Miracle-dz/UniFAR-FTUs huggingface dataset:
OmpC is involved in invasion of epithelial cells by Shigella flexneri

Osmoregulation of the Shigella flexneri ompC gene and the role of OmpC in Shigella virulence have been investigated. OmpC was highly expressed when bacteria were grown in medium of either low or high osmolarity. This constitutive expression is in contrast with the regulation observed in Escherichia coli, in which the expression of OmpC is repressed at low osmolarity and induced at high osmolarity. In addition, the Shigella ompC gene was barely expressed by a delta ompB (delta ompR and delta envZ) mutant. We described in a previous report that such a mutant was severely impaired in virulence both in vitro and in vivo. Starting from this observation, and in order to assess which gene(s) regulated by ompR and envZ are involved in virulence, we constructed an S. flexneri delta ompC mutant. Three S. flexneri mutants, ompF'-lacZ, delta ompC, and delta ompB, were compared for virulence. The ompF'lacZ mutant behaved like the S. flexneri serotype 5 wild-type strain M90T in all in vitro and in vivo virulence tests. On the contrary, the delta ompB and delta ompC strains were considerably impaired in their virulence phenotypes. The ability of these two mutants to spread from cell to cell and to kill epithelial cells was severely affected. Consequently delta ompC, as previously described for delta ompB, was unable to elicit a positive Sereny test. The delta ompB mutant was restored to virulence by introducing a recombinant multicopy plasmid carrying the cloned E. coli ompC gene, indicating that a functional OmpC protein was necessary and sufficient to restore virulence to this mutant of S. flexneri.
Harm Avoidance and Risk of Alzheimer's Disease

Objective: To test the hypothesis that harm avoidance, a trait associated with behavioral inhibition, is associated with the risk of developing Alzheimer's disease (AD). Methods: A total of 791 adults 55 years and older without dementia completed a standard self-report measure of harm avoidance. They then underwent annual evaluations that included detailed cognitive testing and clinical classification of mild cognitive impairment (MCI), dementia, and AD. In a uniform neuropathologic examination of those who died, counts of neuritic plaques, diffuse plaques, and neurofibrillary tangles were standardized and combined to yield a pathologic measure of disease. The relation of harm avoidance to incidence of AD and related outcomes was estimated in analyses adjusted for age, sex, and education. Results: During a mean of 3.5 years of annual observation, 98 people (12.4%) developed incident AD. A high level of harm avoidance (90th percentile) was associated with a more than two-fold increase in risk of AD compared with a low score (10th percentile). Higher harm avoidance was also associated with increased incidence of MCI and more rapid decline in episodic memory, working memory, and perceptual speed (but not semantic memory or visuospatial ability). In 116 participants who died and underwent brain autopsy, harm avoidance was not related to a composite measure of plaques and tangles. Conclusions: A high level of the harm avoidance trait, indicating a tendency toward behavioral inhibition, is related to the risk of developing AD and its precursor, MCI.AD = Alzheimer's disease; MCI = mild cognitive impairment; SD = standard deviation; SE = standard error
Adaptive Architectures for Robust and Efficient Computing

Adaptive Architectures for Robust and Efficient Computing by Shantanu Gupta Chair: Scott A. Mahlke Semiconductor technology scaling has long been a source of d ramatic gains in our computing capabilities. However, as we test the physical limit s of silicon feature size, serious reliability and computational efficiency challenges confr t us. The supply voltage levels have practically stagnated, resulting in increasing power densities and operating temperatures. Given that most semiconductor wearout mechanisms ar e highly dependent on these parameters, significantly higher failure rates are project ed for future technology generations. Further, the rise in power density is also limiting th e number of resources that can be kept active on chip simultaneously, motivating the need for energy-efficient computing. In this landscape of technological challenges, incrementa l architectural improvements to existing designs are likely insufficient, motivating a ne ed to rethink the architectural fabric from the ground up. Towards this end, this thesis pres ents adaptive architecture and compiler solutions that can effectively tackle reliabilit y, performance and energy-efficiency
The mediation of information technology on visitors’ experience at a cultural heritage site

