Miracle-dz/UniFAR-FTUs huggingface dataset:
Crosstalk analysis of an image sensor operating at 1 Gfps

This paper evaluates temporal resolution of an ultra-high-speed image sensor and analyzes crosstalk between image signals when the sensor operates at 1 Giga frames per second (Gfps). The Backside-Illuminated Multi-Collection-Gate (BSI-MCG) structure of the sensor was proposed to achieve ultra-high speed imaging with very high sensitivity. The temporal resolution of the sensor is limited by an electronic factor - the travel time distribution of photoelectrons from their generated positions to a selective collection gate on the front side. To evaluate the travel time at the nanosecond time scale, random motions of electrons are included by using a Monte Carlo simulator in combination with a device simulator. The results show that less than 1ns temporal resolution is achievable. Due to the effect of random motions, crosstalk occurs between the output signals of the sensor. Different types of crosstalk are classified. To estimate the output image signals including crosstalk from other signals, an impulse response method is proposed.
Axonal Transport of the Ca2+‐Dependent Protein Modulator of 3′:5′‐Cyclic‐AMP Phosphodiesterase in the Rabbit Visual System

Abstract: Water‐soluble proteins were extracted from individual retinas, optic nerves, combined optic tracts and lateral geniculate bodies, and superior colliculi of rabbits at 1, 3, and 18 days after injection of [3H]leucine into the right eye. The Ca2+‐dependent protein modulator of 3′:5′‐cyclic‐AMP phos‐phodiesterase (calmodulin) was isolated from these samples by a two‐step polyacrylamide gel electrophoresis procedure. An analysis of the radioactivity incorporated into the total soluble proteins and the calmodulin revealed that most of the calmodulin was axonally transported at a slow rate (2–4 mm/day) and represented about 0.45% of the total transported soluble protein.
Paramyxovirus Infections in Ex Vivo Lung Slice Cultures of Different Host Species

In vivo experiments in animal models of disease are of crucial importance for viral tropism and pathogenesis studies. However, these experiments must be complemented with in vitro and ex vivo experiments. Here, we describe a protocol for the preparation and ex vivo infection of lung slices from different mammalian host species with various respiratory paramyxoviruses expressing fluorescent reporter proteins, and suggest follow-up experiments including immunohistochemistry, flow cytometry and confocal microscopy.
Human L1 element target‐primed reverse transcription in vitro

L1 elements are ubiquitous human transposons that replicate via an RNA intermediate. We have reconstituted the initial stages of L1 element transposition in vitro. The reaction requires only the L1 ORF2 protein, L1 3′ RNA, a target DNA and appropriate buffer components. We detect branched molecules consisting of junctions between transposon 3′ end cDNA and the target DNA, resulting from priming at a nick in the target DNA. 5′ junctions of transposon cDNA and target DNA are also observed. The nicking and reverse transcription steps in the reaction can be uncoupled, as priming at pre‐existing nicks and even double‐strand breaks can occur. We find evidence for specific positioning of the L1 RNA with the ORF2 protein, probably mediated in part by the polyadenosine portion of L1 RNA. Polyguanosine, similar to a conserved region of the L1 3′ UTR, potently inhibits L1 endonuclease (L1 EN) activity. L1 EN activity is also repressed in the context of the full‐length ORF2 protein, but it and a second cryptic nuclease activity are released by ORF2p proteolysis. Additionally, heterologous RNA species such as Alu element RNA and L1 transcripts with 3′ extensions are substrates for the reaction.
A novel function for the IκB inhibitor Cactus in promoting Dorsal nuclear localization and activity in the Drosophila embryo

