Miracle-dz/UniFAR-FTUs huggingface dataset:
Systematic and Molecular Basis of the Antibacterial Action of Quinoxaline 1,4-Di-N-Oxides against Escherichia coli

Quinoxaline 1,4-di-N-oxides (QdNOs) are widely known as potent antibacterial agents, but their antibacterial mechanisms are incompletely understood. In this study, the transcriptomic and proteomic profiles of Escherichia coli exposed to QdNOs were integratively investigated, and the results demonstrated that QdNOs mainly induced an SOS response and oxidative stress. Moreover, genes and proteins involved in the bacterial metabolism, cellular structure maintenance, resistance and virulence were also found to be changed, conferring bacterial survival strategies. Biochemical assays showed that reactive oxygen species were induced in the QdNO-treated bacteria and that free radical scavengers attenuated the antibacterial action of QdNOs and DNA damage, suggesting an oxidative-DNA-damage action of QdNOs. The QdNO radical intermediates, likely carbon-centered and aryl-type radicals, as identified by electron paramagnetic resonance, were the major radicals induced by QdNOs, and xanthine oxidase was one of the QdNO-activating enzymes. This study provides new insights into the action of QdNOs in a systematic manner and increases the current knowledge of bacterial physiology under antibiotic stresses, which may be of great value in the development of new antibiotic-potentiating strategies.
Multidimensional FEM‐FCT schemes for arbitrary time stepping

The flux‐corrected‐transport paradigm is generalized to finite‐element schemes based on arbitrary time stepping. A conservative flux decomposition procedure is proposed for both convective and diffusive terms. Mathematical properties of positivity‐preserving schemes are reviewed. A nonoscillatory low‐order method is constructed by elimination of negative off‐diagonal entries of the discrete transport operator. The linearization of source terms and extension to hyperbolic systems are discussed. Zalesak's multidimensional limiter is employed to switch between linear discretizations of high and low order. A rigorous proof of positivity is provided. The treatment of non‐linearities and iterative solution of linear systems are addressed. The performance of the new algorithm is illustrated by numerical examples for the shock tube problem in one dimension and scalar transport equations in two dimensions. Copyright © 2003 John Wiley & Sons, Ltd.
The Characteristic Trajectory of a Fixing Allele: A Consequence of Fictitious Selection That Arises from Conditioning

This work is concerned with the historical progression, to fixation, of an allele in a finite population. This progression is characterized by the average frequency trajectory of alleles that achieve fixation before a given time, T. Under a diffusion analysis, the average trajectory, conditional on fixation by time T, is shown to be equivalent to the average trajectory in an unconditioned problem involving additional selection. We call this additional selection “fictitious selection”; it plays the role of a selective force in the unconditioned problem but does not exist in reality. It is a consequence of conditioning on fixation. The fictitious selection is frequency dependent and can be very large compared with any real selection that is acting. We derive an approximation for the characteristic trajectory of a fixing allele, when subject to real additive selection, from an unconditioned problem, where the total selection is a combination of real and fictitious selection. Trying to reproduce the characteristic trajectory from the action of additive selection, in an infinite population, can lead to estimates of the strength of the selection that deviate from the real selection by >1000% or have the opposite sign. Strong evolutionary forces may be invoked in problems where conditioning has been carried out, but these forces may largely be an outcome of the conditioning and hence may not have a real existence. The work presented here clarifies these issues and provides two useful tools for future analyses: the characteristic trajectory of a fixing allele and the force that primarily drives this, namely fictitious selection. These should prove useful in a number of areas of interest including coalescence with selection, experimental evolution, time series analyses of ancient DNA, game theory in finite populations, and the historical dynamics of selected alleles in wild populations.
Automatic construction of image operators using a genetic programming approach

This paper presents a methodology for automatic construction of image operators using a linear genetic programming approach, for binary, gray level and color image processing, where the processing solution for a particular application is expressed in terms of the basic morphological operators, dilation and erosion, in conjunction with convolution and logical operators. Genetic Programming (GP), based on concepts of genetics and Darwin's principle of natural selection, to genetically breed and evolve computer programs to solve a wide variety of problems, is a branch of evolutionary computation, and it is consolidating as a promising methodology to be used in applications involving pattern recognition, classification problems and modeling of complex systems. Mathematical morphology is based on the set theory (complete lattice), where the notion of order is very important. This processing technique has proved to be a powerful tool for many computer vision tasks. However, the manual design of complex operations involving image operators is not trivial in practice. Thus, the proposed methodology tries to solve these drawbacks. Some examples of applications are presented and the results are discussed and compared with other methods found in the literature.
Intensity-based Object Localization and Tracking with Wireless Sensors

