gebhart/patrepeval huggingface dataset:
<scp>CD</scp>8 T‐cell priming upon <scp>mRNA</scp> vaccination is restricted to bone‐marrow‐derived antigen‐presenting cells and may involve antigen transfer from myocytes (2015)

Self-amplifying mRNAs (SAM(®) ) are a novel class of nucleic acid vaccines, delivered by a non-viral delivery system. They are effective at eliciting potent and protective immune responses and are being developed as a platform technology with potential to be used for a broad range of targets. However, their mechanism of action has not been fully elucidated. To date, no evidence of in vivo transduction of professional antigen-presenting cells (APCs) by SAM vector has been reported, while the antigen expression has been shown to occur mostly in the muscle fibres. Here we show that bone-marrow-derived APCs rather than muscle cells are responsible for induction of MHC class-I restricted CD8 T cells in vivo, but direct transfection of APCs by SAM vectors is not required. Based on all our in vivo and in vitro data we propose that upon SAM vaccination the antigen is expressed within muscle cells and then transferred to APCs, suggesting cross-priming as the prevalent mechanism for priming the CD8 T-cell response by SAM vaccines.
Transmission Parameters for Candidatus Liberibacter asiaticus by Asian Citrus Psyllid (Hemiptera: Psyllidae) (2010)

The purpose of this investigation was to evaluate acquisition and inoculation (together, transmission) efficiency of Candidatus Liberibacter asiaticus (Las), the pathogen associated with citrus huanglongbing (HLB) by the Asian citrus psyllid, Diaphorina citri (Kuwayama) (Hemiptera: Psyllidae). In laboratory studies, nymphs reared on Las infected plants were more likely to acquire the bacterium than adults. Acquisition by nymphs ranged from 60 to 100%, whereas acquisition by adults only reached 40% after 5 wk of feeding on Las-infected plants. Similar rates of pathogen acquisition by psyllids after nymphal and adult feeding were observed in the field. Transmission of Las from parent to offspring (transovarial) occurred at a rate of 2-6%. One year after psyllid inoculations, successful transmission by individual D. citri ranged from 4 to 10%, whereas groups of 100 or more D. citri transmitted the pathogen at a rate of approximately 88%. In addition, the proportion of Las-positive adult psyllids, determined using quantitative real-time polymerase chain reaction, decreased over time when held on healthy plants. Due to the low rate of pathogen acquisition and long time period required for successful inoculation by adult D. citri, experiments designed to determine the latent period required for replication and successful inoculation of Las by D. citri did not result in Las-infected plants after >1 yr of incubation after inoculation. Collectively, these results indicate that adult D. citri which acquire the HLB pathogen as adults are poor vectors of the pathogen compared with adults that acquired the pathogen as nymphs.
Mucolytic treatment with N-acetylcysteine L-lysinate metered dose inhaler in dogs: airway epithelial function changes (1994)

N-acetylcysteine L-lysinate Nacystelyn (L-NAC) is a newly synthesized mucolytic agent, of which the action in vivo has not been well defined. In six healthy mongrel dogs, the rheological properties of mucus, its mucociliary and cough clearability, and the transepithelial potential difference (PD) of the tracheobronchial epithelium were evaluated after placebo and L-NAC metered dose inhaler (MDI) aerosols. The principal index of mucus rigidity, log G*, decreased at all airway sites with L-NAC administration, i.e. the mucus became less rigid and more deformable (the overall change in G* was 0.29 log units, i.e. ca. twofold decrease). The viscoelasticity-derived mucus transportability parameters, mucociliary (MCI) and cough (CCI) clearability indices, increased with L-NAC MDI, particularly CCI, which predicts the effect of mucus rheology on cough clearability. PD increased significantly with L-NAC administration at all measurement sites, which appears to be a novel effect for a direct acting mucolytic agent. Tracheal mucus linear velocity (TMV) increased after L-NAC compared with placebo, as did the normalized frog palate transport rate (NFPTR). The increase in NFPTR was greater than that predicted from the mucus rheological properties alone, suggesting that L-NAC still resident in the collected mucus stimulated the frog palate cilia. The index of mucus flux, the collection rate in mg.min-1, was higher with L-NAC compared with placebo. From our results, we conclude that L-NAC shows potential benefit in terms of improving mucus rheological properties and clearability. It may act, in part, by stimulating the fresh secretion of mucus of lower viscoelasticity. The stimulation of mucociliary clearance could be related to ion flux changes, as indicated by the increase in PD.
Fluorescence enhancement of the europium(III)-thenoyltrifluoroacetone-trioctylphosphine oxide ternary complex by gadolinium(III) and its application to the determination of europium(III) (1988)

