Detection of recombination in DNA multiple alignments with hidden markov models

CConventional phylogenetic tree estimation methods assume that all sites in a DNA multiple alignment have the same evolutionary history. This assumption is violated in data sets from certain bacteria and viruses due to recombination, a process that leads to the creation of mosaic sequences from different strains and, if undetected, causes systematic errors in phylogenetic tree estimation. In the current work, a hidden Markov model (HMM) is employed to detect recombination events in multiple alignments of DNA sequences. The emission probabilities in a given state are determined by the branching order (topology) and the branch lengths of the respective phylogenetic tree, while the transition probabilities depend on the global recombination probability. The present study improves on an earlier heuristic parameter optimization scheme and shows how the branch lengths and the recombination probability can be optimized in a maximum likelihood sense by applying the expectation maximization (EM) algorithm. The novel algorithm is tested on a synthetic benchmark problem and is found to clearly outperform the earlier heuristic approach. The paper concludes with an application of this scheme to a DNA sequence alignment of the argF gene from four Neisseria strains, where a likely recombination event is clearly detected

Optical computing: introduction by the feature editors

This feature of Applied Optics: Information Processing on optical computing comprises thirty papers. Most of the papers evolved from papers presented at the Fifth Topical Meeting on Optical Computing held in March 1993 in Palm Springs, California

Generalized surface current method in the macroscopic theory of diffraction radiation

The surface current method known in the theory of electromagnetic waves diffraction is generalized to be applied for the problems of diffraction radiation generated by a charged particle moving nearby an ideally-conducting screen in vacuum. An expression for induced surface current density leading to the exact results in the theory of transition radiation is derived, and by using this expression several exact solutions of diffraction radiation problems are found. Limits of applicability for the earlier known models based on the surface current conception are indicated. Properties of radiation from a semi-plane and from a slit in cylinder are investigated at the various distances to observer.Comment: 8 pages, 8 figure

Parental depression and child well-being: Young children's self-reports helped addressing biases in parent reports

Objectives Effects of maternal and paternal depression on child development are typically evaluated using parental reports of child problems. Yet, parental reports may be biased. Methods In a population-based cohort, parents reported lifetime depression (N = 3,178) and depressive symptoms (N = 3,131). Child emotional and behavioral problems were assessed at age 6 years by child self-report using the Berkeley Puppet Interview, by mother report using the Child Behavior Checklist (CBCL), and at age 3 years by father and mother reported CBCLs. Results Both maternal and paternal depression was associated with more child problems. Associations were of similar strength if child problems were obtained by self-reports. However, if parents reported about their own depression or depressive symptoms and about their child's problems, estimates were generally stronger for associations with the reporting parent's depression as the determinant. For instance, if mothers reported child emotional problems, associations were stronger for maternal (B = 0.27; 95% confidence interval (CI) = 0.19, 0.35) than for paternal lifetime depression (B = 0.12; 95% CI = 0.02, 0.21; P-value for difference = 0.02). Conclusion Depression of mothers and fathers affects young children's well-being. However, if parents reported about their own depression and about child problems, associations were inflated. To accurately estimate effects of parental depression, multiple-source data including young children's perspectives must be considered

Gauge Theory on Fuzzy S^2 x S^2 and Regularization on Noncommutative R^4

We define U(n) gauge theory on fuzzy S^2_N x S^2_N as a multi-matrix model, which reduces to ordinary Yang-Mills theory on S^2 x S^2 in the commutative limit N -> infinity. The model can be used as a regularization of gauge theory on noncommutative R^4_\theta in a particular scaling limit, which is studied in detail. We also find topologically non-trivial U(1) solutions, which reduce to the known "fluxon" solutions in the limit of R^4_\theta, reproducing their full moduli space. Other solutions which can be interpreted as 2-dimensional branes are also found. The quantization of the model is defined non-perturbatively in terms of a path integral which is finite. A gauge-fixed BRST-invariant action is given as well. Fermions in the fundamental representation of the gauge group are included using a formulation based on SO(6), by defining a fuzzy Dirac operator which reduces to the standard Dirac operator on S^2 x S^2 in the commutative limit. The chirality operator and Weyl spinors are also introduced.Comment: 39 pages. V2-4: References added, typos fixe

A study of randomness, correlations and collectivity in the nuclear shell model

A variable combination of realistic and random two-body interactions allows the study of collective properties, such as the energy spectra and B(E2) transition strengths in 44Ti, 48Cr and 24Mg. It is found that the average energies of the yrast band states maintain the ordering for any degree of randomness, but the B(E2) values lose their quadrupole collectivity when randomness dominates the Hamiltonian. The high probability of the yrast band to be ordered in the presence of pure random forces exhibits the strong correlations between the different members of the band.Comment: 8 pages, 10 figures, 8 tables, submitted to Physical Review

Advances in silicon phased-array receiver IC's

Phased-Arrays are increasingly used, and require Silicon implementations to result in affordable multi-beam systems. In this paper, CMOS implementations of two novel analogue beamforming multi-channel receivers will be presented. A narrow-band highly linear system exploiting switches and capacitors in advanced CMOS is presented, implementing a fully passive switched capacitor vector modulator exploiting a zero-IF I/Q mixer: This technique is not applicable to very wideband phased-array receivers. These systems require true-time delay beamforming, which is implemented in the second CMOS implementation. An innovative gm-RC implementation of a true-time delay cell is exploited in a four-channel beamforming receiver with more than L.5 GHz bandwidth, in a standard 0.13 um CMOS process. Professional phased-arrays can often not live with the dynamic range limitations imposed by these implementations. To that end a SiGe implementation of an integrated receiver was realized targeting a digital beamforming phased-array. Dynamic range and flexibility of use were the main driving factors. Alltogether, these results show large progress with respect to the feasibility of Silicon-based phased-array front-end implementation for commercial as well as professional phased-arrays. © 2012 IEEE

Miniaturizing the laparoscope: Current applications of micro‐ and minilaparoscopy

Technological advancements have enabled miniaturization of the endoscope without significant compromise to either diagnostic or operative abilities. With a complement of instruments < 5 mm in diameter, newer minimally invasive techniques have been developed to decrease the pain and trauma associated with surgical procedures. These advancements involve additional options for peritoneal access as well as facilitating diagnostic evaluation of the pelvis. Although the robustness and durability of the smaller instruments is an area of concern, a thorough understanding of the clinical advantages and disadvantages has the potential to improve patient outcomes.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/135513/1/ijgo94.pd

Exploring the relation of harsh parental discipline with child emotional and behavioral problems by using multiple informants. The generation R study

Parental harsh disciplining, like corporal punishment, has consistently been associated with adverse mental health outcomes in children. It remains a challenge to accurately assess the consequences of harsh discipline, as researchers and clinicians generally rely on parent report of young children's problem behaviors. If parents rate their parenting styles and their child's behavior this may bias results. The use of child self-report on problem behaviors is not common but may provide extra information about the relation of harsh parental discipline and problem behavior. We examined the independent contribution of young children's self-report above parental report of emotional and behavioral problems in a study of maternal and paternal harsh discipline in a birth cohort. Maternal and paternal harsh discipline predicted both parent reported behavioral and parent reported emotional problems, but only child reported behavioral problems. Associations were not explained by pre-existing behavioral problems at age 3. Importantly, the association with child reported outcomes was independent from parent reported problem behavior. These results suggest that young children's s