gebhart/patrepeval huggingface dataset:
Confocal resonators for measuring the surface resistance of high-temperature superconducting films (1991)

A quasioptical technique of measuring superconductor surface resistance using a confocal resonator has been developed. The method has advantages of nondestructive analysis, high sensitivity, easy extension to higher frequencies, convenient experimental setup, and flexibility in sample size. Tl-Ca-Ba-Cu-O high-temperature superconducting films have been measured with this technique and the measured surface resistances were less than 0.01 Ω at 36.135 GHz and 77 K. The measurements have been performed from 29 to 39 GHz, and all films showed roughly a quadratic dependence of surface resistance with frequency.
Effect of SiO2 on the Reliability of Multilayer Ceramic Capacitors with Ni Electrode. (1993)

Degradation behavior of insulation resistance of BaTi03 based Ni-electrode multilayer ceramic capacitors has been studied with special reference to the dielectric composition and grain boundary chemistry. The degradation behavior shows clear dependence on A/B of grain boundary layer. It is shown that Si02 extracts BaO and Cat) from (Ba1-XCax0)m(Ti1-YZrYO2) and then A/B of grain boundary layer become less than the unity. We have developed high capacitance multilayer ceramic capacitors as 10.50F in 3216 type with superior reliability, using newly developed dielectric material, (BaO),5(Ti1-YZrYO2)+aMnO+bY2O3+cV2O5+dWO3 (Y=0.18, m=1.004, a=0.2wt%, b=0.3wt%, c=0.04wt%, d=0.05wt%).
[Identification of T cell epitopes by reverse immunogenetics]. (1996)

Novel Strategy to identify CTL epitopes called "reverse immunogenetics" was introduced. CTL epitopes were identified as follows; (i) Identification of the motif of HLA class I binding peptides (ii) Selection of sequences matched to the motif of HLA class I binding peptides from HIV proteins and synthesis of peptides (iii) Identification of HLA class I binding peptides by the peptide binding assay (iv) Induction of CTL from PBL of HIV 1 infected individuals by HLA class I binding peptides. Multiple HIV-I epitopes presented by HLA-B35 were identified using this strategy.
Singular spectrum analysis applied to ultrasonic detection and imaging of brachytherapy seeds (2007)

Ultrasound-guided brachytherapy using titanium-shelled radioactive seeds is a popular, effective means of treating prostate cancer. Unfortunately, implantation using needles inserted transperitoneally causes gland movement and distortion, which often results in seed misplacement and dosimetry errors. If actual seed locations could be determined in the operating room, then corrections to dosimetry errors could be made immediately. However, seed specularity, shadowing, and tissue clutter make imaging seeds difficult using conventional ultrasound. Singular spectrum analysis (SSA) shows promise for reliably imaging radioactive seeds implanted in the prostate and enabling additional corrective implantations to be made in the operating room. SSA utilizes eigenvalues derived from the diagonalized correlation matrix of envelope-detected radio-frequency echo signals to yield a P value indicative of the likelihood of a seed-specific repetitive signal. We demonstrated the potential of SSA for seed detection and imaging and illustrated the trade-off considerations for optimization of SSA in clinical applications using simulations assessing performance as a function of different levels of noise and the presence of repetitive signals with various repetition periods; experiments in an ideal scattering environment; and experiments using seeds implanted in beef.
Acoustic model adaptation via Linear Spline Interpolation for robust speech recognition (2010)

We recently proposed a new algorithm to perform acoustic model adaptation to noisy environments called Linear Spline Interpolation (LSI). In this method, the nonlinear relationship between clean and noisy speech features is modeled using linear spline regression. Linear spline parameters that minimize the error the between the predicted noisy features and the actual noisy features are learned from training data. A variance associated with each spline segment captures the uncertainty in the assumed model. In this work, we extend the LSI algorithm in two ways. First, the adaptation scheme is extended to compensate for the presence of linear channel distortion. Second, we show how the noise and channel parameters can be updated during decoding in an unsupervised manner within the LSI framework. Using LSI, we obtain an average relative improvement in word error rate of 10.8% over VTS adaptation on the Aurora 2 task with improvements of 15-18% at SNRs between 10 and 15 dB.
Patch management automation for enterprise cloud (2012)

Applying patches to operating systems, middleware, and applications is considered a major IT pain point due to several reasons. The operating systems and software are of myriad types, there is interdependency among the updates, operating system, and applications, there is lack of standardization among different enterprise customers, and finally testing the applications and operating systems post-update is challenging. As a result, human operator is involved in different stages of the patching process, making it costly and cumbersome. Cloud can help standardize various offerings to customers, and potentially remove human operators. However, it introduces other challenges such as VM time zones and restoring VMs from snapshots which are not present in traditional enterprise environments. We discuss the challenges of achieving patch automation in a Cloud, and then describe our solution.
Genomic organization of GB viruses A and B: two new members of the Flaviviridae associated with GB agent hepatitis (1995)

The genomes of two positive-strand RNA viruses have recently been cloned from the serum of a GB agent-infected tamarin by using representational difference analysis. The two agent, GB viruses A and B (GBV-A and GBV-B, respectively), have genomes of 9,493 and 9,143 nucleotides, respectively, and single large open reading frames that encode potential polyprotein precursors of 2,972 and 2,864 amino acids, respectively. The genomes of these agents are organized much like those of other pestiviruses and flaviviruses, with genes predicted to encode structural and nonstructural proteins located at the 5' and 3' ends, respectively. Amino acid sequence alignments and subsequent phylogenetic analysis of the RNA-dependent RNA polymerases (RdRps) of GBV-A and GBV-B show that they possess conserved sequence motifs associated with supergroup II RNA polymerases of positive-strand RNA viruses. On the basis of similar analyses, the GBV-A- and GBV-B-encoded helicases show significant identity with the supergroup II helicases of positive-strand RNA viruses. Within the supergroup II RNA polymerases and helicases, GBV-A and GBV-B are most closely related to the hepatitis C virus group. Across their entire open reading frames, the GB agents exhibit 27% amino sequence identity to each other, approximately 28% identity to hepatitis C virus type 1, and approximately 20% identity to either bovine viral diarrhea virus or yellow fever virus. The degree of sequence divergence between GBV-A and GBV-B and other Flaviviridae members demonstrates that the GB agents are representatives of two new genera within the Flaviviridae family.
The hybrid volumetric ventriculoid: a model for MR-SPAMM 3-D analysis (2002)