A study of the enhancement of the fluorescence intensity of the EuIII-thenoyltrifluoroacetone (TTA)-trioctylphosphine oxide (TOPS) system by LaIII, GdIII, LuIII and YIII has been carried out in a colloidal-like suspension. Gadolinium(III) caused the largest enhancement of the fluorescence intensity. In the presence of this element the weak fluorescence of the EuIII-TTA-TOPO system was enhanced by a factor of about 18 at a pH of between 5.5 and 6.5. The excitation and emission wavelengths were 343 and 615 nm, respectively. The fluorescence intensity was linear up to 10–8M of europium; the detection limit was found to be 5 × 10–12M and the precision at 8.0 × 10–11M of europium was 1.4%. By stabilising the fluorescence with cetyltrimethylammonium bromide (CTAB), the EuIII-TTA-TOPO-GdIII system together with three other enhancing systems could be applied to the determination of trace amounts of europium in lanthanide oxides and yttrium oxide. The fluorescence intensity of the SmIII-TTA-TOPO system was also enhanced by LaIII, GdIII, LuIII and YIII. The factors influencing the fluorescence enhancement are discussed and a general mechanism involving an intermolecular transfer of energy from the enhancing complex to the fluorescing complex is proposed.
A modified harmonic oscillator approximation scheme for the dielectric constants of Al<i>x</i>Ga1−<i>x</i>As (1991)

The dielectric functions of AlxGa1−xAs have recently been measured for several Al mole fractions over the 1.5–6.0 eV wavelength range [D.E. Aspnes, S. M. Kelso, R. A. Logan, and R. Bhat, J. Appl. Phys. 60, 754 (1986)]. To make use of this data to perform optical modeling for spectroscopic ellipsometry analysis of AlxGa1−xAs-containing samples, and for other optical modeling purposes, a reasonable interpolation scheme is required to estimate the dielectric functions of intermediate compounds. In this work, we will present a modified version of the harmonic oscillator approximation (HOA) of Erman et al. [M. Erman, J. B. Theeten, P. Chambon, S. M. Kelso, and D. E. Aspnes, J. Appl. Phys. 56, 2664 (1984)] to model the experimental data and interpolate between the known compositions over the 1.5–5.0 eV range. Our model uses additional harmonic oscillators and allows each oscillator to have an independent phase. These modifications significantly improve the accuracy of the approximation for photon energies at and below the fundamental band-gap energy. This allows much more accurate modeling of reflection problems for multilayer GaAs/AlGaAs structures. We will present test of this approach with simulations of spectroscopic ellipsometry data using known data, and with measured spectroscopic ellipsometer data on AlxGa1−xAs-containing samples grown by molecular-beam epitaxy and organometallic chemical vapor deposition.
Interleukin-7 stimulates osteoclast formation by up-regulating the T-cell production of soluble osteoclastogenic cytokines (2000)

