Miracle-dz/UniFAR-FTUs huggingface dataset:
Methicillin Resistance Reduces the Virulence of Healthcare-Associated Methicillin-Resistant Staphylococcus aureus by Interfering With the agr Quorum Sensing System

The difficulty in successfully treating infections caused by methicillin-resistant Staphylococcus aureus (MRSA) has led to them being referred to as highly virulent or pathogenic. In our study of one of the major healthcare-associated MRSA (HA-MRSA) clones, we show that expression of the gene responsible for conferring methicillin resistance (mecA) is also directly responsible for reducing the ability of HA-MRSA to secrete cytolytic toxins. We show that resistance to methicillin induces changes in the cell wall, which affects the bacteria's agr quorum sensing system. This leads to reduced toxin expression and, as a consequence, reduced virulence in a murine model of sepsis. This diminished capacity to cause infection may explain the inability of HA-MRSA to move into the community and help us understand the recent emergence of community-associated MRSA (CA-MRSA). CA-MRSA typically express less penicillin-binding protein 2a (encoded by mecA), allowing them to maintain full virulence and succeed in the community environment.
Process warehouses in practice: a goal‐driven method for business process analysis

Process analysis and improvement, one of the core phases in the business process management life cycle, is reaching the top of the agenda for many enterprises and organizations. An emerging approach to analyzing business processes involves the use of process‐oriented data warehouses to collect information about executed processes to enable their detailed analysis and thereby provide bases for possible improvements. However, very little work has been carried out on employing business orientation in the design and utilization of a process warehouse. The approach presented in this study addresses that limitation by proposing a method that relates business goals to the information from the warehouse. To do so, we start by defining a desired goal structure that concerns an existing business process. The obtained goal model is firstly utilized for scoping and designing a corresponding data model for a process warehouse, and further for retrieving the information from the warehouse to examine the fulfillment of the goals of interest. The key benefits of the proposed method are the provision of the relevant and accurate business process information as well as tracing the process‐related goals to the process execution data and further to the analysis of the process. As validation of the proposed method, we develop a prototype, and a healthcare process is used as an illustrative example. Also, to demonstrate the method quality, we perform an experiment on the effectiveness of the information access and retrieval. Copyright © 2011 John Wiley & Sons, Ltd.
TNM residual tumor classification revisited

For cancer patients, prognosis is strongly influenced by the completeness of tumor removal at the time of cancer‐directed surgery or disease remission after nonsurgical treatment with curative intent. These parameters define the relative success of definitive treatment and can be codified by an additional subclassification within the TNM system, the residual tumor (R) classification. Despite the importance of residual tumor status in designing clinical management after treatment, misinterpretation and inconsistent application of the R classification frequently occur that diminish or abrogate its clinical utility.
Direction recognition of moving targets using an IR-UWB radar system

This paper presents a new direction recognition algorithm of moving targets using an impulse radio ultra-wideband (IR-UWB) radar system. To improve the stability of the direction recognition of moving targets, the algorithm divides the whole observation area into three main areas. Each main area consists of three sub-areas. Moreover, we use the mid-point of the effective area as the position of the target instead of the position for the largest peak value of the target signal to enhance the accuracy of the algorithm. The performance comparison between the algorithm based on the mid-point and the algorithm based on the largest peak value is discussed in this paper. Detection error is also discussed in this paper. To prove the performance of the proposed algorithm, the performance analysis is given.
A Probabilistic Model for Fine-Grained Expert Search

Expert search, in which given a query a ranked list of experts instead of documents is returned, has been intensively studied recently due to its importance in facilitating the needs of both information access and knowledge discovery. Many approaches have been proposed, including metadata extraction, expert profile building, and formal model generation. However, all of them conduct expert search with a coarse-grained approach. With these, further improvements on expert search are hard to achieve. In this paper, we propose conducting expert search with a fine-grained approach. Specifically, we utilize more specific evidences existing in the documents. An evidence-oriented probabilistic model for expert search and a method for the implementation are proposed. Experimental results show that the proposed model and the implementation are highly effective.
Molecular Indices of Neuronal and Glial Plasticity in the Hippocampal Formation in a Rodent Model of Age-Induced Spatial Learning Impairment

