gebhart/patrepeval huggingface dataset:
Source Separation by Iterative Rank Reduction - Theory and Applications (2012)

Blended acquisition is quickly becoming an important topic in exploration geophysics because of the economical benefits it promises. The acquisition technique involves firing two or more sources almost simultaneously, effectively increasing spatial sampling per unit of time, but at the expense of cross-contamination from all the individual source energies overlapping one another on the blended shot record. In this expanded abstract we present an innovative method for separating a blended dataset into its constituent source components. The algorithm is an iterative scheme based on matrix rank reduction, during which the individual source components are estimated. The effectiveness of this deblending algorithm is demonstrated using first a synthetically blended dataset and then a real wide-azimuth blended dataset.
Fabry-Perot displacement interferometry for next-generation calculable capacitor (2010)

We describe a Fabry-Perot interferometer system designed to measure the variable spacing between two electrodes in the new NIST calculable capacitor. Using narrow-linewidth telecom lasers, we span a frequency interval of 18 GHz, and achieve a fractional uncertainty of δv/Δ ~1.7 × 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-8</sup> without an optical frequency standard. In the near future we will introduce a rubidium optical standard and frequency comb to make the displacement uncertainty a negligible component of the total target uncertainty of 0.1 zF for capacitance measurements.
Block-quantized kernel matrix for fast spectral embedding (2006)

Eigendecomposition of kernel matrix is an indispensable procedure in many learning and vision tasks. However, the cubic complexity O(N 3) is impractical for large problem, where N is the data size. In this paper, we propose an efficient approach to solve the eigendecomposition of the kernel matrix W. The idea is to approximate W with W that is composed of m 2 constant blocks. The eigenvectors of W, which can be solved in O(m 3) time, is then used to recover the eigenvectors of the original kernel matrix. The complexity of our method is only O(mN + m 3), which scales more favorably than state-ofthe-art low rank approximation and sampling based approaches (O(m 2 N + m 3)), and the approximation quality can be controlled conveniently. Our method demonstrates encouraging scaling behaviors in experiments of image segmentation (by spectral clustering) and kernel principal component analysis. 1.
Multipass amplifiers using optical circulators (1990)

A method of multipassing a pulse of light through an amplifier using an optical circulator, a nonreciprocal component composed of polarization beam splitters and a Faraday rotator, is presented. The pulse can be double, triple, or quadrupole passed through the amplifier depending upon the arrangement of the optical circulator. Numerical calculations and experimental results for multipass amplifiers are presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
RANDOMIZED COMPARATIVE STUDY OF 3 VERSUS 8-MONTH NEOADJUVANT HORMONAL THERAPY BEFORE RADICAL PROSTATECTOMY: BIOCHEMICAL AND PATHOLOGICAL EFFECTS (2001)

Ongoing biochemical and pathological regression of prostate tumors occurs between 3 and 8 months of neoadjuvant hormonal therapy, suggesting that the optimal duration of neoadjuvant hormonal therapy is longer than 3 months. Longer followup is needed to determine whether longer therapy alters PSA recurrence rates.
Assessing Physicochemical Properties of Drug Molecules via Microsolvation Measurements with Differential Mobility Spectrometry (2017)

The microsolvated state of a molecule, represented by its interactions with only a small number of solvent molecules, can play a key role in determining the observable bulk properties of the molecule. This is especially true in cases where strong local hydrogen bonding exists between the molecule and the solvent. One method that can probe the microsolvated states of charged molecules is differential mobility spectrometry (DMS), which rapidly interrogates an ion's transitions between a solvated and desolvated state in the gas phase (i.e., few solvent molecules present). However, can the results of DMS analyses of a class of molecules reveal information about the bulk physicochemical properties of those species? Our findings presented here show that DMS behaviors correlate strongly with the measured solution phase p<i>K</i><sub>a</sub> and p<i>K</i><sub>b</sub> values, and cell permeabilities of a set of structurally related drug molecules, even yielding high-resolution discrimination between isomeric forms of these drugs. This is due to DMS's ability to separate species based upon only subtle (yet predictable) changes in structure: the same subtle changes that can influence isomers' different bulk properties. Using 2-methylquinolin-8-ol as the core structure, we demonstrate how DMS shows promise for rapidly and sensitively probing the physicochemical properties of molecules, with particular attention paid to drug candidates at the early stage of drug development. This study serves as a foundation upon which future drug molecules of different structural classes could be examined.
A novel pillar DRAM cell for 4 Gbit and beyond (2002)

