gebhart/patrepeval huggingface dataset:
Automated quantification of microstructural dimensions of the human kidney using optical coherence tomography (OCT) (2009)

Optical coherence tomography (OCT) is a rapidly emerging imaging modality that can non-invasively provide cross-sectional, high-resolution images of tissue morphology in situ and in real-time. We previously demonstrated that OCT is capable of visualizing characteristic kidney anatomic structures, including blood vessels, uriniferous tubules, glomeruli, and renal capsules on a Munich-Wistar rat model. Because the viability of a donor kidney is closely correlated with its tubular morphology, and a large amount of image datasets are expected when using OCT to scan the entire kidney to provide a global assessment of its viability, it is necessary to develop automatic image analysis methods to quantify the spatially-resolved morphometric parameters such as tubular diameter to provide potential diagnostic information. In this study, we imaged the human kidney in vitro and quantified the diameters of hollow structures such as blood vessels and uriniferous tubules automatically. The microstructures were first segmented from cross-sectional OCT images. Then the spatially-isolated region-of-interest (ROI) was automatically selected to quantify its dimension. This method enables the automatic selection and quantification of spatially-resolved morphometric parameters. The quantification accuracy was validated, and measured features are in agreement with known kidney morphology. This work can enable studies to determine the clinical utility of OCT for kidney imaging, as well as studies to evaluate kidney morphology as a biomarker for assessing kidney's viability prior to transplantation.
Chemical Coupling of a Monoclonal Antisurfactant Protein-B Antibody to Human Urokinase for Targeting Surfactant-Incorporating Alveolar Fibrin (2002)

Intraalveolar fibrin formation is a common histopathological finding in acute inflammatory and chronic interstitial lung diseases. Incorporation of hydrophobic surfactant components into polymerizing fibrin results in a severe loss of surface activity, altered mechanical and structural clot properties, and a reduced susceptibility toward fibrinolytic degradation. Such events have been implicated in atelectasis formation, impairment of gas exchange, and provocation of fibroproliferative changes. In an effort to address the unique features of alveolar fibrin, we designed a hybrid molecule consisting of a monoclonal antibody against surfactant protein SP-B (8B5E) and the catalytic domain of urokinase (B-chain), which was termed MABUC. The urokinase B-chain was prepared by limited reduction of human two-chain-urokinase and subsequent affinity purification and coupled to the antibody using a heterobifunctional cross-linker. Purification of the chimeric protein included gel filtration chromatography and affinity chromatography. An ELISA-like microtiter plate assay, based on the immunological detection of the SP-B moiety and the fibrinolytic activity of the u-PA domain, was developed for the detection of the hybrid molecule. Chromogenic substrate assays, (125)I-based fibrin plate assays, and active site titration were performed to analyze the specific fibrinolytic activity of the conjugate. MABUC was found to fully retain the ability of SP-B binding and the fibrinolytic activity of u-PA. In addition, MABUC was noted to be 1.5-2-fold more effective in the dissolution of surfactant embedding clots and to be approximately 3-fold more resistant against PAI-1, the predominant fibrinolysis inhibitor in the alveolar compartment, as compared to the native u-PA. The superiority of MABUC was particularly prominent (>5-fold efficacy) when investigating clot material incorporating both PAI-1 and surfactant, as a mimicry of alveolar fibrin. We conclude that urokinase and 8B5E can be cross-linked chemically, thus yielding a fibrinolytic enzyme with enhanced substrate specifity for surfactant-containing clots and higher PAI-1 resistance as compared to native u-PA.
Characterization of the <i>sat</i> Operon in <i>Streptococcus mutans</i> : Evidence for a Role of Ffh in Acid Tolerance (2001)

