gebhart/patrepeval huggingface dataset:
A Cell-Based High-Throughput Screen Validates the Plasmodial Surface Anion Channel As an Antimalarial Target (2010)

The plasmodial surface anion channel (PSAC) is an unusual small-conductance ion channel induced on erythrocytes infected with plasmodia, including parasites responsible for human malaria. Although broadly available inhibitors produce microscopic clearance of parasite cultures at high concentrations and suggest that PSAC is an antimalarial target, they have low affinity for the channel and may interfere with other parasite activities. To address these concerns, we developed a miniaturized assay for PSAC activity and carried out a high-throughput inhibitor screen. Approximately 70,000 compounds from synthetic and natural product libraries were screened, revealing inhibitors from multiple structural classes including two novel and potent heterocyclic scaffolds. Single-channel patch-clamp studies indicated that these compounds act directly on PSAC, further implicating a proposed role in transport of diverse solutes. A statistically significant correlation between channel inhibition and in vitro parasite killing by a family of compounds provided chemical validation of PSAC as a drug target. These new inhibitors should be important research tools and may be starting points for much-needed antimalarial drugs.
A transverse shear model of a piezoelectric chemical sensor (1998)

This model of a transverse shear-mode piezoelectric quartz-crystal chemical sensor is based on the fundamental equations of motion and piezoelectricity. The geometry includes the crystal as well as a metal electrode and a polymeric sensing layer immersed in a fluid medium. All of these are considered to be viscoelastic materials, and slip at the three interfaces is included. The model is shown to agree well with both experimental data and published correlations of the series resonant frequency and equivalent series resistance under both mass and liquid loading. In addition, the mechanical resonant behavior is also calculated. The interfacial slip parameter and the complex shear viscosity are shown to be mathematically interchangeable but not physically equivalent. Negative elastic coefficients obtained from the slip parameters for less viscous fluids suggests that interfacial slip is an important process, which dominates viscoelastic effects for these fluids.
Redistribution and Removal of Particles From Drop Surfaces (2009)

It was recently shown by us that particles distributed on the surface of a drop can be concentrated at the poles or equator of the drop by subjecting the latter to a uniform electric field. In this paper, we present experimental results for the dependence of the dielectrophoretic force on the parameters of the system such as the particles’ and drop’s radii and the dielectric properties of the fluids and particles, and define a dimensionless parameter regime for which the technique can work. Specifically, we show that if the drop radius is larger than a critical value, that depends on the physical properties of the drop and ambient fluids and the particles, it is not possible to concentrate particles and thus clean the drop of the particles it carries at its surface because the drop breaks or tip-streams at an electric field intensity smaller than that needed for concentrating particles. However, since the dielectrophoretic force varies inversely with the drop radius, the effectiveness of the concentration mechanism increases with decreasing drop size, and therefore the technique is guaranteed to work provided the drop radius is sufficiently small.
Quantum Dots in Biology and Medicine (2005)

Abstract For Abstract see ChemInform Abstract in Full Text.
Location dependent key management using random key-predistribution in sensor networks (2006)

In this paper we propose a location aware approach for key management in sensor networks. As a result, this approach not only provides for better connectivity of sensor nodes in the network but also provides for containment of node compromise. This approach which we call as location dependent key (LDK) management does not require any knowledge about the deployment of sensor nodes. LDK starts off with loading a random set of keys on each sensor node prior to deployment. The actual keys are then derived from this set after the sensor nodes are deployed. LDK also allows for additions of sensor nodes to the network at any point in time. We study the proposed scheme in detail using simulations. The proposed scheme is also compared with some existing key management schemes designed for sensor networks.
Real-Time Image Processing for Monitoring of Free Weld Pool Surface (1997)