ABSTRACT The evolutionarily conserved Toll signaling pathway controls innate immunity across phyla and embryonic patterning in insects. In the Drosophila embryo, Toll is required to establish gene expression domains along the dorsal-ventral axis. Pathway activation induces degradation of the IκB inhibitor Cactus, resulting in a ventral-to-dorsal nuclear gradient of the NFκB effector Dorsal. Here, we investigate how cactus modulates Toll signals through its effects on the Dorsal gradient and on Dorsal target genes. Quantitative analysis using a series of loss- and gain-of-function conditions shows that the ventral and lateral aspects of the Dorsal gradient can behave differently with respect to Cactus fluctuations. In lateral and dorsal embryo domains, loss of Cactus allows more Dorsal to translocate to the nucleus. Unexpectedly, cactus loss-of-function alleles decrease Dorsal nuclear localization ventrally, where Toll signals are high. Overexpression analysis suggests that this ability of Cactus to enhance Toll stems from the mobilization of a free Cactus pool induced by the Calpain A protease. These results indicate that Cactus acts to bolster Dorsal activation, in addition to its role as a NFκB inhibitor, ensuring a correct response to Toll signals. Summary: During dorsoventral patterning of the Drosophila embryo, ventral and lateral aspects of the embryonic Dorsal/NFκB gradient can behave differently in response to variations in Cactus concentration.
The Pathobiochemistry of Nitrogen Dioxide

Abstract Nitrogen dioxide (NO2) is an oxidizing free radical which can initiate a variety of destructive pathways in living systems, and several diseases are suspected to be connected with both exogenously and endogenously formed NO2. Peroxynitrite (ONOO/ONOOH) is believed to be an important endogenous source of NO2 radicals, but other sources, among them enzymatically ones, have been identified recently. It also became clear during the last few years that in vivo formation of 3-nitrotyrosine strictly depends on the availability of NO2 radicals. Since nitrogen dioxide is a very toxic compound an arsenal of antioxidants (e.g. vitamin C, glutathione, vitamin E, and βcarotene) must eliminate this harmful radical in vivo. Here the recently identified superoxide (O2)dependent formation of peroxynitrate (O2NOO) and the central role of vitamin C are of special importance.
Frictional Moisture Convergence in a Composite Life Cycle of the Madden–Julian Oscillation

Abstract A composite life cycle of the Madden–Julian oscillation (MJO) is constructed using an index based on the first two EOFs of the bandpass-filtered (20–80 days) 850-mb zonal wind averaged from 5°N to 5°S every 2.5° around the equator. Precipitation, 1000-mb convergence, 850-mb wind, and 200-mb wind are composited for the period 1979–95. Water vapor integrated from the surface to 300 mb is composited for the period 1988–92. Frictional moisture convergence at the equator is shown to play an important role in the life cycle of the Madden–Julian oscillation (MJO). Regions of boundary layer convergence foster growth of positive water vapor anomalies to the east of convection. This convergence coincides with 850-mb easterly wind anomalies, as is consistent with Kelvin wave dynamics. Drying of the atmosphere occurs rapidly after the passage of convection with the onset of 850-mb westerly perturbations. Possible mechanisms for this drying include boundary layer divergence and subsidence or horizontal advect.
Modèles hétérogènes en mécanique des fluides : phénomènes de congestion, écoulements granulaires et mouvement collectif

Cette these est dediee a la description et a l'analyse mathematique de phenomenes d'heterogeneites et de congestion dans les modeles de la mecanique des fluides.On montre un lien rigoureux entre des modeles de congestion douce de type Navier-Stokes compressible qui integrent des forces de repulsion a tres courte portee entre composants elementaires; et des modeles de congestion dure de type compressible/incompressible decrivant les transitions entre zones libres et zones congestionnees.On s'interesse ensuite a la modelisation macroscopique de melanges formes par des particules solides immergees dans un fluide.On apporte dans ce cadre une premiere reponse mathematique a la question de la transition entre les regimes de suspensions dictes par les interactions hydrodynamiques et les regimes granulaires dictes par les contacts entre les particules solides.On met par cette demarche en evidence le role crucial joue par les effets de memoire dans le regime granulaire.Cette approche permet egalement un nouveau point de vue pour l'etude mathematique des fluides avec viscosite dependant de la pression.On s'interesse enfin a la modelisation microscopique et macroscopique du trafic routier.Des schemas numeriques originaux sont proposes afin de reproduire des phenomenes de persistance d'embouteillages.
Effect of Different Ratios of Concentrate and Roughage on Lipid Synthesis by Rumen Microorganisms In Vitro

