Miracle-dz/UniFAR-FTUs huggingface dataset:
Mechanisms underlying reduced expulsion of a murine nematode infection during protein deficiency

SUMMARY Balb/c mice infected with the gastrointestinal nematode Heligmosomoides bakeri were fed protein sufficient (PS, 24%) or deficient (PD, 3%) diets to investigate whether diet, infection or dose of larval challenge (0, 100 or 200 larvae) influenced gut pathophysiology and inflammation. Among the PS mice, worms were more posteriorad in the intestine of mice infected with 200 compared with 100 larvae, suggesting active expulsion in the more heavily infected mice. This was consistent with the positive correlation between worm numbers and fluid leakage in PS mice; similar patterns were not detected in the PD mice. Infection also induced villus atrophy, which was more pronounced in PS than in PD mice. Our cytokine screening array indicated that infection in PD mice elevated a wide range of pro-inflammatory cytokines and chemokines. Whereas serum leptin concentrations were higher in PD mice, monocyte chemotactic protein-5 (MCP-5) in serum increased with increasing larval dose and concentrations were lower in PD than PS mice. We suggest that elevated MCP-5 together with villus atrophy may contribute to the apparent dose-dependent expulsion of H. bakeri from PS mice but that delayed expulsion in PD mice appeared related to a predominant Th1 cytokine profile that may be driven by leptin.
YOUTH WELL-BEING INDEX IN THE NEIGHBOURHOOD SPACE: OUTDOOR VS INDOOR SPACE

This paper examines both indoor and outdoor spaces that highly influence the quality index and wellbeing of youth in a marginalized community neighbourhood. The well-being of youth has been measured using quantitative data on the standard of living, physical activity, emotion, safety, youth participation in community activity, space quality and life satisfaction. A total of 530 young people aged between 15 and 25 years old were selected in two different study areas. The highest well-being score indicates the most influence space between outdoor and indoor upon youth quality lifestyle. The male score is slightly higher compared to the female score as the correlation matrix of factor analysis shows that standard of living is suggestively associated with health, physical activity, youth participation and future hope. Thus, the community and stakeholders should take more action and effort to increase youth well-being and quality index in the neighbourhood environmental space.
Towards a Semantic Interoperability in an e-Government Application

Research issues have emerged from the rapid introduction of new technologies in government services in order to deliver efficient and cost effective services, information and knowledge through information and communication technologies. However, the complexity of government services and the diversity of actors involved in the processes make the access to the right information difficult and pose several problems. Some problems are linked to the way of presenting and accessing information. Other problems are linked to interoperability among applications and processes of eGovernment services. The objective of the European TerreGov project is to find a solution to such problems. The project focuses on the semantic requirements of governments at local, intermediate and regional levels, needed to build flexible and interoperable tools to support the change towards eGovernment services. We propose, within this project, an ontology to present knowledge and to achieve the required level of semantic interoperability. We use the ontology to describe the domain knowledge of the organization and to index the resources from which civil servants may receive information. The key point of the system is a unique and multimodal ontology used simultaneously for describing domain knowledge, for adding semantics to agency services, for indexing various documents in knowledge bases used by civil servants and finally for supporting the interaction between the users and the system. We present in this paper the challenges of using ontology in eGovernment environments, such as the lack of expressivity of the formalism chosen for interoperability in the project and the risk of inconsistency when the ontology changes. We propose our solution to such challenges and we demonstrate the use of the ontology by the module in charge of managing complex tasks in the system.
Greedy Õ(C +D) Hot-Potato Routing on Trees

