Miracle-dz/UniFAR-FTUs huggingface dataset:
Tricellular Tight Junction Protein Tricellulin Is Targeted by the Enteropathogenic Escherichia coli Effector EspG1, Leading to Epithelial Barrier Disruption

ABSTRACT Enteropathogenic Escherichia coli (EPEC)-induced diarrhea is often associated with disruption of intestinal epithelial tight junctions. Although studies have shown alterations in the expression and localization of bicellular tight junction proteins during EPEC infections, little is known about whether tricellular tight junction proteins (tTJs) are affected. Using Caco-2 cell monolayers, we investigated if EPEC is capable of targeting the tTJ protein tricellulin. Our results demonstrated that at 4 h postinfection, EPEC induced a significant reduction in tricellulin levels, accompanied by a significant loss of transepithelial resistance (TEER) and a corresponding increase in paracellular permeability. Conversely, cells overexpressing tricellulin were highly resistant to EPEC-induced barrier disruption. Confocal microscopy revealed the distribution of tricellulin into the plasma membrane of infected epithelial cells and confirmed the localization of EPEC aggregates in close proximity to tTJs. Moreover, infections with EPEC strains lacking genes encoding specific type III secreted effector proteins demonstrated a crucial role for the effector EspG1 in modulating tricellulin expression. Complementation studies suggest that the EspG-induced depletion of tricellulin is microtubule dependent. Overall, our results show that EPEC-induced epithelial barrier dysfunction is mediated in part by EspG1-induced microtubule-dependent depletion of tricellulin.
Rethinking Collapsed Variational Bayes Inference for LDA

We propose a novel interpretation of the collapsed variational Bayes inference with a zero-order Taylor expansion approximation, called CVB0 inference, for latent Dirichlet allocation (LDA). We clarify the properties of the CVB0 inference by using the α-divergence. We show that the CVB0 inference is composed of two different divergence projections: α = 1 and -1. This interpretation will help shed light on CVB0 works.
OPTIMIST: A New Conflict Resolution Algorithm for ACT-R

Several studies have suggested recently that a more dynamic conflict resolution mechanism in the ACT–R cognitive architecture (Anderson & Lebiere, 1998) could improve the decision–making behaviour of cognitive models. This part of ACT–R theory is revisited and a new solution is proposed. The new algorithm (OPTIMIST) has been implemented as an overlay to the ACT–R architecture, and can be used as an alternative mechanism. The operation of the new algorithm is tested in a model of the classical Yerkes and Dodson experiment on animals’ learning. When OPTIMIST is used, the resulting model fits the data better than the previous model (e.g. R 2 increases from .85 to .93 in one example).
Strings in flat space and pp waves from N = 4 Super Yang Mills

We explain how the string spectrum in flat space and pp‐waves arises from the large N limit, at fixed gYM2, of U(N) N = 4 super Yang Mills. We reproduce the spectrum by summing a subset of the planar Feynman diagrams. We give a heuristic argument for why we can neglect other diagrams.
Algorithm XXX : Efficient Multiplication of Dense Matrices over GF ( 2 )

We describe an efficient implementation of a hierarchy of algorithms for multiplication of dense matrices over the field with two elements (F2). In particular we present our implementation – in the M4RI library – of Strassen-Winograd matrix multiplication and the “Method of the Four Russians for Multiplication” (M4RM) and compare it against other available implementations. Good performance is demonstrated on AMD’s Opteron processor and particulary good performance on Intel’s Core 2 Duo processor. The open-source M4RI library is available as a stand-alone package as well as part of the Sage mathematics system. In machine terms, addition in F2 is logical-XOR, and multiplication is logical-AND, thus a machine word of 64 bits allows one to operate on 64 elements of F2 in parallel: at most one CPU cycle for 64 parallel additions or multiplications. As such, element-wise operations over F2 are relatively cheap. In fact, in this paper, we conclude that the actual bottlenecks are memory reads and writes and issues of data locality. We present our empirical findings in relation to minimizing these and give an analysis thereof.
The effect of human settlement on the abundance and community structure of ammonia oxidizers in tropical stream sediments

Ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) are a diverse and functionally important group in the nitrogen cycle. Nevertheless, AOA and AOB communities driving this process remain uncharacterized in tropical freshwater sediment. Here, the effect of human settlement on the AOA and AOB diversity and abundance have been assessed by phylogenetic and quantitative PCR analyses, using archaeal and bacterial amoA and 16S rRNA genes. Overall, each environment contained specific clades of amoA and 16S rRNA genes sequences, suggesting that selective pressures lead to AOA and AOB inhabiting distinct ecological niches. Human settlement activities, as derived from increased metal and mineral nitrogen contents, appear to cause a response among the AOB community, with Nitrosomonas taking advantage over Nitrosospira in impacted environments. We also observed a dominance of AOB over AOA in mining-impacted sediments, suggesting that AOB might be the primary drivers of ammonia oxidation in these sediments. In addition, ammonia concentrations demonstrated to be the driver for the abundance of AOA, with an inversely proportional correlation between them. Our findings also revealed the presence of novel ecotypes of Thaumarchaeota, such as those related to the obligate acidophilic Nitrosotalea devanaterra at ammonia-rich places of circumneutral pH. These data add significant new information regarding AOA and AOB from tropical freshwater sediments, albeit future studies would be required to provide additional insights into the niche differentiation among these microorganisms.
The Cost of Equity of Internet Stocks: A Downside Risk Approach

Beta as a measure of risk has been under fire for many years. Although practitioners still widely use the CAPM to estimate the cost of equity of companies, they are aware of its problems and are looking for alternatives. A possible alternative is to estimate the cost of equity based on the semideviation, a well-known and intuitively plausible measure of downside risk. Complementing evidence reported elsewhere about the ability of the semideviation to explain the cross-section of returns in emerging markets and that of industries in emerging markets, this article reports results showing that the semideviation also explains the cross-section of Internet stock returns.
Narrative Support for Technical Documents: Formalising Rhetorical Structure Theory

Business Process Re-engineering (BPR) is an area that requires a lot of technical documents and an important feature of a well-written document is a coherent narrative. Even though computer software has helped authors in many other aspects of writing, support for document narratives is almost non-existent. Therefore, we introduce CANS (Computer-Aided Narrative Support), a tool that uses Rhetorical Structure Theory to enhance the narrative of a document. From this narrative, the tool generates questions to prompt the author for the content of the document. CANS also allows the author to explore alternative narratives for a document. A catalogue of predefined narrative structures for popular types of documents is provided too. Our tool is still in its rudimentary stages but sufficiently complete to be demonstrated.
Inhibition of tumor metastasis by heparanase inhibiting species of heparin.

Heparanase activity correlates with the metastatic potential of lymphoma, melanoma and mammary adenocarcinoma cell lines. We investigated the ability of various modified species of heparin and size-homogeneous oligosaccharides derived from depolymerized heparin to inhibit (1) heparanase-mediated degradation of heparan sulfate in a naturally produced subendothelial extracellular matrix (ECM), and (2) lung colonization of B16-BL6 melanoma cells in C57BL mice. Inhibition of heparanase was best achieved by heparin species containing 16 or more sugar units and having sulfate groups at both the N and O positions. Low-sulfate oligosaccharides were less effective heparanase inhibitors than medium- and high-sulfate fractions of the same-size saccharide. While O-desulfation abolished the heparanase-inhibiting effect of heparin, O-sulfated, N-substituted (e.g. N-acetyl or N-hexanoyl) species of heparin retained high inhibitory activity. Potent inhibitors of heparanase activity were also efficient inhibitors of tumor invasion and lung colonization. Heparin fractions with high and low anticoagulant activity expressed similar high antiheparanase and antimetastatic activities. Structural requirement for the inhibition of melanoma cell heparanase and lung colonization by species of heparin were different from those identified for (1) release of ECM-bound basic fibroblast growth factor (b-FGF) and (2) stimulation of b-FGF receptor binding and mitogenic activity. These results indicate that various nonanticoagulant species of heparin and other polyanionic molecules differing in size, sulfation and substituted groups can be designed to elicit specific effects resulting in the inhibition of cell invasion in tumor metastasis and autoimmunity, or stimulation of neovascularization and wound healing.
A ‘dirty’ business: testing the limitations of terminal restriction fragment length polymorphism (TRFLP) analysis of soil fungi

