Miracle-dz/UniFAR-FTUs huggingface dataset:
Temperate Phages Acquire DNA from Defective Prophages by Relaxed Homologous Recombination: The Role of Rad52-Like Recombinases

Bacteriophages (or phages) dominate the biosphere both numerically and in terms of genetic diversity. In particular, genomic comparisons suggest a remarkable level of horizontal gene transfer among temperate phages, favoring a high evolution rate. Molecular mechanisms of this pervasive mosaicism are mostly unknown. One hypothesis is that phage encoded recombinases are key players in these horizontal transfers, thanks to their high efficiency and low fidelity. Here, we associate two complementary in vivo assays and a bioinformatics analysis to address the role of phage encoded recombinases in genomic mosaicism. The first assay allowed determining the genetic determinants of mosaic formation between lambdoid phages and Escherichia coli prophage remnants. In the second assay, recombination was monitored between sequences on phage λ, and allowed to compare the performance of three different Rad52-like recombinases on the same substrate. We also addressed the importance of homologous recombination in phage evolution by a genomic comparison of 84 E. coli virulent and temperate phages or prophages. We demonstrate that mosaics are mainly generated by homology-driven mechanisms that tolerate high substrate divergence. We show that phage encoded Rad52-like recombinases act independently of RecA, and that they are relatively more efficient when the exchanged fragments are divergent. We also show that accessory phage genes orf and rap contribute to mosaicism. A bioinformatics analysis strengthens our experimental results by showing that homologous recombination left traces in temperate phage genomes at the borders of recently exchanged fragments. We found no evidence of exchanges between virulent and temperate phages of E. coli. Altogether, our results demonstrate that Rad52-like recombinases promote gene shuffling among temperate phages, accelerating their evolution. This mechanism may prove to be more general, as other mobile genetic elements such as ICE encode Rad52-like functions, and play an important role in bacterial evolution itself.
Representing elementary semi-algebraic sets by a few polynomial inequalities: A constructive approach

Let P be an elementary closed semi-algebraic set in R^d, i.e., there exist real polynomials p_1,. ,p_s such that P= \{x \in R^d : p_1(x) \ge 0, >. , p_s(x) \ge 0 \}; in this case p_1,. ,p_s are said to represent P. Denote by $n$ the maximal number of the polynomials from \{p_1,. ,p_s\} that vanish in a point of P. If P is non-empty and bounded, we show that it is possible to construct n+1 polynomials representing P. Furthermore, the number n+1 can be reduced to n in the case when the set of points of P in which n polynomials from \{p_1,. ,p_s\} vanish is finite. Analogous statements are also obtained for elementary open semi-algebraic sets.
Change-Point Monitoring for Secure In-Network Aggregation in Wireless Sensor Networks

Secure in-network aggregation in wireless sensor networks is a necessary and challenging task. In this paper, based on an extended Kalman filter which can facilitate us to set up a normal range of the neighbor's future transmitted aggregated values, we further apply an algorithm of combining cumulative summation and generalized likelihood ratio, which can utilize the cumulative sum of the deviations between measured values and estimated values, and derive a normal range which is more sensitive to attacks. We conduct experiments and simulations to evaluate our proposed local detection mechanisms under different aggregation functions.
Comparing the Quality of Crowdsourced Data Contributed by Expert and Non-Experts

There is currently a lack of in-situ environmental data for the calibration and validation of remotely sensed products and for the development and verification of models. Crowdsourcing is increasingly being seen as one potentially powerful way of increasing the supply of in-situ data but there are a number of concerns over the subsequent use of the data, in particular over data quality. This paper examined crowdsourced data from the Geo-Wiki crowdsourcing tool for land cover validation to determine whether there were significant differences in quality between the answers provided by experts and non-experts in the domain of remote sensing and therefore the extent to which crowdsourced data describing human impact and land cover can be used in further scientific research. The results showed that there was little difference between experts and non-experts in identifying human impact although results varied by land cover while experts were better than non-experts in identifying the land cover type. This suggests the need to create training materials with more examples in those areas where difficulties in identification were encountered, and to offer some method for contributors to reflect on the information they contribute, perhaps by feeding back the evaluations of their contributed data or by making additional training materials available. Accuracies were also found to be higher when the volunteers were more consistent in their responses at a given location and when they indicated higher confidence, which suggests that these additional pieces of information could be used in the development of robust measures of quality in the future.
Huntingtin coordinates the dynein-mediated dynamic positioning of endosomes and lysosomes

