gebhart/patrepeval huggingface dataset:
Isolation and Characterization of Monoclonal Antibodies Specific for Protein Conformational Epitopes Present in Prostate-Specific Membrane Antigen (PSMA) (2000)

Prostate-specific membrane antigen (PSMA) is a 750-amino acid glycoprotein highly expressed in malignant prostate tissues. PSMA reacts with the murine monoclonal antibody 7E11.C5, whose binding epitope has been mapped to the N-terminal of the protein distributed on the cytoplasmic side of the plasma membrane. We have developed murine monoclonal antibodies specific for extracellular epitopes of PSMA. Three of these antibodies--1G9, 3C6, and 4D4--display distinct binding properties consistent with their recognition of conformational epitopes within native PSMA. Results indicate this panel of antibodies binds to native full-length PSMA, but not to fusion proteins containing portions of the linear sequence of the protein. Antibody binding is greatly reduced upon heat denaturation of native PSMA, and these antibodies do not detect PSMA by Western blot. Immunoprecipitation experiments demonstrate the ability of each to bind to full-length PSMA as well as PSM', a form of the protein missing the first 57 amino acids. These results indicate each antibody is specific for an epitope within the extracellular domain, a region spanning residues 44-750. Flow cytometric experiments indicate strong specific binding to live LNCaP cells. Antibody inhibition studies demonstrate that these antibodies recognize at least two distinct epitopes. Taken together, the results demonstrate that these antibodies are specific for native protein conformational epitopes within the extracellular domain. Their properties, in particular strong binding to live cancer cells, make them ideal candidates that are clearly superior to linear sequence epitope specific antibodies for in vivo applications.
Enhanced measurement of broadband nanomechanical property of polymers using atomic force microscope (2013)

A control-based approach to achieve accurate indentation and broadband nanomechanical quantification using atomic force microscope is proposed and utilized to measure four different polymers. For broadband nanomechanical measurement, conventional method is limited by its inability to account for the dynamics effect of the piezoelectric actuator and the cantilever fixture, and the lateral-vertical coupling effect on the cantilever deflection. The proposed approach substantially improved the accuracy of indentation and nanomechanical measurements by utilizing control technique to compensate for these adverse effects. A polydimethylsiloxane sample and three low-density polyethylene samples with different densities were measured by using this approach. The results showed that the viscoelasticity of these four polymer samples can be consistently measured over a large frequency range (100 Hz to 6 kHz) with merely 1 sec. measurement time.
Interaction of Hepatitis C Virus Nonstructural Protein 5A with Core Protein Is Critical for the Production of Infectious Virus Particles (2008)

Nonstructural protein 5A (NS5A) of the hepatitis C virus (HCV) possesses multiple and diverse functions in RNA replication, interferon resistance, and viral pathogenesis. Recent studies suggest that NS5A is involved in the assembly and maturation of infectious viral particles; however, precisely how NS5A participates in virus production has not been fully elucidated. In the present study, we demonstrate that NS5A is a prerequisite for HCV particle production as a result of its interaction with the viral capsid protein (core protein). The efficiency of virus production correlated well with the levels of interaction between NS5A and the core protein. Alanine substitutions for the C-terminal serine cluster in domain III of NS5A (amino acids 2428, 2430, and 2433) impaired NS5A basal phosphorylation, leading to a marked decrease in NS5A-core interaction, disturbance of the subcellular localization of NS5A, and disruption of virion production. Replacing the same serine cluster with glutamic acid, which mimics the presence of phosphoserines, partially preserved the NS5A-core interaction and virion production, suggesting that phosphorylation of these serine residues is important for virion production. In addition, we found that the alanine substitutions in the serine cluster suppressed the association of the core protein with viral genome RNA, possibly resulting in the inhibition of nucleocapsid assembly. These results suggest that NS5A plays a key role in regulating the early phase of HCV particle formation by interacting with core protein and that its C-terminal serine cluster is a determinant of the NS5A-core interaction.
Crocetin: an Agent Derived from Saffron for Prevention and Therapy for Cancer (2011)

