Miracle-dz/UniFAR-FTUs huggingface dataset:
A Novel Sensor Kinase-Response Regulator Hybrid Controls Biofilm Formation and Type VI Secretion System Activity in Burkholderia cenocepacia

ABSTRACT Burkholderia cenocepacia is an important opportunistic pathogen causing serious chronic infections in patients with cystic fibrosis (CF). Adaptation of B. cenocepacia to the CF airways may play an important role in the persistence of the infection. We have identified a sensor kinase-response regulator (BCAM0379) named AtsR in B. cenocepacia K56-2 that shares 19% amino acid identity with RetS from Pseudomonas aeruginosa. atsR inactivation led to increased biofilm production and a hyperadherent phenotype in both abiotic surfaces and lung epithelial cells. Also, the atsR mutant overexpressed and hypersecreted an Hcp-like protein known to be specifically secreted by the type VI secretion system (T6SS) in other gram-negative bacteria. Amoeba plaque assays demonstrated that the atsR mutant was more resistant to Dictyostelium predation than the wild-type strain and that this phenomenon was T6SS dependent. Macrophage infection assays also demonstrated that the atsR mutant induces the formation of actin-mediated protrusions from macrophages that require a functional Hcp-like protein, suggesting that the T6SS is involved in actin rearrangements. Three B. cenocepacia transposon mutants that were found in a previous study to be impaired for survival in chronic lung infection model were mapped to the T6SS gene cluster, indicating that the T6SS is required for infection in vivo. Together, our data show that AtsR is involved in the regulation of genes required for virulence in B. cenocepacia K56-2, including genes encoding a T6SS.
The Smallest Grammar Problem as Constituents Choice and Minimal Grammar Parsing

The smallest grammar problem—namely, finding a smallest context-free grammar that generates exactly one sequence—is of practical and theoretical importance in fields such as Kolmogorov complexity, data compression and pattern discovery. We propose a new perspective on this problem by splitting it into two tasks: (1) choosing which words will be the constituents of the grammar and (2) searching for the smallest grammar given this set of constituents. We show how to solve the second task in polynomial time parsing longer constituent with smaller ones. We propose new algorithms based on classical practical algorithms that use this optimization to find small grammars. Our algorithms consistently find smaller grammars on a classical benchmark reducing the size in 10% in some cases. Moreover, our formulation allows us to define interesting bounds on the number of small grammars and to empirically compare different grammars of small size.
Association fiber pathways to the frontal cortex from the superior temporal region in the rhesus monkey

The projections to the frontal cortex that originate from the various areas of the superior temporal region of the rhesus monkey were investigated with the autoradiographic technique. The results demonstrated that the rostral part of the superior temporal gyrus (areas Pro, Ts1, and Ts2) projects to the proisocortical areas of the orbital and medial frontal cortex, as well as to the nearby orbital areas 13, 12, and 11, and to medial areas 9, 10, and 14. These fibers travel to the frontal lobe as part of the uncinate fascicle. The middle part of the superior temporal gyrus (areas Ts3 and paAlt) projects predominantly to the lateral frontal cortex (areas 12, upper 46, and 9) and to the dorsal aspect of the medial frontal lobe (areas 9 and 10). Only a small number of these fibers terminated within the orbitofrontal cortex. The temporofrontal fibers originating from the middle part of the superior temporal gyrus occupy the lower portion of the extreme capsule and lie just dorsal to the fibers of the uncinate fascicle. The posterior part of the superior temporal gyrus projects to the lateral frontal cortex (area 46, dorsal area 8, and the rostralmost part of dorsal area 6). Some of the fibers from the posterior superior temporal gyrus run initially through the extreme capsule and then cross the claustrum as they ascend to enter the external capsule before continuing their course to the frontal lobe. A larger group of fibers curves round the caudalmost Sylvian fissure and travels to the frontal cortex occupying a position just above and medial to the upper branch of the circular sulcus. This latter pathway constitutes a part of the classically described arcuate fasciculus.
Cingulum bundle asymmetry predicts trait neuroticism: A DTI study

0.204 -0.301 0.043 -0.280 0.063 0.284 0.058 Angry hostility 0.164 -0.308 0.044 -0.337 0.030 -0.026 0.865 Depression 0.216 -0.307 0.038 -0.106 0.469 0.323 0.031 Self-consciousness 0.112 -0.192 0.214 -0.296 0.063 0.158 0.310 Impulsiveness 0.138 -0.076 0.616 -0.353 0.026 0.238 0.125 Vulnerability 0.210 -0.356 0.017 -0.095 0.521 0.259 0.082
Subunit-Specific Trafficking of GABAA Receptors during Status Epilepticus

