gebhart/patrepeval huggingface dataset:
Real-time Imaging of<i>Mycobacterium tuberculosis</i>, Using a Novel Near-Infrared Fluorescent Substrate (2016)

Slow growth of Mycobacterium tuberculosis, the causative agent of tuberculosis, hinders advancement in all areas of research toward prevention and treatment. Real-time imaging with reporter enzyme fluorescence (REF) that uses custom fluorogenic substrates for bacterial enzymes allows rapid and specific detection of M. tuberculosis in live animals. We have synthesized a novel REF substrate, CNIR800, that carries a near-infrared (NIR) fluorochrome IRDye 800CW, with a quencher connected through the lactam ring that is hydrolyzed by the enzyme BlaC (β-lactamase) that is naturally expressed by M. tuberculosis. CNIR800 produces long-wavelength emission at 795 nm upon excitation (745 nm) and exhibits significantly improved signal to noise ratios for detection of M. tuberculosis. The detection threshold with CNIR800 is approximately 100 colony-forming units (CFU) in vitro and <1000 CFU in the lungs of mice. Additionally, fluorescence signal from cleaved CNIR800 reaches maximal levels 4-6 hours after administration in live animals, allowing accurate evaluation of antituberculous drug efficacy. Thus, CNIR800 represents an excellent substrate for accurate detection of M. tuberculosis rapidly and specifically in animals, facilitating research toward understanding pathogenic mechanisms, evaluation of therapeutic outcomes, and screening new vaccines.
Video stabilization based on human visual system (2014)

A video stabilization method based on a new concept inspired by the human visual system is presented. The human eye provides a stable scene by continuously changing the eye’s orientation in a way that always places the focused target in the center of one’s view. Similar to the human eye, the proposed algorithm focuses only on a single target object within a scene and stabilizes the target on the two-dimensional image plane by rotating a camera in three-dimensional space while most previous methods consider all objects in a video. The rotational angles of the camera along the x and y axes are simply predicted from a translational motion vector of the target object on the image plane. Hence, the proposed algorithm can provide a vivid video as if it was seen through the eye. Efficient video stabilization by approximating the human visual system is introduced, a practical method for real-time devices. Experimental results demonstrate that the visual feelings of the compensated videos are different depending on the selected target object and the approximating method provides a reasonable performance.
3D Grain Reconstruction from Boxscan Data (2010)

Abstract : A method for reconstructing the 3D shape of a single grain in a polycrystal from far-field-diffraction data is presented. The reconstruction is performed using an iterative algorithm, algebraic reconstruction technique (ART), to solve a linear system of equations obtained from data from the Boxscan technique. The Boxscan technique is a 3D X-ray diffraction-type scanning technique, which - in geometric tomography terms - provides 2-dimensional X-rays of the object as data. In this paper, we report on the first experimental 3D grain shape reconstruction based on a beta-titanium sample. By comparing our results to high-resolution phase contrast tomography, we find that the average error on the position of the grain boundary in this sample is 2.7 micrometers for a grain radius of 17 micrometers. This result is similar to other current methods.
Spectral differentiation of trace concentrations of NO_2 from NO by laser photofragmentation with fragment ionization at 226 and 452 nm: quantitative analysis of NO–NO_2 mixtures (2000)

Laser-induced photofragmentation with fragment ionization is used to detect and spectrally differentiate trace concentrations of NO(2) from NO in NO-NO(2) mixtures. A laser operating near 226 or 452 nm ionizes the target molecules, and the resulting electrons are collected with miniature electrodes. NO is detected by (1 + 1) resonance-enhanced multiphoton ionization by means of its A (2)?(+) ? X (2)? (0, 0) transitions near 226 nm, whereas NO(2) is detected near 226 nm by laser photofragmentation with subsequent NO fragment ionization by means of both its A (2)?(+) ? X (2)? (0, 0) and (1, 1) transitions. The NO fragment generated from the photolysis of NO(2) is produced rovibrationally excited with a significant population in the first vibrational level of the ground electronic state (X (2)?, upsilon? = 1). In contrast, ambient NO has a room-temperature, Boltzmann population distribution favoring the lowest ground vibrational level (X (2)?, upsilon? = 0). Thus discrimination is possible when the internal energy distributions of both fragment NO and ambient NO are probed. We also demonstrate this approach using visible radiation, further simplifying the experimental apparatus because frequency doubling of the laser radiation is not required. We measured up to three decades of NO-NO(2) mixtures with limits of detection (signal-to-noise ratio of 3) in the low parts per billion for both NO and NO(2) for a 10-s integration time using both ultraviolet or visible radiation.
Adaptive Volumetric Shadow Maps (2010)

