gebhart/patrepeval huggingface dataset:
Adjuvant-free nanogel-based PspA nasal vaccine for the induction of protective immunity against Pneumococcus (166.7) (2012)

Abstract To establish strategically effective and attractive vaccine against pneumococcal respiratory infections, combining the current knowledge and technology for common antigen throughout pneumococcal strains and the new delivery system is essential. Here, we introduce a new pneumococcal nasal vaccine using the advantages of Pneumococcal surface protein A (PspA) antigen and a new adjuvant-free intranasal vaccine-delivery system with a nanometer-sized hydrogel (nanogel) consisting of a cationic type of cholesteryl group-bearing pullulan (cCHP). Nanogel-based PspA nasal vaccination induced high levels of antigen-specific serum IgG, and nasal and bronchial secretory IgA (SIgA) antibodies. The levels of PspA-specific antibodies were as high as those in mice nasally immunized with PspA and mucosal adjuvant, cholera toxin. The nanogel induced PspA-specific immune responses provided protective immunity against the lethal challenge with Streptococcus pneumoniae Xen10. Nanogel-PspA vaccinated group thus had less numbers of pneumococcus on the surface of the bronchial mucosa, and perfectly protected from the pneumococcal invasion of the lung parenchyma. These results demonstrate the effectiveness of the nanogel-based PspA nasal vaccine system as an adjuvant free mucosal vaccine against the respiratory infection of pneumococcus.
The Mechanism Behind Redox Instability of Anodes in High-Temperature SOFCs (2005)

Bulk expansion of the anode upon oxidation is considered to be responsible for the lack of redox stability in high-temperature solid oxide fuel cells SOFCs. The bulk expansion of nickel-yttria stabilized zirconia YSZ anode materials was measured by dilatometry as a function of sample geometry, ceramic component, temperature, and temperature cycling. The strength of the ceramic network and the degree of Ni redistribution appeared to be key parameters of the redox behavior. A model of the redox mechanism in nickel-YSZ anodes was developed based on the dilatometry data and macro-and microstructural observations.
Thereminist robot: Development of a robot theremin player with feedforward and feedback arm control based on a Theremin's pitch model (2009)

We propose a Thereminist robot system that plays the Theremin based on a Theremin's pitch model. The theremin, which is a 1920s electronic musical instrument, is played by moving a player's hand position in the air without touching it. It is difficult to play the Theremin because the relationship between the hand position and Theremin's pitch (pitch characteristics) is non-linear and varies according to the electromagnetic field (hereafter called environment). These characteristics cause two problems: (1) adapting to the environment change is required and (2) a nai¿ve design tends to depend on robot's particular hardware. We implement the coarse-to-fine control system on the Thereminist robot using newly proposed two pitch models: parametric and nonparametric ones. The Thereminist robot works as below: first, the robot calibrates the pitch model by parameter fitting with the Levenberg-Marquardt method. Second, the robot moves its hand in a coarse manner by feedforward control based on the pitch model. Finally, the robot adjusts its position by feedback control (proportional-integral control). In these steps, the robot can play a required pitch quickly, because the robot moves its hand using the pitch model without listening to the Theremin's sound Thus, the time to play the exact pitch is shorter than when only feedback control is used. Three experiments were conducted to evaluate the robustness against the number of samples, environment change, and types of robots. The results revealed that our pitch model describes using only 12 samples of pitches for estimation of the parameters, and adapts if the environment changes. In addition, our system works on two different robots: HRP-2 and ASIMO.
P‐96: Design of Liquid Crystal Displays with 10000: 1 Contrast Ratio over ±85° Viewing Cone (2005)

Abstract A computer simulation model based on oblique angle Jones matrix and Poincaré sphere is developed for optimizing the design of film‐compensated multi‐domain vertical‐alignment liquid crystal display (VA‐LCD). According to this design, a contrast ratio higher than 10000:1 is predicted over the entire ±85° viewing cone for the four‐domain VA‐LCD. Potential application for LCD television is emphasized.
High yield 5-(hydroxymethyl)furfural production from biomass sugars under facile reaction conditions: a hybrid enzyme- and chemo-catalytic technology (2016)

