Species importance in a heterospecific foraging association network

There is a growing recognition of the need to integrate non-trophic interactions into ecological networks for a better understanding of whole-community organization. To achieve this, the first step is to build networks of individual non-trophic interactions. In this study, we analyzed a network of interdependencies among bird species that participated in heterospecific foraging associations (flocks) in an evergreen forest site in the Western Ghats, India. We found the flock network to contain a small core of highly important species that other species are strongly dependent on, a pattern seen in many other biological networks. Further, we found that structural importance of species in the network was strongly correlated to functional importance of species at the individual flock level. Finally, comparisons with flock networks from other Asian forests showed that the same taxonomic groups were important in general, suggesting that species importance was an intrinsic trait and not dependent on local ecological conditions. Hence, given a list of species in an area, it may be possible to predict which ones are likely to be important. Our study provides a framework for the investigation of other heterospecific foraging associations and associations among species in other non-trophic contexts.

Sufficient conditions for formation of a network topology by self-interested agents

Networks such as organizational network of a global company play an important role in a variety of knowledge management and information diffusion tasks. The nodes in these networks correspond to individuals who are self-interested. The topology of these networks often plays a crucial role in deciding the ease and speed with which certain tasks can be accomplished using these networks. Consequently, growing a stable network having a certain topology is of interest. Motivated by this, we study the following important problem: given a certain desired network topology, under what conditions would best response (link addition/deletion) strategies played by self-interested agents lead to formation of a pairwise stable network with only that topology. We study this interesting reverse engineering problem by proposing a natural model of recursive network formation. In this model, nodes enter the network sequentially and the utility of a node captures principal determinants of network formation, namely (1) benefits from immediate neighbors, (2) costs of maintaining links with immediate neighbors, (3) benefits from indirect neighbors, (4) bridging benefits, and (5) network entry fee. Based on this model, we analyze relevant network topologies such as star graph, complete graph, bipartite Turan graph, and multiple stars with interconnected centers, and derive a set of sufficient conditions under which these topologies emerge as pairwise stable networks. We also study the social welfare properties of the above topologies.

CTFS-ForestGEO: a worldwide network monitoring forests in an era of global change

Global change is impacting forests worldwide, threatening biodiversity and ecosystem services including climate regulation. Understanding how forests respond is critical to forest conservation and climate protection. This review describes an international network of 59 long-term forest dynamics research sites (CTFS-ForestGEO) useful for characterizing forest responses to global change. Within very large plots (median size 25ha), all stems 1cm diameter are identified to species, mapped, and regularly recensused according to standardized protocols. CTFS-ForestGEO spans 25 degrees S-61 degrees N latitude, is generally representative of the range of bioclimatic, edaphic, and topographic conditions experienced by forests worldwide, and is the only forest monitoring network that applies a standardized protocol to each of the world's major forest biomes. Supplementary standardized measurements at subsets of the sites provide additional information on plants, animals, and ecosystem and environmental variables. CTFS-ForestGEO sites are experiencing multifaceted anthropogenic global change pressures including warming (average 0.61 degrees C), changes in precipitation (up to +/- 30% change), atmospheric deposition of nitrogen and sulfur compounds (up to 3.8g Nm(-2)yr(-1) and 3.1g Sm(-2)yr(-1)), and forest fragmentation in the surrounding landscape (up to 88% reduced tree cover within 5km). The broad suite of measurements made at CTFS-ForestGEO sites makes it possible to investigate the complex ways in which global change is impacting forest dynamics. Ongoing research across the CTFS-ForestGEO network is yielding insights into how and why the forests are changing, and continued monitoring will provide vital contributions to understanding worldwide forest diversity and dynamics in an era of global change.

