Miracle-dz/UniFAR-FTUs huggingface dataset:
Detection of gyrA mutation among clinical isolates of Campylobacter jejuni isolated in Egypt by MAMA-PCR.

INTRODUCTION Campylobacter spp are the major cause of enteritis in humans and more than 90% of reported infections are caused by Campylobacter jejuni. Fluoroquinolones such as ciprofloxacin are the antibiotics of choice for treatment. An increase in the frequency of ciprofloxacin-resistant Campylobacter has been reported globally due to a single base mutation (C-257 to T) in codon 86 of the quinolone resistance determining region (QRDR) of the gyrA gene altering the amino acid sequence from threonine at position 86 to isoleucine (Thr-86 to Ile). METHODOLOGY Campylobacter spp (n = 118) were selected from a collection of Egyptian isolates spanning 1998 to 2005. The presence of C. jejuni gyrA gene was confirmed in each isolate by a PCR assay amplifying 368 bp portion of the gyrA gene. C to T alteration was detected by the mismatch amplification mutation assay MAMA PCR. The MIC of nalidixic acid (NA) and ciprofloxacin (CIP) was determined by E-test. RESULTS C. jejuni gyrA gene was detected in 100 of the Campylobacter spp studied; the other 18 isolates were found to be Campylobacter coli by lpxA PCR. The mutation was detected in 89 C. jejuni resistant isolates with MIC values (NA; 8 - >256 μg/ml) and (CIP; 4 - >32 μg/ml). The other 11 sensitive C. jejuni isolates with MIC values (NA; 0.38 - 3 µg/ml) and (CIP; 0.03 - 0.125 µg/ml) were not amplified by the MAMA primers. There was 100% congruence with MAMA PCR, MIC results and gyrA gene sequence analysis. CONCLUSIONS In Egypt the main mechanism for resistance to fluoroquinolones is an alteration in the gyrA QRDR. MAMA PCR provides an economical and rapid means for screening fluoroquinolone resistance.
Functional divergence in the caspase gene family and altered functional constraints: statistical analysis and prediction.

In this article, we explore the pattern of type I functional divergence (i.e., altered functional constraints or site-specific rate difference) in the caspase gene family that is important for apoptosis (programmed cell death) and cytokine maturation. By taking advantage of substantial experimental data from caspases, the functional/structural basis of our posterior predictions from sequence analysis was extensively studied. Our results are as follows: (1) Phylogenetic analysis shows that the evolution of major caspase-mediated pathways has been facilitated by gene duplications, (2) type I functional divergence (altered functional constraints) is statistically significant between two major subfamilies, CED-3 and ICE, (3) 4 of 21 predicted amino acid residues (for site-specific rate difference between CED-3 and ICE) have been verified by experimental evidence, and (4) we found that some CED-3 caspases may inherit more ancestral functions, whereas other members may employ some recently derived functions. Our approach can be cost effective in functional genomics to make statistically sound predictions from amino acid sequences.
Convergence theorems of finite-step iteration with errors for non-self asymptotically nonexpansive in the intermediate sense mappings

Let K be a nonempty closed convex nonexpansive retract of a uniformly convex Banach space E with P as a nonexpansive retraction. Let T : K → E be non-self asymptotically nonexpansive in the intermediate sense mapping with F(T) = O. Let {αni}, {βni} and {γni} are sequences in [0, 1] with αn(i) + βn(i) + γn(i) = 1 for all i = 1, 2, . , N. From arbitrary x1 є K , define the sequence {xn } iteratively by (8), where {u(i) } for all i = 1, 2, . , N are bounded sequences in K with P∞ u(i) < ∞. (i) If the dual E
The Need to Belong (NB) in Adolescence: Adaptation of a Scale for its Assessment