Abstract We introduce adaptive volumetric shadow maps (AVSM), a real‐time shadow algorithm that supports high‐quality shadowing from dynamic volumetric media such as hair and smoke. The key contribution of AVSM is the introduction of a streaming simplification algorithm that generates an accurate volumetric light attenuation function using a small fixed memory footprint. This compression strategy leads to high performance because the visibility data can remain in on‐chip memory during simplification and can be efficiently sampled during rendering. We demonstrate that AVSM compression closely approximates the ground‐truth correct solution and performs competitively to existing real‐time rendering techniques while providing higher quality volumetric shadows.
Expression of a plasmid gene of Chlamydia trachomatis encoding a novel 28 kDa antigen (1993)

Plasmid pCT is present in essentially all isolates of Chlamydia trachomatis and may encode factors important for survival in the natural environment. However, no pCT-associated phenotype has been described so far. With the purpose of investigating the possibility of a role of pCT in C. trachomatis pathogenicity we examined the expression of an ORF (ORF3), potentially encoding a 28 kDa polypeptide (pgp3). Analysis of RNA extracted from chlamydia-infected Vero cells detected ORF3-specific transcripts, from 20 h post-infection onwards, mainly as discrete RNA species of 1390 nucleotides comprising the downstream ORF4 sequence. ORF3 DNA was cloned and expressed in Escherichia coli as a 39 kDa fusion protein (MS2/pgp3). Antibodies raised against purified MS2/pgp3, specifically recognized a 28 kDa protein on Western blots of protein from purified chlamydial elementary bodies (EBs). The same antibodies detected chlamydial inclusions in methanol-fixed infected cells by immunofluorescence. Western blot analysis of EBs extracted with 2% Sarkosyl, showed that a large proportion of the 28 kDa antigen is associated with the detergent-insoluble ('membrane') fraction. Antibodies recognizing pgp3 epitopes were detected in sera from patients with chlamydial infections, but not in sero-negative control sera. The finding support the hypothesis that pCT may provide a function related to chlamydial cell physiology.
All Hydrocarbon Composite Resins Based on Cyclopentadiene (1994)

Currently available resins for normal and demanding composite applications often suffer from swelling and/or degradation caused by polar organic solvents and hot, wet environments. One possible means of overcoming these disadvantages is to use all-hydrocarbon matrices that inherently limit interaction and penetration by both organic solvents and water. Polybutadiene is an example of a resin whose inherent hydrophobicity provides excellent hot-wet stability and long term resistance to moisture and saline environments; its use in composites has been limited, however, because of poor physical properties at ambient temperature, We have developed an alternative, inexpensive resin based on multiply-substituted cyclopentadienes
Ultrahigh power compression for X-ray amplification: multiphoton cluster excitation combined with nonlinear channelled propagation (1995)

The ability to apply power densities controllably at or above vigorous thermonuclear levels (>1019 W cm-3) in materials is the basic issue for achieving efficient amplification of X-rays. Recent experimental and theoretical findings concerning (i) the multiphoton production of X-rays from clusters and (ii) high-intensity modes of channelled propagation in plasmas indicate an entirely new method for producing the conditions necessary for strong amplification in the multi-kV range. These two new nonlinear phenomena are being united to produce and control the imperative power compression; the multiphoton mechanism serves to establish the condition locally while the confined propagation provides the required spatial organization. The present work, which experimentally demonstrates the first combined expression of these two complex nonlinear processes through direct X-ray imaging of Xe(M) emission ( approximately 1 keV) in stable self-trapped channels, ( alpha ) reveals the exceptional compatibility of their mutual scaling for realizing the necessary power density, ( beta ) provides confirming evidence for the action of a superstrong coherent multi-electron intense-field interaction in the X-ray generation from the Xe clusters, and ( gamma ) furnishes new detailed information on the dynamics of the radial intensity distributions associated with the channelled propagation. The resulting knowledge of the scaling relations underlying these phenomena enables the optimum conditions for amplification to be specified up to a quantum energy of approximately 5 keV. The harmonious use of these new nonlinear processes is expected to lead to an advanced generation of extraordinarily bright X-ray sources in the multi-kV region having a peak brightness of approximately 1031-1033 gamma s-1 (mrad)-2 (mm)-2 (0.1% BW)-1, a level sufficient for biological holographic imaging capable of providing a high resolution visualization of the molecular anatomy of cells, tissues and organisms in the natural state.
Coherent demodulation for IS-95 uplink (2002)

