gebhart/patrepeval huggingface dataset:
Trispecific antibody against HIV-1 demonstrate anti-viral activity in vivo and have potent Fc-dependent effector functions (2020)

Abstract Broadly neutralizing antibodies (bNAbs) against HIV-1 have been suggested as a complementary immunotherapy to current combination small molecule anti-retroviral therapies (cART) for treatment of HIV-1 infection. Monoclonal bNAbs when used as a monotherapy demonstrate high susceptibility for escape in HIV-1 infected individuals, thus a trispecific bNAb targeting three independent HIV-1 envelope determinants was developed to achieve more robust suppression. Upon treatment of viremic simian-human immunodeficiency virus (SHIV)-infected macaques with the trispecific bNAb, plasma viral suppression of up to 1000-fold was observed. To elucidate a mechanism for the observed plasma viremia control, in vitro assays using the trispecific bNAb were conducted to determine Fc-mediated effector functions. First, we determined that the trispecific bNAb bound to HIV-1 infected cell lines with an equal or higher affinity than its parental bNAbs alone. We then conducted antibody-dependent cell cytotoxicity (ADCC) and antibody-dependent cell phagocytosis (ADCP) assays and found that the trispecific bNAb had comparable or better activity compared to its parental bNAbs alone. Similarly, when we measured direct virolysis of HIV-1 virus using an antibody-dependent complement-mediated virus lysis (ADCML) assay, the trispecific bNAb had comparable or better activity compared to its parental bNAbs alone. These studies demonstrate that the trispecific bNAb shows anti-viral activity in vivo and has potent Fc-dependent effector functions that target both free virus and virally infected cells compared to monoclonal bNAbs alone. Thus, the trispecific bNAb is a promising single immunotherapeutic protein for treatment of HIV-1 infection.
Nucleation of in-grown stacking faults and dislocation half-loops in 4H-SiC epitaxy (2013)

Ultraviolet photoluminescence, transmission electron microscopy and KOH etching were used to characterize extended defects in 4H-SiC epilayers grown at high growth rates (18 μm/h). Layers exhibited high densities of in-grown stacking faults and dislocation half-loops. The stacking faults were 8H Shockley-type faults. The Burgers vector of the dislocation half-loops was in the (0001) basal plane. Both defects nucleate within the epilayer at early stages of growth. Defect nucleation is directly correlated with high initial growth rate and is not related to any defects/heterogeneities in the substrate or epilayer. Epilayer growth by nucleation of two-dimensional islands is proposed as a possible mechanism for the formation of both defects, through nucleation of faulted Si-C bilayers.
Cover Picture: Switching Futile para‐Quinone to Efficient Reactive Oxygen Species Generator: Ubiquitin‐Specific Protease‐2 Inhibition, Electrocatalysis, and Quantification (ChemBioChem 17/2017) (2017)

The cover picture shows that bicyclic para-quinones with a distinct “N-C=O-N” pattern are able to generate reactive oxygen species (ROS) catalyzing the reduction of oxygen, although minor changes in such a skeleton drastically alter its ROS-generating ability. In their article, the authors provide a structure–activity relationship study of these para-quinones and discuss their ability to inhibit ubiquitin-specific protease 2 through ROS production. The substantiation of the mode of action of these inhibitors is supported by cyclic voltammetry and hydrogen peroxide quantification studies. The knowledge acquired in this study should serve as an important guideline for future medicinal chemistry optimization of related structures so as to select the preferred mode of action of para-quinone-based inhibitors. More information can be found in the communication by D. Shabat, Z. Gross, A. Brik, et al. on page 1683 in Issue 17, 2017 (DOI: 10.1002/cbic.201700330).
Bioanalysis ofSyn Dimeric HIV-1 Protease InhibitorN-Benzyl 4-Aryl-1,4-dihydropyridine H19: Metabolic and Cytotoxic Properties in Hep G2 Cells (2000)