ABSTRACT This study identifies perceptual differences between the experiences of using an interactive ubiquitous access tourism service (U-tourism service) at a cultural heritage site and on-site participation-driven services. An interactive U-tourism service, “Hwaseong Haenggung Histour”, a smart phone application, was developed and implemented for this study. The study found (a) visitors who experienced the U-tourism service showed higher recognition on such dimensions as education, novelty, entertainment and fellowships, regarded as important components of on-site experiences, than those who joined on-site participation-driven services and (b) young visitors who used the interactive U-tourism service recorded higher in the dimensions of both education and novelty than those who joined on-site participation-driven services and showed higher satisfaction. These findings provide strong justification for the introduction of U-tourism services, particularly for young visitors. This study contributes to the understanding of a fast-growing and influential electronic tool for cultural heritage sites.
Evaluating diagnostic tests: The area under the ROC curve and the balance of errors

Because accurate diagnosis lies at the heart of medicine, it is important to be able to evaluate the effectiveness of diagnostic tests. A variety of accuracy measures are used. One particularly widely used measure is the AUC, the area under the receiver operating characteristic (ROC) curve. This measure has a well‐understood weakness when comparing ROC curves which cross. However, it also has the more fundamental weakness of failing to balance different kinds of misdiagnoses effectively. This is not merely an aspect of the inevitable arbitrariness in choosing a performance measure, but is a core property of the way the AUC is defined. This property is explored, and an alternative, the H measure, is described. Copyright © 2010 John Wiley & Sons, Ltd.
DREB Genes from Common Bean (Phaseolus vulgaris L.) Show Broad to Specific Abiotic Stress Responses and Distinct Levels of Nucleotide Diversity

We analyzed the nucleotide variability and the expression profile of DREB genes from common bean, a crop of high economic and nutritional value throughout the world but constantly affected by abiotic stresses in cultivation areas. As DREB genes have been constantly associated with abiotic stress tolerance, we systematically categorized 54 putative PvDREB genes distributed in the common bean genome. It involved from AP2 domain location and amino acid conservation analysis (valine at the 14th position) to the identification of conserved motifs within peptide sequences representing six subgroups (A-1 to A-6) of PvDREB proteins. Four genes (PvDREB1F, PvDREB2A, PvDREB5A, and PvDREB6B) were cloned and analyzed for their expression profiles under abiotic stresses and their nucleotide and amino acid diversity in genotypes of Andean and Mesoamerican origin, showing distinct patterns of expression and nucleotide variability. PvDREB1F and PvDREB5A showed high relative inducibilities when genotypes of common bean were submitted to stresses by drought, salt, cold, and ABA. PvDREB2A inducibility was predominantly localized to the stem under drought. PvDREB6B was previously described as an A-2 (DREB2) gene, but a detailed phylogenetic analysis and its expression profile clearly indicated it belongs to group A-6. PvDREB6B was found as a cold- and dehydration-responsive gene, mainly in leaves. Interestingly, PvDREB6B also showed a high nucleotide and amino acid diversity within its coding region, in comparison to the others, implicating in several nonsynonymous amino acid substitutions between Andean and Mesoamerican genotypes. The expression patterns and nucleotide diversity of each DREB found in this study revealed fundamental characteristics for further research aimed at understanding the molecular mechanisms associated with drought, salt, and cold tolerance in common bean, which could be performed based on association mapping and functional analyses.
Clinical characteristics of collagenous and lymphocytic colitis

