Direct CP violation in radiative b decays in and beyond the Standard Model

We consider the partial rate asymmetry in the inclusive decay modes b to s gamma and b to d gamma, concentrating on non-standard models with new charged Higgs interactions. We find that the charged Higgs contribution to the asymmetry for b to s gamma is small in such models due to a universal cancellation mechanism. The asymmetry is therefore difficult to distinguish experimentally from the Standard Model (SM) value, which is also small. The cancellation mechanism is found to be rendered inoperative in supersymmetry due to the presence of chargino loops. Unlike b to s gamma, the rate asymmetry for b to d gamma in Higgs models can be quite different from its SM value, generally ranging from -20% to +20%. Specific model calculations are performed for the Three-Higgs Doublet Model and the ``Top'' Two-Higgs Doublet Model to serve as illustrations. We also offer some suggestions that may be helpful to experimentalists in the detection of the inclusive mode b to d gamma.Comment: RevTex, 24 pages, 6 figures, minor changes, version to appear in PR

Applying advanced data analytics and machine learning to enhance the safety control of dams

The protection of critical engineering infrastructures is vital to today’s so- ciety, not only to ensure the maintenance of their services (e.g., water supply, energy production, transport), but also to avoid large-scale disasters. Therefore, technical and financial efforts are being continuously made to improve the safety control of large civil engineering structures like dams, bridges and nuclear facilities. This con- trol is based on the measurement of physical quantities that characterize the struc- tural behavior, such as displacements, strains and stresses. The analysis of monitor- ing data and its evaluation against physical and mathematical models is the strongest tool to assess the safety of the structural behavior. Commonly, dam specialists use multiple linear regression models to analyze the dam response, which is a well- known approach among dam engineers since the 1950s decade. Nowadays, the data acquisition paradigm is changing from a manual process, where measurements were taken with low frequency (e.g., on a weekly basis), to a fully automated process that allows much higher frequencies. This new paradigm escalates the potential of data analytics on top of monitoring data, but, on the other hand, increases data quality issues related to anomalies in the acquisition process. This chapter presents the full data lifecycle in the safety control of large-scale civil engineering infrastructures (focused on dams), from the data acquisition process, data processing and storage, data quality and outlier detection, and data analysis. A strong focus is made on the use of machine learning techniques for data analysis, where the common multiple linear regression analysis is compared with deep learning strategies, namely recur- rent neural networks. Demonstration scenarios are presented based on data obtained from monitoring systems of concrete dams under operation in Portugal.info:eu-repo/semantics/acceptedVersio

Single Molecule Conformational Memory Extraction: P5ab RNA Hairpin

Extracting kinetic models from single molecule data is an important route to mechanistic insight in biophysics, chemistry, and biology. Data collected from force spectroscopy can probe discrete hops of a single molecule between different conformational states. Model extraction from such data is a challenging inverse problem because single molecule data are noisy and rich in structure. Standard modeling methods normally assume (i) a prespecified number of discrete states and (ii) that transitions between states are Markovian. The data set is then fit to this predetermined model to find a handful of rates describing the transitions between states. We show that it is unnecessary to assume either (i) or (ii) and focus our analysis on the zipping/unzipping transitions of an RNA hairpin. The key is in starting with a very broad class of non-Markov models in order to let the data guide us toward the best model from this very broad class. Our method suggests that there exists a folding intermediate for the P5ab RNA hairpin whose zipping/unzipping is monitored by force spectroscopy experiments. This intermediate would not have been resolved if a Markov model had been assumed from the onset. We compare the merits of our method with those of others

Stress Affects a Gastrin-Releasing Peptide System in the Spinal Cord That Mediates Sexual Function: Implications for Psychogenic Erectile Dysfunction

Many men suffering from stress, including post-traumatic stress disorder (PTSD), report sexual dysfunction, which is traditionally treated via psychological counseling. Recently, we identified a gastrin-releasing peptide (GRP) system in the lumbar spinal cord that is a primary mediator for male reproductive functions.To ask whether an acute severe stress could alter the male specific GRP system, we used a single-prolonged stress (SPS), a putative rat model for PTSD in the present study. Exposure of SPS to male rats decreases both the local content and axonal distribution of GRP in the lower lumbar spinal cord and results in an attenuation of penile reflexes in vivo. Remarkably, pharmacological stimulation of GRP receptors restores penile reflexes in SPS-exposed males, and induces spontaneous ejaculation in a dose-dependent manner. Furthermore, although the level of plasma testosterone is normal 7 days after SPS exposure, we found a significant decrease in the expression of androgen receptor protein in this spinal center.We conclude that the spinal GRP system appears to be a stress-vulnerable center for male reproductive functions, which may provide new insight into a clinical target for the treatment of erectile dysfunction triggered by stress and psychiatric disorders

Differentiating Protein-Coding and Noncoding RNA: Challenges and Ambiguities

The assumption that RNA can be readily classified into either protein-coding or non-protein–coding categories has pervaded biology for close to 50 years. Until recently, discrimination between these two categories was relatively straightforward: most transcripts were clearly identifiable as protein-coding messenger RNAs (mRNAs), and readily distinguished from the small number of well-characterized non-protein–coding RNAs (ncRNAs), such as transfer, ribosomal, and spliceosomal RNAs. Recent genome-wide studies have revealed the existence of thousands of noncoding transcripts, whose function and significance are unclear. The discovery of this hidden transcriptome and the implicit challenge it presents to our understanding of the expression and regulation of genetic information has made the need to distinguish between mRNAs and ncRNAs both more pressing and more complicated. In this Review, we consider the diverse strategies employed to discriminate between protein-coding and noncoding transcripts and the fundamental difficulties that are inherent in what may superficially appear to be a simple problem. Misannotations can also run in both directions: some ncRNAs may actually encode peptides, and some of those currently thought to do so may not. Moreover, recent studies have shown that some RNAs can function both as mRNAs and intrinsically as functional ncRNAs, which may be a relatively widespread phenomenon. We conclude that it is difficult to annotate an RNA unequivocally as protein-coding or noncoding, with overlapping protein-coding and noncoding transcripts further confounding this distinction. In addition, the finding that some transcripts can function both intrinsically at the RNA level and to encode proteins suggests a false dichotomy between mRNAs and ncRNAs. Therefore, the functionality of any transcript at the RNA level should not be discounted

