Miracle-dz/UniFAR-FTUs huggingface dataset:
Translation of non-capped mRNAs in a eukaryotic cell-free system: acceleration of initiation rate in the course of polysome formation

Real-time monitoring of the translation of non-capped luciferase mRNA in a wheat germ cell-free system has been performed by continuous in situ measurement of the luminescence increase in the translation mixture. The phenomenon of acceleration of translation has been revealed. It has been shown that the acceleration is accompanied by the loading of translating polysomes with additional ribosomes, and thus is caused mainly by a rise in the initiation rate, rather than the stimulation of elongation or the involvement of additional mRNA molecules in translation. The acceleration requires a sufficient concentration of mRNA and depends on the sequence of the 5′ untranslated region (UTR). It can be abolished by the addition of excess cap analog (m7GpppGm). As the acceleration does not depend on the preliminary translation of other mRNAs in the same extract, the conclusion has been made that the effect is not due to activation of the ribosome population or other components of the system during translation, but rather it is the consequence of intra-polysomal events. The acceleration observed is discussed in terms of the model of two overlapping initiation pathways in eukaryotic polysomes: translation of non-capped mRNAs starts with eIF4F-independent initiation at 5′ UTR, and after the formation of sufficiently loaded polysomes, they rearrange in such a way that a mechanism of re-initiation of terminating ribosomes switches on. The eIF4F-mediated circularization of polysomes may be considered as a possible event that leads to the re-initiation switch and the resultant acceleration effect.
Real-time video vontent analysis tool for consumer media storage system

— With the growing storage capacities of hard-disks and optical discs, large consumer video databases are gradually developing. The large effective storage capacity using compressed video leads to the application of fast storage and retrieval functions, to enable quick user-friendly searching for and access to specific parts of the video data. We explore the feasibility of a near real-time semantic sports video analyzer for an experimental consumer media server. This tool is able to automatically extract and analyze key events in a video sequence. The analyzer employs several visual cues and a model for real-world coordinates, so that key parameters (e.g. speed and position) of a player can be determined with sufficient accuracy. This special data can be stored as metadata, thereby facilitating intelligent searching of events. The tool consists of four processing steps: (1) playing frame detection, (2) court extraction, as well as a 3-D camera model, (3) player segmentation and tracking, and (4) event-based high-level analysis exploiting visual cues extracted in the real-world. Our system has been evaluated in a new distributed AV content analysis system for home entertainment. We show attractive experimental results indicating the system efficiency and classification skills, thereby offering new analysis and search/retrieval tools to the consumer. 1
Bax Deletion Further Orders the Cell Death Pathway in Cerebellar Granule Cells and Suggests a Caspase-independent Pathway to Cell Death

Dissociated cerebellar granule cells maintained in medium containing 25 mM potassium undergo an apoptotic death when switched to medium with 5 mM potassium. Granule cells from mice in which Bax, a proapoptotic Bcl-2 family member, had been deleted, did not undergo apoptosis in 5 mM potassium, yet did undergo an excitotoxic cell death in response to stimulation with 30 or 100 μM NMDA. Within 2 h after switching to 5 mM K+, both wild-type and Bax-deficient granule cells decreased glucose uptake to <20% of control. Protein synthesis also decreased rapidly in both wild-type and Bax-deficient granule cells to 50% of control within 12 h after switching to 5 mM potassium. Both wild-type and Bax −/− neurons increased mRNA levels of c-jun, and caspase 3 (CPP32) and increased phosphorylation of the transactivation domain of c-Jun after K+ deprivation. Wild-type granule cells in 5 mM K+ increased cleavage of DEVD–aminomethylcoumarin (DEVD-AMC), a fluorogenic substrate for caspases 2, 3, and 7; in contrast, Bax-deficient granule cells did not cleave DEVD-AMC. These results place BAX downstream of metabolic changes, changes in mRNA levels, and increased phosphorylation of c-Jun, yet upstream of the activation of caspases and indicate that BAX is required for apoptotic, but not excitotoxic, cell death. In wild-type cells, Boc-Asp-FMK and ZVAD-FMK, general inhibitors of caspases, blocked cleavage of DEVD-AMC and blocked the increase in TdT-mediated dUTP nick end labeling (TUNEL) positivity. However, these inhibitors had only a marginal effect on preventing cell death, suggesting a caspase-independent death pathway downstream of BAX in cerebellar granule cells.
Monitoring air pollution effects on children for supporting public health policy: the protocol of the prospective cohort MAPEC study