Terminal restriction fragment length polymorphism (TRFLP) is an increasingly popular method in molecular ecology. However, several key limitations of this method have not been fully examined especially when used to study fungi. We investigated the impact of spore contamination, intracollection ribosomal DNA internal transcribed spacer (ITS) region variation, and conserved restriction enzyme recognition loci on the results produced by TRFLP to characterize soil fungal communities. We find that (i) the potential for nontarget structures such as spores to contribute DNA to target sample extractions is high; (ii) multiple fragments (i.e. ‘extra peaks’) per PCR primer‐restriction enzyme combination can be detected that are caused by restriction enzyme inefficiency and intracollection ribosomal DNA ITS variation; and (iii) restriction enzyme digestion in conserved vs. variable gene regions leads to different characterizations of community diversity. Based on these results, we suggest that studies employing TRFLP need to include information from known, identified fungi from sites within which studies take place and not to rely only on TRFLP profiles as a short cut to fungal community description.
Genetic variations of human herpesvirus 7 by analysis of glycoproteins B and H, and R2‐repeat regions

Clinical isolates of human herpesvirus 7 (HHV‐7) from the saliva of healthy individual were investigated for genetic variations in the regions of two immediate‐early (IE) genes, the glycoprotein B (gB) and glycoprotein H (gH) genes, and in R2‐repeat. The genomic DNA of 24 isolates from citizens of Thailand, Japan, and the United States was amplified to detect size variations in the IE‐1 and IE‐2 loci, but none was observed, suggesting that there was no deletion or insertion in these genes, in contrast with an IE gene of human herpesvirus 6 (HHV‐6). The sequences of the gB gene from isolates acquired from 5 Japanese and 8 Thai subject were then compared with those of American strains JI and RK with respect to codons that are known to differentiate gB alleles. All the isolates were found to have gB allele C except for the JI strain, which has allele F. Variability was also observed in five specific gH codons, resulting in 6 different groups. The HHV‐7 isolates might be classified into two major genetic variants by combining their gB and gH allelic groupings. In the present study, only JI belonged to variant 1, while the rest of the isolates appeared to belong to variant 2. In the R2‐repeat region, size heterogeneities were observed among the 24 isolates, due to different repeat numbers (17, 15, 14, 13, or 12 repeats). Therefore, we used the R2‐repeat to identify the origins of isolates in a study of HHV‐7 transmission, and found HHV‐7 to be transmitted within a family from both mothers and fathers to their children. J. Med. Virol. 66:370‐377, 2002. © 2002 Wiley‐Liss, Inc.
Smart Card Information Sharing Platform towards Global Nomadic World

SUMMARY The demand for multi-application smart card platform has been increasing in various business sectors recently. When it comes to the actual implementation of the platform, however, network-based dynamic downloading in a Card Issuer-Service Provider separated environment has not made much progress. This paper introduces the smart card information sharing platform that uses licensing/policy/profile management and PKIbased technologies to enable multiple CIs and multiple SPs to reflect their own business policy flexibly via network. It makes the paradigm shift from card-oriented scheme to service-oriented scheme. By through world’s first implementation of the scheme and some experiments including deployment, we confirmed that this technology is well-accepted and applicable
Magistrates' decision-making : personality, process and outcome

The thesis examined personality and socio-demographic characteristics of individuals and their relationship to the way in which magistrates approach the sentencing of offenders and the choices they make. It was based on a review of the theoretical approaches to models of decision-making and the concept of individual differences. A pluralistic methodology was adopted combining a quasi-experimental approach in the first study, with two further qualitative studies. Study 1 reported the profile data for the participants, all practising magistrates, and their responses to case study vignettes. Study 2 considered participants' perception of the sentencing process and the factors that influenced their decisions using an interpretative phenomenological approach, while Study 3 applied content and discourse analysis to transcripts of a sentencing training exercise in which magistrates had participated. Analyses of the first study were mostly correlational. Modest associations between Locus of Control and Legal Authoriarianism with severity of sentence were demonstrated and also small gender differences in sentencing choice. The study concluded that there was no support for hypotheses linking other personality trait measurements with the severity of sentence or the approach adopted, using an algebraic model to represent the process. In the subsequent studies, evidence emerged to suggest a more holistic approach to sentencing, guided by advice on structured decision-making, while accommodating the influences of probation service reports, diverse sentencing aims and the advice of the legal professionals. The impact of group interactions was also apparent. This varied with individual characteristics and acquired competences necessary for satisfactory appraisal. The interpretation of 'roles' on a sentencing Bench and their potential effects on the process and outcome of sentencing was observed.
Distribution of GABA‐like immunoreactivity in the rat amygdaloid complex

