gebhart/patrepeval huggingface dataset:
Production and Characterization of a Novel Bioflocculant from <i>Bacillus licheniformis</i> (2010)

A bacterium producing an extracellular bioflocculant was isolated from contaminated LB medium and identified as Bacillus licheniformis by 16S rRNA gene sequencing and its biochemical/physiological characteristics. The optimum culture conditions for flocculant production were an initial medium pH of 7.2 and an inoculum size of 4% (vol/vol). The maximum flocculating activity (700 U/ml) was obtained after cultivation at 37 degrees C for 48 h. Chemical analyses of the purified bioflocculant revealed that it was a proteoglycan composed of 89% carbohydrate and 11% protein (wt/wt). The mass ratio of neutral sugar, amino sugar, and uronic acid was measured at 7.9:4:1. Infrared spectrometry further indicated the presence of carboxyl, hydroxyl, and amino groups, typical of heteropolysaccharide. The average mass of the bioflocculant was calculated to be 1.76 x 10(6) Da. Scanning electron microscopy (SEM) images of the bioflocculant showed an irregular structure with netted texture. Its efficient flocculation capabilities suggest potential applications in industry.
The D* Symbolic Differentiation Algorithm (2007)

Functions with densely interconnected expression graphs, which arise in applications such as dynamics, space-time optimization, and PRT, can be difficult to efficiently differentiate using existing symbolic or automatic differentiation techniques. The new algorithm, D*, computes efficient symbolic derivatives for these functions by symbolically executing the expression graph at compile time to eliminate common subexpressions and by exploiting the special nature of the graph that represents the derivative of a function. This graph has a sum of products form; the new algorithm computes a factorization of this derivative graph along with an efficient grouping of product terms into subexpressions. This paper is a revised and expanded version of the paper presented at SIGGRAPH 2007, most recently updated 11/1/2007.
Synthetic Approaches to <i>N</i><sup>δ</sup>-Methylated <scp>l</scp>-Arginine, <i>N</i><sup>ω</sup>-Hydroxy-<scp>l</scp>-arginine, <scp>l</scp>-Citrulline, and <i>N</i><sup>δ</sup>-Cyano-<scp>l</scp>-ornithine (2008)

Nomega-Methylated arginines such as asymmetric dimethyl-L-arginine (ADMA) and monomethyl-l-arginine (NMMA) are known as potent physiological inhibitors of nitric oxide synthases (NOSs). To explore a possible physiological and pharmaceutical relevance of N(delta)-methylated analogues, a synthetic scheme had to be developed that would not lead to N(delta)-methyl-L-arginine only but also to its presumed metabolites of NOS catalysis. Two basic synthetic approaches have been pursued to obtain N(delta)-methylated derivatives of L-ornithine, L-citrulline, L-arginine, and N(omega)-hydroxy-L-arginine. A first attempt utilized conventionally protected L-ornithine, i.e., the tert-butyl ester and Boc-amine, and led to three end compounds in excellent yields. Simultaneous protection of the alpha-amino acid moiety by formation of boroxazolidinones, particularly by employing 9-borabicyclo[3.3.1]nonane (9-BBN-H), proved to be a convenient option to perform side chain modifications and led to all of the desired end compounds. Additionally, enantiomeric excess (ee, %) of crucial synthetic intermediates and end compounds was determined by chiral HPLC.
Synthesis of cyclic carbonates from epoxides and carbon dioxide using bimetallic aluminum(salen) complexes (2012)

Over the last six years, highly active catalysts for the synthesis of cyclic carbonates from epoxides and carbon dioxide have been developed. Initial studies showed that bimetallic aluminium(salen) complexes [Al(salen)]2O formed active catalysts and kinetic studies allowed the catalytic cycle to be determined. The catalysts could be immobilized on silica, allowing them to be used in a gas phase flow reactor as well as in batch reactors. The compatibility of the catalysts with waste carbon dioxide present in power station flue gas has been investigated and studies to enhance the commercial applicability of the catalysts by reducing the cost of their production carried out.
Synthesis and biological effects of novel thiocolchicines. 3. evaluation of N-acyldeacetylthiocolchicines, N-(alkoxycarbonyl)deacetylthiocolchicines, and O-ethyldemethylthiocolchicines. New synthesis of thiodemecolcine and antileukemic effects of 2-demethyl- and 3-demethylthiocolchicine (1985)

