Poisson Approximation and Connectivity in a Scale-free Random Connection Model

We study an inhomogeneous random connection model in the connectivity regime. The vertex set of the graph is a homogeneous Poisson point process $\mathcal{P}_s$ of intensity $s>0$ on the unit cube $S=\left(-\frac{1}{2},\frac{1}{2}\right]^{d},$ $d \geq 2$ . Each vertex is endowed with an independent random weight distributed as $W$, where $P(W>w)=w^{-\beta}1_{[1,\infty)}(w)$, $\beta>0$. Given the vertex set and the weights an edge exists between $x,y\in \mathcal{P}_s$ with probability $\left(1 - \exp\left( - \frac{\eta W_xW_y}{\left(d(x,y)/r\right)^{\alpha}} \right)\right),$ independent of everything else, where $\eta, \alpha > 0$, $d(\cdot, \cdot)$ is the toroidal metric on $S$ and $r > 0$ is a scaling parameter. We derive conditions on $\alpha, \beta$ such that under the scaling $r_s(\xi)^d= \frac{1}{c_0 s} \left( \log s +(k-1) \log\log s +\xi+\log\left(\frac{\alpha\beta}{k!d} \right)\right),$ $\xi \in \mathbb{R}$, the number of vertices of degree $k$ converges in total variation distance to a Poisson random variable with mean $e^{-\xi}$ as $s \to \infty$, where $c_0$ is an explicitly specified constant that depends on $\alpha, \beta, d$ and $\eta$ but not on $k$. In particular, for $k=0$ we obtain the regime in which the number of isolated nodes stabilizes, a precursor to establishing a threshold for connectivity. We also derive a sufficient condition for the graph to be connected with high probability for large $s$. The Poisson approximation result is derived using the Stein's method.Comment: 21 pages, calculations are simplified significantly and results are proved under much weaker condition

Oxygen-regulated transcription factors and their role in pulmonary disease

The transcription factors nuclear factor interleukin-6 (NF-IL6), early growth response-1 (EGR-1) and hypoxia-inducible factor-1 (HIF-1) have important roles in the molecular pathophysiology of hypoxia-associated pulmonary disease. NF-IL6 controls the production of interleukin (IL)-6 in vascular endothelial cells, which may have anti-inflammatory activity by counteracting effects of IL-1 and IL-8. EGR-1 controls the production of tissue factor by macrophages, which triggers fibrin deposition in the pulmonary vasculature. HIF-1 activates the expression of the vasoconstrictor endothelin-1 in vascular endothelial cells. Angiotensin II induces HIF-1 expression and hypertrophy of pulmonary arterial smooth muscle cells. HIF-1 might therefore have multiple roles in the pathogenesis of pulmonary vascular remodeling

Nasal Carriage and Antimicrobial Susceptibility of Staphylococcus aureus in healthy preschool children in Ujjain, India

<p>Abstract</p> <p>Background</p> <p>There is increasing evidence that community acquired <it>S. aureus </it>infections are spreading among healthy children. Nasal colonization with <it>S. aureus </it>plays pivotal role in the increasing prevalence of resistant community acquired <it>S. aureus </it>infections worldwide. A regular surveillance system is important in ensuring quality of patient care. The aim of the study was to assess the prevalence of and the factors associated with nasal carriage of <it>S. aureus </it>and its antibiotic sensitivity pattern among healthy children in Ujjain, India.</p> <p>Methods</p> <p>A prospective study was done in paediatric outpatient clinics of R.D. Gardi medical college Ujjain, India. Healthy children from 1 month to 59 months of age were included. Information on previously known risk factors for nasal colonization was collected using a pre-tested questionnaire. Swabs from anterior nares were collected and transported in Amies transport media with charcoal and cultured on 5% sheep blood agar. Antibiotic sensitivity tests were performed using Kirby Bauer's disc diffusion method according to performance standards of Clinical and Laboratory Standard Institute guidelines.</p> <p>Results</p> <p>Of the 1,562 children from 1-month up-to five years of age included in the study 98 children tested positive for nasal carriage of <it>S. aureus</it>. The prevalence of nasal carriage of <it>S. aureus </it>was 6.3% (95% CI 5.1-7.5) out of which 16.3% (95% CI 8.9-23.8) were methicillin-resistant <it>S. aureus </it>(MRSA). The factors associated with nasal carriage were "child attending preschool" (OR 4.26, 95% CI 2.25-8.03; <it>P </it>= 0.007) or "school" (OR 3.02, 95% CI 1.27-7.18; <it>P </it>< 0.001) and "family size more than 10 members" (OR 2.76 95% CI 1.06-7.15; <it>P </it>= 0.03). The sensitivity pattern of isolated <it>S. aureus </it>showed resistance to commonly used oral antibiotics while resistance to glycopeptides was not noted.</p> <p>Conclusions</p> <p>We found a relatively low rate of nasal carriage of <it>S. aureus </it>in children below five years when compared to children of older age groups in India. Yet, prevalence of MRSA was relatively high.</p

