A network representation of protein structures: Implications for protein stability

This study views each protein structure as a network of noncovalent connections between amino acid side chains. Each amino acid in a protein structure is a node, and the strength of the noncovalent interactions between two amino acids is evaluated for edge determination. The protein structure graphs (PSGs) for 232 proteins have been constructed as a function of the cutoff of the amino acid interaction strength at a few carefully chosen values. Analysis of such PSGs constructed on the basis of edge weights has shown the following: 1), The PSGs exhibit a complex topological network behavior, which is dependent on the interaction cutoff chosen for PSG construction. 2), A transition is observed at a critical interaction cutoff, in all the proteins, as monitored by the size of the largest cluster (giant component) in the graph. Amazingly, this transition occurs within a narrow range of interaction cutoff for all the proteins, irrespective of the size or the fold topology. And 3), the amino acid preferences to be highly connected (hub frequency) have been evaluated as a function of the interaction cutoff. We observe that the aromatic residues along with arginine, histidine, and methionine act as strong hubs at high interaction cutoffs, whereas the hydrophobic leucine and isoleucine residues get added to these hubs at low interaction cutoffs, forming weak hubs. The hubs identified are found to play a role in bringing together different secondary structural elements in the tertiary structure of the proteins. They are also found to contribute to the additional stability of the thermophilic proteins when compared to their mesophilic counterparts and hence could be crucial for the folding and stability of the unique three-dimensional structure of proteins. Based on these results, we also predict a few residues in the thermophilic and mesophilic proteins that can be mutated to alter their thermal stability.

Sensor network deployment for agronomical data gathering in semi-arid regions

We share our experience in planning, designing and deploying a wireless sensor network of one square kilometre area. Environmental data such as soil moisture, temperature, barometric pressure, and relative humidity are collected in this area situated in the semi-arid region of Karnataka, India. It is a hope that information derived from this data will benefit the marginal farmer towards improving his farming practices. Soon after establishing the need for such a project, we begin by showing the big picture of such a data gathering network, the software architecture we have used, the range measurements needed for determining the sensor density, and the packaging issues that seem to play a crucial role in field deployments. Our field deployment experiences include designing with intermittent grid power, enhancing software tools to aid quicker and effective deployment, and flash memory corruption. The first results on data gathering look encouraging.

Simulation of wavelength/time multiple-pulses-per-row fiber-optic CDMA network

Passive wavelength/time fiber-optic code division multiple access (WIT FO-CDMA) network is a viable option for highspeed access networks. Constructions of 2-D codes, suitable for incoherent WIT FO-CDMA, have been proposed to reduce the time spread of the 1-D sequences. The 2-D constructions can be broadly classified as 1) hybrid codes and 2) matrix codes. In our earlier work [141, we had proposed a new family of wavelength/time multiple-pulses-per-row (W/T MPR) matrix codes which have good cardinality, spectral efficiency and at the same time have the lowest off-peak autocorrelation and cross-correlation values equal to unity. In this paper we propose an architecture for a WIT MPR FO-CDAM network designed using the presently available devices and technology. A complete FO-CDMA network of ten users is simulated, for various number of simultaneous users and shown that 0 --> 1 errors can occur only when the number of interfering users is at least equal to the threshold value.

Methodological perspectives for register-based health system performance assessment : Developing a hip fracture monitoring system in Finland

The resources of health systems are limited. There is a need for information concerning the performance of the health system for the purposes of decision-making. This study is about utilization of administrative registers in the context of health system performance evaluation. In order to address this issue, a multidisciplinary methodological framework for register-based data analysis is defined. Because the fixed structure of register-based data indirectly determines constraints on the theoretical constructs, it is essential to elaborate the whole analytic process with respect to the data. The fundamental methodological concepts and theories are synthesized into a data sensitive approach which helps to understand and overcome the problems that are likely to be encountered during a register-based data analyzing process. A pragmatically useful health system performance monitoring should produce valid information about the volume of the problems, about the use of services and about the effectiveness of provided services. A conceptual model for hip fracture performance assessment is constructed and the validity of Finnish registers as a data source for the purposes of performance assessment of hip fracture treatment is confirmed. Solutions to several pragmatic problems related to the development of a register-based hip fracture incidence surveillance system are proposed. The monitoring of effectiveness of treatment is shown to be possible in terms of care episodes. Finally, an example on the justification of a more detailed performance indicator to be used in the profiling of providers is given. In conclusion, it is possible to produce useful and valid information on health system performance by using Finnish register-based data. However, that seems to be far more complicated than is typically assumed. The perspectives given in this study introduce a necessary basis for further work and help in the routine implementation of a hip fracture monitoring system in Finland.

