gebhart/patrepeval huggingface dataset:
WAY‐131256 is an orally active, efficacious, and in vivo functionally selective M1 agonist (1997)

Computer modeling of carbachol docked in the human m1 receptor binding pocket has been used to discover a series of carbamate and thiocarbamate chiral, conformationally restricted analogues of carbachol based on azabicyclo[2.2.1]heptan-3-ol. These molecules have been evaluated for affinity and efficacy at human muscarinic receptors (m1–m5) transfected into a CHO cell line. None of these compounds was selective in binding. Thiocarbamate analogues had greater affinity for the m1 receptor subtype, but lower efficacy based on comparison of their ability to induce phosphoinositide (PI) turnover. Carbamate analogues had lower affinity for m1 receptors than thiocarbamates and varied in efficacy from 10% to 100% of the carbachol response in phosphoinositide (PI) turnover. One of these analogues 3S,4R-azabicyclo[2.2.1]heptan-3-methylcarbamate, WAY-131256, (VI) has been characterized as an m1/m2 agonist in vitro. (VI) was equi-efficacious to the standard m1 agonist, xanomeline (Phase III) in vivo in a scopolamine-impaired radial arm maze paradigm (MED 1 mg/kg, 5.88 mmol/kg for VI and MED 1 mg/kg, 3.55 mmoles/kg for xanomeline) and was approximately equal to xanomeline in an AF64A-impaired radial arm maze paradigm. Despite its lack of m1 selectivity in vitro, in vivo experiments on (VI) indicated no significant effect on blood pressure or heart rate at 10 mg/kg (58.78 mmol/kg) (i.p.), and no peripheral side effects attributed to stimulation of either the m2 or m3 receptors (salivation, lacrimation, and chromodacryorrhea) up to doses of 30 mg/kg, 176.2 mmol/kg. These results may be explained by different receptor densities in various brain regions not accounted for in a transfected cell line or by metabolism of (VI) to a m1 selective agonist in vivo. Drug Dev. Res. 40:185–192, 1997. © 1997 Wiley-Liss, Inc.
HLP (2005)

It is well-known that BGP, the current inter-domain routing protocol, has many deficiencies. This paper describes a hybrid link-state and path-vector protocol called HLP as an alternative to BGP that has vastly better scalability, isolation and convergence properties. Using current BGP routing information, we show that HLP, in comparison to BGP, can reduce the churn-rate of route updates by a factor 400 as well as isolate the effect of routing events to a region 100 times smaller than that of BGP. For a majority of Internet routes, HLP guarantees worst-case linear-time convergence. We also describe a prototype implementation of HLP on top of the XORP router platform. HLP is not intended to be a finished and final proposal for a replacement for BGP, but is instead offered as a starting point for debates about the nature of the next-generation inter-domain routing protocol.
Advanced aggregate computation for large data visualization (2015)

Large data visualization and analysis faces challenges related to performance, operability, degree of discrimination, etc. In this paper, an advanced aggregate computation is proposed to solve these issues from three aspects. By virtue of visualization-based data separation and aggregation, a large dataset is mapped to a visualization-based small dataset for efficient visualization while keeping operability of data. A minimum size of visual primitives for aggregated data is defined to ensure visibility of important but tiny information. And a D3-based rendering implementation improves the performance of consecutive visualizations.
Building a BioChemformatics Database (2008)

The structural registration of chemically modified macromolecules is vital for the development of biopharmaceuticals. However, registration and search of such complex molecules has so far posed formidable challenges performance-wise, since today's chemistry-oriented databases do not scale well to macromolecules. As a practical consequence, macromolecules tend to be stored in protein databases with a focus on protein sequence only, and salient chemistry details are therefore lost. This article describes protein format extensions and the use of pseudoatoms for representing natural amino acids in chemical structures to allow high-performance registration and retrieval of large macromolecules. The representations include exact chemical modifications and enable lossless conversion between chemistry and sequence formats. Registration is done in parallel in both sequence and chemistry formats, and users can register and retrieve molecules in either format as they choose, resulting in what we call a BioChemformatics database. Having both sequence and chemistry formats available on-demand allows for the construction of protein SAR tables with mixed sequence and chemistry information. Likewise, searching may combine sequence and chemistry terms and be performed in standard vendor applications like MDL's ISIS/Base or in-house applications using standard SQL queries.
Preoxidation cleaning optimization for crystalline silicon (solar cell manufacture) (2002)

