The Contribution of Rare Species to Community Phylogenetic Diversity across a Global Network of Forest Plots

Niche differentiation has been proposed as an explanation for rarity in species assemblages. To test this hypothesis requires quantifying the ecological similarity of species. This similarity can potentially be estimated by using phylogenetic relatedness. In this study, we predicted that if niche differentiation does explain the co-occurrence of rare and common species, then rare species should contribute greatly to the overall community phylogenetic diversity (PD), abundance will have phylogenetic signal, and common and rare species will be phylogenetically dissimilar. We tested these predictions by developing a novel method that integrates species rank abundance distributions with phylogenetic trees and trend analyses, to examine the relative contribution of individual species to the overall community PD. We then supplement this approach with analyses of phylogenetic signal in abundances and measures of phylogenetic similarity within and between rare and common species groups. We applied this analytical approach to 15 long-term temperate and tropical forest dynamics plots from around the world. We show that the niche differentiation hypothesis is supported in six of the nine gap-dominated forests but is rejected in the six disturbance-dominated and three gap-dominated forests. We also show that the three metrics utilized in this study each provide unique but corroborating information regarding the phylogenetic distribution of rarity in communities.

ENTANGLEMENT IN A 3-SPIN HEISENBERG-XY CHAIN WITH NEAREST-NEIGHBOR INTERACTIONS, SIMULATED IN AN NMR QUANTUM SIMULATOR

The evolution of entanglement in a 3-spin chain with nearest-neighbor Heisenberg-XY interactions for different initial states is investigated here. In an NMR experimental implementation, we generate multipartite entangled states starting from initial separable pseudo-pure states by simulating nearest-neighbor XY interactions in a 3-spin linear chain of nuclear spin qubits. For simulating XY interactions, we follow algebraic method of Zhang et al. Phys. Rev. A 72 (2005) 012331]. Bell state between end qubits has been generated by using only the unitary evolution of the XY Hamiltonian. For generating W-state and GHZ-state a single qubit rotation is applied on second and all the three qubits, respectively after the unitary evolution of the XY Hamiltonian.

Thermal degradation kinetics of poly(trimethylol propane triacrylate)/poly(hexane diol diacrylate) interpenetrating polymer network

Interpenetrating polymer networks (IPNs) of trimethylol propane triacrylate (TMPTA) and 1,6-hexane diol diacrylate (HDDA) at different weight ratios were synthesized. Temperature modulated differential scanning calorimetry (TMDSC) was used to determine whether the formation resulted in a copolymer or interpenetrating polymer network (IPN). These polymers are used as binders for microstereolithography (MSL) based ceramic microfabrication. The kinetics of thermal degradation of these polymers are important to optimize the debinding process for fabricating 3D shaped ceramic objects by MSL based rapid prototyping technique. Therefore, thermal and thermo-oxidative degradation of these IPNs have been studied by dynamic and isothermal thermogravimetry (TGA). Non-isothermal model-free kinetic methods have been adopted (isoconversional differential and KAS) to calculate the apparent activation energy (E a) as a function of conversion (α) in N 2 and air. The degradation of these polymers in N 2 atmosphere occurs via two mechanisms. Chain end scission plays a dominant role at lower temperature while the kinetics is governed by random chain scission at higher temperature. Oxidative degradation shows multiple degradation steps having higher activation energy than in N 2. Isothermal degradation was also carried out to predict the reaction model which is found to be decelerating. It was shown that the degradation of PTMPTA follows a contracting sphere reaction model in N 2. However, as the HDDA content increases in the IPNs, the degradation reaction follows Avrami-Erofeev model and diffusion governed mechanisms. The intermediate IPN compositions show both type of mechanism. Based on the above study, debinding strategy for MSL based microfabricated ceramic structure has been proposed. © 2012 Elsevier B.V.

Control of a Duct Flow Network for Wind Display in a Virtual Environment

Control of flow in duct networks has a myriad of applications ranging from heating, ventilation, and air-conditioning to blood flow networks. The system considered here provides vent velocity inputs to a novel 3-D wind display device called the TreadPort Active Wind Tunnel. An error-based robust decentralized sliding-mode control method with nominal feedforward terms is developed for individual ducts while considering cross coupling between ducts and model uncertainty as external disturbances in the output. This approach is important due to limited measurements, geometric complexities, and turbulent flow conditions. Methods for resolving challenges such as turbulence, electrical noise, valve actuator design, and sensor placement are presented. The efficacy of the controller and the importance of feedforward terms are demonstrated with simulations based upon an experimentally validated lumped parameter model and experiments on the physical system. Results show significant improvement over traditional control methods and validate prior assertions regarding the importance of decentralized control in practice.