Fracture analysis of stiffened panels under combined tensile, bending, and shear loads

The objective is to present the formulation of numerically integrated modified virtual crack closure integral technique for concentrically and eccentrically stiffened panels for computation of strain-energy release rate and stress intensity factor based on linear elastic fracture mechanics principles. Fracture analysis of cracked stiffened panels under combined tensile, bending, and shear loads has been conducted by employing the stiffened plate/shell finite element model, MQL9S2. This model can be used to analyze plates with arbitrarily located concentric/eccentric stiffeners, without increasing the total number of degrees of freedom, of the plate element. Parametric studies on fracture analysis of stiffened plates under combined tensile and moment loads have been conducted. Based on the results of parametric,studies, polynomial curve fitting has been carried out to get best-fit equations corresponding to each of the stiffener positions. These equations can be used for computation of stress intensity factor for cracked stiffened plates subjected to tensile and moment loads for a given plate size, stiffener configuration, and stiffener position without conducting finite element analysis.

Analysis of connectivity map: Control to glutamate injured and phenobarbital treated neuronal network

We study the responses of a cultured neural network when it is exposed to epileptogenesis glutamate injury causing epilepsy and subsequent treatment with phenobarbital by constructing connectivity map of neurons using correlation matrix. This study is particularly useful in understanding the pharmaceutical drug induced changes in the neuronal network properties with insights into changes at the systems biology level. (C) 2010 American Institute of Physics. [doi:10.1063/1.3398025]

Power Optimal Network-on-Chip Interconnect Design

A large part of today's multi-core chips is interconnect. Increasing communication complexity has made essential new strategies for interconnects, such as Network on Chip. Power dissipation in interconnects has become a substantial part of the total power dissipation. Techniques to reduce interconnect power have thus become a necessity. In this paper, we present a design methodology that gives values of bus width for interconnect links, frequency of operation for routers, in Network on Chip scenario that satisfy required throughput and dissipate minimal switching power. We develop closed form analytical expressions for the power dissipation, with bus width and frequency as variables and then use Lagrange multiplier method to arrive at the optimal values. We present a 4 port router in 90 nm technology library as case study. The results obtained from analysis are discussed.

Generic Routing Rules and a Scalable Access Enhancement for the Network-on-Chip RECONNECT

RECONNECT is a Network-on-Chip using a honeycomb topology. In this paper we focus on properties of general rules applicable to a variety of routing algorithms for the NoC which take into account the missing links of the honeycomb topology when compared to a mesh. We also extend the original proposal [5] and show a method to insert and extract data to and from the network. Access Routers at the boundary of the execution fabric establish connections to multiple periphery modules and create a torus to decrease the node distances. Our approach is scalable and ensures homogeneity among the compute elements in the NoC. We synthesized and evaluated the proposed enhancement in terms of power dissipation and area. Our results indicate that the impact of necessary alterations to the fabric is negligible and effects the data transfer between the fabric and the periphery only marginally.

Search for standard model Higgs boson production in association with a W boson using a neural network discriminant at CDF

We present a search for standard model Higgs boson production in association with a W boson in proton-antiproton collisions at a center of mass energy of 1.96 TeV. The search employs data collected with the CDF II detector that correspond to an integrated luminosity of approximately 1.9 inverse fb. We select events consistent with a signature of a single charged lepton, missing transverse energy, and two jets. Jets corresponding to bottom quarks are identified with a secondary vertex tagging method, a jet probability tagging method, and a neural network filter. We use kinematic information in an artificial neural network to improve discrimination between signal and background compared to previous analyses. The observed number of events and the neural network output distributions are consistent with the standard model background expectations, and we set 95% confidence level upper limits on the production cross section times branching fraction ranging from 1.2 to 1.1 pb or 7.5 to 102 times the standard model expectation for Higgs boson masses from 110 to $150 GeV/c^2, respectively.

Influence of Oxide Particle Network Morphology on Ion Solvation and Transport in ``Soggy Sand''Electrolytes

The role of oxide surface chemical composition and solvent on ion solvation and ion transport of ``soggy sand'' electrolytes are discussed here. A ``soggy sand'' electrolyte system comprising dispersions of hydrophilic/hydrophobic functionalized aerosil silica in lithium perchlorate methoxy polyethylene glycol solution was employed for the study. Static and dynamic rheology measurements show formation of an attractive particle network in the case of the composite with unmodified aerosil silica (i.e., with surface silanol groups) as well as composites with hydrophobic alkane groups. While particle network in the composite with hydrophilic aerosil silica (unmodified) were due to hydrogen bonding, hydrophobic aerosil silica particles were held together via van der Waals forces. The network strength in the latter case (i.e., for hydrophobic composites) were weaker compared with the composite with unmodified aerosil silica. Both unmodified silica as well as hydrophobic silica composites displayed solid-like mechanical strength. No enhancement in ionic conductivity compared to the liquid electrolyte was observed in the case of the unmodified silica. This was attributed to the existence of a very strong particle network, which led to the ``expulsion'' of all conducting entities from the interfacial region between adjacent particles. The ionic conductivity for composites with hydrophobic aerosil particles displayed ionic conductivity dependent on the size of the hydrophobic chemical moiety. No spanning attractive particle network was observed for aerosil particles with surfaces modified with stronger hydrophilic groups (than silanol). The composite resembled a sol, and no percolation in ionic conductivity was observed.

