Inferring molecular function: contributions from functional linkages

In the current era of high-throughput sequencing and structure determination, functional annotation has become a bottleneck in biomedical science. Here, we show that automated inference of molecular function using functional linkages among genes increases the accuracy of functional assignments by >= 8% and enriches functional descriptions in >= 34% of top assignments. Furthermore, biochemical literature supports >80% of automated inferences for previously unannotated proteins. These results emphasize the benefit of incorporating functional linkages in protein annotation.

On the PAPR of cosets of linear codes

Employing an error control code is one of the techniques to reduce the Peak-to-Average Power Ratio (PAPR) in a Orthogonal Frequency Division Multiplexing system, a well known class of such codes being the cosets of Reed-Muller codes. In this paper, we consider the class of such coset-codes of arbitrary linear codes and present a method of doubling the size of such a code without increasing the PAPR, by combining two such binary coset-codes. We identify the conditions under which we can employ this doubling more than once with no marginal increase in the PAPR value. Given a PAPR and length, our method has enabled to get the best coset-code (in terms of the size). Also, we show that the PAPR information of the coset-codes of the extended codes is obtainable from the PAPR of the corresponding coset-codes of the parent code. We have also shown a special type of lengthening is useful in PAPR studies.

Optimal resource allocation in conflicts with the Lanchester linear law (2,1) model

This paper presents a detailed analysis of a model for military conflicts where the defending forces have to determine an optimal partitioning of available resources to counter attacks from an adversary in two different fronts in an area fire situation. Lanchester linear law attrition model is used to develop the dynamical equations governing the variation in force strength. Here we address a static resource allocation problem namely, Time-Zero-Allocation (TZA) where the resource allocation is done only at the initial time. Numerical examples are given to support the analytical results.

Multi-Tone Testing of Linear and Nonlinear Analog Circuits using Polynomial Coefficients

A method of testing for parametric faults of analog circuits based on a polynomial representation of fault-free function of the circuit is presented. The response of the circuit under test (CUT) is estimated as a polynomial in the applied input voltage at relevant frequencies in addition to DC. Classification or Cur is based on a comparison of the estimated polynomial coefficients with those of the fault free circuit. This testing method requires no design for test hardware as might be added to the circuit fly some other methods. The proposed method is illustrated for a benchmark elliptic filter. It is shown to uncover several parametric faults causing deviations as small as 5% from the nominal values.

Evaluating the effectiveness of a self-management exercise intervention on wound healing, functional ability and health-related quality of life outcomes in adults with venous leg ulcers: a randomised controlled trial

Exercise that targets ankle joint mobility may lead to improvement in calf muscle pump function and subsequent healing. The objectives of this research were to assess the impact of an exercise intervention in addition to routine evidence-based care on the healing rates, functional ability and health-related quality of life for adults with venous leg ulcers (VLUs). This study included 63 patients with VLUs. Patients were randomised to receive either a 12-week exercise intervention with a telephone coaching component or usual care plus telephone calls at the same timepoints. The primary outcome evaluated the effectiveness of the intervention in relation to wound healing. The secondary outcomes evaluated physical activity, functional ability and health-related quality of life measures between groups at the end of the 12 weeks. A per protocol analysis complemented the effectiveness (intention-to-treat) analysis to highlight the importance of adherence to an exercise intervention. Intention-to-treat analyses for the primary outcome showed 77% of those in the intervention group healed by 12 weeks compared to 53% of those in the usual care group. Although this difference was not statistically significant due to a smaller than expected sample size, a 24% difference in healing rates could be considered clinically significant. The per protocol analysis for wound healing, however, showed that those in the intervention group who adhered to the exercise protocol 75% or more of the time were significantly more likely to heal and showed higher rates for wound healing than the control group (P = 0·01), that is, 95% of those who adhered in the intervention group healed in 12 weeks. The secondary outcomes of physical activity, functional ability and health-related quality of life were not significantly altered by the intervention. Among the secondary outcomes (physical activity, functional ability and health-related quality of life), intention-to-treat analyses did not support the effectiveness of the intervention. However, per protocol analyses revealed encouraging results with those participants who adhered more than 75% of the time (n = 19) showing significantly improved Range of Ankle Motion from the self-management exercise programme (P = 0·045). This study has shown that those participants who adhere to the exercise programme as an adjunctive treatment to standard care are more likely to heal and have better functional outcomes than those who do not adhere to the exercises in conjunction with usual care.