The arc weld pool is always deformed by plasma jet. In a previous study, a novel sensing mechanism was proposed to sense the free weld pool surface. The specular reflection of pulsed laser stripes from the mirror-like pool surface was captured by a CCD camera. The distorted laser stripes clearly depicted the 3D shape of the free pool surface. To monitor and control the welding process, the on-line acquisition of the reflection pattern is required. In this work, the captured image is analyzed to identify the torch and electrode. The weld pool edges are then detected. Because of the interference of the torch and electrode, the acquired pool boundary may be incomplete. To acquire the complete pool boundary, models have been fitted using the edge points. Finally, the stripes reflected from the weld pool are detected. Currently, the reflection pattern and pool boundary are being related to the weld penetration and used to control the weld penetration.
Non-stoichiometric O-acetylation of Shigella flexneri 2a O-specific polysaccharide: synthesis and antigenicity (2014)

Synthetic functional mimics of the O-antigen from Shigella flexneri 2a are seen as promising vaccine components against endemic shigellosis. Herein, the influence of the polysaccharide non-stoichiometric di-O-acetylation on antigenicity is addressed for the first time. Three decasaccharides, representing relevant internal mono- and di-O-acetylation profiles of the O-antigen, were synthesized from a pivotal protected decasaccharide designed to tailor late stage site-selective O-acetylation. The latter was obtained via a convergent route involving the imidate glycosylation chemistry. Binding studies to five protective mIgGs showed that none of the acetates adds significantly to broad antibody recognition. Yet, one of the five antibodies had a unique pattern of binding. With IC50 in the micromolar to submicromolar range mIgG F22-4 exemplifies a remarkable tight binding antibody against diversely O-acetylated and non-O-acetylated fragments of a neutral polysaccharide of medical importance.
Reconstruction of Sparse Sub-Wavelength Images (2010)

We use compressed sensing to demonstrate theoretically the reconstruction of sub-wavelength features from measured far-field, and provide experimental proof-of-concept. The methods can be applied to non-optical microscopes, provided the information is sparse.
Novel Short Oligonucleotide Conjugates as Inhibitors of Human Telomerase (2004)

Abstract For Abstract see ChemInform Abstract in Full Text.
Effect of foot-and-mouth disease virus 3C protease B2 β-strand proline mutagenesis on expression and processing of the P1 polypeptide using a plasmid expression vector (2019)

The production of experimental molecular vaccines against foot-and-mouth disease virus utilizes the viral encoded 3C protease for processing of the P1 polyprotein. Expression of wild type 3C protease is detrimental to host cells. The molecular vaccine constructs containing the 3C protease L127P mutant significantly reduce adverse effects associated with protease expression while retaining the ability to process and assemble virus-like particles. In published 3C protease crystal structures, the L127 residue is contained within the B2 β-strand as part of the A2-B2 β-sheet. To provide insight into the mechanism by which the L127P mutant alters the properties of the 3C protease, we performed scanning proline mutagenesis of residues 123-128 of the B2 β-strand and monitored expression and P1 processing. Simultaneously, we utilized random mutagenesis of the full 3C sequence to identify additional mutations presenting a phenotype similar to the L127P mutation. Six of the tested mutants enhanced expression over wild type, and the I22P, T100P and V124P mutations surpassed the L127P mutation in certain cell lines. These data areinterpreted in conjunction with published 3C protease crystal structures to provide insight into the mechanism by which these mutations enhance expression.
Damage Detection in Satellite Bolted Joints (2008)

To overcome current limitations of satellite operation timelines, Operationally Responsive Space (ORS) satellites are being developed for rapid configuration and assembly. Time spent on flight qualification tests aimed at assembly verification and launch vehicle integration must be reduced to less than a week. Structural health monitoring (SHM) is seen as a possible avenue for real-time assessment of satellite integrity and qualification before launch. Embedded ultrasonics and magneto-mechanical impedance (MMI) were considered as potential candidates for diagnostics of critical system elements. Piezoelectric wafer active sensors in conjunction with an acousto-elastic SHM were used for assessment of aerospace structures with bolted joints. In the presented analysis, the acousto-elastic behavior of the joint was used as an indicator of structural integrity. Experimental results show changes in the nonlinear response of joints as a result of differing bolt torque. Localization potential of the acousto-elastic technique was demonstrated in a complex structure analogous to a typical satellite panel. The MMI method has shown utility in assessing condition of bolted joints in thin plates and a satellite structure. Experimental data reveal changes in magnitude and position of impedance peaks induced by the difference in structural loads applied to the joint. It is suggested that both the acousto-elastic and MMI methods have indicated possibilities for detecting and characterizing damage in satellite bolted joints.
Tone mapping-based high-dynamic-range image compression: study of optimization criterion and perceptual quality (2013)

