gebhart/patrepeval huggingface dataset:
Integrins Influence the Size and Dynamics of Signaling Microclusters in a Pyk2-dependent Manner (2015)

Integrin engagement on lymphocytes initiates "outside-in" signaling that is required for cytoskeleton remodeling and the formation of the synaptic interface. However, the mechanism by which the "outside-in" signal contributes to receptor-mediated intracellular signaling that regulates the kinetics of granule delivery and efficiency of cytolytic activity is not well understood. We have found that variations in ICAM-1 expression on tumor cells influence killing kinetics of these cells by CD16.NK-92 cytolytic effectors suggesting that changes in integrin ligation on the effector cells regulate the kinetics of cytolytic activity by the effector cells. To understand how variations of the integrin receptor ligation may alter cytolytic activity of CD16.NK-92 cells, we analyzed molecular events at the contact area of these cells exposed to planar lipid bilayers that display integrin ligands at different densities and activating CD16-specific antibodies. Changes in the extent of integrin ligation on CD16.NK-92 cells at the cell/bilayer interface revealed that the integrin signal influences the size and the dynamics of activating receptor microclusters in a Pyk2-dependent manner. Integrin-mediated changes of the intracellular signaling significantly affected the kinetics of degranulation of CD16.NK-92 cells providing evidence that integrins regulate the rate of target cell destruction in antibody-dependent cell cytotoxicity (ADCC).
Blind Equalization and Carrier Phase Recovery in a 16-QAM Optical Coherent System (2009)

Blind equalization and carrier phase recovery in a simulated 14 Gbaud 16-QAM optical coherent system are investigated. Equalization techniques to compensate for linear transmission impairments are presented using the constant modulus algorithm (CMA), the recursive least-squares (RLS)-CMA, and the radius directed equalization (RDE). With 7 T/2-spaced taps, the RDE and the RLS-CMA can compensate up to 1000 ps/nm of CD in the 16-QAM coherent system with performances comparable to the decision-directed (DD) equalizer. We show that the RDE is a promising technique for blind equalization in a 16-QAM coherent system with lower complexity than the RLS-CMA. Blind carrier phase recovery is investigated in a decision-directed-mode. We show that the blind carrier phase recovery algorithm can recover the Square-16-QAM constellation for laser beat linewidths of DeltanuT <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">s</sub> ~ 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-4</sup> in a polarization-multiplexed (POLMUX) 16-QAM coherent system with the RDE algorithm giving better overall performance than the CMA when compensating for CD and differential group delay (DGD). Finally, the dynamical characteristics of the equalizers to track endless polarization rotations are discussed. With the adaptation parameters optimized, the equalizers can track angular rate of rotation ~ 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">5</sup> rad/s.
Efficient in‐gel digestion procedure using 5‐cyclohexyl‐1‐pentyl‐ β ‐ D ‐maltoside as an additive for gel‐based membrane proteomics (2004)

A cycloalkyl aliphatic saccharide, 5-cyclohexyl-1-pentyl-beta-D-maltoside (CYMAL-5), was evaluated as a novel additive in a high-throughput in-gel protein digestion system using 96-well plates. Addition of 0.1% CYMAL-5 (final concentration) during trypsin treatment was compatible with both matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) and liquid chromatography/tandem mass spectrometry (LC/MS/MS) analysis, and gave a better digestion efficiency than n-octylglucoside, which we previously reported. In-gel reduction and alkylation of Cys residues under denaturing conditions also improved the sequence coverage of peptides. In-gel tryptic digestion with the optimum combination of 0.5 mm thick gels, negative staining, alkylation under denaturing conditions (6 M guanidine hydrochloride), and digestion in the presence of CYMAL-5, gave excellent performance especially for membrane protein analysis, where recovery of hydrophobic peptides was markedly enhanced. The new protocol is simple and convenient, and should be widely applicable to gel-based proteomics.
Prevalence of IgE antibody to crude and purified allergens of Japanese cedar pollen among different troops of Japanese monkeys (Macaca fuscata) (1994)