Functional characterization of lysophosphatidic acid phosphatase from Arabidopsis thaliana

Lysophosphatidic acid (LPA) acts as a signaling molecule that regulates diverse cellular processes and it can rapidly be metabolized by phosphatase and acyltransferase LPA phosphatase gene has not been identified and characterized in plants so far The BLAST search revealed that the At3g03520 is similar to phospholipase family. and distantly related to bacterial phosphatases The conserved motif. (J)4XXXNXSFD, was identified in both At3g03520 like phospholipases and acid phosphatases In silico expression analysis of At3g03520 revealed a high expression during phosphate starvation and abiotic stresses. This gene was overexpressed in Escherichia coli and shown to posses LPA specific phosphatase activity These results Suggest that this gene possibly plays a role in signal transduction and storage lipid synthesis.

Evolution of domain combinations in protein kinases and its implications for functional diversity

Protein kinases phosphorylating Ser/Thr/Tyr residues in several cellular proteins exert tight control over their biological functions. They constitute the largest protein family in most eukaryotic species. Protein kinases classified based on sequence similarity in their catalytic domains, cluster into subfamilies, which share gross functional properties. Many protein kinases are associated or tethered covalently to domains that serve as adapter or regulatory modules,naiding substrate recruitment, specificity, and also serve as scaffolds. Hence the modular organisation of the protein kinases serves as guidelines to their functional and molecular properties. Analysis of genomic repertoires of protein kinases in eukaryotes have revealed wide spectrum of domain organisation across various subfamilies of kinases. Occurrence of organism-specific novel domain combinations suggests functional diversity achieved by protein kinases in order to regulate variety of biological processes. In addition, domain architecture of protein kinases revealed existence of hybrid protein kinase subfamilies and their emerging roles in the signaling of eukaryotic organisms. In this review we discuss the repertoire of non-kinase domains tethered to multi-domain kinases in the metazoans. Similarities and differences in the domain architectures of protein kinases in these organisms indicate conserved and unique features that are critical to functional specialization. (C) 2009 Elsevier Ltd. All rights reserved.

Enantioselective syntheses of diquinane and (cis, anti, cis)-linear triquinanes

The enantioselective syntheses of diquinane and cis, anti, cis-linear triquinanes, starting from the readily available (S)-campholenaldehyde, employing an intramolecular rhodium carbenoid CH insertion reaction, are described. (C) 2010 Elsevier Ltd. All rights reserved.

Fluorescent resonant excitation energy transfer in linear polyenes

We have studied the dynamics of excitation transfer between two conjugated polyene molecules whose intermolecular separation is comparable to the molecular dimensions. We have employed a correlated electron model that includes both the charge-charge, charge-bond, and bond-bond intermolecular electron repulsion integrals. We have shown that the excitation transfer rate varies as inverse square of donor-acceptor separation R-2 rather than as R-6, suggested by the Foumlrster type of dipolar approximation. Our time-evolution study alsom shows that the orientational dependence on excitation transfer at a fixed short donor-acceptor separation cannot be explained by Foumlrster type of dipolar approximation beyond a certain orientational angle of rotation of an acceptor polyene with respect to the donor polyene. The actual excitation transfer rate beyond a certain orientational angle is faster than the Foumlrster type of dipolar approximation rate. We have also studied the excitation transfer process in a pair of push-pull polyenes for different push-pull strengths. We have seen that, depending on the push-pull strength, excitation transfer could occur to other dipole coupled states. Our study also allows for the excitation energy transfer to optically dark states which are excluded by Foumlrster theory since the one-photon transition intensity to these states (from the ground state) is zero.

Linear transconductor with flipped voltage follower in 130 nm CMOS

This paper presents a modified design method for linear transconductor circuit in 130 nm CMOS technology to improve linearity, robustness against process induced threshold voltage variability and reduce harmonic distortion. Source follower in the adaptively biased differential pair (ABDP) linear transconductor circuit is replaced with flipped voltage follower to improve the efficiency of the tail current source, which is connected to a conventional differential pair. The simulation results show the performance of the modified circuit also has better speed, noise performance and common mode rejection ratio compared to the ABDP circuit.

Existence and approximations of solutions to some fractional order functional integral equations

In this paper we shall study a fractional order functional integral equation. In the first part of the paper, we proved the existence and uniqueness of mile and global solutions in a Banach space. In the second part of the paper, we used the analytic semigroups theory oflinear operators and the fixed point method to establish the existence, uniqueness and convergence of approximate solutions of the given problem in a separable Hilbert space. We also proved the existence and convergence of Faedo-Galerkin approximate solution to the given problem. Finally, we give an example.