In hot-potato (deflection) routing, nodes in the network have no buffers for packets in transit. A hotpotato routing algorithm is greedy if packets are advanced from their sources toward their destinations whenever possible. The dilation D is the longest distance a packet has to travel; the congestion C is the maximum number of packets that traverse any edge. The routing time of a routing-algorithm is the time for the last packet to reach its destination. A well known lower bound on the routing time is Ω(C +D). When is it possible to design routing algorithms whose routing times match this lower bound? Here, we address this fundamental question within the context of hot-potato routing for the specific case of a tree with n nodes. In particular, we present two greedy, hot-potato routing algorithms: i. A deterministic algorithm, which has a routing time of O((δ ·C+D) lg n), where δ is the maximum node degree; thus, for bounded degree trees, the routing time becomes O((C +D) lg n). ii. A randomized algorithm which has a routing time of O((C + D) lg n) with high probability, for any node degree. Randomization is used for adjusting packet priorities. Both algorithms are online and simple yet efficient. They are built upon the idea of using safe deflections, which are deflections whose net effect is to “recycle” edges from one path to another. These are the first known hot-potato routing algorithms (whether greedy or not) for trees whose routing time is within logarithmic factors of the Ω(C +D) lower bound. Computer Science Department, RPI, 110 8th Street, Troy, NY 12180, USA. Email: buschc@cs.rpi. edu Computer Science Department, RPI, 110 8th Street, Troy, NY 12180, USA. Email: magdon@cs.rpi. edu Computer Science Department, University of Cyprus, P. O. Box 20537, Nicosia CY-1678, Cyprus. Email: mavronic@ucy.ac. cy Computer Science Department, ETH Zurich, 8092 Zurich, Switzerland. Email: wattenhofer@inf.ethz. ch
Action-State Semantics for Practical Reasoning

There are two aspects of practical reasoning which present particular difficulties for current approaches to modelling practical reasoning through argumentation: temporal aspects, and the intrinsic worth of actions. Time is important because actions change the state of the world, we need to consider future states as well as past and present ones. Equally, it is often not what we do but the way that we do it that matters: the same future state may be reachable either through desirable or undesirable actions, and often also actions are done for their own sake rather than for the sake of their consequences. In this paper we will present a semantics for practical reasoning, based on a formalisation developed originally for reasoning about commands, in which actions and states are treated as of equal status. We will show how using these semantics facilitates the handling of the temporal aspects of practical reasoning, and enables, where appropriate, justification of actions without reference to their consequences.
Inhibition by hydroxyl radicals of calcitonin gene-related peptide-mediated neurogenic vasorelaxation in isolated canine lingual artery.

Canine lingual arteries are innervated by calcitonin gene-related peptide (CGRP)-containing vasodilator nerves. Although the vascular system might be considered as the first target of oxygen-derived free radicals in some of the pathophysiological conditions, the effect of oxygen-derived free radicals on neurotransmission in CGRP nerves remains unknown. We, therefore, investigated the role of oxygen-derived free radicals generated from Fenton's reagent (3 x 10(-4) M H2O2 plus 2 x 10(-4) M FeSO4) on CGRP-mediated neurogenic relaxation of canine lingual artery ring preparations. In all experiments, endothelium-denuded preparations (which were suspended in the tissue bath for isometric tension recordings) were treated with guanethidine (5 x 10(-6) M) to block neurogenic constrictor responses. The periarterial nerve stimulation (10 V, 4-16 Hz, for 45 sec), exogenous CGRP (10(-8) M) or the ATP-sensitive K+ channel opener cromakalim (10(-6) M) produced relaxation of the rings at a stable plateau tension by the addition of norepinephrine (10(-5) M); the relaxations elicited by CGRP and cromakalim were human CGRP-(8-37)- and glibenclamide-abolishable, respectively. When the nerve stimulation, CGRP and cromakalim were given after H2O2/FeSO4 exposure (Fenton's reagent was removed from the tissue bath), the observed relaxations were markedly diminished. The effects afforded by the early exposure to H2O2/FeSO4 reaction of the preparations were significantly protected by catalase (100 U/ml, H2O2 scavenger), dimethylthiourea (1 mM, H2O2 and HO. scavenger), dimethyl sulfoxide (100 mM, HO. scavenger), deferoxamine (1 mM, a powerful iron chelator) and by a cocktail of catalase-deferoxamine. Generation of HO. from H2O2/FeSO4 was studied by electron spin resonance spectroscopy using the spintrap 5,5-dimethyl-1-pyrroline-N-oxide. We found that H2O2/ FeSO4 reaction formed a 1:2:2:1 quartet, characteristic of the HO-5,5-dimethyl-1-pyrroline-N-oxide spin adduct. After exposure to capsaicin (10(-5) M) or H2O2/FeSO4 of the artery ring preparations, the intensity of CGRP-like immunoreactivity of the periarterial nerves was reduced drastically; the relaxation caused by the nerve stimulation was nearly fully inhibited by capsaicin and H2O2/FeSO4 reaction. The relaxant response, however, to nitroglycerin (10(-5) M) in the presence of norepinephrine to induce tone was unaffected by the early H2O2/ FeSO4 exposure. The data obtained from the present study indicate that HO. , rather than H2O2, is the active agent in CGRP-mediated neurogenic relaxation. It is suggested that the HO. can deplete endogenous CGRP localized prejunctionally and also damage CGRP-induced relaxation of canine lingual artery preparations that is caused by activation of ATP-sensitive K+ channels at postjunctional sites. It is also postulated that the second messenger system of the relaxation mediated, at least, by cyclic GMP may be less susceptible to HO.
Reinforcement learning of a continuous motor sequence with hidden states