In this paper we present a first evaluation of an application of our intensity-based localization scheme in a real wireless sensor network. We implemented an object localization and tracking algorithm that solely depends on the values gathered by motion detectors. Based on this information and the positions of the observing sensors, the algorithm is not only able to track the position or trace of a moving object by considering the positions of the closest sensor(s) to the object, but is also able to estimate the location or path of the object. With our approach the location of a moving object can be estimated with minimal constraints on both the sensor hardware and the moving object what makes it a very lightweight approach. The applicability of our intensity-based localization algorithm is feasible even with the highly limited hardware implemented on existing sensor nodes.
Attitude Polarization

Psychological evidence suggests that people's learning behavior is often prone to a 'myside bias' or 'irrational belief persistence' in contrast to learning behavior exclusively based on objective data. In the context of Bayesian learning such a bias may result in diverging posterior beliefs and attitude polarization even if agents receive identical information. Such patterns cannot be explained by the standard model of rational Bayesian learning that implies convergent beliefs. As our key contribution, we therefore develop formal models of Bayesian learning with psychological bias as alternatives to rational Bayesian learning. We derive conditions under which beliefs may diverge in the learning process and thus conform with the psychological evidence. Key to our approach is the assumption of ambiguous beliefs that are formalized as non-additive probability measures arising in Choquet expected utility theory. As a speciffc feature of our approach, our models of Bayesian learning with psychological bias reduce to rational Bayesian learning in the absence of ambiguity.
The influence of erythropoietin treatment on oxidative stress parameters in cortex of rats exposed to transient middle cerebral artery occlusion

Introduction: Erythropoietin (Epo) plays a central role in process of erythropoiesis. Recently, its neuroprotective potential was reported in various experimental models of brain damage. However, the mechanism of Epo protection is still unclear. In the present study, we examined the effect of Epo administration on lipid peroxidation levels and antioxidant enzymes’ (superoxide dismutase (SOD) and glutathione peroxidase (GSH-Px) activities in rat cortex following focal cerebral ischemia. Material and Methods: Focal cerebral ischemia was induced in male HanoverWistar rats (250–350 g) by right middle cerebral artery occlusion (MCAO) model for 1 hr. After 23 hrs of reperfusion, ischemic animals were sacrificed and the levels of lipid peroxidation, SOD and GSH-Px activities were determined spectrophotometrically in the right cortex. Ischemic animals received either vehicle or Epo (5000 IU/kg, intraperitoneally) immediately or 3 hrs after MCAO, and were sacrificed 23 hrs or 21 hrs later, respectively. Sham operated, vehicle treated animals served as the control group. Results: Focal cerebral ischemia significantly increased the level of oxidative lipid damage parameters in the right cortex as compared to the control group without affecting SOD and GSH-Px activities. The decrease in level of lipid peroxidation after Epo treatment was registered but it was not statistically significant. Conclusion: Our results indicate that focal cerebral ischemia caused neuronal damage in the right cortex and that Epo treatment was not effective in preventing above mentioned alteration.
Building trust in children

Previous fear of crime studies have rarely considered how fear of crime is learned or the messengers who teach fear of crime to others. This is especially important with children, who often learn about the world from social influences such as parents and teachers. While some work has been done on children’s fear of crime, this work lacks a consideration of the messages parents give children. Further, this research has been restricted to countries such as the US and England. The current research focuses on a country rarely considered in the fear of crime literature – Sweden. In-depth interviews with 14 parents and 10 children are consulted to determine how parents talk to children about safety and what children hear when receiving such messages. Thus, the interplay between parents and their children in the social learning process of safety precautions are considered.
Player perspectives

The term gamer has been applied in various, often simplistic ways to anyone who plays video games as a preferred leisure activity. Being heavily value-laden both socially and culturally, the term has spawned fiery debates on a variety of issues ranging from perpetuation of stereotypes to gender inequality. This paper seeks to understand the gamer tag by charting and critically analysing the gaming journeys of three video game players in an everyday context.The paper uses an ethnographic approach, based on in-depth interviews with and observation of the gaming activity of three individuals over a year. Drawing from Nick Couldry’s Media as Practice approach the gaming practices of the players were examined in relation to how they themselves reflect upon their experience and its various components, and the ways in which they construct and express their gamer/gaming identity. The emergent themes from the analysis have been used to build a tentative framework that could enable a more holistic understanding of the gamer within the gaming world and more generally in popular culture.
In situ phytoplankton distributions in the Amundsen Sea Polynya measured by autonomous gliders