We study the issue of quality assessment in tone mapping-based high-dynamic-range (HDR) image compression. In this, there are two stages at which a decision should be made regarding perceptual visual quality: (a) for finding the optimal parameters of the dynamic range reduction function so that the visual quality is maximized, and (b) visual quality judgment of the decompressed image. We first investigate two objective optimization criteria, namely mean squared error and structural similarity index measure, toward optimization of a tone mapping model-based HDR image compression method. We then conduct a comprehensive subjective study to evaluate the visual quality of the compressed HDR images. Therefore, we consider both objective and subjective aspects for HDR image compression. To our knowledge, no systematic and comprehensive studies exist in the current literature which shed light on the issue of quality assessment in HDR compression. So this study brings in new knowledge and perspective for the relatively less investigated topic of HDR compression from the view point of perceptual quality. We further evaluate the prediction performances of four objective methods on the 140 compressed HDR images that have been subjectively rated.
Multiple enface image averaging for enhanced optical coherence tomography angiography imaging (2018)

Use of multiple image averaging in OCTA enface images was found to be both objectively and subjectively effective for enhancing image quality. These findings may of value for developing optimal OCTA imaging protocols for future studies.
Orienting Ferroelectric Films (2002)

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Sewerage Stormwater Inflow Prediction by Using System Identification Method with Hammerstein Type of Nonlinear Model (2000)

This paper presents a stormwater inflow prediction method based on a rainfall-runoff model. The rainfall-runoff model is derived by using system identification method with a nonlinear model called Hammerstein model, which consists of a static nonlinearity followed by a linear time invariant (LTI) system. It is shown that the Hammerstein model can represent nonlinear phenomena of a rainfall-runoff process effectively, thus the introduction of the Hammerstein model improves the accuracy of inflow prediction results. The effectiveness of the proposed method is illustrated through numerical simulations by using the rainfall-runoff data which is acquired in actual urban catchment and a sewerage treatment plant.
Submillimeter-wave kinetic inductance bolometers on free-standing nanomembranes (2013)

We introduce a microwave submillimeter-wave detector based on an integrated micromesh absorber and superconducting kinetic inductance thermometer on a through-wafer released sub-micron thick membrane. Equilibrium operation achieved by thermal isolation through the membrane geometry enables operation at elevated thermal bath temperatures of 5–10 K. The bolometer operates in a phonon-noise limited regime with a measured noise equivalent temperature difference of below 10 mK at 1 s integration time, which is sufficient for radiometric imaging in terrestrial systems. We also measured and analyzed the bolometer frequency response in the band 0.1–1.4 THz. Performance improvements through further dimensional scale-down and temperature dependency are discussed.
Boosting Salt Resistance of Short Antimicrobial Peptides (2013)

The efficacies of many antimicrobial peptides are greatly reduced under high salt concentrations, therefore limiting their use as pharmaceutical agents. Here, we describe a strategy to boost salt resistance and serum stability of short antimicrobial peptides by adding the nonnatural bulky amino acid β-naphthylalanine to their termini. The activities of the short salt-sensitive tryptophan-rich peptide S1 were diminished at high salt concentrations, whereas the activities of its β-naphthylalanine end-tagged variants were less affected.
A Novel Noncomplementary Active Clamp Flyback Control Technique (2019)