Spatial learning ability was quantitated in young and aged Long–Evans rats, and molecular markers were assessed in the striatum and hippocampal formation using immunocytochemical, immunoblotting, andin situ hybridization histochemical procedures. The mRNA for β-amyloid precursor protein (βAPP), most likely the transcript encoding the 695-amino acid form of this protein, was elevated in pyramidal and granule cells in the hippocampus of aged rats exhibiting poorer spatial learning. In immunoblots of hippocampal protein extracts, however, the level of βAPP-like immunoreactivity was depressed in the more impaired subjects. Similarly, the level in hippocampus of the mRNA for manganese-dependent superoxide dismutase (Mn-SOD), a marker of oxidative stress, was positively correlated with the degree of behavioral impairment, but immunoblotting revealed that Mn-SOD protein was depressed in the aged hippocampus compared with young. The mRNAs for the neuronal form of nitric oxide synthase and for the astrocyte marker glial fibrillary acidic protein (GFAP) were elevated in the hippocampus in correlation with the extent of learning impairment. In the striatum, the levels of mRNA and protein for several candidate genes, including GFAP, were elevated in parallel with the learning index, but these were age effects. Several hippocampal proteins were unchanged (GFAP) or depressed (βAPP and Mn-SOD) in level, despite elevations in corresponding mRNAs. In the aged cohort, hippocampal GFAP mRNA, Mn-SOD mRNA, and βAPP emerged as predictors of behavioral impairment, suggesting the involvement of these hippocampal systems in age-related cognitive impairment.
Hypoxia Enhances the Antiglioma Cytotoxicity of B10, a Glycosylated Derivative of Betulinic Acid

B10 is a glycosylated derivative of betulinic acid with promising activity against glioma cells. Lysosomal cell death pathways appear to be essential for its cytotoxicity. We investigated the influence of hypoxia, nutrient deprivation and current standard therapies on B10 cytotoxicity. The human glioma cell lines LN-308 and LNT-229 were exposed to B10 alone or together with irradiation, temozolomide, nutrient deprivation or hypoxia. Cell growth and viability were evaluated by crystal violet staining, clonogenicity assays, propidium iodide uptake and LDH release assays. Cell death was examined using an inhibitor of lysosomal acidification (bafilomycin A1), a cathepsin inhibitor (CA074-Me) and a short-hairpin RNA targeting cathepsin B. Hypoxia substantially enhanced B10-induced cell death. This effect was sensitive to bafilomycin A1 and thus dependent on hypoxia-induced lysosomal acidification. Cathepsin B appeared to mediate cell death because either the inhibitor CA074-Me or cathepsin B gene silencing rescued glioma cells from B10 toxicity under hypoxia. B10 is a novel antitumor agent with substantially enhanced cytotoxicity under hypoxia conferred by increased lysosomal cell death pathway activation. Given the importance of hypoxia for therapy resistance, malignant progression, and as a result of antiangiogenic therapies, B10 might be a promising strategy for hypoxic tumors like malignant glioma.
Recent progresses in the inspection of aerospace components by infrared thermography

