gebhart/patrepeval huggingface dataset:
DNA G-quadruplex detection system employing a protein fibril ligand (2015)

Thioflavin T (ThT), a typical probe of protein fibrils, also binds human telomeric G-quadruplexes with high specificity for other DNA structures. Upon binding, ThT fluoresces brightly, making it a promising G-quadruplex probe. Because ThT was originally used for detecting protein fibrils, false-positive detection and imaging of DNA G-quadruplexes is possible in the presence of proteins, such as in living cells. We therefore developed a system for the specific discrimination of DNA G-quadruplexes from protein fibrils through measurement of fluorescence resonance energy transfer (FRET) from ThT to a DNA duplex probe. We designed a complementary DNA (cDNA) that hybridizes with the single-stranded region near the DNA G-quadruplex–forming region. Hexidium iodide (HI), a typical DNA duplex fluorescent intercalator, was utilized as an acceptor for FRET from ThT. FRET occurred only when ThT bound the G-quadruplex region and HI bound the duplex region of the cDNA. Fluorescence analysis showed that this system can detect DNA G-quadruplexes even in the presence of protein fibrils.
Multicontrast black‐blood MRI of carotid arteries: Comparison between 1.5 and 3 tesla magnetic field strengths (2006)

This study demonstrated significant improvement in SNR, CNR, and image quality for high- resolution black-blood imaging of carotid arteries at 3T. Morphologic measurements are compatible between 1.5T and 3T.
Growth zones and their boundaries in GaPO4 (2001)

Gallium (ortho)-phosphate (GaPO4) is a piezoelectric material which is grown from hydrothermal solutions. The growth zones, i.e. parts of the crystal grown by different faces, and their boundaries can influence the quality of the grown material. Thus, a theoretical and experimental study of form, size and properties of growth zones and their boundaries in GaPO4 was performed. A program was developed with which the zones in the crystal as well as in any plane cutting through it can be calculated and outlined, simulating the facetted growth using growth rates determined from the crystal habit. This program was applied to spontaneous crystals as well as to crystals growm from seeds. Experimentally, growth zone boundaries which correspond to accumulation of OH were determined by scanning infrared absorption measurements.
Extraction of morphometry and branching angles of porcine coronary arterial tree from CT images (2009)

The morphometry (diameters, length, and angles) of coronary arteries is related to their function. A simple, easy, and accurate image-based method to seamlessly extract the morphometry for coronary arteries is of significant value for understanding the structure-function relation. Here, the morphometry of large (> or = 1 mm in diameter) coronary arteries was extracted from computed tomography (CT) images using a recently validated segmentation algorithm. The coronary arteries of seven pigs were filled with Microfil, and the cast hearts were imaged with CT. The centerlines of the extracted vessels, the vessel radii, and the vessel lengths were identified for over 700 vessel segments. The extraction algorithm was based on a topological analysis of a vector field generated by normal vectors of the extracted vessel wall. The diameters, lengths, and angles of the right coronary artery, left anterior descending coronary artery, and left circumflex artery of all vessels > or = 1 mm in diameter were tabulated for the respective orders. It was found that bifurcations at orders 9-11 are planar ( approximately 90%). The relations between volume and length and area and length were also examined and found to scale as power laws. Furthermore, the bifurcation angles follow the minimum energy hypothesis but with significant scatter. Some of the applications of the semiautomated extraction of morphometric data in applications to coronary physiology and pathophysiology are highlighted.
Rerouting Radical Cascades: Intercepting the Homoallyl Ring Expansion in Enyne Cyclizations via C–S Scission (2014)

The switch from 5-exo- to 6-endo-trig selectivity in the radical cyclization of aromatic enynes was probed via the combination of experimental and computational methods. This transformation occurs by kinetic self-sorting of the mixture of four equilibrating radicals via 5-exo-trig cyclization, followed by homoallyl (3-exo-trig/fragmentation) ring expansion to afford the benzylic radical necessary for the final aromatizing C-C bond fragmentation. The interception of the intermediate 5-exo-trig product via β-scission of a properly positioned weak C-S bond provides direct mechanistic evidence for the 5-exo cyclization/ring expansion sequence. The overall cascade uses alkenes as synthetic equivalents of alkynes for the convenient and mild synthesis of Bu3Sn-functionalized naphthalenes.
Mechanistic and Synthetic Aspects of Atom Transfer Radical Polymerization (1997)