Introduction Genotoxic biomarkers have been studied largely in adult population, but few studies so far have investigated them in children exposed to air pollution. Children are a high-risk group as regards the health effects of air pollution and some studies suggest that early exposure during childhood can play an important role in the development of chronic diseases in adulthood. The objective of the project is to evaluate the associations between the concentration of urban air pollutants and biomarkers of early biological effect in children, and to propose a model for estimating the global risk of early biological effects due to air pollutants and other factors in children. Methods and analysis Two biomarkers of early biological effects, DNA damage by the comet assay and the micronuclei (MN) test, will be investigated in oral mucosa cells of 6–8-year-old children. Concurrently, some toxic airborne pollutants (polycyclic aromatic hydrocarbon (PAH) and nitro-PAH) and in vitro air mutagenicity and toxicity in ultra-fine air particulates (PM0.5) will be evaluated. Furthermore, demographic and socioeconomic variables, other sources of exposures to air pollutants and lifestyle variables will be assessed by a structured questionnaire. The associations between sociodemographic, environmental and other exposure variables and biomarkers of early biological effect using univariate and multivariate models will be analysed. A tentative model for calculating the global absolute risk of having early biological effects caused by air pollution and other variables will be proposed. Ethics and dissemination The project has been approved by the Ethics Committees of the local Health Authorities. The results will be communicated to local Public Health Agencies, for supporting educational programmes and health policy strategies. LIFE+2012 Environment Policy and Governance. LIFE12 ENV/IT/000614.
Série Scientifique Scientific Series Asymptotic Properties of Monte Carlo Estimators of Diffusion Processes Asymptotic Properties of Monte Carlo Estimators of Diffusion Processes*

CIRANO Le CIRANO est un organisme sans but lucratif constitué en vertu de la Loi des compagnies du Québec. Le financement de son infrastructure et de ses activités de recherche provient des cotisations de ses organisations-membres, d'une subvention d'infrastructure du ministère de la Recherche, de la Science et de la Technologie, de même que des subventions et mandats obtenus par ses équipes de recherche. CIRANO is a private non-profit organization incorporated under the Québec Companies Act. Its infrastructure and research activities are funded through fees paid by member organizations, an infrastructure grant from the Ministère de la Recherche, de la Science et de la Technologie, and grants and research mandates obtained by its research teams. ASSOCIÉ AU :. Institut de Finance Mathématique de Montréal (IFM 2). Laboratoires universitaires Bell Canada. Réseau de calcul et de modélisation mathématique [RCM 2 ]. Réseau de centres d'excellence MITACS (Les mathématiques des technologies de l'information et des systèmes complexes) Les cahiers de la série scientifique (CS) visent à rendre accessibles des résultats de recherche effectuée au CIRANO afin de susciter échanges et commentaires. Ces cahiers sont écrits dans le style des publications scientifiques. Les idées et les opinions émises sont sous l'unique responsabilité des auteurs et ne représentent pas nécessairement les positions du CIRANO ou de ses partenaires. This paper presents research carried out at CIRANO and aims at encouraging discussion and comment. The observations and viewpoints expressed are the sole responsibility of the authors. They do not necessarily represent positions of CIRANO or its partners. Résumé / Abstract Dans cet article, nous étudions les distributions limites d'estimateurs de Monte Carlo de processus de diffusion. Nous examinons deux types d'estimateurs. Le premier est fondé sur un schéma d'Euler appliqué aux processus originaux, tandis que le second applique le schéma d'Euler à une transformation des processus qui stabilise la variance. Nous montrons que la transformation augmente la vitesse de convergence du schéma d'Euler. La distribution limite de cet estimateur, dérivée sous forme explicite, se révèle non centrée. Nous étudions également des estimateurs d'espérances conditionnelles de diffusions à partir d'un état initial connu. Nous caractérisons les erreurs d'approximation attendues et utilisons les expressions obtenues pour construire des estimateurs corrigés du biais de deuxième ordre. La correction de ce biais élimine la distorsion de niveau des intervalles de confiance asymptotiques et nous permet d'évaluer l'efficacité relative des estimateurs. Enfin, nous dérivons les distributions limites des estimateurs de …
A Genome-Wide Scan for Carotid Artery Intima-Media Thickness: The Mexican-American Coronary Artery Disease Family Study