An essential protein translocation pathway in Escherichia coli and Bacillus subtilis involves the signal recognition particle (SRP), of which the 54-kDa homolog (Ffh) is an essential component. In a previous study, we found that a transposon insertion in the ylxM-ffh intergenic region of the designated secretion and acid tolerance (sat) operon of Streptococcus mutans resulted in an acid-sensitive phenotype. In the present study, we further characterized this genomic region in S. mutans after construction of bona fide sat operon mutants and confirmed the role of the SRP pathway in acid resistance. Northern blot and primer extension analyses identified an acid-inducible promoter upstream of ylxM that was responsible for upregulating the coordinate expression of all five genes of the sat operon when cells were grown at acid pH. Two constitutive promoters, one immediately upstream of satD and one just 3' to the acid-inducible promoter, were also identified. Except for Ffh, the functions of the sat operon gene products are unknown. SatC, SatD, and SatE have no homology to proteins with known functions, although YlxM may function as a transcriptional regulator linked to genes encoding SRP pathway proteins. Nonpolar mutations created in each of the five genes of the sat locus resulted in viable mutants. Most striking, however, was the finding that a mutation in ffh did not result in loss of cell viability, as is the case in all other microbial species in which this pathway has been described. This mutant also lacked immunologically detectable Ffh and was severely affected in resistance to acid. Complementation of the mutation resulted in restoration of acid tolerance and reappearance of cytoplasmic Ffh. These data provide evidence that the SRP pathway plays an important role in acid tolerance in S. mutans.
Heuristic technique for processor and link assignment in multicomputers (1991)

A graph-based solution to the mapping problem using the simulated annealing optimization heuristic is developed. An automated two-phase mapping strategy is formulated: process annealing assigns parallel processes to processing nodes, and connection annealing schedules traffic connections on network data links so that interprocess communication conflicts are minimized. To evaluate the quality of generated mappings. cost functions suitable for simulated annealing that accurately quantify communications overhead are derived. Communication efficiency is formulated to measure the quality of assignments when the optimal mapping is unknown. The mapping scheme is implemented using the hypercube as a host architecture, and results for several image graphs are presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Seeking the Strongest Rigid Detector (2013)

The current state of the art solutions for object detection describe each class by a set of models trained on discovered sub-classes (so called "components"), with each model itself composed of collections of interrelated parts (deformable models). These detectors build upon the now classic Histogram of Oriented Gradients+linear SVM combo. In this paper we revisit some of the core assumptions in HOG+SVM and show that by properly designing the feature pooling, feature selection, preprocessing, and training methods, it is possible to reach top quality, at least for pedestrian detections, using a single rigid component. Abstract We provide experiments for a large design space, that give insights into the design of classifiers, as well as relevant information for practitioners. Our best detector is fully feed-forward, has a single unified architecture, uses only histograms of oriented gradients and colour information in monocular static images, and improves over 23 other methods on the INRIA, ETH and Caltech-USA datasets, reducing the average miss-rate over HOG+SVM by more than 30%.
Screening Technologies for G Protein-Coupled Receptors: From HTS to uHTS (2009)

The discovery of drugs for G protein-coupled receptors (GPCRs) has traditionally been very successful, even before the structural nature of these molecular targets was elucidated. Over the years, this family of proteins has become more important in the understanding and treatment of different human pathologies, representing today close to 30% of the molecular targets of all marketed drugs. The sequencing of the human genome unveiled the existence of many new GPCRs and this has increased even more the interest of this family of proteins as potential drug targets. Today the search for compounds that interfere or modulate the function of GPCRs is one of the major focuses of pharmaceutical companies. The understanding of the molecular events that take place upon receptor activation, together with the need of testing large chemical libraries, has resulted in the development of a variety of methods and technologies to measure the activity of these receptors. In this chapter we will review most of the assay technologies currently in use for “in vitro” pharmacological screening, their evolution, their capabilities, and their limitations.
PASTEURIZATION OF IGM-ENRICHED IMMUNOGLOBULIN (2004)

