Miracle-dz/UniFAR-FTUs huggingface dataset:
Protection from Ebola Virus Mediated by Cytotoxic T Lymphocytes Specific for the Viral Nucleoprotein

ABSTRACT Cytotoxic T lymphocytes (CTLs) are proposed to be critical for protection from intracellular pathogens such as Ebola virus. However, there have been no demonstrations that protection against Ebola virus is mediated by Ebola virus-specific CTLs. Here, we report that C57BL/6 mice vaccinated with Venezuelan equine encephalitis virus replicons encoding the Ebola virus nucleoprotein (NP) survived lethal challenge with Ebola virus. Vaccination induced both antibodies to the NP and a major histocompatibility complex class I-restricted CTL response to an 11-amino-acid sequence in the amino-terminal portion of the Ebola virus NP. Passive transfer of polyclonal NP-specific antiserum did not protect recipient mice. In contrast, adoptive transfer of CTLs specific for the Ebola virus NP protected unvaccinated mice from lethal Ebola virus challenge. The protective CTLs were CD8+, restricted to the Db class I molecule, and recognized an epitope within amino acids 43 to 53 (VYQVNNLEEIC) in the Ebola virus NP. The demonstration that CTLs can prevent lethal Ebola virus infection affects vaccine development in that protective cellular immune responses may be required for optimal protection from Ebola virus.
The anterior olfactory nucleus: Quantitative study of dendritic morphology

The anterior olfactory nucleus (AON) occupies a crucial position within the olfactory circuit, as it is able to influence function in nearly every major synaptic processing stage of both the ipsilateral and the contralateral pathways. Nevertheless, very little is known about the region's internal organization and circuitry. The present study provides basic quantitative and qualitative data on the morphology of several cell types within the two major regions of the AON, pars externa and pars principalis. In pars externa two types of cells are analyzed, the “classical” cell (type I), containing only apically directed dendrites with large spines, and a previously unreported cell with basilar dendrites and complex, spiny apical processes (type II). In pars principalis the characteristic pyramidal cell is described both on the basis of the depth of the cell bodies in the cell layer comprising the structure and on the basis of their radial location. Several other nonpyramidal neurons are also described. The findings provide useful basic information necessary for understanding and modeling the circuitry of the AON. J. Comp. Neurol. 518:1603–1616, 2010. © 2009 Wiley‐Liss, Inc.
Using genetic markers to estimate the pollen dispersal curve

Pollen dispersal is a critical process that shapes genetic diversity in natural populations of plants. Estimating the pollen dispersal curve can provide insight into the evolutionary dynamics of populations and is essential background for making predictions about changes induced by perturbations. Specifically, we would like to know whether the dispersal curve is exponential, thin‐tailed (decreasing faster than exponential), or fat‐tailed (decreasing slower than the exponential). In the latter case, rare events of long‐distance dispersal will be much more likely. Here we generalize the previously developed twogener method, assuming that the pollen dispersal curve belongs to particular one‐ or two‐parameter families of dispersal curves and estimating simultaneously the parameters of the dispersal curve and the effective density of reproducing individuals in the population. We tested this method on simulated data, using an exponential power distribution, under thin‐tailed, exponential and fat‐tailed conditions. We find that even if our estimates show some bias and large mean squared error (MSE), we are able to estimate correctly the general trend of the curve — thin‐tailed or fat‐tailed — and the effective density. Moreover, the mean distance of dispersal can be correctly estimated with low bias and MSE, even if another family of dispersal curve is used for the estimation. Finally, we consider three case studies based on forest tree species. We find that dispersal is fat‐tailed in all cases, and that the effective density estimated by our model is below the measured density in two of the cases. This latter result may reflect the difficulty of estimating two parameters, or it may be a biological consequence of variance in reproductive success of males in the population. Both the simulated and empirical findings demonstrate the strong potential of twogener for evaluating the shape of the dispersal curve and the effective density of the population (de).
Modeling the mode competition of Yb-doped fiber amplifiers in consideration of photodarkening

In this paper, the numerical steady-state model of mode competition in high power ytterbium-doped fiber amplifiers (YDFA) which considering the distributed photodarkening (PD) loss has been studied and developed for the first time. According to the relationship between PD loss and the upper-state population fraction, the formula of saturated PD loss which can distinguish different modes is established. Based on the rate-equation model considering transverse spatial-hole burning, we calculate the longitudinal distribution and quantitative results of each mode’s PD loss for the first time to the best of our knowledge. The dependence of parameters such as pumping direction, fiber length, and fiber doping composition on YDFA is also investigated and discussed. According to our simulation results, the output power of YDFA is strongly affected by PD loss. Meanwhile, PD increases the loss of higher-order mode (HOM), as well as enhances the ratio between fundamental mode (FM) and HOM. Thus, HOM suppression and improvement of beam quality can be expected within PD effect. In our work, the mode competition of high power YDFA under varying degrees of PD loss has been simulated. Obviously the output power will decrease with increasing the PD loss. However the ratio between FM and HOM has no evident changes with varying the PD loss, which providing guideline on appropriately using PD loss to regulate the mode competition between FM and HOM aiming at effective single-mode output of YDFA.
Lossless Separation of Web Pages into Layout Code and Data