The design of an agent for modelling supply chain network dynamics

A useful insight into managerial decision making can be found from simulation of business systems, but existing work on simulation of supply chain behaviour has largely considered non-competitive chains. Where competitive agents have been examined, they have generally had a simple structure and been used for fundamental examination of stability and equilibria rather than providing practical guidance to managers. In this paper, a new agent for the study of competitive supply chain network dynamics is proposed. The novel features of the agent include the ability to select between competing vendors, distribute orders preferentially among many customers, manage production and inventory, and determine price based on competitive behaviour. The structure of the agent is related to existing business models and sufficient details are provided to allow implementation. The agent is tested to demonstrate that it recreates the main results of the existing modelling and management literature on supply chain dynamics. A brief exploration of competitive dynamics is given to confirm that the proposed agent can respond to competition. The results demonstrate that overall profitability for a supply chain network is maximised when businesses operate collectively. It is possible for an individual business to achieve higher profits by adopting a more competitive stance, but the consequence of this is that the overall profitability of the network is reduced. The agent will be of use for a broad range of studies on the long-run effect of management decisions on their network of suppliers and customers.

Proteomic analysis of the Cdc48/Ubx network identifies a role for Ubx2 in the regulation of lipid biosynthesis

Cdc48/p97 is an essential, highly abundant hexameric member of the AAA (ATPase associated with various cellular activities) family. It has been linked to a variety of processes throughout the cell but it is best known for its role in the ubiquitin proteasome pathway. In this system it is believed that Cdc48 behaves as a segregase, transducing the chemical energy of ATP hydrolysis into mechanical force to separate ubiquitin-conjugated proteins from their tightly-bound partners.

Current models posit that Cdc48 is linked to its substrates through a variety of adaptor proteins, including a family of seven proteins (13 in humans) that contain a Cdc48-binding UBX domain. As such, due to the complexity of the network of adaptor proteins for which it serves as the hub, Cdc48/p97 has the potential to exert a profound influence on the ubiquitin proteasome pathway. However, the number of known substrates of Cdc48/p97 remains relatively small, and smaller still is the number of substrates that have been linked to a specific UBX domain protein. As such, the goal of this dissertation research has been to discover new substrates and better understand the functions of the Cdc48 network. With this objective in mind, we established a proteomic screen to assemble a catalog of candidate substrate/targets of the Ubx adaptor system.

Here we describe the implementation and optimization of a cutting-edge quantitative mass spectrometry method to measure relative changes in the Saccharomyces cerevisiae proteome. Utilizing this technology, and in order to better understand the breadth of function of Cdc48 and its adaptors, we then performed a global screen to identify accumulating ubiquitin conjugates in cdc48-3 and ubxΔ mutants. In this screen different ubx mutants exhibited reproducible patterns of conjugate accumulation that differed greatly from each other, pointing to various unexpected functional specializations of the individual Ubx proteins.

As validation of our mass spectrometry findings, we then examined in detail the endoplasmic-reticulum bound transcription factor Spt23, which we identified as a putative Ubx2 substrate. In these studies ubx2Δ cells were deficient in processing of Spt23 to its active p90 form, and in localizing p90 to the nucleus. Additionally, consistent with reduced processing of Spt23, ubx2Δ cells demonstrated a defect in expression of their target gene OLE1, a fatty acid desaturase. Overall, this work demonstrates the power of proteomics as a tool to identify new targets of various pathways and reveals Ubx2 as a key regulator lipid membrane biosynthesis.

Structural Integration of Tellurium Oxide into Mixed-Network-Former Glasses: Connectivity Distribution in the System NaPO3–TeO2