Adolescents permanently interact with the context they belong to. Family and peer group are considered as two main influential contexts in youths groups [1-3]. The peer group and/ or group of belonging have always played a decisive role in the socialization of the adolescent and it is one of the few youth agents poorly controlled by adults. To Baumeister & Leary [4], the need to belong (NB) is a fundamental human motive and starting point to understand and integrate interpersonal human behavior. To these authors, the NB is a strong drive to form and maintain a minimum amount of meaningful and positive interpersonal relationships. To Osterman [5], it is possible to conclude that belonging is an extremely relevant term since it has a deep impact in motivation and human behavior. To this author, the NB is a human characteristic that drives people to obtain stronger and longer-lasting relationships promoting subjective welfare. To Delle [6] this need includes two aspects: frequent interactions with just a few people and interactions that take place in the context of a stable welfare framework for the subjects. The interactions with a sequence of constant changes will be less satisfactory than repeated interactions with the same person. The loss of belonging could become a real deprivation and cause a number of diseases. The NB goes beyond wanting to be close to other people; it makes it possible for humans to construct culture.
Knowledge Sharing Behavior: Clarifying Its Measurement and Antecedents

vi Chapter 1: Introduction . 1 Learning in organizations . 1 Newcomer socialization . 2 Adaptability. 2 Active learning . 3 Informal learning . 5 Communities of practice . 6 Knowledge sharing . 7 Literature review of knowledge sharing . 8 Definition of rewards . 13 Measurement of knowledge sharing behavior . 14 Rewards and knowledge sharing relationship. 16 Person and situation interaction . 20 Career stage . 22 Goal orientations . 27 Learning goal orientation (LGO) . 27 Performance goal orientation (PGO) . 28 Performance prove orientation (PPO) . 28 Performance avoid orientation (PAO) . 29 Organizational learning culture as a strong situation . 30 Present study . 31 Chapter 2: Study 1 method . 33 Item content validation . 33 Measures . 36 Participants . 37 Exploratory factor analysis . 39 Chapter 3: Study 1 results . 41
2-stage revision of 120 deep infected hip and knee prostheses using gentamicin-PMMA beads

Background and purpose — A 2-stage revision is the most common treatment for late deep prosthesis-related infections and in all cases of septic loosening. However, there is no consensus about the optimal interval between the 2 stages. Patients and methods — We retrospectively studied 120 deep infections of total hip (n = 95) and knee (n = 25) prostheses that had occurred over a period of 25 years. The mean follow-up time was 5 (2–20) years. All infections had been treated with extraction, 1 or more debridements with systemic antibiotics, and implantation of gentamicin-PMMA beads. There had been different time intervals between extraction and reimplantation: median 14 (11–47) days for short-term treatment with uninterrupted hospital stay, and 7 (3–22) months for long-term treatment with temporary discharge. We analyzed the outcome regarding resolution of the infection and clinical results. Results — 88% (105/120) of the infections healed, with no difference in healing rate between short- and long-term treatment. 82 prostheses were reimplanted. In the most recent decade, we treated patients more often with a long-term treatment but reduced the length of time between the extraction and the reimplantation. More reimplantations were performed in long-term treatments than in short-term treatments, despite more having difficult-to-treat infections with worse soft-tissue condition. Interpretation — Patient, wound, and infection considerations resulted in an individualized treatment with different intervals between stages. The 2-stage revision treatment in combination with local gentamicin-PMMA beads gave good results even with difficult prosthesis infections and gentamicin-resistant bacteria.
Local Framings

Framings provide a way to construct Quillen functors from simplicial sets to any given model category. A more structured set-up studies stable frames giving Quillen functors from spectra to stable model categories. We will investigate how this is compatible with Bousfield localisation to gain insight into the deeper structure of the stable homotopy category. We further show how these techniques relate to rigidity questions and how they can be used to study algebraic model categories.
Aggregate uncertainty, disappointment aversion and the business cycle

We investigate the effect of aggregate uncertainty shocks in real variables. More specifically, we introduce a shock in the volatility of productivity in an RBC model with long-run volatility risk and preferences that exhibit generalised disappointment aversion. We find that, when combined with a negative productivity shock, a volatility shock leads to further decline in real variables, such as output, consumption, hours worked and investment. For instance, out of the 2% decrease in output as a result of both shocks, we attribute 0.25% to the effect of an increase in volatility. We also find that this effect is the same as the one obtained in a model with Epstein-ZinWeil preferences, but higher than that of a model with expected utility. Moreover, GDA preferences yield superior asset pricing results, when compared to both Epstein-Zin-Weil preferences and expected utility.
The Role of Genetic Polymorphisms as Related to One-Carbon Metabolism, Vitamin B6, and Gene–Nutrient Interactions in Maintaining Genomic Stability and Cell Viability in Chinese Breast Cancer Patients