An enzyme-catalytic process is introduced for high yield 5-(hydroxymethyl)furfural production from glucose in biomass hydrolysates.
Temperature sculpting in yoctoliter volumes (2013)

The ability to perturb large ensembles of molecules from equilibrium led to major advances in understanding reaction mechanisms in chemistry and biology. Here, we demonstrate the ability to control, measure, and make use of rapid temperature changes in fluid volumes that are commensurate with the size of single molecules. The method is based on attaching gold nanoparticles to a single nanometer-scale pore formed by a protein ion channel. Visible laser light incident on the nanoparticles causes a rapid and large increase of the adjacent solution temperature, which is estimated from the change in the nanopore ionic conductance. The temperature shift also affects the ability of individual molecules to enter into and interact with the nanopore. This technique could significantly improve sensor systems and force measurements based on single nanopores, thereby enabling a method for single molecule thermodynamics and kinetics.
A differential LSI method for document classification (2003)

We have developed an effective probabilistic classifier for document classification by introducing the concept of the differential document vectors and DLSI (differential latent semantics index) spaces. A simple posteriori calculation using the intra- and extra-document statistics demonstrates the advantage of the DLSI space-based probabilistic classifier over the popularly used LSI space-based classifier in classification performance.
The Single-Volume Scatter Camera (2020)

The multi-institution Single-Volume Scatter Camera (SVSC) collaboration led by Sandia National Laboratories (SNL) is developing a compact, high-efficiency double-scatter neutron imaging system. Kinematic emission imaging of fission-energy neutrons can be used to detect, locate, and spatially characterize special nuclear material. Neutron-scatter cameras, analogous to Compton imagers for gamma ray detection, have a wide field of view, good event-by-event angular resolution, and spectral sensitivity. Existing systems, however, suffer from large size and/or poor efficiency. We are developing high-efficiency scatter cameras with small form factors by detecting both neutron scatters in a compact active volume. This effort requires development and characterization of individual system components, namely fast organic scintillators, photodetectors, electronics, and reconstruction algorithms. In this presentation, we will focus on characterization measurements of several SVSC candidate scintillators. The SVSC collaboration is investigating two system concepts: the monolithic design in which isotropically emitted photons are detected on the sides of the volume, and the optically segmented design in which scintillation light is channeled along scintillator bars to segmented photodetector readout. For each of these approaches, we will describe the construction and performance of prototype systems. We will conclude by summarizing lessons learned, comparing and contrasting the two system designs, and outlining plans for the next iteration of prototype design and construction.
Evaluation of an enzyme immunoassay kit for estrogen receptor measurements. (1986)

Using an enzyme immunoassay (EIA) procedure, we evaluated the ability of the glass beads in the ER-EIA kit of Abbott Laboratories, which were coated with monoclonal anti-estrogen receptor (ER) antibodies, to bind hormone-free and hormone-filled Type I ER in cytosols, buffer washes, and 0.4 mol/L KCI extracts of ultracentrifugal pellets of breast cancer tissue homogenates. The unmodified ER-EIA technique yields higher values than does the dextran-coated charcoal (DCC) method for Type I ER. However, the antibody-coated beads fail to bind hormone-free ER and react with only a certain proportion of ER-[3H]estradiol complexes. The antigen saturation limit of the beads could not be determined because the quantity of antigen bound by the beads was disproportionate and unrelated to the total amount of the antigen available in the cytosols. In buffer extracts of tissue pellets that were ER-negative by the DCC assay, the EIA method detected high quantities of ER. We recommend checking the ability of the monoclonal antibodies to recognize proteins other than Type I ER in the extra-nuclear and nuclear compartments of target cells before using them for immunohistochemical detection of ER.
Application of correlation-aided DSA(CDSA) technique to fast cell search in IMT-2000 W-CDMA systems (2000)