In the uplink of the IS-95 mobile communication standard, an orthogonal modulation scheme combined with binary convolutional coding and binary interleaving is defined. In Viterbi et al. (1993), a receiver with non-coherent demodulation is proposed for this transmission system. In this paper, a receiver with coherent demodulation and decision-directed channel estimation is introduced. Comparisons of both schemes show that the use of coherent demodulation leads to a significant gain compared to non-coherent demodulation.
Adsorption of Actives in Ophthalmological Drugs for Over-The-Counter on Soft Contact Lens Surfaces (2009)

The adsorption of various kinds of ionic/nonionic actives, added in ophthalmological drugs (artificial tear, contact lens wetting solution, eye-drops, and eyewash) for over-the-counter (marketable drugs with no need of any medical prescription) , on soft contact lens (SCL) surfaces has been studied as a function of hydrophobicity of the actives. The common logarithm of the 1-octanol/water partitioning coefficient (AC_log P) has been used in order to normalize the hydrophobicity of the actives employed in this study. No significant adsorption occurs for relatively hydrophilic actives, whereas the adsorption rate is gradually increased with an increase in the hydrophobicity of the actives. This suggests that the adsorption is predominantly governed by the hydrophobic interaction of the actives with the SCL surfaces, although an electrostatic interaction plays an additional role for the adsorption. The most effective adsorption occurs in the following active-lens combinations: cationic actives--the anionic and hydrated lens IV (methacrylic acid-based SCL); anionic actives---the nonionic and hydrated lens II (N-vinyl pyrrolidone-based SCL); and nonionic actives--the anionic and less-hydrated lens III (containing hydrophobic silicone monomers).
A phosphatidylinositol-3 kinase binds to platelet-derived growth factor receptors through a specific receptor sequence containing phosphotyrosine. (1991)

Platelet-derived growth factor (PDGF) stimulates autophosphorylation of the PDGF receptor and association of the receptor with several cytoplasmic molecules, including phosphatidylinositol-3 kinase (PI3 kinase). In this study we examined the association of PI3 kinase with immunoprecipitated autophosphorylated PDGF receptor in vitro. The PI3 kinase from cell lysates bound to the wild-type receptor but not to a mutant receptor that had a deletion of the kinase insert region. A protein of an apparent size of 85 kDa bound to the receptor, consistent with previous observations that a protein of this size is associated with PI3 kinase activity. In addition, 110- and 74-kDa proteins bound to the phosphorylated receptor. Dephosphorylated receptors lost the ability to bind PI3 kinase activity as well as the 85-kDa protein. A 20-amino-acid peptide composed of a sequence in the kinase insert region that included one of the autophosphorylation sites of the receptor (tyrosine 719) as well as a nearby tyrosine (Y708) blocked the binding of PI3 kinase to the receptor, but only when the peptide was phosphorylated on tyrosine residues. A scrambled version of the peptide did not block PI3 kinase binding to the receptor even when it was phosphorylated on tyrosine. These tyrosine-phosphorylated peptides did not block binding of phospholipase C-gamma or GTPase-activating protein to the receptor. In separate experiments (receptor blots), soluble radiolabeled receptor bound specifically to an 85-kDa protein present in sodium dodecyl sulfate-polyacrylamide gel electrophoresis-fractionated 3T3 cell lysates that were transferred to nitrocellulose paper. The binding was blocked by the same tyrosine-phosphorylated peptides that prevented binding of PI3 kinase activity to immobilized receptors. These findings show that the PDGF receptor binds directly to an 85-kDa protein and to a PI3 kinase activity through specific sequences in the kinase insert region. The association of a 110-kDa protein with the receptor also involve these sequences, suggesting that this protein may be a subunit of the PI3 kinase. Phosphotyrosine is an essential structure required for the interactions of these proteins with the PDGF receptor.
Regulatory T-cell therapy for transplantation (2012)