Folate-mediated one-carbon metabolism (FMOCM) is linked to DNA synthesis, methylation, and cell proliferation. Vitamin B6 (B6) is a cofactor, and genetic polymorphisms of related key enzymes, such as serine hydroxymethyltransferase (SHMT), methionine synthase reductase (MTRR), and methionine synthase (MS), in FMOCM may govern the bioavailability of metabolites and play important roles in the maintenance of genomic stability and cell viability (GSACV). To evaluate the influences of B6, genetic polymorphisms of these enzymes, and gene–nutrient interactions on GSACV, we utilized the cytokinesis-block micronucleus assay (CBMN) and PCR-restriction fragment length polymorphism (PCR-RFLP) techniques in the lymphocytes from female breast cancer cases and controls. GSACV showed a significantly positive correlation with B6 concentration, and 48 nmol/L of B6 was the most suitable concentration for maintaining GSACV in vitro. The GSACV indexes showed significantly different sensitivity to B6 deficiency between cases and controls; the B6 effect on the GSACV variance contribution of each index was significantly higher than that of genetic polymorphisms and the sample state (tumor state). SHMT C1420T mutations may reduce breast cancer susceptibility, whereas MTRR A66G and MS A2756G mutations may increase breast cancer susceptibility. The role of SHMT, MS, and MTRR genotype polymorphisms in GSACV is reduced compared with that of B6. The results appear to suggest that the long-term lack of B6 under these conditions may increase genetic damage and cell injury and that individuals with various genotypes have different sensitivities to B6 deficiency. FMOCM metabolic enzyme gene polymorphism may be related to breast cancer susceptibility to a certain extent due to the effect of other factors such as stress, hormones, cancer therapies, psychological conditions, and diet. Adequate B6 intake may be good for maintaining genome health and preventing breast cancer.
Biophysical Assessment of Human Aquaporin-7 as a Water and Glycerol Channel in 3T3-L1 Adipocytes

The plasma membrane aquaporin-7 (AQP7) has been shown to be expressed in adipose tissue and its role in glycerol release/uptake in adipocytes has been postulated and correlated with obesity onset. However, some studies have contradicted this view. Based on this situation, we have re-assessed the precise localization of AQP7 in adipose tissue and analyzed its function as a water and/or glycerol channel in adipose cells. Fractionation of mice adipose tissue revealed that AQP7 is located in both adipose and stromal vascular fractions. Moreover, AQP7 was the only aquaglyceroporin expressed in adipose tissue and in 3T3-L1 adipocytes. By overexpressing the human AQP7 in 3T3-L1 adipocytes it was possible to ascertain its role as a water and glycerol channel in a gain-of-function scenario. AQP7 expression had no effect in equilibrium cell volume but AQP7 loss of function correlated with higher triglyceride content. Furthermore it is also reported for the first time a negative correlation between water permeability and the cell non-osmotic volume supporting the observation that AQP7 depleted cells are more prone to lipid accumulation. Additionally, the strong positive correlation between the rates of water and glycerol transport highlights the role of AQP7 as both a water and a glycerol channel and reflects its expression levels in cells. In all, our results clearly document a direct involvement of AQP7 in water and glycerol transport, as well as in triglyceride content in adipocytes.
Power grasp planning for anthropomorphic robot hands

This paper presents an approach for computing power grasps for hands with kinematic structure similar to the human hand, which allows the implementation of strategies inspired in human grasping actions. The proposed method first samples the object surface to look for the best spots for creating an opposing grasp with two or three fingers, and then aligns the other fingers to match the local curvature of the object surface. Different grasp strategies are considered, depending on the relative size of the object with respect to the hand, and on the location of potential obstacles in the environment. Several application examples are provided with two different hand models.
Vector bundle extensions, sheaf cohomology, and the heterotic standard model

