gebhart/patrepeval huggingface dataset:
A Practical Synthesis of Zanamivir Phosphonate Congeners with Potent Anti-influenza Activity (2011)

Two phosphonate compounds 1a (4-amino-1-phosphono-DANA) and 1b (phosphono-zanamivir) are synthesized and shown more potent than zanamivir against the neuraminidases of avian and human influenza viruses, including the oseltamivir-resistant strains. For the first time, the practical synthesis of these phosphonate compounds is realized by conversion of sialic acid to peracetylated phosphono-DANA diethyl ester (5) as a key intermediate in three steps by a novel approach. In comparison with zanamivir, the high affinity of 1a and 1b can be partly attributable to the strong electrostatic interactions of their phosphonate groups with the three arginine residues (Arg118, Arg292, and Arg371) in the active site of neuraminidases. These phosphonates are nontoxic to the human 293T cells; they protect cells from influenza virus infection with EC50 values in low-nanomolar range, including the wild-type WSN (H1N1), the 2009 pandemic (H1N1), the oseltamivir-resistant H274Y (H1N1), RG14 (H5N1), and Udorn (H3N2) influenza strains.
Proteomic Analysis of Pharmacological Preconditioning (2006)

Ischemic preconditioning is characterized by resistance to ischemia reperfusion injury in response to previous short ischemic episodes, a protective effect that can be mimicked pharmacologically. The underlying mechanism of protection remains controversial and requires greater understanding before it can be fully exploited therapeutically. To investigate the overall effect of preconditioning on the myocardial proteome, isolated rabbit ventricular myocytes were treated with drugs known to induce preconditioning, adenosine or diazoxide (each at 100 micromol/L for 60 minutes). Their protein profiles were then compared with vehicle-treated controls (n=4 animals per treatment) using a multitiered 2D gel electrophoresis approach. Of 28 significantly altered protein spots, 19 nonredundant proteins were identified (5 spots remained unidentified). The majority of these proteins are involved in mitochondrial energetics, including subunits of tricarboxylic acid cycle enzymes and oxidative phosphorylation complexes. These changes were not indiscriminate, with only a small number of enzymes or complex subunits altered, indicating a very specific and targeted affect of these 2 preconditioning mimetics. Among the changes were shifts in the extent of posttranslational modification of 4 proteins. One of these, the adenosine-induced phosphorylation of the ATP synthase beta subunit, was fully characterized with the identification of 5 novel phosphorylation sites. This proteomics approach provides an overall assessment of the cellular response to pharmacological treatment with adenosine and diazoxide and identifies a distinct subset of enzymes and protein complex subunit that may underlie the preconditioned phenotype.
High-Throughput Assays Using a Luciferase-Expressing Replicon, Virus-Like Particles, and Full-Length Virus for West Nile Virus Drug Discovery (2005)

Many flaviviruses cause significant human disease worldwide. The development of flavivirus chemotherapy requires reliable high-throughput screening (HTS) assays. Although genetic systems have been developed for many flaviviruses, their usage in antiviral HTS assays has not been well explored. Here we compare three cell-based HTS assays for West Nile virus (WNV) drug discovery: (i) an assay that uses a cell line harboring a persistently replicating subgenomic replicon (containing a deletion of viral structural genes), (ii) an assay that uses packaged virus-like particles containing replicon RNA, and (iii) an assay that uses a full-length reporting virus. A Renilla luciferase gene was engineered into the replicon or into the full-length viral genome to monitor viral replication. Potential inhibitors could be identified through suppression of luciferase signals upon compound incubation. The antiviral assays were optimized in a 96-well format, validated with known WNV inhibitors, and proved useful in identifying a new inhibitor(s) through HTS of a compound library. In addition, because each assay encompasses multiple but discrete steps of the viral life cycle, the three systems could potentially be used to discriminate the mode of action of any inhibitor among viral entry (detected by assays ii and iii but not by assay i), replication (including viral translation and RNA synthesis; detected by assays i to iii), and virion assembly (detected by assay iii but not by assays i and ii). The approaches described in this study should be applicable to the development of cell-based assays for other flaviviruses.
Integration, gap formation, and sharpening of III-V heterostructure nanowires by selective etching (2010)