A novel structure and fabrication process for a DRAM cell for 4 Gbit and beyond is proposed. A poly-Si pillar transistor is formed on top of a trench capacitor with the top of the pillar transistor being directly connected to the bit line. In order to reduce the process steps, word line formation by a spacer etch and self-aligned bit line contact using CMP process are developed. XTEM micrographs show almost single grain and less defect in the small pillars after crystallization annealing of prepatterned /spl alpha/-Si. Electrical measurements show that the pass transistor has good subthreshold slope and Id-Vd characteristics. Improvements in the device performance has been achieved by a sacrificial oxidation and hydrogenation.
Epitope-directed antibody selection by site-specific photocrosslinking (2020)

Currently, there are no methods available offering solutions to select and identify antibodies binding to a specific conformational epitope of an antigen. Here, we developed a method to allow epitope-directed antibody selection from a phage display library by photocrosslinking bound antibodies to a site that specifically incorporates a noncanonical amino acid, <i>p</i>-benzoyl-l-phenylalanine (pBpa), on the target antigen epitope. By one or two rounds of panning against antibody phage display libraries, those hits that covalently bind to the proximity site of pBpa on specific epitopes of target antigens after ultraviolet irradiation are enriched and selected. This method was applied to specific epitopes on human interleukin-1β and complement 5a. In both cases, more than one-third of hits identified bind to the target epitopes, demonstrating the feasibility and versatility of this method.
Cytotoxic T Cell Specificity for Respiratory Syncytial Virus Proteins: Fusion Protein Is an Important Target Antigen (1987)

We examined the specificity of BALB/c cytotoxic T (Tc) cells for respiratory syncytial virus (RSV) components, using recombinant vaccinia viruses (VV) coding for several individual RSV proteins. We found that immunization with the different VVs yielded the following Tc memory cell populations: high levels of RSV-specific Tc cells were induced with the fusion protein VV, but low levels were induced with VV coding for the RSV nucleoprotein. Tc cell recognition of attachment glycoprotein, part of the matrix molecule or 1A internal protein was poor. While high levels of fusion protein-specific Tc cells were induced by the fusion protein VV, they showed poor cross-reactivity between the A2 and 8/60 RSV strains compared with Tc cells primed by RSV infection.
Colorimetric resonant reflection as a direct biochemical assay technique (2003)

A novel approach for the detection of molecular interactions is presented in which a colorimetric resonant diffractive grating surface is used as a surface binding platform. A guided mode resonant phenomenon is used to produce an optical structure that, when illuminated with white light, is designed to reflect only a single wavelength. When molecules are attached to the surface, the reflected wavelength (color) is shifted due to the change of the optical path of light that is coupled into the grating. By linking receptor molecules to the grating surface, complementary binding molecules can be detected without the use of any kind of fluorescent probe or particle label. It is expected that this technology will be most useful in applications where large numbers of biomolecular interactions are measured in parallel, particularly when molecular labels will alter or inhibit the functionality of the molecules under study. High throughput screening of pharmaceutical compound libraries with protein targets, and microarray screening of protein-protein interactions for proteomics are examples of applications that require the sensitivity and throughput afforded by this approach.
NANOTAGS FOR IMPROVED CUTTING DEPTH CORRELATION (2021)