Novel and known analogues of thiocolchicine were evaluated in vitro in a tubulin binding assay and in vivo in mice for acute toxicity and in the P388 lymphocytic leukemia assay. This evaluation included N-acyldeacetylthiocolchicines, N-(alkoxycarbonyl)deacetylthiocolchicines, thiodemecolcine and its methyl carbamate, and O-ethyl ethers of demethylthiocolchicines. Selective ether cleavage of thiodemecolcine with concentrated sulfuric acid at 50 degree C afforded the 2-demethyl congener, characterized as its N,O-diacetyl derivative. Several of the compounds showed high potency in the tubulin binding assay, matching the potency of colchicine. Several N-(alkoxycarbonyl)deacetylcolchicines (carbamates) exhibited strong binding affinity to tubulin but had only weak activities against the P388 tumor system, suggesting that other factors besides tubulin binding may be important for the biological effects. The compounds potent in the tubulin binding assay and in the P388 leukemia assay in mice were generally also toxic to mice in the acute toxicity test, showing thus a similar behavior of thiocolchicines to that observed earlier with colchicines. A considerable amount of data collected for 2-demethyl- and 3-demethylthiocolchicine suggests that the latter represents a broad-spectrum antitumor agent of considerable promise and possibly a less toxic substitute for colchicine.
A linear programming approach to inverse planning in radiosurgery (2018)

Leksell Gamma Knife is a stereotactic radiosurgery system that allows fine-grained control of the delivered dose distribution. However, inverse planning is required to make its full potential clinically accessible. We describe a new inverse planning approach, which both addresses several shortcomings of earlier approaches and unlocks new capabilities. 
We formulate the inverse planning as a convex optimization problem by fixing the isocenter positions and performing sector-duration optimization. The cost function is defined as a weighted sum of objectives, such as coverage, selectivity and beam-on time, where each weight determines the importance of the corresponding objective. By introducing auxiliary variables, we reformulate the objectives corresponding to both the dose and the beam-on time in a way that ultimately results in a linear programming program. Even though linear programming problems are among the simplest optimization problems, we describe two techniques - representative subsampling and dualization - that drastically reduce the dimensionality of the problem and thus further reduce the solution time. 
We illustrate the capabilities of the proposed inverse planner on two cases: a large meningioma with three adjacent organs at risk and a case with six brain metastases. In both cases we found that it was possible to achieve a plan quality at least as good as a clinically acceptable reference plan or to achieve substantially reduced beam-on times at the cost of a small degradation of plan quality. We also show that it is possible to perform dose painting and to create a plan with a homogeneous dose distribution. The optimization times were at most half a minute, but often just a few seconds. 
We propose a new inverse planner for radiosurgery that is fast and convex. It produces reproducible results and can handle both multiple targets and organs at risk.
SSIM-inspired divisive normalization for perceptual video coding (2011)

We propose a perceptual video coding framework based on an SSIM-inspired divisive normalization scheme as an attempt to transform the DCT domain frame prediction residuals to a perceptually uniform space before coding. Based on the residual divisive normalization process, we define a distortion model for mode selection and show that such a divisive normalization strategy largely simplifies the subsequent perceptual rate-distortion optimization procedure. Experiments demonstrate that the proposed scheme can achieve significant gain in terms of rate-SSIM performance in comparison with H.264/AVC.
Highly efficient full-length hepatitis C virus genotype 1 (strain TN) infectious culture system (2012)