Epitaxial growth of heterostructure nanowires allows for the definition of narrow sections with specific semiconductor composition. The authors demonstrate how postgrowth engineering of III-V heterostructure nanowires using selective etching can form gaps, sharpening of tips, and thin sections simultaneously on multiple nanowires. They investigate the potential of combining nanostencil deposition of catalyst, epitaxial III-V heterostructure nanowire growth, and selective etching, as a road toward wafer scale integration and engineering of nanowires with existing silicon technology. Nanostencil lithography is used for deposition of catalyst particles on trench sidewalls and the lateral growth of III-V nanowires is achieved from such catalysts. The selectivity of a bromine-based etch on gallium arsenide segments in gallium phosphide nanowires is examined, using a hydrochloride etch to remove the III-V native oxides. Depending on the etching conditions, a variety of gap topologies and tiplike structures are observed, offering postgrowth engineering of material composition and morphology.
Immunologic Characterization and Quantification of Haemoglobin A<sub>1c</sub> (1978)

Sheep antiserum developed against the human glycohaemoglobin, Hb A1c, distinguishes this fraction from the major component Hb A0. Partial cross reactivity is observed with Hb A1a and Hb A1b, as well as with analogous glycohaemoglobins from mouse and dog haemolysates. The reactivity of the haemoglobins with this specific antiserum is abolished by the reduction of the keto group of the sugar ligand. The immunological specificity displayed provides the basis of a quantitative assay for Hb A1c, suitable for studies of clinical and experimental diabetes.
An effective chip implementation of a real-time eight-channel EEG signal processor based on on-line recursive ICA algorithm (2012)

This paper presents an effective chip implementation of a real-time eight-channel electroencephalogram signal processor based on on-line recursive independent component analysis (ORICA) algorithm. The system architecture is composed of a memory unit, a whitening unit, an ORICA training unit, and an ORICA computation unit. The proposed architecture is implemented using TSMC 90 nm CMOS technology. It occupies a core area of 800×800 μm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> and consumes 4.18 mW at a core supply voltage of 1.0 V and 50 MHz clock operating frequency. Simulated super and sub-Gaussian signals are used to verify the system. The separated signals match those obtained using off-line Matlab-based analysis.
Single-sideband electrooptic modulators and their application in tunable opto-electronic oscillators (2009)

We report on the development of resonant single sideband electro-optical modulators using whispering gallery mode resonators made with electrooptic material. Application of these modulators in compact, widely tunable opto-electronic oscillators and all-optical atomic clocks is discussed.
Crystallization and Properties of Myeloperoxidase from Normal Human Leukocytes (1986)

Myeloperoxidase was purified from normal human leukocytes in a crystalline state. Two types of crystals were obtained by the batchwise and dialysis crystallization methods, one of which had a bipyramidal shape belonging to the orthorhombic system. Three multiple forms of human myeloperoxidase were separated from the crystalline enzyme by CM-Sepharose chromatography with sodium chloride gradient elution. These three multiple forms were found to have very similar enzymatic, spectroscopic, and chemical properties. However, slight differences were observed in their amino acid compositions and the molecular weights of their large subunits determined by sodium dodecyl sulfate (SDS)-polyacrylamide gel electrophoresis. Hemi-myeloperoxidase was prepared from holo-myeloperoxidase by reduction with dithiothreitol and modification with iodoacetamide, and the molecular shapes of the holo- and hemi-enzymes were determined by analytical ultracentrifugation. The axial ratios were calculated to be 2.4-3.5 for the holo-enzyme and 2.9-3.1 for the hemi-enzyme. These results suggest that the shapes of the two enzymes are more spherical in solution than the proposed structural model previously reported.
Carbosilane/carbosiloxane-based ADMET homopolymers and copolymers possessing latent reactivity (2000)

