A novel multiplex PCR system for the detection of virulence associated genes of E. coli O157:H7 from food system

In view of the importance E. coli serotype 0157:H7 in human diseases, an easy and quick system is desirable to detect toxin producing strains. In this report, we describe standardization of a novel multiplex Polymerase Chain Reaction (mPCR) assay for simultaneous detection of four important genes associated with the organism E. coli 0157:H7 viz., stx 1, stx 2, eae A, hly A along with an internal amplification control (IAC). The mPCR method developed in the present study is sensitive enough to detect cells as low as 103 CFU ml-1 or g-1 of the food samples. The E. coli 0157:H7 strains having been identified to contain the gene in the mPCR were unequivocally detected positive for the serological and conventional culture method.  As E. coli 0157:H7 is qualified as biowarfare agent; this mPCR system is of immense help in detecting them during emergencies of biological war and suspected outbreaks.&nbsp

Equivariant map superalgebras

Suppose a group $\Gamma$ acts on a scheme $X$ and a Lie superalgebra $\mathfrak{g}$. The corresponding equivariant map superalgebra is the Lie superalgebra of equivariant regular maps from $X$ to $\mathfrak{g}$. We classify the irreducible finite dimensional modules for these superalgebras under the assumptions that the coordinate ring of $X$ is finitely generated, $\Gamma$ is finite abelian and acts freely on the rational points of $X$, and $\mathfrak{g}$ is a basic classical Lie superalgebra (or $\mathfrak{sl}(n,n)$, $n > 0$, if $\Gamma$ is trivial). We show that they are all (tensor products of) generalized evaluation modules and are parameterized by a certain set of equivariant finitely supported maps defined on $X$. Furthermore, in the case that the even part of $\mathfrak{g}$ is semisimple, we show that all such modules are in fact (tensor products of) evaluation modules. On the other hand, if the even part of $\mathfrak{g}$ is not semisimple (more generally, if $\mathfrak{g}$ is of type I), we introduce a natural generalization of Kac modules and show that all irreducible finite dimensional modules are quotients of these. As a special case, our results give the first classification of the irreducible finite dimensional modules for twisted loop superalgebras.Comment: 27 pages. v2: Section numbering changed to match published version. Other minor corrections. v3: Minor corrections (see change log at end of introduction

Quantifying through-space charge transfer dynamics in \u3c0-coupled molecular systems

understanding the role of intermolecular interaction on through-space charge transfer characteristics in \u3c0-stacked molecular systems is central to the rational design of electronic materials. However, a quantitative study of charge transfer in such systems is often difficult because of poor control over molecular morphology. Here we use the core-hole clock implementation of resonant photoemission spectroscopy to study the femtosecond chargetransfer dynamics in cyclophanes, which consist of two precisely stacked \u3c0-systems held together by aliphatic chains. We study two systems, [2,2]paracyclophane (22PCP) and [4,4]paracyclophane (44PCP), with inter-ring separations of 3.0 and 4.0 \uc5, respectively. We find that charge transfer across the \u3c0-coupled system of 44PCP is 20 times slower than in 22PCP. We attribute this difference to the decreased inter-ring electronic coupling in 44PCP. These measurements illustrate the use of core-hole clock spectroscopy as a general tool for quantifying through-space coupling in \u3c0-stacked systems

Screening, isolation, and decolonisation strategies in the control of meticillin resistant Staphylococcus aureus in intensive care units: cost effectiveness evaluation

Objective To assess the cost effectiveness of screening, isolation, and decolonisation strategies in the control of meticillin resistant Staphylococcus aureus (MRSA) in intensive care units

An Entropy-Based Method with a New Benchmark Dataset for Chinese Textual Affective Structure Analysis

Affective understanding of language is an important research focus in artificial intelligence. The large-scale annotated datasets of Chinese textual affective structure (CTAS) are the foundation for subsequent higher-level analysis of documents. However, there are very few published datasets for CTAS. This paper introduces a new benchmark dataset for the task of CTAS to promote development in this research direction. Specifically, our benchmark is a CTAS dataset with the following advantages: (a) it is Weibo-based, which is the most popular Chinese social media platform used by the public to express their opinions; (b) it includes the most comprehensive affective structure labels at present; and (c) we propose a maximum entropy Markov model that incorporates neural network features and experimentally demonstrate that it outperforms the two baseline models.</jats:p