In this paper, we introduce the correlation-aided distributed sample acquisition (CDSA) scheme for fast cell search in IMT-2000 W-CDMA cellular systems. The proposed scheme incorporates the state symbol correlation process into the comparison-correction based synchronization process of the original DSA scheme to enable fast acquisition even under very poor channel environment. For its realization, each mobile station (MS) has to store in its memory a set of state sample sequences, which are determined by the long-period scrambling sequences used in the system and the sampling interval of the state samples. CDSA based cell search is carried out in two stages: First, the MS first acquires the slot timing by using the primary synch code (PSC) and then identifies the igniter code which conveys the state samples of the current cell. Secondly, the MS identifies the scrambling code and frame timing by taking the comparison-correction based synchronization approach and, if the identification is not done satisfactorily within preset time, it initiates the state symbol correlation process which correlates the received symbol sequence with the pre-stored state sample sequences for a successful identification. As the state symbol SNR is relatively high, the state symbol correlation process enables reliable synchronization even in very low chip-SNR environment. Simulation results show that the proposed CDSA scheme outperforms the 3GPP 3-step approach, requiring the signal power of about 7 dB less for achieving the same acquisition time performance in low-SNR environment. Furthermore, it turns out very robust in the typical synchronization environment where large frequency offset exists.
Functional <i>UQCRC1</i> Polymorphisms Affect Promoter Activity and Body Lipid Accumulation (2007)

Obesity and type 2 diabetes constitute leading public health problems worldwide. Studies have shown that insulin resistance affiliated with these conditions is associated with skeletal muscle lipid accumulation, while the latter is associated with mitochondrial dysfunctions. However, the initiation and regulation of mitochondrial biogenesis rely heavily on approximately 1000 nuclear-encoded mitochondrial regulatory proteins. In this study, we targeted the ubiquinol-cytochrome c reductase core protein I gene, a nuclear-encoded component of mitochondrial complex III, for its association with subcutaneous fat depth (SFD) and skeletal muscle lipid accumulation (SMLA) using cattle as a model. Four promoter polymorphisms were identified and genotyped on approximately 250 Wagyu x Limousin F2 progeny. Statistical analysis revealed that two completely linked polymorphic sites, g.13487C>T and g.13709G>C (r2 = 1), were significantly associated with both SFD (p < 0.01) and SMLA (p < 0.0001). The difference between TTCC and CCGG haplotypes was 0.178 cm for SFD and 0.624 scores for SMLA. Interestingly, the former haplotype produced higher promoter activities than the latter by 43% to 49% in three cell lines (p < 0.05). In addition to Rett syndrome and breast/ovarian cancer observed in other studies, we report evidence for the first time, to our knowledge, that overexpression of ubiquinol-cytochrome c reductase core protein I might affect mitochondrial morphology and/or physiology and lead to development of obesity and related conditions.
A High Molar Extinction Coefficient Sensitizer for Stable Dye-Sensitized Solar Cells (2004)

An amphiphilic heteroleptic polypyridyl ruthenium complex with a high molar extinction coefficient was synthesized and demonstrated as an efficient, thermostable sensitizer in nanocrystalline dye-sensitized solar cells.
Enhancement of photoacoustic tomography by ultrasonic computed tomography based on optical excitation of elements of a full-ring transducer array (2013)

Photoacoustic computed tomography (PACT) is a hybrid technique that combines optical excitation and ultrasonic detection to provide high-resolution images in deep tissues. In the image reconstruction, a constant speed of sound (SOS) is normally assumed. This assumption, however, is often not strictly satisfied in deep tissue imaging, due to acoustic heterogeneities within the object and between the object and the coupling medium. If these heterogeneities are not accounted for, they will cause distortions and artifacts in the reconstructed images. In this Letter, we incorporated ultrasonic computed tomography (USCT), which measures the SOS distribution within the object, into our full-ring array PACT system. Without the need for ultrasonic transmitting electronics, USCT was performed using the same laser beam as for PACT measurement. By scanning the laser beam on the array surface, we can sequentially fire different elements. As a first demonstration of the system, we studied the effect of acoustic heterogeneities on photoacoustic vascular imaging. We verified that constant SOS is a reasonable approximation when the SOS variation is small. When the variation is large, distortion will be observed in the periphery of the object, especially in the tangential direction.
Hepatocyte growth factor, keratinocyte growth factor, their receptors, fibroblast growth factor receptor-2, and the cells of the cornea. (1993)