The distribution of GABA‐like (GABA‐Li) immunoreactivity in the rat amygdaloid complex was studied by using an anti‐GABA antibody. GABA‐Li positive neurons and processes were present in every nucleus of the complex. Three patterns of immunoreactivity were revealed: (1) the intercalated masses and the lateral olfactory tract nucleus exhibited the most intense staining of the neuropil, and virtually every neuron was labeled, (2) the central and medial nuclei contained intensely labeled neuropil and moderately labeled neurons, and (3) in the remaining nuclei, the neuropil was weakly labeled, and relatively numerous GABA‐Li neurons were present. Our results suggest that: (1) the intercalated masses and lateral olfactory tract nucleus consist of large aggregates of GABA‐Li immunoreactive neurons, and (2) the lateral, basal dorsal, and the posterior cortical nuclei may constitute a significant source of GABAergic connections to other amygdaloid nuclei, in particular to the medial and central nuclei.
An Evidence-Based Approach to Spine Surgery

Health care reform will emphasize evidence-based medicine to provide the highest quality care. Recent literature has emerged in spinal surgery that has profoundly increased the evidence base for several spinal procedures. There is now good evidence from randomized controlled trials that surgical treatment of symptomatic lumbar disc herniation, decompression for spinal stenosis, and decompression and fusion for degenerative spondylolisthesis all offer significant clinical benefit in the face of serious back and radicular pain when compared with nonsurgical care. Studies of nonsurgical and surgical treatments for chronic low back pain are inconclusive, limited by study design/methodology. Continuing to increase study quality in the field of spine surgery is more important now than ever before. Optimizing diagnostic specificity, surgical indications, and measuring outcomes with validated instruments should help the spine care community acquire essential data to provide the highest quality evidence-based care, while simultaneously eliminating procedures that lack evidence of efficacy or value.
Useful Simulation Tool for Induction Generators Used In Wind Power Plants

Electric energy generated by wind power plants is the fastest developing and most promising renewable energy source in Europe. Due to the advantages of power electronics wind energy conversion systems equipped with doubly fed induction generators for variable speed wind turbines are one of the most efficient configurations for wind energy conversion. The mathematical model and the simulation programs for such machines to be presented in the paper can help the understanding in this field and can be of real interest for all specialists involved in wind energy exploitation.
Protein Homology Analysis for Function Prediction with Parallel Sub-Graph Isomorphism

To annotate the biological function of a protein molecule, it is essential to have information on its 3D structure. Many successful methods for function prediction are based on determining structurally conserved regions because the functional residues are proved to be more conservative than others in protein evolution. Since the 3D conformation of a protein can be represented by a contact map graph, graph matching, algorithms are often employed to identify the conserved residues in weakly homologous protein pairs. However, the general graph matching algorithm is computationally expensive because graph similarity searching is essentially a NP-hard problem. Parallel implementations of the graph matching are often exploited to speed up the process. In this chapter,the authors review theoretical and computational approaches of graph theory and the recently developed graph matching algorithms for protein function prediction.
Dancing in the Margins

Abstract The purpose of this essay is to illustrate how the complexities, fluidity, and shifting nature of the multiple facets to our identities may shape the very construction of knowledge. Specifically, how researcher positionality and reflexivity influences an understanding of our personal identities related to leisure and social justice research using epiphany moments is examined. It is posited that our socially constructed identities (defined by race, age, gender, sexuality, able-bodied, class, etc.) can have a profound impact on the intersection of our research programs and our commitment to issues of social justice. Emphasis is also placed on understanding the cringe continuum, feelings of unease with research topics, the significance of social justice research in the classroom, and understanding the risks associated with this type of work.
Finding Common Opinions in User-Generated Reviews

