Semistochastic Quadratic Bound Methods

Partition functions arise in a variety of settings, including conditional random fields, logistic regression, and latent gaussian models. In this paper, we consider semistochastic quadratic bound (SQB) methods for maximum likelihood inference based on partition function optimization. Batch methods based on the quadratic bound were recently proposed for this class of problems, and performed favorably in comparison to state-of-the-art techniques. Semistochastic methods fall in between batch algorithms, which use all the data, and stochastic gradient type methods, which use small random selections at each iteration. We build semistochastic quadratic bound-based methods, and prove both global convergence (to a stationary point) under very weak assumptions, and linear convergence rate under stronger assumptions on the objective. To make the proposed methods faster and more stable, we consider inexact subproblem minimization and batch-size selection schemes. The efficacy of SQB methods is demonstrated via comparison with several state-of-the-art techniques on commonly used datasets.Comment: 11 pages, 1 figur

Management of moisture-associated skin damage : a scoping review

BACKGROUND: Protecting the skin against moisture-associated damage is an important component of comprehensive skin and wound care. Based on a review of literature, the authors propose key interventions to protect and prevent damage in the skin folds, perineum, and areas surrounding a wound or stoma. OBJECTIVE: The aim of this scoping review is to identify and provide a narrative integration of the existing evidence related to the management and prevention of moisture-associated skin damage (MASD). METHODS: Study authors searched several databases for a broad spectrum of published and unpublished studies in English, published between 2000 and July 2015. Selected study information was collated in several different formats; ultimately, key findings were aggregated into a thematic description of the evidence to help generate a set of summative statements or recommendations. RESULTS: Based on inclusion criteria, 37 articles were considered appropriate for this review. Findings included functional definitions and prevalence rates of the 4 types of MASD, assessment scales for each, and 7 evidence-based strategies for the management of MASD. CONCLUSIONS: Based on this scoping review of literature, the authors propose key interventions to protect and prevent MASD including the use of barrier ointments, liquid polymers, and cyanoacrylates to create a protective layer that simultaneously maintains hydration levels while blocking external moisture and irritants

Structural and functional analysis of SleL, a peptidoglycan lysin involved in germination of Bacillus spores.

A major event in the germination of Bacillus spores concerns hydrolysis of the cortical peptidoglycan that surrounds the spore protoplast, the integrity of which is essential for maintenance of dormancy. Cortex degradation is initiated in all species of Bacillus spores by the combined activity of two semi-redundant cortex-lytic enzymes, SleB and CwlJ. A third enzyme, SleL, which has N-acetylglucosaminidase activity, cleaves peptidoglycan fragments generated by SleB and CwlJ. Here we present crystal structures of B. cereus and B. megaterium SleL at 1.6 angstroms and 1.7 angstroms, respectively. The structures were determined with a view to identifying the structural basis of differences in catalytic efficiency between the respective enzymes. The catalytic (α/β)8 -barrel cores of both enzymes are highly conserved from a structural perspective, including the spatial distribution of the catalytic residues. Both enzymes are equipped with two N-terminal peptidoglycan-binding LysM domains, which are also structurally highly conserved. However, the topological arrangement of the respective enzymes second LysM domain is markedly different, and this may account for differences in catalytic rates by impacting upon the position of the active sites with respect to their substrates. A chimeric enzyme comprising the B. megaterium SleL catalytic domain plus B. cereus SleL LysM domains displayed enzymatic activity comparable to the native B. cereus protein, exemplifying the importance of the LysM domains to SleL function. Similarly, the reciprocal construct, comprising the B. cereus SleL catalytic domain with B. megaterium SleL LysM domains, showed reduced activity compared with native B. cereus SleL.The crystallographic experiments were performed in the Crystallographic X7ray Facility (CXF) at the Department of Biochemistry, University of Cambridge. DYC was supported by CXF.This is the author accepted manuscript. The final version is available from Wiley via http://dx.doi.org/10.1002/prot.2486

Crystal structure of the PepSY-containing domain of the YpeB protein involved in germination of bacillus spores.

