxtacrine factor ephrin and its receptor. We have found that ephrin-B2 is expressed in the pituitary throughout development but changes its localization pattern. Notably, in the adult pituitary, ephrin-B2 immuno-signals occur in SOX2-, E-cadherin-, and CAR-triple-positive stem/progenitor cells in the niches. Our data suggest that ephrin-B2 signaling has an important role in the formation of pituitary stem/progenitor cell niches and in pituitary organogenesis.

  1. Activin signaling balances proliferation and differentiation of ovarian niche precursors and enables adjustment of niche numbers.

    PubMed

    Lengil, Tamar; Gancz, Dana; Gilboa, Lilach

    2015-03-01

    How the numbers of niches and resident stem cells within a particular organ are determined during development and how they may be modulated or corrected is a question with significant medical implications. In the larval ovary of Drosophila melanogaster, somatic precursors for niches, and germ cells that will become germline stem cells, co-develop. Somatic precursors proliferate during the first 3 days of larval development. By mid-third instar, adult terminal filament (TF) (part of the germline stem cell niche) cells first appear, and differentiation terminates 24 h later when 16-20 TFs fully form. The developmental sequence responsible for TF cell determination and final TF numbers is only partially understood. We show that TF formation proceeds through several, hitherto uncharacterized stages, which include an early exit from the cell cycle to form TF precursors and two steps of cell shape change to form the mature TF cells. The Activin receptor Baboon (Babo) is required for somatic precursor cell proliferation and therefore determines the pool of TF precursors available for TF differentiation. During the final differentiation stage, Babo facilitates TF and germ cell differentiation, and promotes the accumulation of Broad-Z1, which is also a target of the steroid hormone ecdysone. Epistasis analysis shows that Activin controls cell proliferation in an ecdysone-independent manner and TF differentiation by affecting ecdysone targets. We propose that this mode of function allows Activin to balance proliferation and differentiation, and to equilibrate niche numbers. These results suggest a novel model for how niche numbers are corrected during development.

  2. Symbiosis catalyses niche expansion and diversification

    PubMed Central

    Joy, Jeffrey B.

    2013-01-01

    Interactions between species are important catalysts of the evolutionary processes that generate the remarkable diversity of life. Symbioses, conspicuous and inherently interesting forms of species interaction, are pervasive throughout the tree of life. However, nearly all studies of the impact of species interactions on diversification have concentrated on competition and predation leaving unclear the importance of symbiotic interaction. Here, I show that, as predicted by evolutionary theories of symbiosis and diversification, multiple origins of a key innovation, symbiosis between gall-inducing insects and fungi, catalysed both expansion in resource use (niche expansion) and diversification. Symbiotic lineages have undergone a more than sevenfold expansion in the range of host-plant taxa they use relative to lineages without such fungal symbionts, as defined by the genetic distance between host plants. Furthermore, symbiotic gall-inducing insects are more than 17 times as diverse as their non-symbiotic relatives. These results demonstrate that the evolution of symbiotic interaction leads to niche expansion, which in turn catalyses diversification. PMID:23390106

  3. A stem cell niche dominance theorem

    PubMed Central

    2011-01-01

    Background Multilevelness is a defining characteristic of complex systems. For example, in the intestinal tissue the epithelial lining is organized into crypts that are maintained by a niche of stem cells. The behavior of the system 'as a whole' is considered to emerge from the functioning and interactions of its parts. What we are seeking here is a conceptual framework to demonstrate how the "fate" of intestinal crypts is an emergent property that inherently arises from the complex yet robust underlying biology of stem cells. Results We establish a conceptual framework in which to formalize cross-level principles in the context of tissue organization. To this end we provide a definition for stemness, which is the propensity of a cell lineage to contribute to a tissue fate. We do not consider stemness a property of a cell but link it to the process in which a cell lineage contributes towards tissue (mal)function. We furthermore show that the only logically feasible relationship between the stemness of cell lineages and the emergent fate of their tissue, which satisfies the given criteria, is one of dominance from a particular lineage. Conclusions The dominance theorem, conceived and proven in this paper, provides support for the concepts of niche succession and monoclonal conversion in intestinal crypts as bottom-up relations, while crypt fission is postulated to be a top-down principle. PMID:21214945

  4. Neisserial Molecular Adaptations to the Nasopharyngeal Niche.

    PubMed

    Laver, Jay R; Hughes, Sara E; Read, Robert C

    2015-01-01

    The exclusive reservoir of the genus Neisseria is the human. Of the broad range of species that comprise the Neisseria, only two are frequently pathogenic, and only one of those is a resident of the nasopharynx. Although Neisseria meningitidis can cause severe disease if it invades the bloodstream, the vast majority of interactions between humans and Neisseria are benign, with the bacteria inhabiting its mucosal niche as a non-invasive commensal. Understandably, with the exception of Neisseria gonorrhoeae, which preferentially colonises the urogenital tract, the neisseriae are extremely well adapted to survival in the human nasopharynx, their sole biological niche. The purpose of this review is to provide an overview of the molecular mechanisms evolved by Neisseria to facilitate colonisation and survival within the nasopharynx, focussing on N. meningitidis. The organism has adapted to survive in aerosolised transmission and to attach to mucosal surfaces. It then has to replicate in a nutrition-poor environment and resist immune and competitive pressure within a polymicrobial complex. Temperature and relative gas concentrations (nitric oxide and oxygen) are likely to be potent initial signals of arrival within the nasopharyngeal environment, and this review will focus on how N. meningitidis responds to these to increase the likelihood of its survival. PMID:26210107

  5. The perivascular niche regulates breast tumor dormancy

    PubMed Central

    Peinado, Héctor; Mori, Hidetoshi; Matei, Irina R.; Evason, Kimberley J.; Brazier, Hélène; Almeida, Dena; Koller, Antonius; Hajjar, Katherine A.; Stainier, Didier Y.R.; Chen, Emily I.; Lyden, David

    2013-01-01

    In a significant fraction of breast cancer patients, distant metastases emerge after years or even decades of latency. How disseminated tumor cells (DTCs) are kept dormant, and what ‘wakes them up’, are fundamental problems in tumor biology. To address these questions, we utilized metastasis assays in mice to show that dormant DTCs reside upon microvasculature of lung, bone marrow and brain. We then engineered organotypic microvascular niches to determine whether endothelial cells directly influence breast cancer cell (BCC) growth. These models demonstrated that endothelial-derived thrombospondin-1 induces sustained BCC quiescence. This suppressive cue was lost in sprouting neovasculature; time-lapse analysis showed that sprouting vessels not only permit, but accelerate BCC outgrowth. We confirmed this surprising result in dormancy models and in zebrafish, and identified active TGF-β1 and periostin as tumor-promoting, endothelial tip cell-derived factors. Our work reveals that stable microvasculature constitutes a ‘dormant niche,’ whereas sprouting neovasculature sparks micrometastatic outgrowth. PMID:23728425

  6. Available Climate Regimes Drive Niche Diversification during Range Expansion.

    PubMed

    Wüest, Rafael O; Antonelli, Alexandre; Zimmermann, Niklaus E; Linder, H Peter

    2015-05-01

    Climate is a main predictor of biodiversity on a global scale, yet how climate availability affects niche evolution remains poorly explored. Here we assess how intercontinental climate differences may affect the evolution of climate niches and suggest three possible processes: niche truncation along major environmental gradients, intercontinental differences in available climate causing differences in selective regimes, and niche shifts associated with long-distance dispersals leading to a pattern of punctuated evolution. Using the globally distributed danthonioid grasses, we show significant niche differentiation among continents and several instances of niche truncation. The comparison of inferred selective regimes with differences in available climatic space among continents demonstrates adaptation resulting from opportunistic evolution toward available climatic space. Our results suggest that niche evolution in this clade is punctuated, consistent with accelerated niche evolution after long-distance dispersal events. Finally, we discuss how intrinsic constraints (genetic, developmental, or functional) and biotic interactions could have interacted with these three processes during range expansion. Integrating these mechanisms could improve predictions for invasive taxa and long-term evolutionary responses of expanding clades to climate change.

  7. 28. VIEW OF THE SOLDERING NICHE FORMED WITH BRICKS. THE ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    28. VIEW OF THE SOLDERING NICHE FORMED WITH BRICKS. THE BACK OF THE NICHE IS CEMENT FINISHED. THE BOTTOM HAS A 1 INCH THICK ASBESTOS SHELF. THIS PHOTO WAS TAKEN AT THE 3RD FLOOR. - Pacific Telephone & Telegraph Company Building, 1519 Franklin Street, Oakland, Alameda County, CA

  8. Intraspecific genetic variation and competition interact to influence niche expansion

    PubMed Central

    Agashe, Deepa; Bolnick, Daniel I.

    2010-01-01

    Theory and empirical evidence show that intraspecific competition can drive selection favouring the use of novel resources (i.e. niche expansion). The evolutionary response to such selection depends on genetic variation for resource use. However, while genetic variation might facilitate niche expansion, genetically diverse groups may also experience weaker competition, reducing density-dependent selection on resource use. Therefore, genetic variation for fitness on different resources could directly facilitate, or indirectly retard, niche expansion. To test these alternatives, we factorially manipulated both the degree of genetic variation and population density in flour beetles (Tribolium castaneum) exposed to both novel and familiar food resources. Using stable carbon isotope analysis, we measured temporal change and individual variation in beetle diet across eight generations. Intraspecific competition and genetic variation acted on different components of niche evolution: competition facilitated niche expansion, while genetic variation increased individual variation in niche use. In addition, genetic variation and competition together facilitated niche expansion, but all these impacts were temporally variable. Thus, we show that the interaction between genetic variation and competition can also determine niche evolution at different time scales. PMID:20462902

  9. Melanosomes foster a tumour niche by activating CAFs.

    PubMed

    García-Silva, Susana; Peinado, Héctor

    2016-08-30

    Extracellular vesicles, such as exosomes, are important effectors in the formation of tumour-fostering niches. Pigmented melanosomes are now shown to have a relevant role in establishing a tumour niche in primary melanoma by reprogramming dermal fibroblasts into cancer-associated fibroblasts through the transfer of miR-211. PMID:27571736

  10. Using specialty advertising in a niche marketing plan.

    PubMed

    Schwisow, C R

    1992-01-01

    While niche marketing is not a new strategy, an increasing number of competitors are pursuing the same niches, resulting in stiff competition within the health care industry, writes C. Ronald Schwisow. This means marketers need to be resourceful to maximize their communications efforts. One such approach is specialty advertising.

  11. Spatial effects favour the evolution of niche construction.

    PubMed

    Silver, Matt; Di Paolo, Ezequiel

    2006-12-01

    We present an individual-based, spatial implementation of an existing two-locus population genetic model of niche construction. Our analysis reveals that, across a broad range of conditions, niche-construction traits can drive themselves to fixation by simultaneously generating selection that favours 'recipient' trait alleles and linkage disequilibrium between niche-construction and recipient trait alleles. The effect of spatiality is key, since it is the local, resource-mediated interaction between recipient and niche-constructing loci which gives rise to gene linkage. Spatial clustering effects point to a possible mechanism by which an initially rare recipient trait whose selection depends on niche construction could establish in an otherwise hostile environment. The same mechanism could also lead to the spread of an established niche-constructing colony. Similar phenomena are observed in the spatial modelling of two species 'engineering webs'. Here, the activities of two niche-constructing species can combine to drive a particular recipient trait to fixation, or in certain circumstances, maintain the presence of polymorphisms through the preservation of otherwise deleterious alleles. This may have some relevance to ecosystem stability and the maintenance of genetic variation, where the frequencies of key resources are affected by the niche-constructing activities of more than one species. Our model suggests that the stability of multi-species webs in natural populations may increase as the complexity of species-environment interactions increases.

  12. Overcoming Barriers for "Niche" Learners Through Distance Education.

    ERIC Educational Resources Information Center

    Miller, Lawrence G.; Hyatt, Sue Y.; Brennan, Joyce; Bertani, Raymond; Trevor, Thomas

    1999-01-01

    Focuses on students who fit into "niches," and discusses how the Chattanooga State Technical Community College's distance-learning program accommodates these learners. Describes five "niche" learner categories: students with disabilities, power-line maintenance technicians, emergency-service personnel, truckers, and industrial maintenance workers…

  13. Niche divergence accelerates evolution in Asian endemic Procapra gazelles

    PubMed Central

    Hu, Junhua; Jiang, Zhigang; Chen, Jing; Qiao, Huijie

    2015-01-01

    Ecological niche divergence and adaptation to new environments are thought to play important roles in driving speciation. Whether recently evolved species show evidence for niche divergence or conservation is vital towards understanding the role of ecology in the process of speciation. The genus Procapra is an ancient, monophyletic lineage endemic to Asia that contains three extant species (P. gutturosa, P. przewalskii and P. picticaudata). These species mainly inhabit the Qinghai-Tibetan and Mongolian Plateaus, and today have primarily allopatric distributions. We applied a series of geographic information system–based analyses to test for environmental variation and niche divergence among these three species. We found substantial evidence for niche divergence in species’ bioclimatic preferences, which supports the hypothesis that niche divergence accelerates diversification in Procapra. Our results provide important insight into the evolutionary history of ungulates in Asia and help to elucidate how environmental changes accelerate lineage diversification. PMID:25951051

  14. Unifying niche shift studies: insights from biological invasions.

    PubMed

    Guisan, Antoine; Petitpierre, Blaise; Broennimann, Olivier; Daehler, Curtis; Kueffer, Christoph

    2014-05-01

    Assessing whether the climatic niche of a species may change between different geographic areas or time periods has become increasingly important in the context of ongoing global change. However, approaches and findings have remained largely controversial so far, calling for a unification of methods. Here, we build on a review of empirical studies of invasion to formalize a unifying framework that decomposes niche change into unfilling, stability, and expansion situations, taking both a pooled range and range-specific perspective on the niche, while accounting for climatic availability and climatic analogy. This framework provides new insights into the nature of climate niche shifts and our ability to anticipate invasions, and may help in guiding the design of experiments for assessing causes of niche changes.

  15. Niche divergence accelerates evolution in Asian endemic Procapra gazelles.

    PubMed

    Hu, Junhua; Jiang, Zhigang; Chen, Jing; Qiao, Huijie

    2015-01-01

    Ecological niche divergence and adaptation to new environments are thought to play important roles in driving speciation. Whether recently evolved species show evidence for niche divergence or conservation is vital towards understanding the role of ecology in the process of speciation. The genus Procapra is an ancient, monophyletic lineage endemic to Asia that contains three extant species (P. gutturosa, P. przewalskii and P. picticaudata). These species mainly inhabit the Qinghai-Tibetan and Mongolian Plateaus, and today have primarily allopatric distributions. We applied a series of geographic information system-based analyses to test for environmental variation and niche divergence among these three species. We found substantial evidence for niche divergence in species' bioclimatic preferences, which supports the hypothesis that niche divergence accelerates diversification in Procapra. Our results provide important insight into the evolutionary history of ungulates in Asia and help to elucidate how environmental changes accelerate lineage diversification. PMID:25951051

  16. Niche construction initiates the evolution of mutualistic interactions.

    PubMed

    Buser, Claudia C; Newcomb, Richard D; Gaskett, Anne C; Goddard, Matthew R

    2014-10-01

    Niche construction theory explains how organisms' niche modifications may feed back to affect their evolutionary trajectories. In theory, the evolution of other species accessing the same modified niche may also be affected. We propose that this niche construction may be a general mechanism driving the evolution of mutualisms. Drosophilid flies benefit from accessing yeast-infested fruits, but the consequences of this interaction for yeasts are unknown. We reveal high levels of variation among strains of Saccharomyces cerevisiae in their ability to modify fruits and attract Drosophila simulans. More attractive yeasts are dispersed more frequently, both in the lab and in the field, and flies associated with more attractive yeasts have higher fecundity. Although there may be multiple natural yeast and fly species interactions, our controlled assays in the lab and field provide evidence of a mutualistic interaction, facilitated by the yeast's niche modification.

  17. Differential niche dynamics among major marine invertebrate clades

    PubMed Central

    Hopkins, Melanie J; Simpson, Carl; Kiessling, Wolfgang

    2014-01-01

    The degree to which organisms retain their environmental preferences is of utmost importance in predicting their fate in a world of rapid climate change. Notably, marine invertebrates frequently show strong affinities for either carbonate or terrigenous clastic environments. This affinity is due to characteristics of the sediments as well as correlated environmental factors. We assessed the conservatism of substrate affinities of marine invertebrates over geological timescales, and found that niche conservatism is prevalent in the oceans, and largely determined by the strength of initial habitat preference. There is substantial variation in niche conservatism among major clades with corals and sponges being among the most conservative. Time-series analysis suggests that niche conservatism is enhanced during times of elevated nutrient flux, whereas niche evolution tends to occur after mass extinctions. Niche evolution is not necessarily elevated in genera exhibiting higher turnover in species composition. PMID:24313951

  18. [Characteristics, dynamics and niche of insect community in plum orchard].

    PubMed

    Huang, Baohong; Zou, Yunding; Bi, Shoudong; Li, Hengkui; Zhu, Qiaoli

    2005-02-01

    The insect community in plum orchard was investigated on organization level and temporal-spatial niche. The results showed that the insect community was abundant, which included 6 orders, 23 families. The individuals of species, diversity indices, and evenness increased with time. Myzus persicae and Asiaarposina sasokii had the widest spatial niche breadth, while Didesmococcus koreauus borchs had the widest temporal niche breadth. Among the natural enemies, Chilocorus rubidus had the widest both temporal and spatial niche breadth. The niche of Chicocorus rubidus and Didesmococcus koreauus overlapped larger than that of the others, which indicated their synchrony in temporal dimension and their similarity in spatial dimension. As the dominant natural enemies, the two populations should be protected and utilized to control plum pest.