A series of controlled experiments has been performed to evaluate the effect of various chemical surface treatments on the recombination lifetime of crystalline silicon solar cell wafers subjected to high temperature dry oxidation. From this series of experiments, a relatively simple, yet effective, cleaning sequence is deduced. Also evaluated is the effect of different chemical damage-removal etches for improving the recombination lifetime and surface smoothness of mechanically lapped wafers. The methodology used, the experimental results obtained, and the authors' experience using this process on a continuing basis over a period of many months are presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
DNA Cleavage by UVA Irradiation of NADH with Dioxygen via Radical Chain Processes (2006)

Efficient DNA cleaving-activity is observed by UVA irradiation of an O2-saturated aqueous solution of NADH (β-nicotinamide adenine dinucleotide, reduced form). No DNA cleavage has been observed without NADH under otherwise the same experimental conditions. In the presence of NADH, energy transfer from the triplet excited state of NADH (3NADH*) to O2 occurs to produce singlet oxygen (1O2) that is detected by the phosphorescence emission at 1270 nm. No quenching of 1O2 by NADH was observed as indicated by no change in the intensity of phosphorescence emission of 1O2 at 1270 nm in the presence of various concentrations of NADH. In addition to the energy transfer, photoinduced electron transfer from 3NADH* to O2 occurs to produce NADH•+ and O2•-, both of which was observed by ESR. The quantum yield of the photochemical oxidation of NADH with O2 increases linearly with increasing concentration of NADH but decreases with increasing the light intensity absorbed by NADH. Such unusual dependence of the quantum yield on concentration of NADH and the light intensity absorbed by NADH indicates that the photochemical oxidation of NADH with O2 proceeds via radical chain processes. The O2•- produced in the photoinduced electron transfer is in the protonation equilibrium with HO2•, which acts as a chain carrier for the radical chain oxidation of NADH with O2 to produce NAD+ and H2O2, leading to the DNA cleavage.
Neural Pose Transfer by Spatially Adaptive Instance Normalization (2020)

Pose transfer has been studied for decades, in which the pose of a source mesh is applied to a target mesh. Particularly in this paper, we are interested in transferring the pose of source human mesh to deform the target human mesh, while the source and target meshes may have different identity information. Traditional studies assume that the paired source and target meshes are existed with the point-wise correspondences of user annotated landmarks/mesh points, which requires heavy labelling efforts. On the other hand, the generalization ability of deep models is limited, when the source and target meshes have different identities. To break this limitation, we proposes the first neural pose transfer model that solves the pose transfer via the latest technique for image style transfer, leveraging the newly proposed component -- spatially adaptive instance normalization. Our model does not require any correspondences between the source and target meshes. Extensive experiments show that the proposed model can effectively transfer deformation from source to target meshes, and has good generalization ability to deal with unseen identities or poses of meshes. Code is available at https://github.com/jiashunwang/Neural-Pose-Transfer .
Fluorescence In Situ Hybridization Using 16S rRNA-Targeted Oligonucleotides Reveals Localization of Methanogens and Selected Uncultured Bacteria in Mesophilic and Thermophilic Sludge Granules (1999)

