gebhart/patrepeval huggingface dataset:
Discovery of Imidazo[1,5-<i>a</i>]pyrido[3,2-<i>e</i>]pyrazines as a New Class of Phosphodiesterase 10A Inhibitiors (2010)

Novel imidazo[1,5-a]pyrido[3,2-e]pyrazines have been synthesized and characterized as both potent and selective phosphodiesterase 10A (PDE10A) inhibitors. For in vitro characterization, inhibition of PDE10A mediated cAMP hydrolysis was used and a QSAR model was established to analyze substitution effects. The outcome of this analysis was complemented by the crystal structure of PDE10A in complex with compound 49. Qualitatively new interactions between inhibitor and binding site were found, contrasting with previously published crystal structures of papaverine-like inhibitors. In accordance with the known antipsychotic potential of PDE10A inhibitors, MK-801 induced stereotypy and hyperactivity in rats were reversed by selected compounds. Thus, a promising compound class has been identified for the treatment of schizophrenia that could circumvent side effects connected with current therapies.
Optimization of Potent Hepatitis C Virus NS3 Helicase Inhibitors Isolated from the Yellow Dyes Thioflavine S and Primuline (2012)

A screen for hepatitis C virus (HCV) NS3 helicase inhibitors revealed that the commercial dye thioflavine S was the most potent inhibitor of NS3-catalyzed DNA and RNA unwinding in the 827-compound National Cancer Institute Mechanistic Set. Thioflavine S and the related dye primuline were separated here into their pure components, all of which were oligomers of substituted benzothiazoles. The most potent compound (P4), a benzothiazole tetramer, inhibited unwinding >50% at 2 ± 1 μM, inhibited the subgenomic HCV replicon at 10 μM, and was not toxic at 100 μM. Because P4 also interacted with DNA, more specific analogues were synthesized from the abundant dimeric component of primuline. Some of the 32 analogues prepared retained ability to inhibit HCV helicase but did not appear to interact with DNA. The most potent of these specific helicase inhibitors (compound 17) was active against the replicon and inhibited the helicase more than 50% at 2.6 ± 1 μM.
Optimal Sizing of Second Life Battery to Reduce CO2 Emissions (2012)

Batteries used in electric vehicles cannot be used in the vehicle once the battery capacity falls to 70% to 80%. The remaining capacity of these batteries can be used in various applications so that they can be kept out of landfills. One of the applications is to use the second life batteries to reduce carbon dioxide (CO2) emissions from the grid. The CO2 emissions from the grid are high during the non-peak hours when only the base plants are operating. We charge the second life battery when the power from renewable resources is available and discharge the battery when there is peak load. With the increase in renewable generation such as photo voltaic, wind energy the carbon foot print changes with the hour of the day. The demonstrated technique optimizes the use of second life battery to reduce the emissions considering uncertainties in the load and availability of renewable power.
The Distributed Object Consistency Protocol Version 1.0 (1999)

This report describes a protocol for improving content consistency in web proxy cache servers, which leads to reduced response time and server load. The Distributed Object Consistency Protocol (DOCP) is an extension to HTTP, replacing some of HTTP’s current cache control mechanism. It supports incremental evolution: proxy servers that implement the protocol can interoperate with non-DOCP proxy servers and gradually learn about peers as they are deployed in the network. The DOCP uses a publish/subscribe mechanism with server invalidation when objects change instead of client validation to test for changes. Stronger semantic consistency assures content providers that pages served from cache are the same as are on the master origin server, and assures end users that the information they are getting is fresh, limiting the need to “Reload”. Strong consistency is difficult to achieve in wide area networks, so the DOCP provides “delta consistency”, where an object is consistent for all but a short, bounded time after a modification. This allows the DOCP to meet web user expectations for content availability and responsiveness. Protocol simulation shows that DOCP consumes fewer network and server resources than the current HTTP cache consistency protocol does, while providing greatly improved consistency. DOCP eliminates the need for users and content providers to guess at correct values for HTTP cache control headers by providing a clean framework for wide area web object replication.
Comparative Molecular Field Analysis of the Binding of the Stereoisomers of Fenoterol and Fenoterol Derivatives to the β<sub>2</sub> Adrenergic Receptor (2007)