Human plasma proteins are important for therapy or prophylaxis of human diseases. Due to the preparation of human plasma proteins from human plasma pools and risk of contamination with human viruses, different viral reduction treatments such as: pasteurization, solvent/detergent, dry heat treatment, steam treatment, beta-propiolactone/UV and nanofiltration have been implemented. As pasteurization can be performed for liquid protein, this method (a 10-hour heat treatment of the aqueous solutions at 60°C) was introduced into the manufacturing procedure of IgM-enriched immunoglobulin, to improve its safety further. The efficiency of this method for inactivation of viruses was evaluated by the use of Foot-and-Mouth Disease Virus (a non-enveloped virus) and Infectious Bovine Rhinotracheitis (IBR) Virus (a lipid-enveloped virus). Pasteurization inactivated Foot-and-Mouth Disease Virus by 7 log10 and for IBR Virus by 5log10. These findings show a significant added measure of virus safety associated with pasteurization of IgM-enriched immunoglobulin preparation.
The Life Settlement Market is an Opportunity (2006)

Life settlements provide life insurance policy owners a viable alternative to surrendering the life policy. The authors address the misunderstandings of many early entrants regarding the inner workings of life insurance products, the terminology, and the applicability of certain actuarial assumptions. The authors point out that insurance companies, rather than portraying life settlement transactions as an attack on policyholder equity, ought to take more responsibility in creating a disciplined and orderly secondary market for life insurance policies that can benefit their policyholders. A mature life settlement market—with attention paid to consumer needs, a technically correct understanding of the risks, responsible pricing, and maintenance of high ethical standards—will thrive and every participant will be well served. Who is better equipped to do this than the insurance companies? <b>TOPICS:</b>Other real assets, exchanges/markets/clearinghouses, credit risk management
A novel side-gated ultrathin-channel nanopore FET (SGNAFET) sensor for direct DNA sequencing (2013)

A novel side-gated ultrathin-channel nanopore FET (SGNAFET), for fast and label-free DNA sequencing with high resolution and sensitivity, is proposed. The goal of the SGNAFET is to identify the four types of nucleotides in DNA by changes in the channel current of the SGNAFET. Aiming to reach that goal, a SGNAFET with channel thickness (t <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">ch.</sub> ) of 2 or 4 nm was successfully operated and could detect DNA translocations through its nanopore on the basis of changes in its channel current.
Corona poling of nonlinear polymer thin films for electro-optic modulators (1994)

We have developed an experimental technique for corona poling a nonlinear polymer thin film for use in electro-optic modulators. This method eliminates the pinhole and surface roughness damage that has been observed when corona poling a nonlinear polymer deposited on a conducting substrate. Electro-optic modulators have been constructed to compare this corona poling technique to the contact poling technique commonly used with electro-optic devices. Experimental results are presented that demonstrate that the corona poled electro-optic devices were poled with electric fields near the dielectric breakdown of the thin polymer films—fields that are often difficult to achieve with contact poling.
Structural and functional analysis of the riboflavin synthesis genes encoding GTP cyclohydrolase II (ribA), DHBP synthase (ribBA), riboflavin synthase (ribC), and riboflavin deaminase/reductase (ribD) from Helicobacter pylori strain P1 (2000)

The functions of the riboflavin synthesis gene homologues ribA, ribBA, ribC, and ribD from Helicobacter pylori strain P1 were confirmed by complementation of defined Escherichia coli mutant strains. The H. pylori ribBA gene, which is similar to bifunctional ribBA genes of Gram-positive bacteria, fully complemented the ribB mutation and partially restored growth in a ribC mutant. However, ribBA did not complement the ribA mutation in E. coli, thus explaining the presence of the additional separate copy of the ribA gene in the H. pylori chromosome. In E. coli exclusively ribA conferred hemolytic activity and gave rise to production of molecules with fluorescence characteristics similar to flavins, as observed earlier. The E. coli hemolysin ClyA was not involved in causing the hemolytic phenotype. No riboflavin synthesis genes on plasmids conferred iron uptake functions to a siderophore-deficient mutant of E. coli. Marker exchange mutagenesis of the genes in H. pylori was not successful indicating that riboflavin synthesis is essential for basic metabolic functions of the gastric pathogen.
A Quarter-Square Multiplier Using a Segmented Parabolic Characteristic (1951)