The effect of different feeding ratios of concentrate to roughage on ruminal lipid synthesis in vitro was examined. Three sheep fitted with a rumen fistula were fed three different ratios (8:2, 4:6 and 0:10) of concentrate and roughage, and their rumen liquor were used for incubation. 13 C-labeled glucose or sodium acetate as substrate was added to cultures of rumen liquor, and they were incubated for 6 h. The total lipid in the culture of the rumen liquor was extracted, and the percentage of 13 C excess was analyzed. The percentage of 13 C excess recovered when incubated with glucose increased with increased ratio of concentrate in the diet. The values of cultures incubated with glucose were higher than those incubated with sodium acetate except the roughage-only feeding. In the roughage-only diet, the percentage of 13 C excess when incubated with sodium acetate was highest of all diets. The recovery percentage of 13 C from glucose increased with increased ratio of concentrate. The recovery percentage of 13 C from sodium acetate addition in only roughage feeding was highest among the three diets. The recovery percentage of 13 C from glucose was markedly higher than that of sodium acetate addition in all feedings. The results indicate that high concentrate feeding facilitates lipid synthesis by rumen microorganisms, and that glucose may be the precursor for lipid synthesis rather than acetic acid. (Asian-Aust. J. Anim. Sci. 2003. Vol 16, No. 1 : 36-38)
Méthodes d’analyse de survie, valeurs manquantes et fractions attribuables temps dépendantes : application aux décès par cancer de la prostate

Le terme analyse de survie fait reference aux methodes utilisees pour modeliser le temps d'apparition d'un ou plusieurs evenements en tenant compte de la censure. L'evenement d’interet peut etre l'apparition, la recidive d'une maladie, ou le deces. Les causes de deces peuvent presenter des valeurs absentes, une situation qui peut etre modelisee par des methodes d’imputation. Dans la premiere partie de cette these nous avons passer en revue les methodes de gestion des donnees manquantes. Puis nous avons detaille les procedures qui permettent une imputation multiple des causes de deces. Nous avons developpe ces methodes dans une cohorte issue d’une etude europeenne, l’ERSPC (European Randomized Study of Screening for Prostate Cancer), qui etudiait le depistage et la mortalite par cancer de la prostate. Nous avons propose une formulation theorique des regles de Rubin apres transformation log-log complementaire afin de combiner les estimations de survie. De plus, nous mettons a disposition le code R afferent. Dans la deuxieme partie, nous presentons les methodes d'analyse de survie, en proposant une ecriture unifiee basee sur les definitions des survies brute et nette, que l’on s'interesse a toutes les causes de deces ou a une seule cause. Cela implique la prise en compte de la censure qui peut alors etre informative. Nous avons considere les methodes dites classiques (Kaplan-Meier, Nelson-Aalen, Cox et parametriques), les methodes des risques competitifs (en considerant un modele multi-etats ou un modele de temps latents), les methodes dites specifiques avec correction IPCW (Inverse Ponderation Censoring Weighting) et les methodes de survie relative. Les methodes dites classiques reposent sur l'hypothese de censure non informative. Quand on s'interesse aux deces de toutes causes, cette hypothese est souvent valide. En revanche, pour un deces de cause particuliere, les deces d'autres causes sont consideres comme une censure, et cette censure par deces d'autres causes est en general informative. Nous introduisons une approche basee sur la methode IPCW afin de corriger cette censure informative, et nous fournissons une fonction R qui permet d’appliquer cette approche directement. Toutes les methodes presentees dans ce chapitre sont appliquees aux bases de donnees completees par imputation multiple.Enfin, dans une derniere partie nous avons cherche a determiner le pourcentage de deces explique par une ou plusieurs variables en utilisant les fractions attribuables. Nous presentons les formulations theoriques des fractions attribuables, independantes du temps puis dependantes du temps qui s’expriment sous la forme de survie. Nous illustrons ces concepts en utilisant toutes les methodes de survie de la partie precedente et comparons les resultats. Les estimations obtenues avec les differentes methodes sont tres proches.
Uso da Inteligência Coletiva para Identificação de Mensagens Relevantes em um Bate-papo Gamificado