Background and Purpose— Carotid artery intima-media thickness (CIMT), a subclinical measure of atherosclerosis, is associated with coronary artery disease (CAD), and stroke. CIMT is also an important predictor of clinical cardiovascular events. To systematically identify the genetic determinants of CIMT, we performed a genome-wide scan using data from 91 2-generation Mexican American families ascertained via a parent with CAD diagnosed. Methods— CIMT was measured in 274 adult offspring (mean age, 34.6 years) using high-resolution B-mode ultrasound; 413 subjects, including adult offspring and their parents, were genotyped using Marshfield screen set 12 (380 microsatellite markers at ≈10-cM interval). Heritability was estimated using the variance component approach implemented in SOLAR. Linkage analyses were performed using both the sib-pair regression approach and the variance component approach. Results— The estimated heritability was 0.68, 0.45, and 0.40 for unadjusted, gender- and age-adjusted, and multivariate-adjusted CIMT, respectively. The strongest evidence of linkage was found on chromosome 2 at D2S2944 (logarithm of the odds [LOD]=3.08). Other suggestive linkages were also found on chromosome 6 at D6S1022 to D6S2410 (LOD=2.21) and chromosome 13 at D13S796 to D13S895 (LOD=1.34). Conclusions— These results show that there is a strong genetic effect on CIMT in these Mexican American CAD families. The linkage peak on chromosome 2 suggests that there is a gene (or genes) at this chromosome location influencing CIMT.
Algorithms for Lipschitz Learning on Graphs

We develop fast algorithms for solving regression problems on graphs where one is given the value of a function at some vertices, and must find its smoothest possible extension to all vertices. The extension we compute is the absolutely minimal Lipschitz extension, and is the limit for large $p$ of $p$-Laplacian regularization. We present an algorithm that computes a minimal Lipschitz extension in expected linear time, and an algorithm that computes an absolutely minimal Lipschitz extension in expected time $\widetilde{O} (m n)$. The latter algorithm has variants that seem to run much faster in practice. These extensions are particularly amenable to regularization: we can perform $l_{0}$-regularization on the given values in polynomial time and $l_{1}$-regularization on the initial function values and on graph edge weights in time $\widetilde{O} (m^{3/2})$.
Journal of Geophysical Research: Solid Earth Patterns of Rupture Directivity of Subduction Zone Earthquakes in Northern Chile

We perform a systematic directivity analysis of local seismic events west oﬀ the coast of northern Chile. An empirical Green’s function technique is applied to a selection of events from a time period from 2008 to 2016 in the vicinity of the rupture area of the M W 8.1 Iquique megathrust earthquake in 2014. We compute rupture directivity for 293 events of magnitudes between M L 2.6 and M L 5.3. We ﬁnd a strong preference of rupture orientations subparallel to the convergence vector of the Nazca plate relative to the South-American plate. The preferred rupture direction is downdip. We speculate that the reason for the dominating rupture direction could be a lateral limitation of available rupture directions by the repeating earthquake-like nature of the observed events combined with a material contrast at the subduction interface which, according to the bimaterial eﬀect, favors the downdip rupture direction. controls the directivity of earthquakes. rupture directivity of multiple small to medium (M L 2.6–M L 5.3) events in the northern Chile subduction zone, which were recorded by the Integrated Plate boundary Observatory Chile. On the M W 8.1 Iquique megathrust earthquake occurred in the southern Peru- northern Chile seismic gap event by a large number of foreshocks aftershocks, aftershock seismicity rate Multiple large events L ≥ seismic sequence strong unilateral directivity megathrust foreshock aftershock data set also constitutes rich for here presented comprehensive study on rupture directivity even for events of signiﬁcantly smaller magnitude. In this we describe how we compute waveform similarity-based empirical Green’s function (EGF) pairs and then reconstruct the source time functions at all recording stations. Further, the amplitudes of these source time functions are analyzed for azimuthal variations corresponding to the directivity eﬀect of unilateral ruptures. The procedure is tested with a synthetic event catalog in order to ensure the robustness of theapproachforthegivensource-receivergeometryinnorthernChile. Theresultingcatalogisﬁnallyanalyzed for spatiotemporal dependencies of rupture direction and
Priority Assignment for Global Fixed Priority Pre-Emptive Scheduling in Multiprocessor Real-Time Systems