Human corneal epithelial, stromal fibroblasts, and endothelial cells produce messenger RNA coding for HGF and KGF, although low levels appear to be present in the epithelial cells. All three major cell types of the cornea produce messenger RNA coding for HGF receptor, KGF receptor, and FGF receptor-2. The proliferation of human corneal epithelial and endothelial cells, but not stromal fibroblasts, was stimulated by exogenous HGF and KGF. HGF and KGF likely have intracrine, autocrine, and/or paracrine functions in the cornea. Exogenous HGF and KGF may be useful in corneal preservation and for regulating corneal wound healing.
Isolation and Characterization of a New Vitamin C Producing Enzyme (<scp>L</scp>-Gulono-<i>γ</i>-lactone Dehydrogenase) of Bacterial Origin (1995)

For the first time we found that the bacterial strain Gluconobacter oxydans DSM 4025 produced L-ascorbic acid from L-gulono-γ-lactone and therefore we isolated and purified the enzyme L-gulono-γ-lactone dehydrogenase catalyzing the oxidation reaction. G. oxydans DSM 4025 produced 8.57 and 13.9 mg of L-ascorbic acid per ml from 70.3 and 89.3 mg of L-gulono-γ-lactone per ml in the growing and resting cell systems, respectively. The enzyme was isolated from the soluble fraction of the cells of G. oxydans DSM 4025 by DEAE-cellulose, Q-Sepharose, hydroxylapatite, and Sephacryl S-300 column chromatographies. The molecular weight of the enzyme was 110, 000 and it consisted of three kinds of subunits of 61, 000, 32, 500, and 16, 5000. L-Gulono-γ-lactone was oxidized to L-ascorbic acid very rapidly in the presence of dyes, such as 2, 6-dichlorophenolindophenol or phenazine methosulfate, but oxygen was not available as an electron acceptor. The absorption spectrum of the reduced form of the native enzyme showed maxima at 416, 521, and 552 nm in the visible region, indicating the presence of cytochrome c. The enzyme isolated from G. oxydans DSM 4025 was entirely different from isofunctional enzymes of eucaryotic organisms.
Information-Flow Matting (2017)

We present a novel, purely affinity-based natural image matting algorithm. Our method relies on carefully defined pixel-to-pixel connections that enable effective use of information available in the image. We control the information flow from the known-opacity regions into the unknown region, as well as within the unknown region itself, by utilizing multiple definitions of pixel affinities. Among other forms of information flow, we introduce color-mixture flow, which builds upon local linear embedding and effectively encapsulates the relation between different pixel opacities. Our resulting novel linear system formulation can be solved in closed-form and is robust against several fundamental challenges of natural matting such as holes and remote intricate structures. While our method is primarily designed as a standalone matting tool, we show that it can also be used for regularizing mattes obtained by sampling-based methods. The formulation is also extended to layer color estimation and we show that the use of multiple channels of flow increases the layer color quality. We also demonstrate our performance in green-screen keying and analyze the characteristics of the utilized affinities.
Identification of apilimod as a first-in-class PIKfyve kinase inhibitor for treatment of B-cell non-Hodgkin lymphoma (2017)