During a drilling operation, rock cuttings are often sampled off a shale shaker for lithology and petrophysical characterization. These analyses play an important role in describing the subsurface; and it is important that the depth origin of the cuttings be accurately determined. Traditionally, mud-loggers determine the depth origin of the sampled cuttings by calculating the lag time required for the cuttings to travel from the bit to the surface. These calculations, however, can contain inaccuracies in the depth correlation due to the shuffling and settling of cuttings as they travel with drilling fluid to the surface, due to unplanned conditions like drilling an overgauge hole, and due to other unforeseen drilling events, especially critical in horizontal sections. We therefore aimed to remedy these inaccuracies by developing a series of styrene-based nanoparticles that tagged the cuttings as they were generated at the drillbit. These “NanoTags” were tested while drilling in Q4, 2019; and the results indicated that the NanoTags did in fact have the potential to identify some systematic errors compared with traditional mud logging calculations.
An Algorithm Measuring Donor Cell-Free DNA in Plasma of Cellular and Solid Organ Transplant Recipients That Does Not Require Donor or Recipient Genotyping (2016)

Cell-free DNA (cfDNA) has significant potential in the diagnosis and monitoring of clinical conditions. However, accurately and easily distinguishing the relative proportion of DNA molecules in a mixture derived from two different sources (i.e., donor and recipient tissues after transplantation) is challenging. In human cellular transplantation, there is currently no useable method to detect <i>in vivo</i> engraftment, and blood-based non-invasive tests for allograft rejection in solid organ transplantation are either non-specific or absent. Elevated levels of donor cfDNA have been shown to correlate with solid organ rejection, but complex methodology limits implementation of this promising biomarker. We describe a cost-effective method to quantify donor cfDNA in recipient plasma using a panel of high-frequency single nucleotide polymorphisms, next-generation (semiconductor) sequencing, and a novel mixture model algorithm. <i>In vitro</i>, our method accurately and rapidly determined donor:recipient DNA admixture. For <i>in vivo</i> testing, donor cfDNA was serially quantified in an infant with a urea cycle disorder after receiving six daily infusions of donor liver cells. Donor cfDNA isolated from 1 to 2 ml of recipient plasma was detected as late as 24 weeks after infusion suggesting engraftment. The percentage of circulating donor cfDNA was also assessed in pediatric and adult heart transplant recipients undergoing routine endomyocardial biopsy with levels observed to be stable over time and generally measuring <1% in cases without moderate or severe cellular rejection. Unlike existing non-invasive methods used to define the proportion of donor cfDNA in solid organ transplant patients, our assay does not require sex mismatch, donor genotyping, or whole-genome sequencing and potentially has broad application to detect cellular engraftment or allograft injury after transplantation.
ESCAPE OF HUMAN IMMUNODEFICIENCY VIRUS FROM IMMUNE CONTROL (1997)

Cytotoxic T lymphocytes (CTL) play a crucial role in the attempt to control infection with human immunodeficiency virus (HIV). Variation in epitopes recognized by CTL is common and frequently offers potential escape routes for mutant virus. Proof of escape, however, requires demonstration of increased frequency of virus particles or provirus that carry the escape sequence. There are now several recorded examples of virus variants that escape from CTL and are then selected. Most dramatic are those in which the CTL response has been dominated by CTL recognizing a single epitope that has suddenly changed, resulting in escape to fixation. This has been seen both early and late in the infection, leaving no doubt that escape occurs. Such escape is likely to be favored when the antiviral CTL response is oligoclonal and focused on a small number of immunodominant epitopes. The heterogeneous CTL response seen in many HIV-infected patients may result from successive waves of virus escape followed by new CTL responses specific for subdominant epitopes. Mutant virus can escape by several different routes, including failure of the mutated peptide to bind to the presenting HLA molecule and altered interactions with T cell receptors (TCR), including antagonism.
Phosphorylation and proteolytic modification of specific cytoskeletal proteins in human neutrophils stimulated by phorbol 12-myristate 13-acetate. (1987)