Stereoisomers of fenoterol and six fenoterol derivatives have been synthesized and their binding affinities for the beta2 adrenergic receptor (Kibeta2-AR), the subtype selectivity relative to the beta1-AR (Kibeta1-AR/Kibeta2-AR) and their functional activities were determined. Of the 26 compounds synthesized in the study, submicromolar binding affinities were observed for (R,R)-fenoterol, the (R,R)-isomer of the p-methoxy, and (R,R)- and (R,S)-isomers of 1-naphthyl derivatives and all of these compounds were active at submicromolar concentrations in cardiomyocyte contractility tests. The Kibeta1-AR/Kibeta2-AR ratios were >40 for (R,R)-fenoterol and the (R,R)-p-methoxy and (R,S)-1-naphthyl derivatives and 14 for the (R,R)-1-napthyl derivative. The binding data was analyzed using comparative molecular field analysis (CoMFA), and the resulting model indicated that the fenoterol derivatives interacted with two separate binding sites and one steric restricted site on the pseudo-receptor and that the chirality of the second stereogenic center affected Kibeta2 and subtype selectivity.
Near-infrared fluorescence contrast-enhanced imaging with area illumination and area detection: the forward imaging problem (2003)

Fluorescence frequency-domain photon migration measurements were acquired from tissue phantoms, each containing a fluorescent target, by means of area illumination and area detection on the same surface and for the first time, to our knowledge, compared with predictions computed with a numerical solution to the coupled photon diffusion equations. We accomplished area illumination and area detection using a planar, intensity-modulated excitation light source and a gain-modulated intensified charge-coupled device camera, respectively. A 1-ml vessel containing 1-microm solution of Indocyanine Green in 1% Liposyn was immersed 1 cm deep in each 512-ml tissue phantom. For most tissue phantoms, the background surrounding the 1-ml target was composed of Liposyn solution containing Indocyanine Green or 3,3'-Diethylthiatricarbocyanine Iodide such that the target-to-background ratio of fluorescence yield was > or = 10:1. Measurements of fluorescence modulation amplitude and phase were predicted with a mean error ranging from 10.1% to 13.6% and 0.56 degrees to 1.72 degrees, respectively. These numbers are similar to those obtained by use of single-pixel frequency-domain photon migration techniques and validate the potential use of area illumination and area detection for biomedical imaging of tissues. Results also demonstrate that target-to-background ratios of fluorescence yield and fluorescence lifetime significantly affect target detectability.
A new approach to very high resolution mini-brain PET using a small number of large detectors (1990)

A novel very-high-resolution positron emission tomography (PET) using only a small number of large detectors in a circular ring format with collimating apertures is proposed, and a design example is given. The proposed system is ideally suited for very-high-resolution brain imaging, i.e. close to 2 mm FWHM (full width at half maximum) resolution, and can be converted to a medium-resolution system by simply changing the size of the collimating aperture if higher-sensitivity operation is desired. The basic concept of the system design is the optimization of the detector size and system diameter. The former relates to the detection efficiency and photon spillage and penetration to adjacent crystals, while the latter (system diameter) relates to the overall system sensitivity. Since conventional sampling schemes are unlikely to satisfy the sampling requirements for such a system where only a small number of large detectors are arranged in a circular ring format, a sequentially arranged collimating aperture rotating-ring detector (SCARD) scheme has been developed. This scheme makes it possible to sample the object space finely enough for image reconstruction.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
High Frequency Power Distribution Unit (HFPDU) for MRI systems (2017)

To reduce the cost and footprint of a Magnetic Resonant Imaging (MRI) scanner setup in a hospital, a modification in the existing power architecture of the MRI system has been proposed. A high frequency alternative for the frontend bulky low frequency transformer has been proposed. The implementation challenges and workaround solutions for the High Frequency Power Distribution Unit (HFPDU) has been explored and the experimental setup and results are discussed in the paper.
100 Gb/s per-channel free-space optical transmission with coherent detection and MIMO processing (2009)