Reinforcement learning is the scheme for unsupervised learning in which robots are expected to acquire behavior skills through self-explorations based on reward signals. There are some difficulties, however, in applying conventional reinforcement learning algorithms to motion control tasks of a robot because most algorithms are concerned with discrete state space and based on the assumption of complete observability of the state. Real-world environments often have partial observablility; therefore, robots have to estimate the unobservable hidden states. This paper proposes a method to solve these two problems by combining the reinforcement learning algorithm and a learning algorithm for a continuous time recurrent neural network (CTRNN). The CTRNN can learn spatio-temporal structures in a continuous time and space domain, and can preserve the contextual flow by a self-organizing appropriate internal memory structure. This enables the robot to deal with the hidden state problem. We carried out an experiment on the pendulum swing-up task without rotational speed information. As a result, this task is accomplished in several hundred trials using the proposed algorithm. In addition, it is shown that the information about the rotational speed of the pendulum, which is considered as a hidden state, is estimated and encoded on the activation of a context neuron.
Evidence on the Formation of Singlet Oxygen in the Donor Side Photoinhibition of Photosystem II: EPR Spin-Trapping Study

When photosystem II (PSII) is exposed to excess light, singlet oxygen (1O2) formed by the interaction of molecular oxygen with triplet chlorophyll. Triplet chlorophyll is formed by the charge recombination of triplet radical pair 3[P680•+Pheo•−] in the acceptor-side photoinhibition of PSII. Here, we provide evidence on the formation of 1O2 in the donor side photoinhibition of PSII. Light-induced 1O2 production in Tris-treated PSII membranes was studied by electron paramagnetic resonance (EPR) spin-trapping spectroscopy, as monitored by TEMPONE EPR signal. Light-induced formation of carbon-centered radicals (R•) was observed by POBN-R adduct EPR signal. Increased oxidation of organic molecules at high pH enhanced the formation of TEMPONE and POBN-R adduct EPR signals in Tris-treated PSII membranes. Interestingly, the scavenging of R• by propyl gallate significantly suppressed 1O2. Based on our results, it is concluded that 1O2 formation correlates with R• formation on the donor side of PSII due to oxidation of organic molecules (lipids and proteins) by long-lived P680•+/TyrZ•. It is proposed here that the Russell mechanism for the recombination of two peroxyl radicals formed by the interaction of R• with molecular oxygen is a plausible mechanism for 1O2 formation in the donor side photoinhibition of PSII.
Antibodies Against Anthrax: Mechanisms of Action and Clinical Applications