Cancer is one of the leading causes of death in the United States and accounts for approximately 8 million deaths per year worldwide. Although there is an increasing number of therapeutic options available for patients with cancer, their efficacy is time-limited and non-curative. Approximately 50-60% cancer patients in the United States utilize agents derived from different parts of plants or nutrients (complementary and alternative medicine), exclusively or concurrently with traditional therapeutic regime such as chemotherapy and/or radiation therapy. The need for new drugs has prompted studies evaluating possible anti-cancer agents in fruits, vegetables, herbs and spices. Saffron, a spice and a food colorant present in the dry stigmas of the plant Crocus sativus L., has been used as an herbal remedy for various ailments including cancer by the ancient Arabian, Indian and Chinese cultures. Crocetin, an important carotenoid constituent of saffron, has shown significant potential as an anti-tumor agent in animal models and cell culture systems. Crocetin affects the growth of cancer cells by inhibiting nucleic acid synthesis, enhancing anti-oxidative system, inducing apoptosis and hindering growth factor signaling pathways. This review discusses the studies on cancer preventive potential of crocetin and its future use as an anticancer agent.
Antireflection dielectric overcoated high-spatial-frequency rectangular-groove surface-relief gratings on lossy materials (1987)

Zero-reflectivity surfaces on lossy materials are useful for eliminating unwanted reflections. Surface-relief gratings on metal surfaces can produce unity transmissivity and thus total absorption. A rigorous impedance matching approach is used. The zero reflectivity condition and the equivalence of the homogeneous layer and the grating in the long-wavelength limit produce a system of nonlinear transcendental equations. First, the required thickness and complex refractive index for a single homogeneous lossy layer antireflection coating are calculated. Then the filling factor and groove depth of the equivalent high-spatial-frequency rectangular-groove surface-relief grating are determined. The analysis includes multiple dielectric overlayers for grating protection and for broad banding the antireflection characteristics. It is shown that multiple zero reflectivity solutions exist for both TE and TM polarizations for arbitrary angles of incidence and for any complex refractive-index substrate. Necessary and sufficient conditions in the parametric space are also computed. The inclusion of one or more dielectric overlayers gives additional design flexibility. The sensitivity of the antireflection design as a function of the angle of incidence and wavelength is presented.
Parallel classification for data mining on shared-memory multiprocessors (1999)

Presents parallel algorithms for building decision-tree classifiers on shared-memory multiprocessor (SMP) systems. The proposed algorithms span the gamut of data and task parallelism. The data parallelism is based on attribute scheduling among processors. This basic scheme is extended with task pipelining and dynamic load balancing to yield faster implementations. The task-parallel approach uses dynamic subtree partitioning among processors. Our performance evaluation shows that the construction of a decision-tree classifier can be effectively parallelized on an SMP machine with good speedup.
Multi-Codebook Based Beamforming and Scheduling for MIMO-OFDM Systems with Limited Feedback (2008)

Transmit beamforming can exploit the spatial diversity afforded by multiple-input multiple-output (MIMO) systems with low complexity. To apply this technique in more practical systems with the constraint of limited feedback, codebook based beamforming and vector quantization technique have been considered in various papers. On the other hand, multi-user scheduling is able to achieve another form of diversity arising from the independence of fading for different users, however, has not been fully taken into account in existing codebook based beamforming schemes. In this letter, a multi-codebook based beamforming and scheduling scheme is proposed, which exploits both spatial diversity and multi-user diversity by switching the codebook for different resource blocks. Meanwhile, the multi-codebook design issue is addressed, the corresponding theoretical analysis is provided, and the performance gain of proposed scheme is simulated. Furthermore, the impacts of related parameters on the performance gain are also investigated.
Photoelectric dye-based retinal prosthesis (OUReP) as a novel type of artificial retina (2021)