  19. NICHE: The non-imaging Cherenkov array

    NASA Astrophysics Data System (ADS)

    Bergman, Douglas; Krizmanic, John

    2013-02-01

    The accurate measurement of the Cosmic Ray (CR) nuclear composition around and above the Knee (~ 1015.5 eV) has been difficult due to uncertainties inherent to the measurement techniques and/or dependence on hadronic Monte Carlo simulation models required to interpret the data. Measurement of the Cherenkov air shower signal, calibrated with air fluorescence measurements, offers a methodology to provide an accurate measurement of the nuclear composition evolution over a large energy range. NICHE will use an array of widely-spaced, non-imaging Cherenkov counters to measure the amplitude and time-spread of the air shower Cherenkov signal to extract CR nuclear composition measurements and to cross-calibrate the Cherenkov energy and composition measurements with TA/TALE fluorescence and surface detector measurements.

  20. Exometabolite niche partitioning among sympatric soil bacteria

    SciTech Connect

    Baran, Richard; Brodie, Eoin L.; Mayberry-Lewis, Jazmine; Hummel, Eric; Da Rocha, Ulisses Nunes; Chakraborty, Romy; Bowen, Benjamin P.; Karaoz, Ulas; Cadillo-Quiroz, Hinsby; Garcia-Pichel, Ferran; Northen, Trent R.

    2015-09-22

    Soils are arguably the most microbially diverse ecosystems. Physicochemical properties have been associated with the maintenance of this diversity. Yet, the role of microbial substrate specialization is largely unexplored since substrate utilization studies have focused on simple substrates, not the complex mixtures representative of the soil environment. Here we examine the exometabolite composition of desert biological soil crusts (biocrusts) and the substrate preferences of seven biocrust isolates. The biocrust's main primary producer releases a diverse array of metabolites, and isolates of physically associated taxa use unique subsets of the complex metabolite pool. Individual isolates use only 13-26% of available metabolites, with only 2 out of 470 used by all and 40% not used by any. An extension of this approach to a mesophilic soil environment also reveals high levels of microbial substrate specialization. In conclusion, these results suggest that exometabolite niche partitioning may be an important factor in the maintenance of microbial diversity.

  1. Exometabolite niche partitioning among sympatric soil bacteria

    PubMed Central

    Baran, Richard; Brodie, Eoin L.; Mayberry-Lewis, Jazmine; Hummel, Eric; Da Rocha, Ulisses Nunes; Chakraborty, Romy; Bowen, Benjamin P.; Karaoz, Ulas; Cadillo-Quiroz, Hinsby; Garcia-Pichel, Ferran; Northen, Trent R.

    2015-01-01

    Soils are arguably the most microbially diverse ecosystems. Physicochemical properties have been associated with the maintenance of this diversity. Yet, the role of microbial substrate specialization is largely unexplored since substrate utilization studies have focused on simple substrates, not the complex mixtures representative of the soil environment. Here we examine the exometabolite composition of desert biological soil crusts (biocrusts) and the substrate preferences of seven biocrust isolates. The biocrust's main primary producer releases a diverse array of metabolites, and isolates of physically associated taxa use unique subsets of the complex metabolite pool. Individual isolates use only 13−26% of available metabolites, with only 2 out of 470 used by all and 40% not used by any. An extension of this approach to a mesophilic soil environment also reveals high levels of microbial substrate specialization. These results suggest that exometabolite niche partitioning may be an important factor in the maintenance of microbial diversity. PMID:26392107

  2. Exometabolite niche partitioning among sympatric soil bacteria

    DOE PAGES

    Baran, Richard; Brodie, Eoin L.; Mayberry-Lewis, Jazmine; Hummel, Eric; Da Rocha, Ulisses Nunes; Chakraborty, Romy; Bowen, Benjamin P.; Karaoz, Ulas; Cadillo-Quiroz, Hinsby; Garcia-Pichel, Ferran; et al

    2015-09-22

    Soils are arguably the most microbially diverse ecosystems. Physicochemical properties have been associated with the maintenance of this diversity. Yet, the role of microbial substrate specialization is largely unexplored since substrate utilization studies have focused on simple substrates, not the complex mixtures representative of the soil environment. Here we examine the exometabolite composition of desert biological soil crusts (biocrusts) and the substrate preferences of seven biocrust isolates. The biocrust's main primary producer releases a diverse array of metabolites, and isolates of physically associated taxa use unique subsets of the complex metabolite pool. Individual isolates use only 13-26% of available metabolites,more » with only 2 out of 470 used by all and 40% not used by any. An extension of this approach to a mesophilic soil environment also reveals high levels of microbial substrate specialization. In conclusion, these results suggest that exometabolite niche partitioning may be an important factor in the maintenance of microbial diversity.« less

  3. Pathogen evolution and the immunological niche

    PubMed Central

    Cobey, Sarah

    2014-01-01

    Host immunity is a major driver of pathogen evolution and thus a major determinant of pathogen diversity. Explanations for pathogen diversity traditionally assume simple interactions between pathogens and the immune system, a view encapsulated by the susceptible–infected–recovered (SIR) model. However, there is growing evidence that the complexity of many host–pathogen interactions is dynamically important. This revised perspective requires broadening the definition of a pathogen's immunological phenotype, or what can be thought of as its immunological niche. After reviewing evidence that interactions between pathogens and host immunity drive much of pathogen evolution, I introduce the concept of a pathogen's immunological phenotype. Models that depart from the SIR paradigm demonstrate the utility of this perspective and show that it is particularly useful in understanding vaccine-induced evolution. This paper highlights questions in immunology, evolution, and ecology that must be answered to advance theories of pathogen diversity. PMID:25040161

  4. Animal personality due to social niche specialisation.

    PubMed

    Bergmüller, Ralph; Taborsky, Michael

    2010-09-01

    The existence of 'animal personality', i.e. consistent individual differences in behaviour across time and contexts, is an evolutionary puzzle that has recently generated considerable research interest. Although social factors are generally considered to be important, it is as yet unclear how they might select for personality. Drawing from ecological niche theory, we explore how social conflict and alternative social options can be key factors in the evolution and development of consistent individual differences in behaviour. We discuss how animal personality research might benefit from insights into the study of alternative tactics and illustrate how selection can favour behavioural diversification and consistency due to fitness benefits resulting from conflict reduction among social partners.

  5. Language, embodiment, and the cognitive niche.

    PubMed

    Clark, Andy

    2006-08-01

    Embodied agents use bodily actions and environmental interventions to make the world a better place to think in. Where does language fit into this emerging picture of the embodied, ecologically efficient agent? One useful way to approach this question is to consider language itself as a cognition-enhancing animal-built structure. To take this perspective is to view language as a kind of self-constructed cognitive niche: a persisting but never stationary material scaffolding whose crucial role in promoting thought and reason remains surprisingly poorly understood. It is the very materiality of this linguistic scaffolding, I suggest, that gives it some key benefits. By materializing thought in words, we create structures that are themselves proper objects of perception, manipulation, and (further) thought.

  6. The social brain: scale-invariant layering of Erdős-Rényi networks in small-scale human societies.

    PubMed

    Harré, Michael S; Prokopenko, Mikhail

    2016-05-01

    The cognitive ability to form social links that can bind individuals together into large cooperative groups for safety and resource sharing was a key development in human evolutionary and social history. The 'social brain hypothesis' argues that the size of these social groups is based on a neurologically constrained capacity for maintaining long-term stable relationships. No model to date has been able to combine a specific socio-cognitive mechanism with the discrete scale invariance observed in ethnographic studies. We show that these properties result in nested layers of self-organizing Erdős-Rényi networks formed by each individual's ability to maintain only a small number of social links. Each set of links plays a specific role in the formation of different social groups. The scale invariance in our model is distinct from previous 'scale-free networks' studied using much larger social groups; here, the scale invariance is in the relationship between group sizes, rather than in the link degree distribution. We also compare our model with a dominance-based hierarchy and conclude that humans were probably egalitarian in hunter-gatherer-like societies, maintaining an average maximum of four or five social links connecting all members in a largest social network of around 132 people.

  7. The social brain: scale-invariant layering of Erdős-Rényi networks in small-scale human societies.

    PubMed

    Harré, Michael S; Prokopenko, Mikhail

    2016-05-01

    The cognitive ability to form social links that can bind individuals together into large cooperative groups for safety and resource sharing was a key development in human evolutionary and social history. The 'social brain hypothesis' argues that the size of these social groups is based on a neurologically constrained capacity for maintaining long-term stable relationships. No model to date has been able to combine a specific socio-cognitive mechanism with the discrete scale invariance observed in ethnographic studies. We show that these properties result in nested layers of self-organizing Erdős-Rényi networks formed by each individual's ability to maintain only a small number of social links. Each set of links plays a specific role in the formation of different social groups. The scale invariance in our model is distinct from previous 'scale-free networks' studied using much larger social groups; here, the scale invariance is in the relationship between group sizes, rather than in the link degree distribution. We also compare our model with a dominance-based hierarchy and conclude that humans were probably egalitarian in hunter-gatherer-like societies, maintaining an average maximum of four or five social links connecting all members in a largest social network of around 132 people. PMID:27194482

  8. Large Amplitude Spatial and Temporal Gradients in Atmospheric Boundary Layer CO2 Mole Fractions Detected With a Tower-Based Network in the U.S. Upper Midwest

    SciTech Connect

    Miles, Natasha; Richardson, S. J.; Davis, Kenneth J.; Lauvaux, Thomas; Andrews, A.; West, Tristram O.; Bandaru, Varaprasad; Crosson, Eric R.

    2012-02-21

    This study presents observations of atmospheric CO{sub 2} mole fraction from a nine-tower, regional network deployed during the North American Carbon Program's Mid-Continent Intensive during 2007-2009. Within this network in a largely agricultural area, mean atmospheric CO{sub 2} gradients were strongly correlated with both ground-based inventory data and estimates from satellite remote sensing. The average seasonal drawdown for corn-dominated sites (35 ppm) is significantly larger than has been observed at other continental boundary layer sites. Observed growing-season median CO{sub 2} gradients are strongly dependent on local flux. The gradients between cross-vegetation site-pairs, for example, average 2.0 ppm/100 km, four times larger than the similar-vegetation site-pair average. Daily-timescale gradients are as large as 5.5 ppm/100 km, but dominated by advection rather than local flux. Flooding in 2008 led to a region-wide 23 week delay in growing-season minima. The observations show that regional-scale CO{sub 2} mole fraction networks yield large, coherent signals governed largely by regional sources and sinks of CO{sub 2}.

  9. Life history, cognition and the evolution of complex foraging niches.

    PubMed

    Schuppli, Caroline; Graber, Sereina M; Isler, Karin; van Schaik, Carel P

    2016-03-01

    Animal species that live in complex foraging niches have, in general, improved access to energy-rich and seasonally stable food sources. Because human food procurement is uniquely complex, we ask here which conditions may have allowed species to evolve into such complex foraging niches, and also how niche complexity is related to relative brain size. To do so, we divided niche complexity into a knowledge-learning and a motor-learning dimension. Using a sample of 78 primate and 65 carnivoran species, we found that two life-history features are consistently correlated with complex niches: slow, conservative development or provisioning of offspring over extended periods of time. Both act to buffer low energy yields during periods of learning, and may thus act as limiting factors for the evolution of complex niches. Our results further showed that the knowledge and motor dimensions of niche complexity were correlated with pace of development in primates only, and with the length of provisioning in only carnivorans. Accordingly, in primates, but not carnivorans, living in a complex foraging niche requires enhanced cognitive abilities, i.e., a large brain. The patterns in these two groups of mammals show that selection favors evolution into complex niches (in either the knowledge or motor dimension) in species that either develop more slowly or provision their young for an extended period of time. These findings help to explain how humans constructed by far the most complex niche: our ancestors managed to combine slow development (as in other primates) with systematic provisioning of immatures and even adults (as in carnivorans). This study also provides strong support for the importance of ecological factors in brain size evolution. PMID:26989019

  10. Ecology of Enterococcus faecalis and niche adapted or non-niche-adapted Enterococcus faecium in continuous-flow anaerobic cultures

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Objectives: To study the survivability of niche adapted Enterococcus faecium I.3rif (I.3rif) vs. non-niche adapted Enterococcus faecium (GRE47) in cultures that contain Enterococcus faecalis I.2. Methods: An anaerobic continuous-flow culture of chicken microflora (CCF) that models the chicken gastr...

  11. Using Ecological Niche Models and Niche Analyses to Understand Speciation Patterns: The Case of Sister Neotropical Orchid Bees

    PubMed Central

    Silva, Daniel P.; Vilela, Bruno; De Marco, Paulo; Nemésio, André

    2014-01-01

    The role of past connections between the two major South American forested biomes on current species distribution has been recognized a long time ago. Climatic oscillations that further separated these biomes have promoted parapatric speciation, in which many species had their continuous distribution split, giving rise to different but related species (i.e., different potential distributions and realized niche features). The distribution of many sister species of orchid bees follow this pattern. Here, using ecological niche models and niche analyses, we (1) tested the role of ecological niche differentiation on the divergence between sister orchid-bees (genera Eulaema and Eufriesea) from the Amazon and Atlantic forests, and (2) highlighted interesting areas for new surveys. Amazonian species occupied different realized niches than their Atlantic sister species. Conversely, species of sympatric but distantly related Eulaema bees occupied similar realized niches. Amazonian species had a wide potential distribution in South America, whereas Atlantic Forest species were more limited to the eastern coast of the continent. Additionally, we identified several areas in need of future surveys. Our results show that the realized niche of Atlantic-Amazonian sister species of orchid bees, which have been previously treated as allopatric populations of three species, had limited niche overlap and similarity. These findings agree with their current taxonomy, which treats each of those populations as distinct valid species. PMID:25422941

  12. Synthesis, characterization and structure determination of two isotypes of a layered aluminophosphate with a new 2D network topology

    SciTech Connect

    Tuel, A. . E-mail: tuel@catalyse.cnrs.fr; Lorentz, Ch.; Gramlich, V.; Baerlocher, Ch.

    2005-07-15

    Two isotypes of a new layered aluminophosphate, further denoted MDAP-3 and MDAE-1, have been synthesized under hydrothermal conditions using N-methyl-1,3-propanediamine and N-methyl-ethylenediamine, respectively. MDAP-3, with the empirical formula [Al{sub 2}(HPO{sub 4})(PO{sub 4}){sub 2}](C{sub 4}N{sub 2}H{sub 14})(H{sub 2}O), crystallizes in the orthorhombic space group Pna2(1) (No. 33) with a=9.602(16)A, b=9.26(2)A, c=16.03(3)A, Z=4, R{sub 1}=0.0498 and wR{sub 2}=0.1217. The second solid, MDAE-1, with the empirical formula [Al{sub 2}(HPO{sub 4})(PO{sub 4}){sub 2}](C{sub 3}N{sub 2}H{sub 12})(H{sub 2}O), crystallizes in the same space group with a=9.4250(19)A, b=9.3170(19)A, c=15.907(3)A, Z=4, R{sub 1}=0.0407 and wR{sub 2}=0.0954. The two compounds possess the same layer topology. Inorganic layers contain PO{sub 3}=O, PO{sub 3}OH, AlO{sub 4} and AlO{sub 6} polyhedra, linked together to generate a new 4x8 net. MDAP-3 and MDAE-1 represent the first examples of two-dimensional layered aluminophosphates with the Al{sub 2}P{sub 3}O{sub 12} stoichiometry, and containing AlO{sub 6} octahedra.

  13. 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.

  14. Conversion of quiescent niche cells to somatic stem cells causes ectopic niche formation in the Drosophila testis

    PubMed Central

    Hétié, Phylis; de Cuevas, Margaret; Matunis, Erika

    2014-01-01

    Summary Adult stem cells reside in specialized regulatory microenvironments, or niches, where local signals ensure stem cell maintenance. The Drosophila testis contains a well-characterized niche wherein signals from post-mitotic hub cells promote maintenance of adjacent germline stem cells and somatic cyst stem cells (CySCs). Hub cells were considered to be terminally differentiated; here we show that they can give rise to CySCs. Genetic ablation of CySCs triggers hub cells to transiently exit quiescence, delaminate from the hub, and convert into functional CySCs. Ectopic Cyclin D-Cdk4 expression in hub cells is also sufficient to trigger their conversion into CySCs. In both cases, this conversion causes the formation of multiple ectopic niches over time. Therefore, our work provides a model for understanding how oncogenic mutations in quiescent niche cells could promote loss of quiescence, changes in cell fate, and aberrant niche expansion more generally. PMID:24746819

  15. Dynamics of bacterial community succession in a salt marsh chronosequence: evidences for temporal niche partitioning

    PubMed Central

    Dini-Andreote, Francisco; de Cássia Pereira e Silva, Michele; Triadó-Margarit, Xavier; Casamayor, Emilio O; van Elsas, Jan Dirk; Salles, Joana Falcão

    2014-01-01

    The mechanisms underlying community assembly and promoting temporal succession are often overlooked in microbial ecology. Here, we studied an undisturbed salt marsh chronosequence, spanning over a century of ecosystem development, to understand bacterial succession in soil. We used 16S rRNA gene-based quantitative PCR to determine bacterial abundance and multitag 454 pyrosequencing for community composition and diversity analyses. Despite 10-fold lower 16S rRNA gene abundances, the initial stages of soil development held higher phylogenetic diversities than the soil at late succession. Temporal variations in phylogenetic β-diversity were greater at initial stages of soil development, possibly as a result of the great dynamism imposed by the daily influence of the tide, promoting high immigration rates. Allogenic succession of bacterial communities was mostly driven by shifts in the soil physical structure, as well as variations in pH and salinity, which collectively explained 84.5% of the variation concerning community assemblage. The community assembly data for each successional stage were integrated into a network co-occurrence analysis, revealing higher complexity at initial stages, coinciding with great dynamism in turnover and environmental variability. Contrary to a spatial niche-based perspective of bacterial community assembly, we suggest temporal niche partitioning as the dominant mechanism of assembly (promoting more phylotype co-occurrence) in the initial stages of succession, where continuous environmental change results in the existence of multiple niches over short periods of time. PMID:24739625

  16. Experiments with humans indicate that decision accuracy drives the evolution of niche width.

    PubMed

    Tosh, Colin R; Ruxton, Graeme D; Krause, Jens; Franks, Daniel W

    2011-12-01

    One theory to explain the high incidence of niche specialization in many animals is that it reduces attentional load during resource-seeking behaviour and thus leads to more accurate resource selection. A recent neural network model refined the predictions of this theory, indicating that a cognitive advantage in specialists is likely to occur under realistic ecological conditions, namely when 'mistakes' (i.e. selection of non-host resources) contribute moderately but positively to fitness. Here, we present a formal empirical test of the predictions of this model. Using a human-computer interactive, we demonstrate that the central prediction of the model is supported: specialist humans are more accurate decision-makers than generalists when their mistakes are rewarded, but not when mistakes are punished. The idea that increased decision accuracy drives the evolution of niche width in animals has been supported in almost all empirical systems in which it has been investigated. Theoretical work supports the idea, and now the predictions of a key theoretical model have been demonstrated in a real biological information-processing system. Considering these interlocking pieces of evidence, we argue that specialization through increased decision accuracy may contribute significantly, along with other mechanisms, to promote niche specialization in animals.