The use NonDestructive Testing and Evaluation (NDT&E) techniques for the inspection of aerospace materials has progressively increase in the last few decades as commercial and military aircrafts exceed their initial design life. Aerospace components are typically made of aluminium, honeycomb structures, composites or fibre metal laminates (FML), which are affected by different types of anomalies, namely: delaminations, disbonds, water ingress, node failure and core crushing. Possible causes are either material contamination introduced during manufacture, e.g. dirt, solvents, moisture, oils, etc.; or by damages caused during in-flight operation, e.g. after impact. Infrared thermography techniques have proven to be an effective way to detect and, in many cases, to quantify the degree of surface and subsurface damage on such components. Several configurations have been proposed to achieve an active thermography inspection ranging from passive inspection, i.e. without applying any external stimulation, to active approaches, in which an external source of energy is used to produce a thermal contrast between the non-defective and the defective material. The thermal stimulation can be delivered to the specimen surface by optical, mechanical, electromagnetic or other means. The physics and the practical considerations behind these approaches are different in all cases, and the selection of one or another will depend on the specific application and the availability of the equipment. In this paper, a review of recent developments on the thermographic inspection of aerospace materials is proposed. Some guidelines, supported with examples on real and academic specimens, are provided to illustrate the most suitable technique to be considered for some conventional applications.
Towards Optimized TCP/IP Covert Channels Detection, IDS and Firewall Integration

Covert channels exist in most communications systems and allow individuals to communicate truly undetectable and exchange hidden information. That's why their detection seems to be a big deal for security systems. However, till now, security systems do not include dedicated processes for covert channel detection. In this paper, we first propose mechanisms to detect common covert channels. Then, within a whole security system, we propose an optimized order regarding the execution of the three major security processes: Firewall, Intrusion Detection System (IDS) and Covert Channel Detection System (CCDS). It will be demonstrated that the proposed order would allow security systems to offer better processing performances.
Neodymium-complex-doped steady-state polymer waveguide lasers

Channel waveguides based on a polymer, 6-fluorinated-dianhydride/epoxy, which is actively doped with a rare-earth-ion-doped complex, Nd(thenoyltrifluoroacetone)3 1,10-phenanthroline, have been fabricated. Luminescence and loss spectra of the channel waveguides have been experimentally investigated. By optimization of the fabrication procedure of both, host material and optical structure, steady-state laser emission has been demonstrated from a channel waveguide near 1060 nm, which provides up to 440 µW of output power from the waveguide structures developed.
Recurrent Neural Net Regression Models with space-varying coefficients for pedotransfer function estimation and prediction of soil properties

The paper aim is to propose a new regression model for relating soil variables of difficult or complex measurement with other variables easier to measure, in order to predict the first one based on data about the last ones. The measurements are taken along soil lines called transects. The study of these relations (pedotransfer functions) presents the complexity of simultaneous presence of 3 elements: data spatial dependence, soil non-homogeneity and non-linearity of the relationship. The main models usually considered in the literature for such relations (namely, linear state-space and feedforward neural nets) have the limitation of expressing only two of these 3 characteristics of the problem. In order to overcome such limitations, it is proposed here a regression model for pedotransfer mapping based on recurrent neural nets (the feedback helps to better express the spatial dependence), but with weights varying smoothly along the space in order to incorporate the soil non-homogeneity. The algorithm developed for model estimation and prediction is based on a second order non-linear extension of the Kalman filter in Bayesian form. The comparative advantages of the proposed model in relation to the other ones are shown, considering different prediction performance measures for the transect extremes.
French validation of the Barcelona Music Reward Questionnaire

Background. The Barcelona Music Reward Questionnaire (BMRQ) questionnaire investigates the main facets of music experience that could explain the variance observed in how people experience reward associated with music. Currently, only English and Spanish versions of this questionnaire are available. The objective of this study is to validate a French version of the BMRQ. Methods. The original BMRQ was translated and adapted into an international French version. The questionnaire was then administered through an online survey aimed at adults aged over 18 years who were fluent in French. Statistical analyses were performed and compared to the original English and Spanish version for validation purposes. Results. A total of 1,027 participants completed the questionnaire. Most responses were obtained from France (89.4%). Analyses revealed that congruence values between the rotated loading matrix and the ideal loading matrix ranged between 0.88 and 0.96. Factor reliabilities of subscales (i.e., Musical Seeking, Emotion Evocation, Mood Regulation, Social Reward and Sensory-Motor) also ranged between 0.88 and 0.96. In addition, reliability of the overall factor score (i.e., Music reward) was 0.91. Finally, the internal consistency of the overall scale was 0.85. The factorial structure obtained in the French translation was similar to that of the original Spanish and English samples. Conclusion. The French version of the BMRQ appears valid and reliable. Potential applications of the BMRQ include its use as a valuable tool in music reward and emotion research, whether in healthy individuals or in patients suffering from a wide variety of cognitive, neurologic and auditory disorders.
Clearance and Safety of the Radiocontrast Medium Iopamidol in Peritoneal Dialysis Patients