We have developed the world's first novel type of artificial retina, OUReP (Okayama University Retinal Prosthesis), in which a photoelectric dye that converts light energy into electric potential is covalently bonded to the surface of a polyethylene thin film as an insulator. The receptor that absorbs light and the output device that generates displacement current to stimulate nearby neurons are integrated in a sheet of thin film. It has become possible to measure the surface potential of the artificial retina OUReP using a Kelvin probe that measures the surface potential of semiconductors. When light is turned on and off to the artificial retina OUReP, the surface potential changes rapidly. As the light intensity is increased, the potential change on the surface of the artificial retina becomes larger. As for safety, the artificial retina OUReP was not toxic in all tests for biological evaluation of medical devices. As for efficacy, the artificial retina OUReP was implanted under the retina by vitreous surgery in monkey eyes which had chemically-induced macular degeneration with photoreceptor cell loss. Over the next 6 months, retinal detachment did not occur during the course, and the artificial retina was in contact with the retinal tissue. The amplitude of the visual evoked potential attenuated by macular degeneration recovered 1 month after implantation of the artificial retina, and the recovery of amplitude was maintained until 6 months after the implantation. By using multielectrode array-mounted dish recording system, it has been proved that action potential spikes are induced when the artificial retina is placed on degenerative retinal tissue of retinal dystrophic rats or mice and exposed to light, which is used as an index of the effectiveness of the artificial retina. We have established manufacturing and quality control of the device in a clean room facility, proved the safety and efficacy, and are preparing for first-in-human investigator-initiated clinical trials.
Biocontrol Activity of Acremonium strictum BCP Against Botrytis Diseases (2009)

Biological control activity of Acremonium strictum BCP, a mycoparasite on Botrytis cinerea, was examined against six plant diseases such as rice blast, rice sheath blight, cucumber gray mold, tomato late blight, wheat leaf rust, and barley powdery mildew in growth chambers. The spore suspension of strain BCP showed strong control activities against five plant diseases except against wheat leaf rust. On the other hand, the culture filtrate of A. strictum BCP was effective in controlling only cucumber gray mold and barley powdery mildew. Further in vivo biocontrol activities of A. strictum BCP against tomato gray mold were investigated under greenhouse conditions. Control efficacy of the fungus on tomato gray mold increased in a concentration-dependent manner. Treatment of more than <TEX>$1{\times}10^6$</TEX> spores/ml significantly controlled the disease both in tomato seedlings and in adult plants. The high disease control activity was obtained from protective application of the strain BCP, whereas the curative application did not control the disease. Foliar infections of B. cinerea were controlled with <TEX>$1{\times}10^8$</TEX> spores/ml of A. strictum BCP applied up to 7 days before inoculation. In a commercial greenhouse, application of A. strictum BCP exhibited the similar control efficacy with fungicide procymidone (recommended rate, <TEX>$500{\mu}g/ml$</TEX>) against strawberry gray mold. These results indicate that A. strictum BCP could be developed as a biofungicide for Botrytis diseases under greenhouse conditions.
Characterizing and Alleviating Substrate Limitations for Improved <i>in vitro</i> Ribosome Construction (2014)

Complete cell-free synthesis of ribosomes could make possible minimal cell projects and the construction of variant ribosomes with new functions. Recently, we reported the development of an integrated synthesis, assembly, and translation (iSAT) method for in vitro construction of Escherichia coli ribosomes. iSAT allows simultaneous rRNA synthesis, ribosome assembly, and reporter protein expression as a measure of ribosome activity. Here, we explore causes of iSAT reaction termination to improve efficiency and yields. We discovered that phosphoenolpyruvate (PEP), the secondary energy substrate, and nucleoside triphosphates (NTPs) were rapidly degraded during iSAT reactions. In turn, we observed a significant drop in the adenylate energy charge and termination of protein synthesis. Furthermore, we identified that the accumulation of inorganic phosphate is inhibitory to iSAT. Fed-batch replenishment of PEP and magnesium glutamate (to offset the inhibitory effects of accumulating phosphate by repeated additions of PEP) prior to energy depletion prolonged the reaction duration 2-fold and increased superfolder green fluorescent protein (sfGFP) yield by ~75%. By adopting a semi-continuous method, where passive diffusion enables substrate replenishment and byproduct removal, we prolonged iSAT reaction duration 5-fold and increased sfGFP yield 7-fold to 7.5 ± 0.7 μmol L(-1). This protein yield is the highest ever reported for iSAT reactions. Our results underscore the critical role energy substrates play in iSAT and highlight the importance of understanding metabolic processes that influence substrate depletion for cell-free synthetic biology.
A microstructure-fiber-based 10-GHz synchronized tunable optical parametric oscillator in the 1550-nm regime (2003)

