Creating a specialist protein resource network: a meeting report for the protein bioinformatics and community resources retreat

During 11-12 August 2014, a Protein Bioinformatics and Community Resources Retreat was held at the Wellcome Trust Genome Campus in Hinxton, UK. This meeting brought together the principal investigators of several specialized protein resources (such as CAZy, TCDB and MEROPS) as well as those from protein databases from the large Bioinformatics centres (including UniProt and RefSeq). The retreat was divided into five sessions: (1) key challenges, (2) the databases represented, (3) best practices for maintenance and curation, (4) information flow to and from large data centers and (5) communication and funding. An important outcome of this meeting was the creation of a Specialist Protein Resource Network that we believe will improve coordination of the activities of its member resources. We invite further protein database resources to join the network and continue the dialogue.

An approximation to the QoS aware throughput region of a tree network under IEEE 802.15.4 CSMA/CA with application to wireless sensor network design

In the context of wireless sensor networks, we are motivated by the design of a tree network spanning a set of source nodes that generate packets, a set of additional relay nodes that only forward packets from the sources, and a data sink. We assume that the paths from the sources to the sink have bounded hop count, that the nodes use the IEEE 802.15.4 CSMA/CA for medium access control, and that there are no hidden terminals. In this setting, starting with a set of simple fixed point equations, we derive explicit conditions on the packet generation rates at the sources, so that the tree network approximately provides certain quality of service (QoS) such as end-to-end delivery probability and mean delay. The structures of our conditions provide insight on the dependence of the network performance on the arrival rate vector, and the topological properties of the tree network. Our numerical experiments suggest that our approximations are able to capture a significant part of the QoS aware throughput region (of a tree network), that is adequate for many sensor network applications. Furthermore, for the special case of equal arrival rates, default backoff parameters, and for a range of values of target QoS, we show that among all path-length-bounded trees (spanning a given set of sources and the data sink) that meet the conditions derived in the paper, a shortest path tree achieves the maximum throughput. (C) 2015 Elsevier B.V. All rights reserved.

Ultra-small sulphur nanoparticles configured inside a flexible organic mixed conducting network as a cathode for lithium-sulphur batteries

The major challenges in Li-S batteries are the formation of soluble polysulphides during the reversible conversion of S-8 <-> Li2S, large changes in sulphur particle volume during lithiation and extremely poor charge transport in sulphur. We demonstrate here a novel and simple strategy to overcome these challenges towards practical realization of a stable high performance Li-S battery. For the first time, a strategy is developed which does away with the necessity of pre-fabricated high surface area hollow-structured adsorbates and also multiple nontrivial synthesis steps related to sulphur loading inside such adsorbates. A lithiated polyethylene glycol (PEG) based surfactant tethered on ultra-small sulphur nanoparticles and wrapped up with polyaniline (PAni) (abbreviated as S-MIEC) is demonstrated here as an exceptional cathode for Li-S batteries. The PEG and PAni network around the sulphur nanoparticles serves as an efficient flexible trap for sulphur and polysulphides and also provides distinct pathways for electrons (through PAni) and ions (through PEG) during battery operation. Contrary to the cathodes demonstrated based on various carbon-sulphur composites, the mixed conducting S-MIEC showed an extremely high loading of 75%. The S-MIEC exhibited a stable capacity of nearly 900 mA h g(-1) at the end of 100 cycles at a 1C current rate.

As-You-Go Deployment of a 2-Connected Wireless Relay Network for Sensor-Sink Interconnection

A person walks along a line (which could be an idealisation of a forest trail, for example), placing relays as he walks, in order to create a multihop network for connecting a sensor at a point along the line to a sink at the start of the line. The potential placement points are equally spaced along the line, and at each such location the decision to place or not to place a relay is based on link quality measurements to the previously placed relays. The location of the sensor is unknown apriori, and is discovered as the deployment agent walks. In this paper, we extend our earlier work on this class of problems to include the objective of achieving a 2-connected multihop network. We propose a network cost objective that is additive over the deployed relays, and accounts for possible alternate routing over the multiple available paths. As in our earlier work, the problem is formulated as a Markov decision process. Placement algorithms are obtained for two source location models, which yield a discounted cost MDP and an average cost MDP. In each case we obtain structural results for an optimal policy, and perform a numerical study that provides insights into the advantages and disadvantages of multi-connectivity. We validate the results obtained from numerical study experimentally in a forest-like environment.