We experimentally demonstrate the first 100 Gb/s per-channel free-space optical transmission using polarization-multiplexed QPSK, coherent detection, and MIMO processing. This is the highest per-channel FSO rate yet reported, highly-suitable for short-distance 100 Gb/s fiber backhaul.
Stabilizer and surgical arm design for cardiac surgery (2002)

Presents the design of a cardiac tissue stabilizing device with fixating surgical arm, developed for open-heart cardiac surgery to stabilize anastomosis sites during off-pump coronary artery bypass grafting surgeries. The stabilization device is a "C"-shaped hollow ring that holds the heart using vacuum pressure. The arm is a seven link, 18-DOF, redundant, passive, serial linkage. As it attaches directly to the patient on the chest retractor, the arm has a stable mechanical ground protecting the patient from injury should they move during surgery. Measured forces and torques from two pigs' hearts were scaled to human magnitudes to determine stabilizer lifting and arm braking requirements.
Rectifying rolling shutter video from hand-held devices (2011)

This paper presents a method for rectifying video sequences from rolling shutter (RS) cameras. In contrast to previous RS rectification attempts we model distortions as being caused by the 3D motion of the camera. The camera motion is parametrised as a continuous curve, with knots at the last row of each frame. Curve parameters are solved for using non-linear least squares over inter-frame correspondences obtained from a KLT tracker. We have generated synthetic RS sequences with associated ground-truth to allow controlled evaluation. Using these sequences, we demonstrate that our algorithm improves over two previously published methods. The RS dataset is available on the web to allow comparison with other methods.
Development of Methicillin Resistance in Clinical Isolates of <i>Staphylococcus sciuri</i> by Transcriptional Activation of the <i>mecA</i> Homologue Native to the Species (2003)

The beta-lactam resistance gene mecA was acquired by Staphylococcus aureus from an extraspecies source. The search for the possible origin of this gene has led to the identification of a close structural homologue of mecA as a native gene in the animal species Staphylococcus sciuri. Surprisingly, the overwhelming majority of S. sciuri isolates were fully susceptible to beta-lactam antibiotics in spite of the ubiquitous presence of the mecA homologue in the bacteria. We now describe two unusual S. sciuri strains isolated from humans-SS-37 and SS-41-that showed resistance to methicillin associated with high rates of transcription of the mecA homologue and production of a protein resembling penicillin binding protein 2a, the gene product of S. aureus mecA. In strain SS-37 increased transcription of the mecA homologue was related to insertion of an IS256 element upstream of the structural gene, and strain SS-41 had single nucleotide alterations in the promoter region of the mecA homologue which appear to be related to up-regulation of the rate of transcription. A third methicillin-resistant human isolate of S. sciuri that carries both the native mecA homologue and a methicillin-resistant S. aureus (MRSA) type mecA, strain K3, was now shown to be unstable in the absence of drug selection, causing the segregation of antibiotic-susceptible cells accompanied by the loss of the MRSA type mecA. These observations illustrate the remarkable variety of strategies available to bacteria for acquiring mechanisms of drug resistance in the in vivo environment.
Abstract 5520: Therapeutic vaccination with epitope-enhanced and wild-type TARP peptides in stage D0 prostate cancer (2011)