It is feasible to grow human alloantigen-reactive Tregs up to billions, an optimal number to achieve therapeutic efficacy. Better understanding of Treg lineage commitment and further technological investments are needed to ease the implementation and ensure consistency in Treg manufacturing.
Novel FEXT Cancellation and Equalization for High Speed Ethernet Transmission (2008)

In high-speed multi-pair wireline communication systems, such as 10 gigabit Ethernet over Copper (10GBASE-T), far-end crosstalk (FEXT) becomes a major impairment and needs to be suppressed to increase data rates. Conventional techniques based on crosstalk cancellation are not suitable for FEXT due to the fact that the disturbing source of FEXT is generally unknown to the victims. This paper presents two different approaches to efficiently deal with FEXT over unshielded twisted-pair (UTP) copper cables. To eliminate the error propagation problem in practice, both approaches use the Tomlinson-Harashima precoding (THP) technique which however makes the transceiver design nontrivial. In the first approach, FEXT is treated as noise and a new feedforward FEXT canceller is proposed. Compared with conventional techniques, the proposed FEXT canceller can mitigate the non-causal part of FEXT, thus leading to better FEXT cancellation performance. In the second approach, FEXT is treated as signal, and the general multi-input multi-output (MIMO) equalization technique is combined with the TH precoding technique to deal with both intersymbol interference (ISI) and FEXT. Different from the existing works, the proposed designs comply with the 10GBASE-T standard and they are suitable in real applications. Simulation results verify that the proposed approaches can achieve much better performance in terms of decision-point signal-to-noise ratio (DP-SNR) than conventional techniques. It is also shown that the hardware complexity of the transceiver can be reduced by about 37.2% by utilizing the increased DP-SNR in the proposed designs.
Acrolein Microspheres Are Bonded To Large-Area Substrates (1988)

Reactive cross-linked microspheres produced under influence of ionizing radiation in aqueous solutions of unsaturated aldehydes, such as acrolein, with sodium dodecyl sulfate. Diameters of spheres depend on concentrations of ingredients. If polystyrene, polymethylmethacrylate, or polypropylene object immersed in solution during irradiation, microspheres become attached to surface. Resulting modified surface has grainy coating with reactivity similar to free microspheres. Aldehyde-substituted-functional microspheres react under mild conditions with number of organic reagents and with most proteins. Microsphere-coated macrospheres or films used to immobilize high concentrations of proteins, enzymes, hormones, viruses, cells, and large number of organic compounds. Applications include separation techniques, clinical diagnostic tests, catalytic processes, and battery separators.
Identification of a new Bradyrhizobium japonicum gene (frxA) encoding a ferredoxinlike protein (1988)

An open reading frame of 74 codons was identified downstream of the nifB gene of Bradyrhizobium japonicum 110. The predicted amino acid sequence shared 63% similarity with the Rhodopseudomonas palustris ferredoxin I sequence. We propose to name the gene frxA. The frxA gene was found to be cotranscribed with the nifB gene. An insertion mutation within frxA hardly affected nitrogen fixation activity.
Solubilization of Sulfhydryl Oxidase, A Bovine Skim Milk Membrane Enzyme (1982)

Sulfhydryl oxidase of bovine milk was prepared by gel chromatography of crude skim milk membranes obtained by ammonium sulfate fractionation of whey. A variety of detergents were screened for their potential effectiveness as enzymesolubilizing agents. Anionic detergents, such as sodium dodecyl sulfate and sodium octyl sulfate, inactivated the enzyme concomitantly with solubilization. Nonionic detergents, however, were generally effective in solubilizing sulfhydryl oxidase near their critical micelle concentrations. Polyoxyethylene-9-1auryl ether and /3-octyl-D-glucoside afforded the best solubilization of sulfhydryl oxidase among the detergents tested; enzymic activity was retained fully at detergent concentrations producing over 80% solubilization.
Design and performance characterization of a novel low-pole dual-stator flux switching permanent magnet machine (2015)