Chronic infection with hepatitis C virus (HCV) is an important cause of end stage liver disease worldwide. In the United States, most HCV-related disease is associated with genotype 1 infection, which remains difficult to treat. Drug and vaccine development was hampered by inability to culture patient isolates representing HCV genotypes 1-7 and subtypes; only a recombinant 2a genome (strain JFH1) spontaneously replicated in vitro. Recently, we identified three mutations F1464L/A1672S/D2979G (LSG) in the nonstructural (NS) proteins, essential for development of full-length HCV 2a (J6) and 2b (J8) culture systems in Huh7.5 cells. Here, we developed a highly efficient genotype 1a (strain TN) full-length culture system. We initially found that the LSG substitutions conferred viability to an intergenotypic recombinant composed of TN 5' untranslated region (5'UTR)-NS5A and JFH1 NS5B-3'UTR; recovered viruses acquired two adaptive mutations located in NS3 and NS4B. Introduction of these changes into a replication-deficient TN full-length genome, harboring LSG, permitted efficient HCV production. Additional identified NS4B and NS5B mutations fully adapted the TN full-length virus. Thus, a TN genome with 8 changes (designated TN cell-culture derived, TNcc) replicated efficiently and released infectious particles of ∼5 log(10) focus-forming units per mL; passaged TNcc did not require additional changes. IFN-α and directly acting antivirals targeting the HCV protease, NS5A, and NS5B, each inhibited full-length TN infection dose-dependently. Given the unique importance of genotype 1 for pathogenesis, this infectious 1a culture system represents an important advance in HCV research. The approach used and the mutations identified might permit culture development for other HCV isolates, thus facilitating vaccine development and personalized treatment.
Power supply voltage detection and clamping circuit for 3-D integrated circuits (2014)

A circuit that detects and sets the power supply voltage of a given device plane in a 3-D IC is proposed. The circuit consists of 1) a ring oscillator in each voltage domain located in each device plane, and 2) a power module placed in a dedicated power plane. The power module consists of four components; a divide-by-40 clock divider, a frequency detector, a voltage ramp generator, and a voltage peak detector circuit. The power module provides a stable reference voltage equal to the power supply voltage of the targeted voltage domain in the device plane. SPICE simulations of the circuit indicate that power supply voltages of less than 1 V are successfully set and provided as a reference to an on-chip voltage regulator within 500 ns and with reference voltage variation of less than 1%. The power module is integrated with on-chip voltage regulators which require a precise voltage reference. The proposed implementation permits dynamic voltage and frequency scaling and point of load power delivery.
Comprehensive detection of counterfeit ICs via on-chip sensor and post-fabrication authentication policy (2017)

Counterfeit integrated circuits (ICs) have posed a major security and safety threat on commercial and mission-critical systems. In this paper, we propose to develop a comprehensive counterfeit ICs detection and prevention strategy, consisting of an innovative multi-functional on-chip sensor and a related post-fabrication authentication methodology. We target at many counterfeit ICs including the recycled/remarked/out-of-spec ICs, as well as cloned and over-produced ICs. First, the new sensor consists of antifuse memory and aging sensors to reduce reference circuit related area overhead of those sensor circuits. Second, the new sensor combines both the ring-oscillator based aging sensor with recently proposed electromigration(EM)-based aging sensor so that it can be effective for estimation of both short and long period time of chip usage. Third, on top of the new sensor, we propose a new post-fabrication authentication methodology to detect and prevent non-defective counterfeit ICs. Simulation results show the advantage of the proposed multi-functional sensor against existing on-chip sensors in terms of functionality, detection coverage and usage time estimation range and accuracy.
An in-the-ear platform for recording electroencephalogram (2011)

We introduce a novel approach to brain monitoring based on electroencephalogram (EEG) recordings from within the ear canal. While existing clinical and wearable systems are limited in terms of portability and ease of use, the proposed in-the-ear (ITE) recording platform promises a number of advantages including ease of implementation, minimally intrusive electrodes and enhanced accuracy (fixed electrode positions). It thus facilitates a crucial step towards the design of brain computer interfaces that integrate naturally with daily life. The feasibility of the ITE concept is demonstrated with recordings made from electrodes embedded on an earplug which are benchmarked against conventional scalp electrodes for a classic EEG paradigm.
Dye Stabilization and Enhanced Photoelectrode Wettability in Water-Based Dye-Sensitized Solar Cells through Post-assembly Atomic Layer Deposition of TiO<sub>2</sub> (2013)