Syn dimeric N-benzyl 4-aryl-1,4-dihydropyridine H19 is a nonpeptidic HIV-1 protease inhibitor of the dihydroxyethylene type representing novel C2-symmetric inhibitors. Great interest was focussed on the extent of metabolism of these novel inhibitory structures as their functional groups are similar to certain peptidic and non-peptidic HIV-1 protease inhibitors with poor bioavailability due to extensive metabolism. Thus, early characterization of metabolic and toxic properties decisively determines the future prospects of those novel HIV-1 protease inhibitors. Both metabolism and toxicity were evaluated in Hep G2 monolayers. While no phase-I metabolites were found the extent of conjugation in phase-II of biotransformation was poor. Moreover, cytotoxic evaluation of protein and DNA decrease and, furthermore, of membrane toxicity characterized the novel inhibitors as non-toxic. Consequently, the favourable poor metabolism and non-toxic properties encourage further development of these novel HIV-1 protease inhibitors.
A low complexity reweighted proportionate affine projection algorithm with memory and row action projection (2015)

A new reweighted proportionate affine projection algorithm (RPAPA) with memory and row action projection (MRAP) is proposed in this paper. The reweighted PAPA is derived from a family of sparseness measures, which demonstrate performance similar to mu-law and the l 0 norm PAPA but with lower computational complexity. The sparseness of the channel is taken into account to improve the performance for dispersive system identification. Meanwhile, the memory of the filter’s coefficients is combined with row action projections (RAP) to significantly reduce computational complexity. Simulation results demonstrate that the proposed RPAPA MRAP algorithm outperforms both the affine projection algorithm (APA) and PAPA, and has performance similar to l 0 PAPA and mu-law PAPA, in terms of convergence speed and tracking ability. Meanwhile, the proposed RPAPA MRAP has much lower computational complexity than PAPA, mu-law PAPA, and l 0 PAPA, etc., which makes it very appealing for real-time implementation.
Tracking Single Cells in Live Animals Using a Photoconvertible Near-Infrared Cell Membrane Label (2013)

We describe a novel photoconversion technique to track individual cells in vivo using a commercial lipophilic membrane dye, DiR. We show that DiR exhibits a permanent fluorescence emission shift (photoconversion) after light exposure and does not reacquire the original color over time. Ratiometric imaging can be used to distinguish photoconverted from non-converted cells with high sensitivity. Combining the use of this photoconvertible dye with intravital microscopy, we tracked the division of individual hematopoietic stem/progenitor cells within the calvarium bone marrow of live mice. We also studied the peripheral differentiation of individual T cells by tracking the gain or loss of FoxP3-GFP expression, a marker of the immune suppressive function of CD4(+) T cells. With the near-infrared photoconvertible membrane dye, the entire visible spectral range is available for simultaneous use with other fluorescent proteins to monitor gene expression or to trace cell lineage commitment in vivo with high spatial and temporal resolution.
The high efficiency transformer-less PV inverter topologies derived from NPC topology (2009)

<p style="text-align: left">The grid-connected photovoltaic (PV) systems are an important part of renewable energy sources and their integration is getting more and more widespread. In order to improve the efficiency, practicality and reliability of the PV systems, many kinds of new inverter topologies have been proposed to avoid using a grid isolation transformer. The NPC topology and two other derived topologies are presented and analyzed in this paper. Validated by experiments, it has been proven that they are very suitable for using in transformer-less PV applications due to high efficiency, low leakage current and EMI. Simulations using Simulink and the PLECS toolbox have been done for evaluating efficiency of different NPC topologies and some experimental results are presented in this paper to validate the operation of the different topologies.
Phase II Evaluation of Paclitaxel and Carboplatin in the Treatment of Carcinosarcoma of the Uterus: A Gynecologic Oncology Group Study (2010)

Paclitaxel plus carboplatin demonstrates antitumor activity against uterine carcinosarcoma with acceptable toxicity and warrants further evaluation in phase III randomized trials.
Nanocomposites with Structure Domains of 0.5 to 3 nm by Polymerization of Silicon Spiro Compounds (2009)