Stimulation of intact human neutrophils with phorbol 12-myristate 13-acetate results in the selective phosphorylation of two cytoskeletal protein components with molecular masses of 20 and 48 kDa. After phosphorylation the 48-kDa protein is no longer recovered as a component of the cytoskeletal fraction but is present as a fully soluble phosphoprotein. Phosphorylation of the 20-kDa protein (probably myosin light chains) signals a proteolytic conversion, catalyzed by calpain, to a smaller species having a molecular mass of approximately 15 kDa. Phosphorylation of both the 48- and 20-kDa proteins is related to the conversion of protein kinase C, also catalyzed by calpain, to the soluble fully active form. Leupeptin, an inhibitor of calpain, blocks both the phosphorylation of the target proteins and the proteolytic modification of the 20-kDa polypeptide. Thus, phosphorylation of cytoskeletal proteins and signal-directed proteolysis appear to be related processes that follow stimulation of human neutrophils by phorbol esters. The resulting changes in cytoskeletal organization may be involved in the expression of some neutrophil functions, such as exocytosis of specific granules.
Conditional routing of information to the cortex: A model of the basal ganglia’s role in cognitive coordination. (2010)

The basal ganglia play a central role in cognition and are involved in such general functions as action selection and reinforcement learning. Here, we present a model exploring the hypothesis that the basal ganglia implement a conditional information-routing system. The system directs the transmission of cortical signals between pairs of regions by manipulating separately the selection of sources and destinations of information transfers. We suggest that such a mechanism provides an account for several cognitive functions of the basal ganglia. The model also incorporates a possible mechanism by which subsequent transfers of information control the release of dopamine. This signal is used to produce novel stimulus-response associations by internalizing transferred cortical representations in the striatum. We discuss how the model is related to production systems and cognitive architectures. A series of simulations is presented to illustrate how the model can perform simple stimulus-response tasks, develop automatic behaviors, and provide an account of impairments in Parkinson's and Huntington's diseases.
Tomographic imaging of the angular‐dependent coherent‐scatter cross section (1997)

A new special-purpose computed tomographic (CT) imaging system is described which produces images based on measurements of the low-angle (0-10 degrees) x-ray diffraction properties of an object. Low-angle scatter in the diagnostic x-ray energy range is dominated by coherent scatter, and the system uses first-generation CT geometry to acquire a diffraction pattern for each pencil beam. The patterns are used to reconstruct a series of images which represent the coherent-scatter intensity at a series of scatter angles. To demonstrate the potential of coherent-scatter CT (CSCT), the scanner has been built and used to image a phantom consisting of a water-filled Lucite cylinder containing rods of polyethylene, Lucite, polycarbonate, and nylon. In this paper, the system is described and a sequence of CSCT images of this phantom is shown. Coherent-scatter cross sections of these materials are generated for each pixel from this sequence of images and compared with cross sections measured separately. The resulting excellent agreement shows that the angular-dependent coherent-scatter cross section can be accurately imaged in a tomographic slice through an object. These cross sections give material-specific information about the object. The long-term goal of this research is to make measurements of bone-mineral content for every pixel in a tomographic slice.
Waveguide-Coupled Graphene Optoelectronics (2013)

An overview of waveguide-coupled graphene optoelectronics is provided. A review of the optical properties of graphene is first provided and a motivation for waveguide-coupled graphene optoelectronics is given. This motivation is largely based upon the increased interaction length that can be achieved using such geometries. A derivation of the optical absorption for graphene interacting with a guided waveguide mode wave is provided. Device concepts for waveguide-coupled graphene optoelectronic devices, including optical modulators, photodetectors, and polarizers operating in the near- and mid-infrared regimes, are then described. This discussion provides a specific emphasis on the effect of disorder on the expected performance and energy consumption of graphene-based optical modulators. Finally, an outlook for future areas of exploration is given.
Real-Time Ultrasound Thermography and Thermometry [Life Sciences] (2018)

This article describes the basic principles of ultrasound thermography (UST) and its real-time implementation using graphics processing unit (GPU)-enabled software architecture. In medicine, the term thermography is mostly associated with heat-sensing infrared cameras for recording surface temperature changes. In this article, we use this term to describe the qualitative noninvasive imaging of tissue temperature change using any imaging modality. Examples of these modalities include microwave radiometry, magnetic resonance imaging (MRI), US imaging, and photoacoustic tomography. Of these imaging methods, US and MR are the most widely investigated. Table S1 in "Real-Time Thermography in Medicine" lists some US- and MRbased methods for tissue thermography reported in recent literature.
Comparative study of fully depleted and body-grounded non fully depleted SOI MOSFETs for high performance analog and mixed signal circuits (1995)