Optimal Hop Distance and Power Control for a Single Cell, Dense, Ad Hoc Wireless Network

We consider a dense, ad hoc wireless network, confined to a small region. The wireless network is operated as a single cell, i.e., only one successful transmission is supported at a time. Data packets are sent between source-destination pairs by multihop relaying. We assume that nodes self-organize into a multihop network such that all hops are of length d meters, where d is a design parameter. There is a contention-based multiaccess scheme, and it is assumed that every node always has data to send, either originated from it or a transit packet (saturation assumption). In this scenario, we seek to maximize a measure of the transport capacity of the network (measured in bit-meters per second) over power controls (in a fading environment) and over the hop distance d, subject to an average power constraint. We first motivate that for a dense collection of nodes confined to a small region, single cell operation is efficient for single user decoding transceivers. Then, operating the dense ad hoc wireless network (described above) as a single cell, we study the hop length and power control that maximizes the transport capacity for a given network power constraint. More specifically, for a fading channel and for a fixed transmission time strategy (akin to the IEEE 802.11 TXOP), we find that there exists an intrinsic aggregate bit rate (Theta(opt) bits per second, depending on the contention mechanism and the channel fading characteristics) carried by the network, when operating at the optimal hop length and power control. The optimal transport capacity is of the form d(opt)((P) over bar (t)) x Theta(opt) with d(opt) scaling as (P) over bar (t) (1/eta), where (P) over bar (t) is the available time average transmit power and eta is the path loss exponent. Under certain conditions on the fading distribution, we then provide a simple characterization of the optimal operating point. Simulation results are provided comparing the performance of the optimal strategy derived here with some simple strategies for operating the network.

A study of epileptogenic network structures in rat hippocampal cultures using first spike latencies during synchronization events

Study of hypersynchronous activity is of prime importance for combating epilepsy. Studies on network structure typically reconstruct the network by measuring various aspects of the interaction between neurons and subsequently measure the properties of the reconstructed network. In sub-sampled networks such methods lead to significant errors in reconstruction. Using rat hippocampal neurons cultured on a multi-electrode array dish and a glutamate injury model of epilepsy in vitro, we studied synchronous activity in neuronal networks. Using the first spike latencies in various neurons during a network burst, we extract various recurring spatio-temporal onset patterns in the networks. Comparing the patterns seen in control and injured networks, we observe that injured networks express a wide diversity in their foci (origin) and activation pattern, while control networks show limited diversity. Furthermore, we note that onset patterns in glutamate injured networks show a positive correlation between synchronization delay and physical distance between neurons, while control networks do not.

A study of epileptogenic network structures in rat hippocampal cultures using first spike latencies during synchronization events

Study of hypersynchronous activity is of prime importance for combating epilepsy. Studies on network structure typically reconstruct the network by measuring various aspects of the interaction between neurons and subsequently measure the properties of the reconstructed network. In sub-sampled networks such methods lead to significant errors in reconstruction. Using rat hippocampal neurons cultured on a multi-electrode array dish and a glutamate injury model of epilepsy in vitro, we studied synchronous activity in neuronal networks. Using the first spike latencies in various neurons during a network burst, we extract various recurring spatio-temporal onset patterns in the networks. Comparing the patterns seen in control and injured networks, we observe that injured networks express a wide diversity in their foci (origin) and activation pattern, while control networks show limited diversity. Furthermore, we note that onset patterns in glutamate injured networks show a positive correlation between synchronization delay and physical distance between neurons, while control networks do not.

Understanding the Magnetization Reversal in Six-Fold Anisotropic Hexagonal Networks

Isolated magnetic nanowires have been studied extensively and the magnetization reversal mechanism is well understood in these systems. But when these nanowires are joined together in different architectures, they behave differently and can give novel properties. Using this approach, one can engineer the network architectures to get artificial anisotropy. Here, we report six-fold anisotropy by joining the magnetic nanowires into hexagonal network. For this study, we also benchmark the widely used micromagnetic packages: OOMMF, Nmag, and LLG-simulator. Further, we propose a local hysteresis method by post processing the spatial magnetization information. With this approach we obtained the hysteresis of nanowires to understand the six-fold anisotropy and the reversal mechanism within the hexagonal networks.

Multi-Port Network Approach for the Analysis of Dual Band Fractal Microstrip Antennas

The multiport network approach is extended to analyze the behavior of microstrip fractal antennas. The capacitively fedmicrostrip square ring antenna has the side opposite to the feed arm replaced with a fractal Minkowski geometry. Dual frequency operation is achieved by suitably choosing the indentation of this fractal geometry. The width of the two sides adjacent to this is increased to further control the resonant characteristics and the ratio of the two resonance frequencies of this antenna. The impedance matrix for the multiport network model of this antenna is simplified exploiting self-similarity of the geometry with greater accuracy and reduced analysis time. Experimentally validated results confirm utility of the approach in analyzing the input characteristics of similar multi-frequency fractal microstrip antennas with other fractal geometries.