We investigated the role of the membrane-associated scaffolding protein huntingtin (Htt) in the dynein-mediated transport of early, recycling, and late endosomes and lysosomes. Our observations support a model of Htt as a facilitator of dynein-mediated trafficking that can regulate the cytoskeletal association of dynamic organelles.
Donor- and Ligand-Dependent Differences in C-C Chemokine Receptor 5 Reexpression

ABSTRACT N-terminal modifications of the chemokine RANTES bind to C-C chemokine receptor 5 (CCR5) and block human immunodeficiency virus type 1 (HIV-1) infection with greater efficacy than native RANTES. Modified RANTES compounds induce rapid CCR5 internalization and much slower receptor reexpression than native RANTES, suggesting that receptor sequestration is one mode of anti-HIV activity. The rates of CCR5 internalization and reexpression were compared using the potentn-nonanoyl (NNY)-RANTES derivative and CD4+ T cells derived from donors with different CCR5 gene polymorphisms. NNY-RANTES caused even more rapid receptor internalization and slower reexpression than aminooxypentane (AOP)-RANTES. Polymorphisms in the promoter and coding regions of CCR5 significantly affected the receptor reexpression rate after exposure of cells to NNY-RANTES. These observations may be relevant for understanding the protective effects of different CCR5 genotypes against HIV-1 disease progression.
Is a Robot a Better Walking Partner if it Associates Utterances with Visual Scenes?

We aim to develop a walking partner robot with the capability to select small-talk topics that are associative to visual scenes. We first collected video sequences from five different locations and prepared a dataset about small-talk topics associated to visual scenes. Then we developed a technique to associate the visual scenes with the small-talk topics. We converted visual scenes into lists of words using an off-the-shelf vision library and formed a topic space with a Latent Dirichlet Allocation (LDA) method in which a list of words is transformed to a topic vector. Finally, the system selects the most similar utterance in the topic vectors. We tested our developed technique with a dataset, which successfully selected 72% appropriate utterances, and conducted a user study outdoors where participants took a walk with a small robot on their shoulder and engaged in small talk. We confirmed that the participants more highly perceived the robot with our developed technique because it selected appropriate utterances than a robot that randomly selected utterances. Further, they also felt that the former type of robot is a better walking partner.
Workplace Spirituality, Commitment, and Self‐Reported Individual Performance: An Empirical Study

This paper shows how the perceptions of people regarding five dimensions of workplace spirituality (team’s sense of community, alignment with organizational values, sense of contribution to society, enjoyment at work, and opportunities for inner life) predict affective, normative, and continuance commitment, as well as self‐reported individual performance. One sample in Portugal and another in Brazil were collected. The findings show that employees’ perceptions of workplace spirituality predict significant variance of commitment and individual performance in both samples. The empirical evidence suggests that workplace spirituality is a pertinent construct for researchers and an important concern to be taken into account by managers.
A Novel Form of Presynaptic Plasticity Based on the Fast Reactivation of Release Sites Switched Off during Low-Frequency Depression