A modern web page is often served by running layout code on data, producing an HTML document that enhances the data with front/back matters and layout/style operations. In this paper, we consider the opposite task: separating a given web page into a data component and a layout program. This separation has various important applications: page encoding may be significantly more compact (reducing web traffic), data representation is normalized across web designs (facilitating wrapping, retrieval and extraction), and repetitions are diminished (expediting site updates and redesign). We present a framework for defining the separation task, and devise an algorithm for synthesizing layout code from a web page while distilling its data in a lossless manner. The main idea is to synthesize layout code hierarchically for parts of the page, and use a combined program-data representation cost to decide whether to align intermediate programs. When intermediate programs are aligned, they are transformed into a single program, possibly with loops and conditionals. At the same time, differences between the aligned programs are captured by the data component such that executing the layout code on the data results in the original page. We have implemented our approach and conducted a thorough experimental study of its effectiveness. Our experiments show that our approach features state of the art (and higher) performance in both size compression and record extraction.
A 1V 830μW full-band ZigBee receiver front-end with current-reuse and Gm-boosting techniques

A low-voltage low-power CMOS ZigBee receiver front-end supporting 780/868/915/2400MHz bands is presented in this paper. The wideband common-gate (CG) low noise amplifier (LNA) and the I/Q current-commutating mixer are merged in a single circuit, sharing the bias current. Active trans-conductance (gm) boosting technique is utilized in the design of the presented receiver front-end. The topology and optimization method of the presented front-end are shown. Post-layout simulation results for 180nm RF CMOS implementations show the conversion gain is 26.5dB at 780/868/915MHz bands and 19.5dB at 2400MHz band. The minimum simulated NF is 6.5dB. The receiver front-end consumes 830μW from a 1V DC supply and the active size of core circuit is 0.0276mm2.
The Tobit Kalman Filter: An Estimator for Censored Measurements

Tobit model censored data arise in multiple engineering applications through saturating sensors, limit-of-detection effects, and image frame effects. In this brief, we introduce a novel formulation of the Kalman filter for Tobit Type 1 censored measurements. Our proposed formulation, called the Tobit Kalman filter, is identical to the standard Kalman filter in the no-censoring case. At or near the censored region, the Tobit Kalman filter utilizes a local approximation of the probability of censoring in order to provide a fully recursive estimate of the state and state error covariance. The additional computational burden of the method compared with the standard Kalman filter is limited to the calculation of m normal probability density functions and m normal cumulative density functions per update, where m is the number of measurements.
A tissue factor-cascade-targeted nanoparticle forsite-directed inducing thrombosis

Tissue factor is an upstream component of the cascade and a high-expressing factor under phathological conditions. In this study, a tissue factor cascade-targeted strategy for inducing local thrombosis was developed by combining ENP-HMME and photochemistry. In vitro study showed that protein EGFP-EGF1 conjugation to the nanoparticles could significantly contribute to the uptake of nanoparticles by tissue factor over-expressed brain capillary endothelial cells. Three-dimensional imaging and specklegram of brains in vivo showed that tissue factor cascade-targeted strategy successfully induced thrombosis of expected position. As shown by the in vivo multispectral fluorescent imaging, when ENP-HMME was combined with photochemistry, higher accumulation in the infarction hemisphere was observed, which might suggest that the photochemistry inducing tissue factor cascade recruited more ENP-HMME than HMME-loaded nanoparticles (NP-HMME). The data indicated the tissue factor cascade-targeted strategy has potential to induce local thrombosis, and might be applied in the treatment of a variety of hypervascular diseases.
Recent developments and applications of quantitative laser light sheet measuring techniques in turbomachinery components