The crystal structure of the C-terminal domain of the Bacillus megaterium YpeB protein has been solved by X-ray crystallography to 1.80-Å resolution. The full-length protein is essential in stabilising the SleB cortex lytic enzyme in Bacillus spores, and may have a role in regulating SleB activity during spore germination. The YpeB-C crystal structure comprises three tandemly repeated PepSY domains, which are aligned to form an extended laterally compressed molecule. A predominantly positively charged region located in the second PepSY domain may provide a site for protein interactions that are important in stabilising SleB and YpeB within the spore.The author acknowledges support from various sources including the new lecturers' start up funding from Cambridge University and a donation from the Government Decontamination Service.This is the author accepted manuscript. The final version is available from Wiley via http://dx.doi.org/10.1002/prot.2486

Comparison of Nitrogen Oxide Metabolism among Diverse Ammonia-Oxidizing Bacteria

Ammonia-oxidizing bacteria (AOB) have well characterized genes that encode and express nitrite reductases (NIR) and nitric oxide reductases (NOR). However, the connection between presence or absence of these and other genes for nitrogen transformations with the physiological production of nitric oxide (NO) and nitrous oxide (N2O) has not been tested across AOB isolated from various trophic states, with diverse phylogeny, and with closed genomes. It is therefore unclear if genomic content for nitrogen oxide metabolism is predictive of net N2O production. Instantaneous microrespirometry experiments were utilized to measure NO and N2O emitted by AOB during active oxidation of ammonia (NH3) or hydroxylamine (NH2OH) and through a period of anoxia. This data was used in concert with genomic content and phylogeny to assess whether taxonomic factors were predictive of nitrogen oxide metabolism. Results showed that two oligotrophic AOB strains lacking annotated NOR-encoding genes released large quantities of NO and produced N2O abiologically at the onset of anoxia following NH3-oxidation. Furthermore, high concentrations of N2O were measured during active O2-dependent NH2OH oxidation by the two oligotrophic AOB in contrast to non-oligotrophic strains that only produced N2O at the onset of anoxia. Therefore, complete nitrifier denitrification did not occur in the two oligotrophic strains, but did occur in meso- and eutrophic strains, even in Nitrosomonas communis Nm2 that lacks an annotated NIR-encoding gene. Regardless of mechanism, all AOB strains produced measureable N2O under tested conditions. This work further confirms that AOB require NOR activity to enzymatically reduce NO to N2O in the nitrifier denitrification pathway, and also that abiotic reactions play an important role in N2O formation, in oligotrophic AOB lacking NOR activity

N=2 SU Quiver with USP Ends or SU Ends with Antisymmetric Matter

We consider the four dimensional scale invariant N=2 SU quiver gauge theories with USp(2N) ends or SU(2N) ends with antisymmetric matter representations. We argue that these theories are realized as six dimensional A_{2N-1} (0,2) theories compactified on spheres with punctures. With this realization, we can study various strongly coupled cusps in moduli space and find the S-dual theories. We find a class of isolated superconformal field theories with only odd dimensional operators $D(\phi)\geq3$ and superconformal field theories with only even dimensional operators $D(\phi)\geq4$.Comment: Minor changes are made; refrences are added; 21 pages, 18 figure

Conceptual study for a sub-pupil instrument having 4 high order adaptive optics paths for parallel multi-wavelength high contrast imaging, and medium resolution spectrometry

We present the concept of an instrument that will create 4 circular sub-pupils of 3 m in diameter. Each sub-pupil path will be corrected by a high order adaptive optics system (SR~80% in H) without spider and M2 obstruction. These four independent channels, obviously all pointed towards the same field, allows the possibility of covering totally different parts of the electromagnetic spectrum simultaneously without compromising Signal to Noise Ratio. Each channel can be dedicated to very specialized but complementary purposes: high contrast imaging, pseudo-wide field imaging, high precision multi-color photometry, medium-resolution spectroscopy, polarimetry and sparse-aperture masking

In vivo silencing of genes coding for dTip60 chromatin remodeling complex subunits affects polytene chromosome organization and proper development in Drosophila melanogaster

Chromatin organization is developmentally regulated by epigenetic changes mediated by histone‐modifying enzymes and chromatin remodeling complexes. In Drosophila melanogaster, the Tip60 chromatin remodeling complex (dTip60) play roles in chromatin regulation, which are shared by evolutionarily‐related complexes identified in animal and plants. Recently, it was found that most subunits previously assigned to the dTip60 complex are shared by two related complexes, DOM‐A.C and DOM‐B.C, defined by DOM‐A and DOM‐B isoforms, respectively. In this work, we combined classical genetics, cell biology, and reverse genetics approaches to further investigate the biological roles played during Drosophila melanogaster development by a number of subunits originally assigned to the dTip60 complex

Group Theory Approach to Band Structure: Scarf and Lame Hamiltonians

The group theoretical treatment of bound and scattering state problems is extended to include band structure. We show that one can realize Hamiltonians with periodic potentials as dynamical symmetries, where representation theory provides analytic solutions, or which can be treated with more general spectrum generating algebraic methods. We find dynamical symmetries for which we derive the transfer matrices and dispersion relations. Both compact and non-compact groups are found to play a role.Comment: 4 pages + 2 figs. Revtex/epsf. To appear: Phys Rev Lett, v.83 199