16S rRNA-targeted in situ hybridization combined with confocal laser scanning microscopy was used to elucidate the spatial distribution of microbes within two types of methanogenic granular sludge, mesophilic (35 degrees C) and thermophilic (55 degrees C), in upflow anaerobic sludge blanket reactors fed with sucrose-, acetate-, and propionate-based artificial wastewater. The spatial organization of the microbes was visualized in thin sections of the granules by using fluorescent oligonucleotide probes specific to several phylogenetic groups of microbes. In situ hybridization with archaeal- and bacterial-domain probes within granule sections clearly showed that both mesophilic and thermophilic granules had layered structures and that the outer layer harbored mainly bacterial cells while the inner layer consisted mainly of archaeal cells. Methanosaeta-, Methanobacterium-, Methanospirillum-, and Methanosarcina-like cells were detected with oligonucleotide probes specific for the different groups of methanogens, and they were found to be localized inside the granules, in both types of which dominant methanogens were members of the genus Methanosaeta. For specific detection of bacteria which were previously detected by whole-microbial-community 16S ribosomal DNA (rDNA)-cloning analysis (Y. Sekiguchi, Y. Kamagata, K. Syutsubo, A. Ohashi, H. Harada, and K. Nakamura, Microbiology 144:2655-2665, 1998) we designed probes specific for clonal 16S rDNAs related to unidentified green nonsulfur bacteria and clones related to Syntrophobacter species. The probe designed for the cluster closely related to Syntrophobacter species hybridized with coccoid cells in the inner layer of the mesophilic granule sections. The probe for the unidentified bacteria which were clustered with the green nonsulfur bacteria detected filamentous cells in the outermost layer of the thermophilic sludge granule sections. These results revealed the spatial organizations of methanogens and uncultivated bacteria and their in situ morphologies and metabolic functions in both mesophilic and thermophilic granular sludges.
Modelling Behaviour of a Carbon Epoxy Composite Exposed to Fire: Part I—Characterisation of Thermophysical Properties (2017)

Thermophysical properties of a carbon-reinforced epoxy composite laminate (T700/M21 composite for aircraft structures) were evaluated using different innovative characterisation methods. Thermogravimetric Analysis (TGA), Simultaneous Thermal analysis (STA), Laser Flash analysis (LFA), and Fourier Transform Infrared (FTIR) analysis were used for measuring the thermal decomposition, the specific heat capacity, the anisotropic thermal conductivity of the composite, the heats of decomposition and the specific heat capacity of released gases. It permits to get input data to feed a three-dimensional (3D) model given the temperature profile and the mass loss obtained during well-defined fire scenarios (model presented in Part II of this paper). The measurements were optimised to get accurate data. The data also permit to create a public database on an aeronautical carbon fibre/epoxy composite for fire safety engineering.
Coronary vessel detection methods for organ‐mounted robots (2021)

Through the use of two machine learning algorithms, HeartLander has shown the ability to identify different sized vasculature proximally above turbulent flow. These results indicate that it is feasible to use Doppler ultrasound to identify and avoid coronary vasculature during cardiac interventions using HeartLander.
Synthesis of Tetracyclic Heterocompounds as Selective Estrogen Receptor Modulators. Part 2. Process Improvement for Scale-Up Of 2,5,8-Substituted 11,12-Dihydro-5H-6,13-dioxabenzo[3,4]cyclohepta-[1,2-a]naphthalene Derivatives (2007)

An improved, reproducible nonchromatographic process for scale-up synthesis of 2,5,8-substituted 11,12-dihydro-5H-6,13-dioxabenzo[3,4]cyclohepta[1,2-a]naphthalene derivatives as selective estrogen receptor modulators (SERMs) is described. The titled compounds were prepared in 9−21% overall yield with high chemical purity (>97%) after nine consecutive synthetic steps.
Estradiol and phytoestrogens differently influence the rodent postmenopausal mammary gland (2006)

The differences observed in the histological pattern, hormonal receptor status regulation, and Ki67 modulation suggest a different role for phytoestrogens and 17beta-estradiol in postmenopausal rodent mammary glands.
Revisión del apoyo del Banco al sector agropecuario, 2002-2014: Evidencias de áreas temáticas clave (2015)

El objetivo de la presente evaluacion es examinar la funcion del apoyo brindado por el Banco Interamericano de Desarrollo (BID o Banco) al desarrollo agropecuario en la region desde 2002. En ella se analizan la pertinencia del apoyo global del BID y la pertinencia, implementacion y eficacia de determinados proyectos en tres areas tematicas clave, a saber, apoyo directo a los agricultores, sanidad animal y vegetal e inocuidad alimentaria, y administracion y regularizacion de tierras. Ademas, se procura identificar los factores que afectan el exito de varios tipos de intervenciones en diferentes contextos y formular recomendaciones acerca de la manera en que el Banco puede incrementar su apoyo al sector. Una finalidad de la evaluacion es la de ofrecer orientacion para la actualizacion del Documento de Marco Sectorial en 2016.
Genetic Approaches to Defining Signaling by the CML-associated Tyrosine Kinase BCR-ABL (1994)