We measured specific IgE antibodies to the crude allergen as well as two purified allergens (Cry j I and Cry j II) of Japanese cedar (Cryptomeria japonica--CJ) pollen in the serum of 276 Japanese monkeys in nine troops. Of 45 monkeys with CJ specific IgE in eight of nine troops, 23 (51%) were found to have IgE to both Cry j I and Cry j II, 21 (47%) only to Cry j I, and one (2.2%) only to Cry j II. The positive rate of specific IgE antibody to each allergen varied among the troops.
Atomic Structures and Gram Scale Synthesis of Three Tetrahedral Quantum Dots (2014)

Luminescent semiconducting quantum dots (QDs) are central to emerging technologies that range from tissue imaging to solid-state lighting. However, existing samples are heterogeneous, which has prevented atomic-resolution determination of their structures and obscured the relationship between their atomic and electronic structures. Here we report the synthesis, isolation, and structural characterization of three cadmium selenide QDs with uniform compositions (Cd35Se20(X)30(L)30, Cd56Se35(X)42(L)42, Cd84Se56(X)56(L)56; X = O2CPh, L = H2N-C4H9). Their UV-absorption spectra show a lowest energy electronic transition that decreases in energy (3.54 eV, 3.26 eV, 3.04 eV) and sharpens as the size of the QD increases (fwhm = 207 meV, 145 meV, 115 meV). The photoluminescence spectra of all three QDs are broad with large Stokes shifts characteristic of trap-luminescence. Using a combination of single-crystal X-ray diffraction and atomic pair distribution function analysis, we determine the structures of their inorganic cores, revealing a series of pyramidal nanostuctures with cadmium terminated {111} facets. Theoretical and experimental studies on these materials will open the door to a deeper fundamental understanding of structure-property relationships in quantum-confined semiconductors.
Safeness of carbon nanotubes (2006)

Carbon nanotubes (CNTs) have single- or multi-cylindrical graphene structures that possess diameters of a few nanometers, while the length can be up to a few micrometers. Single-walled carbon nanotubes (SWCNTs) and multi-walled carbon nanotubes (MWCNTs) possess a high tensile strength and ultra-light weight, and have excellent chemical and thermal stability. They also possess semiconducting and metallic conductive properties. These anomalous features have led to many proposed applications in the biomedical field, including biosensors, drug and vaccine delivery. However, CNTs could have unusual toxicological properties, in that they share intermediate morphological characteristics of both fibers and nanoparticles. This review presents the cytotoxicity and biocompatibility of CNTs. Finally, we report the activation of the human acute monocytic leukemia cell line THP-1 in vitro and the response in subcutaneous tissue in vivo to MWCNTs of different lengths.
An In Vivo Comparison of the Potential for Extravertebral Cement Leak After Vertebroplasty and Kyphoplasty (2002)

The findings showed less vascular and transcortical extravasation of injected contrast with kyphoplasty than with vertebroplasty. Although leakage of contrast may not correlate precisely with polymethylmethacrylate leakage, the authors believe this study highlights the relative safety of these procedures.
Synthesis of manufacturable analog circuits (1994)

We describe a synthesis system that takes operating range constraints and inter- and intra-circuit parametric manufacturing variations into account while designing a sized and biased analog circuit. Previous approaches to CAD for analog circuit synthesis have concentrated on nominal analog circuit design, and subsequent optimization of these circuits for statistical fluctuations and operating point ranges. Our approach simultaneously synthesizes and optimizes for operating and manufacturing variations by mapping the circuit design problem into an Infinite Programming problem and solving it using an annealing within annealing formulation. We present circuits designed by this integrated synthesis system, and show that they indeed meet their operating range and parametric manufacturing constraints.
Stable Boron-Modified ZSM-22 Zeolite Catalyst for Selective Production of Propylene from Methanol (2019)

The effects of boron incorporation on the ZSM-22 particle size, morphology, and acidity were investigated via a microwave-assisted synthesis method (MAHyS). The in situ addition of boron into the TON framework resulted in ZSM-22 zeolite (TON framework) with the same needle-shape morphology but smaller particles size as observed from the scanning electron microscopy (SEM) and transmission electron microscopy (TEM) images. The incorporation of boron into ZSM-22 zeolite resulted in enhanced textural properties as indicated by N2 adsorption–desorption measurements. The temperature-programmed desorption of ammonia (NH3-TPD) analysis showed insignificant changes in the acidity properties, while pyridine Fourier-transform infrared (FTIR) analysis showed a slight enhancement in the boron-incorporated ZSM-22 zeolite acidity. The boron-incorporated ZSM-22 zeolite sample showed extended catalytic activity in methanol conversion to light olefins.
Adaptive nonlinear output feedback tracking with a reduced order high-gain observer (2005)