A circuit for multiplying two varying voltages based on the ``quarter-square'' method has been developed. A segmented nonlinear element is used for squaring, and a time-sharing scheme permits the use of a single squaring element instead of duplicate elements as in previous designs. The circuit has a time delay of less than 40 microseconds (0–67 percent) and has an accuracy of better than ±1 percent. The original circuit was designed to operate only in the first quadrant. Various methods for including the four quadrants are discussed.
Three-Dimensional Mapping of Chorioretinal Vascular Oxygen Tension in the Rat (2009)

Three-dimensional mapping of chorioretinal oxygen tension allowed quantitative P(O2) measurements in large retinal blood vessels and in retinal capillaries. This method has the potential to facilitate better understanding of retinal oxygenation in health and disease.
Dynamics of Passive-Scalar Turbulence (2005)

We present the first study of the dynamic scaling or multiscaling of passive-scalar turbulence. For the Kraichnan version of passive-scalar turbulence we show analytically, in both Eulerian and quasi-Lagrangian frameworks, that simple dynamic scaling is obtained but with different dynamic exponents. By developing the multifractal model we show that dynamic multiscaling occurs in passive-scalar turbulence only if the advecting velocity field is itself multifractal. We substantiate our results by detailed numerical simulations in shell models of passive-scalar advection.
Current Efficiency Studies of the Hooker Type S Chlorine Cell (1944)

A study was made to determine the relative magnitude of the various processes causing loss of current efficiency in Hooker Type S chlorine cells. Loss of <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline" id="ML1" overflow="scroll"> <mml:mi mathvariant="normal">NaOH</mml:mi> </mml:math> production from theoretical is due almost entirely to migration of <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline" id="ML2" overflow="scroll"> <mml:msup> <mml:mo>OH</mml:mo> <mml:mrow> <mml:mo>−</mml:mo> </mml:mrow> </mml:msup> </mml:math> ions through the diaphragm from the catholyte to the anolyte. The alkali, NaOH, from the catholyte tends to decrease the hydrogen ion concentration of the anolyte, whereas several processes at the anode and in the anolyte tend to increase it. Consequently, a certain pH is established which, it is shown, depends principally upon the current efficiency, the <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline" id="ML3" overflow="scroll"> <mml:mi mathvariant="normal">NaCl</mml:mi> </mml:math> concentration and the type and condition of the anode. The determination of anolyte pH is shown to be a convenient approximate test for the determination of current efficiency for control purposes. Calculation of current efficiency from the oxygen and carbon dioxide content of the cell gas, as determined by an accurate and relatively quick analytical method, is a convenient means of determining current efficiency which compares favorably in accuracy with usual methods employing caustic liquor and current measurements. In connection with studies to determine the effect of operating the Hooker Type S chlorine cell under various conditions, the relationships between current efficiency loss and various reactions occurring in the cell were investigated and quantitative relationships between ion concentrations and current efficiency loss were developed. Methods of testing for experimental work and for control were worked out. All work was done with standard Type S cells in regular operation, and varying conditions from normal by means of a separate brine supply for the cell being tested. However, methods and fundamental principles would be applicable, with some modification, to any type diaphragm cell.
Neutrophil attractant/activation protein‐1 (interleukin‐8) induces <i>in vitro</i> neutrophil migration by haptotactic mechanism (1993)