Social identity, social networks and recovery capital in emerging adulthood: a pilot study

Background It has been argued that recovery from substance dependence relies on a change in identity, with past research focused on ‘personal identity’. This study assessed support for a social identity model of recovery in emerging adults through examining associations between social identity, social networks, recovery capital, and quality of life. Methods Twenty participants aged 18–21 in residential treatment for substance misuse were recruited from four specialist youth drug treatment services - three detoxification facilities and one psychosocial rehabilitation facility in Victoria, Australia. Participants completed a detailed social network interview exploring the substance use of groups in their social networks and measures of quality of life, recovery capital, and social identity. Results Lower group substance use was associated with higher recovery capital, stronger identification with non-using groups, and greater importance of non-using groups in the social network. Additionally, greater identification with and importance of non-using groups were associated with better environmental quality of life, whereas greater importance conferred on using groups was associated with reduced environmental quality of life. Conclusions Support was found for the role of social identity processes in reported recovery capital and quality of life. Future research in larger, longitudinal samples is required to improve understanding of social identity processes during treatment and early recovery and its relationship to recovery stability. Keywords Social network Social identity Emerging adult Substance use Treatment Recovery Quality of lif

pcaGoPromoter - An R Package for Biological and Regulatory Interpretation of Principal Components in Genome-Wide Gene Expression Data

Analyzing data obtained from genome-wide gene expression experiments is challenging due to the quantity of variables, the need for multivariate analyses, and the demands of managing large amounts of data. Here we present the R package pcaGoPromoter, which facilitates the interpretation of genome-wide expression data and overcomes the aforementioned problems. In the first step, principal component analysis (PCA) is applied to survey any differences between experiments and possible groupings. The next step is the interpretation of the principal components with respect to both biological function and regulation by predicted transcription factor binding sites. The robustness of the results is evaluated using cross-validation, and illustrative plots of PCA scores and gene ontology terms are available. pcaGoPromoter works with any platform that uses gene symbols or Entrez IDs as probe identifiers. In addition, support for several popular Affymetrix GeneChip platforms is provided. To illustrate the features of the pcaGoPromoter package a serum stimulation experiment was performed and the genome-wide gene expression in the resulting samples was profiled using the Affymetrix Human Genome U133 Plus 2.0 chip. Array data were analyzed using pcaGoPromoter package tools, resulting in a clear separation of the experiments into three groups: controls, serum only and serum with inhibitor. Functional annotation of the axes in the PCA score plot showed the expected serum-promoted biological processes, e.g., cell cycle progression and the predicted involvement of expected transcription factors, including E2F. In addition, unexpected results, e.g., cholesterol synthesis in serum-depleted cells and NF-κB activation in inhibitor treated cells, were noted. In summary, the pcaGoPromoter R package provides a collection of tools for analyzing gene expression data. These tools give an overview of the input data via PCA, functional interpretation by gene ontology terms (biological processes), and an indication of the involvement of possible transcription factors

Resolving the paradox of shame: differentiating among specific appraisal-feeling combinations explains pro-social and self-defensive motivation