Stable, holomorphic vector bundles are constructed on an torus fibered, non-simply connected Calabi-Yau threefold using the method of bundle extensions. Since the manifold is multiply connected, we work with equivariant bundles on the elliptically fibered covering space. The cohomology groups of the vector bundle, which yield the low energy spectrum, are computed using the Leray spectral sequence and fit the requirements of particle phenomenology. The physical properties of these vacua were discussed previously. In this paper, we systematically compute all relevant cohomology groups and explicitly prove the existence of the necessary vector bundle extensions. All mathematical details are explained in a pedagogical way, providing the technical framework for constructing heterotic standard model vacua.
The metallicity dependence of the Cepheid PL-relation

A sample of 37 Galactic, 10 LMC and 6 SMC cepheids is compiled for which individual metallicity estimates exist and BVIK photometry in almost all cases. The Galactic cepheids all have an individual distance estimate available. For the MC objects different sources of photometry are combined to obtain improved periods and mean magnitudes. A multi-parameter Period-Luminosity relation is fitted to the data which also solves for the distance to the LMC and SMC. When all three galaxies are considered, without metallicity effect, a significant quadratic term in $\log P$ is found, as previously observed and also predicted in some theoretical calculations. For the present sample it is empirically determined that for $\log P PL -relations may be adopted, but this restricts the sample to only 4 LMC and 1 SMC cepheid. Considering the Galactic sample a metallicity effect is found in the zero point in the VIWK PL -relation ($-0.6 \pm 0.4$ or $-0.8 \pm 0.3$ mag/dex depending on the in- or exclusion of one object), in the sense that metal-rich cepheids are brighter. The small significance is mostly due to the fact that the Galactic sample spans a narrow metallicity range. The error is to a significant part due to the error in the metallicity determinations and not to the error in the fit. Including the 5 MC cepheids broadens the observed metallicity range and a metallity effect of about $-0.27 \pm 0.08$ mag/dex in the zero point is found in VIWK , in agreement with some previous empirical estimates, but now derived using direct metallicity determinations for the cepheids themselves.
H E ] 1 0 Ju l 2 01 1 Formatted to JCAP style Searches for Dark Matter annihilation signatures in the Segue 1 satellite galaxy with the MAGIC-I telescope MAGIC Collaboration

We report the results of the observation of the nearby satellite galaxy Segue 1 performed by the MAGIC-I ground-based gamma-ray telescope between November 2008 and March 2009 for a total of 43.2 hours. No significant gamma-ray emission was found above the background. Differential upper limits on the gamma-ray flux are derived assuming various power-law slopes for the possible emission spectrum. Integral upper limits are also calculated for several power-law spectra and for different energy thresholds. The values are of the order of 10−11 ph cm−2 s−1 above 100 GeV and 10−12 ph cm−2 s−1 above 200 GeV. Segue 1 is currently considered one of the most interesting targets for indirect dark matter searches. In these terms, the upper limits have been also interpreted in the context of annihilating dark matter particles. For such purpose, we performed a grid scan over a reasonable portion of the parameter space for the minimal SuperGravity model and computed the flux upper limit for each point separately, taking fully into account the peculiar spectral features of each model. We found that in order to match the experimental upper limits with the model predictions, a minimum flux boost of 103 is required, and that the upper limits are quite dependent on the shape of the gamma-ray energy spectrum predicted by each specific model. Finally we compared the upper limits with the predictions of some dark matter models able to explain the PAMELA rise in the positron ratio, finding that Segue 1 data are in tension with the dark matter explanation of the PAMELA spectrum in the case of a dark matter candidate annihilating into τ+τ−. A complete exclusion however is not possible due to the uncertainties in the Segue 1 astrophysical factor.
Efficient protocol for isolation of functional RNA from different grape tissue rich in polyphenols and polysaccharides for gene expression studies

Electronic Journal of Biotechnology ISSN: 0717-3458 Vol.11 No.3, Issue of July 15, 2008 © 2008 by Pontificia Universidad Catolica de Valparaiso -- Chile Received April 15, 2007 / Accepted January 23, 2008
Back up the organisation: how employees and information systems re-member organizational practice