Detachment (desorption) of molecular dyes from photoelectrodes is one of the major limitations for the long-term operation of dye-sensitized solar cells. Here we demonstrate a method to greatly inhibit this loss by growing a transparent metal oxide (TiO2) on the dye-coated photoelectrode via atomic layer deposition (ALD). TiO2-enshrouded sensitizers largely resist detachment, even in pH 10.7 ethanol, a standard solution for intentional removal of molecular dyes from photoelectrodes. Additionally, the ALD post-treatment renders the otherwise hydrophobic dye-coated surface hydrophilic, thereby enhancing photoelectrode pore-filling with aqueous solution.
Dual Sagnac loop mirror SOA-based widely tunable dual-output port fiber laser (2009)

A widely tunable (30 nm) fiber laser based on a double Sagnac loop mirror configuration is proposed and demonstrated. A semiconductor optical amplifier (SOA) placed between the two loop mirrors acts as the gain medium. The fiber laser has two output ports with adjustable optical power outputs. Wavelength tunability is obtained through the use of a thin film tunable filter, while optical power adjustability is accomplished by proper adjustment of each of the loop mirror reflectivity via a polarization controller. A total output power of + 9 dBm is measured and the potential for higher output powers is discussed. Optical power stability of better than +/- 0.15 dB is measured for 6 hours.
Model checking of hierarchical state machines (2001)

Model checking is emerging as a practical tool for detecting logical errors in early stages of system design. We investigate the model checking of sequential hierarchical (nested) systems, i.e., finite-state machines whose states themselves can be other machines. This nesting ability is common in various software design methodologies, and is available in several commercial modeling tools. The straightforward way to analyze a hierarchical machine is to flatten it (thus incurring an exponential blow up) and apply a model-checking tool on the resulting ordinary FSM. We show that this flattening can be avoided. We develop algorithms for verifying linear-time requirements whose complexity is polynomial in the size of the hierarchical machine. We also address the verification of branching time requirements and provide efficient algorithms and matching lower bounds.
Immunobiology of Myasthenia Gravis, Experimental Autoimmune Myasthenia Gravis, and Lambert-Eaton Syndrome (1985)

Exhausted CD8 T (Tex) cells are a distinct cell lineage that arise during chronic infections and cancers in animal models and humans. Tex cells are characterized by progressive loss of effector functions, high and sustained inhibitory receptor expression, ...Read More
P2P Live Streaming Towards Best Video Quality (2008)

While the overall bandwidth of peer-to-peer live video streaming system scales automatically as peers collectively contribute the bandwidth, each peer also demands to download at the specified video playback rate so as to play the video smoothly. Therefore, a fundamental problem arisen is how to balance the bandwidth supply and demand in the peer-to-peer system to enjoy peers with the best video quality. To address this problem, we propose a fully distributed peer-to-peer video streaming framework which automatically adapts the network towards full bandwidth utilization. Our design possesses two unique features. First, a special <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">link-level homogenous</i> overlay network is formed in which all the overlay links approach to have an identical bandwidth value. With such a feature, video flowing through the overlay links will not encounter any bottlenecks, and peers can thus achieve the guaranteed downloading rates. Second, based on the peer downloading rate observed locally at the streaming server, the server can adaptively adjust the video playback rate so that peers can achieve the best video quality with full bandwidth utilization. The effectiveness of our framework is verified through extensive simulations.
A surgically-implanted intramuscular electrode for an implantable neuromuscular stimulation system (1994)

An intramuscular electrode has been developed for use with an implantable neuromuscular stimulator. In vitro tests indicate that the electrode will maintain a stable position within the muscle, but is capable of being removed intact. When tested in a buffered saline environment at the maximum stimulation parameters (0.4 /spl mu/C/mm/sup 2//phase), there was no corrosion of the stimulating surface. In vivo evaluations were conducted, in which four sets of 4 intramuscular electrodes and 4 epimysial electrodes, were surgically implanted in the forelimb of 4 dogs. Each set was connected to an implanted neuromuscular stimulator. All but 1 of the 16 intramuscular electrodes operated properly throughout the study, producing responses functionally indistinguishable from epimysial electrodes. One electrode fractured due to improper surgical placement. After removal, some pitting corrosion was observed in 2 of the 15 retrieved intramuscular electrodes, possibly due to minute surface defects resulting from the electrode manufacturing process.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Characterization of Noribogaine at nAChRs and Effect on Nicotine Self‐Administration in Rats (2015)