Repetitive firing of neurons at a low frequency often leads to a decrease in synaptic strength. The mechanism of this low-frequency depression (LFD) is poorly understood. Here, LFD was studied at Aplysia cholinergic synapses. The absence of a significant change in the paired-pulse ratio during LFD, together with the facts that neither the time course nor the extent of LFD were affected by the initial release probability, suggests that LFD is not related to a depletion of the ready-to-fuse synaptic vesicles (SVs) or to a decrease in the release probability, but results from the silencing of a subpopulation of release sites. A subset of SVs or release sites, which acquired a high release probability status during LFD, permits synapses to rapidly and temporarily recover the initial synaptic strength when the stimulation is stopped. However, the recovery of the full capacity of the synapse to sustain repetitive stimulations is slow and involves spontaneous reactivation of the silent release sites. Application of tetanic stimulations accelerates this recovery by immediately switching on the silent sites. This high-frequency-dependent phenomenon underlies a new form of synaptic plasticity that allows resetting of presynaptic efficiency independently of the recent history of the synapse. Microinjection of a mutated Aplysia synapsin that cannot be phosphorylated by cAMP-dependent protein kinase (PKA), or a PKA inhibitor both prevented high-frequency-dependent awakening of release sites. Changes in the firing pattern of neurons appear to be able to regulate the on–off status of release sites via a molecular cascade involving PKA-dependent phosphorylation of synapsin.
Pricing and Hedging Electricity Swing Contracts

In this master thesis, an e cient and exible model for pricing and hedging swing contracts, in an incomplete market, is presented. The model supports an hourly withdrawal strategy and includes all available future and forward contracts in the market. The model is a two stage stochastic optimization model, constructed to price and hedge simultaneously. It uses exogenous spot prices and swap contracts, and the scope is limited for one kind of swing contracts; exible load contracts. The model is a good foundation to develop into a multi stage stochastic model. The models exibility makes it possible to use a time resolution of blocks of hours, in order to value and hedge other swing contracts, and use di erent price models for the spot and swap prices. A block resolution of small number of hours is preferred, compared to an hourly resolution, due to a large decrease in computation time at the expense of a minimal loss of value. However, a daily or larger resolution of the withdrawal schedule and spot price will drastically reduce the value of the optimization. Because of the incompleteness in the electricity market, the market player's risk aversion will in uence the hedging and withdrawal strategy, and therefore also the value of the contract. We look at several volume risk functions and a CVaR pro t risk function, and we optimize a exible load contract by creating a static hedge. A utility function minimizing the pro t risk, results in a better reduction of downside risk in an optimization compared to a hedge created by a volume risk aversion model.
The promise of cryogenic solid-state lasers

Cryogenic cooling of solid-state lasers has a number of important benefits, including the near vanishing of optical distortion in high average power lasers, as well as enhanced spectroscopic and lasing properties. These benefits are just beginning to be exploited to produce compact high average power lasers whose output is scalable, near diffraction limited, and whose efficiencies will exceed those of modern bulk solid-state lasers. In this paper, we review the history of cryogenically cooled solid-state lasers and the benefits of cryogenic cooling, including optical and laser properties and thermal and thermooptic properties; examine cryogenic amplifiers and cooling methods, including a straight-through propagation thin-disk configuration that does not perform well at room temperature, and summarize the experimental performance demonstrated to date. As a specific example, we examine the spectroscopic and lasing properties of Yb:YAG and show that compact high efficiency and high average power, near diffraction limited lasers (>100 kW) can be realized in the near future using presently available technology.
ENIGMA: a testbed for MPLS and QoS integration on IP networks

ENIGMA is a network configuration and management environment that provides end to end QoS (quality of service) across an MPLS transport network for UMTS services. As a result, a new concept of transport network is defined, which links the new trends in IP with the operator's needs. This solution will allow an improvement in the mobile user experience thanks to QoS and traffic engineering provisioning. This paper describes the project and explores the state of the art of the technology. It also introduces how the management software works and finishes with a testbed proposal and results
Model collisions in the dissimilarity SOM

We investigate in this paper the problem of model collisions in the Dissimilarity Self Organizing Map (SOM). This extension of the SOM to dissimilarity data suffers from constraints imposed on the model representation, that lead to some strong map folding: several units share a common prototype. We propose in this paper an efficient way to address this problem via a branch and bound approach.
Knowledge Representation in the Large