FSodium phosphate tellurite glasses in the system (NaPO3)(x)(TeO2)(1-x) were prepared and structurally characterized by thermal analysis, vibrational spectroscopy, X-ray photoelectron spectroscopy (XPS) and a variety of complementary solid-state nuclear magnetic resonance (NMR) techniques. Unlike the situation in other mixed-network-former glasses, the interaction between the two network formers tellurium oxide and phosphorus oxide produces no new structural units, and no sharing of the network modifier Na2O takes place. The glass structure can be regarded as a network of interlinked metaphosphate-type P(2) tetrahedral and TeO4/2 antiprismotic units. The combined interpretation of the O 1s XPS data and the P-31 solid-state NMR spectra presents clear quantitative evidence for a nonstatistical connectivity distribution. Rather the formation of homootomic P-O-P and Te-O-Te linkages is favored over mixed P-O-Te connectivities. As a consequence of this chemical segregation effect, the spatial sodium distribution is not random, as also indicated by a detailed analysis of P-31/No-23 rotational echo double-resonance (REDOR) experiments. ACHTUNGTRENUNG(TeO2)1 x were prepared and structurally characterized by thermal analysis,vibrat ional spectroscopy,X-ray photoelectron spectroscopy (XPS) and a variety of complementary solid-state nuclear magnetic resonance (NMR) techniques. Unlike the situation in other mixed-network-former glasses,the interaction between the two network formers tellurium oxide and phosphorus oxide produces no new structural units,and no sharing of the network modifier Na2O takes place. The glass structure can be regarded as a network of interlinked metaphosphate-type P(2) tetrahedral and TeO4/2 antiprismatic units. The combined interpretation of the O 1s XPS data and the 31P solid-state NMR spectra presents clear quantitative evidence for a nonstatistical connectivity distribution. Rather,the formation of homoatomic P O P and Te O Te linkages is favored over mixed P O Te connectivities. As a consequence of this chemical segregation effect,the spatial sodium distribution is not random,as also indicated by a detailed analysis of 31P/23Na rotational echo double-resonance (REDOR) experiments.

Extraction of fibre network architecture by X-ray tomography and prediction of elastic properties using an affine analytical model

This paper proposes a method for extracting reliable architectural characteristics from complex porous structures using micro-computed tomography (μCT) images. The work focuses on a highly porous material composed of a network of fibres bonded together. The segmentation process, allowing separation of the fibres from the remainder of the image, is the most critical step in constructing an accurate representation of the network architecture. Segmentation methods, based on local and global thresholding, were investigated and evaluated by a quantitative comparison of the architectural parameters they yielded, such as the fibre orientation and segment length (sections between joints) distributions and the number of inter-fibre crossings. To improve segmentation accuracy, a deconvolution algorithm was proposed to restore the original images. The efficacy of the proposed method was verified by comparing μCT network architectural characteristics with those obtained using high resolution CT scans (nanoCT). The results indicate that this approach resolves the architecture of these complex networks and produces results approaching the quality of nanoCT scans. The extracted architectural parameters were used in conjunction with an affine analytical model to predict the axial and transverse stiffnesses of the fibre network. Transverse stiffness predictions were compared with experimentally measured values obtained by vibration testing. © 2011 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Evaluating the impacts of iteration on PD processes by transforming task network models into System Dynamics models

Iteration is unavoidable in the design process and should be incorporated when planning and managing projects in order to minimize surprises and reduce schedule distortions. However, planning and managing iteration is challenging because the relationships between its causes and effects are complex. Most approaches which use mathematical models to analyze the impact of iteration on the design process focus on a relatively small number of its causes and effects. Therefore, insights derived from these analytical models may not be robust under a broader consideration of potential influencing factors. In this article, we synthesize an explanatory framework which describes the network of causes and effects of iteration identified from the literature, and introduce an analytic approach which combines a task network modeling approach with System Dynamics simulation. Our approach models the network of causes and effects of iteration alongside the process architecture which is required to analyze the impact of iteration on design process performance. We show how this allows managers to assess the impact of changes to process architecture and to management levers which influence iterative behavior, accounting for the fact that these changes can occur simultaneously and can accumulate in non-linear ways. We also discuss how the insights resulting from this analysis can be visualized for easier consumption by project participants not familiar with simulation methods. Copyright © 2010 by ASME.

Controlled organization of silver nanoparticles into network assemblies by tuning pH values

We demonstrate the pH-induced assembly of 2-mercaptosuccinic acid-functionalized silver nanoparticles (MSA-Ag NPs) in the absence of hard or soft template. Two-dimensional (2D) and three-dimensional (3D) networks of silver NPs were achieved by tuning pH of the medium. The assembly process was monitored using atomic forces microscopy. The key factor affects the formation of network of silver NPs may be intermolecular hydrogen bonding between two carboxylic acid groups of MSA on two adjacent silver NPs.