This paper compared the performance of conventional fully depleted (FD) SOI MOSFETs and body-grounded nonfully depleted (NFD) SOI MOSFETs for analog applications, A new low-barrier body-contact (LBBC) technology has been developed to provide effective body contact. Experimental results show that the NFD MOSFET's with LBBC structure give one order of magnitude higher output resistance, significantly lower flicker noise, improved subthreshold characteristics, and minimal threshold voltage variation compared with conventional FD SOI MOSFETs. The device characteristics of the LBBC MOSFET's are more desirable for fabricating high performance analog or mixed analog/digital CMOS circuits.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Comparison of Different PCR Approaches for Typing of Francisella tularensis Strains (2000)

In this study, we evaluated three PCR methods for epidemiological typing of Francisella tularensis: repetitive extragenic palindromic element PCR (REP-PCR), enterobacterial repetitive intergenic consensus sequence PCR (ERIC-PCR), and random amplified polymorphic DNA (RAPD) assay with both M13 and T3-T7 primers. The analysis was performed with 40 strains of F. tularensis isolated from hares, humans, ticks, and a vole. On the basis of the combination of REP, ERIC, and RAPD fingerprints, F. tularensis strains were divided into 17 genetic groups (designated A to Q), and one Francisella novicida strain was classified in group R. The F. novicida strain is of special concern, since previous genetic methods have been unable to clearly distinguish between F. tularensis and F. novicida. The F. tularensis isolates recovered from hares were included in groups A to J, M, and P; those recovered from humans were included in groups A, D, G, J, L, O, and N; those isolated from ticks were included in groups B and Q; and that recovered from a vole was in group K. The diversities calculated for the 40 F. tularensis isolates, according to Simpson's index, were 0.14 for REP-PCR, 0.52 for ERIC-PCR, 0.39 for RAPD assay with the M13 primer (RAPD/M13-PCR), and 0.65 for RAPD/T3-T7-PCR, and the diversity increased up to 0.90 when ERIC-PCR, RAPD/M13-PCR, and RAPD/T3-T7-PCR were combined. Our results suggest that although limited genetic heterogeneity among F. tularensis strains was observed, this small variation is enough to validate the PCR methods used in this study and their combinations, because they can provide safe, useful, and rapid tools for the typing of F. tularensis.
Oxcarbazepine: Preclinical Anticonvulsant Profile and Putative Mechanisms of Action (1994)

Oxcarbazepine (OCBZ, Trileptal) and its main human monohydroxy metabolite (MHD) protected mice and rats against generalized tonic-clonic seizures induced by electroshock with ED50 values between 13.5 and 20.5 mg/kg p.o. No tolerance toward this anticonvulsant effect was observed when rats were treated with OCBZ or MHD daily for 4 weeks. The therapeutic indices were 4 (OCBZ) and > 6 (MHD) for sedation (observation test, mice and rats) and 8 (MHD) or 10 (OCBZ) for motor impairment (rotorod test, mice). Both compounds were less potent in suppressing chemically induced seizures and did not significantly influence rat kindling development. At doses of 50 mg/kg p.o. and 20 mg/kg i.m. and higher, OCBZ and, to a lesser extent, MHD protected Rhesus monkeys from aluminum-induced chronically recurring partial seizures. In vitro, OCBZ and MHD suppressed sustained high-frequency repetitive firing of sodium-dependent action potentials in mouse neurons in cell culture with equal potency (medium effective concentration 5 x 10(-8) M/L). This effect is probably due in part to a direct effect on sodium channels. Patch-clamp studies on rat dorsal root ganglia cells revealed that up to a concentration of 3 x 10(-4) M, MHD did not significantly interact with L-type calcium currents, whereas OCBZ diminished them by about 30% at the concentration of 3 x 10(-4) M. In biochemical investigations, no brain neurotransmitter or modulator receptor site responsible for the anticonvulsant mechanism of action of OCBZ and MHD was identified.(ABSTRACT TRUNCATED AT 250 WORDS)