A large and growing body of user-generated reviews is available on the Internet, from product reviews at sites like Amazon.com to restaurant reviews at sites like Yelp.com. For users making a purchasing or dining decision, the opinions of others can be an important factor. Although some aggregate information -like average-star ratings -for multiple reviews is sometimes available, in general the only way to determine common views among users is by reading through many reviews. As the number of reviews for a single product or restaurant becomes large (on the order of hundreds), it becomes increasingly impractical to read every review. Some techniques are commonly employed to compensate for this, such as ranking reviews by usefulness, as determined by readers. Since readers are most likely to read only the topranked reviews, however, this approach likely leads to a reinforcement of existing useful reviews, while relegating new, unread reviews to the bottom of the list.
A murine transmembrane tumor necrosis factor (TNF) transgene induces arthritis by cooperative p55/p75 TNF receptor signaling

The arthritogenic activities of tumor necrosis factor (TNF) and its p55TNF‐receptor (R) have been well documented in experimental animal models of arthritis, and in transgenic mice expressing wild‐type or mutant transmembrane human TNF proteins in their joints. In this study we show that chronic inflammatory arthritis also develops in transgenic mice made to overexpress a mutant transmembrane from of the murine TNF protein (muTNFΔ1–12) which is known to utilize efficiently both the p55 and the p75TNFR. Cross‐breeding of the transgene into a TNF knockout background did not alter development of disease. Analysis of TNF bioactivity in sera from lipopolysaccharide‐stimulated mice or ex vivo macrophage cultures demonstrated that the muTNFΔ1–12 protein accumulates on the cell surface and is not processed to bioactive soluble TNF, indicating that transmembrane TNF is by itself sufficient to mediate pathogenesis of arthritis. Furthermore, using TNFR knockout mice, it is shown that development of transmembrane TNF‐mediated arthritis requires the presence of the p55TNFR but is significantly delayed in the absence of the p75TNFR, suggesting a positive cooperation between the two TNFR in the arthritogenic process. These results indicate that blocking the activities of both soluble and transmembrane TNF may be required to effectively neutralize the pathogenic potential of this cytokine in arthritis.
Effects of $\hbox{Al}_{2}\hbox{O}_{3}$ Dielectric Cap and Nitridation on Device Performance, Scalability, and Reliability for Advanced High- $\kappa$/Metal Gate pMOSFET Applications

A pFET threshold-voltage (<i>Vt</i>) reduction of about 200 mV is demonstrated by inserting a thin Al<sub>2</sub>O<sub>3</sub> layer between the high-k dielectric and the TiN gate without noticeable degradation of other electrical properties. HfSiO<sub>prop</sub>capped with 9 Aring of thin Al<sub>2</sub>O<sub>3</sub>obtains a low long-channel V<i>t</i> of -0.37 V (the lowest among those with TiN gate), a high mobility of 59 cm<sup>2</sup> /V ldr s at 0.8 MV/cm (92% of universal value), a negligible equivalent- oxide-thickness (EOT) increase of 0.1 Aring (compared to the uncapped reference), and a low Vt instability of 4.8 mV at 7 MV/cm. It also passes the ten-year negative-bias-temperature-instability (NBTI) lifetime specification with a gate overdrive of -0.7 V. This indicates that thin Al<sub>2</sub>O<sub>3</sub>obtains caps are beneficial to the pFET applications. In contrast, nitrogen incorporation in the Al<sub>2</sub>O<sub>3</sub>-capped HfSiO<sub>prop</sub> is not favorable because it increases the Vt by 50-140 mV, degrades the mobility by 10%-22%, increases the EOT by 0.5-0.8 Aring and the Vt instability by 5-13 mV, and reduces the NBTI lifetime by four to five orders of magnitude. Compared to postcap nitridation, high-k nitridation results in more severe degradation of these properties by incorporating nitrogen closer to the Si/SiO<sub>2</sub> interface.