This paper proposes an innovative non-complementary control method for an active clamp flyback converter. The proposed method recovers the leakage inductance energy and achieves soft switching for all the switches, while obtaining a lower RMS current compared to previous complementary or noncomplementary active clamp flyback control methods. In order to improve power density while reducing the profile of the transformer, a planar transformer with PCB-litz windings is developed for this converter.
Antimicrobial efficacy of chlorhexidine digluconate alone and in combination with eucalyptus oil, tea tree oil and thymol against planktonic and biofilm cultures of Staphylococcus epidermidis (2008)

The results from this study suggest that there may be a role for essential oils, in particular EO, for improved skin antisepsis when combined with CHG.
Two-Channel Bioimpedance Monitor for Impedance Cardiography (2006)

In this paper we introduce our conception of a two-channel bioimpedance monitor for the impedance cardiography. We describe the design of a homemade device which is based on a direct digital synthesizer and a digital down converter. This solution enables us to obtain a high-quality bioimpedance signal, which can be used for computing the cardiac output beat per beat. It further enables us to analyze impedance phase changes beat per beat. Our device allows simultaneous measuring of complex impedance in two arbitrary directions on human/animal body without any interference between channels. The setting of the main parameters of the measurement like the amplitude and the frequency of the measurement current depends on the user
Isolation and Identification of Vesicular-Arbuscular Mycorrhiza-Stimulatory Compounds from Clover ( <i>Trifolium repens</i> ) Roots (1991)

Two isoflavonoids isolated from clover roots grown under phosphate stress were characterized as formononetin (7-hydroxy,4'-methoxy isoflavone) and biochanin A (5,7-dihydroxy,4'-methoxy isoflavone). At 5 ppm, these compounds stimulated hyphal growth in vitro and root colonization of an undescribed vesicular-arbuscular mycorrhiza, a Glomus sp. (INVAM-112). The permethylated products of the two compounds were inactive. These findings suggest that the isoflavonoids studied may act as signal molecules in vesicular-arbuscular mycorrhiza symbiosis.
<i>p</i> -channel LDMOS transistor using new taperedfield oxidation technology (1998)

The on-resistance of p-channel RESURF (reduced surface field) LDMOS (lateral double-diffused MOS) transistors has been improved by using a new tapered TEOS field oxide in the drift region of the devices. With similar breakdown voltage, at Vgs = –5.0 V, the specific on-resistance of the LDMOS with tapered field oxide is ~31.5 mΩ·cm2, while that of the LDMOS with conventional field oxide is ~57 mΩ·cm2.
Regular Expression Matching with Multi-Strings and Intervals (2010)

Regular expression matching is a key task (and often computational bottleneck) in a variety of software tools and applications. For instance, the standard grep and sed utilities, scripting languages such as perl, internet traffic analysis, XML querying, and protein searching. The basic definition of a regular expression is that we combine characters with union, concatenation, and kleene star operators. The length m is proportional to the number of characters. However, often the initial operation is to concatenate characters in fairly long strings, e.g., if we search for certain combinations of words in a firewall. As a result, the number k of strings in the regular expression is significantly smaller than m. Our main result is a new algorithm that essentially replaces m with k in the complexity bounds for regular expression matching. More precisely, after an O(m log k) time and O(m) space preprocessing of the expression, we can match it in a string presented as a stream of characters in time per character, where w is the number of bits in a memory word. For large w, this corresponds to the previous best bound of . Prior to this work no O(k) bound per character was known. We further extend our solution to efficiently handle character class interval operators C{x, y}. Here, C is a set of characters and C{x, y}, where x and y are integers such that 0 ≤ x ≤ y, represents a string of length between x and y from C. These character class intervals generalize variable length gaps which are frequently used for pattern matching in computational biology applications.
Ionic-to-electronic conductivity transition in an oxide glass doped with gold (2009)