It is proposed that a reduced surface expression of GABAA receptors (GABARs) contributes to the pathogenesis of status epilepticus (SE), a condition characterized by prolonged seizures. This hypothesis was based on the finding that prolonged epileptiform bursting (repetitive bursts of prolonged depolarizations with superimposed action potentials) in cultures of dissociated hippocampal pyramidal neurons (dissociated cultures) results in the increased intracellular accumulation of GABARs. However, it is not known whether this rapid modification in the surface-expressed GABAR pool results from selective, subunit-dependent or nonselective, subunit-independent internalization of GABARs. In hippocampal slices obtained from animals undergoing prolonged SE (SE-treated slices), we found that the surface expression of the GABAR β2/3 and γ2 subunits was reduced, whereas that of the δ subunit was not. Complementary electrophysiological recordings from dentate granule cells in SE-treated slices demonstrated a reduction in GABAR-mediated synaptic inhibition, but not tonic inhibition. A reduction in the surface expression of the γ2 subunit, but not the δ subunit was also observed in dissociated cultures and organotypic hippocampal slice cultures when incubated in an elevated KCl external medium or an elevated KCl external medium supplemented with NMDA, respectively. Additional studies demonstrated that the reduction in the surface expression of the γ2 subunit was independent of direct ligand binding of the GABAR. These findings demonstrate that the regulation of surface-expressed GABAR pool during SE is subunit-specific and occurs independent of ligand binding. The differential modulation of the surface expression of GABARs during SE has potential implications for the treatment of this neurological emergency.
Topology and dynamics of boolean networks with strong inhibition

A major challenge in systems biology is to understand interactions within biological systems. Such a system often consists of units with various levels of activities that evolve over time, mathematically represented by the dynamics of the system. The interaction between units is mathematically represented by the topology of the system. We carry out some mathematical analysis on the connections between topology and dynamics of such networks. We focus on a specific Boolean network model - the Strong Inhibition Model. This model defines a natural map from the space of all possible topologies on the network to the space of all possible dynamics on the same network. We prove this map is neither surjective nor injective. We introduce the notions of "redundant edges" and "dormant vertices" which capture the non-injectiveness of the map. Using these, we determine exactly when two different topologies yield the same dynamics and we provide an algorithm that determines all possible network solutions given a dynamics.
L'Observatoire des sciences et des techniques : activités - définition - méthodologie

Dans cet article, les auteurs rendent compte des m�thodes et indicateurs mis en oeuvre par l'Observatoire des sciences et des techniques. Ils indiquent les types de visibilit� qui s'en suivent et sugg�rent ce que pourrait �tre une herm�neutique strat�gique prenant appui sur des m�thodes de type infom�trique dans le domaine des acteurs-r�seaux techno-�conomiques.
Model Checking Meets Probability: A Gentle Introduction

This paper considers fully probabilistic system models. Each transition is quantified with a probability—its likelihood of occurrence. Properties are expressed as automata that either accept or reject system runs. The central question is to determine the fraction of accepted system runs. We also consider probabilistic timed system models. Their properties are timed automata that accept timed runs iff all timing constraints resent in the automaton are met; otherwise it rejects. The central question is to determine the fraction of accepted timed system runs.
Introduction to Special Theme Issue

The last 2 decades have witnessed a relative explosion of research on cognition in schizophrenia, using a variety of approaches that range from the use of large neuropsychological batteries to focused cognitive experimental techniques. There are several reasons for this surge of research on cognitive function in schizophrenia. One reason is the growing body of research suggesting that cognitive function in schizophrenia is one of the most critical determinants of quality of life in schizophrenia, potentially more so than the severity of other aspects/symptoms of schizophrenia such as hallucinations, delusions, or even negative symptoms.1 A second reason is the hope that understanding the nature of cognitive dysfunction in schizophrenia will give us insight into the neurobiological mechanisms that contribute to the development of this disorder, spurred by the advances made in understanding the neural mechanisms supporting intact cognitive function. A third reason is the hope that cognitive deficits will serve as endophenotypic markers that will help identify genetic or environmental risk factors for the development of schizophrenia. A fourth reason is the hope that understanding the mechanisms leading to cognitive dysfunction in schizophrenia will spur novel drug development and discoveries that may improve cognitive and life function in this illness. As articulated by Gottesman and Hanson,2 the clinical traits used to diagnose schizophrenia, or the subclinical phenomena often used to identify those at risk for schizophrenia, have little biological reality, making it difficult to link them to genetic mechanisms. If at least some cognitive functions have an identifiable link to neurobiological and genetic mechanisms (as recent cognitive neuroscience and functional genomics research suggests), then cognitive deficits may serve as promising endophenotypic markers in the search for the etiology of schizophrenia.3–5
SENSO E NON SENSO DELLA SCUOLA TRA ISTITUZIONE E ORGANIZZAZIONE