The Amundsen Sea Polynya is characterized by large phytoplankton blooms, which makes this region disproportionately important relative to its size for the biogeochemistry of the Southern Ocean. In situ data on phytoplankton are limited, which is problematic given recent reports of sustained change in the Amundsen Sea. During two field expeditions to the Amundsen Sea during austral summer 2010–2011 and 2014, we collected physical and bio-optical data from ships and autonomous underwater gliders. Gliders documented large phytoplankton blooms associated with Antarctic Surface Waters with low salinity surface water and shallow upper mixed layers (< 50 m). High biomass was not always associated with a specific water mass, suggesting the importance of upper mixed depth and light in influencing phytoplankton biomass. Spectral optical backscatter and ship pigment data suggested that the composition of phytoplankton was spatially heterogeneous, with the large blooms dominated by Phaeocystis and non-bloom waters dominated by diatoms. Phytoplankton growth rates estimated from field data (≤ 0.10 day−1) were at the lower end of the range measured during ship-based incubations, reflecting both in situ nutrient and light limitations. In the bloom waters, phytoplankton biomass was high throughout the 50-m thick upper mixed layer. Those biomass levels, along with the presence of colored dissolved organic matter and detritus, resulted in a euphotic zone that was often < 10 m deep. The net result was that the majority of phytoplankton were light-limited, suggesting that mixing rates within the upper mixed layer were critical to determining the overall productivity; however, regional productivity will ultimately be controlled by water column stability and the depth of the upper mixed layer, which may be enhanced with continued ice melt in the Amundsen Sea Polynya.
Metacognitive functions in patients who has obsessive compulsive disorder and major depressive disorder: a controlled study

Objective: The aim of this study was to compare metacognitive functions of patients with obsessive compulsive disorder (OCD) and major depressive disorder (MDD) and their relationship to clinical symptoms with those of the control group. Methods: The study included 50 patients with OCD and 50 patients with MDD who were admitted to Firat University, Clinic of Psychiatry and who met the study criteria and 50 healthy controls. The Structured Clinical Interview (SCID-I) for DSM-IV Axis I Disorders, Sociodemographic and Clinical Data Form, and Metacognition Questionnaire-30 (MCQ-30) were administered to patients and control groups; additionally, the Beck Depression Inventory (BDI) and the Beck Anxiety Inventory (BAI) were also administered to patients with MDD whereas the Yale-Brown obsessive compulsive scale (Y-BOCS) and the Obsessive Beliefs Questionnaire-44 (OBS-44) were administered to patients with OCD. Results: Total metacognition scores were found to be significant in both disease groups as compared to the control group. Metacognition subscales of ‘uncontrollability and danger’ and ‘need to control’ were significantly higher in patients with OCD, whereas, the subscale of cognitive confidence was significantly higher in patients with MDD as compared to the control group. In addition, there was a positive correlation between Y-BOCS subscale of compulsion and need to control, between the OBQ-44 factor of perfectionism/certainty and uncontrollability between danger and the subscale of cognitive awareness in patients with OCD. On the other hand, there was a positive correlation between BDI scores and metacognition subscales of positive belief, cognitive confidence and uncontrollability and danger in patients with MDD. Conclusion: The findings of our study demonstrated significant differences in the parameters of metacognition questionnaire between patients with depression and those with OCD. Future studies are warranted to elucidate the causal relationship of these differences to MDD and OCD.
Collaborative Null-Steering Beamforming for Uniformly Distributed Wireless Sensor Networks

Null-steering transmit beamformers aim to maximize the received signal power in the direction of the intended receiver while substantially reducing the power impinging on the unintended receivers located in other directions. The existing null-steering beamformers may not be directly applied in wireless sensor networks (WSNs) as they do not conform with the decentralized nature of WSNs and require every node to be aware of the locations of all other nodes in the network. This manuscript presents a novel collaborative null-steering beamformer that can be implemented in uniformly distributed WSNs in which each node is oblivious of other nodes' locations. The average beampattern expression of the proposed beamformer is derived and it is shown that the beampattern associated with any arbitrary realization of the nodes' locations converges with probability one to the so-obtained average beampattern as the number of collaborating nodes grows large. Properties of the average beampattern are analytically studied. In particular, it is proven that the average gain of the proposed beamformer is inversely proportional to the number of collaborating nodes in the directions of unintended receivers and further, if a mild condition is satisfied, it is approximately equal to that of the collaborative conventional beamformer in the directions with far angular distance from any unintended receiver. It is argued that if virtual unintended receivers are assumed at proper directions, then the proposed collaborative null-steering beamformer can form an average beampattern with sidelobe peaks substantially smaller than those of the average beampattern of the collaborative conventional beamformer. To substantiate this argument, the optimal direction of a virtual unintended receiver is obtained such that its associated collaborative null-steering beamformer forms an average beam-pattern with minimal largest side-lobe peak. Depending on the number of collaborating nodes, it is further shown that the largest average sidelobe peak of the latter beamformer is up to 6.6 (dB) less than that of the collaborative conventional beamformer.
Equilibrium temperature distribution and Hadley circulation in an axisymmetric model