Concerns output-feedback adaptive controllers for nonlinear systems which require observers with the high gain. This may pose a problem if the measured output is corrupted by noise. In order to reduce the effect of noise a new class of adaptive controllers is proposed which uses a reduced order high-gain observer to estimate only the first r, (r<n) derivatives of the output. This approach is feasible if, in certain coordinates, nonlinearities in the system depend only on the first r derivatives of the output. Semiglobal adaptive output-feedback tracking is achieved under the assumption that the regressor matrix is persistently exciting.
MAFIA: Machine Learning Acceleration on FPGAs for IoT Applications (2021)

Recent breakthroughs in ML have produced new classes of models that allow ML inference to run directly on milliwatt-powered IoT devices. On one hand, existing ML-to-FPGA compilers are designed for deep neural-networks on large FPGAs. On the other hand, general-purpose HLS tools fail to exploit properties specific to ML inference, thereby resulting in suboptimal performance. We propose MAFIA, a tool to compile ML inference on small form-factor FPGAs for IoT applications. MAFIA provides native support for linear algebra operations and can express a variety of ML algorithms, including state-of-the-art models. We show that MAFIA-generated programs outperform best-performing variant of a commercial HLS compiler by 2.5 × on average.
Modification of proteoglycans during maturation of fibroblast substratum adhesion sites (1983)

Newly formed adhesion sites, left bound to the tissue culture substratum after [ethylenebis(oxyethylenenitrilo)] tetraacetic acid mediated detachment of simian virus 40 transformed Balb/c 3T3 cells, have been extracted with 0.5 M guanidine hydrochloride or Zwittergent (3-12), extractions which identify different subfractions of proteoglycans in these sites. The compositions of these extracts were then compared to similar extracts of "maturing" adhesion sites in an effort to identify structural and metabolic changes which may occur with time and which may play a role in altering adhesion during cell movement. Guanidine hydrochloride (0.5 M) extracts both hyaluronate and chondroitin sulfate proteoglycan from newly formed sites (but which are not complexed in an aggregate similar to that found in cartilage) but only hyaluronate from fully matured sites, indicating that the chondroitin sulfate proteoglycans somehow become resistant to extraction with time. Both high and low molecular weight forms of hyaluronate also accumulate in sites with time. Zwittergent 3-12 solubilizes free chains of heparan sulfate but not heparan sulfate proteoglycan from either class of sites. Most of the heparan sulfate in newly formed sites occurs as a large proteoglycan excludable from Sepharose CL-6B columns under stringent dissociative conditions; however, as adhesion sites "mature", a portion of this proteoglycan appears to be converted by some unknown mechanism to free heparan sulfate chains. This process may very well weaken the close adhesive contacts between the cell and substratum mediated by fibronectin's binding to the highly multivalent heparan sulfate proteoglycans. These studies further indicate that there is considerable metabolism and changing intermolecular associations of proteoglycans within these sites during movement of fibroblasts over this model extracellular matrix.
A Single N66S Mutation in the PB1-F2 Protein of Influenza A Virus Increases Virulence by Inhibiting the Early Interferon Response In Vivo (2010)