This paper addresses the problem of priority assignment in multiprocessor real-time systems using global fixed task-priority pre-emptive scheduling. In this paper, we prove that Audsley's Optimal Priority Assignment (OPA) algorithm, originally devised for uniprocessor scheduling, is applicable to the multiprocessor case, provided that three conditions hold with respect to the schedulability tests used. Our empirical investigations show that the combination of optimal priority assignment policy and a simple compatible schedulability test is highly effective, in terms of the number of tasksets deemed to be schedulable. We also examine the performance of heuristic priority assignment policies such as Deadline Monotonic, and an extension of the TkC priority assignment policy called DkC that can be used with any schedulability test. Here we find that Deadline Monotonic priority assignment has relatively poor performance in the multiprocessor case, while DkC priority assignment is highly effective.
Multiyear Observations of Gravity Wave Momentum Fluxes in the Midlatitude Mesosphere and Lower Thermosphere Region by Meteor Radar

Multiyear high‐frequency gravity wave (GW) momentum fluxes and variances in the mesosphere and lower thermosphere region are revealed using four meteor radars along 120°E longitude at Northern Hemisphere midlatitudes for the first time, which are located at Mohe (53.5°N, 122.3°E), Beijing (40.3°N, 116.2°E), Mengcheng (33.3°N, 116.5°E), and Wuhan (30.5°N, 114.2°E), respectively. The seasonal and latitudinal variations of GW momentum fluxes in the midlatitude are discussed. The directions of the monthly mean zonal momentum fluxes are mostly against the background mean zonal winds, which agree well with the selective filtering mechanism. The seasonal variations of meridional momentum fluxes have similar trends over all four stations. The latitudinal variations in the seasonal variation of GW momentum fluxes are mainly due to the latitudinal variations of background winds and GW sources. The unexpected eastward momentum fluxes in winter over Beijing are likely caused by the secondary GWs propagating eastward from the source region over the Tibetan Plateau (25°–40°N, 70–100°E). The GW variances show a V‐shaped structure indicating annual and semiannual variations over four stations in zonal component. A quasi‐4‐month oscillation was observed over Mohe, Mengcheng, and Wuhan in meridional component. The background winds play decisive roles in these GW variance structures.
Privacy enhanced cellular access security

The 3G cellular access security architectures do not provide satisfactorily user privacy and fail to fully include all three principal entities involved in the security context. In this paper we propose a beyond-3G Privacy Enhanced 3-Way Authentication and Key Agreement (PE3WAKA) protocol that provides substantially improved user privacy and a 3-way security context. By integrating selected Mobility Management procedures and the PE3WAKA protocol this is achieved with fewer round-trips than the 3G equivalent.
Forces for Morphogenesis Investigated with Laser Microsurgery and Quantitative Modeling

We investigated the forces that connect the genetic program of development to morphogenesis in Drosophila. We focused on dorsal closure, a powerful model system for development and wound healing. We found that the bulk of progress toward closure is driven by contractility in supracellular “purse strings” and in the amnioserosa, whereas adhesion-mediated zipping coordinates the forces produced by the purse strings and is essential only for the end stages. We applied quantitative modeling to show that these forces, generated in distinct cells, are coordinated in space and synchronized in time. Modeling of wild-type and mutant phenotypes is predictive; although closure in myospheroid mutants ultimately fails when the cell sheets rip themselves apart, our analysis indicates that βPS integrin has an earlier, important role in zipping.
Modeling and analysis of DC traction system under light of current developments in HPC and virtual reality

