gebhart/patrepeval huggingface dataset:
SomatiCA: Identifying, Characterizing and Quantifying Somatic Copy Number Aberrations from Cancer Genome Sequencing Data (2013)

Whole genome sequencing of matched tumor-normal sample pairs is becoming routine in cancer research. However, analysis of somatic copy-number changes from sequencing data is still challenging because of insufficient sequencing coverage, unknown tumor sample purity and subclonal heterogeneity. Here we describe a computational framework, named SomatiCA, which explicitly accounts for tumor purity and subclonality in the analysis of somatic copy-number profiles. Taking read depths (RD) and lesser allele frequencies (LAF) as input, SomatiCA will output 1) admixture rate for each tumor sample, 2) somatic allelic copy-number for each genomic segment, 3) fraction of tumor cells with subclonal change in each somatic copy number aberration (SCNA), and 4) a list of substantial genomic aberration events including gain, loss and LOH. SomatiCA is available as a Bioconductor R package at http://www.bioconductor.org/packages/2.13/bioc/html/SomatiCA.html.
Parallel push-pull hybrid circuit. (1963)

This paper deals with a new hybrid circuit for signal branching or combining in parallel push-pull amplifiers. The purpose of the new hybrid circuit is to perform the branching or combining of two pairs of signals for parallel push-pull operation, each consisting of two oppositely phased, balanced signals. The advantage of combining two pairs of parallel push-pull signals by a single component of new hybrid circuit is clear; one would require a multiplicity of conventional rat-race circuits to do the same job, inasmuch as the basic rat-race circuit is limited to only one pair of push-pull signals. The new hybrid circuit is further elaborated to improve the performance for combining unbalanced push-pull signals by: (1) showing that the combination of unbalanced push-pull signals is equivalent to the super-position of cophase components on the balanced antiphase components; (2) analyzing the effect of the cophase components in the hybrid circuit; and (3) devising means of improving the adverse effects of the cophase components. Finally, an evaluation is made of a parallel push-pull amplifier using the new hybrid circuit in comparison with the conventional rat-race circuits required for the same parallel push-pull operation.
Knocking down Interferon Induced Transmembrane protein 1 (IFITM1) Inhibited Cell Proliferation and Invasion in Glioma Cells (2010)

Here we investigated the role of Interferon Induced Transmembrane Protein 1 (IFITM1) in glioma carcinogenesis. We determined the expression levels of IFITM1 in different glioma cell lines, examined its role in cell proliferation/cell migration & invasion, and the corresponding molecular mechanism in glioma cells. Our results showed that IFITM1 mRNA level was elevated in four of five widely used glioma cell lines and positively correlated with their tumorigenic abilities. Suppression of IFITM1 by siIFITM1 inhibited the proliferation of U‐373 MG and U‐87 MG glioma cells lines in a time dependent manner. The growth inhibition effect of siIFITM1 was mediated not by apoptosis but G1 to S phase cell cycle arrest, which are mediated via decreased G1/S‐specific cylin‐D1, cyclin‐dependent kinase 2 (CDK2) and increased cyclin‐dependent kinase inhibitor 1B (p27kip1). Furthermore, IFITM1 knockdown significantly inhibit the migration and invasion of U‐373 MG and U‐87 MG cells, which was mediated by decreased MMP9 expression and activity. Taken together, these results suggested IFITM1 might be a potential candidate oncogene in glioma.
Balanced antipodal Vivaldi antenna for breast cancer detection (2007)

A new ultra-wideband antenna for tissue sensing adaptive radar system is presented in this paper. The antenna is based on a balanced antipodal Vivaldi design. The measurements showed that the antenna has better that -10 dB return loss above 2.4 GHz. Simulation indicated that the antennas is capable of sending very short pulses with fidelity above 0.96 at a distance of 20 mm and up to 0.994 further away from the antenna aperture. 70% of the accepted energy is radiated in the endfire direction with a beamwidth of 34 mm by 44 mm on a plane 20 mm away. (5 pages)
Structural Characterization of Vulcanizates Part X. Thiol-Disulfide Interchange for Cleaving Disulfide Crosslinks in Natural Rubber Vulcanizates (1970)