  17. Root niche separation can explain avoidance of seasonal drought stress and vulnerability of overstory trees to extended drought in a mature Amazonian forest

    NASA Astrophysics Data System (ADS)

    Ivanov, Valeriy Y.; Hutyra, Lucy R.; Wofsy, Steven C.; Munger, J. William; Saleska, Scott R.; de Oliveira, Raimundo C., Jr.; de Camargo, Plínio B.

    2012-12-01

    Large areas of Amazonian evergreen forest experience seasonal droughts extending for three or more months, yet show maximum rates of photosynthesis and evapotranspiration during dry intervals. This apparent resilience is belied by disproportionate mortality of the large trees in manipulations that reduce wet season rainfall, occurring after 2-3 years of treatment. The goal of this study is to characterize the mechanisms that produce these contrasting ecosystem responses. A mechanistic model is developed based on the ecohydrological framework of TIN (Triangulated Irregular Network)-based Real Time Integrated Basin Simulator + Vegetation Generator for Interactive Evolution (tRIBS+VEGGIE). The model is used to test the roles of deep roots and soil capillary flux to provide water to the forest during the dry season. Also examined is the importance of "root niche separation," in which roots of overstory trees extend to depth, where during the dry season they use water stored from wet season precipitation, while roots of understory trees are concentrated in shallow layers that access dry season precipitation directly. Observational data from the Tapajós National Forest, Brazil, were used as meteorological forcing and provided comprehensive observational constraints on the model. Results strongly suggest that deep roots with root niche separation adaptations explain both the observed resilience during seasonal drought and the vulnerability of canopy-dominant trees to extended deficits of wet season rainfall. These mechanisms appear to provide an adaptive strategy that enhances productivity of the largest trees in the face of their disproportionate heat loads and water demand in the dry season. A sensitivity analysis exploring how wet season rainfall affects the stability of the rainforest system is presented.

  18. Networks.

    ERIC Educational Resources Information Center

    Cerf, Vinton G.

    1991-01-01

    The demands placed on the networks transporting the information and knowledge generated by the increased diversity and sophistication of computational machinery are described. What is needed to support this increased flow, the structures already in place, and what must be built are topics of discussion. (KR)

  19. Tempo and mode of climatic niche evolution in Primates.

    PubMed

    Duran, Andressa; Pie, Marcio R

    2015-09-01

    Climatic niches have increasingly become a nexus in our understanding of a variety of ecological and evolutionary phenomena, from species distributions to latitudinal diversity gradients. Despite the increasing availability of comprehensive datasets on species ranges, phylogenetic histories, and georeferenced environmental conditions, studies on the evolution of climate niches have only begun to understand how niches evolve over evolutionary timescales. Here, using primates as a model system, we integrate recently developed phylogenetic comparative methods, species distribution patterns, and climatic data to explore primate climatic niche evolution, both among clades and over time. In general, we found that simple, constant-rate models provide a poor representation of how climatic niches evolve. For instance, there have been shifts in the rate of climatic niche evolution in several independent clades, particularly in response to the increasingly cooler climates of the past 10 My. Interestingly, rate accelerations greatly outnumbered rate decelerations. These results highlight the importance of considering more realistic evolutionary models that allow for the detection of heterogeneity in the tempo and mode of climatic niche evolution, as well as to infer possible constraining factors for species distributions in geographical space. PMID:26178157

  20. Tempo and mode of climatic niche evolution in Primates.

    PubMed

    Duran, Andressa; Pie, Marcio R

    2015-09-01

    Climatic niches have increasingly become a nexus in our understanding of a variety of ecological and evolutionary phenomena, from species distributions to latitudinal diversity gradients. Despite the increasing availability of comprehensive datasets on species ranges, phylogenetic histories, and georeferenced environmental conditions, studies on the evolution of climate niches have only begun to understand how niches evolve over evolutionary timescales. Here, using primates as a model system, we integrate recently developed phylogenetic comparative methods, species distribution patterns, and climatic data to explore primate climatic niche evolution, both among clades and over time. In general, we found that simple, constant-rate models provide a poor representation of how climatic niches evolve. For instance, there have been shifts in the rate of climatic niche evolution in several independent clades, particularly in response to the increasingly cooler climates of the past 10 My. Interestingly, rate accelerations greatly outnumbered rate decelerations. These results highlight the importance of considering more realistic evolutionary models that allow for the detection of heterogeneity in the tempo and mode of climatic niche evolution, as well as to infer possible constraining factors for species distributions in geographical space.

  1. The spermatogonial stem cell niche in the collared peccary (Tayassu tajacu).

    PubMed

    Campos-Junior, Paulo Henrique A; Costa, Guilherme M J; Lacerda, Samyra M S N; Rezende-Neto, José V; de Paula, Ana M; Hofmann, Marie-Claude; de França, Luiz R

    2012-05-01

    In the seminiferous epithelium, spermatogonial stem cells (SSCs) are located in a particular environment called the "niche" that is controlled by the basement membrane, key testis somatic cells, and factors originating from the vascular network. However, the role of Leydig cells (LCs) as a niche component is not yet clearly elucidated. Recent studies showed that peccaries (Tayassu tajacu) present a peculiar LC cytoarchitecture in which these cells are located around the seminiferous tubule lobes, making the peccary a unique model for investigating the SSC niche. This peculiarity allowed us to subdivide the seminiferous tubule cross-sections in three different testis parenchyma regions (tubule-tubule, tubule-interstitium, and tubule-LC contact). Our aims were to characterize the different spermatogonial cell types and to determine the location and/or distribution of the SSCs along the seminiferous tubules. Compared to differentiating spermatogonia, undifferentiated spermatogonia (A(und)) presented a noticeably higher nuclear volume (P < 0.05), allowing an accurate evaluation of their distribution. Immunostaining analysis demonstrated that approximately 93% of A(und) were GDNF receptor alpha 1 positive (GFRA1(+)), and these cells were preferentially located adjacent to the interstitial compartment without LCs (P < 0.05). The expression of colony-stimulating factor 1 was observed in LCs and peritubular myoid cells (PMCs), whereas its receptor was present in LCs and in GFRA1(+) A(und). Taken together, our findings strongly suggest that LCs, different from PMCs, might play a minor role in the SSC niche and physiology and that these steroidogenic cells are probably involved in the differentiation of A(und) toward type A(1) spermatogonia.

  2. A Hypothesis-Testing Framework for Studies Investigating Ontogenetic Niche Shifts Using Stable Isotope Ratios

    PubMed Central

    Hammerschlag-Peyer, Caroline M.; Yeager, Lauren A.; Araújo, Márcio S.; Layman, Craig A.

    2011-01-01

    Ontogenetic niche shifts occur across diverse taxonomic groups, and can have critical implications for population dynamics, community structure, and ecosystem function. In this study, we provide a hypothesis-testing framework combining univariate and multivariate analyses to examine ontogenetic niche shifts using stable isotope ratios. This framework is based on three distinct ontogenetic niche shift scenarios, i.e., (1) no niche shift, (2) niche expansion/reduction, and (3) discrete niche shift between size classes. We developed criteria for identifying each scenario, as based on three important resource use characteristics, i.e., niche width, niche position, and niche overlap. We provide an empirical example for each ontogenetic niche shift scenario, illustrating differences in resource use characteristics among different organisms. The present framework provides a foundation for future studies on ontogenetic niche shifts, and also can be applied to examine resource variability among other population sub-groupings (e.g., by sex or phenotype). PMID:22073265

  3. Mutually connected component of networks of networks with replica nodes

    NASA Astrophysics Data System (ADS)

    Bianconi, Ginestra; Dorogovtsev, Sergey N.; Mendes, José F. F.

    2015-01-01

    We describe the emergence of the giant mutually connected component in networks of networks in which each node has a single replica node in any layer and can be interdependent only on its replica nodes in the interdependent layers. We prove that if, in these networks, all the nodes of one network (layer) are interdependent on the nodes of the same other interconnected layer, then, remarkably, the mutually connected component does not depend on the topology of the network of networks. This component coincides with the mutual component of the fully connected network of networks constructed from the same set of layers, i.e., a multiplex network.

  4. Hematopoietic stem cell niche maintenance during homeostasis and regeneration

    PubMed Central

    Mendelson, Avital; Frenette, Paul S

    2015-01-01

    The bone marrow niche has mystified scientists for many years, leading to widespread investigation to shed light into its molecular and cellular composition. Considerable efforts have been devoted toward uncovering the regulatory mechanisms of hematopoietic stem cell (HSC) niche maintenance. Recent advances in imaging and genetic manipulation of mouse models have allowed the identification of distinct vascular niches that have been shown to orchestrate the balance between quiescence, proliferation and regeneration of the bone marrow after injury. Here we highlight the recently discovered intrinsic mechanisms, microenvironmental interactions and communication with surrounding cells involved in HSC regulation, during homeostasis and in regeneration after injury and discuss their implications for regenerative therapy. PMID:25100529

  5. Niche construction: evolutionary implications for parasites and hosts.

    PubMed

    Lymbery, Alan J

    2015-04-01

    Organisms can determine the environment they experience through the process of niche construction. This may have important evolutionary consequences by exposing them to new selection pressures, producing a faster response to selection, and building suites of coadapted traits. Traits of the parasite which influence the likelihood of encountering different host environments, or which change the host environment, can be regarded as niche construction traits, as can traits of the host which influence the likelihood of the host being infected by parasites. A niche construction perspective may provide new insights into the evolution of host/parasite interactions; this is illustrated with several examples from the viewpoint of both parasite and host traits.

  6. The evolution of the cancer niche during multistage carcinogenesis.

    PubMed

    Barcellos-Hoff, Mary Helen; Lyden, David; Wang, Timothy C

    2013-07-01

    The concept of the tumour microenvironment recognizes that the interplay between cancer cells and stromal cells is a crucial determinant of cancer growth. In this Perspectives article, we propose the novel concept that the tumour microenvironment is built through rate-limiting steps during multistage carcinogenesis. Construction of a 'precancer niche' is a necessary and early step that is required for initiated cells to survive and evolve; subsequent niche expansion and maturation accompany tumour promotion and progression, respectively. As such, cancer niches represent an emergent property of a tumour that could be a robust target for cancer prevention and therapy.

  7. Extensive subglacial hydrological network and basal temperate layer in Southwest Greenland: an integrated approach of radar analysis and ice sheet modeling

    NASA Astrophysics Data System (ADS)

    Chu, W.; Schroeder, D. M.; Seroussi, H. L.; Bell, R. E.; Creyts, T. T.

    2015-12-01

    Meltwater storage in and beneath the ice sheet exerts strong control on ice flow velocity by modifying the ice thermal structure and basal sliding. However, observations of meltwater storage in Greenland are sparse and mostly limited to the margins of the ice sheet, providing an incomplete view on how water is distributed. To address this shortcoming, we use an integrated approach of radar analyses, and thermal and subglacial hydrology modeling to produce the first, catchment-wide characterization of the subglacial hydrological network. Our study focuses on a 1450 km2 section of Russell Glacier and Isunnguata Sermia. We use the depth profiles of ice temperature from a thermal model to correct radar englacial attenuation losses, and produce maps of relative basal reflectivity from radar bed echoes. We examine the reflectivity relative to a subglacial hydrology model, and show that substantial volumes of water store in an extensive subglacial hydrological network. Data from mid-April show that subglacial water concentrates along the basal valleys in the lower catchment directly below where numerous moulins open later in the season. Additionally, we identify an unusually low apparent reflectivity feature at the catchment boundary of Russell and Isunnguata. We suggest that the apparent reflectivity anomaly is a result of high englacial attenuation losses associated with a basal temperate layer ~250 m thick and ~14 km2 in area. This temperate layer was previously observed in another melt season from boreholes temperature measurements, suggesting that it is likely is a persistent and contiguous feature. Our results demonstrate the integration of observations and modeling are a powerful approach to characterize Greenland hydrology and its effect on ice sheet thermal state that may modify ice dynamics critically.

  8. Stem cell autotomy and niche interaction in different systems

    PubMed Central

    Dorn, David C; Dorn, August

    2015-01-01

    The best known cases of cell autotomy are the formation of erythrocytes and thrombocytes (platelets) from progenitor cells that reside in special niches. Recently, autotomy of stem cells and its enigmatic interaction with the niche has been reported from male germline stem cells (GSCs) in several insect species. First described in lepidopterans, the silkmoth, followed by the gipsy moth and consecutively in hemipterans, foremost the milkweed bug. In both, moths and the milkweed bug, GSCs form finger-like projections toward the niche, the apical cells (homologs of the hub cells in Drosophila). Whereas in the milkweed bug the projection terminals remain at the surface of the niche cells, in the gipsy moth they protrude deeply into the singular niche cell. In both cases, the projections undergo serial retrograde fragmentation with progressing signs of autophagy. In the gipsy moth, the autotomized vesicles are phagocytized and digested by the niche cell. In the milkweed bug the autotomized vesicles accumulate at the niche surface and disintegrate. Autotomy and sprouting of new projections appears to occur continuously. The significance of the GSC-niche interactions, however, remains enigmatic. Our concept on the signaling relationship between stem cell-niche in general and GSC and niche (hub cells and cyst stem cells) in particular has been greatly shaped by Drosophila melanogaster. In comparing the interactions of GSCs with their niche in Drosophila with those in species exhibiting GSC autotomy it is obvious that additional or alternative modes of stem cell-niche communication exist. Thus, essential signaling pathways, including niche-stem cell adhesion (E-cadherin) and the direction of asymmetrical GSC division - as they were found in Drosophila - can hardly be translated into the systems where GSC autotomy was reported. It is shown here that the serial autotomy of GSC projections shows remarkable similarities with Wallerian axonal destruction, developmental axon

  9. Stem cell autotomy and niche interaction in different systems.

    PubMed

    Dorn, David C; Dorn, August

    2015-07-26

    The best known cases of cell autotomy are the formation of erythrocytes and thrombocytes (platelets) from progenitor cells that reside in special niches. Recently, autotomy of stem cells and its enigmatic interaction with the niche has been reported from male germline stem cells (GSCs) in several insect species. First described in lepidopterans, the silkmoth, followed by the gipsy moth and consecutively in hemipterans, foremost the milkweed bug. In both, moths and the milkweed bug, GSCs form finger-like projections toward the niche, the apical cells (homologs of the hub cells in Drosophila). Whereas in the milkweed bug the projection terminals remain at the surface of the niche cells, in the gipsy moth they protrude deeply into the singular niche cell. In both cases, the projections undergo serial retrograde fragmentation with progressing signs of autophagy. In the gipsy moth, the autotomized vesicles are phagocytized and digested by the niche cell. In the milkweed bug the autotomized vesicles accumulate at the niche surface and disintegrate. Autotomy and sprouting of new projections appears to occur continuously. The significance of the GSC-niche interactions, however, remains enigmatic. Our concept on the signaling relationship between stem cell-niche in general and GSC and niche (hub cells and cyst stem cells) in particular has been greatly shaped by Drosophila melanogaster. In comparing the interactions of GSCs with their niche in Drosophila with those in species exhibiting GSC autotomy it is obvious that additional or alternative modes of stem cell-niche communication exist. Thus, essential signaling pathways, including niche-stem cell adhesion (E-cadherin) and the direction of asymmetrical GSC division - as they were found in Drosophila - can hardly be translated into the systems where GSC autotomy was reported. It is shown here that the serial autotomy of GSC projections shows remarkable similarities with Wallerian axonal destruction, developmental axon

  10. A synthesis of transplant experiments and ecological niche models suggests that range limits are often niche limits.

    PubMed

    Lee-Yaw, Julie A; Kharouba, Heather M; Bontrager, Megan; Mahony, Colin; Csergő, Anna Mária; Noreen, Annika M E; Li, Qin; Schuster, Richard; Angert, Amy L

    2016-06-01

    Global change has made it important to understand the factors that shape species' distributions. Central to this area of research is the question of whether species' range limits primarily reflect the distribution of suitable habitat (i.e. niche limits) or arise as a result of dispersal limitation. Over-the-edge transplant experiments and ecological niche models are commonly used to address this question, yet few studies have taken advantage of a combined approach for inferring the causes of range limits. Here, we synthesise results from existing transplant experiments with new information on the predicted suitability of sites based on niche models. We found that individual performance and habitat suitability independently decline beyond range limits across multiple species. Furthermore, inferences from transplant experiments and niche models were generally concordant within species, with 31 out of 40 cases fully supporting the hypothesis that range limits are niche limits. These results suggest that range limits are often niche limits and that the factors constraining species' ranges operate at scales detectable by both transplant experiments and niche models. In light of these findings, we outline an integrative framework for addressing the causes of range limits in individual species. PMID:27111656

  11. A physically meaningful equivalent circuit network model of a lithium-ion battery accounting for local electrochemical and thermal behaviour, variable double layer capacitance and degradation

    NASA Astrophysics Data System (ADS)

    von Srbik, Marie-Therese; Marinescu, Monica; Martinez-Botas, Ricardo F.; Offer, Gregory J.