Abstract Mechanistic and synthetic aspects of atom transfer radical polymerization (ATRP) are reviewed. This controlled/“living” system polymerizes many monomers including styrenes, (meth)acrylates, acrylonitrile and dienes. The halogen end groups can be converted to other functional groups such as amines and azides. In addition to producing well-defined linear homopolymers, statistical copolymers, block copolymers, and gradient copolymers, ATRP can be used to synthesize graft and hyperbranched copolymers through copolymerization with functionalized monomers. Selection of appropriate conditions for ATRP depends on targeted molecular weight and degree of polymer chain end-functionality and includes considering the monomer(s) to be polymerized, initiator structure/reactivity, amount of catalyst/deactivator used, halogen end-group used, and temperature.
Reduction in blood pressure in normal and spontaneously hypertensive rats by lergotrile mesylate (1979)

Abstract The acute administration of lergotrile mesylate to normal or spontaneously-hypertensive rats (SHR) causes a prompt reduction in blood pressure. In SHR, doses as small as 0·05 mg kg−1 are effective; maximal reductions in blood pressure are obtained at a dose of 0·25 mg kg−1. Lergotrile may be administered intraperitoneally or orally. Its efficacy as an antihypertensive agent in rats does not diminish significantly when administered twice daily for 7 days. Although lergotrile has been reported to be a dopamine agonist, the present data do not establish the mechanism by which the drug lowers blood pressure.
Bimodal multicast (1999)

There are many methods for making a multicast protocol “reliable.” At one end of the spectrum, a reliable multicast protocol might offer tomicity guarantees, such as all-or-nothing delivery, delivery ordering, and perhaps additional properties such as virtually synchronous addressing. At the other are protocols that use local repair to overcome transient packet loss in the network, offering “best effort” reliability. Yet none of this prior work has treated stability of multicast delivery as a basic reliability property, such as might be needed in an internet radio, television, or conferencing application. This article looks at reliability with a new goal: development of a multicast protocol which is reliable in a sense that can be rigorously quantified and includes throughput stability guarantees. We characterize this new protocol as a “bimodal multicast” in reference to its reliability model, which corresponds to a family of bimodal probability distributions. Here, we introduce the protocol, provide a theoretical analysis of its behavior, review experimental results, and discuss some candidate applications. These confirm that bimodal multicast is reliable, scalable, and that the protocol provides remarkably stable delivery throughput.
Three-Dimensionally Engineered Normal Human Lung Tissue-Like Assemblies: Target Tissues for Human Respiratory Viral Infections (2008)

In vitro three-dimensional (3D) human lung epithelio-mesenchymal tissue-like assemblies (3D hLEM TLAs) from this point forward referred to as TLAs were engineered in Rotating Wall Vessel (RWV) technology to mimic the characteristics of in vivo tissues thus providing a tool to study human respiratory viruses and host cell interactions. The TLAs were bioengineered onto collagen-coated cyclodextran microcarriers using primary human mesenchymal bronchial-tracheal cells (HBTC) as the foundation matrix and an adult human bronchial epithelial immortalized cell line (BEAS-2B) as the overlying component. The resulting TLAs share significant characteristics with in vivo human respiratory epithelium including polarization, tight junctions, desmosomes, and microvilli. The presence of tissue-like differentiation markers including villin, keratins, and specific lung epithelium markers, as well as the production of tissue mucin, further confirm these TLAs differentiated into tissues functionally similar to in vivo tissues. Increasing virus titers for human respiratory syncytial virus (wtRSVA2) and the detection of membrane bound glycoproteins over time confirm productive infection with the virus. Therefore, we assert TLAs mimic aspects of the human respiratory epithelium and provide a unique capability to study the interactions of respiratory viruses and their primary target tissue independent of the host s immune system.
Multispectral skin imaging for biometrics (2004)

