Quantum Optical Systems for the Implementation of Quantum Information Processing

We review the field of Quantum Optical Information from elementary considerations through to quantum computation schemes. We illustrate our discussion with descriptions of experimental demonstrations of key communication and processing tasks from the last decade and also look forward to the key results likely in the next decade. We examine both discrete (single photon) type processing as well as those which employ continuous variable manipulations. The mathematical formalism is kept to the minimum needed to understand the key theoretical and experimental results

Differential Trends in the Codon Usage Patterns in HIV-1 Genes

Host-pathogen interactions underlie one of the most complex evolutionary phenomena resulting in continual adaptive genetic changes, where pathogens exploit the host's molecular resources for growth and survival, while hosts try to eliminate the pathogen. Deciphering the molecular basis of host–pathogen interactions is useful in understanding the factors governing pathogen evolution and disease propagation. In host-pathogen context, a balance between mutation, selection, and genetic drift is known to maintain codon bias in both organisms. Studies revealing determinants of the bias and its dynamics are central to the understanding of host-pathogen evolution. We considered the Human Immunodeficiency Virus (HIV) type 1 and its human host to search for evolutionary signatures in the viral genome. Positive selection is known to dominate intra-host evolution of HIV-1, whereas high genetic variability underlies the belief that neutral processes drive inter-host differences. In this study, we analyze the codon usage patterns of HIV-1 genomes across all subtypes and clades sequenced over a period of 23 years. We show presence of unique temporal correlations in the codon bias of three HIV-1 genes illustrating differential adaptation of the HIV-1 genes towards the host preferred codons. Our results point towards gene-specific translational selection to be an important force driving the evolution of HIV-1 at the population level

Gene expression clines reveal local adaptation and associated trade-offs at a continental scale

Local adaptation, where fitness in one environment comes at a cost in another, should lead to spatial variation in trade-offs between life history traits and may be critical for population persistence. Recent studies have sought genomic signals of local adaptation, but often have been limited to laboratory populations representing two environmentally different locations of a species' distribution. We measured gene expression, as a proxy for fitness, in males of Drosophila subobscura, occupying a 20° latitudinal and 11 °C thermal range. Uniquely, we sampled six populations and studied both common garden and semi-natural responses to identify signals of local adaptation. We found contrasting patterns of investment: transcripts with expression positively correlated to latitude were enriched for metabolic processes, expressed across all tissues whereas negatively correlated transcripts were enriched for reproductive processes, expressed primarily in testes. When using only the end populations, to compare our results to previous studies, we found that locally adaptive patterns were obscured. While phenotypic trade-offs between metabolic and reproductive functions across widespread species are well-known, our results identify underlying genetic and tissue responses at a continental scale that may be responsible for this. This may contribute to understanding population persistence under environmental change

Incremental grouping of image elements in vision

One important task for the visual system is to group image elements that belong to an object and to segregate them from other objects and the background. We here present an incremental grouping theory (IGT) that addresses the role of object-based attention in perceptual grouping at a psychological level and, at the same time, outlines the mechanisms for grouping at the neurophysiological level. The IGT proposes that there are two processes for perceptual grouping. The first process is base grouping and relies on neurons that are tuned to feature conjunctions. Base grouping is fast and occurs in parallel across the visual scene, but not all possible feature conjunctions can be coded as base groupings. If there are no neurons tuned to the relevant feature conjunctions, a second process called incremental grouping comes into play. Incremental grouping is a time-consuming and capacity-limited process that requires the gradual spread of enhanced neuronal activity across the representation of an object in the visual cortex. The spread of enhanced neuronal activity corresponds to the labeling of image elements with object-based attention

The Flux-Line Lattice in Superconductors

Magnetic flux can penetrate a type-II superconductor in form of Abrikosov vortices. These tend to arrange in a triangular flux-line lattice (FLL) which is more or less perturbed by material inhomogeneities that pin the flux lines, and in high-$T_c$ supercon- ductors (HTSC's) also by thermal fluctuations. Many properties of the FLL are well described by the phenomenological Ginzburg-Landau theory or by the electromagnetic London theory, which treats the vortex core as a singularity. In Nb alloys and HTSC's the FLL is very soft mainly because of the large magnetic penetration depth: The shear modulus of the FLL is thus small and the tilt modulus is dispersive and becomes very small for short distortion wavelength. This softness of the FLL is enhanced further by the pronounced anisotropy and layered structure of HTSC's, which strongly increases the penetration depth for currents along the c-axis of these uniaxial crystals and may even cause a decoupling of two-dimensional vortex lattices in the Cu-O layers. Thermal fluctuations and softening may melt the FLL and cause thermally activated depinning of the flux lines or of the 2D pancake vortices in the layers. Various phase transitions are predicted for the FLL in layered HTSC's. The linear and nonlinear magnetic response of HTSC's gives rise to interesting effects which strongly depend on the geometry of the experiment.Comment: Review paper for Rep.Prog.Phys., 124 narrow pages. The 30 figures do not exist as postscript file

Comparison of hemolytic activity of the intermediate subunit of Entamoeba histolytica and Entamoeba dispar lectins

Galactose and N-acetyl-D-galactosamine-inhibitable lectin of Entamoeba histolytica has roles in pathogenicity and induction of protective immunity in rodent models of amoebiasis. Recently, the intermediate subunit of the lectin, Igl1, of E. histolytica has been shown to have hemolytic activity. However, the corresponding lectin is also expressed in a non-virulent species, Entamoeba dispar, and another subunit, Igl2, is expressed in the protozoa. Therefore, in this study, we compared the activities of Igl1 and Igl2 subunits from E. histolytica and E. dispar using various regions of recombinant Igl proteins expressed in Escherichia coli. The recombinant E. dispar Igl proteins had comparable hemolytic activities with those of E. histolytica Igl proteins. Furthermore, Igl1 gene-silenced E. histolytica trophozoites showed less hemolytic activity compared with vector-transfected trophozoites, indicating that the expression level of Igl1 protein influences the activity. These results suggest that the lower hemolytic activity in E. dispar compared with E. histolytica reflects the lower expression level of Igl1 in the E. dispar parasite