This article analyses the current relaity of schooling, highlighting some of the major changing factors: factors of turbolence (i.e. the reform processes) and negative attitudes towards the change, expressed by teachers, headmasters, parents and extra-school agencies); processes of de-structuration of the institutional stability; processes of fragmentation and lost of motivation within the social actors within the school establishments. It follows the interpretation of this frame on the base of the ambivalence "institution versus organisation", that can explain part of this increasing complexity. Finally, to cope with the complexity it is proposed a model of solution as process of "institutionalization bottom-up", based on th sense making capability of the social actors in school.
Modified One Cycle Controlled Scheme for Single-Phase Grid Connected Pv-Fc Hybrid System

AC to DC converters based on one cycle control exhibit instability in current control. In this paper modified one cycle control(MOOC) for bidirectional ac to dc is proposed. The sum of fictitious current and the actual load current is compared with a sawtooth waveform to generate the generating switches. In order to interface the inverter with the grid service of a phase locked loop(PLL) is required. Designing a phase locked loop for interfacing with a weak grid is always a difficult proposition considering the nonidealities like frequency variation and harmonic distortions in the line voltages. Renewable energy is currently widely used one of these resources is solar energy. The pv array normally uses a maximum power point tracking (MPPT) technique to continuously deliver the highest power to the load when there are variations in irradiation and temperature, making it an uncontrollable source. The disadvantage of pv energy is that the pv output power depends on weather conditions and cell temperature further it is not available during night. In order to over these drawbacks alternative source such as proton exchange membrane fuel cell (PEMFC) should be installed in the hybrid system by changing the fuel cell output power the hybrid sources output becomes controllable. Keywods: Maximum power point tracking (MPPT), One cycle control (OCC), Bidirectional ac to dc converter, PV Array, Proton exchange membrane fuel cell(PEMFC).
Region-Based Color Correction of Images

This paper proposes a region-based color correction method that corrects color-shifted images based on a reference image with a standard background. When correcting images without foreground objects, i.e., objects not in the reference image, both the reference image and the color-shifted image are segmented into several regions. A color correction process based on principal component analysis (PCA) is performed between the corresponding regions on the reference image and color-shifted image. The key concept of the color correction process is to align the color distribution of regions on the color-shifted image with the corresponding ones on the reference image by an Affine transform. The proposed color correction is also applicable to those images with foreground objects. In the experiments, the effectiveness of the proposed method is verified by testing some simple images and real-world images with and without foreground objects. Particularly, the proposed method effectively improves the skin-color area identification in a face detector, which is an important issue in many computer vision applications
The yjeQ Gene Is Required for Virulence of Staphylococcus aureus

ABSTRACT Gene products required for in vivo growth and survival of Staphylococcus aureus and other pathogens represent new targets for antimicrobial chemotherapy. In this study we created a Staphylococcus aureus yjeQ deletion strain and tested its virulence using a mouse kidney abscess infection model. The yjeQ deletion strain was compromised for growth in vitro and severely attenuated for virulence. We concluded that yjeQ is an attractive and novel new drug target.
An Architecture for Learning "Potential Field" Cognitive Maps with an Application to Mobile Robotics