Human chronic myelogenous leukemia (CML) is a cancer that is associated with a specific cytogenetic marker known as the Philadelphia (Ph1) chromosome (Nowell and Hungerford 1960; Rowley 1973; for review, see Kurzrock et al. 1988). Cells of multiple lineages carry Ph1, suggesting that the disease originates in a pluripotent stem cell. Ph1 is the result of a reciprocal translocation of chromosomes 9 and 22, which results in the fusion of two cellular genes encoding BCR and c-ABL (Shtivelman et al. 1985; Clark et al. 1988). The resulting fusion gene (see Fig. 1) encodes BCR-ABL, an activated protein tyrosine kinase. The tyrosine kinase activity of BCR-ABL is deregulated when compared to c-ABL (Konopka and Witte 1985) and is the most essential feature for its transforming activity. In nature, two fusion products are detected. P210 BCR-ABL is associated with CML and P185 BCR-ABL is associated with the more aggressive acute lymphocytic leukemia...
Writer identification using text line based features (2002)

We present a system for writer identification. From handwritten lines of text, twelve features are extracted which are used to recognize persons, based on their handwriting. The features extracted mainly correspond to visible characteristics of the writing, for example, the width, the slant and the height of the three main writing zones. Additionally, features based on the fractal behavior of the writing, which are correlated with the writing's legibility, are used. With these features two classifiers are applied: a k-nearest neighbor and a feedforward neural network classifier. In the experiments, 100 pages of text written by 20 different writers are used. By classifying individual text lines, an average recognition rate of 87.8% for the k-nearest neighbor and 90.7% for the neural network is measured. By a simple maximum ranking over all lines of a page, all texts are correctly assigned to the corresponding writers. Compared to these results, an average recognition rate of 98% was measured when humans assigned persons to the text lines.
Mechanical Properties of a SiC-Fiber Reinforced CVI-SiC Composite (1991)

Mechanical properties of a commercial SiC-fiber/CVI-SiC composite were examined. The composite showed high fracture toughness (12.5MPa·m1/2) and low strength (162MPa in tensile strength) comparing to those far other engineering ceramics, resulting from fracture behavior dependent on the microstructure. The high fracture toughness is a result of fiber debonding and pull-out effects, however, the low strength is associated with porous microstructure.
Distinct Graft-Specific TCR Avidity Profiles during Acute Rejection and Tolerance (2018)

Mechanisms implicated in robust transplantation tolerance at the cellular level can be broadly categorized into those that inhibit alloreactive T cells intrinsically (clonal deletion and dysfunction) or extrinsically through regulation. Here, we investigated whether additional population-level mechanisms control T cells by examining whether therapeutically induced peripheral transplantation tolerance could influence T cell populations' avidity for alloantigens. Whereas T cells with high avidity preferentially accumulated during acute rejection of allografts, the alloreactive T cells in tolerant recipients retained a low-avidity profile, comparable to naive mice despite evidence of activation. These contrasting avidity profiles upon productive versus tolerogenic stimulation were durable and persisted upon alloantigen re-encounter in the absence of any immunosuppression. Thus, peripheral transplantation tolerance involves control of alloreactive T cells at the population level, in addition to the individual cell level. Controlling expansion or eliminating high-affinity, donor-specific T cells long term may be desirable to achieve robust transplantation tolerance in the clinic.
Asad Abidi, Mark Horowitz and Teresa Meng Elected to U.S. National Academy of Engineering (2007)

Former SSCS officers and AdCom members Asad Abidi, Mark Horowitz, and Teresa Meng were among 64 Americans and nine foreign associates elected in January to the National Academy of Engineering Class of 2007.
Learning from Live Coding (2016)