Frame knowledge representation systems lack two important capabilities that prevent them from scaling up to large applications: they do not support fast access to large knowledge bases (KBs), nor do they provide concurrent multiuser access to shared KBs. We describe the design and implementation of a storage subsystem that submerges a database management system (DBMS) within a knowledge representation system. The storage subsystem incrementally loads referenced frames from the DBMS, and can save to the DBMS only those frames that have been updated in a given session. We present experimental results that show our approach to be an improvement over the use of flat files, and that evaluate several variations of our approach.
Neural Network Modeling of Speech and Music Signals

Time series prediction is one of the major applications of neural networks. After a short introduction into the basic theoretical foundations we argue that the iterated prediction of a dynamical system may be interpreted as a model of the system dynamics. By means of RBF neural networks we describe a modeling approach and extend it to be able to model instationary systems. As a practical test for the capabilities of the method we investigate the modeling of musical and speech signals and demonstrate that the model may be used for synthesis of musical and speech signals.
Sampling Strategies for Particle Filtering SLAM

We describe several new sampling strategies for Rao-Blackwellized particle filtering SLAM. Two of the strategies, called fixed-lag roughening and the block proposal distribution, attempt to exploit “future” information, when it becomes available, to improve the filter’s estimation for previous time steps. Fixed-lag roughening perturbs trajectory samples over a fixed lag time according to a Markov Chain Monte Carlo kernel. The block proposal distribution directly samples poses over a fixed lag from their fully joint distribution conditioned on all the available data. Our results indicate that the proposed strategies, especially the block proposal, yield significant improvements in filter consistency and a reduction in particle degeneracies compared to standard sampling techniques such as the improved proposal distribution of FastSLAM 2. In addition, we examine the effectiveness of two new resampling techniques, residual resampling and generalized resampling, as applied to RBPF SLAM. These drop-in-place techniques are simple to use and (in the case of residual resampling) computationally cheaper than the standard random resampling approach. However, our results show that they offer no real improvement in performance over random resampling in SLAM. This is an extended version of a paper (Beevers and Huang, 2007) previously submitted for publication.
Robust calibration of an ultralow-cost inertial measurement unit and a camera: Handling of severe system uncertainty

Recently, mobile devices such as smart phones and quad-copters are being equipped with inertial measurement units (IMUs) because of advances in micro-electro-mechanical systems technology. This has increased the importance of IMU- camera fusion for vision-based applications. However, ultralow-cost IMUs take much less accurate measurements than low-cost and high-cost IMUs. This uncertainty degrades the accuracy and reliability of IMU-camera calibration, which is the most important step for IMU-camera fusion technology. In this paper, we propose three effective algorithms for robust IMU- camera calibration with uncertain measurements: boundary constraint, adaptive prediction, and angular velocity constraint. These algorithms incorporate a Bayesian filtering framework to estimate calibration parameters more efficiently. The experimental results on both simulation and real data demonstrated the superiority of the proposed algorithms.
Notas sobre la complejidad en la Psicología.

Este trabajo presenta algunas reflexiones sobre el concepto de complejidad tal como ha venido apareciendo en la ciencia occidental. Se hace especial hincapie en su concepcion mas reciente, en terminos de no linealidad, y se observa el papel central que desempena una concepcion geometrica-topologica de la realidad. Se senalan, despues, algunas repercusiones de tales ideas en la Psicologia. El desarrollo y el funcionamiento, tanto normal como patologico, del psiquismo del ser humano y su comportamiento - manifestacion contextualizada de aquel- aparecen concebidos como sistemas complejos, dinamicos, abiertos y autoorganizados. En esta linea, la teoria de sistemas dinamicos se muestra como el marco idoneo para la construccion de una metodologia adecuada para la Psicologia. Aun considerando unicamente su aspecto mas puramente verbalconceptual, la teoria de sistemas dinamicos ofrece, como minimo, unas posibilidades de reformulacion de muchas de las nociones mas importantes de la Psicologia que constituyen una valiosa fuente de ideas e hipotesis prometedoras.
Determining Maximum Stack Usage in Preemptive Shared Stack Systems