Noribogaine, a polypharmacological drug with activities at opioid receptors, ionotropic nicotinic receptors, and serotonin reuptake transporters, is being investigated for treatment of substance abuse‐related disorders. In this study, noribogaine molecular activity at neuronal nicotinic acetylcholine receptors (nAChRs) was characterized. Noribogaine inhibited α3β4, α7 nAChRs, and endogenously expressed habenula‐type α3‐(α5, β2, β4) nAChRs populations. Anti‐addictive compounds ibogaine, 18MC‐ a synthetic derivative of coronaridine, and mecamylamine were tested in parallel. Then, noribogaine was tested for use as a treatment for nicotine dependence in a nicotine self‐administration study in rats in comparison to varenicline, an approved medication for smoking cessation. After initial food pellet training, followed by 26 sessions of nicotine self‐administration training, the rats were administered noribogaine (12.5, 25 or 50 mg/kg p.o.), noribogaine vehicle, varenicline or saline using a within‐subject design with a latin square test schedule. Noribogaine dose‐dependently decreased nicotine self‐administration by up to 64% of saline treated rats levels and was equi‐effective to varenicline. Noribogaine pharmacological profiling at the nAChRs receptor population and its ability to dose‐dependently attenuate drug‐taking behavior for nicotine supports future studies to assess its potential usefulness in multiple therapeutic arenas, including smoking cessation, substance abuse related disorders, and anxiety related disorders.
High-performance InAs/GaSb superlattice photodiodes for the very long wavelength infrared range (2001)

We report on the demonstration of high-performance p-i-n photodiodes based on type-II InAs/GaSb superlattices with 50% cut-off wavelength λc=16 μm operating at 80 K. Material is grown by molecular beam epitaxy on GaSb substrates with excellent crystal quality as evidenced by x-ray diffraction and atomic force microscopy. The processed devices show a current responsivity of 3.5 A/W at 80 K leading to a detectivity of ∼1.51×1010 cmHz1/2/W. The quantum efficiency of these devices is about 35% which is comparable to HgCdTe detectors with a similar active layer thickness.
Scanning polarization force microscopy: A technique for imaging liquids and weakly adsorbed layers (1995)

The atomic force microscope is used to measure dielectric polarization forces on surfaces induced by a charged tip. On insulators, the major contribution to the surface polarizability at low frequencies is from surface ions. The mobility of these ions depends strongly on the humidity. Using polarization forces we have been able to image liquid films, droplets, and other weakly adsorbed material.
N-version temperature-aware scheduling and binding (2009)

Technology scaling to nanometer nodes causes growing increase in power density and especially leakage that in turn result in locally hot regions on the chip. In this paper, we introduce a novel methodology for temperature-aware design. The methodology embeds N-versions of the scheduler and binder such that the thermal profiles of the versions are distant from each other. Next, instead of using only one version of the scheduler and binder, a rotation of N-versions of the scheduler and binder is constructed for balancing the thermal profile of the chip. We propose a linear programming framework that takes the multiple versions as the input, and constructs the thermal-aware rotational scheduling and binding by selecting the N most efficient versions and by determining the duration of each version. Our experimental evaluation shows a very low overhead and an average 5% decrease in the steady-state peak temperature produced on the benchmark designs compared to using a schedule that balances the amount of usage of different modules.
ChemInform Abstract: STEREOSELECTIVE TOTAL SYNTHESIS OF 1α,25S,26‐TRIHYDROXYCHOLECALCIFEROL (1984)

Abstract Ausgehend von dem lndanderivat (I) wird das Nitron (X) hergestellt, das mit Meth ylacrylat (XI) das Isoxazolidin (XII) bildet.
Discovery of Aminofurazan-azabenzimidazoles as Inhibitors of Rho-Kinase with High Kinase Selectivity and Antihypertensive Activity (2006)

The discovery, proposed binding mode, and optimization of a novel class of Rho-kinase inhibitors are presented. Appropriate substitution on the 6-position of the azabenzimidazole core provided subnanomolar enzyme potency in vitro while dramatically improving selectivity over a panel of other kinases. Pharmacokinetic data was obtained for the most potent and selective examples and one (6n) has been shown to lower blood pressure in a rat model of hypertension.