We identified apilimod as an antiproliferative compound by high-throughput screening of clinical-stage drugs. Apilimod exhibits exquisite specificity for phosphatidylinositol-3-phosphate 5-kinase (PIKfyve) lipid kinase and has selective cytotoxic activity in B-cell non-Hodgkin lymphoma (B-NHL) compared with normal cells. Apilimod displays nanomolar activity in vitro, and in vivo studies demonstrate single-agent efficacy as well as synergy with approved B-NHL drugs. Using biochemical and knockdown approaches, and discovery of a kinase domain mutation conferring resistance, we demonstrate that apilimod-mediated cytotoxicity is driven by PIKfyve inhibition. Furthermore, a critical role for lysosome dysfunction as a major factor contributing to apilimod's cytotoxicity is supported by a genome-wide CRISPR screen. In the screen, <i>TFEB</i> (master transcriptional regulator of lysosomal biogenesis) and endosomal/lysosomal genes <i>CLCN7</i>, <i>OSTM1</i>, and <i>SNX10</i> were identified as important determinants of apilimod sensitivity. These findings thus suggest that disruption of lysosomal homeostasis with apilimod represents a novel approach to treat B-NHL.
Urine analysis by laser Raman spectroscopy (2001)

Both normal Raman and SERS approaches have been investigated for total urine-nitrogen determination, urine urea-nitrogen determination, and for the urea/creatinine excretion ratio.
Device For Perception Of Polarization (1993)

Polarized image viewed through rotating polarizing filter appears to pulsate. Optical device enables human observer to perceive polarization of light. Used alone for viewing in real time and/or in conjunction with video or movie camera to record for subsequent detailed quantitative analysis of polarization in scene. Device used in remote sensing to classify portions of scenes according to polarization characteristics, to enhance viewing through atmosphere and oceans and to enhance contrasts. Used to monitor oilspill from air and detect changes in soil moisture and to map wetlands, among many other possible civilian and military applications.
Data storage using peptide sequences (2021)

Humankind is generating digital data at an exponential rate. These data are typically stored using electronic, magnetic or optical devices, which require large physical spaces and cannot last for a very long time. Here we report the use of peptide sequences for data storage, which can be durable and of high storage density. With the selection of suitable constitutive amino acids, designs of address codes and error-correction schemes to protect the order and integrity of the stored data, optimization of the analytical protocol and development of a software to effectively recover peptide sequences from the tandem mass spectra, we demonstrated the feasibility of this method by successfully storing and retrieving a text file and the music file Silent Night with 40 and 511 18-mer peptides respectively. This method for the first time links data storage with the peptide synthesis industry and proteomics techniques, and is expected to stimulate the development of relevant fields.
Methods for reducing memristor crossbar simulation time (2015)

Memristor crossbars have the potential to perform parallel resistive computations in the analog domain, and they can be used to develop high density neural network algorithms. However, accurately simulating large memristor crossbars in SPICE (with more than 256 devices) is very difficult and time consuming. This paper discusses using Xyce (a parallel SPICE platform developed by Sandia Labs) to speed up memristor crossbar simulation. Using Xyce, we were able to successfully train neuromorphic memristor crossbars containing 10,096 memristors to learn a large array of linearly separable logic functions. Large memristor crossbars were also used for pattern recognition using both the MNIST and CBCL face datasets. To further reduce training time, a memristor crossbar approximation was simulated in MATLAB. Modeling a crossbar in MATLAB takes significantly less time, but is slightly less accurate. The trained resistance values determined by MATLAB were then downloaded to the more precise crossbar simulated in Xyce (which contains input drivers, comparator circuits, and wire resistance). The classification accuracy found in Xyce was then compared to the accuracy determined when testing the approximated crossbar in MATLAB, as well as a traditional software neural network implementation. To the best of our knowledge, this is the first published result that describes using XYCE to simulate a neuromorphic memristor crossbar using accurate memristor modeling techniques.
<title>Imaging proximity assays</title> (1998)

Scintillation Proximity Assay is an established radioisotopic assay technique widely used in high throughput screening laboratories. The requirement for miniaturization of these arrays has led to the development of microplates containing 384, 864, 1536 or even higher numbers of wells. Imaging is the only practical detection method for quantifying the assays in such high density plates.