The PB1-F2 protein of influenza A virus can contribute to viral pathogenesis of influenza virus strains. Of note, an N66S amino acid mutation in PB1-F2 has been shown to increase the pathogenesis associated with H5N1 Hong Kong/1997 and H1N1 Brevig Mission/1918 influenza viruses. To identify the mechanism of enhanced immunopathology, we evaluated the host response to two isogenic viruses that differ by a single amino acid at position 66 of the PB1-F2 protein. Various components of the adaptive immune response were ruled out as factors contributing to pathogenesis through knockout mouse studies. Transcriptional profiling of lungs from PB1-F2 66S-infected mice revealed an early delay in innate immune responses. In particular, enhanced activation of type I interferon (IFN) pathway genes, including IFN-β, RIG-I, and numerous interferon-inducible genes, was not observed until day 3 postinfection. The N66S mutant virus caused increased cellularity in the lungs, as a result of monocyte and neutrophil infiltration. Furthermore, numerous cytokines and chemokines related to monocyte and neutrophil migration and maturation were upregulated. The cellular infiltration and increased cytokine expression corresponded to increased PB1-F2 66S titer. These data suggest that PB1-F2 N66S may contribute to the delay of innate immune responses, allowing for unchecked viral growth and ultimately severe immunopathology observed in the lungs.
Low-loss, low-threshold 0.98 μm wavelength InGaAsP/InGaP/GaAs broadened waveguide lasers grown by GSMBE (2002)

We describe the design and experimental results for broadened waveguide (BW) high-power, low-loss, low threshold current 0.98 /spl mu/m-aluminum-free InGaAsP/InGaP/GaAs lasers. The dramatic decrease in the internal losses with an increase in the width of the waveguide layer for a SCH-MQW structure, is attributed to lower free-carrier absorption due to the reduced overlap of the optical mode with the highly doped cladding regions. The BW lasers grown with both InGaAsP and GaAs waveguides show lower internal loss and threshold current than those designed for optimum optical confinement factor within the QW region. We report a record low internal loss of 2.2 cm/sup -1/ and highest CW output power of 6.8 W for a InGaP/GaAs laser grown by GSMBE. We also report the highest quasi-continuous output power of 13.3 W measured for a single 100 /spl mu/m aperture, 0.8-0.98 /spl mu/m Al-free laser diode, grown by either MBE or MOCVD.
Will a chip every day keep the doctor away? (2001)

"We can rebuild him. We have the technology. We have the capability to make the world's first Bionic man." So began each episode of 1970s TV show Six Million Dollar Man, as surgeons attempted to rebuild aeroplane crash victim Steve Austin by fitting him with bionic limbs and eagle-eye vision. As the popularity of the show proved, the concept of integrating man and machine has long fuelled our imagination. It has also been the subject of many other science-fiction movies and shows, including Bionic Woman, Robocop and Inspector Gadget.
ORAL, BUT NOT INTRAVENOUS, ALLOANTIGEN PREVENTS ACCELERATED ALLOGRAFT REJECTION BY SELECTIVE INTRAGRAFT TH2 CELL ACTIVATION (1993)

We studied the mechanisms by which oral or intravenous administration of allogeneic splenocytes prevents sensitization by skin allografts and development of accelerated rejection of subsequent cardiac allografts. LEW rats were sensitized with BN skin allografts 7 days prior to receiving heterotopic (LEW x BN)F1 vascularized cardiac allografts. While unsensitized cardiac allografts are rejected on days 6-8, control sensitized grafts were rejected within 24 to 48 hr. Oral administration of BN splenocytes during the sensitization phase (between skin and heart grafting) has been found to prevent accelerated allograft rejection and prolong cardiac allograft survival to 7 days. An alternative route of antigen exposure, specifically intravenous administration of BN splenocytes (50 x 10(6) daily for 5 days starting on the day of skin grafting), also prevented accelerated cardiac allograft rejection and prolonged allograft survival to 9 +/- 1 days (n = 5). Immunoperoxidase studies of cardiac allografts harvested 24-48 hr posttransplant showed that, when compared with sensitized controls, animals that received oral splenocytes had reduced deposition of IgG (end-point titer of 1/1000 vs. 1/4000), IgM (1/1000 vs. 1/16000), C3 (1/4000 vs. 1/16000), and fibrin (1/4000 vs. 1/16000). There was also decreased infiltration by macrophages (18 +/- 8 vs. 37 +/- 8 cells/HPF, P < 0.01), T cells (5 +/- 3 vs. 19 +/- 7, P < 0.01), and IL-2R+ T cells (5 +/- 3 vs. 15 +/- 4, P < 0.01), and a significant reduction in the numbers and extent of intragraft mononuclear cells stained with antibodies to IL-1, IL-2, IL-6, IL-8, IFN-gamma, and TNF-alpha. In contrast, these grafts showed markedly increased IL-4 staining (including most mononuclear and all endothelial cells), as compared with control grafts (< 20% of mononuclear cells and only focal endothelial staining). Immunoperoxidase studies of cardiac allografts harvested from rats receiving intravenous splenocytes also showed markedly reduced humoral deposits and cellular infiltrates, comparable to that found in the oral splenocytes-treated group, but showed significantly different cytokine expression. In particular, some intragraft mononuclear cell labeling for IFN-gamma remained, and IL-4 staining was not increased relative to control grafts. Attempts were then made to abrogate spleen cell-induced prolongation of cardiac allograft survival by daily injections of CD4 monoclonal antibody (BWH-4 mAb, 700 micrograms) from the time of cardiac transplantation, therapy previously shown unable to prolong cardiac survival in this model when commenced after skin graft-induced sensitization has occurred.(ABSTRACT TRUNCATED AT 400 WORDS)
Rotationally-invariant non-local means for image denoising and tomography (2015)