    2016-09-01

    A novel electrical circuit analogy is proposed modelling electrochemical systems under realistic automotive operation conditions. The model is developed for a lithium ion battery and is based on a pseudo 2D electrochemical model. Although cast in the framework familiar to application engineers, the model is essentially an electrochemical battery model: all variables have a direct physical interpretation and there is direct access to all states of the cell via the model variables (concentrations, potentials) for monitoring and control systems design. This is the first Equivalent Circuit Network -type model that tracks directly the evolution of species inside the cell. It accounts for complex electrochemical phenomena that are usually omitted in online battery performance predictors such as variable double layer capacitance, the full current-overpotential relation and overpotentials due to mass transport limitations. The coupled electrochemical and thermal model accounts for capacity fade via a loss in active species and for power fade via an increase in resistive solid electrolyte passivation layers at both electrodes. The model's capability to simulate cell behaviour under dynamic events is validated against test procedures, such as standard battery testing load cycles for current rates up to 20 C, as well as realistic automotive drive cycle loads.

  12. Recruitment and Consolidation of Cell Assemblies for Words by Way of Hebbian Learning and Competition in a Multi-Layer Neural Network.

    PubMed

    Garagnani, Max; Wennekers, Thomas; Pulvermüller, Friedemann

    2009-06-01

    Current cognitive theories postulate either localist representations of knowledge or fully overlapping, distributed ones. We use a connectionist model that closely replicates known anatomical properties of the cerebral cortex and neurophysiological principles to show that Hebbian learning in a multi-layer neural network leads to memory traces (cell assemblies) that are both distributed and anatomically distinct. Taking the example of word learning based on action-perception correlation, we document mechanisms underlying the emergence of these assemblies, especially (i) the recruitment of neurons and consolidation of connections defining the kernel of the assembly along with (ii) the pruning of the cell assembly's halo (consisting of very weakly connected cells). We found that, whereas a learning rule mapping covariance led to significant overlap and merging of assemblies, a neurobiologically grounded synaptic plasticity rule with fixed LTP/LTD thresholds produced minimal overlap and prevented merging, exhibiting competitive learning behaviour. Our results are discussed in light of current theories of language and memory. As simulations with neurobiologically realistic neural networks demonstrate here spontaneous emergence of lexical representations that are both cortically dispersed and anatomically distinct, both localist and distributed cognitive accounts receive partial support.

  13. Brine network structural metamorphosis and sea ice bottom layer permeability change induced by sea water penetration under a surface pressure field

    NASA Astrophysics Data System (ADS)

    Hudier, E. J.

    2013-12-01

    Sea ice presents two roughness scales: one in the millimetre range and the other up to several meters due to ridging. The larger roughness elements are the result of compression and sheer, causing ice blocks to pile up and down at the line of contact between converging ice floes. In terms of boundary limit dynamic, they create obstacles that induce, in their wake, a pressure gradient at the ice water interface. Sea ice is a porous medium and as such, is permeable when subject to pressure gradients. Models have shown that, at spring, when ice permeability increases, sea water can be forced through the ice water interface into the bottom ice layer while brine is pumped out of it under obstacle induced pressure gradients. These results suggest that ice ocean heat budgets have to include a porous flow component and its associated latent heat import/export caused by through volume melting/thawing inside the bottom ice layer subject to sea water infiltration. With the initiation of a melt/thaw dynamic within the porous bottom ice layer, the porous network restructures. Our research show an enlargement of the larger brine channels while smaller ones close due ice growth. Similarly, ice volume of smaller cross size tend to disappear while larger ones evolve slowly. As heat fluxes due to latent heat exchanges become several orders of magnitude larger than any other exterior forcing, such as radiation, heat budgets within ice individual volumes balance fluxes in and out caused by melting/thaw on channel walls. Our simulations were run from an early spring C shape temperature profile to an isothermal state showing that structural change becomes significant only after the temperature profile becomes positive upward.

  14. Host specialist clownfishes are environmental niche generalists.

    PubMed

    Litsios, Glenn; Kostikova, Anna; Salamin, Nicolas

    2014-11-22

    Why generalist and specialist species coexist in nature is a question that has interested evolutionary biologists for a long time. While the coexistence of specialists and generalists exploiting resources on a single ecological dimension has been theoretically and empirically explored, biological systems with multiple resource dimensions (e.g. trophic, ecological) are less well understood. Yet, such systems may provide an alternative to the classical theory of stable evolutionary coexistence of generalist and specialist species on a single resource dimension. We explore such systems and the potential trade-offs between different resource dimensions in clownfishes. All species of this iconic clade are obligate mutualists with sea anemones yet show interspecific variation in anemone host specificity. Moreover, clownfishes developed variable environmental specialization across their distribution. In this study, we test for the existence of a relationship between host-specificity (number of anemones associated with a clownfish species) and environmental-specificity (expressed as the size of the ecological niche breadth across climatic gradients). We find a negative correlation between host range and environmental specificities in temperature, salinity and pH, probably indicating a trade-off between both types of specialization forcing species to specialize only in a single direction. Trade-offs in a multi-dimensional resource space could be a novel way of explaining the coexistence of generalist and specialists. PMID:25274370

  15. Phylogenetic niche conservatism in C4 grasses.

    PubMed

    Liu, Hui; Edwards, Erika J; Freckleton, Robert P; Osborne, Colin P

    2012-11-01

    Photosynthetic pathway is used widely to discriminate plant functional types in studies of global change. However, independent evolutionary lineages of C(4) grasses with different variants of C(4) photosynthesis show different biogeographical relationships with mean annual precipitation, suggesting phylogenetic niche conservatism (PNC). To investigate how phylogeny and photosynthetic type differentiate C(4) grasses, we compiled a dataset of morphological and habitat information of 185 genera belonging to two monophyletic subfamilies, Chloridoideae and Panicoideae, which together account for 90 % of the world's C(4) grass species. We evaluated evolutionary variance and covariance of morphological and habitat traits. Strong phylogenetic signals were found in both morphological and habitat traits, arising mainly from the divergence of the two subfamilies. Genera in Chloridoideae had significantly smaller culm heights, leaf widths, 1,000-seed weights and stomata; they also appeared more in dry, open or saline habitats than those of Panicoideae. Controlling for phylogenetic structure showed significant covariation among morphological traits, supporting the hypothesis of phylogenetically independent scaling effects. However, associations between morphological and habitat traits showed limited phylogenetic covariance. Subfamily was a better explanation than photosynthetic type for the variance in most morphological traits. Morphology, habitat water availability, shading, and productivity are therefore all involved in the PNC of C(4) grass lineages. This study emphasized the importance of phylogenetic history in the ecology and biogeography of C(4) grasses, suggesting that divergent lineages need to be considered to fully understand the impacts of global change on plant distributions. PMID:22569558

  16. Pseudomonas biofilm matrix composition and niche biology

    PubMed Central

    Mann, Ethan E.; Wozniak, Daniel J.

    2014-01-01

    Biofilms are a predominant form of growth for bacteria in the environment and in the clinic. Critical for biofilm development are adherence, proliferation, and dispersion phases. Each of these stages includes reinforcement by, or modulation of, the extracellular matrix. Pseudomonas aeruginosa has been a model organism for the study of biofilm formation. Additionally, other Pseudomonas species utilize biofilm formation during plant colonization and environmental persistence. Pseudomonads produce several biofilm matrix molecules, including polysaccharides, nucleic acids, and proteins. Accessory matrix components shown to aid biofilm formation and adaptability under varying conditions are also produced by pseudomonads. Adaptation facilitated by biofilm formation allows for selection of genetic variants with unique and distinguishable colony morphology. Examples include rugose small-colony variants and wrinkly spreaders (WS), which over produce Psl/Pel or cellulose, respectively, and mucoid bacteria that over produce alginate. The well-documented emergence of these variants suggests that pseudomonads take advantage of matrix-building subpopulations conferring specific benefits for the entire population. This review will focus on various polysaccharides as well as additional Pseudomonas biofilm matrix components. Discussions will center on structure–function relationships, regulation, and the role of individual matrix molecules in niche biology. PMID:22212072

  17. Invasive plants have broader physiological niches.

    PubMed

    Higgins, Steven I; Richardson, David M

    2014-07-22

    Invasive species cost the global economy billions of dollars each year, but ecologists have struggled to predict the risk of an introduced species naturalizing and invading. Although carefully designed experiments are needed to fully elucidate what makes some species invasive, much can be learned from unintentional experiments involving the introduction of species beyond their native ranges. Here, we assess invasion risk by linking a physiologically based species distribution model with data on the invasive success of 749 Australian acacia and eucalypt tree species that have, over more than a century, been introduced around the world. The model correctly predicts 92% of occurrences observed outside of Australia from an independent dataset. We found that invasiveness is positively associated with the projection of physiological niche volume in geographic space, thereby illustrating that species tolerant of a broader range of environmental conditions are more likely to be invasive. Species achieve this broader tolerance in different ways, meaning that the traits that define invasive success are context-specific. Hence, our study reconciles studies that have failed to identify the traits that define invasive success with the urgent and pragmatic need to predict invasive success.

  18. 45. EXPOSEDAGGREGATE CONCRETE AT NICHE, NORTH BOUNDARY, SEVERAL TEXTURES POURED ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    45. EXPOSED-AGGREGATE CONCRETE AT NICHE, NORTH BOUNDARY, SEVERAL TEXTURES POURED AT ONE TIME, October 1987 - Meridian Hill Park, Bounded by Fifteenth, Sixteenth, Euclid & W Streets, Northwest, Washington, District of Columbia, DC

  19. 24. NICHE IN GREAT WALL AT TOP OF WEST ASCENT, ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    24. NICHE IN GREAT WALL AT TOP OF WEST ASCENT, NOTE SHELL SPILL, October 1987 - Meridian Hill Park, Bounded by Fifteenth, Sixteenth, Euclid & W Streets, Northwest, Washington, District of Columbia, DC

  20. INTERIOR VIEW OF THE HALL. NOTE THE TELEPHONE NICHE, TONGUEANDGROOVE ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    INTERIOR VIEW OF THE HALL. NOTE THE TELEPHONE NICHE, TONGUE-AND-GROOVE WOOD FLOORING, AND DOUBLE DOOR OF THE LINEN CLOSET. VIEW FACING SOUTHWEST. - Hickam Field, Officers' Housing Type F, 602 Beard Avenue, Honolulu, Honolulu County, HI

  1. Detail of upper part of statuary niche, Federal Street lobby. ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    Detail of upper part of statuary niche, Federal Street lobby. Wood storage platform in foreground divides Federal Street lobby into upper and lower sections - Stamford Post Office, 421 Atlantic Street, Stamford, Fairfield County, CT

  2. Mini-gut organoids: reconstitution of the stem cell niche.

    PubMed

    Date, Shoichi; Sato, Toshiro

    2015-01-01

    In the adult mammalian body, self-renewal of tissue stem cells is regulated by extracellular niche environments in response to the demands of tissue organization. Intestinal stem cells expressing Lgr5 constantly self-renew in their specific niche at the crypt bottom to maintain rapid turnover of the epithelium. Niche-regulated stem cell self-renewal is perturbed in several mouse genetic models and during human tumorigenesis, suggesting roles for EGF, Wnt, BMP/TGF-β, and Notch signaling. In vitro niche reconstitution capitalizing on this knowledge has enabled the growth of single intestinal stem cells into mini-gut epithelial organoids comprising Lgr5(+) stem cells and all types of differentiated lineages. The mini-gut organoid culture platform is applicable to various types of digestive tissue epithelium from multiple species. The mechanism of self-renewal in organoids provides novel insights for organogenesis, regenerative medicine, and tumorigenesis of the digestive system. PMID:26436704

  3. Niche construction drives social dependence in hermit crabs.

    PubMed

    Laidre, Mark E

    2012-10-23

    Organisms can receive not only a genetic inheritance from their ancestors but also an ecological inheritance, involving modifications their ancestors made to the environment through niche construction. Ecological inheritances may persist as a legacy, potentially generating selection pressures that favor sociality. Yet, most proposed cases of sociality being impacted by an ecological inheritance come from organisms that live among close kin and were highly social before their niche construction began. Here, I show that in terrestrial hermit crabs (Coenobita compressus)--organisms that do not live with kin and reside alone, each in its own shell--niche-construction drives social dependence, such that individuals can only survive in remodeled shells handed down from conspecifics. These results suggest that niche construction can be an important initiator of evolutionary pressures to socialize, even among unrelated and otherwise asocial organisms.

  4. EvoDevo and niche construction: building bridges.

    PubMed

    Laland, Kevin N; Odling-Smee, John; Gilbert, Scott F

    2008-11-15

    Evolutionary developmental biology and niche-construction theory have much in common, despite independent intellectual origins. Both place emphasis on the role of ontogenetic processes in evolution. The same historical events shaped them, and similar philosophical and sociological barriers hindered their respective advances. Both perspectives maintain that neo-Darwinism needs a theory of macroevolutionary variation and that such a theory can now be adduced from developmental biology. Some proponents of both EvoDevo and niche construction propose additional evolutionary mechanisms, and specify a key role for stable extra-genetic forms of inheritance. Similarly, proponents of each lay emphasis on "reciprocal causation" in the relationship between organism and environment. We illustrate here how EvoDevo and niche construction could gain "added value" from each other, and demonstrate how the niche-construction perspective potentially provides a useful conduit to integrate evolutionary and developmental biology.

  5. Interior of niche with small sink and cabinets behind original ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    Interior of niche with small sink and cabinets behind original nurses' station - U.S. Naval Base, Pearl Harbor, Type "B" Casualty Dressing & Decontamination Station, Intersection of Eighth Street, Avenue E & Central Avenue, Pearl City, Honolulu County, HI

  6. INVASIVE SPECIES: PREDICTING GEOGRAPHIC DISTRIBUTIONS USING ECOLOGICAL NICHE MODELING

    EPA Science Inventory

    Present approaches to species invasions are reactive in nature. This scenario results in management that perpetually lags behind the most recent invasion and makes control much more difficult. In contrast, spatially explicit ecological niche modeling provides an effective solut...

  7. Aging of the subventricular zone neural stem cell niche.

    PubMed

    Conover, Joanne C; Shook, Brett A

    2011-02-01

    The persistence of an active subventricular zone neural stem cell niche in the adult mammalian forebrain supports its continued role in the production of new neurons and in generating cells to function in repair through adulthood. Unfortunately, with increasing age the niche begins to deteriorate, compromising these functions. The reasons for this decline are not clear. Studies are beginning to define the molecular and physiologic changes in the microenvironment of the aging subventricular zone niche. New revelations from aging studies will allow for a more thorough understanding of which reparative functions are lost in the aged brain, the progression of niche demise and the possibility for therauptic intervention to improve aging brain function. PMID:22396866

  8. Niche separation of thaumarchaeotes from sea surface to hadal ocean.

    NASA Astrophysics Data System (ADS)

    Nunoura, T.

    2015-12-01

    Niche separation of the marine thaumarchaeal subgroups such as α (Nitrosopumiluscluster), β, γ and δ subgroups, along vertical water column has been observed in Arctic to tropical oceans (Sintes et al. 2013 and references therein). Availability of ammonia most likely influence on niche separation of thaumarchaeal communities, and thus the niche separation would be a signature of geochemical interface in oceanic environments. In the Challenger Deep, thaumarchaeal communities in hadal water were distinct from those in the overlying abyssal water, and the niche separation of thaumarchaeotes was consistent with the enrichments of heterotrophic populations in the hadal water (Nunoura et al. 2015). Moreover, we have compared hadal microbial ecosystems in distinct trench environments at the Northwest Pacific; the Japan and Izu-Ogasawara Trenches, by using multiple molecular techniques including single-cell genomic analysis. A series of the molecular environmental studies for hadal environments provides novel insights into the molecular machineries of thaumarchaeotes that adapt and dominate in aphotic oceanic waters.

  9. IGF-1-mediated osteoblastic niche expansion enhances long-term hematopoietic stem cell engraftment after murine bone marrow transplantation.

    PubMed

    Caselli, Anna; Olson, Timothy S; Otsuru, Satoru; Chen, Xiaohua; Hofmann, Ted J; Nah, Hyun-Duck; Grisendi, Giulia; Paolucci, Paolo; Dominici, Massimo; Horwitz, Edwin M

    2013-10-01

    The efficiency of hematopoietic stem cell (HSC) engraftment after bone marrow (BM) transplantation depends largely on the capacity of the marrow microenvironment to accept the transplanted cells. While radioablation of BM damages osteoblastic stem cell niches, little is known about their restoration and mechanisms governing their receptivity to engraft transplanted HSCs. We previously reported rapid restoration and profound expansion of the marrow endosteal microenvironment in response to marrow radioablation. Here, we show that this reorganization represents proliferation of mature endosteal osteoblasts which seem to arise from a small subset of high-proliferative, relatively radio-resistant endosteal cells. Multiple layers of osteoblasts form along the endosteal surface within 48 hours after total body irradiation, concomitant with a peak in marrow cytokine expression. This niche reorganization fosters homing of the transplanted hematopoietic cells to the host marrow space and engraftment of long-term-HSC. Inhibition of insulin-like growth factor (IGF)-1-receptor tyrosine kinase signaling abrogates endosteal osteoblast proliferation and donor HSC engraftment, suggesting that the cytokine IGF-1 is a crucial mediator of endosteal niche reorganization and consequently donor HSC engraftment. Further understanding of this novel mechanism of IGF-1-dependent osteoblastic niche expansion and HSC engraftment may yield clinical applications for improving engraftment efficiency after clinical HSC transplantation.