We demonstrate a microstructure-fiber (MF)-based supercontinuum source and a synchronously pumped optical parametric oscillator in the 1550-nm regime. By using a 12.5-m-long MF, we obtained a 10-GHz repetition-rate picosecond-pulse source that is capable of /spl sim/120-nm wavelength tunability due to the wide-gain bandwidth of the combined processes of stimulated Raman scattering and parametric four-wave mixing.
Prostacyclin, biological role and therapeutic potential (1981)

Conference Abstract| April 01 1981 Prostacyclin, biological role and therapeutic potential S. Moncada S. Moncada 1Dept. of Prostaglandin Research, Wellcome Research Laboratories, Langley Court, Beckenham, Kent BR3 3BS Search for other works by this author on: This Site PubMed Google Scholar Biochem Soc Trans (1981) 9 (2): 73P. https://doi.org/10.1042/bst009073p Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Facebook Twitter LinkedIn MailTo Cite Icon Cite Get Permissions Citation S. Moncada; Prostacyclin, biological role and therapeutic potential. Biochem Soc Trans 1 April 1981; 9 (2): 73P. doi: https://doi.org/10.1042/bst009073p Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAll JournalsBiochemical Society Transactions Search Advanced Search This content is only available as a PDF. © 1981 Biochemical Society1981 Article PDF first page preview Close Modal You do not currently have access to this content.
Convolutional Recurrent Neural Networks for Small-Footprint Keyword Spotting (2017)

Keyword spotting (KWS) constitutes a major component of human-technology interfaces. Maximizing the detection accuracy at a low false alarm (FA) rate, while minimizing the footprint size, latency and complexity are the goals for KWS. Towards achieving them, we study Convolutional Recurrent Neural Networks (CRNNs). Inspired by large-scale state-of-the-art speech recognition systems, we combine the strengths of convolutional layers and recurrent layers to exploit local structure and long-range context. We analyze the effect of architecture parameters, and propose training strategies to improve performance. With only ~230k parameters, our CRNN model yields acceptably low latency, and achieves 97.71% accuracy at 0.5 FA/hour for 5 dB signal-to-noise ratio.
Active Water Management for Proton Exchange Membrane Fuel Cells Using an Integrated Electroosmotic Pump (2005)

We have developed proton exchange membrane fuel cells (PEMFC’s) with integrated planar electroosmotic pumping structures that actively remove liquid water from cathode flow channels. Recent experimental and numerical investigations on PEMFC’s emphasize water management as a critical factor in the design of robust, high efficiency fuel cells. Although various passive water management strategies have been proposed, water is still typically removed by pumping air into cathode channels at flow rates significantly larger than those required by fuel cell stoichiometry. This method of water removal is thermodynamically unfavorable and constrains cathode flow channel design. EO pumps can relieve cathode design barriers and simplify water management in fuel cells. EO pumps have no moving parts, scale across a wide range of operation, and result in low parasitic power. We demonstrate and quantify the efficacy of EO water pumping using a single-pass fuel cell test channel. Our results show that removing water from the cathode using integrated EO pumping structures improves fuel cell performance and stability. These pumps enable operation with air flow rates of just two to three times stoichiometric requirements.
Generalized auto-calibrating technique for image reconstruction from sensitivity encoded MRI data (2006)