Reactive methoxy-functionalized carbosilane and carbosiloxane dienes can be either homopolymerized or copolymerized via acyclic diene metathesis (ADMET) polycondensation chemistry to produce reactive materials with mechanical behavior dependent on the molar ratios of the comonomers. The methoxy-functional group within the polycarbosilane repeat unit remains inert during the metathesis polymerization and can be triggered subsequently with water to generate crosslinks between polymer chains. In this way, linear, thermoplastic copolymers can be prepared with ADMET chemistry and converted into crosslinked, thermoset copolymers upon exposure to moisture. Crosslinked films containing 5–10% of the crosslinked hard segment are soft and flexible materials. © 2000 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 38: 1544–1550, 2000
Vapor Sensing Characteristics of Nanoelectromechanical Chemical Sensors Functionalized Using Surface-Initiated Polymerization (2014)

Surface-initiated polymerization has been used to grow thick, uniform poly(methyl methacrylate) films on nanocantilever sensors. Cantilevers with these coatings yielded significantly greater sensitivity relative to bare devices as well as relative to devices that had been coated with drop-cast polymer films. The devices with surface-initiated polymer films also demonstrated high selectivity toward polar analytes. Surface-initiated polymerization can therefore provide a straightforward, reproducible method for large-scale functionalization of nanosensors.
Isotropic wavevector domain image filters by a photonic crystal slab device (2018)

We show that several types of isotropic image filters in the wavevector domain can be implemented with a single photonic crystal slab device. Such a slab is designed so that the guided resonance near the Γ point exhibits an isotropic band structure. Depending on the light frequency and the choice of transmission or reflection mode, the device realizes isotropic high-pass, low-pass, band-reject, and band-pass filtering in wavevector space. These filter functions are important for various image processing tasks, including edge detection, smoothing, white noise suppression, and suppression or extraction of periodic noises. We numerically demonstrate these filter functionalities by simulations of a slab structure that is designed to operate in the visible wavelength range. Our work expands the application of nanophotonics-based optical analog computing for image processing.
Network-assisted D2D communications: Implementing a technology prototype for cellular traffic offloading (2014)

Currently, cellular operators are struggling to relieve congestion on their networks in the face of rapidly growing mobile data traffic. While deploying an increasing number of base stations is expected to mitigate the disproportion between user demand and available radio resources, this solution is costly and plagued with many practical challenges. An attractive alternative is to enable cellular traffic offloading onto device-to-device (D2D) connections in the unlicensed bands, as current multi-radio user devices are already capable of establishing concurrent LTE and WiFi links. However, WiFi lacks a fast, efficient method of device/service discovery, and it is not equipped to efficiently manage numerous D2D connections. In our research, we have found that a limited amount of network assistance for D2D communications can overcome these limitations; and in this paper we describe our network-assisted D2D technology prototype. Specifically, we outline a complete standards-compliant solution that provides a seamless D2D connectivity experience to the end user. Our solution utilizes WiFi Direct as the link-layer technology for proximal D2D connections. However, the challenges faced during the design phase are universal to all D2D link-layer protocols, thus the proposed solutions are applicable to other potential D2D technologies.
Variational calculation of force-frequency constants of doubly rotated quartz resonators (1978)

The calculus of variations has been used to obtain solutions for the statics tress distributions in circular quartz resonator blanks caused by forces acting along the blank diameter. The resulting static stress distributionsh ave been used with nonlinear elastic calculations (third-order elastic constants) to predict the force sensitivity of the resonant frequency of thickness shear resonators. The present results are shown to agree more favorably with experiment than results obtained by previous theories where the quartz was assumed to be isotropic for the statics tress solution. General theoretical results and supporting experimental results argeiv en for the force-frequency constants of doubly rotated family (yxωl)ϕ,θ along the technologically important zero temperature coefficient branch which contains the AT-, FC-, IT-, SC-, and rotated X-cuts The results will be useful for choosing the location of bonding pads for two-point mountss o that the mounting stress effectsc an be minimized in frequency control applications or maximized in force transducer applications.
High-resolution DNA melting analysis in clinical research and diagnostics (2010)