Este artigo tem como objetivo apresentar um sistema de bate-papo desenvolvido para o contexto educacional com base em principios de gamificacao e de inteligencia coletiva. Para promover o engajamento e a avaliacao das mensagens sao utilizadas reacoes, tal qual ocorrem no Sistema de Rede Social Facebook. Para a execucao desta pesquisa, o paradigma epistemologico usado foi a Design Science Research. Para a avaliacao do artefato proposto foi executado um estudo de caso no grupo de pesquisa que os autores do artigo participam e, apos as analises qualitativas e quantitativas, concluiu-se que os beneficios da inteligencia coletiva podem ser potencializados se a gamificacao for bem projetada e aplicada.
Caries Trends in Brazilian Non-Privileged Preschool Children in 1996 and 2006

The aims were to analyse caries trends in Brazilian non- privileged preschool children from 1996 to 2006 and to test the hypothesis that a decline in caries prevalence would manifest itself as a reduction in the rate of caries progression. Subjects were 1- to 5-year-old children born in and life time residents of the Federal District of Brazil (cohort 1996 = 1,465) and (cohort 2006 = 2,511). The clinical examination determined whether the tooth surfaces were sound, presented active lesions (non cavitated and cavitated), inactive lesions (non-cavitated and cavitated), fillings, were indicated for extraction or had been extracted. Intra- and inter-examiner reliability of caries scores showed κ values ranging from 0.71–0.93. A significant increase in the percentage of children who were free from any form of untreated or treated caries was observed (p < 0.05; χ2 test). Caries prevalence decreased by almost a half from 1996 to 2006. Differences in the mean caries scores at surface level, which included non-cavitated lesions, were observed for all age groups (p < 0.002; Mann-Whitney test) indicating a reduction in the rate of caries progression. In conclusion, since this population has access to fluoride and presents moderate caries prevalence, other measures to reduce the rate of caries progression are required to further improve oral health in non-privileged children.
Testing the Standard Fireball Model of Gamma-Ray Bursts Using Late X-Ray Afterglows Measured by Swift

We show that all X-ray decay curves of γ-ray bursts (GRBs) measured by Swift can be fitted using one or two components, both of which have exactly the same functional form comprised of an early falling exponential phase followed by a power-law decay. The first component contains the prompt γ-ray emission and the initial X-ray decay. The second component appears later, has a much longer duration, and is present for ≈80% of GRBs. It most likely arises from the external shock that eventually develops into the X-ray afterglow. In the remaining ≈20% of GRBs the initial X-ray decay of the first component fades more slowly than the second and dominates at late times to form an afterglow. The temporal decay parameters and γ/X-ray spectral indices derived for 107 GRBs are compared to the expectations of the standard fireball model including a search for possible "jet breaks. " For ~50% of GRBs the observed afterglow is in accord with the model, but for the rest the temporal and spectral indices do not conform to the expected closure relations and are suggestive of continued, late, energy injection. We identify a few possible jet breaks, but there are many examples where such breaks are predicted but are absent. The time Ta at which the exponential phase of the second component changes to a final power-law decay afterglow is correlated with the peak of the γ-ray spectrum, Epeak. This is analogous to the Ghirlanda relation, indicating that this time is in some way related to optically observed break times measured for pre-Swift bursts.
Trust Based Routing in DSR over Mobile Ad-hoc Network

: A mobile ad-hoc network is a self-configuring network or infrastructure-less network of mobile nodes connected by wireless links which together form a random topology. Due to absence of centralized control, multi-hop communications and dynamic network topology, the provision of making routing secure in mobile ad hoc networks is much more challenging than the security in wired network or infrastructure based networks. Nodes in mobile Ad Hoc Network (MANET) do not depend on a central infrastructure but relay packets originated by other mobile nodes. Mobile ad hoc networks can work properly only if the participating nodes cooperate in routing and forwarding. For individual nodes it might be advantageous not to cooperate, though. In this research paper, we propose a new approach based on relationship among the mobile nodes which makes them to cooperate in an infrastructure-less environment. The faith unit is used to calculate the faith values of each node in the network. The calculated faith values are being used by the relationship estimator to determine the relationship status of mobile nodes. The proposed enhanced protocol was compared with the standard DSR protocol and the results are analyzed using the MATLAB-R2008a.
Asymptomatic microbleeds as a risk factor for aspirin-associated intracerebral hemorrhages