Multispectral imaging of skin represents a novel method to make an improved biometric determination of identity. Multispectral imaging provides a means to image both the surface characteristics and subsurface skin features, offering the promise of a sensor that has improved performance, works under adverse conditions and is difficult to spoof.
Outdoor measurement of SAR (specific absorption rate) in a full-sized human model exposed to 29. 9 MHz in the near field (1989)

Localized and averaged specific absorption rates (SARs) were obtained in a full-size muscle-equivalent human model exposed to near-field 29.9-MHz irradiation at an outdoor facility. The model was positioned erect on a metallic groundplane 1.22 m (4 ft) from the base of a 10.8-m (35 ft) whip antenna with an input power of 1.0 kW. For whole-body SAR, a mean value of 0.83 W/kg was determined using two gradient-layer calorimeters in a twin-well configuration. The localized SARs at 12 body locations were measured using nonperturbing temperature probes and were highest in the ankle region. It is concluded that average SAR measurements in a full-size phantom are feasible using a twin-calorimeter approach; measurements in the field are practical when human-size (183 x 61 x 46 cm) calorimeters are used.
Diffractive optical elements for spectral imaging (2000)

Diffractive optical elements fabricated on flat and non-flat substrates frequently act as dispersive elements in imaging spectrometers. We describe the design and electron-beam fabrication of blazed and computer-generated-hologram gratings for slit and tomographic imaging spectrometers.
Novel Hybrid Inorganic-Organic Abrasion-Resistant Coatings Prepared by a Sol-Gel Process (1994)

Abstract Novel abrasion-resistant coatings prepared by a sol-gel process have been developed and applied on the polymeric substrate Bisphenol A polycarbonate. In general, coatings utilize either 4,4′-diaminodiphenyl sulfone (DDS) or diethylenetriamine (DETA) that are then functionalized at their amine groups with 3-isocyanatopropyltriethoxysilane. Following functionalization, these coating materials are then spin coated onto bisphenol A polycarbonate sheet and cured. These reactants undergo a comparable sol-gel reaction similar to typical metal alkoxide chemistry, thereby producing an insoluble network material containing a good dispersion of the functionalized organic along with the hydrolyzed and condensed silicon alkoxide groups. The final coating is transparent and of a few microns in thickness. Following curing, an index of the abrasion resistance is assessed by an optical method, and the adhesion behavior of the coatings is investigated and quantified. It is demonstrated that these thin transparent coatings do provide considerable abrasion resistance over and above that of the uncoated polymeric substrate.
Hybrid backscatter communication for wireless powered communication networks (2016)

We propose hybrid backscatter communication for wireless powered communication networks (WPCNs) to increase transmission range and provide uniform rate distribution in heterogeneous network (HetNet) environment. In such HetNet where the TV tower or high-power base station (macrocell) coexists with densely deployed small-power access points (e.g., small-cells or WiFi), users can operate in either dedicated bistatic scatter or ambient backscatter, given that the harvested energy from the dedicated or ambient RF signals may not be sufficient to support the existing harvest-then-transmit (HTT) protocol for WPCNs. Considering this dual mode operation, we formulate throughput maximization problem depending on the user location, namely indoor or outdoor zone. After showing the optimal time allocation for the dual mode operation, we show that the performance of the proposed hybrid backscatter communication is superior to the other schemes.
Distilling Knowledge from Deep Networks with Applications to Healthcare Domain (2015)

Exponential growth in Electronic Healthcare Records (EHR) has resulted in new opportunities and urgent needs for discovery of meaningful data-driven representations and patterns of diseases in Computational Phenotyping research. Deep Learning models have shown superior performance for robust prediction in computational phenotyping tasks, but suffer from the issue of model interpretability which is crucial for clinicians involved in decision-making. In this paper, we introduce a novel knowledge-distillation approach called Interpretable Mimic Learning, to learn interpretable phenotype features for making robust prediction while mimicking the performance of deep learning models. Our framework uses Gradient Boosting Trees to learn interpretable features from deep learning models such as Stacked Denoising Autoencoder and Long Short-Term Memory. Exhaustive experiments on a real-world clinical time-series dataset show that our method obtains similar or better performance than the deep learning models, and it provides interpretable phenotypes for clinical decision making.
Automatic multi-phase digital pulse width modulator (2010)