Although the characteristics and safety of radiocontrast media in peritoneal dialysis (PD) patients are not yet well defined, their use in PD patients is considered generally safe. In this study, we evaluated clearance and adverse events of iopamidol in PD patients. We measured the iopamidol concentration in the plasma, dialysate, and urine of 11 patients. Iopamidol clearance from patient plasma was delayed with a half-life of 33.3 h, and the elimination ratio was 83.6% for 96 h. We retrospectively investigated adverse events occurring in a total of 50 stable PD patients who underwent a total of 64 angiographic computed tomography (CT) scans. In 64 angiographic CT scans, two cases of adverse events were observed. Our results suggest that iopamidol can be eliminated by regular PD and careful observation for adverse events are necessary for the safe use of radiocontrast media.
Efficient Machine-Independent Programming of High-Performance Multiprocessors

A major component of the success of scientific computing is the rapid increase in computing capability. Parallel computing can provide the next great leap in the computation power scientists and engineers need to solve many important problems. The proliferation of parallel architectures, however, discourages users from writing parallel applications. Recent advances in automatic parallelization and parallel languages provide a means for users to write portable programs that protect software investment. Unfortunately, current systems frequently experience poor performance because they fail to fully exploit the features of the underlying parallel architecture. For uniprocessors, compilers have been quite successful in mapping machine-independent programs (e.g., Fortran, C) down to the complex features of today's microprocessors. I believe that compilers are also well-suited for customizing portable parallel programs. The objective of my research is to develop compilation techniques to support efficient machine-independent programming of high-performance multiprocessors. I plan to implement and evaluate these effectiveness of these techniques in COSMIC, a Communication-Optimizing, Shared-Memory Integrated Compiler. COSMIC will target a shared-memory programming model because it provides the best combination of flexibility and performance. Experiments show that simply exploiting parallelism is no longer sufficient for achieving the best performance, mainly because the cost of interprocessor communication is too great compared to computation and local memory accesses [74, 77]. To achieve high performance, COSMIC will perform communication analysis and apply optimizations for locality, synchronization, communication, and memory system effects. COSMIC follows two basic guidelines. First, it uses compilation techniques for message-passing machines to retain most of the benefits of explicit messages. Second, it exploits architectural and operating system support available in shared-memory multiprocessors to improve flexibility and performance. A novel characteristic of COSMIC will be its ability to take advantage of the multiple coherence protocols and hybrid message-passing support found in software Distributed-Shared-Memory (DSM) systems and Flexible-Shared-Memory (FSM) machines. To evaluate the impact on the performance on scientific applications, I will test COSMIC on programs from Flame) from fields such as computational chemistry, computational fluid dynamics, sparse matrix codes, and computational combustion. I will measure the impact of the optimizations on application performance for the IBM SP-2, DEC Alpha multiprocessor, and clusters of Alpha workstations. My goal is to significantly improve on current compilers for shared-memory architectures and match or exceed the performance of message-passing programs on distributed-memory architectures. This project will make several important contributions, including: 1) a sophisticated optimizing compiler for shared-memory machines, 2) a prototype …
General Graph Data De-Anonymization