The purpose of this paper is to characterize the performance of a novel dual-stator six slot four pole (6/4) flux switching permanent magnet machine. The proposed dual-stator 6/4 topology eliminates even order harmonics in the flux linkage and back electromotive force, which are present in the conventional single stator topology. The resulting back electromotive forces of the proposed dual-stator machine are balanced and sinusoidal waveforms. Sizing equations for the machine are studied based on the flux linkage harmonic contents and generalized sizing laws and performance of the machine is characterized. Various loss components such as copper loss, iron loss, and magnet loss are evaluated. The properties of the proposed machine are verified by finite element analysis studies.
Avirulent <i>Toxoplasma gondii</i> Generates Therapeutic Antitumor Immunity by Reversing Immunosuppression in the Ovarian Cancer Microenvironment (2013)

Reversing tumor-associated immunosuppression seems necessary to stimulate effective therapeutic immunity against lethal epithelial tumors. Here, we show this goal can be addressed using cps, an avirulent, nonreplicating uracil auxotroph strain of the parasite Toxoplasma gondii (T. gondii), which preferentially invades immunosuppressive CD11c(+) antigen-presenting cells in the ovarian carcinoma microenvironment. Tumor-associated CD11c(+) cells invaded by cps were converted to immunostimulatory phenotypes, which expressed increased levels of the T-cell receptor costimulatory molecules CD80 and CD86. In response to cps treatment of the immunosuppressive ovarian tumor environment, CD11c(+) cells regained the ability to efficiently cross-present antigen and prime CD8(+) T-cell responses. Correspondingly, cps treatment markedly increased tumor antigen-specific responses by CD8(+) T cells. Adoptive transfer experiments showed that these antitumor T-cell responses were effective in suppressing solid tumor development. Indeed, intraperitoneal cps treatment triggered rejection of established ID8-VegfA tumors, an aggressive xenograft model of ovarian carcinoma, also conferring a survival benefit in a related aggressive model (ID8-Defb29/Vegf-A). The therapeutic benefit of cps treatment relied on expression of IL-12, but it was unexpectedly independent of MyD88 signaling as well as immune experience with T. gondii. Taken together, our results establish that cps preferentially invades tumor-associated antigen-presenting cells and restores their ability to trigger potent antitumor CD8(+) T-cell responses. Immunochemotherapeutic applications of cps might be broadly useful to reawaken natural immunity in the highly immunosuppressive microenvironment of most solid tumors.
Self-healing catalysts: Co<sub>3</sub>O<sub>4</sub> nanorods for Fischer–Tropsch synthesis (2014)

We combine kinetic and spectroscopic data to demonstrate the concept of a self-healing catalyst, which effectively eliminates the need for catalyst regeneration. The observed self-healing is triggered by controlling the crystallographic orientation at the catalyst surface.
<title>Optical lightpipe sensor based on surface plasmon resonance</title> (1996)

In this paper, a novel optical sensor using surface plasmon resonance in a symmetrical planar lightpipe is introduced. The new design utilizes a microscope slide with beveled ends as the sensor substrate. Collimated TM polarized white light is used to interrogate the sensing surface at a single angle. Preliminary experimental results for glycerol solutions from 0.6%<SUB>wt</SUB> to 16%<SUB>wt</SUB> demonstrate a concentration sensitivity of 3.4 multiplied by 10<SUP>-4</SUP> by weight. The corresponding refractive index sensitivity is estimated as 4 by 10<SUP>-5</SUP>.
A real-time and protocol-aware reactive jamming framework built on software-defined radios (2014)

This paper develops a software-defined radio (SDR) framework for real-time reactive adversarial jamming in wireless networks. The system consists of detection and RF response infrastructure, implemented in the FPGA of a USRP N210 and designed to function with the open source GNU Radio SDR library. The framework can be used to implement a fast turnaround reactive jamming system capable of timely RF response within \textit{80ns} of signal detection. Our framework also allows for full control and feedback from the FPGA hardware to the GNU Radio-based cognitive radio backend, making it applicable to a wide range of preamble-based wireless communication schemes. This paper presents the capabilities, design, and experimental evaluation of this framework. Using this platform, we demonstrate real-time reactive jamming capabilities in both WiFi (802.11g) and mobile WiMAX (802.16e) networks and quantify jamming performances by measuring the network throughput using the iperf software tool. The results indicate that our system works reliably in real time as a reactive jammer and can be used for practical assessments of modern jamming and secure communication techniques.