Concerning the further development of gas turbine engines, advances of the aero-thermodynamic design can be achieved most efficiently by co-operative efforts aimed at the improvement of both the numerical simulation methods and the experimental test and measurement techniques. Rapid development of numerical capability is accompanied by increasing demands on experimental data. In this context significant instrumentation research efforts are being conducted to develop the needed measurement technologies. Because of the need for reduced experimental costs planar measurement techniques have undergone a rapid pace of development. Three newly developed quantitative light sheet techniques utilizing the scattered light of tracer particles are described in this paper. First a Doppler global velocimetry (DGV) system optimized for time-averaged three component velocity measurements is presented. The system, which uses a single viewing direction in conjunction with three different illumination directions enables very accurate velocity measurements. Second a quantitative light sheet (QLS) technique for quantitative mass fraction measurements in mixing processes is treated. To apply the technique the inflow of the mixing experiment must consist at least of two separate flows, one of which can be seeded while the other remains unseeded. DGV and QLS results obtained from experimental investigation in a model combuster are presented. Third a method named tracer-based shock visualization (TSV) is described which is capable of determining the shape and structure of shock waves in transonic flows by analysing the sudden increase of flow density across a shock. Results taken in a transonic compressor are presented.
PHYSIOLOGICAL PERFORMANCE OF FLOATING GIANT KELP MACROCYSTIS PYRIFERA (PHAEOPHYCEAE): LATITUDINAL VARIABILITY IN THE EFFECTS OF TEMPERATURE AND GRAZING 1

Rafts of Macrocystis pyrifera (L.) C. Agardh can act as an important dispersal vehicle for a multitude of organisms, but this mechanism requires prolonged persistence of floating kelps at the sea surface. When detached, kelps become transferred into higher temperature and irradiance regimes at the sea surface, which may negatively affect kelp physiology and thus their ability to persist for long periods after detachment. To examine the effect of water temperature and herbivory on the photosynthetic performance, pigment composition, carbonic anhydrase (CA) activity, and the nitrogen (N) and carbon (C) content of floating M. pyrifera, experiments were conducted at three sites (20° S, 30° S, 40° S) along the Chilean Pacific coast. Sporophytes of M. pyrifera were maintained at three different temperatures (ambient, ambient − 4°C, ambient + 4°C) and in presence or absence of the amphipod Peramphithoe femorata for 14 d. CA activity decreased at 20° S and 30° S, where water temperatures and irradiances were highest. At both sites, pigment contents were substantially lower in the experimental algae than in the initial algae, an effect that was enhanced by grazers. Floating kelps at 20° S could not withstand water temperatures >24°C and sank at day 5 of experimentation. Maximal quantum yield decreased at 20° S and 30° S but remained high at 40° S. It is concluded that environmental stress is low for kelps floating under moderate temperature and irradiance conditions (i.e., at 40° S), ensuring their physiological integrity at the sea surface and, consequently, a high dispersal potential for associated biota.
Experimental Implementation of An Intrusion Detection System using WLAN Signals

In this paper, we experimentally implement an intrusion detection system using WLAN under the situation where many base stations are observed. Our system detects an event by measuring the received signal strength indication (RSSI) of a WLAN signal. The detection algorithm and the decision rule are presented and the effectiveness of the system is demonstrated through the measurement results.
Extending dynamic range of monochrome and color images through fusion

This paper presents an approach to enhance the dynamic range of monochromatic and color images. The goal of this method is that of overcoming the inherent physical limitations of the acquisition process. The approach uses pattern-selective image fusion as a means to integrate information from images acquired under different shutter speeds or apertures. The result of this process is a composite in which none of the portions of the image is over or under saturated and the underlying information has been preserved. The results show the performance of this enhancement process from imagery taken from consumer-grade video camera equipment.
Designing for yield: a defect-tolerant approach to high-level synthesis

Defect-tolerant techniques can be effectively applied to regular structures which allow a very simple reconfiguration technique. A typical example is represented by memories, where algorithms for row and column elimination grant very good results with a limited area overhead (namely, a limited number of spare rows and columns). The reconfiguration technologies developed for memories could be applied to other devices only if the two conditions of regularity and simplicity can be transferred to their architectures. In the present paper we propose a methodology aiming at designing an intrinsically regular data path thus achieving defect-tolerance with a limited area increase, both in terms of spare functional units and memories and in terms of augmented interconnection network.
Discovery of Single Nucleotide Polymorphisms in Complex Genomes Using SGSautoSNP

Single nucleotide polymorphisms (SNPs) are becoming the dominant form of molecular marker for genetic and genomic analysis. The advances in second generation DNA sequencing provide opportunities to identify very large numbers of SNPs in a range of species. However, SNP identification remains a challenge for large and polyploid genomes due to their size and complexity. We have developed a pipeline for the robust identification of SNPs in large and complex genomes using Illumina second generation DNA sequence data and demonstrated this by the discovery of SNPs in the hexaploid wheat genome. We have developed a SNP discovery pipeline called SGSautoSNP (Second-Generation Sequencing AutoSNP) and applied this to discover more than 800,000 SNPs between four hexaploid wheat cultivars across chromosomes 7A, 7B and 7D. All SNPs are presented for download and viewing within a public GBrowse database. Validation suggests an accuracy of greater than 93% of SNPs represent polymorphisms between wheat cultivars and hence are valuable for detailed diversity analysis, marker assisted selection and genotyping by sequencing. The pipeline produces output in GFF3, VCF, Flapjack or Illumina Infinium design format for further genotyping diverse populations. As well as providing an unprecedented resource for wheat diversity analysis, the method establishes a foundation for high resolution SNP discovery in other large and complex genomes.
Cone Trees: animated 3D visualizations of hierarchical information

