Making Classical Ground State Spin Computing Fault-Tolerant

We examine a model of classical deterministic computing in which the ground state of the classical system is a spatial history of the computation. This model is relevant to quantum dot cellular automata as well as to recent universal adiabatic quantum computing constructions. In its most primitive form, systems constructed in this model cannot compute in an error free manner when working at non-zero temperature. However, by exploiting a mapping between the partition function for this model and probabilistic classical circuits we are able to show that it is possible to make this model effectively error free. We achieve this by using techniques in fault-tolerant classical computing and the result is that the system can compute effectively error free if the temperature is below a critical temperature. We further link this model to computational complexity and show that a certain problem concerning finite temperature classical spin systems is complete for the complexity class Merlin-Arthur. This provides an interesting connection between the physical behavior of certain many-body spin systems and computational complexity.Comment: 24 pages, 1 figur

The traditional, the ideal and the unexplored: sport coaches’ social identity constructs in film

The sport coaching construct within mainstream fiction films has been described as stereotypical, reinforcing the traditional notion of the sport coach as a technician who conquers all, or a hapless individual, open to ridicule from athletes and fans. Although this depiction is also prevalent in some independent fiction films and documentaries, film sub genres such as social realism and “fly on the wall” style documentaries move away from the “Hollywood sports film structure” towards stories that focus on everyday coaching moments. Through a critical discourse analysis of two U.K. films (Bend it Like Beckham and Twenty Four Seven), both featuring sport coaches in central roles, we reflect critically on these mass media multidimensional representations in terms of the sport coaching professionalisation agenda in the U.K. and the social identification process of sport coaches within their sporting environments. Keywords: Sport coaching, film, social identification, professionalisation, coaching roles

Data Publication with the Structural Biology Data Grid Supports Live Analysis

Access to experimental X-ray diffraction image data is fundamental for validation and reproduction of macromolecular models and indispensable for development of structural biology processing methods. Here, we established a diffraction data publication and dissemination system, Structural Biology Data Grid (SBDG; data.sbgrid.org), to preserve primary experimental data sets that support scientific publications. Data sets are accessible to researchers through a community driven data grid, which facilitates global data access. Our analysis of a pilot collection of crystallographic data sets demonstrates that the information archived by SBDG is sufficient to reprocess data to statistics that meet or exceed the quality of the original published structures. SBDG has extended its services to the entire community and is used to develop support for other types of biomedical data sets. It is anticipated that access to the experimental data sets will enhance the paradigm shift in the community towards a much more dynamic body of continuously improving data analysis

Data Publication with the Structural Biology Data Grid Supports Live Analysis

Access to experimental X-ray diffraction image data is fundamental for validation and reproduction of macromolecular models and indispensable for development of structural biology processing methods. Here, we established a diffraction data publication and dissemination system, Structural Biology Data Grid (SBDG; data.sbgrid.org), to preserve primary experimental data sets that support scientific publications. Data sets are accessible to researchers through a community driven data grid, which facilitates global data access. Our analysis of a pilot collection of crystallographic data sets demonstrates that the information archived by SBDG is sufficient to reprocess data to statistics that meet or exceed the quality of the original published structures. SBDG has extended its services to the entire community and is used to develop support for other types of biomedical data sets. It is anticipated that access to the experimental data sets will enhance the paradigm shift in the community towards a much more dynamic body of continuously improving data analysis

Verification of model simulated mass balance, flow fields and tabular calving events of the Antarctic ice sheet against remotely sensed observations

The Antarctic ice sheet (AIS) has the greatestpotential for global sea level rise. This study simulates AISice creeping, sliding, tabular calving, and estimates the totalmass balances, using a recently developed, advanced icedynamics model, known as SEGMENT-Ice. SEGMENTIceis written in a spherical Earth coordinate system.Because the AIS contains the South Pole, a projectiontransfer is performed to displace the pole outside of thesimulation domain. The AIS also has complex ice-watergranularmaterial-bedrock configurations, requiringsophisticated lateral and basal boundary conditions.Because of the prevalence of ice shelves, a ‘girder yield’type calving scheme is activated. The simulations of presentsurface ice flow velocities compare favorably with InSARmeasurements, for various ice-water-bedrock configurations.The estimated ice mass loss rate during 2003–2009agrees with GRACE measurements and provides morespatial details not represented by the latter. The modelestimated calving frequencies of the peripheral ice shelvesfrom 1996 (roughly when the 5-km digital elevation andthickness data for the shelves were collected) to 2009compare well with archived scatterometer images. SEGMENT-Ice’s unique, non-local systematic calving schemeis found to be relevant for tabular calving. However, theexact timing of calving and of iceberg sizes cannot besimulated accurately at present. A projection of the futuremass change of the AIS is made, with SEGMENT-Iceforced by atmospheric conditions from three differentcoupled general circulation models. The entire AIS is estimatedto be losing mass steadily at a rate of*120 km3/a atpresent and this rate possibly may double by year 2100