Among nucleic acid analytical methods, high-resolution melting analysis is gaining more and more attention. High-resolution melting provides simple, homogeneous solutions for variant scanning and genotyping, addressing the needs of today's overburdened laboratories with rapid turnaround times and minimal cost. The flexibility of the technique has allowed it to be adopted by a wide range of disciplines for a variety of applications. In this review we examine the broad use of high-resolution melting analysis, including gene scanning, genotyping (including small amplicon, unlabeled probe and snapback primers), sequence matching and methylation analysis. Four major application arenas are examined to demonstrate the methods and approaches commonly used in particular fields. The appropriate usage of high-resolution melting analysis is discussed in the context of known constraints, such as sample quality and quantity, with a particular focus placed on proper experimental design in order to produce successful results.
LATS: a load-adaptive threshold scheme for tracking mobile users (1999)

Mobile user tracking is a major issue. We propose a novel approach for user tracking, in which the tracking activity is adapted to both user and system activity. The basic idea is to make the user-location update-rate dependent not only on the user activity (such as the call profile and mobility pattern). Rather, it is also made dependent on the signaling load, which reflects the actual cost of the update operation. Thus, at low-signaling load locations, the users are to transmit location update messages more frequently. To carry out this approach, we propose a load-adaptive threshold scheme (LATS): the network determines for each cell a registration threshold level (which depends on the cell load) and announces it, as a broadcast message, to the users. The user computes its own registration priority and then transmits a registration message only if its priority exceeds the announced threshold level. Thus, whenever the local load on the cell is low, the registration activity increases, while in loaded cells the registration activity decreases. Our analysis shows that the LATS reduces the paging cost, in comparison with other dynamic methods, without increasing the wireless cost of registration. Moreover, if higher user density is coupled with less mobility (e.g., consider vehicles), then the LATS strategy offers further performance improvement. The load-adaptive strategy can be used in addition to any other dynamic tracking strategy. Furthermore, the computational complexity imposed on the user is identical to that required by an equivalent load-insensitive scheme.
In Vitro Measurements of Physiological Glucose Concentrations in Biological Fluids Using Mid-Infrared Spectroscopy (2013)

Predictions of glucose concentrations throughout the physiological range are obtained in vitro using partial least squares regression analysis of mid-infrared transmission spectra. Concentrations as low as 30 mg/dL are predicted to clinical accuracy.
FPGA-Based Embedded Motion Estimation Sensor (2008)

Accurate real-time motion estimation is very critical to many computer vision tasks. However, because of its computational power and processing speed requirements, it is rarely used for real-time applications, especially for micro unmanned vehicles. In our previous work, a FPGA system was built to process optical flow vectors of 64 frames of<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:mn>640</mml:mn><mml:mo>×</mml:mo><mml:mn>480</mml:mn></mml:mrow></mml:math>image per second. Compared to software-based algorithms, this system achieved much higher frame rate but marginal accuracy. In this paper, a more accurate optical flow algorithm is proposed. Temporal smoothing is incorporated in the hardware structure which significantly improves the algorithm accuracy. To accommodate temporal smoothing, the hardware structure is composed of two parts: the derivative (DER) module produces intermediate results and the optical flow computation (OFC) module calculates the final optical flow vectors. Software running on a built-in processor on the FPGA chip is used in the design to direct the data flow and manage hardware components. This new design has been implemented on a compact, low power, high performance hardware platform for micro UV applications. It is able to process 15 frames of<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:mn>640</mml:mn><mml:mo>×</mml:mo><mml:mn>480</mml:mn></mml:mrow></mml:math>image per second and with much improved accuracy. Higher frame rate can be achieved with further optimization and additional memory space.
On the Design of Robust Steerable Frequency-Invariant Beampatterns with Concentric Circular Microphone Arrays (2018)