The pace of engagement with new digital technologies in music education is proving to be slow. A key issue - and a major barrier to entry - is teacher skills and confidence to work with technology creatively. Following a concerted campaign from the technology industry, in spring 2013 the UK government agreed to introduce the subject of computing into the national curriculum for all children at the age of five. This chapter describes, interprets and theorises the digital skills and engagement with live coding performance in music.
Helicobacter pylori toxin VacA induces vacuole formation by acting in the cell cytosol (1997)

Cells exposed to Helicobacter pylori toxin VacA develop large vacuoles that originate from massive swelling of membranous compartments of late stages of the endocytic pathway. To determine if the toxin is active from the cell cytosol, cells were either microinjected with toxin or transfected with plasmids encoding VacA. Both procedures cause formation of intracellular vacuoles. Cytosolic localization of the toxin was assessed by indirect immunofluorescence with specific antibodies and by expression of an active green fluorescence protein (GFP)-VacA chimera. Vacuoles induced by internally produced VacA are morphologically and functionally identical to those induced by externally added toxin. It is concluded that VacA is a toxin acting intracellularly by altering a cytosol-exposed target, possibly involved in the control of membrane trafficking.
Design and analysis of 6 DOF handheld micromanipulator (2012)

This paper presents the design and analysis of a handheld manipulator for vitreoretinal microsurgery and other biomedical applications. The design involves a parallel micromanipulator utilizing six piezoelectric linear actuators, combining compactness with a large range of motion and relatively high stiffness. Given the available force of the actuators, the overall dimension of the micromanipulator was optimized considering realistic external loads on a remote center of motion representing the point of expected contact with the sclera of the eye during microsurgery. Based on optimization and workspace analysis, a benchtop version of the micromanipulator was built with a base diameter of 25 mm and a height of 50 mm. It provides a hemispherical workspace of 4.0 mm diameter at the tool tip. The manipulation performance of the constructed manipulator was measured under a lateral load applied at the remote center of motion. The micromanipulator tolerated side loads up to 200 mN.
Leakage scaling in deep submicron CMOS for SoC (2002)

In this paper, we demonstrate the effects of CMOS technology scaling on the high temperature characteristics (from 25/spl deg/C to 125/spl deg/C) of the four components of off-state drain leakage (I/sub off/) (i.e. subthreshold leakage (I/sub sub/), gate edge-direct-tunneling leakage (I/sub EDT/), gate-induced drain-leakage (I/sub GIDL/), and bulk band-to-band-tunneling leakage (I/sub B-BTBT/)). In addition, the high temperature characteristics of I/sub off/ with reverse body bias (V/sub B/) for the further reduction of the standby leakage are also demonstrated. The discussion is based on the data measured from three CMOS logic technologies (i.e., low-voltage and high performance (LV), low-power (LP), and ultra-low-power (ULP)) and three generations (0.18 /spl mu/m, 0.15 /spl mu/m, and 0.13 /spl mu/m). Experiments show that the optimum V/sub B/, which minimizes I/sub off/, is a function of temperature. The experiments also show that for CMOS logic technologies of the next generations, it is important to control I/sub B-BTBT/ and I/sub GIDL/ by reducing effective doping concentration and doping gradient. It seems that in order to conform on-state gate leakage (I/sub G-on/) and I/sub EDT/ specifications and to retain a 10-20% performance improvement at the same time, it is indispensable to use high-quality and high-dielectric-constant materials to reduce effective oxide thickness (EOT). The role of each leakage component in SRAM standby current (I/sub SB/) is also analyzed.
Search for new physics ineμXdata at DØ using SLEUTH: A quasi-model-independent search strategy for new physics (2000)

We present a quasi-model-independent search for the physics responsible for electroweak symmetry breaking. We define final states to be studied, and construct a rule that identifies a set of relevant variables for any particular final state. A new algorithm (``SLEUTH'') searches for regions of excess in those variables and quantifies the significance of any detected excess. After demonstrating the sensitivity of the method, we apply it to the semi-inclusive channel $e\ensuremath{\mu}X$ collected in 108 ${\mathrm{pb}}^{\ensuremath{-}1}$ of $p\overline{p}$ collisions at $\sqrt{s}=1.8$ TeV at the D\O{} experiment during 1992--1996 at the Fermilab Tevatron. We find no evidence of new high ${p}_{T}$ physics in this sample.