Two from one: It is possible to form two different, interpenetrating polymer structures—silicon dioxide and a phenolic resin—simultaneously in a single step without the formation of by-products by using a readily polymerizable, organic silicon spiro compound. This new polymerization process enables the fabrication of materials with domain sizes of 0.5 to 3 nm.
Development of Thermoreversible Crosslinking Rubber using Supramolecular Hydrogen Bonding Networks (2005)

Thermoreversible Hydrogen-bond crosslinking isoprene rubber (THC-IR) was synthesized by modification of isoprene rubber (IR) with maleic anhydride followed by the addition of 3-amino-1, 2, 4-triazole(ATA), in solid phase. The mechanical properties of the resulting rubber were more similar to the sulfur-vulcanized rubber than general thermoplastic elastomers (ex. SEBS). Although the tensile strength and elongation at break were lower than those of a corresponding sulfur-cured rubber, the moduli were as high as those of sulfur-cured rubber. Reforming could be repeated more than 10 times without significantly changing its mechanical properties. Differential scanning calorimetry (DSC) revealed that the superior mechanical properties and good recyclability are attributable to the strong hydrogen bonding. The TRC-IR showed an endothermic transition peak at around 185°C on the DSC chart, indicating cleavage of the hydrogen bonding. Moreover, small angle X-ray scattering (SAXS) clarified the crosslinking point is aggregated structure of ca. 5nm by supramolecular hydrogen bonding. A hypothetical model was suggested which comprises strong crosslinking moiety formed by the seven points hydrogen bonds. The thermoreversible crosslinking system could be applied to EPM and AEM, as well. These rubbers also showed superior mechanical properties as well as excellent recyclability.
S3Pool: Pooling with Stochastic Spatial Sampling (2016)

Feature pooling layers (e.g., max pooling) in convolutional neural networks (CNNs) serve the dual purpose of providing increasingly abstract representations as well as yielding computational savings in subsequent convolutional layers. We view the pooling operation in CNNs as a two-step procedure: first, a pooling window (e.g., $2\times 2$) slides over the feature map with stride one which leaves the spatial resolution intact, and second, downsampling is performed by selecting one pixel from each non-overlapping pooling window in an often uniform and deterministic (e.g., top-left) manner. Our starting point in this work is the observation that this regularly spaced downsampling arising from non-overlapping windows, although intuitive from a signal processing perspective (which has the goal of signal reconstruction), is not necessarily optimal for \emph{learning} (where the goal is to generalize). We study this aspect and propose a novel pooling strategy with stochastic spatial sampling (S3Pool), where the regular downsampling is replaced by a more general stochastic version. We observe that this general stochasticity acts as a strong regularizer, and can also be seen as doing implicit data augmentation by introducing distortions in the feature maps. We further introduce a mechanism to control the amount of distortion to suit different datasets and architectures. To demonstrate the effectiveness of the proposed approach, we perform extensive experiments on several popular image classification benchmarks, observing excellent improvements over baseline models. Experimental code is available at https://github.com/Shuangfei/s3pool.
The nonlinear influence of design parameters on the performance of brushless PM machines (2012)

The present paper describes a large-scale unitary-study for a generic topology of brushless motors operated from sine-wave current regulated drives. Firstly, a parametric model of the SPM machine, employing nine independent variables is introduced. A sensitivity analysis based on the Response Surface (RS) method is carried out to identify the non-linear correlation between the independent variables and the output functions. Finally, a multi-criteria optimization for the three specific output functions is performed through a Differential Evolution (DE) algorithm. The optimization method demonstrated in the paper is generally applicable to a wide class of brushless SPM machines. At the same time, the boundaries of the 3D pareto front are lined up with the expectations derived from the sensitivity study confirming the effectiveness of the DE algorithm. Other approaches for employing the optimization method for more practical application-dependent design studies are briefly discussed.
Resolution enhancement and separation of reverberation from target echo with the time reversal operator decomposition (2003)

Time reversal operator (TRO) decompositions are performed in a model of an ocean wave guide containing a target and having different kinds of bottom. The objective is to study the effects of bottom reverberation and absorption by means of ultrasonic experiments. It is shown experimentally that the echo from a target can be separated from the bottom reverberation. Reverberation eigenvectors are back propagated in the wave guide leading to focus on the bottom. An amplitude correction is applied to both reverberation and signal eigenvectors to compensate for bottom absorption and thus to improve target resolution.
A highly miniturized single-chip MOEMS scanner for all-in-one imaging solution (2018)