In unstimulated conditions osteoclast renewal occurs as a result of the stromal cell production of the key osteoclastogenic factors, receptor activator of NFkB ligand (RANKL) and macrophage colony-stimulating factor (M-CSF). Inflammation is known to cause increased osteoclastogenesis; however, the mechanisms responsible for this phenomenon are poorly understood. We now show that interleukin-1 (IL-1) and tumor necrosis factor alpha (TNFalpha), cytokines typically produced in inflammatory conditions, increase the stromal cell production of IL-7. This factor, in turn, up-regulates production of osteoclastogenic cytokines by T cells leading to stimulation of osteoclast (OC) formation. Although T cells were found to produce soluble forms of both RANKL and M-CSF, saturating concentrations of osteoprotegerin failed to inhibit approximately 40% of the OC formation, suggesting that IL-7 acts via both RANKL-dependent and RANKL-independent pathways. Despite the identification of T-cell-secreted M-CSF, this cytokine was not essential for either RANKL-dependent or -independent OC formation, suggesting that T cells secrete other cytokines capable of substituting for M-CSF action. On the basis of our data, we propose a novel mechanism for inflammatory bone loss in which induction of IL-7 from stromal cells by IL-1 and TNFalpha leads to the production of soluble osteoclastogenic cytokines by T cells. Thus, the mechanism by which IL-7 causes bone resorption involves the activation of T cells and the T-cell-dependent augmentation of osteoclastogenesis. (Blood. 2000;96:1873-1878)
Oil palm genome sequence reveals divergence of interfertile species in Old and New worlds (2013)

Oil palm is the most productive oil-bearing crop. Although it is planted on only 5% of the total world vegetable oil acreage, palm oil accounts for 33% of vegetable oil and 45% of edible oil worldwide, but increased cultivation competes with dwindling rainforest reserves. We report the 1.8-gigabase (Gb) genome sequence of the African oil palm Elaeis guineensis, the predominant source of worldwide oil production. A total of 1.535 Gb of assembled sequence and transcriptome data from 30 tissue types were used to predict at least 34,802 genes, including oil biosynthesis genes and homologues of WRINKLED1 (WRI1), and other transcriptional regulators, which are highly expressed in the kernel. We also report the draft sequence of the South American oil palm Elaeis oleifera, which has the same number of chromosomes (2n = 32) and produces fertile interspecific hybrids with E. guineensis but seems to have diverged in the New World. Segmental duplications of chromosome arms define the palaeotetraploid origin of palm trees. The oil palm sequence enables the discovery of genes for important traits as well as somaclonal epigenetic alterations that restrict the use of clones in commercial plantings, and should therefore help to achieve sustainability for biofuels and edible oils, reducing the rainforest footprint of this tropical plantation crop.
Surveillance of <i>Salmonella</i> Prevalence in Animal Feeds and Characterization of the <i>Salmonella</i> Isolates by Serotyping and Antimicrobial Susceptibility (2012)

This article presents the surveillance data from the Feed Contaminants Program (2002-2009) and Salmonella Assignment (2007-2009) of the U.S. Food and Drug Administration (FDA), which monitor the trend of Salmonella contamination in animal feeds. A total of 2,058 samples were collected from complete animal feeds, feed ingredients, pet foods, pet treats, and supplements for pets in 2002-2009. These samples were tested for the presence of Salmonella. Those that were positive for Salmonella underwent serotyping and testing for antimicrobial susceptibility. Of the 2,058 samples, 257 were positive for Salmonella (12.5%). The results indicate a significant overall Salmonella reduction (p≤0.05) in animal feeds from 18.2% (187 samples tested) in 2002 to 8.0% (584 samples tested) in 2009. Among these samples, feed ingredients and pet foods/treats had the most significant reduction (p≤0.05). Of the 45 Salmonella serotypes identified, Salmonella Senftenberg and Salmonella Montevideo were the top two common serotypes (8.9%). Of the 257 Salmonella isolates obtained, 54 isolates (21%) were resistant to at least one antimicrobial. The findings provide the animal feed industries with Salmonella prevalence information that can be used to address Salmonella contamination problems. Our findings can also be used to educate pet owners when handling pet foods and treats at home to prevent salmonellosis.
A C++ class library for telescope pointing (2006)