  10. A hypoxic ticket to the bone metastatic niche.

    PubMed

    Vanharanta, Sakari

    2015-09-04

    Hypoxia is a well-characterized driver of aggressive cancer phenotypes, including metastasis. Accumulating evidence suggests that, in addition to having local effects, the consequences of tumour hypoxia can be systemic, leading to the formation of pre-metastatic niches that can later foster metastatic colonization in distant organs. Recent findings have demonstrated that such niches can also form in the bone, possibly revealing new avenues for therapeutic intervention.

  11. Shape and evolution of the fundamental niche in marine Vibrio

    PubMed Central

    Materna, Arne C; Friedman, Jonathan; Bauer, Claudia; David, Christina; Chen, Sara; Huang, Ivy B; Gillens, April; Clarke, Sean A; Polz, Martin F; Alm, Eric J

    2012-01-01

    Hutchinson's fundamental niche, defined by the physical and biological environments in which an organism can thrive in the absence of inter-species interactions, is an important theoretical concept in ecology. However, little is known about the overlap between the fundamental niche and the set of conditions species inhabit in nature, and about natural variation in fundamental niche shape and its change as species adapt to their environment. Here, we develop a custom-made dual gradient apparatus to map a cross-section of the fundamental niche for several marine bacterial species within the genus Vibrio based on their temperature and salinity tolerance, and compare tolerance limits to the environment where these species commonly occur. We interpret these niche shapes in light of a conceptual model comprising five basic niche shapes. We find that the fundamental niche encompasses a much wider set of conditions than those strains typically inhabit, especially for salinity. Moreover, though the conditions that strains typically inhabit agree well with the strains' temperature tolerance, they are negatively correlated with the strains' salinity tolerance. Such relationships can arise when the physiological response to different stressors is coupled, and we present evidence for such a coupling between temperature and salinity tolerance. Finally, comparison with well-documented ecological range in V. vulnificus suggests that biotic interactions limit the occurrence of this species at low-temperature—high-salinity conditions. Our findings highlight the complex interplay between the ecological, physiological and evolutionary determinants of niche morphology, and caution against making inferences based on a single ecological factor. PMID:22832347

  12. Pollination niche overlap between a parasitic plant and its host.

    PubMed

    Ollerton, Jeff; Stott, Adrian; Allnutt, Emma; Shove, Sam; Taylor, Chloe; Lamborn, Ellen

    2007-03-01

    Niche theory predicts that species which share resources should evolve strategies to minimise competition for those resources, or the less competitive species would be extirpated. Some plant species are constrained to co-occur, for example parasitic plants and their hosts, and may overlap in their pollination niche if they flower at the same time and attract the same pollinators. Using field observations and experiments between 1996 and 2006, we tested a series of hypotheses regarding pollination niche overlap between a specialist parasitic plant Orobanche elatior (Orobanchaceae) and its host Centaurea scabiosa (Asteraceae). These species flower more or less at the same time, with some year-to-year variation. The host is pollinated by a diverse range of insects, which vary in their effectiveness, whilst the parasite is pollinated by a single species of bumblebee, Bombus pascuorum, which is also an effective pollinator of the host plant. The two species therefore have partially overlapping pollination niches. These niches are not finely subdivided by differential pollen placement, or by diurnal segregation of the niches. We therefore found no evidence of character displacement within the pollination niches of these species, possibly because pollinators are not a limiting resource for these plants. Direct observation of pollinator movements, coupled with experimental manipulations of host plant inflorescence density, showed that Bombus pascuorum only rarely moves between inflorescences of the host and the parasite and therefore the presence of one plant is unlikely to be facilitating pollination in the other. This is the first detailed examination of pollination niche overlap in a plant parasite system and we suggest avenues for future research in relation to pollination and other shared interactions between parasitic plants and their hosts.

  13. Shape and evolution of the fundamental niche in marine Vibrio.

    PubMed

    Materna, Arne C; Friedman, Jonathan; Bauer, Claudia; David, Christina; Chen, Sara; Huang, Ivy B; Gillens, April; Clarke, Sean A; Polz, Martin F; Alm, Eric J

    2012-12-01

    Hutchinson's fundamental niche, defined by the physical and biological environments in which an organism can thrive in the absence of inter-species interactions, is an important theoretical concept in ecology. However, little is known about the overlap between the fundamental niche and the set of conditions species inhabit in nature, and about natural variation in fundamental niche shape and its change as species adapt to their environment. Here, we develop a custom-made dual gradient apparatus to map a cross-section of the fundamental niche for several marine bacterial species within the genus Vibrio based on their temperature and salinity tolerance, and compare tolerance limits to the environment where these species commonly occur. We interpret these niche shapes in light of a conceptual model comprising five basic niche shapes. We find that the fundamental niche encompasses a much wider set of conditions than those strains typically inhabit, especially for salinity. Moreover, though the conditions that strains typically inhabit agree well with the strains' temperature tolerance, they are negatively correlated with the strains' salinity tolerance. Such relationships can arise when the physiological response to different stressors is coupled, and we present evidence for such a coupling between temperature and salinity tolerance. Finally, comparison with well-documented ecological range in V. vulnificus suggests that biotic interactions limit the occurrence of this species at low-temperature-high-salinity conditions. Our findings highlight the complex interplay between the ecological, physiological and evolutionary determinants of niche morphology, and caution against making inferences based on a single ecological factor.

  14. Stochastic Dynamics of Interacting Haematopoietic Stem Cell Niche Lineages

    PubMed Central

    Székely, Tamás; Burrage, Kevin; Mangel, Marc; Bonsall, Michael B.

    2014-01-01

    Since we still know very little about stem cells in their natural environment, it is useful to explore their dynamics through modelling and simulation, as well as experimentally. Most models of stem cell systems are based on deterministic differential equations that ignore the natural heterogeneity of stem cell populations. This is not appropriate at the level of individual cells and niches, when randomness is more likely to affect dynamics. In this paper, we introduce a fast stochastic method for simulating a metapopulation of stem cell niche lineages, that is, many sub-populations that together form a heterogeneous metapopulation, over time. By selecting the common limiting timestep, our method ensures that the entire metapopulation is simulated synchronously. This is important, as it allows us to introduce interactions between separate niche lineages, which would otherwise be impossible. We expand our method to enable the coupling of many lineages into niche groups, where differentiated cells are pooled within each niche group. Using this method, we explore the dynamics of the haematopoietic system from a demand control system perspective. We find that coupling together niche lineages allows the organism to regulate blood cell numbers as closely as possible to the homeostatic optimum. Furthermore, coupled lineages respond better than uncoupled ones to random perturbations, here the loss of some myeloid cells. This could imply that it is advantageous for an organism to connect together its niche lineages into groups. Our results suggest that a potential fruitful empirical direction will be to understand how stem cell descendants communicate with the niche and how cancer may arise as a result of a failure of such communication. PMID:25188267

  15. Advances and Limitations of Disease Biogeography Using Ecological Niche Modeling.

    PubMed

    Escobar, Luis E; Craft, Meggan E

    2016-01-01

    Mapping disease transmission risk is crucial in public and animal health for evidence based decision-making. Ecology and epidemiology are highly related disciplines that may contribute to improvements in mapping disease, which can be used to answer health related questions. Ecological niche modeling is increasingly used for understanding the biogeography of diseases in plants, animals, and humans. However, epidemiological applications of niche modeling approaches for disease mapping can fail to generate robust study designs, producing incomplete or incorrect inferences. This manuscript is an overview of the history and conceptual bases behind ecological niche modeling, specifically as applied to epidemiology and public health; it does not pretend to be an exhaustive and detailed description of ecological niche modeling literature and methods. Instead, this review includes selected state-of-the-science approaches and tools, providing a short guide to designing studies incorporating information on the type and quality of the input data (i.e., occurrences and environmental variables), identification and justification of the extent of the study area, and encourages users to explore and test diverse algorithms for more informed conclusions. We provide a friendly introduction to the field of disease biogeography presenting an updated guide for researchers looking to use ecological niche modeling for disease mapping. We anticipate that ecological niche modeling will soon be a critical tool for epidemiologists aiming to map disease transmission risk, forecast disease distribution under climate change scenarios, and identify landscape factors triggering outbreaks. PMID:27547199

  16. Introducing BioSARN - an ecological niche model refinement tool.

    PubMed

    Heap, Marshall J

    2016-08-01

    Environmental niche modeling outputs a biological species' potential distribution. Further work is needed to arrive at a species' realized distribution. The Biological Species Approximate Realized Niche (BioSARN) application provides the ecological modeler with a toolset to refine Environmental niche models (ENMs). These tools include soil and land class filtering, niche area quantification and novelties like enhanced temporal corridor definition, and output to a high spatial resolution land class model. BioSARN is exemplified with a study on Fraser fir, a tree species with strong land class and edaphic correlations. Soil and land class filtering caused the potential distribution area to decline 17%. Enhanced temporal corridor definition permitted distinction of current, continuing, and future niches, and thus niche change and movement. Tile quantification analysis provided further corroboration of these trends. BioSARN does not substitute other established ENM methods. Rather, it allows the experimenter to work with their preferred ENM, refining it using their knowledge and experience. Output from lower spatial resolution ENMs to a high spatial resolution land class model is a pseudo high-resolution result. Still, it maybe the best that can be achieved until wide range high spatial resolution environmental data and accurate high precision species occurrence data become generally available. PMID:27547356

  17. Advances and Limitations of Disease Biogeography Using Ecological Niche Modeling

    PubMed Central

    Escobar, Luis E.; Craft, Meggan E.

    2016-01-01

    Mapping disease transmission risk is crucial in public and animal health for evidence based decision-making. Ecology and epidemiology are highly related disciplines that may contribute to improvements in mapping disease, which can be used to answer health related questions. Ecological niche modeling is increasingly used for understanding the biogeography of diseases in plants, animals, and humans. However, epidemiological applications of niche modeling approaches for disease mapping can fail to generate robust study designs, producing incomplete or incorrect inferences. This manuscript is an overview of the history and conceptual bases behind ecological niche modeling, specifically as applied to epidemiology and public health; it does not pretend to be an exhaustive and detailed description of ecological niche modeling literature and methods. Instead, this review includes selected state-of-the-science approaches and tools, providing a short guide to designing studies incorporating information on the type and quality of the input data (i.e., occurrences and environmental variables), identification and justification of the extent of the study area, and encourages users to explore and test diverse algorithms for more informed conclusions. We provide a friendly introduction to the field of disease biogeography presenting an updated guide for researchers looking to use ecological niche modeling for disease mapping. We anticipate that ecological niche modeling will soon be a critical tool for epidemiologists aiming to map disease transmission risk, forecast disease distribution under climate change scenarios, and identify landscape factors triggering outbreaks. PMID:27547199

  18. Modulating the stem cell niche for tissue regeneration

    PubMed Central

    Lane, Steven W; Williams, David A; Watt, Fiona M

    2015-01-01

    The field of regenerative medicine holds considerable promise for treating diseases that are currently intractable. Although many researchers are adopting the strategy of cell transplantation for tissue repair, an alternative approach to therapy is to manipulate the stem cell microenvironment, or niche, to facilitate repair by endogenous stem cells. The niche is highly dynamic, with multiple opportunities for intervention. These include administration of small molecules, biologics or biomaterials that target specific aspects of the niche, such as cell-cell and cell–extracellular matrix interactions, to stimulate expansion or differentiation of stem cells, or to cause reversion of differentiated cells to stem cells. Nevertheless, there are several challenges in targeting the niche therapeutically, not least that of achieving specificity of delivery and responses. We envisage that successful treatments in regenerative medicine will involve different combinations of factors to target stem cells and niche cells, applied at different times to effect recovery according to the dynamics of stem cell–niche interactions. PMID:25093887

  19. Perspective: seven reasons (not) to neglect niche construction.

    PubMed

    Laland, Kevin N; Sterelny, Kim

    2006-09-01

    The niche-construction perspective within evolutionary biology places emphasis on the changes that organisms bring about in their selective environments. Advocates of this viewpoint argue that there is both accuracy and utility in treating niche construction as an evolutionary process in its own right, rather than merely as a product of evolution. Here we discuss and assess seven putative weaknesses of the niche-construction perspective. Niche construction has been neglected or rejected on the grounds that (1) it is not prevalent, (2) its study is not tractable, (3) it is not a process, (4) it is caused by natural selection, (5) it does not change our understanding of evolution in any fundamental way, (6) it does not bring about adaptation, and (7) it is not a single phenomenon. In each case, we critically evaluate the theoretical standing of these arguments and consider the empirical evidence that can be brought to bear on the debate. We conclude that none of these are strong criticisms of the niche-construction perspective and maintain that there are compelling reasons for treating niche construction as a major evolutionary process.

  20. Advances and Limitations of Disease Biogeography Using Ecological Niche Modeling.

    PubMed

    Escobar, Luis E; Craft, Meggan E

    2016-01-01

    Mapping disease transmission risk is crucial in public and animal health for evidence based decision-making. Ecology and epidemiology are highly related disciplines that may contribute to improvements in mapping disease, which can be used to answer health related questions. Ecological niche modeling is increasingly used for understanding the biogeography of diseases in plants, animals, and humans. However, epidemiological applications of niche modeling approaches for disease mapping can fail to generate robust study designs, producing incomplete or incorrect inferences. This manuscript is an overview of the history and conceptual bases behind ecological niche modeling, specifically as applied to epidemiology and public health; it does not pretend to be an exhaustive and detailed description of ecological niche modeling literature and methods. Instead, this review includes selected state-of-the-science approaches and tools, providing a short guide to designing studies incorporating information on the type and quality of the input data (i.e., occurrences and environmental variables), identification and justification of the extent of the study area, and encourages users to explore and test diverse algorithms for more informed conclusions. We provide a friendly introduction to the field of disease biogeography presenting an updated guide for researchers looking to use ecological niche modeling for disease mapping. We anticipate that ecological niche modeling will soon be a critical tool for epidemiologists aiming to map disease transmission risk, forecast disease distribution under climate change scenarios, and identify landscape factors triggering outbreaks.

  1. The Perivascular Niche and Self-Renewal of Stem Cells

    PubMed Central

    Oh, Min; Nör, Jacques E.

    2015-01-01

    Postnatal stem cells are typically found in niches that provide signaling cues to maintain their self-renewal and multipotency. While stem cell populations may serve distinct purposes within their tissue of origin, understanding the conserved biology of stem cells and their respective niches provides insights to the behavior of these cells during homeostasis and tissue repair. Here, we discuss perivascular niches of two distinct stem cell populations (i.e., hematopoietic stem cells, mesenchymal stem cells) and explore mechanisms that sustain these stem cells postnatally. We highlight work that demonstrates the impact of cellular crosstalk to stem cell self-renewal and maintenance of functional perivascular niches. We also discuss the importance of the crosstalk within the perivascular niche to the biology of stem cells, and describe the regenerative potential of perivascular cells. We postulate that signaling events that establish and/or stabilize the perivascular niche, particularly through the modulation of self-renewing factors, are key to the long-term success of regenerated tissues. PMID:26696901

  2. Introducing BioSARN - an ecological niche model refinement tool.

    PubMed

    Heap, Marshall J

    2016-08-01

    Environmental niche modeling outputs a biological species' potential distribution. Further work is needed to arrive at a species' realized distribution. The Biological Species Approximate Realized Niche (BioSARN) application provides the ecological modeler with a toolset to refine Environmental niche models (ENMs). These tools include soil and land class filtering, niche area quantification and novelties like enhanced temporal corridor definition, and output to a high spatial resolution land class model. BioSARN is exemplified with a study on Fraser fir, a tree species with strong land class and edaphic correlations. Soil and land class filtering caused the potential distribution area to decline 17%. Enhanced temporal corridor definition permitted distinction of current, continuing, and future niches, and thus niche change and movement. Tile quantification analysis provided further corroboration of these trends. BioSARN does not substitute other established ENM methods. Rather, it allows the experimenter to work with their preferred ENM, refining it using their knowledge and experience. Output from lower spatial resolution ENMs to a high spatial resolution land class model is a pseudo high-resolution result. Still, it maybe the best that can be achieved until wide range high spatial resolution environmental data and accurate high precision species occurrence data become generally available.

  3. The prediction of bacteria type and culture growth phase by an electronic nose with a multi-layer perceptron network

    NASA Astrophysics Data System (ADS)

    Gardner, J. W.; Craven, M.; Dow, C.; Hines, E. L.

    1998-01-01

    An investigation into the use of an electronic nose to predict the class and growth phase of two potentially pathogenic micro-organisms, Eschericha coli ( E. coli) and Staphylococcus aureus ( S. aureus), has been performed. In order to do this we have developed an automated system to sample, with a high degree of reproducibility, the head space of bacterial cultures grown in a standard nutrient medium. Head spaces have been examined by using an array of six different metal oxide semiconducting gas sensors and classified by a multi-layer perceptron (MLP) with a back-propagation (BP) learning algorithm. The performance of 36 different pre-processing algorithms has been studied on the basis of nine different sensor parameters and four different normalization techniques. The best MLP was found to classify successfully 100% of the unknown S. aureus samples and 92% of the unknown E. coli samples, on the basis of a set of 360 training vectors and 360 test vectors taken from the lag, log and stationary growth phases. The real growth phase of the bacteria was determined from optical cell counts and was predicted from the head space samples with an accuracy of 81%. We conclude that these results show considerable promise in that the correct prediction of the type and growth phase of pathogenic bacteria may help both in the more rapid treatment of bacterial infections and in the more efficient testing of new anti-biotic drugs.