The learning architecture described in this article autonomously acquires a topographical (metric) map that encodes a measure of "value" for xy-Cartesian locations in an environment. There are two reasons for the creation of low value areas. Direct negative reinforcement from the environment will result from the robot discovering obstacles or having other "unpleasant" experiences. - The other source of negative reinforcement is internally generated by the learning algorithm, as it identifies regions that are a long distance away from the "pleasant" places in the environment. Conversely example "pleasant" places, where positive environmental reward is received, might be energy-charging sites or simply locations that the robot should visit in executing its daily tasks. In general what the robot learns is a map of "motivational" tendencies, or "expectancies". In such a map, the value attached to a place comes to reflect a balance between the good and bad rewards attainable from that position. When the Temporal Difference learning part of the architecture is turned on, that measure of value comes to include an estimate of how far, in travel time, it is to positive reinforcement. The architecture is loosely based on an Adaptive Heuristic Critic structure. Exploration of a continuous-valued search space is conducted by an Evolution Strategy, tuned for fast and approximate optimization. Knowledge acquired autonomously from this exploration is stored in a Radial Basis Function (RBF) neural network. Inherent features of this neural network type lead to the creation of a "potential field" structure that exerts appetitive and aversive "forces"on the robot as it moves around in the environment. The results of simulation experiments are presented, with a view to illustrating the strengths and weaknesses of the architecture. The map building architecture proposed here is intended to form part of an overall navigational system. In future work it will be integrated with a self-localization algorithm, landmark-based topological mapping, and a reactive system for dealing with local dynamics in the environment.
Hustling, Hassling and Making it Happen: Researching Consultants in a Small Firm Context

The investigation of work in small consultancy firms poses particular challenges for researchers. These include the omnipotence of the founding entrepreneur, estrangement from the academic community, a lack of time, an ambiguous knowledge base and the ostensibly unitarist nature of work relations in such settings. Drawing on the experience of an intensive fieldwork study of employment relations in three small consultancy firms, this paper examines how an `entrepreneurial' approach was used to address such contingencies. Key features of this process were the enactment of fieldwork opportunities, the potential creation of a `joint venture' and the subsequent management of relations in the field. A degree of manipulation is an inherent feature of such an enterprise; but this should be seen in the context of a relationship of `symmetry' between researcher and researched.
Detection of Cognitive States from fMRI Data Using Machine Learning Techniques

Over the past decade functional Magnetic Resonance Imaging (fMRI) has emerged as a powerful technique to locate activity of human brain while engaged in a particular task or cognitive state. We consider the inverse problem of detecting the cognitive state of a human subject based on the fMRI data. We have explored classification techniques such as Gaussian Naive Bayes, k-Nearest Neighbour and Support Vector Machines. In order to reduce the very high dimensional fMRI data, we have used three feature selection strategies. Discriminating features and activity based features were used to select features for the problem of identifying the instantaneous cognitive state given a single fMRI scan and correlation based features were used when fMRI data from a single time interval was given. A case study of visuo-motor sequence learning is presented. The set of cognitive states we are interested in detecting are whether the subject has learnt a sequence, and if the subject is paying attention only towards the position or towards both the color and position of the visual stimuli. We have successfully used correlation based features to detect position-color related cognitive states with 80% accuracy and the cognitive states related to learning with 62.5% accuracy.
Television and party political dissent: intra-party competition and the formation of news agendas

This paper re-examines the formation of political news agendas on British television. It argues that studies of news agenda formation in political communication have been overly focused on general election campaigns and the competition between the main political parties to set the news agenda. It suggests that such studies see political parties as either homogeneous or focus exclusively on the activities of communication elites and therefore miss another important aspect of the modern political communication process. Using the British party conferences as a case study, this paper argues that in order to capture the complexities of agenda formation outside election periods, political parties have to be seen as heterogeneous organisations, consisting of various ‘claim-makers’. News agendas in certain situations have to be understood as the product of intra-party competition between the leadership and dissenting voices. While this competition is imperfect, favouring resource rich party elites, on certain newsworthy issues broadcasting professionals act as a counterweight to leadership resource advantages, and help shape the outcome of intra-party competition. In conclusion the paper suggests that dissenting actors within political parties, when newsworthy, can make a substantial contribution to the formation of television news agendas despite the resistance of party leaderships. Taking account of the communicative activity of these actors and of news values will provide further insights into the formation of political news agendas between general elections. Copyright © 2001 Henry Stewart Publications
Research Project : Packing Problems in Combinatorial Optimization submitted to the Probral DAAD – CAPES Program

In this project we plan to develop new approaches and algorithms to solve hard combinatorial optimization problems. Many of these problems have important applications in practice. For instance, many problems that arise in the design of VLSI circuits can be formulated as combinatorial optimization problems (see [26]). We are specially interested in packing problems. Such problems have been broadly investigated not only because of their interesting theoretical aspects, but also due to their many practical applications, such as in cloth, glass, paper and wood industries. They also have applications in design of VLSI circuits, warehouse storage, newspapers paging, production of alcohol in the sugar cane industry, and in several other contexts. In this project we intend to develop new algorithms for a variety of packing problems. All participants have ongoing experience on this subject, and this project is a natural attempt to combine their skills to solve new hard problems.