When people utilize social applications and services, their privacy suffers a potential serious threat. In this article, we present a novel, robust, and effective de-anonymization attack to mobility trace data and social data. First, we design a Unified Similarity (US) measurement, which takes account of local and global structural characteristics of data, information obtained from auxiliary data, and knowledge inherited from ongoing de-anonymization results. By analyzing the measurement on real datasets, we find that some data can potentially be de-anonymized accurately and the other can be de-anonymized in a coarse granularity. Utilizing this property, we present a US-based De-Anonymization (DA) framework, which iteratively de-anonymizes data with accuracy guarantee. Then, to de-anonymize large-scale data without knowledge of the overlap size between the anonymized data and the auxiliary data, we generalize DA to an Adaptive De-Anonymization (ADA) framework. By smartly working on two core matching subgraphs, ADA achieves high de-anonymization accuracy and reduces computational overhead. Finally, we examine the presented de-anonymization attack on three well-known mobility traces: St Andrews, Infocom06, and Smallblue, and three social datasets: ArnetMiner, Google+, and Facebook. The experimental results demonstrate that the presented de-anonymization framework is very effective and robust to noise. The source code and employed datasets are now publicly available at SecGraph [2015].
EEG asymmetry and symptom response to cognitive behavioral herapy in patients with social anxiety disorder avid

Although previous studies have shown that socially anxious individuals exhibit greater relative right frontal electroencephalogram (EEG) activity at rest, no studies have investigated whether improvements in symptoms as a result of treatment are associated with concomitant changes in resting brain activity. Regional EEG activity was measured at rest in 23 patients with social anxiety disorder (SAD) before and after cognitive behavioral therapy (CBT). Results indicated that patients shifted significantly from EG asymmetry ocial anxiety ocial phobia ognitive behavioral therapy eurobiology rontal cortex greater relative right to greater relative left resting frontal brain activity from preto posttreatment. Greater left frontal EEG activity at pretreatment predicted greater reduction in social anxiety from preto posttreatment and lower posttreatment social anxiety after accounting for pretreatment symptoms. These relations were specific to the frontal alpha EEG asymmetry metric. These preliminary findings suggest that resting frontal EEG asymmetry may be a predictor of symptom change and endstate functioning in SAD patients who undergo efficacious psychological treatment.
Endothelial Cell Senescence in Human Atherosclerosis: Role of Telomere in Endothelial Dysfunction

Background—The functional changes associated with cellular senescence may be involved in human aging and age-related vascular disorders. We have shown the important role of telomere and telomerase in vascular cell senescence in vitro. Progressive telomere shortening in vivo has been observed in the regions susceptible to atherosclerosis, implying contributions to atherogenesis. However, whether senescent vascular cells are present in the vasculature and contribute to the pathogenesis of atherosclerosis remains unclear. Methods and Results—Senescence-associated &bgr;-galactosidase (&bgr;-gal) activity was examined in the coronary arteries and the internal mammary arteries retrieved from autopsied individuals who had had ischemic heart diseases. Strong &bgr;-gal stainings were observed in atherosclerotic lesions of the coronary arteries but not in the internal mammary arteries. An immunohistochemical analysis using anti-factor VIII antibody demonstrated that &bgr;-gal stained cells are vascular endothelial cells. To determine whether endothelial cell senescence causes endothelial dysfunction, we induced senescence in human aortic endothelial cells (HAECs) by inhibiting telomere function and examined the expression of intercellular adhesion molecule (ICAM)-1 and endothelial nitric oxide synthase (eNOS) activity. Senescent HAECs exhibited increased ICAM-1 expression and decreased eNOS activity, both of which are alterations implicated in atherogenesis. In contrast, introduction of telomerase catalytic component significantly extended the life span and inhibited the functional alterations associated with senescence in HAECs. Conclusions—Vascular endothelial cells with senescence-associated phenotypes are present in human atherosclerotic lesions, and endothelial cell senescence induced by telomere shortening may contribute to atherogenesis.