Background: Microscopic colitides (MC), collagenous colitis (CC) and lymphocytic colitis (LC) share clinical features, but their mutual relationship is unclear, and clinical comparative studies are rare. We aimed to examine the clinical features in CC and LC by focusing on concomitant diseases. Methods: Patients with MC (30 with CC, 54 with LC) were identified in the pathology databases and by reviewing biopsies. Controls included 84 age‐ and sex‐matched persons. The clinical data collected from patient records were prospectively completed by interviews. Results: The female:male ratio was 2:1 in CC and 5.75:1 in LC. Mean age at diagnosis was 53 in CC and 55.4 years in LC. There were no differences in the pattern of symptoms. Concomitant autoimmune diseases were more common in CC (53.3%) than in LC (25.9%; P = 0.017). Celiac disease was common in both CC (20%) and LC (14.8%). Bronchial asthma was associated with LC (25.9%), but not with CC (6.7%; P = 0.042). Colon diverticulosis was rare in MC (16%) compared with the controls (39%; P = 0.001). Hypolactasia was common in MC (45%; 76% in CC, 54% in LC) compared to its prevalence in the Finnish general population (17%). Conclusions: CC and LC are largely similar clinically, but the differences in the occurrence of autoimmune conditions and bronchial asthma suggest that they differ in immunopathogenesis. MC is associated with reduced lactose tolerance and shows a negative association with diverticular disease, possibly related to the small intestinal pathology and abnormal stool consistency.
Comparison : Monolithic vs . Modular SoC Testing

THE MODULAR DESIGN approach, which partitions a design into smaller blocks, has successfully ameliorated the increasing complexity of VLSI designs. Such a divide-and-conquer design style also supports the import of external design expertise by integrating third-party design blocks, also known as cores. Both the design and the test approach for a large SoC can be modular; various modules and cores are then tested as stand-alone units. Modular testing typically involves wrapping test modules for controllability and observability purposes and connecting all test wrappers to SoC pins through one or more test access mechanisms (TAMs). IEEE Std 1500 has standardized wrappers, allowing wrapped cores from multiple sources within one SoC to interoperate. Embedded nonlogic blocks, such as memories and analog, require dedicated tests to ensure test quality. Their defects, fault models, and hence test patterns differ from regular standard-cell logic. Hard cores and encrypted cores, for which no implementation netlist is available to the SoC integrator, must be tested with the test patterns delivered by their core provider, and thus also require stand-alone testing. However, even for logic-only SoCs for which the entire netlist is available, modular testing, enabled by IEEE1500-based wrappers, has attractive benefits. Modular test generation involves breaking up a large monolithic SoC into smaller design netlists, which become tractable for ATPG and fault-simulation tools. (The ‘‘Related Work’’ sidebar discusses two approaches, hierarchical ATPG and modular testing, in which test generation can capitalize on ATPG results previously obtained for SoC modules.) Modular test enables test reuse, which is particularly beneficial if subsequent SoC design derivatives are based on a family concept. Moreover, modular SoC testing enables optimizations in test time, power consumption, IR drop, and so on, through proper scheduling of the various component tests. In this article, we compare monolithic and modular testing with respect to test data volume. (This article is an expanded version of a preliminary paper we presented at the 2008 Design, Automation and Test in Europe [DATE] conference.) We also reuse some experimental data (results for AMD’s Athlon processor), from another paper we presented at the 2007 International Test Conference (ITC), which originally focused on a test application time comparison between monolithic and modular testing. Our comparative theoretical study shows that modular testing requires a significantly smaller test data volume than monolithic testing. Most test access architectures based on wrappers and TAMs allow cores that are not being tested to be disconnected from the TAM, which
Housing price changes, general equilibrium and welfare

This paper explores the aggregate welfare effects of housing price changes in the heterogeneous agent general equilibrium model with multi-sector production side. The model includes two types of households: credit-constrained households and unconstrained households. These types differ not only because of the presence or absence of credit constraints but also from the point of view of their time preference rates and factors of production which they own. The modeling of the production side of the economy is based on Davis and Heathcote (2005) and includes a composite good production sector housing production sector and intermediate goods production sector. Besides welfare comparisons between steady states, the welfare changes during transition between steady states are also calculated.
Epilepsy from the Patient's Perspective: Review of Results of a Community-Based Survey

