Signature, a web server for taxonomic characterization of sequence samples using signature genes

Signature genes are genes that are unique to a taxonomic clade and are common within it. They contain a wealth of information about clade-specific processes and hold a strong evolutionary signal that can be used to phylogenetically characterize a set of sequences, such as a metagenomics sample. As signature genes are based on gene content, they provide a means to assess the taxonomic origin of a sequence sample that is complementary to sequence-based analyses. Here, we introduce Signature (http://www.cmbi.ru.nl/signature), a web server that identifies the signature genes in a set of query sequences, and therewith phylogenetically characterizes it. The server produces a list of taxonomic clades that share signature genes with the set of query sequences, along with an insightful image of the tree of life, in which the clades are color coded based on the number of signature genes present. This allows the user to quickly see from which part(s) of the taxonomy the query sequences likely originate

Sum rules of codon usage probabilities

In the crystal basis model of the genetic code, it is deduced that the sum of usage probabilities of the codons with C and A in the third position for the quartets and/or sextets is independent of the biological species for vertebrates. A comparison with experimental data shows that the prediction is satisfied within about 5 %.Comment: 7 page

Addition-Deletion Networks

We study structural properties of growing networks where both addition and deletion of nodes are possible. Our model network evolves via two independent processes. With rate r, a node is added to the system and this node links to a randomly selected existing node. With rate 1, a randomly selected node is deleted, and its parent node inherits the links of its immediate descendants. We show that the in-component size distribution decays algebraically, c_k ~ k^{-beta}, as k-->infty. The exponent beta=2+1/(r-1) varies continuously with the addition rate r. Structural properties of the network including the height distribution, the diameter of the network, the average distance between two nodes, and the fraction of dangling nodes are also obtained analytically. Interestingly, the deletion process leads to a giant hub, a single node with a macroscopic degree whereas all other nodes have a microscopic degree.Comment: 8 pages, 5 figure

Fitness landscape of the cellular automata majority problem: View from the Olympus

In this paper we study cellular automata (CAs) that perform the computational Majority task. This task is a good example of what the phenomenon of emergence in complex systems is. We take an interest in the reasons that make this particular fitness landscape a difficult one. The first goal is to study the landscape as such, and thus it is ideally independent from the actual heuristics used to search the space. However, a second goal is to understand the features a good search technique for this particular problem space should possess. We statistically quantify in various ways the degree of difficulty of searching this landscape. Due to neutrality, investigations based on sampling techniques on the whole landscape are difficult to conduct. So, we go exploring the landscape from the top. Although it has been proved that no CA can perform the task perfectly, several efficient CAs for this task have been found. Exploiting similarities between these CAs and symmetries in the landscape, we define the Olympus landscape which is regarded as the ''heavenly home'' of the best local optima known (blok). Then we measure several properties of this subspace. Although it is easier to find relevant CAs in this subspace than in the overall landscape, there are structural reasons that prevent a searcher from finding overfitted CAs in the Olympus. Finally, we study dynamics and performance of genetic algorithms on the Olympus in order to confirm our analysis and to find efficient CAs for the Majority problem with low computational cost

Rank Statistics in Biological Evolution

We present a statistical analysis of biological evolution processes. Specifically, we study the stochastic replication-mutation-death model where the population of a species may grow or shrink by birth or death, respectively, and additionally, mutations lead to the creation of new species. We rank the various species by the chronological order by which they originate. The average population N_k of the kth species decays algebraically with rank, N_k ~ M^{mu} k^{-mu}, where M is the average total population. The characteristic exponent mu=(alpha-gamma)/(alpha+beta-gamma)$ depends on alpha, beta, and gamma, the replication, mutation, and death rates. Furthermore, the average population P_k of all descendants of the kth species has a universal algebraic behavior, P_k ~ M/k.Comment: 4 pages, 3 figure

Optimum power transfer in RF front end systems using adaptive impedance matching technique

Matching the antenna's impedance to the RF-front-end of a wireless communications system is challenging as the impedance varies with its surround environment. Autonomously matching the antenna to the RF-front-end is therefore essential to optimize power transfer and thereby maintain the antenna's radiation efficiency. This paper presents a theoretical technique for automatically tuning an LC impedance matching network that compensates antenna mismatch presented to the RF-front-end. The proposed technique converges to a matching point without the need of complex mathematical modelling of the system comprising of non-linear control elements. Digital circuitry is used to implement the required matching circuit. Reliable convergence is achieved within the tuning range of the LC-network using control-loops that can independently control the LC impedance. An algorithm based on the proposed technique was used to verify its effectiveness with various antenna loads. Mismatch error of the technique is less than 0.2%. The technique enables speedy convergence (<5 s) and is highly accurate for autonomous adaptive antenna matching networks

A comprehensive survey on 'circular polarized antennas' for existing and emerging wireless communication technologies