  4. Aircraft optical cable plant program plan: the approach for the physical layer for fly-by-light control networks

    NASA Astrophysics Data System (ADS)

    Weaver, Thomas L.; Murdock, John K.

    1995-05-01

    A program was created with joint industry and government funding to apply fiber optic technologies to aircraft. The technology offers many potential benefits. Among them are increased electromagnetic interference immunity and the possibility of reduced weight, increased reliability, and enlarged capability by redesigning architectures to use the large bandwidth of fiber optics. Those benefits will only be realized if fiber optics meets the unique requirements of aircraft networks. Over the past two decades, considerable effort has been expended on applying photonic technologies to aircraft. Great successes have occurred in optoelectronic components development. In the development of these systems to link those components, known as the cable plant, progress has also been made, but only recently has it been organized in a coordinated, systems-oriented fashion. The FLASH program will expand on the nascent cable plant systems efforts by building upon recent work in individual components, and integrating that work into a cohesive aircraft cable plant. Therefore, the FLASH program will develop the low cost, reliable cables, connectors, splices, backplanes, manufacturing and installation methods, test methods, support equipment, and training systems needed to form a true optical cable plant for transport aircraft, tactical aircraft, and helicopters.

  5. The Global Terrestrial Network for Permafrost Database: metadata statistics and prospective analysis on future permafrost temperature and active layer depth monitoring site distribution

    NASA Astrophysics Data System (ADS)

    Biskaborn, B. K.; Lanckman, J.-P.; Lantuit, H.; Elger, K.; Streletskiy, D. A.; Cable, W. L.; Romanovsky, V. E.

    2015-03-01

    The Global Terrestrial Network for Permafrost (GTN-P) provides the first dynamic database associated with the Thermal State of Permafrost (TSP) and the Circumpolar Active Layer Monitoring (CALM) programs, which extensively collect permafrost temperature and active layer thickness data from Arctic, Antarctic and Mountain permafrost regions. The purpose of the database is to establish an "early warning system" for the consequences of climate change in permafrost regions and to provide standardized thermal permafrost data to global models. In this paper we perform statistical analysis of the GTN-P metadata aiming to identify the spatial gaps in the GTN-P site distribution in relation to climate-effective environmental parameters. We describe the concept and structure of the Data Management System in regard to user operability, data transfer and data policy. We outline data sources and data processing including quality control strategies. Assessment of the metadata and data quality reveals 63% metadata completeness at active layer sites and 50% metadata completeness for boreholes. Voronoi Tessellation Analysis on the spatial sample distribution of boreholes and active layer measurement sites quantifies the distribution inhomogeneity and provides potential locations of additional permafrost research sites to improve the representativeness of thermal monitoring across areas underlain by permafrost. The depth distribution of the boreholes reveals that 73% are shallower than 25 m and 27% are deeper, reaching a maximum of 1 km depth. Comparison of the GTN-P site distribution with permafrost zones, soil organic carbon contents and vegetation types exhibits different local to regional monitoring situations on maps. Preferential slope orientation at the sites most likely causes a bias in the temperature monitoring and should be taken into account when using the data for global models. The distribution of GTN-P sites within zones of projected temperature change show a high

  6. Meninges: from protective membrane to stem cell niche

    PubMed Central

    Decimo, Ilaria; Fumagalli, Guido; Berton, Valeria; Krampera, Mauro; Bifari, Francesco

    2012-01-01

    Meninges are a three tissue membrane primarily known as coverings of the brain. More in depth studies on meningeal function and ultrastructure have recently changed the view of meninges as a merely protective membrane. Accurate evaluation of the anatomical distribution in the CNS reveals that meninges largely penetrate inside the neural tissue. Meninges enter the CNS by projecting between structures, in the stroma of choroid plexus and form the perivascular space (Virchow-Robin) of every parenchymal vessel. Thus, meninges may modulate most of the physiological and pathological events of the CNS throughout the life. Meninges are present since the very early embryonic stages of cortical development and appear to be necessary for normal corticogenesis and brain structures formation. In adulthood meninges contribute to neural tissue homeostasis by secreting several trophic factors including FGF2 and SDF-1. Recently, for the first time, we have identified the presence of a stem cell population with neural differentiation potential in meninges. In addition, we and other groups have further described the presence in meninges of injury responsive neural precursors. In this review we will give a comprehensive view of meninges and their multiple roles in the context of a functional network with the neural tissue. We will highlight the current literature on the developmental feature of meninges and their role in cortical development. Moreover, we will elucidate the anatomical distribution of the meninges and their trophic properties in adult CNS. Finally, we will emphasize recent evidences suggesting the potential role of meninges as stem cell niche harbouring endogenous precursors that can be activated by injury and are able to contribute to CNS parenchymal reaction. PMID:23671802

  7. Meninges: from protective membrane to stem cell niche.

    PubMed

    Decimo, Ilaria; Fumagalli, Guido; Berton, Valeria; Krampera, Mauro; Bifari, Francesco

    2012-01-01

    Meninges are a three tissue membrane primarily known as coverings of the brain. More in depth studies on meningeal function and ultrastructure have recently changed the view of meninges as a merely protective membrane. Accurate evaluation of the anatomical distribution in the CNS reveals that meninges largely penetrate inside the neural tissue. Meninges enter the CNS by projecting between structures, in the stroma of choroid plexus and form the perivascular space (Virchow-Robin) of every parenchymal vessel. Thus, meninges may modulate most of the physiological and pathological events of the CNS throughout the life. Meninges are present since the very early embryonic stages of cortical development and appear to be necessary for normal corticogenesis and brain structures formation. In adulthood meninges contribute to neural tissue homeostasis by secreting several trophic factors including FGF2 and SDF-1. Recently, for the first time, we have identified the presence of a stem cell population with neural differentiation potential in meninges. In addition, we and other groups have further described the presence in meninges of injury responsive neural precursors. In this review we will give a comprehensive view of meninges and their multiple roles in the context of a functional network with the neural tissue. We will highlight the current literature on the developmental feature of meninges and their role in cortical development. Moreover, we will elucidate the anatomical distribution of the meninges and their trophic properties in adult CNS. Finally, we will emphasize recent evidences suggesting the potential role of meninges as stem cell niche harbouring endogenous precursors that can be activated by injury and are able to contribute to CNS parenchymal reaction.

  8. Characterising the effect of a variety of surface roughness on boundary layer wind and dynamics within the scanning Doppler lidar network in Finland

    NASA Astrophysics Data System (ADS)

    Hirsikko, Anne; O'Connor, Ewan J.; Wood, Curtis R.; Vakkari, Ville

    2013-04-01

    Aerosol particle and trace gas atmospheric content is controlled by natural and anthropological emissions. However, further dispersion in the atmosphere is driven by wind and dynamic mixing. Atmospheric surface and boundary layer dynamics have direct and indirect effects on weather, air quality and processes affecting climate (e.g. gas exchange between ecosystem and atmosphere). In addition to the amount of solar energy and prevailing meteorological condition, the surface topography has a strong influence on the close to surface wind field and turbulence, particularly in urban areas (e.g. Barlow and Coceal, 2009). In order to characterise the effect of forest, urban and coastal surfaces on boundary layer wind and mixing, we have utilised the Finnish Doppler lidar network (Hirsikko et al., 2013). The network consists of five 1.5 μm Doppler lidars (HALO Photonics, Pearson et al., 2009), of which four are capable of full hemispheric scanning and are located at Helsinki (60.12°N, 25.58°E, 45 m asl.), Utö island (59.47°N, 21.23°E, 8 m asl.), SMEAR II at Hyytiälä (61.50°N, 24.17°E, 181 m asl.) and Kuopio (62.44°N, 27.32°E, 190 m asl.). The fifth lidar at Sodankylä (67.37°N, 26.63°E, 171 m asl.) is a new model designed for the Arctic environment with no external moving parts, but still retains limited scan capability. Investigation of boundary layer wind and mixing condition can now be extended beyond vertical profiles of horizontal wind, and dissipation rate of turbulent kinetic energy (O'Connor et al., 2010) throughout the boundary layer. We have applied custom designed scanning routines for 3D-observation of the wind fields and simultaneous aerosol particle distribution continuously for over one year at Helsinki and Utö, and began similar scanning routines at Kuopio and Hyytiälä in spring 2013. In this long term project, our aims are to 1) characterise the effect of the land-sea interface and the urban environment on the wind and its turbulent nature

  9. Transient nonlinear optically-thick radiative-convective double-diffusive boundary layers in a Darcian porous medium adjacent to an impulsively started surface: Network simulation solutions

    NASA Astrophysics Data System (ADS)

    Anwar Bég, O.; Zueco, J.; Takhar, H. S.; Bég, T. A.; Sajid, A.

    2009-11-01

    A boundary-layer model is described for the two-dimensional nonlinear transient thermal convection heat and mass transfer in an optically-thick fluid in a Darcian porous medium adjacent to an impulsively started vertical surface, in the presence of significant thermal radiation and buoyancy forces in an (X∗,Y∗,t∗) coordinate system. An algebraic approximation is employed to simplify the integro-differential equation of radiative transfer for unidirectional flux normal to the plate into the boundary-layer regime, by incorporating this flux term in the energy conservation equation. The conservation equations are non-dimensionalized into an (X,Y,T) coordinate system and solved using the Network Simulation Method (NSM), a robust numerical technique which demonstrates high efficiency and accuracy. The transient variation of non-dimensional streamwise velocity component (u) and temperature (T) and concentration (C) functions is computed for various selected values of Stark number (radiation-conduction interaction parameter) and Darcy number. Transient velocity (u) and steady-state local skin friction (τX) are also studied for various thermal Grashof number (Gr), species Grashof number (Gm), Schmidt number (Sc) and Stark number (N) values. These computations for the infinite permeability case (Da → ∞) are compared with previous finite difference solutions [Prasad et al. Int J Therm Sci 2007;46(12):1251-8] and shown to be in excellent agreement. An increase in Darcy number is seen to accelerate the flow and boost velocity. A decrease in Stark number (corresponding to an increase in thermal radiation heat transfer contribution) is shown to increase the velocity values. Temperature function is observed to fall in value with a rise in Da and increase with decrease in N (corresponding to an increase in thermal radiation heat transfer contribution). Applications of the study include rocket combustion chambers, astrophysical flows, spacecraft thermal fluid dynamics in

  10. Niche restriction in parasites: proximate and ultimate causes.

    PubMed

    Rohde, K

    1994-01-01

    Hutchinson's (1957) definition of an ecological niche as a multidimensional hypervolume determined by a number of physical and biotic variables is adopted. The number of niche dimensions is very great, but as a working hypothesis it is assumed that a few are sufficient to characterize the niche of a parasite species to a high degree of accuracy. They are host species, microhabitat(s), macrohabitat(s), geographical range, sex and age of host, season, food and hyperparasites. Methods to measure niche width, in particular specificity indices, are discussed, and some examples of niche restriction are described. Proximate and ultimate causes of niche restriction are discussed, mainly using marine parasites as examples. Among proximate causes of one niche dimension, host specificity, are ecological factors restricting exposure to infection to certain host species; host-specific chemical factors that induce hatching, direct infective stages to a host and bring about settlement of a parasite; factors that lead to mortality in or on the wrong host; morphological adaptations that guarantee survival in or on the 'correct' host; and availability of suitable hosts. Many factors are likely to be responsible for microhabitat specificity, but have been little studied, except for some physiological and morphological adaptations to particular microhabitats. Macrohabitats and geographical range may be determined by the distribution of intermediate hosts and certain food items, and by a variety of chemical and physical factors. Hosts of different sexes may differ in feeding habits and the composition of the skin, and thus acquire parasites differentially. Hosts of different age may be differentially infected due to accumulation of parasites with age, loss of parasites due to developing resistance (or immunity), and different size and feeding habits. Among ultimate causes of niche restriction and segregation are avoidance of competition, predation and hyperparasites; facilitation of

  11. Natural and Unnatural Oil Layers on the Surface of the Gulf of Mexico Detected and Quantified in Synthetic Aperture RADAR Images with Texture Classifying Neural Network Algorithms

    NASA Astrophysics Data System (ADS)

    MacDonald, I. R.; Garcia-Pineda, O. G.; Morey, S. L.; Huffer, F.

    2011-12-01

    Effervescent hydrocarbons rise naturally from hydrocarbon seeps in the Gulf of Mexico and reach the ocean surface. This oil forms thin (~0.1 μm) layers that enhance specular reflectivity and have been widely used to quantify the abundance and distribution of natural seeps using synthetic aperture radar (SAR). An analogous process occurred at a vastly greater scale for oil and gas discharged from BP's Macondo well blowout. SAR data allow direct comparison of the areas of the ocean surface covered by oil from natural sources and the discharge. We used a texture classifying neural network algorithm to quantify the areas of naturally occurring oil-covered water in 176 SAR image collections from the Gulf of Mexico obtained between May 1997 and November 2007, prior to the blowout. Separately we also analyzed 36 SAR images collections obtained between 26 April and 30 July, 2010 while the discharged oil was visible in the Gulf of Mexico. For the naturally occurring oil, we removed pollution events and transient oceanographic effects by including only the reflectance anomalies that that recurred in the same locality over multiple images. We measured the area of oil layers in a grid of 10x10 km cells covering the entire Gulf of Mexico. Floating oil layers were observed in only a fraction of the total Gulf area amounting to 1.22x10^5 km^2. In a bootstrap sample of 2000 replications, the combined average area of these layers was 7.80x10^2 km^2 (sd 86.03). For a regional comparison, we divided the Gulf of Mexico into four quadrates along 90° W longitude, and 25° N latitude. The NE quadrate, where the BP discharge occurred, received on average 7.0% of the total natural seepage in the Gulf of Mexico (5.24 x10^2 km^2, sd 21.99); the NW quadrate received on average 68.0% of this total (5.30 x10^2 km^2, sd 69.67). The BP blowout occurred in the NE quadrate of the Gulf of Mexico; discharged oil that reached the surface drifted over a large area north of 25° N. Performing a

  12. Neutrality, niches, and dispersal in a temperate forest understory

    PubMed Central

    Gilbert, Benjamin; Lechowicz, Martin J.

    2004-01-01

    A fundamental goal of ecology is to understand what controls the distribution and abundance of species. Both environmental niches and trade-offs among species in dispersal and competitive ability have traditionally been cited as determinants of plant community composition. More recently, neutral models have shown that communities of species with identical life-history characteristics and no adaptation to environmental niches can form spatial distribution patterns similar to those found in nature, so long as the species have a limited dispersal distance. If there is a strong correlation between geographic distance and change in environmental conditions, however, such spatial patterns can arise through either neutral or niche-based processes. To test these competing theories, we developed a sampling design that decoupled distance and environment in the understory plant communities of an old-growth, temperate forest. We found strong evidence of niche-structuring but almost no support for neutral predictions. Dispersal limitation acted in conjunction with environmental gradients to determine species' distributions, and both functional and phylogenetic constraints appear to contribute to the niche differentiation that structures community assembly. Our results indicate that testing a neutral hypothesis without accounting for environmental gradients will at best cause unexplained variation in plant distributions and may well provide misleading support for neutrality because of a correlation between geographic distance and environment. PMID:15128948

  13. Testicular Niche Required for Human Spermatogonial Stem Cell Expansion

    PubMed Central

    Smith, James F.; Yango, Pamela; Altman, Eran; Choudhry, Shweta; Poelzl, Andrea; Zamah, Alberuni M.; Rosen, Mitchell; Klatsky, Peter C.

    2014-01-01

    Prepubertal boys treated with high-dose chemotherapy do not have an established means of fertility preservation because no established in vitro technique exists to expand and mature purified spermatogonial stem cells (SSCs) to functional sperm in humans. In this study, we define and characterize the unique testicular cellular niche required for SSC expansion using testicular tissues from men with normal spermatogenesis. Highly purified SSCs and testicular somatic cells were isolated by fluorescence-activated cell sorting using SSEA-4 and THY1 as markers of SSCs and somatic cells. Cells were cultured on various established niches to assess their role in SSC expansion in a defined somatic cellular niche. Of all the niches examined, cells in the SSEA-4 population exclusively bound to adult testicular stromal cells, established colonies, and expanded. Further characterization of these testicular stromal cells revealed distinct mesenchymal markers and the ability to undergo differentiation along the mesenchymal lineage, supporting a testicular multipotent stromal cell origin. In vitro human SSC expansion requires a unique niche provided exclusively by testicular multipotent stromal cells with mesenchymal properties. These findings provide an important foundation for developing methods of inducing SSC growth and maturation in prepubertal testicular tissue, essential to enabling fertility preservation for these boys. PMID:25038247

  14. The importance of niche differentiation for coexistence on large scales.

    PubMed

    Tang, Junfeng; Zhou, Shurong

    2011-03-21

    It is widely accepted that niche differentiation plays a key role in coexistence on relatively small scales. With regard to a large community scale, the recently propounded neutral theory suggests that species abundances are more influenced by history and chance than they are by interspecies competition. This inference is mainly based on the probability that competitive exclusion is largely slowed by recruitment limitation, which may be common in species rich communities. In this respect, a theoretical study conducted by Hurtt and Pacala (1995) for a niche differentiated community has been frequently cited to support neutral coexistence. In this paper, we focused on the effect of symmetric recruitment limitation on delaying species competitive exclusion caused by both symmetric and asymmetric competition in a large homogeneous habitat. By removing niche differentiation in space, we found that recruitment limitation could delay competitive exclusion to some extent, but the effect was rather limited compared to that predicted by Hurtt and Pacala's model for a niche differentiated community. Our results imply that niche differentiation may be important for species coexistence even on large scales and this has already been confirmed in some species rich communities.