Amplification of antigen-antibody interactions based on biotin labeled protein-streptavidin network complex using impedance spectroscopy

Antibody was covalently immobilized by amine coupling method to gold surfaces modified with a self-assembled monolayer of thioctic acid. The electrochemical measurements of cyclic voltammetry and impedance spectroscopy showed that the hexacyanoferrate redox reactions on the gold surface were blocked due to the procedures of self-assembly of thioctic acid and antibody immobilization. The binding of a specific antigen to antibody recognition layer could be detected by measurements of the impedance change. A new amplification strategy was introduced for improving the sensitivity of impedance measurements using biotin labeled protein- streptavidin network complex. This amplification strategy is based on the construction of a molecular complex between streptavidin and biotin labeled protein. This complex can be formed in a cross-linking network of molecules so that the amplification of response signal will be realized due to the big molecular size of complex. The results show that this amplification strategy causes dramatic improvement of the detection sensitivity of hIgG and has good correlation for detection of hIgG in the range of 2-10 mug/ml. (C) 2001 Elsevier Science B.V. All rights reserved.

Structural Saliency: The Detection of Globally Salient Structures Using a Locally Connected Network

Certain salient structures in images attract our immediate attention without requiring a systematic scan. We present a method for computing saliency by a simple iterative scheme, using a uniform network of locally connected processing elements. The network uses an optimization approach to produce a "saliency map," a representation of the image emphasizing salient locations. The main properties of the network are: (i) the computations are simple and local, (ii) globally salient structures emerge with a small number of iterations, and (iii) as a by-product of the computations, contours are smoothed and gaps are filled in.

Exploring the relationship between social network sites and the consumption of cultural goods through the lens of affordances

This thesis presents research theorising the use of social network sites (SNS) for the consumption of cultural goods. SNS are Internet-based applications that enable people to connect, interact, discover, and share user-generated content. They have transformed communication practices and are facilitating users to present their identity online through the disclosure of information on a profile. SNS are especially effective for propagating content far and wide within a network of connections. Cultural goods constitute hedonic experiential goods with cultural, artistic, and entertainment value, such as music, books, films, and fashion. Their consumption is culturally dependant and they have unique characteristics that distinguish them from utilitarian products. The way in which users express their identity on SNS is through the sharing of cultural interests and tastes. This makes cultural good consumption vulnerable to the exchange of content and ideas that occurs across an expansive network of connections within these social systems. This study proposes the lens of affordances to theorise the use of social network sites for the consumption of cultural goods. Qualitative case study research using two phases of data collection is proposed in the application of affordances to the research topic. The interaction between task, technology, and user characteristics is investigated by examining each characteristic in detail, before investigating the actual interaction between the user and the artifact for a particular purpose. The study contributes to knowledge by (i) improving our understanding of the affordances of social network sites for the consumption of cultural goods, (ii) demonstrating the role of task, technology and user characteristics in mediating user behaviour for user-artifact interactions, (iii) explaining the technical features and user activities important to the process of consuming cultural goods using social network sites, and (iv) theorising the consumption of cultural goods using SNS by presenting a theoretical research model which identifies empirical indicators of model constructs and maps out affordance dependencies and hierarchies. The study also provides a systematic research process for applying the concept of affordances to the study of system use.

Prospective surveillance for invasive fungal infections in hematopoietic stem cell transplant recipients, 2001-2006: overview of the Transplant-Associated Infection Surveillance Network (TRANSNET) Database.