The task of managing and accessing large information spaces is a problem in large scale cognition. Enwrging technologies for 3D visualization and interactive aninlaiion offer potential solutions to this problenl, especially when the structure of the information can be visualized. We describe one of these Information Visualtzaiion techniques, called the Cone Tree, which is used for visualizing hierarchical information structures. The hierarchy is presented in 3D to nlaxilnize effective use of available screen space and enable visualization of the whole structure. Interactive aninlation is used (,o shift sonle of the user’s cognitive load to the human perceptual system,
Efficacy of intratracheal instillation of a meropenem/perfluorochemical suspension in acute lung injury

Perfluorochemical (PFC) is theoretically a good vehicle for delivering biological agents to the lungs. This study was designed to investigate the efficacy of intratracheal (IT) instillation of meropenem using PFC liquid as a vehicle in a piglet model of acute lung injury (ALI). Eighteen piglets were injured with lung lavages to induce ALI, and randomly assigned to intravenous (IV) infusion or IT instillation groups, the latter using either PFC or normal saline (NS) as a delivery vehicle for meropenem. Blood samples were obtained at 0, 15, 30, and 60 min, and then hourly for 6 hr. Sera and extracts of lung tissues were assayed for meropenem content using high‐performance liquid chromatography. We found that the IV group had significantly higher serum concentrations of meropenem during the first hour after dosing (P < 0.05). There was no significant difference between IT‐PFC and IT‐NS groups regarding changes in serum meropenem concentrations during the experimental period. Meropenem content in lung tissue was highest in the IT‐PFC group, lower in the IT‐NS group, and undetectable in the IV group (P < 0.05). The IT‐NS group had the highest peak inspiratory pressure (P < 0.05), but there were no significant differences in other cardiopulmonary parameters among the three groups studied. In conclusion, meropenem can be safely administered to injured lungs by IT instillation in a meropenem/PFC suspension. Using PFC liquid as an IT vehicle to carry meropenem provides better pulmonary drug depositions than IV injection or IT instillation with NS in ALI. Pediatr Pulmonol. 2012; 47:189–198. © 2011 Wiley Periodicals, Inc.
An Approach to Identify the Number of Clusters

In this technological age, vast amounts of data are generated. Various statistical methods are used to find patterns in data, including clustering. Many common methods for cluster analysis, such as k-means and Nonnegative Matrix Factorization, require input of the number of clusters in the data. However, usually that number is unknown. There exists a method that uses eigenvalues to compute the number of clusters, but sometimes it underestimates that number. In this paper, we propose a complementary method to identify the number of clusters. This method is used to analyze three data sets and gives fairly accurate estimates of the number of clusters.
L4-LINUX BASED SYSTEM AS A PLATFORM FOR EPICS IOC-CORE

The EPICS Input/Output Controller (IOC) coreprogram, iocCore [1], is now portable to multiplatforms. The Linux operating system, among them, seems to be a promising candidate for a platform to run iocCore, considering the recent high appreciation in desktop and server use as well as control fields. The Linux kernel, however, is not suitable for timecritical applications, since it responds to external events with unpredictable latency. We summarize three known causes of the latency, and then discuss some of the different solutions and how they affect the functionality of iocCore. As a possible alternative, we propose an approach that dispatches user-level processes by a real-time kernel aiming at a consistency of availability with predictable responsiveness.
A Neural Network Component for an Intrusion Detection System Herv

In this paper, we present a possible application of neural networks as a component of an intrusion detection system. Neural network algorithms are emerging nowadays as a new arnficial intelligence techm”quethat can be applied to real-l~e problems. We present an approach of user behavior modeling that takes advantage of the properties of neural algorithms and display results obtained on preliminary testing of our approach.
Unified Definition of Heuristics for Classical Planning

In many types of planning algorithms distance heuristics play an important role. Most of the earlier works restrict to STRIPS operators, and their application to a more general language with disjunctivity and conditional effects first requires an exponential size reduction to STRIPS operators. I present direct formalizations of a number of distance heuristics for a general operator description language in a uniform way, avoiding the exponentiality inherent in earlier reductive approaches. The formalizations use formulae to represent the conditions under which operators have given effects. The exponentiality shows up in satisfiability tests with these formulae, but would appear to be a minor issue because of the small size of the formulae.