A total of 1023 individuals with epilepsy responded to a community-based questionnaire survey. Relative to U.S. population norms, respondents had lower household incomes and lesser levels of educational and vocational attainment. Although 89% of respondents reported that their seizures were, in their estimation, at least somewhat controlled, 57% reported having suffered at least one seizure in the preceding year. Of the many concerns that accompanied life with epilepsy, fear (of a seizure, of embarrassment, even of death) was the issue most frequently reported. Eighty-eight percent of respondents reported having health insurance, and this insurance covered epilepsy treatment in 93% of cases. The majority of respondents said that they were satisfied with the medical care they were receiving but wished for more information about epilepsy. Despite advances in epilepsy therapy, freedom from seizures and optimal quality of life eludes many.
Neuroimmune processes associated with Wallerian degeneration support neurotrophin‐3‐induced axonal sprouting in the injured spinal cord

Lesions of the spinal cord cause two distinctive types of neuroimmune responses, a response at the lesion site that leads to additional tissue destruction and a more subtle response, termed Wallerian degeneration (WD), that occurs distal to the lesion site. We have evidence that the neuroimmune response associated with WD may support tissue repair. Previously, we found that overexpression of neurotrophin‐3 (NT‐3) induced axonal growth in the spinal cord after a unilateral corticospinal tract (CST) lesion, but only if the immune system was intact and activated. We reasoned that a neuroimmune response associated with WD was involved in this neuroplasticity. To test this, we compared NT‐3‐induced axonal sprouting in athymic nude rats that lack functional T cells with rats with functional T cells and in nude rats grafted with CD4+ T cells or CD8+ T cells. There was no sprouting in nude rats and in nude rats grafted with CD8+ T cells. However, nude rats grafted with CD4+ T cells mounted a sprouting response. To determine which CD4+ subtype, type 1 T helper (Th1) or type 2 T helper (Th2) cells, was responsible, we grafted Th1 and Th2 cells into nude rats and tested whether they would support sprouting. Axonal sprouting was greater in rats grafted with Th2 cells, demonstrating that the Th2 subtype was responsible for supporting axonal sprouting. These data suggest that WD activates Th2 cells that, along with the direct effects of NT‐3 on CST axons, act to support axonal sprouting in the lesioned spinal cord. © 2013 Wiley Periodicals, Inc.
Vijjana: A collaborative agent model for creating a knowledge advantage machine

In this paper we describe the Discovery Agent of Vijjana, an umbrella project for creating a person-specific knowledge repository based on classification and analysis. Vijjana provides a framework designed for building collaborative knowledge networks that are domain specific and well bounded in search categories. Using the Vijjana model, we can envision creating an intelligent agent that presents context based information that is drawn from a personalized knowledge base. We call such an agent a Knowledge Advantage Machine (KaM) as it enables a user to take advantage of the personalized knowledge base to perform the task at hand more effectively - in much the same way mechanical advantage had been helping industrial workers. In this paper we discuss only the first part, namely the discovery agent. In this part the focus is on a conceptual way to bridge the gap between the presentation layer and the data access layer which is discussed here using the Object Relational Mapping through the Hibernate framework.
Optimization of corona ring structure for UHV composite insulator using finite element method and PSO algorithm

The optimization method combining Finite Element Method (FEM) and particle swarm optimization (PSO) algorithm has been applied to design of corona ring structure for composite insulator used along Ultra High Voltage (UHV) transmission line in the present work. Firstly, corona discharges have been investigated by means of ultraviolet imager (UVI) observation which indicates improper corona structure and installation. Next, E-field distributions along composite insulator and on surface of corona ring have been computed and analyzed with three-dimensional FEM calculation model of UHV tangent tower on which hangs suspension and tension composite insulators in single-circuit transmission line using commercial software ANSYS. Finally, an objective function which can evaluate nonlinear relationship between maximum electric field strength and corona ring structure parameters has been established based on initial calculating results, On the other hand, PSO algorithm also has been implemented using APDL language in ANSYS computing environment, then optimization of corona ring structure for UHV composite insulator can be converted to seek minimum value of objective function utilized programmed PSO algorithm. The results show that the proposed optimization process can be conducted automatically and efficiently, moreover, the electric field strength along insulator and around corona rings after optimization is less than that before optimization, and the optimal rings improve electric field distribution along composite insulators.
Variables affecting convection-enhanced delivery to the striatum: a systematic examination of rate of infusion, cannula size, infusate concentration, and tissue-cannula sealing time.