A highly miniaturized, single-chip, large scanning range MOEMS scanner is demonstrated. This intrinsically-aligned, monolithically integrated device uses small angular displacement to provide a linear scanning range of 2000 μm in the lateral and 1000 μm in the vertical direction, at a working distance of 2 cm, with an average operating power lower than 170 mW. Within a footprint of only 7×10 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> , the presented system fully integrates a photonic interferometer comprising a mirror, a silicon microlens and the MEMS actuator into a single chip, thus offering an unprecedentedly miniaturized scanning solution. The monolithic integration of all photonic components provides intrinsic alignment and excludes coupling losses often encountered in systems composed of discrete parts. No additional attenuation of the optical signal is observed during device operation. This small and high-performance device is suitable as complete system-on-chip for commercial, portable imaging applications.
EBV latency III immortalization program sensitizes B cells to induction of CD95-mediated apoptosis via LMP1: role of NF- B, STAT1, and p53 (2005)

Epstein-Barr virus (EBV) induces CD95 expression and the CD95 gene (FAS) is regulated by NF-kappaB, STAT1, and/or p53. To understand the contribution of these factors in the regulation of CD95 by EBV in lymphoblastoid cell lines (LCLs), we cloned dominant-active IkappaBalpha, active (STAT1alpha) and inactive (STAT1beta) forms of STAT1, p53, a dominant-negative mutant of LMP1, and wild-type LMP1 into a novel double-inducible episomal vector, pRT-1. These plasmids were stably transfected either into wild-type LCLs or EREB2-5 cells, an LCL with an estrogen-regulatable EBNA2 protein. Inhibition of LMP1 signaling decreased expression of CD95, whereas overexpression of LMP1 markedly increased it. Induction of the latency III program in EREB2-5 cells correlated with activation of NF-kappaB, STAT1, and p53. CD95 expression was regulated by these 3 transcriptional systems. STAT1 and p53 activation were secondary to NF-kappaB activation. CD95 surface expression sensitized EBV-infected B cells to the induction of CD95-mediated apoptosis. In vitro inhibition of CD95-CD95 ligand interaction was found to reverse T-cell killing of EBV-infected B cells. Therefore, LMP1 activation of NF-kappaB sensitizes infected B cells to CD95-mediated apoptosis and renders EBV latency III-immortalized B cells susceptible to elimination by the immune system, contributing to the establishment of a host/virus equilibrium.
A solidly mounted, high frequency, thickness shear mode bulk acoustic wave resonator using X-LiTaO3 thin plate and SiO2/Ta multilayer acoustic films (2021)

Abstract This paper describes a bulk acoustic wave (BAW) high-frequency resonator with a solidly mounted structure using a single crystal LiTaO 3 (LT) thin plate. A Bragg reflector solidly supports the LT thin plate, which is fragile if self-suspended. The BAW resonator uses a thickness shear mode in 1.5 μ m thick X-LT. The Bragg reflector is made of four pairs of SiO 2 and Ta films, i.e. eight layers in total. The fabricated device works at a resonance frequency of 1.14 GHz and an antiresonance frequency of 1.23 GHz, showing a bandwidth of 7.9% and a low-temperature coefficient of frequency of −16 ppm °C −1 and −26 ppm °C −1 at the maximum and minimum admittances, respectively. The measured impedance ratio is 61 dB, although the structure and fabrication process are not optimized yet, suggesting a high potential for this device.
A Plasticizer Removal Method in Electroceramic Green Bodies Using Supercritical Carbon Dioxide (2003)

