Random Surfing Without Teleportation

In the standard Random Surfer Model, the teleportation matrix is necessary to ensure that the final PageRank vector is well-defined. The introduction of this matrix, however, results in serious problems and imposes fundamental limitations to the quality of the ranking vectors. In this work, building on the recently proposed NCDawareRank framework, we exploit the decomposition of the underlying space into blocks, and we derive easy to check necessary and sufficient conditions for random surfing without teleportation.Comment: 13 pages. Published in the Volume: "Algorithms, Probability, Networks and Games, Springer-Verlag, 2015". (The updated version corrects small typos/errors

Correlative multi-scale imaging of shales: A review and future perspectives

As the fastest growing energy sector globally, shale and shale reservoirs have attracted the attention of both industry and scholars. However, the strong heterogeneity at different scales and the extremely fine-grained nature of shales makes macroscopic and microscopic characterization highly challenging. Recent advances in imaging techniques have provided many novel characterization opportunities of shale components and microstructures at multiple scales. Correlative imaging, where multiple techniques are combined, is playing an increasingly important role in the imaging and quantification of shale microstructures (e.g. one can combine optical microscopy, scanning electron microscopy/transmission electron microscopy and X-ray radiography in 2D, or X-ray computed tomography and electron microscopy in 3D). Combined utilization of these techniques can characterize the heterogeneity of shale microstructures over a large range of scales, from macroscale to nanoscale (c. 100-10-9 m). Other chemical and physical measurements can be correlated to imaging techniques to provide complementary information for minerals, organic matter and pores. These imaging techniques and subsequent quantification methods are critically reviewed to provide an overview of the correlative imaging workflow. Applications of the above techniques for imaging particular features in different shales are demonstrated, and key limitations and benefits summarized. Current challenges and future perspectives in shale imaging techniques and their applications are discussed

XBorne 2016: A Brief Introduction

International audienceWe present the new version of XBorne a software tool for the probabilistic modeling with Markov chains. The tool which has been developed initially as a testbed for the algorithmic stochastic comparisons of stochastic matrices and Markov chains, is now a general purpose framework which can be used for the Markovian modelling in education and research

Synchrotron tomographic quantification of strain and fracture during simulated thermal maturation of an organic-rich shale, UK Kimmeridge Clay

Analyzing the development of fracture networks in shale is important to understand both hydrocarbon migration pathways within and from source rocks and the effectiveness of hydraulic stimulation upon shale reservoirs. Here we use time‐resolved synchrotron X‐ray tomography to quantify in four dimensions (3‐D plus time) the development of fractures during the accelerated maturation of an organic‐rich mudstone (the UK Kimmeridge Clay), with the aim of determining the nature and timing of crack initiation. Electron microscopy (EM, both scanning backscattered and energy dispersive) was used to correlatively characterize the microstructure of the sample preheating and postheating. The tomographic data were analyzed by using digital volume correlation (DVC) to measure the three‐dimensional displacements between subsequent time/heating steps allowing the strain fields surrounding each crack to be calculated, enabling crack opening modes to be determined. Quantification of the strain eigenvectors just before crack propagation suggests that the main mode driving crack initiation is the opening displacement perpendicular to the bedding, mode I. Further, detailed investigation of the DVC measured strain evolution revealed the complex interaction of the laminar clay matrix and the maximum principal strain on incipient crack nucleation. Full field DVC also allowed accurate calculation of the coefficients of thermal expansion (8 × 10−5/°C perpendicular and 6.2 × 10−5/°C parallel to the bedding plane). These results demonstrate how correlative imaging (using synchrotron tomography, DVC, and EM) can be used to elucidate the influence of shale microstructure on its anisotropic mechanical behavior

Analysis of finite-buffer state-dependent bulk queues

<p>In this paper, we consider a general state-dependent finite-buffer bulk queue in which the rates and batch sizes of arrivals and services are allowed to depend on the number of customers in queue and service batch sizes. Such queueing systems have rich applications in manufacturing, service operations, computer and telecommunication systems. Interesting examples include batch oven processes in the aircraft and semiconductor industry; serving of passengers by elevators, shuttle buses, and ferries; and congestion control mechanisms to regulate transmission rates in packet-switched communication networks. We develop a unifying method to study the performance of this general class of finite-buffer state-dependent bulk queueing systems. For this purpose, we use semi-regenerative analysis to develop a numerically stable method for calculating the limiting probability distribution of the queue length process. Based on the limiting probabilities, we present various performance measures for evaluating admission control and batch service policies, such as the loss probability for an arriving group of customers and for individual customers within a group. We demonstrate our method by means of numerical examples.</p>

SHARPIN Negatively Associates with TRAF2-Mediated NFκB Activation

NFκB is an inducible transcriptional factor controlled by two principal signaling cascades and plays pivotal roles in diverse physiological processes including inflammation, apoptosis, oncogenesis, immunity, and development. Activation of NFκB signaling was detected in skin of SHAPRIN-deficient mice and can be diminished by an NFκB inhibitor. However, in vitro studies demonstrated that SHARPIN activates NFκB signaling by forming a linear ubiquitin chain assembly complex with RNF31 (HOIP) and RBCK1 (HOIL1). The inconsistency between in vivo and in vitro findings about SHARPIN's function on NFκB activation could be partially due to SHARPIN's potential interactions with downstream molecules of NFκB pathway. In this study, 17 anti-flag immunoprecipitated proteins, including TRAF2, were identified by mass spectrum analysis among Sharpin-Flag transfected mouse fibroblasts, B lymphocytes, and BALB/c LN stroma 12 cells suggesting their interaction with SHARPIN. Interaction between SHARPIN and TRAF2 confirmed previous yeast two hybridization reports that SHARPIN was one TRAF2's partners. Furthermore, luciferase-based NFκB reporter assays demonstrated that SHARPIN negatively associates with NFκB activation, which can be partly compensated by over-expression of TRAF2. These data suggested that other than activating NFκB signaling by forming ubiquitin ligase complex with RNF31 and RBCK1, SHARPIN may also negatively associate with NFκB activation via interactions with other NFκB members, such as TRAF2