This paper studies the problem of frequency-invariant beamforming with concentric circular microphone arrays (CCMAs). We develop a beamforming algorithm based on an optimal approximation of the beamformer's beampattern with the Jacobi-Anger expansion. In comparison with the existing frequency-invariant beamformers with either circular microphone arrays (CMAs) or CCMAs, the developed algorithm offers the following advantages: 1) it can mitigate the deep-null problem encountered in CMAs and therefore has a consistent directivity factor over the frequency range of speech signals; 2) it is more flexible in terms of steering flexibility and the resulting beampattern can be steered to any direction; and 3) it does not require the microphones in different rings of the CCMA to be aligned, which is very useful in practice, particularly when microphone arrays with small and compact apertures have to be used.
2007 Young Investigator Award (2008)

FSGS is a pathologic lesion that frequently causes the nephrotic syndrome and ensuing renal failure. The cause remains unknown in the majority of individuals; however, in the past two decades, rare familial forms have been identified. It has been suggested that known genetic causes of the hereditary form of this disease account for upwards of 18% of cases. Mutations in five genes have been found to cause inherited nephrotic syndromes and FSGS. In this article, I discuss the phenotypic characteristics of hereditary FSGS and the transient receptor potential cation channel 6 (TRPC6) protein, which is the genetic impetus for an autosomal dominant form of FSGS. The TRP channels have been implicated in varied biologic functions such as mechanosensation, ion homeostasis, cell growth, and phospholipase C-dependent calcium entry into cells. The mutated ion channel causes an increase in calcium transients. Current evidence also suggests that blocking TRPC6 channels may be of therapeutic benefit in idiopathic FSGS, a disease with a generally poor prognosis. Preliminary experiments reveal that the commonly used immunosuppressive agent FK-506 can inhibit TRPC6 activity in vivo. This creates the intriguing possibility that blocking TRPC6 channels within the podocyte may translate into long-lasting clinical benefits in patients with FSGS.
Comparative performance analysis of two picture adjustment methods: HSV vs. YC b C r (2011)

Picture adjustment is referred to those adjustments that affect the four main subjective perceptual image attributes: Hue, Saturation, Brightness (sometimes called Intensity) and Contrast--HSIC adjustments. The common method used for this type of adjustments in a display processing pipe is based on YC<sub>b</sub>C<sub>r</sub> color space and a 3x4 color adjustment matrix. Picture adjustments based on this method, however, leads to multiple problems such as adjusting one attribute leads to degradation of other attributes. As an alternative, other color spaces such as HSV can be used to generate more consistent and effective picture adjustments. In this paper, the results of a comparative performance analysis between the two methods based on YC<sub>b</sub>C<sub>r</sub> and HSV color spaces (for HSIC adjustments) are presented.
Intelligent control of an exercise machine (2002)

The control of a one degree of freedom exercise machine is considered. The control objective is to cause the human user to exercise at a rate which optimizes a prescribed weighted power criterion. The optimality condition is determined by the muscle mechanics which is assumed to satisfy a force-velocity relationship. In general, the parameters of this relationship are unknown and vary with the configuration of the exercise machine. As a consequence, the control scheme must simultaneously (i) identify the parameters, (ii) optimize the controller, and (iii) stabilize the system to the estimated optimal states. In this paper we derive a controller which is in the form of a nonlinear dynamic damper and makes the controlled system interact passively with the user. Assuming that the human's force-velocity muscular biomechanics relationship is known, this controller allows the user to exercise in an optimal manner.
Clinical Feasibility of a Fully Automated 3D Reconstruction of Rotational Coronary X-Ray Angiograms (2010)

Fully automated reconstruction of rotational coronary x-ray angiograms is feasible, produces 3D volumetric images that overcome some of the limitations of standard 2D angiography, and is ready for further implementation and study in the clinical environment.
Highly Efficient JFH1‐Based Cell‐Culture System for Hepatitis C Virus Genotype 5a: Failure of Homologous Neutralizing‐Antibody Treatment to Control Infection (2008)

The SA13/JFH1 culture permits genotype 5a-specific studies of Core-NS2 function and interfering agents. The ability of HCV to spread in vivo during treatment with neutralizing antibodies was confirmed in vitro.