B. anthracis is a bioweapon of primary importance and its pathogenicity depends on its lethal and edema toxins, which belong to the A-B model of bacterial toxins, and on its capsule. These toxins are secreted early in the course of the anthrax disease and for this reason antibiotics must be administered early, in addition to other limitations. Antibodies (Abs) may however neutralize those toxins and target this capsule to improve anthrax treatment, and many Abs have been developed in that perspective. These Abs act at various steps of the cell intoxication and their mechanisms of action are detailed in the present review, presented in correlation with structural and functional data. The potential for clinical application is discussed for Abs targeting each step of entry, with four of these molecules already advancing to clinical trials. Paradoxically, certain Abs may also enhance the lethal toxin activity and this aspect will also be presented. The unique paradigm of Abs neutralizing anthrax toxins thus exemplifies how they may act to neutralize A-B toxins and, more generally, be active against infectious diseases.
Examination of Broad Symptom Improvement Resulting From Mindfulness-Based Stress Reduction in Breast Cancer Survivors: A Randomized Controlled Trial.

PURPOSE The purpose of this randomized trial was to evaluate the efficacy of the Mindfulness-Based Stress Reduction for Breast Cancer (MBSR[BC]) program in improving psychological and physical symptoms and quality of life among breast cancer survivors (BCSs) who completed treatment. Outcomes were assessed immediately after 6 weeks of MBSR(BC) training and 6 weeks later to test efficacy over an extended timeframe. PATIENTS AND METHODS A total of 322 BCSs were randomly assigned to either a 6-week MBSR(BC) program (n = 155) or a usual care group (n = 167). Psychological (depression, anxiety, stress, and fear of recurrence) and physical symptoms (fatigue and pain) and quality of life (as related to health) were assessed at baseline and at 6 and 12 weeks. Linear mixed models were used to assess MBSR(BC) effects over time, and participant characteristics at baseline were also tested as moderators of MBSR(BC) effects. RESULTS Results demonstrated extended improvement for the MBSR(BC) group compared with usual care in both psychological symptoms of anxiety, fear of recurrence overall, and fear of recurrence problems and physical symptoms of fatigue severity and fatigue interference (P < .01). Overall effect sizes were largest for fear of recurrence problems (d = 0.35) and fatigue severity (d = 0.27). Moderation effects showed BCSs with the highest levels of stress at baseline experienced the greatest benefit from MBSR(BC). CONCLUSION The MBSR(BC) program significantly improved a broad range of symptoms among BCSs up to 6 weeks after MBSR(BC) training, with generally small to moderate overall effect sizes.
Automatic prostate segmentation on MR images with deep network and graph model

Automated prostate diagnoses and treatments have gained much attention due to the high mortality rate of prostate cancer. In particular, unsupervised (automatic) prostate segmentation is an active and challenging research. Most conventional works usually utilize handcrafted (low-level) features for prostate segmentation; however they often fail to extract the intrinsic structure of the prostate, especially on images with blurred boundaries. In this paper, we propose a novel automated prostate segmentation model with learned features from deep network. Specifically, we first generate a set of prostate proposals in transverse plane via recognizing the position and coarse estimate of the shape of the prostate on the global prostate image and using the deep network to extract highly effective features for the boundary refinement in a finer scale. With consideration of the correlations among different sequential images, we then construct a graph to select the best prostate proposals from proposal set for its use in 3D prostate segmentation. Experimental evaluation demonstrates that our proposed deep network and graph based method is superior to state-of-the-art couterparts, in terms of both dice similarity coefficient and Hausdorff distance, on public dataset.
CcpA-Mediated Catabolite Activation of the Bacillus subtilis ilv-leu Operon and Its Negation by Either CodY- or TnrA-Mediated Negative Regulation