A case study of an organizational memory information system located within a Portuguese bank is described and analyzed. It shows how the development of effective organizational memory and performance can be rendered problematic by such a system and how such problems were alleviated through the provision of formal and informal back up mechanisms and improvisations. The paper concludes with a consideration of these findings for the theory and practice of organizational memory information system development.
Neuroimaging in Multiple Sclerosis

Multiple sclerosis (MS) is a chronic disabling autoimmune disorder of the central nervous system histopathologically characterized by inflammation, multifocal demyelination, axonal damage and neuronal loss. Focal intensive demyelination and white matter infiltration by lymphocytes and mononuclear cells are pathological hallmarks of the disease (Ferguson et al., 1997; Lucchinetti et al., 2000). Complementary to the clinical evaluation, conventional magnetic resonance imaging (cMRI) plays a prominent role for diagnosis and assessment of patients with multiple sclerosis. It provides reliable detection and quantitative estimation of focal white matter lesions in vivo. Modern criteria involve MRI parameters for the diagnosis of MS and for predicting conversion to clinically definite MS in patients who present with a first clinical episode (eg, unilateral optic neuritis) suggestive of disease onset. A diagnosis of multiple sclerosis is based on showing disease dissemination in space and time and excluding other neurological disorders that can clinically and radiologically mimic multiple sclerosis. However, neurological impairment of patients with MS is poorly associated with the lesion load observed on conventional MRI scans. The discrepancy between clinical and conventional MRI findings in MS is explained, at least partially, by the low sensitivity of conventional MRI in the detection of grey-matter involvement and diffuse damage in white matter. In order to overcome these limitations new uses of conventional MRI methods have evolved and nonconventional MRI techniques have been developed. These advances are expected to help in understanding the underlying disease processes and the accumulation of irreversible disability and therefore are promising tools in studies of disease evolution and clinical trials. Optical coherence tomography (OCT) -a new, sensitive and non-invasive transpupillary imaging methodis able to provide accurate and quantitative measurements of axonal loss in retina and therefore holds promise as a biomarker for neurodegeneration in MS. This chapter reviews the use of cMRI techniques to diagnosis and follow-up of patients with MS. It also summarizes the evolving non-conventional MRI and non-invasive optical techniques, which are sensitive to different aspects of MS pathology and are promising to further increase our understanding of disease pathophysiology and the mechanisms accounting for the accumulation of irreversible disability.
Human Activity Recognition from Video: modeling, feature selection and classification architecture

In this paper, we address the problem of recognizing human activities, such as {Active, Inactive, Walking, Running, Fighting}from video sequences, with a particular emphasis on the problems of feature selection, data modeling and classifier structure. The need for such systems is increasing everyday, with the number of (hundreds or thousands) of surveillance cameras deployed in public spaces. This massive number of cameras calls for systems able to detect, categorize and recognize human activity, requesting human attention only when necessary. Our work is focused on three fundamental issues: (i) the design of a classifier and data modeling for activity recognition; (ii) how to perform feature selection and (iii) how to define the structure of a classifier. We use of a Bayesian classifier, and model the likelihood functions as Gaussian mixtures, adequate to cope with complex data distributions, that are learned automatically. As for feature selection, we propose several (suboptimal) methods to evaluate the recognition rate achieved with different feature combinations, with the Bayesian classifier. Finally, we investigate the use of hierarchical classifiers (including the possibility of automatic generation). Our results were based on nearly 16,000 images of five activities and we achieved an error rate as low as 1.5%. These experiments clearly demonstrate the importance of powerful methodologies for data modeling and how intertwined feature selection, classifier design and the structure of the classifier are.
The polynomial method in circuit complexity

The basic techniques for using polynomials in complexity theory are examined, emphasizing intuition at the expense of formality. The focus is on the connections to constant-depth circuits, at the expense of polynomial-time Turing machines. The closure properties, upper bounds, and lower bounds obtained by this approach are surveyed. <<ETX>>