tpk is a C++ class library, layered on TCSpk and slalib that implements virtual telescope objects for generating mount and rotator position (and optionally, velocity and acceleration) demands, predicting the position of guide probes etc. in the focal plane and tip and tilt for steerable optics. These objects allocate and manage storage for the kernel context in a thread safe manner enabling a pointing kernel for a specific telescope configuration to be constructed simply by creating the necessary objects and calling their "fast", "medium" and "slow" update methods at the appropriate rates. Additional facilities include: Tracking of solar system objects using orbital elements as tabulated by the Minor Planet Center, the JPL Horizons system and the Astronomical Almanac or the for the major planets, built-in ephemeredes due to Chapront and Francou - Management of pointing models including the logging of pointing test data capable of being read into TPOINT, catalogues of pointing reference stars and pointing adjustments from handsets and guiders including the necessary digital filters - Generation of world coordinate system mappings and FITS keywords for instruments. The library can be tailored for a particular operating environment by replacing the mutex and clock classes. For "off-line" or otherwise non time-critical application the existing Posix and Windows implementations can be used.
Detection, Recognition and Tracking of Moving Objects from Real-time Video via SP Theory of Intelligence and Species Inspired PSO (2017)

In this paper, we address the basic problem of recognizing moving objects in video images using SP Theory of Intelligence. The concept of SP Theory of Intelligence which is a framework of artificial intelligence, was first introduced by Gerard J Wolff, where S stands for Simplicity and P stands for Power. Using the concept of multiple alignment, we detect and recognize object of our interest in video frames with multilevel hierarchical parts and subparts, based on polythetic categories. We track the recognized objects using the species based Particle Swarm Optimization (PSO). First, we extract the multiple alignment of our object of interest from training images. In order to recognize accurately and handle occlusion, we use the polythetic concepts on raw data line to omit the redundant noise via searching for best alignment representing the features from the extracted alignments. We recognize the domain of interest from the video scenes in form of wide variety of multiple alignments to handle scene variability. Unsupervised learning is done in the SP model following the DONSVIC principle and natural structures are discovered via information compression and pattern analysis. After successful recognition of objects, we use species based PSO algorithm as the alignments of our object of interest is analogues to observation likelihood and fitness ability of species. Subsequently, we analyze the competition and repulsion among species with annealed Gaussian based PSO. We have tested our algorithms on David, Walking2, FaceOcc1, Jogging and Dudek, obtaining very satisfactory and competitive results.
TOPOGRAPHY-PRESERVING, NON-LINEAR INPAINTING FOR AUTONOMOUS BARE EARTH DIGITAL ELEVATION MODEL (DEM) RECONSTRUCTION (2006)

Harris describes a novel way to autonomously inpaint missing data into high resolution single reflective surfaces utilizing a variant of the Navier-Stokes equations. One product of this process is a high-resolution bare earth Digital Elevation Model (DEM) with the same resolution as the input data. Inpainting allows generation of high resolution bare earth DEMs in both high and low frequency terrain environments for urban 3-D modeling. Having this bare earth DEM accounts for a dramatic increase in accuracy in all other steps of the urban 3-D modeling process. The LiteSite™ toolkit has the capability to automatically extract buildings and vegetation from an urban scene. The resulting DEM from this step of the process acts as input to the inpainting process. The expected building and vegetation base heights can then be inpainted into the area of extraction where data is now missing. The inpainting process maintains building and vegetation base height consistency in the inpainted regions and performs high accuracy interpolation and edge propagation on DEMs. Inpainting is highly effective for data sets where the occurrence of missing data is common and undesired. Examples of such data include Shuttle Radar Topography Mission (SRTM), LIDAR, IFSAR, correlated DEMs from imagery, or any other single reflectance collection data set. This technology preserves height contours. A more accurate bare earth product allows for better automated building vector extraction and therefore reduces manual building vector editing. Automated texturing of 3D model products with aerial or satellite imagery is accomplished using Harris’ RealSite TM Toolkit.
A priority-driven concurrency control protocol based on data contention rates for distributed real-time database systems (2002)