Energy analysis of chemistry for correct insertion by DNA polymerase beta

X-ray crystallographic structures of human DNA polymerase β with nonhydrolyzable analogs containing all atoms in the active site required for catalysis provide a secure starting point for a theoretical analysis (quantum mechanics/molecular mechanics) of the mechanism of chemistry without biasing of modeling assumptions as required in previous studies. These structures provide the basis for a detailed quantum mechanics/molecular mechanics study of the path for the complete transfer of a monophosphate nucleoside donor to the sugar acceptor in the active site. The reaction is largely associative with the main energetic step preceded by proton transfer from the terminal primer deoxyribose O3′ to Asp-256. The key residues that provide electrostatic stabilization of the transition state are identified and compared with those identified by mutational studies

Influence of Nanoparticle Size and Shape on Oligomer Formation of an Amyloidogenic Peptide

Understanding the influence of macromolecular crowding and nanoparticles on the formation of in-register $\beta$-sheets, the primary structural component of amyloid fibrils, is a first step towards describing \emph{in vivo} protein aggregation and interactions between synthetic materials and proteins. Using all atom molecular simulations in implicit solvent we illustrate the effects of nanoparticle size, shape, and volume fraction on oligomer formation of an amyloidogenic peptide from the transthyretin protein. Surprisingly, we find that inert spherical crowding particles destabilize in-register $\beta$-sheets formed by dimers while stabilizing $\beta$-sheets comprised of trimers and tetramers. As the radius of the nanoparticle increases crowding effects decrease, implying smaller crowding particles have the largest influence on the earliest amyloid species. We explain these results using a theory based on the depletion effect. Finally, we show that spherocylindrical crowders destabilize the ordered $\beta$-sheet dimer to a greater extent than spherical crowders, which underscores the influence of nanoparticle shape on protein aggregation

A Plasma Biomarker Panel of Four MicroRNAs for the Diagnosis of Prostate Cancer

© 2018 The Author(s). Prostate cancer is diagnosed in over 1 million men every year globally, yet current diagnostic modalities are inadequate for identification of significant cancer and more reliable early diagnostic biomarkers are necessary for improved clinical management of prostate cancer patients. MicroRNAs (miRNAs) modulate important cellular processes/pathways contributing to cancer and are stably present in body fluids. In this study we profiled 372 cancer-associated miRNAs in plasma collected before (∼60% patients) and after/during commencement of treatment (∼40% patients), from age-matched prostate cancer patients and healthy controls, and observed elevated levels of 4 miRNAs - miR-4289, miR-326, miR-152-3p and miR-98-5p, which were validated in an independent cohort. The miRNA panel was able to differentiate between prostate cancer patients and controls (AUC = 0.88). Analysis of published miRNA transcriptomic data from clinical samples demonstrated low expression of miR-152-3p in tumour compared to adjacent non-malignant tissues. Overexpression of miR-152-3p increased proliferation and migration of prostate cancer cells, suggesting a role for this miRNA in prostate cancer pathogenesis, a concept that was supported by pathway analysis of predicted miR-152-3p target genes. In summary, a four miRNA panel, including miR-152-3p which likely targets genes with key roles in prostate cancer pathogenesis, has the potential to improve early prostate cancer diagnosis

Slabs of stabilized jellium: Quantum-size and self-compression effects

We examine thin films of two simple metals (aluminum and lithium) in the stabilized jellium model, a modification of the regular jellium model in which a constant potential is added inside the metal to stabilize the system for a given background density. We investigate quantum-size effects on the surface energy and the work function. For a given film thickness we also evaluate the density yielding energy stability, which is found to be slightly higher than the equilibrium density of the bulk system and to approach this value in the limit of thick slabs. A comparison of our self-consistent calculations with the predictions of the liquid-drop model shows the validity of this model.Comment: 7 pages, 6 figures, to appear in Phys. Rev.