The authors measured the presence and extent of asymptomatic microbleeds on gradient-recalled-echo MRI in 21 aspirin users who developed intracerebral hemorrhage and 21 aspirin users without history of intracerebral hemorrhage. Microbleeds were more frequent (19 vs 7, p < 0.001) and more extensive (mean number of microbleeds 13.3 vs 0.4, p < 0.001) in the intracerebral hemorrhage group than in the control group. Asymptomatic microbleeds may be a risk factor for aspirin-associated intracerebral hemorrhage.
The US Food and Drug Administration Provides a Pathway for Licensing Vaccines for Global Diseases

Responding to an urgency for new vaccines for global diseases, in September 2008 the Center for Biologics Evaluation and Research (CBER) at the US Food and Drug Administration (FDA) published an important FDA Guidance Document (see Box 1), ‘‘General Principles for the Development of Vaccines to Protect Against Global Infectious Diseases,’’ [1] that should expand the FDA’s role in facilitating the development of new vaccines for global bacterial, viral, and parasitic diseases affecting millions of people in developing countries worldwide. In part, this action is in response to a changing paradigm in advocacy for global diseases and recognition on the part of developed nations that the facilitation of vaccines and other products for neglected diseases disproportionately affecting those living in poverty is an effort that benefits industrialized as well as low-income countries. Moreover, through the effort of researchers, the pharmaceutical and biotechnology industries, and guided by nongovernmental product development partnerships, many funded by the Bill & Melinda Gates Foundation, preventative vaccines for global diseases are becoming a reality. Recent progress in this area is exemplified by both a meningococcal vaccine [2] and a new malaria vaccine moving forward into phase III efficacy trials in several African nations [3] and by several candidate vaccines for the prevention of tuberculosis being tested in phase I and II trials [4]. Vaccines and therapeutics for other viral [5], bacterial [6], and parasitic [7] neglected diseases are also in various stages of progress. As these new products enter into clinical trials, it has become clear to product development partners that it is critically important to identify regulatory pathways leading to the timely evaluation and acceptance of safe and effective life-saving interventions. However, this effort is impeded by the fact that regulatory agencies in developing countries where tropical diseases are endemic often lack the capacity to review applications for new vaccines, resulting in lengthy delays in obtaining permission to conduct clinical trials. Better-resourced regulatory agencies such as the US FDA, Health Canada, and the European Union’s European Medicines Agency (EMEA) have been willing to help strengthen regulatory authorities in developing countries, mostly through capacity-building and training programs coordinated by the World Health Organization (WHO), yet their ability to license new vaccines for global diseases has been restricted by the paucity of these diseases within their countries [8]. Some new approaches are being undertaken by the EMEA and by WHO and are briefly described here. In 2004 the European Union introduced a resolution (Article 58) stating that the EMEA could provide a scientific opinion equivalent to a marketing authorization in cooperation with WHO for the evaluation of medicinal products intended
Replica Placement Strategy for Data Grid Environment

Data Grid is an infrastructure that manages huge amount of data files, and provides intensive computational resources across geographically distributed collaboration. To increase resource availability and to ease resource sharing in such environment, there is a need for replication services. Data replication is one of the methods used to improve the performance of data access in distributed systems by replicating multiple copies of data files in the distributed sites. Replica placement mechanism is the process of identifying where to place copies of replicated data files in a Grid system. Existing work identifies the suitable sites based on number of requests and read cost of the required file. Such approaches consume large bandwidth and increases the computational time. The authors propose a replica placement strategy RPS that finds the best locations to store replicas based on four criteria, namely, 1 Read Cost, 2 File Transfer Time, 3 Sites' Workload, and 4 Replication Sites. OptorSim is used to evaluate the performance of this replica placement strategy. The simulation results show that RPS requires less execution time and consumes less network usage compared to existing approaches of Simple Optimizer and LFU Least Frequently Used.