Genetic and Computational Identification of a Conserved Bacterial Metabolic Module

We have experimentally and computationally defined a set of genes that form a conserved metabolic module in the α-proteobacterium Caulobacter crescentus and used this module to illustrate a schema for the propagation of pathway-level annotation across bacterial genera. Applying comprehensive forward and reverse genetic methods and genome-wide transcriptional analysis, we (1) confirmed the presence of genes involved in catabolism of the abundant environmental sugar myo-inositol, (2) defined an operon encoding an ABC-family myo-inositol transmembrane transporter, and (3) identified a novel myo-inositol regulator protein and cis-acting regulatory motif that control expression of genes in this metabolic module. Despite being encoded from non-contiguous loci on the C. crescentus chromosome, these myo-inositol catabolic enzymes and transporter proteins form a tightly linked functional group in a computationally inferred network of protein associations. Primary sequence comparison was not sufficient to confidently extend annotation of all components of this novel metabolic module to related bacterial genera. Consequently, we implemented the Graemlin multiple-network alignment algorithm to generate cross-species predictions of genes involved in myo-inositol transport and catabolism in other α-proteobacteria. Although the chromosomal organization of genes in this functional module varied between species, the upstream regions of genes in this aligned network were enriched for the same palindromic cis-regulatory motif identified experimentally in C. crescentus. Transposon disruption of the operon encoding the computationally predicted ABC myo-inositol transporter of Sinorhizobium meliloti abolished growth on myo-inositol as the sole carbon source, confirming our cross-genera functional prediction. Thus, we have defined regulatory, transport, and catabolic genes and a cis-acting regulatory sequence that form a conserved module required for myo-inositol metabolism in select α-proteobacteria. Moreover, this study describes a forward validation of gene-network alignment, and illustrates a strategy for reliably transferring pathway-level annotation across bacterial species

A Genetically Encoded Tag for Correlated Light and Electron Microscopy of Intact Cells, Tissues, and Organisms

Electron microscopy (EM) achieves the highest spatial resolution in protein localization, but specific protein EM labeling has lacked generally applicable genetically encoded tags for in situ visualization in cells and tissues. Here we introduce “miniSOG” (for mini Singlet Oxygen Generator), a fluorescent flavoprotein engineered from Arabidopsis phototropin 2. MiniSOG contains 106 amino acids, less than half the size of Green Fluorescent Protein. Illumination of miniSOG generates sufficient singlet oxygen to locally catalyze the polymerization of diaminobenzidine into an osmiophilic reaction product resolvable by EM. MiniSOG fusions to many well-characterized proteins localize correctly in mammalian cells, intact nematodes, and rodents, enabling correlated fluorescence and EM from large volumes of tissue after strong aldehyde fixation, without the need for exogenous ligands, probes, or destructive permeabilizing detergents. MiniSOG permits high quality ultrastructural preservation and 3-dimensional protein localization via electron tomography or serial section block face scanning electron microscopy. EM shows that miniSOG-tagged SynCAM1 is presynaptic in cultured cortical neurons, whereas miniSOG-tagged SynCAM2 is postsynaptic in culture and in intact mice. Thus SynCAM1 and SynCAM2 could be heterophilic partners. MiniSOG may do for EM what Green Fluorescent Protein did for fluorescence microscopy

Blue and Red Light Modulates SigB-Dependent Gene Transcription, Swimming Motility and Invasiveness in Listeria monocytogenes

Background: In a number of gram-positive bacteria, including Listeria, the general stress response is regulated by the alternative sigma factor B (SigB). Common stressors which lead to the activation of SigB and the SigB-dependent regulon are high osmolarity, acid and several more. Recently is has been shown that also blue and red light activates SigB in Bacillus subtilis. Methodology/Principal Findings: By qRT-PCR we analyzed the transcriptional response of the pathogen L. monocytogenes to blue and red light in wild type bacteria and in isogenic deletion mutants for the putative blue-light receptor Lmo0799 and the stress sigma factor SigB. It was found that both blue (455 nm) and red (625 nm) light induced the transcription of sigB and SigB-dependent genes, this induction was completely abolished in the SigB mutant. The blue-light effect was largely dependent on Lmo0799, proving that this protein is a genuine blue-light receptor. The deletion of lmo0799 enhanced the red-light effect, the underlying mechanism as well as that of SigB activation by red light remains unknown. Blue light led to an increased transcription of the internalin A/B genes and of bacterial invasiveness for Caco-2 enterocytes. Exposure to blue light also strongly inhibited swimming motility of the bacteria in a Lmo0799- and SigB-dependent manner, red light had no effect there. Conclusions/Significance: Our data established that visible, in particular blue light is an important environmental signal with an impact on gene expression and physiology of the non-phototrophic bacterium L. monocytogenes. In natural environments these effects will result in sometimes random but potentially also cyclic fluctuations of gene activity, depending on the light conditions prevailing in the respective habitat