Abstract Background: T-cell receptor alternate reading frame protein (TARP) is immunogenic, is expressed in ∼95% of prostate cancer specimens and hence is a good candidate for therapeutic vaccination. The immunogenicity of HLA-A*0201 binding TARP peptides can be improved through epitope-enhancement achieved by amino acid substitutions that result in increased HLA binding affinity and immunogenicity at least in mice. We conducted a pilot study to determine the safety and immunogenicity of TARP peptide vaccination and its impact on PSA doubling time (PSADT) in men with Stage D0 prostate cancer. Methods: HLA-A*0201 positive men were randomized to receive epitope-enhanced (29-37-9V) or wild type (27-35) TARP peptides administered as a peptide emulsion with Montanide ISA 51VG plus GM-CSF (Arm A) or as an autologous peptide-pulsed dendritic cell vaccine (Arm B). Vaccines are administered q 3 weeks for a total of 5 vaccines with an optional 6th dose of vaccine at 36 weeks based on immune response or PSADT criteria and a booster dose of vaccine for all patients at 48 weeks. Results: 26 patients have enrolled in the study to date (n = 14 Arm A, n = 12 Arm B) with a mean on study duration of 7.5 months. Mean baseline cohort characteristics: age 63 yrs, PSA 4.43, PSADT 7.3 months and Gleason Score 6.7 with 19 of 26 s/p radical prostatectomy. TARP vaccination was safe and well tolerated with adverse events limited to local injection site reactions &lt; Grade 2. Nine of 18 patients (50%) reaching 24 weeks on study were documented to have an increase in their PSADT compared to baseline. Mean Percent Increase/Prolongation in PSADT: Surprisingly TARP-specific IFN-γ ELISPOT responses have been detected ex vivo in only 3 of 14 (21%) patients examined to date. Conclusion: Vaccination with wild type and epitope-enhanced TARP peptides results in prolongation of PSADT in a substantial fraction of patients. The immunologic correlates responsible for PSADT lengthening are poorly understood and require additional study. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 5520. doi:10.1158/1538-7445.AM2011-5520
Sample Treatment Considerations in the Analysis of Organic Colorants by Surface-Enhanced Raman Scattering (2012)

The introduction of surface-enhanced Raman spectroscopy (SERS) in the field of cultural heritage has significantly improved the analysis of the organic dyes and their complexes that have been used as textile dyes and pigments in paintings and other polychrome works of art since antiquity. Over the last five years, a number of different procedures have been developed by various research groups. In this Article, we evaluate the effect of pretreating samples by exposing them to hydrofluoric acid (HF) vapor prior to SERS analysis, a step designed to hydrolyze the dye-metal complexes and increase analyte adsorption on the nanosized metallic support, thus enhancing the SERS signal. Materials studied include pure colorants, commercial lake pigments, and fibers from dyed textiles, as well as actual aged samples, such as microscopic fragments of lakes on paper and ancient pigments and glazes from several works of art, covering a wide range of time, from the second century B.C. to the early 20th century. In each case, SERS spectra obtained with or without HF hydrolysis were critically evaluated. The pretreatment with HF vapor resulted in faster analysis and increased sensitivity in most cases, with the exception of dyed silk fibers, where silk protein hydrolyzates were found to interfere with SERS analysis. As a final point, a two-step procedure including SERS on untreated and treated samples is proposed as a standard approach: by analyzing a sample first without hydrolysis, and then, following removal of the colloid, upon HF treatment, the best and most reliable results for a great number of dyes and substrates are assured.
Complex stiffness quantification using ultrasound stimulated vibrometry (2004)

The propagation speed of shear waves is related to frequency and the complex stiffness (shear elasticity and viscosity) of the medium. A method is presented to solve for complex stiffness of a homogeneous medium by measuring shear wave speed dispersion. Harmonic radiation force, introduced by modulating the energy density of incident ultrasound, is used to generate shear waves of various frequencies in a homogeneous medium. The speed of shear waves is measured from phase shift detected over the distance propagated. Measurements of shear wave speed at multiple frequencies are fit with the theoretical model to solve for the shear elasticity and viscosity of the medium. A laser vibrometer is used in experiments to detect the vibration within gelatin phantoms, which shows promising results validated by an independent complex-stiffness quantification method. Practical considerations and challenges in possible medical applications are discussed.
Replacing and safeguarding pancreatic β cells for diabetes (2015)

Pluripotent stem cells are a scalable source of pancreatic cells for transplantation into patients with diabetes. Here, we describe how the field is gaining momentum toward a β cell replacement therapy.
Formation of large-area GaN nanostructures with controlled geometry and morphology using top-down fabrication scheme (2012)