Network approaches to drug discovery

Introduction: Advances in genomics technologies are providing a very large amount of data on genome-wide gene expression profiles, protein molecules and their interactions with other macromolecules and metabolites. Molecular interaction networks provide a useful way to capture this complex data and comprehend it. Networks are beginning to be used in drug discovery, in many steps of the modern discovery pipeline, with large-scale molecular networks being particularly useful for the understanding of the molecular basis of the disease. Areas covered: The authors discuss network approaches used for drug target discovery and lead identification in the drug discovery pipeline. By reconstructing networks of targets, drugs and drug candidates as well as gene expression profiles under normal and disease conditions, the paper illustrates how it is possible to find relationships between different diseases, find biomarkers, explore drug repurposing and study emergence of drug resistance. Furthermore, the authors also look at networks which address particular important aspects such as off-target effects, combination-targets, mechanism of drug action and drug safety. Expert opinion: The network approach represents another paradigm shift in drug discovery science. A network approach provides a fresh perspective of understanding important proteins in the context of their cellular environments, providing a rational basis for deriving useful strategies in drug design. Besides drug target identification and inferring mechanism of action, networks enable us to address new ideas that could prove to be extremely useful for new drug discovery, such as drug repositioning, drug synergy, polypharmacology and personalized medicine.

Interaction Signatures Stabilizing the NAD(P)-Binding Rossmann Fold: A Structure Network Approach

The fidelity of the folding pathways being encoded in the amino acid sequence is met with challenge in instances where proteins with no sequence homology, performing different functions and no apparent evolutionary linkage, adopt a similar fold. The problem stated otherwise is that a limited fold space is available to a repertoire of diverse sequences. The key question is what factors lead to the formation of a fold from diverse sequences. Here, with the NAD(P)-binding Rossmann fold domains as a case study and using the concepts of network theory, we have unveiled the consensus structural features that drive the formation of this fold. We have proposed a graph theoretic formalism to capture the structural details in terms of the conserved atomic interactions in global milieu, and hence extract the essential topological features from diverse sequences. A unified mathematical representation of the different structures together with a judicious concoction of several network parameters enabled us to probe into the structural features driving the adoption of the NAD(P)-binding Rossmann fold. The atomic interactions at key positions seem to be better conserved in proteins, as compared to the residues participating in these interactions. We propose a ``spatial motif'' and several ``fold specific hot spots'' that form the signature structural blueprints of the NAD(P)-binding Rossmann fold domain. Excellent agreement of our data with previous experimental and theoretical studies validates the robustness and validity of the approach. Additionally, comparison of our results with statistical coupling analysis (SCA) provides further support. The methodology proposed here is general and can be applied to similar problems of interest.

Smart Network Interface Selection for E-DTNs

We implement two energy models that accurately and comprehensively estimates the system energy cost and communication energy cost for using Bluetooth and Wi-Fi interfaces. The energy models running on a system is used to smartly pick the most energy optimal network interface so that data transfer between two end points is maximized.

A scalable network port scan detection system on FPGA

With ever increasing network speed, scalable and reliable detection of network port scans has become a major challenge. In this paper, we present a scalable and flexible architecture and a novel algorithm, to detect and block port scans in real time. The proposed architecture detects fast scanners as well as stealth scanners having large inter-probe periods. FPGA implementation of the proposed system gives an average throughput of 2 Gbps with a system clock frequency of 100 MHz on Xilinx Virtex-II Pro FPGA. Experimental results on real network trace show the effectiveness of the proposed system in detecting and blocking network scans with very low false positives and false negatives.

Smoothed functional and Quasi-Newton algorithms for routing in multi-stage queueing network with constraints

We consider the problem of optimal routing in a multi-stage network of queues with constraints on queue lengths. We develop three algorithms for probabilistic routing for this problem using only the total end-to-end delays. These algorithms use the smoothed functional (SF) approach to optimize the routing probabilities. In our model all the queues are assumed to have constraints on the average queue length. We also propose a novel quasi-Newton based SF algorithm. Policies like Join Shortest Queue or Least Work Left work only for unconstrained routing. Besides assuming knowledge of the queue length at all the queues. If the only information available is the expected end-to-end delay as with our case such policies cannot be used. We also give simulation results showing the performance of the SF algorithms for this problem.

An adaptive reliable transport protocol based on automatic reSend reQuest(ASQ) technique for wireless sensor networks

There are many wireless sensor network(WSN) applications which require reliable data transfer between the nodes. Several techniques including link level retransmission, error correction methods and hybrid Automatic Repeat re- Quest(ARQ) were introduced into the wireless sensor networks for ensuring reliability. In this paper, we use Automatic reSend request(ASQ) technique with regular acknowledgement to design reliable end-to-end communication protocol, called Adaptive Reliable Transport(ARTP) protocol, for WSNs. Besides ensuring reliability, objective of ARTP protocol is to ensure message stream FIFO at the receiver side instead of the byte stream FIFO used in TCP/IP protocol suite. To realize this objective, a new protocol stack has been used in the ARTP protocol. The ARTP protocol saves energy without affecting the throughput by sending three different types of acknowledgements, viz. ACK, NACK and FNACK with semantics different from that existing in the literature currently and adapting to the network conditions. Additionally, the protocol controls flow based on the receiver's feedback and congestion by holding ACK messages. To the best of our knowledge, there has been little or no attempt to build a receiver controlled regularly acknowledged reliable communication protocol. We have carried out extensive simulation studies of our protocol using Castalia simulator, and the study shows that our protocol performs better than related protocols in wireless/wire line networks, in terms of throughput and energy efficiency.