ABSTRACT The Bacillus subtilis ilv-leu operon functions in the biosynthesis of branched-chain amino acids. It undergoes catabolite activation involving a promoter-proximal cre which is mediated by the complex of CcpA and P-Ser-HPr. This activation of ilv-leu expression is negatively regulated through CodY binding to a high-affinity site in the promoter region under amino acid-rich growth conditions, and it is negatively regulated through TnrA binding to the TnrA box under nitrogen-limited growth conditions. The CcpA-mediated catabolite activation of ilv-leu required a helix face-dependent interaction of the complex of CcpA and P-Ser-HPr with RNA polymerase and needed a 19-nucleotide region upstream of cre for full activation. DNase I footprinting indicated that CodY binding to the high-affinity site competitively prevented the binding of the complex of CcpA and P-Ser-HPr to cre. This CodY binding not only negated catabolite activation but also likely inhibited transcription initiation from the ilv-leu promoter. The footprinting also indicated that TnrA and the complex of CcpA and P-Ser-HPr simultaneously bound to the TnrA box and the cre site, respectively, which are 112 nucleotides apart; TnrA binding to its box was likely to induce DNA bending. This implied that interaction of TnrA bound to its box with the complex of CcpA and P-Ser-HPr bound to cre might negate catabolite activation, but TnrA bound to its box did not inhibit transcription initiation from the ilv-leu promoter. Moreover, this negation of catabolite activation by TnrA required a 26-nucleotide region downstream of the TnrA box.
SemEval-2010 Task 8: Multi-Way Classification of Semantic Relations Between Pairs of Nominals

We present a brief overview of the main challenges in the extraction of semantic relations from English text, and discuss the shortcomings of previous data sets and shared tasks. This leads us to introduce a new task, which will be part of SemEval-2010: multi-way classification of mutually exclusive semantic relations between pairs of common nominals. The task is designed to compare different approaches to the problem and to provide a standard testbed for future research, which can benefit many applications in Natural Language Processing.
Online smoothing of live video transmissions

In this paper, we consider the problem of online smoothing of live video transmissions, where low latency is critical. To address the low latency requirement, our approach is to wait for a small smoothing window of video frames to be generated, and smooth them prior to their transmission. We present two classes of techniques that adapt an optimal offline algorithm[11] for online use: jumping window algorithms, in which an algorithm executes on consecutive non-overlapping smoothing windows, and sliding window algorithms, in which an algorithm executes on overlapping smoothing windows. We then evaluate these techniques using MPEG-1 traces. We find that the videos smoothed by these techniques show dramatic reduction in their peak rate, coefficient of variation and effective bandwidth. Furthermore, these reductions can be obtained by using very small window sizes, from 1 s to 5 s, indicating that even live video applications that have extremely tight latency requirements can benefit tremendously from using online smoothing. It is also of interest to note that these reductions in peak rate, coefficient of variation and effective bandwidth are very close to those obtained by the optimal offline algorithm. This implies that most of the smoothing benefits that can possibly be seen by a live video transmission can be attained by online smoothing operating on a very small smoothing window, thus incurring only a very small additional latency.
Potential of zebrafish as a model for exploring the role of the amygdala in emotional memory and motivational behavior

Emotion is a key aspect of behavior, enabling humans and animals to assign either positive or negative values to sensory inputs and thereby to make appropriate decisions. Classical experiments in mammalian models, mainly in primates and rodents, have shown that the amygdala is essential for appetitive and aversive associative processing and that dysfunction of this brain region leads to various psychiatric conditions, including depression, generalized anxiety disorder, panic disorder, phobias, autism, and posttraumatic stress disorder. In the past 2 decades, the zebrafish (Danio rerio; Cyprinidae) has emerged as a versatile, reliable vertebrate model organism for the in vivo study of development, gene function, and numerous aspects of human pathologies. Small size, high fecundity, rapid external development, transparency, genetic tractability, and high genetic and physiologic homology with humans are among the factors that have contributed to the success with this small fish in different biomedical research areas. Recent findings indicate that, despite the anatomical differences in the brain structure of teleosts and tetrapods, fish possess a structure homologous to the mammalian amygdala, a hypothesis that is supported by the expression of molecular markers, analyses of neuronal projections in different brain areas, and behavioral studies. This Review summarizes this evidence and highlights a number of relevant bioassays in zebrafish to study emotional memory and motivational behavior. © 2016 Wiley Periodicals, Inc.