Abstract The thiol-disulfide exchange reaction is shown to be applicable to cleavage of disulfide crosslinks in accelerated sulfur vulcanizates of natural rubber. The reaction, in conjunction with the previously reported selective cleavage of polysulfide crosslinks, is used to determine the distribution of crosslink types for several accelerated sulfur vulcanization systems as a function of cure time. Discrepancies between the results and published results obtained using the reagent sodium di- n -butyl phosphite for disulfide crosslink cleavage are discussed.
An empirical assessment of the relationships between service quality, satisfaction and value : a tourism study (2002)

This study considers the interplay between customer satisfaction, service quality and value in a tourism environment. The basic point of departure is that the business of marketing is still customer satisfaction, and that customer satisfaction will determine value perceptions and thus eventually behavioural intentions such as actual buying. However, marketers and particularly tourism marketers need to develop accurate models of the process by which these constructs interact. A theoretical model of the hypothesised relationships in the customer's service assessment process is proposed and empirically tested in a tourism environment. The findings of this study provide considerable empirical support for the Experiential Model of Service Evaluation. The model suggests a definite causal ordering : that service quality influences customer satisfaction, which in turn determines value perceptions.
DARPA interest in diffractive sensors (2007)

The Defense Advanced Research Projects Agency (DARPA) is in a unique position to question traditional sensing architectures and concepts while possessing both the charter and funding to explore and develop the technologies necessary to accomplish both existing and desired applications. This paper describes the logical flow from the need for long-term tracking of an extremely large number of vehicles in an urban environment, through the fundamental requirements and the application to the phenomenology tradespace.
Space-Time Video Super-Resolution Using Temporal Profiles (2020)

In this paper, we propose a novel space-time video super-resolution method, which aims to recover a high-frame-rate and high-resolution video from its low-frame-rate and low-resolution observation. Existing solutions seldom consider the spatial-temporal correlation and the long-term temporal context simultaneously and thus are limited in the restoration performance. Inspired by the epipolar-plane image used in multi-view computer vision tasks, we first propose the concept of temporal-profile super-resolution to directly exploit the spatial-temporal correlation in the long-term temporal context. Then, we specifically design a feature shuffling module for spatial retargeting and spatial-temporal information fusion, which is followed by a refining module for artifacts alleviation and detail enhancement. Different from existing solutions, our method does not require any explicit or implicit motion estimation, making it lightweight and flexible to handle any number of input frames. Comprehensive experimental results demonstrate that our method not only generates superior space-time video super-resolution results but also retains competitive implementation efficiency.
Digital current sharing method for mulitiphase DC-DC converters using the peak input voltage (2011)

This paper describes a new digital current sharing method to overcome the inaccuracy of the current sensing circuitry for multiphase dc-dc converters. The difference between sensed current values causes the unequal current distribution in multiphase dc-dc converters even though they are controlled by the same current reference. The proposed digital minimum peak voltage tracking (MPVT) algorithm calculates the required current reference adjustment value using only the peak input ripple voltage information without an additional input current sensing circuit. The MPVT algorithm achieves the equal current distribution between phases of the converter with high parameter insensitivity. For the experimental verification, a 500W two phase interleaved synchronous buck dc-dc converter with 30-42V input range and 24V (20A) output is implemented.
The Regulation of Energy Balance: An Overview (2009)

10.1002/9780470712221.ch5.abs This chapter contains sections titled: Regulation of body fat and composition Regulation of energy intake and expenditure Lessons from other species: informative or misleading? Causes of obesity References
SecA2-dependent secretion of autolytic enzymes promotes <i>Listeria monocytogenes</i> pathogenesis (2003)