The paper presents a priority-driven concurrency control protocol to schedule active transactions accessing distributed real-time databases based on priority information. This protocol controls real-time transactions with different priority more effectively. By combining flexible synchronization techniques for desirable real-time conflict resolution, it intends to avoid unnecessary aborts or blocking of conflicting transactions. Thus, flexible priority-driven scheduling enables this protocol to interleave and complete as many transactions as possible without sacrificing data or timing constraints. Performance is achieved by increasing the number of transactions, especially with higher priority.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Velocity model building from raw shot gathers using machine learning (2019)

Summary We present a machine learning setup that can estimate a velocity model from raw seismic shot gathers without the need for an initial velocity model. Our setup is based on a convolutional neural network (CNN) trained on pairs of random generated synthetic velocity models and corresponding forward modelled synthetic shot gathers. The network is trained to predict the correct velocity model for a given input shot gather. We evaluate the performance of the trained network on both synthetic and real seismic data, and observe that the system is able to estimate background velocity trends directly from the raw shot gathers without need for preprocessing or preconditioning. Once trained, the network is very fast to run, and can deliver a velocity model in seconds running on a single GPU. The preciscion and resolution of the estimated velocity models is not on par with state of the art velocity model building techniques such as FWI and/or reflection tomography, but shows that machine learning can robustly extract meaningful velocity information from raw shot gathers, and that there might be potential in using such methods for velocity model building.
Stimulation of Agrobacterium tumefaciens T-DNA transfer by overdrive depends on a flanking sequence but not on helical position with respect to the border repeat (1991)

T-DNA transfer by Agrobacterium tumefaciens depends on the right border repeat of the T-DNA and is greatly stimulated by overdrive, an adjacent sequence. We report that the function of overdrive does not depend on helical position with respect to the border repeat. A synthetic 24-bp overdrive and a 12-bp region containing a fully conserved 8-bp core overdrive sequence stimulated virulence equally, but full function required additional bases to the left of the 24-bp sequence.
Effect of HPHT processing on the structure, and thermoelectric properties of Co<sub>4</sub>Sb<sub>12</sub> co-doped with Te and Sn (2015)

Te–Sn co-doped Co<sub>4</sub>Sb<sub>12</sub> bulk polycrystalline materials Co<sub>4</sub>Sb<sub>11.7−x</sub>Te<sub>x</sub>Sn<sub>0.3</sub> have been prepared using a high pressure and high temperature method and then characterized using X-ray diffraction.
Double or Nothing: Multiplicative Incentive Mechanisms for Crowdsourcing (2014)

Crowdsourcing has gained immense popularity in machine learning applications for obtaining large amounts of labeled data. Crowdsourcing is cheap and fast, but suffers from the problem of low-quality data. To address this fundamental challenge in crowdsourcing, we propose a simple payment mechanism to incentivize workers to answer only the questions that they are sure of and skip the rest. We show that surprisingly, under a mild and natural no-free-lunch requirement, this mechanism is the one and only incentive-compatible payment mechanism possible. We also show that among all possible incentive-compatible mechanisms (that may or may not satisfy no-free-lunch), our mechanism makes the smallest possible payment to spammers. Interestingly, this unique mechanism takes a multiplicative form. The simplicity of the mechanism is an added benefit. In preliminary experiments involving over several hundred workers, we observe a significant reduction in the error rates under our unique mechanism for the same or lower monetary expenditure.
On the use of machine learning for identifying botnet network traffic (2016)

During the last decade significant scientific efforts have been invested in the development of methods that could provide efficient and effective botnet detection. As a result, an array of detection methods based on diverse technical principles and targeting various aspects of botnet phenomena have been defined. As botnets rely on the Internet for both communicating with the attacker as well as for implementing different attack campaigns, network traffic analysis is one of the main means of identifying their existence. In addition to relying on traffic analysis for botnet detection, many contemporary approaches use machine learning techniques for identifying malicious traffic. This paper presents a survey of contemporary botnet detection methods that rely on machine learning for identifying botnet network traffic. The paper provides a comprehensive overview on the existing scientific work thus contributing to the better understanding of capabilities, limitations and opportunities of using machine learning for identifying botnet traffic. Furthermore, the paper outlines possibilities for the future development of machine learning-based botnet detection systems.