OBJECT Although recent studies have shown that convection can be used to distribute macromolecules within the central nervous system (CNS) in a homogeneous, targeted fashion over clinically significant volumes and that the volume of infusion and target location (gray as opposed to white matter) influence distribution, little is known about other factors that may influence optimum use of convection-enhanced distribution. To understand the variables that affect convective delivery more fully, we examined the rate of infusion, delivery cannula size, concentration of infusate, and preinfusion sealing time. METHODS The authors used convection to deliver 4 microl of 14C-albumin to the striatum of 40 rats. The effect of the rate of infusion (0.1, 0.5, 1, and 5 microl/minute), cannula size (32, 28, and 22 gauge), concentration of infusate (100%, 50%, and 25%), and preinfusion sealing time (0 and 70 minutes) on convective delivery was examined using quantitative autoradiography, National Institutes of Health image analysis software, scintillation analysis, and histological analysis. Higher rates of infusion (1 and 5 microl/minute) caused significantly (p < 0.05) more leakback of infusate (22.7+/-11.7% and 30.3+/-7.8% [mean+/-standard deviation], respectively) compared with lower rates (0.1 microl/minute [4+/-3.6%] and 0.5 microl/minute [5.2+/-3.6%]). Recovery of infusate was significantly (p < 0.05) higher at the infusion rate of 0.1 microl/minute (95.1+/-2.8%) compared with higher rates (85.2+/-4%). The use of large cannulae (28 and 22 gauge) produced significantly (p < 0.05) more leakback (35.7+/-8.1% and 21.1+/-7.5%, respectively) than the smaller cannula (32 gauge [5.2+/-3.6%]). Varying the concentration of the infusate and the preinfusion sealing time did not alter the volume of distribution, regional distribution, or infusate recovery. CONCLUSIONS Rate of infusion and cannula size can significantly affect convective distribution of molecules, whereas preinfusion sealing time and variations in infusate concentration have no effect in this small animal model. Understanding the parameters that influence convective delivery within the CNS can be used to enhance delivery of potentially therapeutic agents in an experimental setting and to indicate the variables that will need to be considered for optimum use of this approach for drug delivery in the clinical setting.
Selective deficit of angiogenic growth factors characterises pregnancies complicated by pre-eclampsia.

OBJECTIVE To compare serum levels of angiogenic growth factors vascular endothelial growth factor (VEGF), placental growth factor (PlGF) and angiogenin in pre-eclamptic women and matched controls. DESIGN Retrospective analysis of -70 degrees C stored serum of women who developed pre-eclampsia and matched controls. SETTING Department of Gynaecology and Obstetrics, St Elisabeth Hospital, Curaçao, Netherlands Antilles. SAMPLE Thirty women with pre-eclampsia and 30 normotensive controls matched for age and gestation. RESULTS VEGF and PIGF serum levels were significantly lower in pre-eclamptic pregnancies, compared with controls (VEGF 0.31 +/- 1.20 vs 18.30 +/- 24.97 pg/mL, P = 0.0004; PlGF 54.19 +/- 32.05 vs 497.95 +/- 340.51 pg/mL, P < 0.0001). Matched couple analysis showed VEGF serum concentrations to be lower in the majority of pre-eclamptic women and PlGF concentrations to be lower in all pre-eclamptic women. Angiogenin serum levels showed no statistical significant difference between pre-eclamptic pregnancies and controls (523.68 +/- 367.55 vs 670.41 +/- 251.54 ng/mL, P = 0.058), with matched couple analysis showing no clear pattern. CONCLUSIONS Decreased serum levels of VEGF and PIGF characterise, and therefore seem to be of importance during (the development of), pre-eclampsia. This selective deficit of angiogenic growth factors might in part explain the shallow placentation found in this pregnancy complication.