Fracture behavior of concrete–concrete interface using acoustic emission technique

The fracture behavior of concrete–concrete interface is characterized using acoustic emission (AE). Beams of different sizes having jointed interface between two different strengths of concrete are tested. The results of load, displacement, CMOD, AE-events and AE-energy are analyzed. The width of fracture process zone and damage zone are computed using AE-data and are found to be independent of size. It is observed that, as the difference in compressive strength of concrete on either side of interface increases, the load carrying capacity, number of AE-events, AE-energy, width of fracture process zone and damage zone decreases.

The fracture toughness of bulk metallic glasses

Stiffness, strength, and toughness are the three primary attributes of a material, in terms of its mechanical properties. Bulk metallic glasses (BMGs) are known to exhibit elastic moduli at a fraction lower than crystalline alloys and have extraordinary strength. However, the reported values of fracture toughness of BMGs are highly variable; some BMGs such as the Zr-based ones have toughness values that are comparable to some high strength steels and titanium alloys, whereas there are also BMGs that are almost as brittle as silicate glasses. Invariably, monolithic BMGs exhibit no or low crack growth resistance and tend to become brittle upon structural relaxation. Despite its critical importance for the use of BMGs as structural materials, the fracture toughness of BMGs is relatively poorly understood. In this paper, we review the available literature to summarize the current understanding of the mechanics and micromechanisms of BMG toughness and highlight the needs for future research in this important area.

Conflicts when Competitors Cooperate: Exploring Elements of Conflicts from a Business Network Perspective

Most of the existing research within the business network approach is based on companies that are operating on different levels within the same value chain, as a buyer and a supplier. Intercompetitor cooperation, i.e. cooperation between companies occupying the same level within different value chains, has not been studied to the same extent. Moreover scholars within the business network approach have usually described industrial relationships as long term, consisting of mutual commitment and trust. Industrial relationships are not static, but dynamic, and they contain situations of both harmony and conflict. There is consequently a need for more research both concerning intercompetitor cooperation and conflicts. The purpose of this study is to develop our theoretical and empirical understanding of the nature of conflicts in intercompetitor cooperation from a business network perspective. The focus of the study lies on issue and intensity of conflict. The issue of a conflict can be divided into cause and topic, while the intensity comprises the importance and outcome of a conflict. The empirical part of the study is based on two case studies of groups of cooperating competitors from two different industries. The applied research method is interviews. According to the findings of this study causes of conflicts in intercompetitor cooperation can be divided into three groups: focus, awareness and capacity. Topics of conflict can be related to domain, delivery, advertising or cooperation. Moreover the findings show that conflict situations may be grouped into not important, important or very important. Some conflicts may also be of varying importance, meaning that the importance varies from one point of time to another. Based on the findings of the study the outcome or status of a conflict can be analyzed both on a concrete and general level. The findings also indicate that several conflicts are partly hidden, which means that only one or some of the involved actors perceive the conflict. Furthermore several conflict situations can be related to external network actors.

Adaptation in a Business Network Cooperation Context (summary section only)

In today’s business one can say that competition does not take place inside the network, but between networks. Change and dynamics are central issues in network studies, and a company, due its changing environment, can identify opportunities and threats and respond to them accordingly. These opportunities are vital, but also complex and demanding for the management. Earlier research has identified a shortcoming in explanations of how the micro-level interactions to macro-level patterns are connected. The IMP-group has been trying to fill this research gap with research on interactions within business networks. In this area of research lies the focus of research on relationships between organizations. Adaptation in cooperation is a central concept within business network research. Adaptation has been dealt with in previous literature, but the focus of the studies has mainly been outside this phenomenon, and it has mostly had a supporting role. Most literature has also described the buyers' point of view in studied supply networks, whereas much less attention has been paid to the suppliers' view on them. This study focuses on this research gap. The results of the study stress that adaptation should be included to a greater extent in the strategy work of companies. The adaptations should be carefully planned and, as far as possible, made consciously. Conscious, well-planned adaptations can be seen as investments into present and future relationships, and resources should be invested into something that does not increase the company’s dependence, but divides the power in the relationship between the companies. Adaptations should be planned so that they result in a more offensive way of responding to the demands that are placed upon the companies. In this way, the actions can be viewed and analyzed in accordance with whether the actions make the company weaker or stronger.

A comparative study of dynamic,ductile fracture initiation in two specimen configurations

In this work a single edge notched plate (SEN(T)) subjected to a tensile stress pulse is analysed, using a 2D plane strain dynamic finite element procedure. The interaction of the notch with a pre-nucleated hole ahead of it is examined. The background material is modelled by the Gurson constitutive law and ductile failure by microvoid coalescence in the ligament connecting the notch and the hole is simulated. Both rate independent and rate dependent material behaviour is considered. The notch tip region is subjected to a range of loading rates j by varying the peak value and the rise time of the applied stress pulse. The results obtained from these simulations are compared with a three point bend (TPB) specimen subjected to impact loading analysed in an earlier work [3] The variation of J at fracture initiation, J(c), with average loading rate j is obtained from the finite element simulations. It is found that the functional relationship between J(c) and j is fairly independent of the specimen geometry and is only dependent on material behaviour.