Circular polarized (CP) antennas are well suited for long-distance transmission attainment. In order to be adaptable for beyond 5G communication, a detailed and systematic investigation of their important conventional features is required for expected enhancements. The existing designs employing millimeter wave, microwave, and ultra-wideband (UWB) frequencies form the elementary platform for future studies. The 3.4-3.8 GHz frequency band has been identified as a worthy candidate for 5G communications because of spectrum availability. This band comes under UWB frequencies (3.1-10.6 GHz). In this survey, a review of CP antennas in the selected areas to improve the understanding of early-stage researchers specially experienced antenna designers has presented for the first time as best of our knowledge. Design implementations involving size, axial ratio, efficiency, and gain improvements are covered in detail. Besides that, various design approaches to realize CP antennas including (a) printed CP antennas based on parasitic or slotted elements, (b) dielectric resonator CP antennas, (c) reconfigurable CP antennas, (d) substrate integrated waveguide CP antennas, (e) fractal CP antennas, (f) hybrid techniques CP antennas, and (g) 3D printing CP antennas with single and multiple feeding structures have investigated and analyzed. The aim of this work is to provide necessary guidance for the selection of CP antenna geometries in terms of the required dimensions, available bandwidth, gain, and useful materials for the integration and realization in future communication systems

A Comprehensive Survey on 'Various Decoupling Mechanisms with Focus on Metamaterial and Metasurface Principles Applicable to SAR and MIMO Antenna Systems'

Nowadays synthetic aperture radar (SAR) and multiple-input-multiple-output (MIMO) antenna systems with the capability to radiate waves in more than one pattern and polarization are playing a key role in modern telecommunication and radar systems. This is possible with the use of antenna arrays as they offer advantages of high gain and beamforming capability, which can be utilized for controlling radiation pattern for electromagnetic (EM) interference immunity in wireless systems. However, with the growing demand for compact array antennas, the physical footprint of the arrays needs to be smaller and the consequent of this is severe degradation in the performance of the array resulting from strong mutual-coupling and crosstalk effects between adjacent radiating elements. This review presents a detailed systematic and theoretical study of various mutual-coupling suppression (decoupling) techniques with a strong focus on metamaterial (MTM) and metasurface (MTS) approaches. While the performance of systems employing antenna arrays can be enhanced by calibrating out the interferences digitally, however it is more efficient to apply decoupling techniques at the antenna itself. Previously various simple and cost-effective approaches have been demonstrated to effectively suppress unwanted mutual-coupling in arrays. Such techniques include the use of defected ground structure (DGS), parasitic or slot element, dielectric resonator antenna (DRA), complementary split-ring resonators (CSRR), decoupling networks, P.I.N or varactor diodes, electromagnetic bandgap (EBG) structures, etc. In this review, it is shown that the mutual-coupling reduction methods inspired By MTM and MTS concepts can provide a higher level of isolation between neighbouring radiating elements using easily realizable and cost-effective decoupling configurations that have negligible consequence on the arrays characteristics such as bandwidth, gain and radiation efficiency, and physical footprint

Metamaterial-inspired antenna array for application in microwave breast imaging systems for tumor detection

This paper presents a study of a planar antenna-array inspired by the metamaterial concept where the resonant elements have sub-wavelength dimensions for application in microwave medical imaging systems for detecting tumors in biological tissues. The proposed antenna consists of square-shaped concentric-rings which are connected to a central patch through a common feedline. The array structure comprises several antennas that are arranged to surround the sample breast model. One antenna at a time in the array is used in transmission-mode while others are in receive-mode. The antenna array operates over 2-12 GHz amply covering the frequency range of existing microwave imaging systems. Measured results show that compared to a standard patch antenna array the proposed array with identical dimensions exhibits an average radiation gain and efficiency improvement of 4.8 dBi and 18%, respectively. The average reflection-coefficient of the array over its operating range is better than S-11 <= -20 dB making it highly receptive to weak signals and minimizing the distortion encountered with the transmission of short duration pulse-trains. Moreover, the proposed antenna-array exhibits high-isolation on average of 30dB between radiators. This means that antennas in the array (i) can be closely spaced to accommodate more radiators to achieve higher-resolution imaging scans, and (ii) the imagining scans can be done over a wider frequency range to ascertain better contrast in electrical parameters between malignant tumor-tissue and the surrounding normal breast-tissue to facilitate the detection of breast-tumor. It is found that short wavelength gives better resolution. In this experimental study a standard biomedical breast model that mimics a real-human breast in terms of dielectric and optical properties was used to demonstrate the viability of the proposed antenna over a standard patch antenna in the detection and the localization of tumor. These results are encouraging for clinical trials and further refinement of the antenna-array

Bandwidth and gain enhancement of composite right left handed metamaterial transmission line planar antenna employing a non foster impedance matching circuit board

The paper demonstrates an effective technique to significantly enhance the bandwidth and radiation gain of an otherwise narrowband composite right/left-handed transmission-line (CRLH-TL) antenna using a non-Foster impedance matching circuit (NF-IMC) without affecting the antenna's stability. This is achieved by using the negative reactance of the NF-IMC to counteract the input capacitance of the antenna. Series capacitance of the CRLH-TL unit-cell is created by etching a dielectric spiral slot inside a rectangular microstrip patch that is grounded through a spiraled microstrip inductance. The overall size of the antenna, including the NF-IMC at its lowest operating frequency is 0.335 lambda (0)x0.137 lambda (0)x0.003 lambda (0), where lambda (0) is the free-space wavelength at 1.4 GHz. The performance of the antenna was verified through actual measurements. The stable bandwidth of the antenna for |S-11|<= -18 dB is greater than 1 GHz (1.4-2.45 GHz), which is significantly wider than the CRLH-TL antenna without the proposed impedance matching circuit. In addition, with the proposed technique the measured radiation gain and efficiency of the antenna are increased on average by 3.2 dBi and 31.5% over the operating frequency band