MRI with multiple receiver coils (parallel MRI) has been extensively used to achieve higher spatial and temporal resolution, suppress imaging artifacts, and reduced scan time. A number of techniques have been proposed to reconstruct images from reduced (undersampled) k-space datasets acquired by multiple coils. All the techniques require some type of calibration information to describe image encoding by spatially varying coil sensitivities. This information can be derived from supplementary calibration scans. However, this approach increases scan time and can be erroneous due to patient motion between calibration and imaging scans. Auto-calibrating techniques such as the commonly used GRAPPA, do not require calibration scans and estimate reconstruction coefficients directly from acquired k-space data. GRAPPA typically gives good quality results for low undersampling rates. However, strong noise amplification and non-resolved aliasing artifacts makes the technique less applicable in cases of high undersampling. In this work, we have proposed a novel auto-calibrating technique for image reconstruction from sensitivity encoded MRI data that overcomes limitations of the existing auto-calibrating techniques. In the proposed technique (GARSE), specifics of coil sensitivity representation in the image and k-space domains are utilized in the reconstruction in such a way that more trustworthy reconstruction coefficients can be identified resulting in improved image quality. GARSE reconstruction coefficients are spatially variable and adjusted according to local coil sensitivities characteristics, whereas GRAPPA reconstruction coefficients are spatially invariant and, therefore, sub-optimal. Results from MRI studies of phantoms and humans demonstrate substantial advantages of GARSE in comparison with GRAPPA, especially for high undersampling rates.
Analysis of tRNA-Directed Transcription Antitermination in the T Box System In Vivo (2009)

Regulation of gene expression in bacteria by cis-acting RNA elements can be investigated both in vivo and in vitro. Analyses in vivo can focus on changes in mRNA transcript levels or in protein production. Systems that are regulated at the level of premature termination of transcription are best analyzed by monitoring expression of a fusion to an easily assayable reporter gene construct or by direct measurement of the terminated and readthrough transcripts. These experimental approaches are described in the context of the Bacillus subtilis T box mechanism, which responds to uncharged tRNA as the effector, and are readily adaptable to other regulatory systems that respond to other signal molecules, and other experimental systems.
Analysis of Diffractive Optical Neural Networks and Their Integration With Electronic Neural Networks (2019)

Optical machine learning offers advantages in terms of power efficiency, scalability and computation speed. Recently, an optical machine learning method based on Diffractive Deep Neural Networks (D<sup>2</sup>NNs) has been introduced to execute a function as the input light diffracts through passive layers, designed by deep learning using a computer. Here we introduce improvements to D<sup>2</sup>NNs by changing the training loss function and reducing the impact of vanishing gradients in the error back-propagation step. Using five phase-only diffractive layers, we numerically achieved a classification accuracy of 97.18% and 89.13% for optical recognition of handwritten digits and fashion products, respectively; using both phase and amplitude modulation (complex-valued) at each layer, our inference performance improved to 97.81% and 89.32%, respectively. Furthermore, we report the integration of D<sup>2</sup>NNs with electronic neural networks to create hybrid-classifiers that significantly reduce the number of input pixels into an electronic network using an ultra-compact front-end D<sup>2</sup>NN with a layer-to-layer distance of a few wavelengths, also reducing the complexity of the successive electronic network. Using a 5-layer phase-only D<sup>2</sup>NN jointly-optimized with a single fully-connected electronic layer, we achieved a classification accuracy of 98.71% and 90.04% for the recognition of handwritten digits and fashion products, respectively. Moreover, the input to the electronic network was compressed by >7.8 times down to 10×10 pixels. Beyond creating low-power and high-frame rate machine learning platforms, D<sup>2</sup>NN-based hybrid neural networks will find applications in smart optical imager and sensor design.
Fiber Optic Sensor For Temperature Measurement In Gas Flow And Steam Turbines (1987)

The development of a fiber optic interferometer for static temperature sensing in gas or steam flows and in steam turbines is reported. This paper contains informations from the initial motivations to the test procedures of the prototype. A Michelson interferometer single physical arm, combined with an active phase tracking heterodyne detection has been conceived. Tests of the semi-industrial prototype in a supersonic air pipe are described (resolution 0.5 K, dynamic 50 K). The design of an optical probe for steam turbine measurement is reported and an outline of future experiments of the optical system is given.