  15. Size, shape, and the thermal niche of endotherms

    PubMed Central

    Porter, Warren P.; Kearney, Michael

    2009-01-01

    A key challenge in ecology is to define species' niches on the basis of functional traits. Size and shape are important determinants of a species' niche but their causal role is often difficult to interpret. For endotherms, size and shape define the thermal niche through their interaction with core temperature, insulation, and environmental conditions, determining the thermoneutral zone (TNZ) where energy and water costs are minimized. Laboratory measures of metabolic rate used to describe TNZs cannot be generalized to infer the capacity for terrestrial animals to find their TNZ in complex natural environments. Here, we derive an analytical model of the thermal niche of an ellipsoid furred endotherm that accurately predicts field and laboratory data. We use the model to illustrate the relative importance of size and shape on the location of the TNZ under different environmental conditions. The interaction between body shape and posture strongly influences the location of the TNZ and the expected scaling of metabolic rate with size at constant temperature. We demonstrate that the latter relationship has a slope of approximately ½ rather than the commonly expected surface area/volume scaling of ⅔. We show how such functional traits models can be integrated with spatial environmental datasets to calculate null expectations for body size clines from a thermal perspective, aiding mechanistic interpretation of empirical clines such as Bergmann's Rule. The combination of spatially explicit data with biophysical models of heat exchange provides a powerful means for studying the thermal niches of endotherms across climatic gradients. PMID:19846790

  16. Step back! Niche dynamics in cave-dwelling predators

    NASA Astrophysics Data System (ADS)

    Mammola, Stefano; Piano, Elena; Isaia, Marco

    2016-08-01

    The geometry of the Hutchinson's hypervolume derives from multiple selective pressures defined, on one hand, by the physiological tolerance of the species, and on the other, by intra- and interspecific competition. The quantification of these evolutionary forces is essential for the understanding of the coexistence of predators in light of competitive exclusion dynamics. We address this topic by investigating the ecological niche of two medium-sized troglophile spiders (Meta menardi and Pimoa graphitica). Over one year, we surveyed several populations in four subterranean sites in the Western Italian Alps, monitoring monthly their spatial and temporal dynamics and the associated physical and ecological variables. We assessed competition between the two species by means of multi regression techniques and by evaluating the intersection between their multidimensional hypervolumes. We detected a remarkable overlap between the microclimatic and trophic niche of M. menardi and P. graphitica, however, the former -being larger in size- resulted the best competitor in proximity of the cave entrance, causing the latter to readjust its spatial niche towards the inner part, where prey availability is scarcer ("step back effect"). In parallel to the slight variations in the subterranean microclimatic condition, the niche of the two species was also found to be seasonal dependent, varying over the year. With this work, we aim at providing new insights about the relationships among predators, demonstrating that energy-poor environments such as caves maintain the potential for diversification of predators via niche differentiation and serve as useful models for theoretical ecological studies.

  17. Grassland species loss resulting from reduced niche dimension.

    PubMed

    Harpole, W Stanley; Tilman, David

    2007-04-12

    Intact ecosystems contain large numbers of competing but coexisting species. Although numerous alternative theories have provided potential explanations for this high biodiversity, there have been few field experiments testing between these theories. In particular, theory predicts that higher diversity of coexisting competitors could result from greater niche dimensionality, for example larger numbers of limiting resources or factors. Alternatively, diversity could be independent of niche dimensionality because large numbers of species can coexist when limited by just one or two factors if species have appropriate trade-offs. Here we show that plant coexistence and diversity result from the 'niche dimensionality' of a habitat. Plant species numbers decreased with increasing numbers of added limiting soil resources (soil moisture, nitrogen, phosphorus and base cations), which is consistent with theoretical predictions that an increased supply of multiple limiting resources can reduce niche dimension. An observational field study gave similar results. The niche dimension hypothesis also explained diversity changes in the classic Park Grass Experiment at Rothamsted. Our results provide an alternative mechanistic explanation for the effects of nutrient eutrophication on the diversity of terrestrial, freshwater and marine ecosystems.

  18. Qualitative and quantitative high performance thin layer chromatography analysis of Calendula officinalis using high resolution plate imaging and artificial neural network data modelling.

    PubMed

    Agatonovic-Kustrin, S; Loescher, Christine M

    2013-10-10

    Calendula officinalis, commonly known Marigold, has been traditionally used for its anti-inflammatory effects. The aim of this study was to investigate the capacity of an artificial neural network (ANN) to analyse thin layer chromatography (TLC) chromatograms as fingerprint patterns for quantitative estimation of chlorogenic acid, caffeic acid and rutin in Calendula plant extracts. By applying samples with different weight ratios of marker compounds to the system, a database of chromatograms was constructed. A hundred and one signal intensities in each of the HPTLC chromatograms were correlated to the amounts of applied chlorogenic acid, caffeic acid, and rutin using an ANN. The developed ANN correlation was used to quantify the amounts of 3 marker compounds in calendula plant extracts. The minimum quantifiable level (MQL) of 610, 190 and 940 ng and the limit of detection (LD) of 183, 57 and 282 ng were established for chlorogenic, caffeic acid and rutin, respectively. A novel method for quality control of herbal products, based on HPTLC separation, high resolution digital plate imaging and ANN data analysis has been developed. The proposed method can be adopted for routine evaluation of the phytochemical variability in calendula extracts.

  19. EEG-Based Classification of New Imagery Tasks Using Three-Layer Feedforward Neural Network Classifier for Brain-Computer Interface

    NASA Astrophysics Data System (ADS)

    Phothisonothai, Montri; Nakagawa, Masahiro

    2006-10-01

    In this paper proposes the classification method of new imagery tasks for simple binary commands approach to a brain-computer interface (BCI). An analysis of imaginary tasks as “yes/no” have been proposed. Since BCI is very helpful technology for the patients who are suffering from severe motor disabilities. The BCI applications can be realized by using an electroencephalogram (EEG) signals recording at the scalp surface through the electrodes. Six healthy subjects (three males and three females), aged 23-30 years, were volunteered to participate in the experiment. During the experiment, 10-questions were used to be stimuli. The feature extraction of the event-related synchronization and event-related desynchronization (ERD/ERS) responses can be determined by the slope coefficient and Euclidian distance (SCED) method. The method uses the three-layer feedforward neural network based on a simple backpropagation algorithm to classify the two feature vectors. The experimental results of the proposed method show the average accuracy rates of 81.5 and 78.8% when the subjects imagine to “yes” and “no”, respectively.

  20. Microbial mats: an ecological niche for fungi

    PubMed Central

    Cantrell, Sharon A.; Duval-Pérez, Lisabeth

    2013-01-01

    Fungi were documented in tropical hypersaline microbial mats and their role in the degradation of complex carbohydrates (exopolymeric substance – EPS) was explored. Fungal diversity is higher during the wet season with Acremonium, Aspergillus, Cladosporium, and Penicillium among the more common genera. Diversity is also higher in the oxic layer and in young and transient mats. Enrichments with xanthan (a model EPS) show that without antibiotics (full community) degradation is faster than enrichments with antibacterial (fungal community) and antifungal (bacterial community) agents, suggesting that degradation is performed by a consortium of organisms (bacteria and fungi). The combined evidence from all experiments indicates that bacteria carried out approximately two-third of the xanthan degradation. The pattern of degradation is similar between seasons and layers but degradation is faster in enrichments from the wet season. The research suggests that fungi thrive in these hypersaline consortia and may participate in the carbon cycle through the degradation of complex carbohydrates. PMID:23577004

  1. Mapping the potential risk of mycetoma infection in Sudan and South Sudan using ecological niche modeling.

    PubMed

    Samy, Abdallah M; van de Sande, Wendy W J; Fahal, Ahmed Hassan; Peterson, A Townsend

    2014-10-01

    In 2013, the World Health Organization (WHO) recognized mycetoma as one of the neglected tropical conditions due to the efforts of the mycetoma consortium. This same consortium formulated knowledge gaps that require further research. One of these gaps was that very few data are available on the epidemiology and transmission cycle of the causative agents. Previous work suggested a soil-borne or Acacia thorn-prick-mediated origin of mycetoma infections, but no studies have investigated effects of soil type and Acacia geographic distribution on mycetoma case distributions. Here, we map risk of mycetoma infection across Sudan and South Sudan using ecological niche modeling (ENM). For this study, records of mycetoma cases were obtained from the scientific literature and GIDEON; Acacia records were obtained from the Global Biodiversity Information Facility. We developed ENMs based on digital GIS data layers summarizing soil characteristics, land-surface temperature, and greenness indices to provide a rich picture of environmental variation across Sudan and South Sudan. ENMs were calibrated in known endemic districts and transferred countrywide; model results suggested that risk is greatest in an east-west belt across central Sudan. Visualizing ENMs in environmental dimensions, mycetoma occurs under diverse environmental conditions. We compared niches of mycetoma and Acacia trees, and could not reject the null hypothesis of niche similarity. This study revealed contributions of different environmental factors to mycetoma infection risk, identified suitable environments and regions for transmission, signaled a potential mycetoma-Acacia association, and provided steps towards a robust risk map for the disease. PMID:25330098

  2. Stroke Increases Neural Stem Cells and Angiogenesis in the Neurogenic Niche of the Adult Mouse

    PubMed Central

    Zhang, Rui Lan; Chopp, Michael; Roberts, Cynthia; Liu, Xianshuang; Wei, Min; Nejad-Davarani, Siamak P.; Wang, Xinli; Zhang, Zheng Gang

    2014-01-01

    The unique cellular and vascular architecture of the adult ventricular-subventricular zone (V/SVZ) neurogenic niche plays an important role in regulating neural stem cell function. However, the in vivo identification of neural stem cells and their relationship to blood vessels within this niche in response to stroke remain largely unknown. Using whole-mount preparation of the lateral ventricle wall, we examined the architecture of neural stem cells and blood vessels in the V/SVZ of adult mouse over the course of 3 months after onset of focal cerebral ischemia. Stroke substantially increased the number of glial fibrillary acidic protein (GFAP) positive neural stem cells that are in contact with the cerebrospinal fluid (CSF) via their apical processes at the center of pinwheel structures formed by ependymal cells residing in the lateral ventricle. Long basal processes of these cells extended to blood vessels beneath the ependymal layer. Moreover, stroke increased V/SVZ endothelial cell proliferation from 2% in non-ischemic mice to 12 and 15% at 7 and 14 days after stroke, respectively. Vascular volume in the V/SVZ was augmented from 3% of the total volume prior to stroke to 6% at 90 days after stroke. Stroke-increased angiogenesis was closely associated with neuroblasts that expanded to nearly encompass the entire lateral ventricular wall in the V/SVZ. These data indicate that stroke induces long-term alterations of the neural stem cell and vascular architecture of the adult V/SVZ neurogenic niche. These post-stroke structural changes may provide insight into neural stem cell mediation of stroke-induced neurogenesis through the interaction of neural stem cells with proteins in the CSF and their sub-ependymal neurovascular interaction. PMID:25437857

  3. Ecological Niche Modeling for the Prediction of the Geographic Distribution of Cutaneous Leishmaniasis in Tunisia

    PubMed Central

    Chalghaf, Bilel; Chlif, Sadok; Mayala, Benjamin; Ghawar, Wissem; Bettaieb, Jihène; Harrabi, Myriam; Benie, Goze Bertin; Michael, Edwin; Salah, Afif Ben

    2016-01-01

    Cutaneous leishmaniasis is a very complex disease involving multiple factors that limit its emergence and spatial distribution. Prediction of cutaneous leishmaniasis epidemics in Tunisia remains difficult because most of the epidemiological tools used so far are descriptive in nature and mainly focus on a time dimension. The purpose of this work is to predict the potential geographic distribution of Phlebotomus papatasi and zoonotic cutaneous leishmaniasis caused by Leishmania major in Tunisia using Grinnellian ecological niche modeling. We attempted to assess the importance of environmental factors influencing the potential distribution of P. papatasi and cutaneous leishmaniasis caused by L. major. Vectors were trapped in central Tunisia during the transmission season using CDC light traps (John W. Hock Co., Gainesville, FL). A global positioning system was used to record the geographical coordinates of vector occurrence points and households tested positive for cutaneous leishmaniasis caused by L. major. Nine environmental layers were used as predictor variables to model the P. papatasi geographical distribution and five variables were used to model the L. major potential distribution. Ecological niche modeling was used to relate known species' occurrence points to values of environmental factors for these same points to predict the presence of the species in unsampled regions based on the value of the predictor variables. Rainfall and temperature contributed the most as predictors for sand flies and human case distributions. Ecological niche modeling anticipated the current distribution of P. papatasi with the highest suitability for species occurrence in the central and southeastern part of Tunisian. Furthermore, our study demonstrated that governorates of Gafsa, Sidi Bouzid, and Kairouan are at highest epidemic risk. PMID:26856914

  4. Habitat suitability and ecological niches of different plankton functional types in the global ocean

    NASA Astrophysics Data System (ADS)

    Vogt, Meike; Brun, Philipp; Payne, Mark R.; O'Brien, Colleen J.; Bednaršek, Nina; Buitenhuis, Erik T.; Doney, Scott C.; Leblanc, Karine; Le Quéré, Corinne; Luo, Yawei; Moriarty, Róisín; O'Brien, Todd D.; Schiebel, Ralf; Swan, Chantal

    2013-04-01

    Marine plankton play a central role in the biogeochemical cycling of important elements such as carbon, nitrogen, and sulphur. While our knowledge about marine ecosystem structure and functioning is still scarce and episodic, several recent observational studies confirm that marine ecosystems have been changing due to recent climate change, overfishing, and coastal eutrophication. In order to better understand marine ecosystem dynamics, the MAREDAT initiative has recently collected abundance and biomass data for 5 autotrophic (diatoms, Phaeocystis, coccolithophores, nitrogen fixers, picophytoplankton), and 6 heterotrophic plankton functional types (PFTs; bacteria, micro-, meso- and macrozooplankton, foraminifera and pteropods). Species distribution models (SDMs) are statistical tools that can be used to derive information about species habitats in space and time. They have been used extensively for a wide range of ecological applications in terrestrial ecosystems, but here we present the first global application in the marine realm, which was made possible by the MAREDAT data synthesis effort. We use a maximum entropy SDM to simulate global habitat suitability, habitat extent and ecological niches for different PFTs in the modern ocean. Present habitat suitability is derived from presence-only MAREDAT data and the observed annual and monthly mean levels of physiologically relevant variables such as SST, nutrient concentration or photosynthetic active radiation received in the mixed layer. This information can then be used to derive ecological niches for different species or taxa within each PFT, and to compare the ecological niches of different PFTs. While these results still need verification because data was not available for all ocean regions for all PFTs, they can give a first indication what present and future plankton habitats may look like, and what consequences we may have to expect for future marine ecosystem functioning and service provision in a warmer

  5. Ecological Niche Modeling for the Prediction of the Geographic Distribution of Cutaneous Leishmaniasis in Tunisia.

    PubMed

    Chalghaf, Bilel; Chlif, Sadok; Mayala, Benjamin; Ghawar, Wissem; Bettaieb, Jihène; Harrabi, Myriam; Benie, Goze Bertin; Michael, Edwin; Salah, Afif Ben

    2016-04-01

    Cutaneous leishmaniasis is a very complex disease involving multiple factors that limit its emergence and spatial distribution. Prediction of cutaneous leishmaniasis epidemics in Tunisia remains difficult because most of the epidemiological tools used so far are descriptive in nature and mainly focus on a time dimension. The purpose of this work is to predict the potential geographic distribution of Phlebotomus papatasi and zoonotic cutaneous leishmaniasis caused by Leishmania major in Tunisia using Grinnellian ecological niche modeling. We attempted to assess the importance of environmental factors influencing the potential distribution of P. papatasi and cutaneous leishmaniasis caused by L. major. Vectors were trapped in central Tunisia during the transmission season using CDC light traps (John W. Hock Co., Gainesville, FL). A global positioning system was used to record the geographical coordinates of vector occurrence points and households tested positive for cutaneous leishmaniasis caused by L. major. Nine environmental layers were used as predictor variables to model the P. papatasi geographical distribution and five variables were used to model the L. major potential distribution. Ecological niche modeling was used to relate known species' occurrence points to values of environmental factors for these same points to predict the presence of the species in unsampled regions based on the value of the predictor variables. Rainfall and temperature contributed the most as predictors for sand flies and human case distributions. Ecological niche modeling anticipated the current distribution of P. papatasi with the highest suitability for species occurrence in the central and southeastern part of Tunisian. Furthermore, our study demonstrated that governorates of Gafsa, Sidi Bouzid, and Kairouan are at highest epidemic risk. PMID:26856914

  6. Ecological Niche Modeling for the Prediction of the Geographic Distribution of Cutaneous Leishmaniasis in Tunisia.

    PubMed

    Chalghaf, Bilel; Chlif, Sadok; Mayala, Benjamin; Ghawar, Wissem; Bettaieb, Jihène; Harrabi, Myriam; Benie, Goze Bertin; Michael, Edwin; Salah, Afif Ben

    2016-04-01

    Cutaneous leishmaniasis is a very complex disease involving multiple factors that limit its emergence and spatial distribution. Prediction of cutaneous leishmaniasis epidemics in Tunisia remains difficult because most of the epidemiological tools used so far are descriptive in nature and mainly focus on a time dimension. The purpose of this work is to predict the potential geographic distribution of Phlebotomus papatasi and zoonotic cutaneous leishmaniasis caused by Leishmania major in Tunisia using Grinnellian ecological niche modeling. We attempted to assess the importance of environmental factors influencing the potential distribution of P. papatasi and cutaneous leishmaniasis caused by L. major. Vectors were trapped in central Tunisia during the transmission season using CDC light traps (John W. Hock Co., Gainesville, FL). A global positioning system was used to record the geographical coordinates of vector occurrence points and households tested positive for cutaneous leishmaniasis caused by L. major. Nine environmental layers were used as predictor variables to model the P. papatasi geographical distribution and five variables were used to model the L. major potential distribution. Ecological niche modeling was used to relate known species' occurrence points to values of environmental factors for these same points to predict the presence of the species in unsampled regions based on the value of the predictor variables. Rainfall and temperature contributed the most as predictors for sand flies and human case distributions. Ecological niche modeling anticipated the current distribution of P. papatasi with the highest suitability for species occurrence in the central and southeastern part of Tunisian. Furthermore, our study demonstrated that governorates of Gafsa, Sidi Bouzid, and Kairouan are at highest epidemic risk.