This paper presents a novel method to determine the maximum stack memory used in preemptive, shared stack, real-time systems. We provide a general and exact problem formulation applicable for any preemptive system model based on dynamic (run-time) properties. We also show how to safely approximate the exact stack usage by using static (compile time) information about the system model and the underlying run-time system on a relevant and commercially available system model: a hybrid, statically and dynamically, scheduled system. Comprehensive evaluations show that our technique significantly reduces the amount of stack memory needed compared to existing analysis techniques. For typical task sets a decrease in the order of 70% is typical
Nonsteroidal Anti-Inflammatory Drug Effects on Osteoblastic Cell Cycle, Cytotoxicity, and Cell Death

Previous studies indicated that nonsteroidal anti-inflammatory drugs (NSAIDs) suppress bone repair, growth, and remodeling in vivo. Our previous in vitro study demonstrated that indomethacin and ketorolac inhibited osteoblast proliferation. In this study, we further investigated the influences of 4 NSAIDs on cell cycle kinetics, cytotoxicity, and cell death pattern in osteoblast cultures from rat fetal calvaria. Our results showed that NSAIDs significantly arrested cell cycle at the G0/G1 phase and induced cytotoxicity and cell death of osteoblasts. Apoptosis was more pronounced than necrosis caused by NSAIDs. Among these NSAIDs, piroxicam showed the least effect to produce osteoblastic dysfunction. Moreover, we found that the cytotoxic and apoptotic effects of NSAIDs on osteoblasts might not be prostaglandin related. These results suggest that the NSAID effects on cell cycle arrest and cell death induction in osteoblasts may be one of the important mechanisms contributing to their suppressive effect on bone formation.
Calcimimetic R-568 and Its Enantiomer S-568 Increase Nitric Oxide Release in Human Endothelial Cells

Background Calcimimetics, such as R-568, are thought to activate G protein-linked Ca2+-sensing receptor (CaSR) by allosterically increasing the affinity of the receptor for Ca2+ allowing for efficient control of uremic hyperparathyroidism. Several recent studies suggest they possess additional vascular actions. Although it has been postulated that calcimimetics may have a direct effect on CaSR in the blood vessels, further studies are needed to elucidate their vascular CaSR-dependent versus CaSR-independent effects. Methodology/Principal Findings Focusing on human umbilical vein endothelial cells (HUVECs), we studied the CaSR expression and distribution by Immunofluorescence and Western Blot analysis. CaSR function was evaluated by measuring the potential effect of calcimimetic R-568 and its enantiomer S-568 upon the modulation of intracellular Ca2+ levels (using a single cell approach and FURA-2AM), in the presence or absence of Calhex-231, a negative modulator of CaSR. To address their potential vascular functions, we also evaluated R- and S-568-stimulated enzymatic release of Nitric Oxide (NO) by DAF-2DA, by Nitric Oxide Synthase (NOS) radiometric assay (both in HUVECs and in Human Aortic Endothelial Cells) and by measuring eNOS-ser1177 phosphorylation levels (Immunoblotting). We show that, although the CaSR protein was expressed in HUVECs, it was mainly distributed in cytoplasm while the functional CaSR dimers, usually localized on the plasma membrane, were absent. In addition, regardless of the presence or absence of Calhex-231, both R- and S-568 significantly increased intracellular Ca2+ levels by mobilization of Ca2+ from intracellular stores, which in turn augmented NO release by a time- and Ca2+-dependent increase in eNOS-ser1177 phosphorylation levels. Conclusions/Significance Taken together, these data indicate that in human endothelium there is no stereoselectivity in the responses to calcimimetics and that CaSR is probably not involved in the action of R- and S-568. This suggests an additional mechanism in support of the CaSR-independent role of calcimimetics as vasculotrope agents.