Epidemiology and risk factors for Staphylococcus aureus colonization in children in the post-PCV7 era

<p>Abstract</p> <p>Background</p> <p>The incidence of community-associated methicillin-resistant <it>Staphylococcus aureus </it>(MRSA) has risen dramatically in the U.S., particularly among children. Although <it>Streptococcus pneumoniae </it>colonization has been inversely associated with <it>S. aureus </it>colonization in unvaccinated children, this and other risk factors for <it>S. aureus </it>carriage have not been assessed following widespread use of the heptavalent pneumococcal conjugate vaccine (PCV7). Our objectives were to (1) determine the prevalence of <it>S. aureus </it>and MRSA colonization in young children in the context of widespread use of PCV7; and (2) examine risk factors for <it>S. aureus </it>colonization in the post-PCV7 era, including the absence of vaccine-type <it>S. pneumoniae </it>colonization.</p> <p>Methods</p> <p>Swabs of the anterior nares (<it>S. aureus</it>) were obtained from children enrolled in an ongoing study of nasopharyngeal pneumococcal colonization of healthy children in 8 Massachusetts communities. Children 3 months to <7 years of age seen for well child or sick visits in primary care offices from 11/03–4/04 and 10/06–4/07 were enrolled. <it>S. aureus </it>was identified and antibiotic susceptibility testing was performed. Epidemiologic risk factors for <it>S. aureus </it>colonization were collected from parent surveys and chart reviews, along with data on pneumococcal colonization. Multivariate mixed model analyses were performed to identify factors associated with <it>S. aureus </it>colonization.</p> <p>Results</p> <p>Among 1,968 children, the mean age (SD) was 2.7 (1.8) years, 32% received an antibiotic in the past 2 months, 2% were colonized with PCV7 strains and 24% were colonized with non-PCV7 strains. The prevalence of <it>S. aureus </it>colonization remained stable between 2003–04 and 2006–07 (14.6% vs. 14.1%), while MRSA colonization remained low (0.2% vs. 0.9%, p = 0.09). Although absence of pneumococcal colonization was not significantly associated with <it>S. aureus </it>colonization, age (6–11 mo vs. ≥5 yrs, OR 0.39 [95% CI 0.24–0.64]; 1–1.99 yrs vs. ≥5 yrs, OR 0.35 [0.23–0.54]; 2–2.99 yrs vs. ≥5 yrs, OR 0.45 [0.28–0.73]; 3–3.99 yrs vs. ≥5 yrs, OR 0.53 [0.33–0.86]) and recent antibiotic use were significant predictors in multivariate models.</p> <p>Conclusion</p> <p>In Massachusetts, <it>S. aureus </it>and MRSA colonization remained stable from 2003–04 to 2006–07 among children <7 years despite widespread use of pneumococcal conjugate vaccine. <it>S. aureus </it>nasal colonization varies by age and is inversely correlated with recent antibiotic use.</p

Whole-body tissue stabilization and selective extractions via tissue-hydrogel hybrids for high-resolution intact circuit mapping and phenotyping

To facilitate fine-scale phenotyping of whole specimens, we describe here a set of tissue fixation-embedding, detergent-clearing and staining protocols that can be used to transform excised organs and whole organisms into optically transparent samples within 1–2 weeks without compromising their cellular architecture or endogenous fluorescence. PACT (passive CLARITY technique) and PARS (perfusion-assisted agent release in situ) use tissue-hydrogel hybrids to stabilize tissue biomolecules during selective lipid extraction, resulting in enhanced clearing efficiency and sample integrity. Furthermore, the macromolecule permeability of PACT- and PARS-processed tissue hybrids supports the diffusion of immunolabels throughout intact tissue, whereas RIMS (refractive index matching solution) grants high-resolution imaging at depth by further reducing light scattering in cleared and uncleared samples alike. These methods are adaptable to difficult-to-image tissues, such as bone (PACT-deCAL), and to magnified single-cell visualization (ePACT). Together, these protocols and solutions enable phenotyping of subcellular components and tracing cellular connectivity in intact biological networks

Rasd1 Modulates the Coactivator Function of NonO in the Cyclic AMP Pathway

All living organisms exhibit autonomous daily physiological and behavioural rhythms to help them synchronize with the environment. Entrainment of circadian rhythm is achieved via activation of cyclic AMP (cAMP) and mitogen-activated protein kinase signaling pathways. NonO (p54nrb) is a multifunctional protein involved in transcriptional activation of the cAMP pathway and is involved in circadian rhythm control. Rasd1 is a monomeric G protein implicated to play a pivotal role in potentiating both photic and nonphotic responses of the circadian rhythm. In this study, we have identified and validated NonO as an interacting partner of Rasd1 via affinity pulldown, co-immunoprecipitation and indirect immunofluorescence studies. The GTP-hydrolysis activity of Rasd1 is required for the functional interaction. Functional interaction of Rasd1-NonO in the cAMP pathway was investigated via reporter gene assays, chromatin immunoprecipitation and gene knockdown. We showed that Rasd1 and NonO interact at the CRE-site of specific target genes. These findings reveal a novel mechanism by which the coregulator activity of NonO can be modulated