Research has shown that people can respond both self-defensively and pro-socially when they experience shame. We address this paradox by differentiating among specific appraisals (of specific self-defect and concern for condemnation) and feelings (of shame, inferiority, and rejection) often reported as part of shame. In two Experiments (Study 1: N = 85; Study 2: N = 112), manipulations that put participants’ social-image at risk increased their appraisal of concern for condemnation. In Study 2, a manipulation of moral failure increased participants’ appraisal that they suffered a specific self-defect. In both studies, mediation analyses showed that effects of the social-image at risk manipulation on self-defensive motivation were explained by appraisal of concern for condemnation and felt rejection. In contrast, the effect of the moral failure manipulation on pro-social motivation in Study 2 was explained by appraisal of a specific self-defect and felt shame. Thus, distinguishing among the appraisals and feelings tied to shame enabled clearer prediction of pro-social and self-defensive responses to moral failure with and without risk to social-image

Resistance of Leishmania (Viannia) braziliensis to nitric oxide: correlation with antimony therapy and TNF-α production

<p>Abstract</p> <p>Background</p> <p>Nitric oxide (NO) produced in macrophages plays a pivotal role as a leishmanicidal agent. A previous study has demonstrated that 20% of the <it>L. (V.) braziliensis </it>isolated from initial cutaneous lesions of patients from the endemic area of Corte de Pedra, Bahia, Brazil, were NO resistant. Additionally, 5 to 11% of the patients did not respond to three or more antimony treatments" (refractory patients). The aim of this study is to investigate if there is an association between the resistance of <it>L. (V.) braziliensis </it>to NO and nonresponsiveness to antimony therapy and cytokine production.</p> <p>Methods</p> <p>We evaluated the <it>in vitro </it>toxicity of NO against the promastigotes stages of <it>L. (V.) braziliensis </it>isolated from responsive and refractory patients, and the infectivity of the amastigote forms of these isolates against human macrophages. The supernatants from <it>Leishmania </it>infected macrophage were used to measure TNF-α and IL-10 levels.</p> <p>Results</p> <p>Using NaNO₂(pH 5.0) as the NO source, <it>L. (V.) braziliensis </it>isolated from refractory patients were more NO resistant (IC50 = 5.8 ± 4.8) than <it>L. (V.) braziliensis </it>isolated from responsive patients (IC50 = 2.0 ± 1.4). Four isolates were selected to infect human macrophages: NO-susceptible and NO-resistant <it>L. (V.) braziliensis </it>isolated from responsive and refractory patients. NO-resistant <it>L. (V.) braziliensis </it>isolated from refractory patients infected more macrophages stimulated with LPS and IFN-γ at 120 hours than NO-susceptible <it>L. (V.) braziliensis </it>isolated from refractory patients. Also, lower levels of TNF-α were detected in supernatants of macrophages infected with NO-resistant <it>L. (V.) braziliensis </it>as compared to macrophages infected with NO-susceptible <it>L. (V.) braziliensis </it>(p < 0.05 at 2, 24 and 120 hours), while no differences were detected in IL-10 levels.</p> <p>Conclusion</p> <p>These data suggest that NO resistance could be related to the nonresponsiveness to antimony therapy seen in American Tegumentary Leishmaniasis.</p

High Resolution Detection and Analysis of CpG Dinucleotides Methylation Using MBD-Seq Technology

Methyl-CpG binding domain protein sequencing (MBD-seq) is widely used to survey DNA methylation patterns. However, the optimal experimental parameters for MBD-seq remain unclear and the data analysis remains challenging. In this study, we generated high depth MBD-seq data in MCF-7 cell and developed a bi-asymmetric-Laplace model (BALM) to perform data analysis. We found that optimal efficiency of MBD-seq experiments was achieved by sequencing ∼100 million unique mapped tags from a combination of 500 mM and 1000 mM salt concentration elution in MCF-7 cells. Clonal bisulfite sequencing results showed that the methylation status of each CpG dinucleotides in the tested regions was accurately detected with high resolution using the proposed model. These results demonstrated the combination of MBD-seq and BALM could serve as a useful tool to investigate DNA methylome due to its low cost, high specificity, efficiency and resolution