Pathogenic bacteria secrete proteins that promote invasion of host tissues and resistance to immune responses. However, secretion mechanisms that contribute to the enormous morbidity and mortality of Gram-positive bacteria are largely undefined. An auxiliary protein secretion system (SecA2) has recently emerged in Listeria monocytogenes and eight other Gram-positive pathogens. Here, a proteomics approach identified seventeen SecA2-dependent secreted and surface proteins of L. monocytogenes, the two most abundant of which [the p60 and N-acetylmuramidase (NamA) autolysins] hydrolyze bacterial peptidoglycan (PGN) and contribute to host colonization. SecA2-deficient (DeltaSecA2) bacteria were rapidly cleared after systemic infection of murine hosts, and in cultured cells showed reduced cell-cell spread. p60 or NamA deficiencies (Deltap60 and DeltaNamA) caused intermediate reductions in bacterial virulence in vivo, yet showed no defect for infection of cultured cells. Restoration of virulence in Deltap60 bacteria required full-length p60 with an intact catalytic domain, suggesting that PGN hydrolysis by p60 is crucial for L. monocytogenes virulence. Coordinated PGN hydrolysis by p60 and NamA activities is predicted to generate a muramyl glycopeptide, glucosaminylmuramyl dipeptide (GMDP), which is known to modify host inflammatory responses. Thus, SecA2-dependent secretion may promote release of muramyl peptides that subvert host pattern recognition.
Phonon-based scalable quantum computing and sensing (Presentation Video) (2015)

Quantum computing fundamentally depends on the ability to concurrently entangle and individually address/control a large number of qubits. In general, the primary inhibitors of large scale entanglement are qubit dependent; for example inhomogeneity in quantum dots, spectral crowding brought about by proximity-based entanglement in ions, weak interactions of neutral atoms, and the fabrication tolerances in the case of Si-vacancies or SQUIDs. We propose an inherently scalable solid-state qubit system with individually addressable qubits based on the coupling of a phonon with an acceptor impurity in a high-Q Phononic Crystal resonant cavity. Due to their unique nonlinear properties, phonons enable new opportunities for quantum devices and physics. We present a phononic crystal-based platform for observing the phonon analogy of cavity quantum electrodynamics, called phonodynamics, in a solid-state system. Practical schemes involve selective placement of a single acceptor atom in the peak of the strain field in a high-Q phononic crystal cavity that enables strong coupling of the phonon modes to the energy levels of the atom. A qubit is then created by entangling a phonon at the resonance frequency of the cavity with the atomic acceptor states. We show theoretical optimization of the cavity design and excitation waveguides, along with estimated performance figures of the phoniton system. Qubits based on this half-sound, half-matter quasi-particle, may outcompete other quantum architectures in terms of combined emission rate, coherence lifetime, and fabrication demands.
Protein kinase C isoenzymes display differential affinity for phorbol esters. Analysis of phorbol ester receptors in B cell differentiation (1992)

Protein kinase C (PKC) comprises a family of distinct isoenzymes that are involved in signal transduction pathways linking the cell to triggers perceived via membrane receptors. These isoenzymes differ in their tissue distribution, activation requirements, and substrate specificity. One common denominator among different PKC subspecies is their activation by phorbol esters. We have developed a sensitive method permitting the measurement of phorbol ester binding sites, their quantitation, as well as their dissociation kinetics, by performing cytofluorometric analyses on intact cells or on isolated PKC associated to phosphatidylserine vesicles incubated in the presence of fluorochrome-labeled phorbol ester. Both PKC isozymes beta I/beta II and alpha from brain and spleen after incorporation into phosphatidylserine vesicles, display affinities with apparent Kd of 120 and 50 nM, respectively; although PKC gamma from brain exhibits a Kd of 210 nM. In addition to these receptors, on PKC isozymes from spleen, an intermediate affinity phorbol ester receptor (Kd of 3 nM) and an additional high affinity phorbol ester binding site with a Kd of 0.1 to 0.5 nM were also detected. This latter receptor comigrates with high m.w. PKC isoforms. In different cell lines, the phorbol ester binding patterns, as well as the expression of individual PKC isoenzymes, could be positively correlated.
Crystalline Bacterial Cell Surface Layers (S-Layers): A Versatile Self-Assembly System (2005)

I. Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 583 II. Location and Ultrastructure of S-Layers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 584 III. Isolation, Chemical Characterization, and Molecular Biology . . . . . . . . . . . . . . . . . . . . . . 585 IV. Dynamic Process of Assembly of S-Layers During Cell Growth . . . . . . . . . . . . . . . . . . . . 588A. Incorporation of New Subunits into Closed Surface Crystals . . . . . . . . . . . . . . . . . . . 588 V. Self-Assembly of Isolated S-Layer Subunits . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 591A. Self-Assembly in Suspension . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 591 B. Self-Assembly on Lipid Films and at the Air-Water Interface . . . . . . . . . . . . . . . . . . 596 C. Self-Assembly on Solid Supports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 601 D. Lipid Membranes on Porous and Solid Supports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 602 E. Self-Assembly on Liposomes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 604VI. Patterning of S-Layers Recrystallized on Solid Supports . . . . . . . . . . . . . . . . . . . . . . . . . . 606 VII. S-Layers as Matrices for the Immobilization of Functional Moleculesand Functional S-Layer-Fusion Proteins . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 608 VIII. S-Layers as Templates in the Formation of Regularly Arranged Nanoparticles . . . . . . . . 609 IX. Conclusions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 611 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 612I. INTRODUCTIONSelf-assembly of molecules into monomolecular arrays is a new and rapidly growing transdisciplinary scientific and engineering field. Particularly the immobilization of biomolecules in an ordered fashion on solid substrates and their controlled confinement in definite areas of nanometer dimensions are key requirements for many applications in molecular nanotechnology and nanobiotechnology including the development of bioanalytical sensors, molecular electronics, biocompatible surfaces, and signal processing between cells and integrated circuits.
Total Synthesis of (±)‐Wortmannin (2002)

A potent and specific phosphoinositide 3-kinase inhibitor (±)-wortmannin has been achieved through an intramolecular Heck reaction for the construction of an allylic quaternary carbon center and a diosphenol–Claisen rearrangement (see scheme). SEM=2-(Trimethylsilyl)ethoxymethyl. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2002/z50016_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Improved Inspection Techniques for Steel Prestressing/Post-tensioning Strand : Volume I (2012)

Post-tensioned bridges require a detailed inspection of their post-tensioning systems since damage in these systems is not evident and can result in costly repairs/replacements, loss of integrity and reduction in safety of the bridge. Different nondestructive evaluation (NDE) techniques can be used for the inspection of post-tensioning systems however; there is no systematic way by which a particular NDE technology may be selected for a particular job. This project presents elements and foundation for development of a systematic, job specific approach for the selection of NDE technology for inspection of the post-tensioning systems. In order to achieve this goal, factors affecting the performance of NDE techniques used for the condition assessment of the post-tensioning systems are identified. NDE techniques are then grouped according to their underlying phenomenological bases to put forth the working principles, and pros and cons that can be used for the development of a ranking system. It has been found that the major difference in grouting practice before and after 2000 affects the selection of NDE technique for the inspection of post-tensioning systems. Other factors affecting the performance of the NDE techniques are the duct system, geometrically difficult zones, and the types of defects. Separate sets of NDE technique are recommended for the internal/external ducts positioned along the traffic and geometrically difficult zones. A job specific Ranking Index is proposed for the selection of NDE that takes into account not only the above mentioned factors, but also the cost of conducting NDE. Based on the project findings a roadmap to develop comprehensive methodology to effectively assess the condition of post-tensioned bridge systems is presented.
Cannabis XVIII: Isolation and synthesis of olivetol derivatives formed in the pyrolysis of cannabidiol (1978)