  7. The Spermatogonial Stem Cell Niche in the Collared Peccary (Tayassu tajacu)1

    PubMed Central

    Campos-Junior, Paulo Henrique A.; Costa, Guilherme M.J.; Lacerda, Samyra M.S.N.; Rezende-Neto, José V.; de Paula, Ana M.; Hofmann, Marie-Claude; de França, Luiz R.

    2012-01-01

    ABSTRACT In the seminiferous epithelium, spermatogonial stem cells (SSCs) are located in a particular environment called the “niche” that is controlled by the basement membrane, key testis somatic cells, and factors originating from the vascular network. However, the role of Leydig cells (LCs) as a niche component is not yet clearly elucidated. Recent studies showed that peccaries (Tayassu tajacu) present a peculiar LC cytoarchitecture in which these cells are located around the seminiferous tubule lobes, making the peccary a unique model for investigating the SSC niche. This peculiarity allowed us to subdivide the seminiferous tubule cross-sections in three different testis parenchyma regions (tubule-tubule, tubule-interstitium, and tubule-LC contact). Our aims were to characterize the different spermatogonial cell types and to determine the location and/or distribution of the SSCs along the seminiferous tubules. Compared to differentiating spermatogonia, undifferentiated spermatogonia (Aund) presented a noticeably higher nuclear volume (P < 0.05), allowing an accurate evaluation of their distribution. Immunostaining analysis demonstrated that approximately 93% of Aund were GDNF receptor alpha 1 positive (GFRA1+), and these cells were preferentially located adjacent to the interstitial compartment without LCs (P < 0.05). The expression of colony-stimulating factor 1 was observed in LCs and peritubular myoid cells (PMCs), whereas its receptor was present in LCs and in GFRA1+ Aund. Taken together, our findings strongly suggest that LCs, different from PMCs, might play a minor role in the SSC niche and physiology and that these steroidogenic cells are probably involved in the differentiation of Aund toward type A1 spermatogonia. PMID:22262689

  8. Macrophages Contribute to the Spermatogonial Niche in the Adult Testis.

    PubMed

    DeFalco, Tony; Potter, Sarah J; Williams, Alyna V; Waller, Brittain; Kan, Matthew J; Capel, Blanche

    2015-08-18

    The testis produces sperm throughout the male reproductive lifespan by balancing self-renewal and differentiation of spermatogonial stem cells (SSCs). Part of the SSC niche is thought to lie outside the seminiferous tubules of the testis; however, specific interstitial components of the niche that regulate spermatogonial divisions and differentiation remain undefined. We identified distinct populations of testicular macrophages, one of which lies on the surface of seminiferous tubules, in close apposition to areas of tubules enriched for undifferentiated spermatogonia. These macrophages express spermatogonial proliferation- and differentiation-inducing factors, such as colony-stimulating factor 1 (CSF1) and enzymes involved in retinoic acid (RA) biosynthesis. We show that transient depletion of macrophages leads to a disruption in spermatogonial differentiation. These findings reveal an unexpected role for macrophages in the spermatogonial niche in the testis and raise the possibility that macrophages play previously unappreciated roles in stem/progenitor cell regulation in other tissues.

  9. Macrophages Contribute to the Spermatogonial Niche in the Adult Testis

    PubMed Central

    DeFalco, Tony; Potter, Sarah J.; Williams, Alyna V.; Waller, Brittain; Kan, Matthew J.; Capel, Blanche

    2015-01-01

    Summary The testis produces sperm throughout the male reproductive lifespan by balancing self-renewal and differentiation of spermatogonial stem cells (SSCs). Part of the SSC niche is thought to lie outside the seminiferous tubules of the testis; however, specific interstitial components of the niche that regulate spermatogonial divisions and differentiation remain undefined. We identified distinct populations of testicular macrophages, one of which lies on the surface of seminiferous tubules in close apposition to areas of tubules enriched for undifferentiated spermatogonia. These macrophages express spermatogonial proliferation- and differentiation-inducing factors, such as colony stimulating factor 1 (CSF1) and enzymes involved in retinoic acid (RA) biosynthesis. We show that transient depletion of macrophages leads to a disruption in spermatogonial differentiation. These findings reveal an unexpected role for macrophages in the spermatogonial niche in the testis, and raise the possibility that macrophages play previously unappreciated roles in stem/progenitor cell regulation in other tissues. PMID:26257171

  10. Reticulate evolution is favored in influenza niche switching.

    PubMed

    Ma, Eric J; Hill, Nichola J; Zabilansky, Justin; Yuan, Kyle; Runstadler, Jonathan A

    2016-05-10

    Reticulate evolution is thought to accelerate the process of evolution beyond simple genetic drift and selection, helping to rapidly generate novel hybrids with combinations of adaptive traits. However, the long-standing dogma that reticulate evolutionary processes are likewise advantageous for switching ecological niches, as in microbial pathogen host switch events, has not been explicitly tested. We use data from the influenza genome sequencing project and a phylogenetic heuristic approach to show that reassortment, a reticulate evolutionary mechanism, predominates over mutational drift in transmission between different host species. Moreover, as host evolutionary distance increases, reassortment is increasingly favored. We conclude that the greater the quantitative difference between ecological niches, the greater the importance of reticulate evolutionary processes in overcoming niche barriers. PMID:27114508

  11. Lymphatic vessels arise from specialized angioblasts within a venous niche.

    PubMed

    Nicenboim, J; Malkinson, G; Lupo, T; Asaf, L; Sela, Y; Mayseless, O; Gibbs-Bar, L; Senderovich, N; Hashimshony, T; Shin, M; Jerafi-Vider, A; Avraham-Davidi, I; Krupalnik, V; Hofi, R; Almog, G; Astin, J W; Golani, O; Ben-Dor, S; Crosier, P S; Herzog, W; Lawson, N D; Hanna, J H; Yanai, I; Yaniv, K

    2015-06-01

    How cells acquire their fate is a fundamental question in developmental and regenerative biology. Multipotent progenitors undergo cell-fate restriction in response to cues from the microenvironment, the nature of which is poorly understood. In the case of the lymphatic system, venous cells from the cardinal vein are thought to generate lymphatic vessels through trans-differentiation. Here we show that in zebrafish, lymphatic progenitors arise from a previously uncharacterized niche of specialized angioblasts within the cardinal vein, which also generates arterial and venous fates. We further identify Wnt5b as a novel lymphatic inductive signal and show that it also promotes the ‘angioblast-to-lymphatic’ transition in human embryonic stem cells, suggesting that this process is evolutionarily conserved. Our results uncover a novel mechanism of lymphatic specification, and provide the first characterization of the lymphatic inductive niche. More broadly, our findings highlight the cardinal vein as a heterogeneous structure, analogous to the haematopoietic niche in the aortic floor.

  12. Viral niche construction alters hosts and ecosystems at multiple scales.

    PubMed

    Hamblin, Steven R; White, Peter A; Tanaka, Mark M

    2014-11-01

    The classical picture of viruses focuses on pathogenic viruses damaging the host's cells and physiology and host-pathogen immune coevolution. However, a broader picture of viruses is emerging that includes weakly pathogenic, commensal, or even mutualistic viruses and includes gross behavioural manipulations and viral effects on ecosystems. In this paper, we argue for niche construction as a unifying perspective on viral evolution. As obligate intracellular parasites, viruses are always modifying their environment, and these modifications drive evolutionary feedback between the virus and its environment across multiple scales from cells to ecosystems. We argue that niche construction will provide new insights into viral evolution, and that virology is a powerful source of empirical tests for niche construction.

  13. Ecological niche modeling of lyme disease in British Columbia, Canada.

    PubMed

    Mak, Sunny; Morshed, Muhammad; Henry, Bonnie

    2010-01-01

    The purpose of this study was to describe the geographic distribution and model the ecological niche for Borrelia burgdorferi (Johnson, Schmidt, Hyde, Steigerwaldt & Brenner), Ixodes pacificus (Cooley & Kohls), and Ixodes angustus (Neumann), the bacterium and primary tick vectors for Lyme disease, in British Columbia (BC), Canada. We employed a landscape epidemiology approach using geographic information systems mapping and ecological niche modeling (Genetic Algorithm for Rule-set Prediction) to identify geographical areas of disease transmission risk. Forecasted optimal ecological niche areas for B. burgdorferi are focused along the coast of Vancouver Island, the southwestern coast of the BC mainland, and in valley systems of interior BC roughly along and below the N51 degree line of latitude. These findings have been used to increase public and physician awareness of Lyme disease risk, and prioritize future field sampling for ticks in BC. PMID:20180315

  14. Climatic Niche Evolution in New World Monkeys (Platyrrhini)

    PubMed Central

    Duran, Andressa; Meyer, Andreas L. S.; Pie, Marcio R.

    2013-01-01

    Despite considerable interest in recent years on species distribution modeling and phylogenetic niche conservatism, little is known about the way in which climatic niches change over evolutionary time. This knowledge is of major importance to understand the mechanisms underlying limits of species distributions, as well as to infer how different lineages might be affected by anthropogenic climate change. In this study we investigate the tempo and mode climatic niche evolution in New World monkeys (Platyrrhini). Climatic conditions found throughout the distribution of 140 primate species were investigated using a principal component analysis, which indicated that mean temperature (particularly during the winter) is the most important climatic correlate of platyrrhine geographical distributions, accounting for nearly half of the interspecific variation in climatic niches. The effects of precipitation were associated with the second principal component, particularly with respect to the dry season. When models of trait evolution were fit to scores on each of the principal component axes, significant phylogenetic signal was detected for PC1 scores, but not for PC2 scores. Interestingly, although all platyrrhine families occupied comparable regions of climatic space, some aotid species such as Aotus lemurinus, A. jorgehernandezi, and A. miconax show highly distinctive climatic niches associated with drier conditions (high PC2 scores). This shift might have been made possible by their nocturnal habits, which could serve as an exaptation that allow them to be less constrained by humidity during the night. These results underscore the usefulness of investigating explicitly the tempo and mode of climatic niche evolution and its role in determining species distributions. PMID:24376729

  15. Climatic niche evolution in New World monkeys (Platyrrhini).

    PubMed

    Duran, Andressa; Meyer, Andreas L S; Pie, Marcio R

    2013-01-01

    Despite considerable interest in recent years on species distribution modeling and phylogenetic niche conservatism, little is known about the way in which climatic niches change over evolutionary time. This knowledge is of major importance to understand the mechanisms underlying limits of species distributions, as well as to infer how different lineages might be affected by anthropogenic climate change. In this study we investigate the tempo and mode climatic niche evolution in New World monkeys (Platyrrhini). Climatic conditions found throughout the distribution of 140 primate species were investigated using a principal component analysis, which indicated that mean temperature (particularly during the winter) is the most important climatic correlate of platyrrhine geographical distributions, accounting for nearly half of the interspecific variation in climatic niches. The effects of precipitation were associated with the second principal component, particularly with respect to the dry season. When models of trait evolution were fit to scores on each of the principal component axes, significant phylogenetic signal was detected for PC1 scores, but not for PC2 scores. Interestingly, although all platyrrhine families occupied comparable regions of climatic space, some aotid species such as Aotus lemurinus, A. jorgehernandezi, and A. miconax show highly distinctive climatic niches associated with drier conditions (high PC2 scores). This shift might have been made possible by their nocturnal habits, which could serve as an exaptation that allow them to be less constrained by humidity during the night. These results underscore the usefulness of investigating explicitly the tempo and mode of climatic niche evolution and its role in determining species distributions.

  16. The transition between the niche and neutral regimes in ecology

    PubMed Central

    Fisher, Charles K.; Mehta, Pankaj

    2014-01-01

    An ongoing debate in ecology concerns the impacts of ecological drift and selection on community assembly. Here, we show that there is a transition in diverse ecological communities between a selection-dominated regime (the niche phase) and a drift-dominated regime (the neutral phase). Simulations and analytic arguments show that the niche phase is favored in communities with large population sizes and relatively constant environments, whereas the neutral phase is favored in communities with small population sizes and fluctuating environments. Our results demonstrate how apparently neutral populations may arise even in communities inhabited by species with varying traits. PMID:25157131

  17. The stem cell niche finds its true north.

    PubMed

    Kirkeby, Agnete; Perlmann, Thomas; Pereira, Carlos-Filipe

    2016-08-15

    The third 'Stem Cell Niche' meeting, supported by The Novo Nordisk Foundation, was held this year on May 22-26 and brought together 185 selected participants from 24 different countries to Hillerød, Denmark. Diverse aspects of embryonic and adult stem cell biology were discussed, including their respective niches in ageing, disease and regeneration. Many presentations focused on emerging technologies, including single-cell analysis, in vitro organogenesis and direct reprogramming. Here, we summarize the data presented at this exciting and highly enjoyable meeting, where speakers as well as kitchen chefs were applauded at every session. PMID:27531947

  18. Niche-dependent genetic diversity in Antarctic metaviromes

    PubMed Central

    Zablocki, Olivier; van Zyl, Lonnie; Adriaenssens, Evelien M; Rubagotti, Enrico; Tuffin, Marla; Cary, Stephen C; Cowan, Don

    2014-01-01

    The metaviromes from 2 different Antarctic terrestrial soil niches have been analyzed. Both hypoliths (microbial assemblages beneath transluscent rocks) and surrounding open soils showed a high level diversity of tailed phages, viruses of algae and amoeba, and virophage sequences. Comparisons of other global metaviromes with the Antarctic libraries showed a niche-dependent clustering pattern, unrelated to the geographical origin of a given metavirome. Within the Antarctic open soil metavirome, a putative circularly permuted, ∼42kb dsDNA virus genome was annotated, showing features of a temperate phage possessing a variety of conserved protein domains with no significant taxonomic affiliations in current databases. PMID:26458512

  19. Predators determine how weather affects the spatial niche of lizard prey: exploring niche dynamics at a fine scale.

    PubMed

    Lopez-Darias, Marta; Schoener, Thomas W; Spiller, David A; Losos, Jonathan B

    2012-12-01

    Although abiotic and biotic factors can interact to shape the spatial niche of a species, studies that explore the interactive effects of both at a local scale are rare. We demonstrate that one of the main axes (perch height) characterizing the spatial niche of a common lizard, Anolis sagrei, varies according to the interactive effects of weather and the activity of a larger predatory lizard, Leiocephalus carinatus. Results were completely consistent: no matter how favorable the weather conditions for using the ground (mainly characterized by temperature, humidity, wind speed, rain), A. sagrei did not do so if the predator was present. Hence, great behavioral plasticity enabled A. sagrei to adjust its use of space very quickly. To the best of our knowledge, these results constitute the first field demonstration for anoles (and possibly for other animals as well) of how time-varying environmental conditions and predator presence interact to produce short-term changes in utilization along a major niche axis.

  20. Phylogenetic patterns of climatic, habitat and trophic niches in a European avian assemblage

    PubMed Central

    Pearman, Peter B; Lavergne, Sébastien; Roquet, Cristina; Wüest, Rafael; Zimmermann, Niklaus E; Thuiller, Wilfried

    2014-01-01

    Aim The origins of ecological diversity in continental species assemblages have long intrigued biogeographers. We apply phylogenetic comparative analyses to disentangle the evolutionary patterns of ecological niches in an assemblage of European birds. We compare phylogenetic patterns in trophic, habitat and climatic niche components. Location Europe. Methods From polygon range maps and handbook data we inferred the realized climatic, habitat and trophic niches of 405 species of breeding birds in Europe. We fitted Pagel's lambda and kappa statistics, and conducted analyses of disparity through time to compare temporal patterns of ecological diversification on all niche axes together. All observed patterns were compared with expectations based on neutral (Brownian) models of niche divergence. Results In this assemblage, patterns of phylogenetic signal (lambda) suggest that related species resemble each other less in regard to their climatic and habitat niches than they do in their trophic niche. Kappa estimates show that ecological divergence does not gradually increase with divergence time, and that this punctualism is stronger in climatic niches than in habitat and trophic niches. Observed niche disparity markedly exceeds levels expected from a Brownian model of ecological diversification, thus providing no evidence for past phylogenetic niche conservatism in these multivariate niches. Levels of multivariate disparity are greatest for the climatic niche, followed by disparity of the habitat and the trophic niches. Main conclusions Phylogenetic patterns in the three niche components differ within this avian assemblage. Variation in evolutionary rates (degree of gradualism, constancy through the tree) and/or non-random macroecological sampling probably lead here to differences in the phylogenetic structure of niche components. Testing hypotheses on the origin of these patterns requires more complete phylogenetic trees of the birds, and extended ecological data on