Current demands on switched-mode power supplies to deliver higher output power with improved efficiency are leading to an increased use of multi-phase power converters. With an increasing number of phases, special multi-phase digital pulse width modulators (DPWMs) prove advantageous over the parallel use of conventional DPWMs. In this paper a ¿smart¿ multi-phase DPWM is presented which incorporates a duty cycle distribution algorithm. This algorithm is based on the fastest execution of the duty cycle input command with respect to the number of switching actions per phase and switching cycle. The system provides good dynamic current sharing during transients and enables the use of ¿faster¿ digital loop compensators. Intrinsic support of a variable number of active phases (phase-shedding operation) and improved scalability over conventional designs complete the feature set. The proposed system has been implemented on an FPGA system and tested with a four-phase buck converter.
Microwave multipolar plasmas excited by distributed electron cyclotron resonance: Concept and performance (1988)

Distributed electron cyclotron resonance or DECR, a new plasma excitation technique well adapted to microwave multipolar plasmas, is described. The novel reactor concept is based upon the use of several microwave linear applicators working at the ECR mode along the multipolar confinement magnets. At a microwave frequency of 2.45 GHz, large volumes of highly homogeneous plasmas with an electron temperature of the order of 3 eV and ion densities better than 1011 cm−3 are currently being produced in DECR reactors.
Rational engineering of a native hyperthermostable lactonase into a broad spectrum phosphotriesterase (2017)

The redesign of enzyme active sites to alter their function or specificity is a difficult yet appealing challenge. Here we used a structure-based design approach to engineer the lactonase SsoPox from Sulfolobus solfataricus into a phosphotriesterase. The five best variants were characterized and their structure was solved. The most active variant, αsD6 (V27A-Y97W-L228M-W263M) demonstrates a large increase in catalytic efficiencies over the wild-type enzyme, with increases of 2,210-fold, 163-fold, 58-fold, 16-fold against methyl-parathion, malathion, ethyl-paraoxon, and methyl-paraoxon, respectively. Interestingly, the best mutants are also capable of degrading fensulfothion, which is reported to be an inhibitor for the wild-type enzyme, as well as others that are not substrates of the starting template or previously reported W263 mutants. The broad specificity of these engineered variants makes them promising candidates for the bioremediation of organophosphorus compounds. Analysis of their structures reveals that the increase in activity mainly occurs through the destabilization of the active site loop involved in substrate binding, and it has been observed that the level of disorder correlates with the width of the enzyme specificity spectrum. This finding supports the idea that active site conformational flexibility is essential to the acquisition of broader substrate specificity.
A 1 cm/spl times/1 cm In/sub 0.53/Ga/sub 0.47/As-In/sub 0.52/Al/sub 0.48/As avalanche photodiode array (2005)

We report a 1 cm/spl times/1 cm array of 100 In/sub 0.53/Ga/sub 0.47/As-In/sub 0.52/Al/sub 0.48/As avalanche photodiodes (APD). The average breakdown voltage was 28.7 V with a standard deviation of less than 0.5 V. The distribution of breakdown voltage across the area followed a radial pattern consistent with a slight epitaxial growth nonuniformity. The mean dark current at a gain of 10, or 6.1 A/W, was 10.3 nA, and none of the 100 APDs had a dark current of more than 25 nA. The bandwidth at a gain of 10 was 6.2 GHz, and the maximum gain-bandwidth product was 140 GHz. This technology is ideally suited for next-generation three-dimensional imaging applications.
Closed-Loop Asynchronous Neuromuscular Electrical Stimulation Prolongs Functional Movements in the Lower Body (2015)

