Evolutionary footprint of coevolving positions in genes

Motivation: The analysis of molecular coevolution provides information on the potential functional and structural implication of positions along DNA sequences, and several methods are available to identify coevolving positions using probabilistic or combinatorial approaches. The specific nucleotide or amino acid profile associated with the coevolution process is, however, not estimated, but only known profiles, such as the Watson-Crick constraint, are usually considered a priori in current measures of coevolution. Results: Here, we propose a new probabilistic model, Coev, to identify coevolving positions and their associated profile in DNA sequences while incorporating the underlying phylogenetic relationships. The process of coevolution is modeled by a 16 × 16 instantaneous rate matrix that includes rates of transition as well as a profile of coevolution. We used simulated, empirical and illustrative data to evaluate our model and to compare it with a model of ‘independent' evolution using Akaike Information Criterion. We showed that the Coev model is able to discriminate between coevolving and non-coevolving positions and provides better specificity and specificity than other available approaches. We further demonstrate that the identification of the profile of coevolution can shed new light on the process of dependent substitution during lineage evolution. Availability: http://www2.unil.ch/phylo/bioinformatics/coev Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics onlin

A comprehensive theoretical and experimental study of coplanar waveguide shunt stubs

A comprehensive theoretical and experimental study of straight and bent coplanar waveguide (CPW) shunt stubs is presented. In the theoretical analysis, the CPW is assumed to be inside a cavity, while, the experiments are performed on open structures. A hybrid technique was developed to analyze the CPW discontinuities which proved to be accurate since the theoretical and experimental results agree very well. The effect of the cavity resonances on the behavior of the stubs with and without air-bridges is investigated. In addition, the encountered radiation loss due to the discontinuities is evaluated experimentally

A Novel Transition Between Rectangular Waveguide and Layered Ridge Dielectric Waveguide

A novel transition between rectangular waveguide and layered ridge dielectric waveguide (LRDW) is reported. The transition is also suitable for use with image guide, insulated image guide, dielectric ridge waveguide and other open dielectric waveguides. Both experimental and theoretical data are presented which compare the new transition to three transitions reported in the literature

Broadband Uniplanar Microstrip to Slot-Line Transitions

New in line uniplanar microstrip-to-slotline transitions for MIC/MMIC and phased array slotline antenna applications are described. Such transactions are compact and suitable to be used in an open environment or inside a package or a multichip module. The transitions share the concept of using a balun which consists of two microstrip lines connected to a slotline through a pair of coupled microstrips. The transitions are studied theoretically using the finite difference time domain (FDTD) technique and measured experimentally using an HP8510C Network Analyzer. For a back-to-back configuration, an insertion loss of less than 1.3 dB per transition is achieved over a 40% 3-dB bandwidth with a minimum of 0.6 dB at the design frequency

A theoretical and experimental study of coplanar waveguide shunt stubs

A comprehensive theoretical and experimental study of straight and bent coplanar waveguide (CPW) shunt stubs is presented. In the theoretical analysis, the CPW is assumed to be inside a cavity while, the experiments are performed on open structures. For the analysis of CPW discontinuities with air-bridges, a hybrid technique was developed which was validated through extensive theoretical and experimental comparisons. The effect of the cavity resonances on the behavior of the stubs with and without air-bridges is investigated. In addition, the encountered radiation loss due to the discontinuities is evaluated experimentally

Coplanar stripline components for high frequency application

In this paper, coplanar stripline discontinuities such as a slit, a right angle bend and a T-junction are characterized and their performance is parameterized with respect to frequency and geometry. Lumped equivalent circuits are presented for some of them. The element values are obtained from the measured discontinuity scattering (S) parameters. The experimental results are compared with theoretical data obtained using the Finite Difference Time Domain (FD-TD) technique for validation and show very good agreement

Selection on the Major Color Gene Melanocortin-1-Receptor Shaped the Evolution of the Melanocortin System Genes.

Modular genetic systems and networks have complex evolutionary histories shaped by selection acting on single genes as well as on their integrated function within the network. However, uncovering molecular coevolution requires the detection of coevolving sites in sequences. Detailed knowledge of the functions of each gene in the system is also necessary to identify the selective agents driving coevolution. Using recently developed computational tools, we investigated the effect of positive selection on the coevolution of ten major genes in the melanocortin system, responsible for multiple physiological functions and human diseases. Substitutions driven by positive selection at the melanocortin-1-receptor (MC1R) induced more coevolutionary changes on the system than positive selection on other genes in the system. Contrarily, selection on the highly pleiotropic POMC gene, which orchestrates the activation of the different melanocortin receptors, had the lowest coevolutionary influence. MC1R and possibly its main function, melanin pigmentation, seems to have influenced the evolution of the melanocortin system more than functions regulated by MC2-5Rs such as energy homeostasis, glucocorticoid-dependent stress and anti-inflammatory responses. Although replication in other regulatory systems is needed, this suggests that single functional aspects of a genetic network or system can be of higher importance than others in shaping coevolution among the genes that integrate it

Theoretical and Experimental Study of Microstrip-to-Slot Line Uniplanar Transition

Recent advances in MMCI technology make it possible to construct transitions from CPW-to-microstrip with via hole, microstrip-to-slot line and microshield line-to-CPW all of which have potential applications in the feed network of antennas. In this study we investigate the characteristics of the microstrip-to-slot line uniplanar transition using the finite element methods (FEM) and finite difference time domain (FDTD) techniques, and compared the theoretical results with the measurements. In both cases, the results agree with the measurements within a few percent

Consensus definition and diagnostic criteria for neonatal encephalopathy-study protocol for a real-time modified delphi study

BACKGROUND: 'Neonatal encephalopathy' (NE) describes a group of conditions in term infants presenting in the earliest days after birth with disturbed neurological function of cerebral origin. NE is aetiologically heterogenous; one cause is peripartum hypoxic ischaemia. Lack of uniformity in the terminology used to describe NE and its diagnostic criteria creates difficulty in the design and interpretation of research and complicates communication with families. The DEFINE study aims to use a modified Delphi approach to form a consensus definition for NE, and diagnostic criteria.METHODS: Directed by an international steering group, we will conduct a systematic review of the literature to assess the terminology used in trials of NE, and with their guidance perform an online Real-time Delphi survey to develop a consensus diagnosis and criteria for NE. A consensus meeting will be held to agree on the final terminology and criteria, and the outcome disseminated widely.DISCUSSION: A clear and consistent consensus-based definition of NE and criteria for its diagnosis, achieved by use of a modified Delphi technique, will enable more comparability of research results and improved communication among professionals and with families.IMPACT: The terms Neonatal Encephalopathy and Hypoxic Ischaemic Encephalopathy tend to be used interchangeably in the literature to describe a term newborn with signs of encephalopathy at birth. This creates difficulty in communication with families and carers, and between medical professionals and researchers, as well as creating difficulty with performance of research. The DEFINE project will use a Real-time Delphi approach to create a consensus definition for the term 'Neonatal Encephalopathy'. A definition formed by this consensus approach will be accepted and utilised by the neonatal community to improve research, outcomes, and parental experience.</p