Protein Structure and Function: Looking through the Network of Side-Chain Interactions

Network theory has become an excellent method of choice through which biological data are smoothly integrated to gain insights into complex biological problems. Understanding protein structure, folding, and function has been an important problem, which is being extensively investigated by the network approach. Since the sequence uniquely determines the structure, this review focuses on the networks of non-covalently connected amino acid side chains in proteins. Questions in structural biology are addressed within the framework of such a formalism. While general applications are mentioned in this review, challenging problems which have demanded the attention of scientific community for a long time, such as allostery and protein folding, are considered in greater detail. Our aim has been to explore these important problems through the eyes of networks. Various methods of constructing protein structure networks (PSN) are consolidated. They include the methods based on geometry, edges weighted by different schemes, and also bipartite network of protein-nucleic acid complexes. A number of network metrics that elegantly capture the general features as well as specific features related to phenomena, such as allostery and protein model validation, are described. Additionally, an integration of network theory with ensembles of equilibrium structures of a single protein or that of a large number of structures from the data bank has been presented to perceive complex phenomena from network perspective. Finally, we discuss briefly the capabilities, limitations, and the scope for further explorations of protein structure networks.

Ultrasonic Guided Wave Sensor Network Optimization for Monitoring Rivet Line

Guided waves using piezo-electric wafer active sensors (PWAS) is one of the useful techniques of damage detection. Sensor network optimization with minimal network hardware footprint and maximal area of coverage remains a challenging problem. PWAS sensors are placed at discrete locations in order to inspect damages in plates and the idea has the potential to be extended to assembled structures. Various actuator-sensor configurations are possible within the network in order to identify and locate damages. In this paper we present a correlation based approach to monitor cracks emanating from rivet line using a simulated guided wave signal whose sensor is operating in pulse echo mode. Discussions regarding the identification of phase change due to reflections from the crack are also discussed in this paper.

Wireless Network-Coded Accumulate-Compute-and-Forward Two-Way Relaying

For the physical-layer network-coded wireless two-way relaying, it was observed by Koike-Akino et al. that adaptively changing the network coding map used at the relay according to channel conditions greatly reduces the impact of multiple-access interference, which occurs at the relay, and all these network coding maps should satisfy a requirement called exclusive law. We extend this approach to an accumulate-compute-and-forward protocol, which employs two phases: a multiple access (MA) phase consisting of two channel uses with independent messages in each channel use and a broadcast (BC) phase having one channel use. Assuming that the two users transmit points from the same 4-phase-shift keying (PSK) constellation, every such network coding map that satisfies the exclusive law can be represented by a Latin square of side 16, and conversely, this relationship can be used to get the network coding maps satisfying the exclusive law. Two methods of obtaining this network coding map to be used at the relay are discussed. Using the structural properties of the Latin squares for a given set of parameters, the problem of finding all the required maps is reduced to finding a small set of maps for the case. Having obtained all the Latin squares, a criterion is provided to select a Latin square for a given realization of fade state. This criterion turns out to be the same as the one used byMuralidharan et al. for two-stage bidirectional relaying.

Application of the Conjugate Gradient Optimization Algorithm of Neural Network on Laser Machining

在应用激光技术加工复杂曲面时,通常以采样点集为插值点来建立曲面函数,然后实现曲面上任意坐标点的精确定位。人工神经网络的BP算法能实现函数插值,但计算精度偏低,往往达不到插值精确要求,造成较大的加工误差。提出人工神经网络的共轭梯度最优化插值新算法,并通过实例仿真,证明了这种曲面精确定位方法的可行性,从而为激光加工的三维精确定位提供了一种良好解决方案。这种方法已经应用在实际中。

Three-Dimensional Network Model And Its Parameter Calibration

A material model, whose framework is parallel spring-bundles oriented in 3-D space, is proposed. Based on a discussion of the discrete schemes and optimum discretization of the solid angles, a 3-D network cell consisted of one-dimensional components is developed with its geometrical and physical parameters calibrated. It is proved that the 3-D network model is able to exactly simulate materials with arbitrary Poisson ratio from 0 to 1/2, breaking through the limit that the previous models in the literature are only suitable for materials with Poisson ratio from 0 to 1/3. A simplified model is also proposed to realize high computation accuracy within low computation cost. Examples demonstrate that the 3-D network model has particular superiority in the simulation of short-fiber reinforced composites.