This paper details the fabrication of GaN nanoscale structures using deep ultraviolet lithography and inductively coupled plasma (ICP) etching techniques. The authors controlled the geometry (dimensions and shape) and surface morphology of such nanoscale structures through selection of etching parameters. The authors compared seven different chlorine-based etch chemistries: Cl2, Ar, Cl2/N2, Cl2/Ar, Cl2/N2/Ar, Cl2/H2/Ar, and Cl2/He/Ar. The authors found that nitrogen plays a significant role in fabricating high quality etched GaN nanostructures. This paper presents the effects of varying the etch parameters, including gas chemistry, gas flow rate, ICP power, rf power, chamber pressure, and substrate temperature, on the etch characteristics, including etch rate, sidewall angle, anisotropy, mask erosion, and surface roughness. Dominant etch mechanisms in relation to the observed characteristics of the etched features are discussed. Utilizing such methods, the authors demonstrated the fabrication of nanoscale structures with designed shapes and dimensions over large area. Nanocolumns with diameter of 120 nm and height of 1.6 μm with sidewall angle of 86° (90° represent a vertical sidewall) were fabricated. Nanocones with tip diameter of 30 nm and height of 1.6 μm with sidewall angle of 70° were demonstrated. Such structures could potentially be used in light-emitting diodes, laser diodes, photodetectors, vertical transistors, field emitters, and photovoltaic devices. This study indicates the feasibility of top-down methods in the fabrication of next-generation nitride-based nanoscale devices, with large-area uniformity and scalability.
Analysis of Downhole Asphaltene Gradients in Oil Reservoirs with a New Bimodal Asphaltene Distribution Function (2011)

Downhole fluid analysis (DFA) has been successfully used to describe reservoir connectivity and fluid properties. DFA not only measures bulk fluid properties such as the gas−oil ratio (GOR), density, and light-end compositions of CO2, CH4, C2H6, C3H8−C5H12 fraction, and hexane and heavier (hexane +) fractions but also color (optical density) that is related to the heavy ends (asphaltenes and resins) in real time at downhole conditions. Therefore, color gradient analysis in oil columns becomes essential to determine reservoir complexities. In this paper, a new bimodal Γ-distribution function (asphaltene molecules + nanoaggregates and clusters) was proposed to characterize asphaltene components. A thermodynamic asphaltene-grading model was also developed to describe equilibrium distributions of heavy ends (heavy resins and asphaltenes) in oil columns using the multicomponent Flory−Huggins regular solution model coupled with a gravitational contribution. The variations of oil properties (such as molar volume, molar mass, solubility parameter, and density) with depth were calculated by the equation of state (EOS). The primary factors governing asphaltene distribution in reservoirs are the gravitational term, which is determined in part by the size of the asphaltene colloidal particle, and the solubility term, which is determined in large part by the GOR (composition). Consequently, it is critical to accurately measure both the fluid coloration and the GOR (composition) to understand the asphaltene gradient in oil columns. The results obtained in this work are in accordance with the Yen−Mullins model in asphaltene science. In particular, if asphaltenes are equilibrated in an oil reservoir, then a massive fluid flow through the reservoir had to have taken place, and permeable rocks are required, thereby implying connectivity, because asphaltenes necessarily enter the reservoir out of their ultimate equilibrium at the beginning of the reservoir charging. Therefore, a new powerful approach is established for conducting DFA color and GOR gradient analysis by coupling advanced asphaltene science with DFA technology (profiling of fluids) to address reservoir connectivity.
Urine nitrification and sewer discharge to realize in-sewer denitrification to simplify sewage treatment in Hong Kong (2011)

The chemically enhanced primary treatment works in Hong Kong will be upgraded for biological nitrogen removal. This study proposed a novel approach to waive the upgrading by urine source-separation, onsite nitrification and discharge of nitrified urine into sewers to achieve in-sewer denitrification. Human urine was collected and a lab-scale experiment for full urine nitrification was conducted. The results showed that full nitrification was achieved with alkaline addition. Simulation of nitrified urine discharge into an 8-km pressure main in Hong Kong was conducted with a quasi-2D dynamic sewer model developed from a previously calibrated sewer biofilm model. It was assumed that 70% of the residents' urine was collected and fully nitrified on-site. The simulation results revealed that the proposed approach is effective in removal of nitrogen within the sewer, which decreases ammonia-N at the sewer outlet to a level required for secondary effluent discharge in Hong Kong.