Gold doped ruby glasses are classical examples of metal-glass nanocomposites that have been investigated for their striking optical properties. For the example of weakly Au doped lithium-borate glasses these materials are shown to exhibit a transition from ionic to electronic conduction within the same sample. It is achieved via appropriate heat treatment, presumably by introducing polarons formed from the trapping of electrons at partially ionized gold atoms. This unique electrical response is expected to introduce new functionality to this class of nanocomposites.
Aberration-Compensation Methods for 0.85-Numerical-Aperture (<i>NA</i>) Single-Element Objective Lens (2002)

We have fabricated a high-numerical-aperture objective lens that consists of only a single-element. This lens has a large working distance and does not require assembly procedures in comparison to a two-element objective lens already proposed. We have also developed aberration-compensation methods for coma and spherical aberration. Spherical aberration is compensated automatically by using a servo circuit. A signal read-out obtained from a high-density optical disk is demonstrated using this single-element objective lens.
Magnetorheological platform dampers for mountain bikes (2009)

Full suspension mountain bicycles exhibit unwanted suspension movement during pedalling. Damper manufacturers frequently adopt what is known as platform damping to overcome this problem. Such dampers resist low frequency pedalling inputs due to the presence of a threshold or 'platform' damping level. However, this platform compromises shock absorption ability over rougher terrain. In this paper, the authors describe a prototype rear shock absorber that utilises magnetorheological (MR) fluids to implement semi-active platform damping. Results from recent field trials will be presented, and the current status of commercialising the system will be discussed.
Al1.3Sb3Te material for phase change memory application (2011)

Comparing with Ge2Sb2Te5, Al1.3Sb3Te is proved to be a promising candidate for phase-change memory use because of its higher crystallization temperature (∼210 °C), larger crystallization activation energy (3.32 eV), and better data retention ability (124 °C for 10 yr). Furthermore, Al1.3Sb3Te shows fast phase change speed and crystallizes into a uniformly embedded crystal structure. As short as 10 ns width, voltage pulse can realize reversible operations for Al1.3Sb3Te based phase-change memory cell. Moreover, phase-change memory cell based on Al1.3Sb3Te material also has good endurance (∼2.5 × 104 cycles) and an enough resistance ratio of ∼102.
<title>Efficacy of pyropheophorbide-a-hexyl ether for photodynamic therapy of rat 9L gliosarcoma</title> (1993)

In preliminary studies, the efficacy of a new photosensitizer, pyropheophorbide-(alpha) - hexyl ether (HPPH #23), for use in photodynamic therapy (PDT) was assessed using the rat 9L gliosarcoma tumor model in subcutaneous flank tumors, intracranial tumors, and in vivo. Flank and intracranial tumors were irradiated with 75 - 203 J/cm<SUP>2</SUP> 24 hours after 0.3 - 0.6 mg/kg IV injection of HPPH #23. At 24 hours post-PDT, and flank tumors showed a range of necrosis at the highest laser dose from 50 - 100%. The overlying skin and underlying muscle were spared. Intracranial tumors exhibited moderate to severe hemorrhagic necrosis. Areas of brain adjacent to tumor within the irradiated field also showed some damage. In vitro phototoxicity of HPPH #23 was compared to that of Photofrin II (PhII). Cells growing in culture dishes were exposed to HPPH #23 or PhII for 20 hours, washed free of unbound drug, then irradiated at 2.5 J/cm<SUP>2</SUP>, 17 mW/cm<SUP>2</SUP> at 665 nm (HPPH #23) or 630 nm (PhII). Irradiated cultures were maintained in dark incubators for an additional 4 - 5 days, and phototoxic inhibition of cell proliferation was quantified by the sulphorhodamine B spectrophotometric assay. Under identical irradiation conditions, the IC<SUB>50</SUB> for HPPH #23 (0.25 (mu) g/ml) was 10-fold lower than that of PhII (2.5 (mu) g/ml). Complete cell kill was achieved at sensitizer doses of 0.5 (mu) g/ml (HPPH #23) and 5.0 (mu) g/ml (PhII).