We have developed a library for simulation of DC traction system. The modeling, installation and reliability aspects of Traction system in purview of current developments in HPC and Virtual reality can be implemented on the proposed protocol. We have proposed a model to predict and analyze traction system more comprehensively and put a modeling structure regarding the same. Distribution of various computations is shown in an HPC setup and has been implemented. The advantages of Virtual reality in installation in city and intercity, driving has been implemented on C#. Installation of VR framework for installation of DC traction thus has been implemented in the current technologies that are being developed in areas of HPC and VR.
Applying perceptually driven cognitive mapping to virtual urban environments

This paper describes a method for building a cognitive map of a virtual urban environment. Our routines enable virtual humans to map their environment using a realistic model of perception. We based our implementation on a computational framework proposed by Yeap and Jefferies (Yeap & Jefferies 1999) for representing a local environment as a structure called an Absolute Space Representation (ASR). Their algorithms compute and update ASRs from a 2-1/2D sketch of the local environment, and then connect the ASRs together to form a raw cognitive map. Our work extends the framework developed by Yeap and Jefferies in three important ways. First, we implemented the framework in a virtual training environment, the Mission Rehearsal Exercise (Swartout et al. 2001). Second, we describe a method for acquiring a 2- 1/2D sketch in a virtual world, a step omitted from their framework, but which is essential for computing an ASR. Third, we extend the ASR algorithm to map regions that are partially visible through exits of the local space. Together, the implementation of the ASR algorithm along with our extensions will be useful in a wide variety of applications involving virtual humans and agents who need to perceive and reason about spatial concepts in urban environments.
Approaches in Gene Therapy of Cancer and Cardiovascular Diseases

In this chapter we will focus on few topics. First, we summarize and discuss angiogenic gene therapy of cancer and cardiovascular diseases, with RNA interference in a separate section. Second, we briefly review delivering systems in gene therapy, their advatages and limitations and further focus on bacterial vectors. Last, we summarize antioxidant gene therapy of cardiovascular diseases and hypertension. Considering the fact that the fundamental discoveries and new findings in medicine are being crystallized on genetic and genomic levels, gene therapy is one of the potential mechanisms for therapeutic intervention. Gene therapy in a broad sense, i.e. all the therapeutic strategies employing nucleic acids as carriers of genetic information, found its utilization in most areas of medicine, including angiogenesis research. Similarly to classical “non-gene“ therapy, the research in gene therapy is happening on the preclinical level using appropriate animal models, with cancer and cardiovascular diseases being the most abundant indications. There are several different strategies known. Besides the delivery of therapeutic gene (replacement of the mutated gene by a functional one or delivery of the gene because of lack of the gene product), novel strategies are also being widely used based on blocking the function of a specific gene by application of RNA interference inducing sequences, antisense inhibition etc. One of the key advantages of gene approaches is the endogenous production of the therapeutic molecule. Furthermore, targeted gene delivery specifically into the target tissue or only to a certain cell type can dramatically decrease the likelihood of adverse effects. Along with the development of new vectors and regulatory systems, the ability to control the expression of therapeutic gene in time and space is being improved. This is of great importance in affecting such complex and complicated processes as angiogenesis. Currently, almost three quarters of indications addressed by gene therapy clinical trials are represented by cancer and cardiovascular diseases
An Easy Setup for Parallel Medical Image Processing: Using Taverna and ARC

Medical image processing is known as a computationally expensive and data intensive domain. It is thus well-suited for Grid computing. However, Grid computing usually requires the applications to be designed for parallel processing, which is a challenge for medical imaging researchers in hospitals that are most often not used to this. Making parallel programming methods easier to apply can promote Grid technologies in clinical environments. Readily available, functional tools with an intuitive interface are required to really promote healthgrids. Moreover, the tools need to be well integrated with the Grid infrastructure. To facilitate the adoption of Grids in the Geneva University Hospitals we have set up a develop environment based on the Taverna workflow engine. Its usage with a medical imaging application on the hospitals' internal Grid cluster is presented in this paper.