Abstract. The impact of the equilibrium temperature distribution, θE, on the Hadley circulation simulated by an axisymmetric model is studied. The θE distributions that drive the model are modulated here by two parameters, n and k, the former controlling the horizontal broadness and the latter controlling the vertical stratification of θE. In the present study, variations in the θE distribution mimic changes in the energy input of the atmospheric system, leaving as almost invariant the Equator–poles θE difference. Both equinoctial and time-dependent Hadley circulations are simulated and the results compared. The results give evidence that concentrated θE distributions enhance the meridional circulation and jet wind speed intensities, even with a lower energy input. The meridional circulation and the subtropical jet stream widths are controlled by the broadness of horizontal θE rather than by the vertical stratification, which is important only when θE distribution is concentrated at the Equator. The jet stream position does not show any dependence with n and k, except when the θE distribution is very wide (n = 3) and, in such a case, the jet is located at the mid-latitudes and the model temperature clamps to forcing θE. Using n = 2 and k = 1, we have the formulation of the potential temperature adopted in the classical literature. A comparison with other works is performed, and our results show that the model running in different configurations (equinoctial, solstitial and time dependent) yields results similar to one another.
Formal verification of obstacle avoidance and navigation of ground robots

This article answers fundamental safety questions for ground robot navigation: under which circumstances does which control decision make a ground robot safely avoid obstacles? Unsurprisingly, the answer depends on the exact formulation of the safety objective, as well as the physical capabilities and limitations of the robot and the obstacles. Because uncertainties about the exact future behavior of a robot’s environment make this a challenging problem, we formally verify corresponding controllers and provide rigorous safety proofs justifying why the robots can never collide with the obstacle in the respective physical model. To account for ground robots in which different physical phenomena are important, we analyze a series of increasingly strong properties of controllers for increasingly rich dynamics and identify the impact that the additional model parameters have on the required safety margins. We analyze and formally verify: (i) static safety, which ensures that no collisions can happen with stationary obstacles; (ii) passive safety, which ensures that no collisions can happen with stationary or moving obstacles while the robot moves; (iii) the stronger passive-friendly safety, in which the robot further maintains sufficient maneuvering distance for obstacles to avoid collision as well; and (iv) passive orientation safety, which allows for imperfect sensor coverage of the robot, i.e., the robot is aware that not everything in its environment will be visible. We formally prove that safety can be guaranteed despite sensor uncertainty and actuator perturbation. We complement these provably correct safety properties with liveness properties: we prove that provably safe motion is flexible enough to let the robot navigate waypoints and pass intersections. To account for the mixed influence of discrete control decisions and the continuous physical motion of the ground robot, we develop corresponding hybrid system models and use differential dynamic logic theorem-proving techniques to formally verify their correctness. Since these models identify a broad range of conditions under which control decisions are provably safe, our results apply to any control algorithm for ground robots with the same dynamics. As a demonstration, we also synthesize provably correct runtime monitor conditions that check the compliance of any control algorithm with the verified control decisions.
Activation of clinically used anthracyclines by the formaldehyde-releasing prodrug pivaloyloxymethyl butyrate

The anthracycline group of compounds is extensively used in current cancer chemotherapy regimens and is classified as topoisomerase II inhibitor. However, previous work has shown that doxorubicin can be activated to form DNA adducts in the presence of formaldehyde-releasing prodrugs and that this leads to apoptosis independently of topoisomerase II–mediated damage. To determine which anthracyclines would be useful in combination with formaldehyde-releasing prodrugs, a series of clinically relevant anthracyclines (doxorubicin, daunorubicin, idarubicin, and epirubicin) were examined for their capacity to form DNA adducts in MCF7 and MCF7/Dx (P-glycoprotein overexpressing) cells in the presence of the formaldehyde-releasing drug pivaloyloxymethyl butyrate (AN-9). All anthracyclines, with the exception of epirubicin, efficiently yielded adducts in both sensitive and resistant cell lines, and levels of adducts were similar in mitochondrial and nuclear genomes. Idarubicin was the most active compound in both sensitive and resistant cell lines, whereas adducts formed by doxorubicin and daunorubicin were consistently lower in the resistant compared with sensitive cells. The adducts formed by doxorubicin, daunorubicin, and idarubicin showed the same DNA sequence specificity in sensitive and resistant cells as assessed by λ-exonuclease–based sequencing of α-satellite DNA extracted from drug-treated cells. Growth inhibition assays were used to show that doxorubicin, daunorubicin, and idarubicin were all synergistic in combination with AN-9, whereas the combination of epirubicin with AN-9 was additive. Although apoptosis assays indicated a greater than additive effect for epirubicin/AN-9 combinations, this effect was much more pronounced for doxorubicin/AN-9 combinations. [Mol Cancer Ther 2007;6(4):1450–9]