Neuromuscular electrical stimulation (NMES) is commonly used in rehabilitative settings and is also used for assistive purposes to create functional movements, where it is termed functional electrical stimulation (FES). One limitation of NMES/FES is early onset of muscle fatigue. NMES-induced fatigue can be reduced by switching between multiple stimulation channels that target different motor units or synergistic muscles (i.e., asynchronous stimulation). However, switching stimulation channels introduces additional complexity due to the need to consider the switching dynamics and differing muscle response to stimulation. The objective of this study was to develop and test a closed-loop controller for asynchronous stimulation. The developed closed-loop controller yields asymptotic tracking of a desired trajectory for a person's knee-shank complex despite switching between stimulation channels. The developed controller was implemented on four able-bodied individuals with four-channel asynchronous stimulation as well as single-channel conventional stimulation. The results indicate that asynchronous stimulation extends the duration that functional movements can be performed during feedback control. This result is promising for the implementation of asynchronous stimulation in closed-loop rehabilitative procedures and in assistive devices as a method to reduce muscle fatigue while maintaining a person's ability to track a desired limb trajectory.
Determination of calibration parameters of a VRX CT system using an "Amoeba" algorithm. (2004)

Efforts to improve the spatial resolution of CT scanners have focused mainly on reducing the source and detector element sizes, ignoring losses from the size of the secondary-ionization charge "clouds" created by the detected x-ray photons, i.e., the "physics limit." This paper focuses on implementing a technique called "projective compression." which allows further reduction in effective cell size while overcoming the physics limit as well. Projective compression signifies detector geometries in which the apparent cell size is smaller than the physical cell size, allowing large resolution boosts. A realization of this technique has been developed with a dual-arm "variable-resolution x-ray" (VRX) detector. Accurate values of the geometrical parameters are needed to convert VRX outputs to formats ready for optimal image reconstruction by standard CT techniques. The required calibrating data are obtained by scanning a rotating pin and fitting a theoretical parametric curve (using a multi-parameter minimization algorithm) to the resulting pin sinogram. Excellent fits are obtained for both detector-arm sections with an average (maximum) fit deviation of ~0.05 (0.1) detector cell width. Fit convergence and sensitivity to starting conditions are considered. Pre- and post-optimization reconstructions of the alignment pin and a biological subject reconstruction after calibration are shown.
Anode‐Supported Tubular Micro‐Solid Oxide Fuel Cell (2007)

A tubular anode‐supported “micro‐solid oxide fuel cell” (μSOFC) has been developed for producing high volumetric power density (VPD) SOFC systems featuring rapid turn on/off capability. An electrophoretic deposition (EPD)‐based, facile manufacturing process is being refined to produce the anode support, anode functional and electrolyte layers of a single cell. μSOFCs (diameter <5 mm) have two main potential advantages, a substantial increase in the electrolyte surface area per unit volume of a stack and also rapid start‐up. As fuel cell power is directly proportional to the active electrolyte surface area, a μSOFC stack can substantially increase the VPD of an SOFC device. A decrease in tube diameter allows for a reduction in wall thickness without any degradation of a cell's mechanical properties. Owing to its thin wall, a μSOFC has an extremely high thermal shock resistance and low thermal mass. These two characteristics are fundamental in reducing start‐up and turn‐off time for the SOFC stack. Traditionally, SOFC has not been considered for portable applications due to its high thermal mass and low thermal shock resistance (start‐up time in hours), but with μSOFCs' potential for rapid start‐up, new possibilities for portable and transportable applications open up.
Cyclomarins A−C, New Antiinflammatory Cyclic Peptides Produced by a Marine Bacterium (<i>Streptomyces</i> sp.) (1999)

Three new cyclic heptapeptides, cyclomarins A−C (1−3), were isolated from extracts of a cultured marine bacterium collected in the vicinity of San Diego, CA. The major metabolite, cyclomarin A (1), contains three common and four unusual (or unique) amino acids. The structures of the new metabolites were determined using 1D and 2D NMR methods, and the stereochemistry was determined from an X-ray crystal structure of the diacetate derivative of 1. Cyclomarin A (1) displays significant antiinflammatory activity in both in vivo and in vitro assays.