The role of leukocyte migration induced by the substrate-bound attractants is obscured by the inability of standard methods for the study of leukocyte migration to dissociate chemotaxis and haptotaxis, migration in response to soluble and surface-bound gradients of attractants. Here we show that the gradient of neutrophil attractant/activation protein-1 (interleukin-8, NAP-1/IL-8) induces directed in vitro neutrophil migration when bound to the polycarbonate filter. In addition, we suggest that haptotaxis is responsible for neutrophil migration induced by NAP-1/IL-8 in standard Boyden-type chemotaxis assays and, in light of the ability of NAP-1/IL-8 to bind to the endothelial cell surface and the extracellular matrix, could also be of great significance in vivo.
Erratum: A femtojoule calorimeter using micromechanical sensors [Rev. Sci. Instrum. <b>65</b>, 3793 (1994)] (1995)

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Addition of Silane-Functionalized Carbon Nanotubes for Improved Rate Capability of LiNi<sub>1/3</sub>Co<sub>1/3</sub>Mn<sub>1/3</sub>O<sub>2</sub>Cathodes for Lithium Ion Batteries (2012)

This paper reports the preparation and characterization of LiNi1/3Co1/3Mn1/3O2 (NCM) cathodes containing multi-walled carbon nanotubes (MWCNTs) with different types of functionalization, including acid treatment, amino functionalization and silanization. Among these MWCNTs, the silane-functionalized CNTs give rise to significant reduction in inner electronic resistance and improvements in both capacity retention and rate capability of the nanocomposite cathodes. This finding is attributed to the synergy to form 3D spatial conductive networks among the active NCM particles by the well-dispersed MWCNTs and carbon black. (C) 2012 The Electrochemical Society. [DOI: 10.1149/2.013301jes] All rights reserved.
Photon-stimulated field emission from semiconducting (10,0) and metallic (5,5) carbon nanotubes (2002)

We present three-dimensional simulations of field emission through an oscillating barrier from ideally open (10,0) and (5,5) carbon nanotubes without adsorption, by using a transfer-matrix methodology. By introducing pseudopotentials for the representation of carbon atoms and by repeating periodically a basic unit of the nanotube, band-structure effects are manifested in the energy distributions. The total-energy distributions also exhibit oscillations, which are related to stationary waves in the structure. The current enhancement due to the photon-stimulation process reaches a saturation plateau for photon energies larger than 5 eV and decreases when the photon energy exceeds 9 eV. The results indicate a maximal current enhancement at a photon energy of 8.4 eV. This maximum may correspond to the best compromise between increasing width of the energy distribution and decreasing efficiency of the photon stimulation. In addition, a resonant photon-stimulation process seems associated with the maximum. For a power flux density of $5.96\ifmmode\times\else\texttimes\fi{}{10}^{12}{\mathrm{W}/\mathrm{m}}^{2}$ and a local field of 2.5 V/nm, a relative current enhancement up to ${10}^{9}$ is achieved with the semiconducting (10,0) nanotube while it is only of 140% for the metallic (5,5), this large difference being explained by the semiconducting (10,0) nanotube having an intrinsic emission (without photonic stimulation) $5\ifmmode\times\else\texttimes\fi{}{10}^{8}$ times lower than that of the metallic (5,5). These results indicate that photon-stimulated field emission from semiconducting carbon nanotubes may lead to important technological applications, like THz amplifiers (if a femtosecond modulation of the radiation can be achieved).
Metabolic imaging in the anesthetized rat brain using hyperpolarized [1‐<sup>13</sup>C] pyruvate and [1‐<sup>13</sup>C] ethyl pyruvate (2010)

Formulation, polarization, and dissolution conditions were developed to obtain a stable hyperpolarized solution of [1-(13)C]-ethyl pyruvate. A maximum tolerated concentration and injection rate were determined, and (13)C spectroscopic imaging was used to compare the uptake of hyperpolarized [1-(13)C]-ethyl pyruvate relative to hyperpolarized [1-(13)C]-pyruvate into anesthetized rat brain. Hyperpolarized [1-(13)C]-ethyl pyruvate and [1-(13)C]-pyruvate metabolic imaging in normal brain is demonstrated and quantified in this feasibility and range-finding study.