Abstract Pyrolysis of cannabidiol results in the formation of several new cannabinoids and cracking products. In an earlier paper several structures were proposed for the cracking products based on GCMS measurements. In this paper the isolation and synthesis of the majority of these cracking products ‐ which are in general C (2) ‐substituted olivetol derivatives ‐ is described. 2,6‐Dimethoxy‐4‐pentylphenyl‐lithium and the cuprates derived therefrom proved to be very promising intermediates for the synthesis of olivetol derivatives specifically substituted at C (2) . The versatility of these reagents is illustrated by several examples.
Herpesvirus proteinase: site-directed mutagenesis used to study maturational, release, and inactivation cleavage sites of precursor and to identify a possible catalytic site serine and histidine (1993)

The cytomegalovirus maturational proteinase is synthesized as a precursor that undergoes at least three processing cleavages. Two of these were predicted to be at highly conserved consensus sequences--one near the carboxyl end of the precursor, called the maturational (M) site, and the other near the middle of the precursor, called the release (R) site. A third less-well-conserved cleavage site, called the inactivation (I) site, was also identified near the middle of the human cytomegalovirus 28-kDa assemblin homolog. We have used site-directed mutagenesis to verify all three predicted sequences in the simian cytomegalovirus proteinase, and have shown that the proteinase precursor is active without cleavage at these sites. We have also shown that the P4 tyrosine and the P2 lysine of the R site were more sensitive to substitution than the other R- and M-site residues tested: substitution of alanine for P4 tyrosine at the R site severely reduced cleavage at that site but not at the M site, and substitution of asparagine for lysine at P2 of the R site reduced M-site cleavage and nearly eliminated I-site cleavage but had little effect on R-site cleavage. With the exception of P1' serine, all R-site mutations hindered I-site cleavage, suggesting a role for the carboxyl end of assemblin in I-site cleavage. Pulse-chase radiolabeling and site-directed mutagenesis indicated that assemblin is metabolically unstable and is degraded by cleavage at its I site. Fourteen amino acid substitutions were also made in assemblin, the enzymatic amino half of the proteinase precursor. Among those tested, only 2 amino acids were identified as essential for activity: the single absolutely conserved serine and one of the two absolutely conserved histidines. When the highly conserved glutamic acid (Glu22) was substituted, the proteinase was able to cleave at the M and I sites but not at the R site, suggesting either a direct (e.g., substrate recognition) or indirect (e.g., protein conformation) role for this residue in determining substrate specificity.
Anti-Allergic Properties of the Natural PAF Antagonist Yangambin (1997)

In this study we examined the ability of the furofuran lignan yangambin to influence the local and systemic responses induced by antigen or PAF in actively sensitized or normal rats. Given intraperitoneally 1 h before stimulation, yangambin inhibited the pleural neutrophil and eosinophil infiltration evoked by the i.pl. injection of PAF or antigen into normal or 14 daysensitized rats whereas plasma exudation evoked by both stimuli was unaffected. The pleural neutrophil influx (6 h) after LTB4 stimulation was also significantly inhibited by yangambin. We also evidenced that the hemoconcentration, thrombocytopenia, and leucocytosis noted after i.v. PAF were all attenuated by yangambin. In actively sensitized rats, pretreatment with yangambin failed to modify the antigen-induced hemoconcentration and leucocytosis, but dose-dependently abrogated the thrombocytopenia noted 1 h post-stimulation. In vitro, the anaphylactic contraction of longitudinal jejunal segments to antigen challenge was significantly inhibited by yangambin (10(-5)-10(-4) M). Likewise, the contraction of jejunal segments from normal rats to PAF was markedly blocked by yangambin under conditions where the response to 5-hydroxytryptamine (5-HT) was not altered. In conclusion, our results show that antigen- and PAF-induced pleural neutrophil and eosinophil accumulation, but not exudation, is sensitive to treatment with yangambin. In addition, yangambin also suppressed the pleural neutrophil infiltration triggered by LTB4 as well as the blood thrombocytopenia and intestinal anaphylaxis elicited by antigen in rats. Thus, our findings indicate that yangambin shows an antagonistic action on receptors other than those of PAF, i.e., LTB4, and strongly suggest that it may be a useful drug in the treatment of some allergic inflammatory responses.