A novel selective removal method for plasticizer in green bodies of electroceramic components using supercritical carbon dioxide has been proposed and successfully demonstrated. The effects of temperature, pressure, and carbon dioxide flow rate on the weight decrease factor were investigated. The plasticizer was effectively removed by treatment with supercritical carbon dioxide at 10 MPa in the low-temperature region below 50°C and in the high-temperature region above 150°C. The extract collected in the collector cylinder after experimentation at 40°C and 10 MPa was confirmed by infrared spectroscopy to be plasticizer originating in the green bodies. The key parameters governing the plasticizer removal rate were identified as the carbon dioxide density in the low-temperature region and the vapor pressure of the plasticizer in the high-temperature region. The proposed method is as yet imperfect, since some defects were frequently detected on the surface of the green bodies after completion of the experiments. However, the proposed removal method is likely to have significant industrial potential, since it would enable a fabrication process that is both efficient and environmentally friendly. © 2003 The Electrochemical Society. All rights reserved.
An adaptive strategy via reinforcement learning for the prisoner dilemma game (2017)

The iterated prisoner's dilemma (IPD) is an ideal model for analyzing interactions between agents in complex networks. It has attracted wide interest in the development of novel strategies since the success of tit-for-tat in Axelrod's tournament. This paper studies a new adaptive strategy of IPD in different complex networks, where agents can learn and adapt their strategies through reinforcement learning method. A temporal difference learning method is applied for designing the adaptive strategy to optimize the decision making process of the agents. Previous studies indicated that mutual cooperation is hard to emerge in the IPD. Therefore, three examples which based on square lattice network and scale-free network are provided to show two features of the adaptive strategy. First, the mutual cooperation can be achieved by the group with adaptive agents under scale-free network, and once evolution has converged mutual cooperation, it is unlikely to shift. Secondly, the adaptive strategy can earn a better payoff compared with other strategies in the square network. The analytical properties are discussed for verifying evolutionary stability of the adaptive strategy.
Impact of Refinery Stream Gasoline Property Variation on Load Sensitivity of the HCCI Combustion (2012)

The HCCI combustion process is highly reliant upon a favorable in-cylinder thermal environment in an engine, for a given fuel. Commercial fuels can differ considerably in composition and auto-ignition chemistry, hence strategies intended to bring HCCI to market must account for this fuel variability. To this end, a test matrix consisting of eight gasoline fuels comprised of blends made solely from refinery streams were run in an experimental, single cylinder HCCI engine. All fuels contained 10% ethanol by volume and were representative of a cross-section of fuels one would expect to find at gasoline pumps across the United States. The properties of the fuels were varied according to research octane number (RON), sensitivity (S=RON-MON) and volumetric content of aromatics and olefins. For each fuel, a sweep of load (mass of fuel injected per cycle) was conducted and the intake air temperature was adjusted in order to keep the crank angle of the 50% mass fraction burned point (CA50) constant. By analyzing the amount of temperature compensation required to maintain constant combustion phasing, it was possible to determine the sensitivity of HCCI to changes in load for various fuels. In addition, the deviation of fuel properties brought about variations in important engine performance metrics like specific fuel consumption. Though the injected energy content per cycle was matched at the baseline point across the test fuel matrix, thermodynamic differences resulted in a spread of specific fuel consumption for the fuels tested.
Properties of recombinant adenosine receptors (1993)

Abstract Four subtypes of adenosine receptors have been cloned in several laboratories. The receptors all interact with G proteins and span the plasma membrane 7 times. They range in size from 319 to 412 amino acids. Conservation of structure among 10 different receptor clones for various species suggests that ligand recognition sites involve amino acids in the 2, 3, and 7 transmembrane segments of receptors. Species differences in ligand binding to A 1 receptors in tissues are very similar; for bovine receptors the affinity is R ‐PIA ≫ NECA, for canine receptors NECA ≥ R ‐PIA. Purified bovine A 1 receptors functionally couple to the pertussis toxin sensitive recombinant G proteins, G i1 , G i2 , G i3 , and G o . © 1993 Wiley‐Liss, Inc.
2,3′,4,4′,5′‐Pentamethoxy‐trans‐stilbene, a resveratrol derivative, inhibits colitis‐associated colorectal carcinogenesis in mice (2010)

PMS effectively suppressed colon carcinogenesis in an AOM/DSS animal model and may merit further clinical investigation as a chemoprophylactic agent against colitis-associated colon cancer in humans.