BACKGROUND: The incidence and epidemiology of invasive fungal infections (IFIs), a leading cause of death among hematopoeitic stem cell transplant (HSCT) recipients, are derived mainly from single-institution retrospective studies. METHODS: The Transplant Associated Infections Surveillance Network, a network of 23 US transplant centers, prospectively enrolled HSCT recipients with proven and probable IFIs occurring between March 2001 and March 2006. We collected denominator data on all HSCTs preformed at each site and clinical, diagnostic, and outcome information for each IFI case. To estimate trends in IFI, we calculated the 12-month cumulative incidence among 9 sequential subcohorts. RESULTS: We identified 983 IFIs among 875 HSCT recipients. The median age of the patients was 49 years; 60% were male. Invasive aspergillosis (43%), invasive candidiasis (28%), and zygomycosis (8%) were the most common IFIs. Fifty-nine percent and 61% of IFIs were recognized within 60 days of neutropenia and graft-versus-host disease, respectively. Median onset of candidiasis and aspergillosis after HSCT was 61 days and 99 days, respectively. Within a cohort of 16,200 HSCT recipients who received their first transplants between March 2001 and September 2005 and were followed up through March 2006, we identified 718 IFIs in 639 persons. Twelve-month cumulative incidences, based on the first IFI, were 7.7 cases per 100 transplants for matched unrelated allogeneic, 8.1 cases per 100 transplants for mismatched-related allogeneic, 5.8 cases per 100 transplants for matched-related allogeneic, and 1.2 cases per 100 transplants for autologous HSCT. CONCLUSIONS: In this national prospective surveillance study of IFIs in HSCT recipients, the cumulative incidence was highest for aspergillosis, followed by candidiasis. Understanding the epidemiologic trends and burden of IFIs may lead to improved management strategies and study design.

Evaluation of the new ESR network software for the retrieval of direct sun products from cimel ce318 and prede pom01 sun-sky radiometers.

The European Skynet Radiometers network (EuroSkyRad or ESR) has been recently established as a research network of European PREDE sun-sky radiometers. Moreover, ESR is federated with SKYNET, an international network of PREDE sun-sky radiometers mostly present in East Asia. In contrast to SKYNET, the European network also integrates users of the CIMEL CE318 sky–sun photometer. Keeping instrumental duality in mind, a set of open source algorithms has been developed consisting of two modules for (1) the retrieval of direct sun products (aerosol optical depth, wavelength exponent and water vapor) from the sun extinction measurements; and (2) the inversion of the sky radiance to derive other aerosol optical properties such as size distribution, single scattering albedo or refractive index. In this study we evaluate the ESR direct sun products in comparison with the AERosol RObotic NETwork (AERONET) products. Specifically, we have applied the ESR algorithm to a CIMEL CE318 and PREDE POM simultaneously for a 4-yr database measured at the Burjassot site (Valencia, Spain), and compared the resultant products with the AERONET direct sun measurements obtained with the same CIMEL CE318 sky–sun photometer. The comparison shows that aerosol optical depth differences are mostly within the nominal uncertainty of 0.003 for a standard calibration instrument, and fall within the nominal AERONET uncertainty of 0.01–0.02 for a field instrument in the spectral range 340 to 1020 nm. In the cases of the Ångström exponent and the columnar water vapor, the differences are lower than 0.02 and 0.15 cm, respectively. Therefore, we present an open source code program that can be used with both CIMEL and PREDE sky radiometers and whose results are equivalent to AERONET and SKYNET retrievals.

Strategy in a religious network: A bourdieuian critique of the sociology of spirituality

Within the sociology of religion there has emerged a discourse on spirituality that views contemporary developments as involving the assertion of individuals’ self-authority. This perspective’s theoretical roots have been persistently criticised for their conceptualisation of agency; in contrast, this paper draws upon Bourdieu’s concept of strategy to examine action in an English religious network of the sort often classified ‘New Age’. In particular, one informant is discussed in order to provide focus for an understanding of what Lahire calls sociology at the level of the individual. Her actions, better explained as strategic improvisations than as choices made on the basis of self-authority, help to illuminate the peculiarities of this religious setting, which is characterised in terms of ‘nonformativeness’. By emphasising social contextualisation, this approach addresses people’s meaningful actions in a way that may be applied not only more widely within the religious field but also in other fields of action.