Bifidobacterium Infantis 35624 Protects Against Salmonella-Induced Reductions in Digestive Enzyme Activity in Mice by Attenuation of the Host Inflammatory Response

OBJECTIVES: Salmonella-induced damage to the small intestine may decrease the villi-associated enzyme activity, causing malabsorption of nutrients and diarrhea, and thus contribute to the symptoms of infection. The objective of this study was to determine the mechanism by which different doses and durations of Salmonella infection and lipopolysaccharide (LPS) affect brush border enzyme activity in the mouse, and to determine if the probiotic Bifidobacterium longum subspecies infantis 35624 could attenuate the intestinal damage. METHODS: BALB/c mice were challenged with Salmonella enterica serovar Typhimurium UK1 at various doses (10(2)-10(8) colony-forming unit (CFU)) and durations (10(6) CFU for 1-6 days). Mice were also treated with B. longum subsp. infantis 35624 for 2 weeks before and during a 6-day S. Typhimurium challenge (10(6) CFU), or before injection of LPS. The small intestine was assessed for morphological changes, mRNA expression of cytokines, and activity of the brush border enzymes sucrase-isomaltase, maltase, and alkaline phosphatase. RESULTS: S. Typhimurium infection significantly reduced the activity of all brush border enzymes in a dose- and time-dependent manner (P<0.05). This also occurred following injection of LPS. Pre-treatment with B. longum subsp. infantis 35624 prevented weight loss, protected brush border enzyme activity, reduced the small intestinal damage, and inhibited the increase in interleukin (IL)-10 and IL-8 expression due to Salmonella challenge. CONCLUSIONS: Salmonella infection reduces the small intestinal brush border enzyme activity in mice, with the level of reduction and associated weight loss increasing with dose and duration of infection. B. longum subsp. infantis 35624 treatment attenuated the effect of Salmonella infection on brush border enzyme activity and weight loss, which may be due to modulation of the host immune response

Identification of Rice Transcription Factors Associated with Drought Tolerance Using the Ecotilling Method

The drought tolerance (DT) of plants is a complex quantitative trait. Under natural and artificial selection, drought tolerance represents the crop survival ability and production capacity under drought conditions (Luo, 2010). To understand the regulation mechanism of varied drought tolerance among rice genotypes, 95 diverse rice landraces or varieties were evaluated within a field screen facility based on the ‘line–source soil moisture gradient’, and their resistance varied from extremely resistant to sensitive. The method of Ecotype Targeting Induced Local Lesions in Genomes (Ecotilling) was used to analyze the diversity in the promoters of 24 transcription factor families. The bands separated by electrophoresis using Ecotilling were converted into molecular markers. STRUCTURE analysis revealed a value of K = 2, namely, the population with two subgroups (i.e., indica and japonica), which coincided very well with the UPGMA clusters (NTSYS-pc software) using distance-based analysis and InDel markers. Then the association analysis between the promoter diversity of these transcription factors and the DT index/level of each variety was performed. The results showed that three genes were associated with the DT index and that five genes were associated with the DT level. The sequences of these associated genes are complex and variable, especially at approximately 1000 bp upstream of the transcription initiation sites. The study illuminated that association analysis aimed at Ecotilling diversity of natural groups could facilitate the isolation of rice genes related to complex quantitative traits

EMT Inducers Catalyze Malignant Transformation of Mammary Epithelial Cells and Drive Tumorigenesis towards Claudin-Low Tumors in Transgenic Mice

The epithelial-mesenchymal transition (EMT) is an embryonic transdifferentiation process consisting of conversion of polarized epithelial cells to motile mesenchymal ones. EMT–inducing transcription factors are aberrantly expressed in multiple tumor types and are known to favor the metastatic dissemination process. Supporting oncogenic activity within primary lesions, the TWIST and ZEB proteins can prevent cells from undergoing oncogene-induced senescence and apoptosis by abolishing both p53- and RB-dependent pathways. Here we show that they also downregulate PP2A phosphatase activity and efficiently cooperate with an oncogenic version of H-RAS in malignant transformation of human mammary epithelial cells. Thus, by down-regulating crucial tumor suppressor functions, EMT inducers make cells particularly prone to malignant conversion. Importantly, by analyzing transformed cells generated in vitro and by characterizing novel transgenic mouse models, we further demonstrate that cooperation between an EMT inducer and an active form of RAS is sufficient to trigger transformation of mammary epithelial cells into malignant cells exhibiting all the characteristic features of claudin-low tumors, including low expression of tight and adherens junction genes, EMT traits, and stem cell–like characteristics. Claudin-low tumors are believed to be the most primitive breast malignancies, having arisen through transformation of an early epithelial precursor with inherent stemness properties and metaplastic features. Challenging this prevailing view, we propose that these aggressive tumors arise from cells committed to luminal differentiation, through a process driven by EMT inducers and combining malignant transformation and transdifferentiation