Many samples imaged in structural biology and material science contain several similar particles at random locations and orientations. Model-based iterative reconstruction (MBIR) methods can in principle be used to exploit such redundancies in images through log prior probabilities that accurately account for non-local similarity between the particles. However, determining such a log prior term can be challenging. Several denoising algorithms like non-local means (NLM) successfully capture such non-local redundancies, but the problem is two-fold: NLM is not explicitly formulated as a cost function, and neither can it capture similarity between randomly oriented particles. In this paper, we propose a rotationally-invariant nonlocal means (RINLM) algorithm, and describe a method to implement RINLM as a prior model using a novel framework that we call plug-and-play priors. We introduce the idea of patch pre-rotation to make RINLM computationally tractable. Finally, we showcase image denoising and 2D tomography results, using the proposed RINLM algorithm, as we highlight high reconstruction quality, image sharpness, and artifact suppression.
High durability fuel cell components with cerium salt additives (2023)

A fuel cell membrane electrode assembly is provided comprising a polymer electrolyte membrane which comprises a polymer that comprises bound anionic functional groups, wherein the polymer electrolyte membrane additionally comprises cerium cations. In another aspect, a fuel cell membrane electrode assembly is provided comprising a polymer electrolyte membrane which comprises a polymer that comprises bound anionic functional groups, wherein at least a portion of the anionic functional groups are in acid form and at least a portion of the anionic functional groups are neutralized by cerium cations. In another aspect, a polymer electrolyte membrane is provided which comprises a polymer that comprises bound anionic functional groups, wherein the polymer electrolyte membrane additionally comprises cerium cations, and wherein the amount of cerium cations present is between 0.001 and 0.5 charge equivalents based on the molar amount of acid functional groups present in the polymer electrolyte, more typically between 0.005 and 0.2, more typically between 0.01 and 0.1, and more typically between 0.02 and 0.05.
Homogeneous decomposition of vinyl ethers. The heat of formation of ethanal‐2‐yl (1979)

Abstract The thermal unimolecular decomposition of three vinylethers has been studied in a VLPP apparatus. The high‐pressure rate constant for the retro‐ene reaction of ethylvinylether was fit by log k (sec −1 ) = (11.47 + 0.25) ‐ (43.4 ± 1.0)/2.303 RT at &lt; T &gt; = 900 K and that of t ‐ butylvinylether by log k (sec −1 ) = (12.00 ± 0.27) ‐ (38.4 ± 1.0)/2.303 RT at &lt; T &gt; = 800 K. No evidence for the competition of the higher energy homolytic bond‐fission process could be obtained from the experimental data. The rate constant compatible with the CO bond scission reaction in the case of benzylvinylether was log k (sec −1 ) = (16.63 ± 0.30) ‐ (53.74 ± 1.0)/2.303 RT at &lt; T &gt; = 750 K. Together with Δ H f ,300 0 (benzyl·) = 47.0 kcal/mol, the activation energy for this reaction results in Δ H f ,300 0 (CH 2 CHO) = +3.0 ± 2.0 kcal/mol and a corresponding resonance stabilization energy of 3.2 ± 2.0 kcal/mol for 2‐ethanalyl radical.