The authors introduce the Hybrid Volumetric Ventriculoid (HVV), a model for quantitatively analysing 3-D Left Ventricular (LV) geometry and motion from tagged MR (SPAMM) images. It is the first model (in parallel with Park et al., 1995) which is both hybrid and volumetric. It is hybrid in that it is comprised of a global (parametric) component and a local (explicit) component which form a composite model capable of resembling an LV with arbitrary precision. Among other advantages, this formulation allows the model to provide a concise description of the LV's gross shape for comparison with a "normal" population while at the same time being detailed enough to recover local material measures (i.e., strain). Since the HVV is volumetric it may be deformed directly from myocardial MR tag intersection displacements without prior processing. Deformation is cast as an energy minimization in which lower energies imply a better fit. The authors' paradigm extends the state of the art myocardial motion recovery to directly include myocardial contour information. This improves the overall model fit by helping to overcome the inherent sparsity of MR-tag data. the authors apply an HVV to volunteer multi-slice, multi-phase SPAMM data sets taken from orthogonal views and report LV strain, as well as motion parameters quantifying myocardial thickening.
, a Novel Gene Preferentially Expressed in Aortic Smooth Muscle Cells, Is Down-regulated by Vascular Injury (1996)

Despite the importance of phenotypic alterations in arterial smooth muscle cells (ASMC) during the pathogenesis of arteriosclerosis, little is known about genes that define differentiated ASMC. Using differential mRNA display, we isolated a novel gene preferentially expressed in the rat aorta and termed this gene APEG-1. The cDNA of rat APEG-1 contained an open reading frame encoding 113 amino acids, which would predict a basic protein of 12.7 kDa. The amino acid sequence of rat APEG-1 was highly conserved among human and mouse homologues (97 and 98%, respectively). Using an APEG-1 fusion protein containing an N-terminal c-Myc tag, we identified APEG-1 as a nuclear protein. By in situ hybridization, APEG-1 mRNA was expressed in rat ASMC. Although APEG-1 was expressed highly in differentiated ASMC in vivo, its expression was quickly down-regulated and disappeared in dedifferentiated ASMC in culture. In vivo, APEG-1 mRNA levels decreased by more than 80% in response to vascular injury as ASMC changed from a quiescent to a proliferative phenotype. Taken together, these data indicate that APEG-1 is a novel marker for differentiated ASMC and may have a role in regulating growth and differentiation of this cell type.
Ribosomal Synthesis of Natural‐Product‐Like Bicyclic Peptides in <i>Escherichia coli</i> (2015)

Methods to access natural-product-like macrocyclic peptides can disclose new opportunities for the exploration of this important structural class for chemical biology and drug discovery applications. Here, the scope and mechanism of a novel strategy for directing the biosynthesis of thioether-bridged bicyclic peptides in bacterial cells was investigated. This method entails split intein-catalyzed head-to-tail cyclization of a ribosomally produced precursor peptide, combined with inter-side-chain crosslinking through a genetically encoded cysteine-reactive amino acid. This strategy could be successfully applied to achieve formation of structurally diverse bicyclic peptides with high efficiency and selectivity in Escherichia coli. Insights into the sequence of reactions underlying the peptide bicyclization process were gained from time-course experiments. Finally, the potential utility of this methodology toward the discovery of macrocyclic peptides with enhanced functional properties was demonstrated through the isolation of a bicyclic peptide with sub-micromolar affinity for streptavidin.
Design of synthetic oligoribonucleotide-based agonists of Toll-like receptor 3 and their immune response profiles in vitro and in vivo (2012)

Double-stranded RNA of viral origin and enzymatically synthesized poly I:C act as agonists of TLR3 and induce immune responses. We have designed and synthesized double-stranded synthetic oligoribonucleotides (dsORNs) which act as agonists of TLR3. Each strand of dsORN contains two distinct segments, namely an alignment segment composed of a heteronucleotide sequence and an oligo inosine (I) or an oligo cytidine (C) segment. We report here the results of studies of dsORNs containing varying lengths and compositions of alignment and oligo I/oligo C segments. dsORNs of 50-mer length with a 15-mer alignment segment and a 35-mer oligo I/oligo C segment form stable duplexes under physiological conditions and induce TLR3-mediated immune responses. dsORNs activated the IRF3 signaling pathway in J774 cells, induced production of cytokines, including IFN-β, IFN-α, IP-10, IL-12 and IL-6, in murine and human cell-based assays and also induced multiple cytokines following systemic administration in mice and non-human primates.
Sensitive Cell-Based Assay for Determination of Human Immunodeficiency Virus Type 1 Coreceptor Tropism (2013)

CCR5 antagonists are a powerful new class of antiretroviral drugs that require a companion assay to evaluate the presence of CXCR4-tropic (non-R5) viruses prior to use in human immunodeficiency virus (HIV)-infected individuals. In this study, we have developed, characterized, verified, and prevalidated a novel phenotypic test to determine HIV-1 coreceptor tropism (VERITROP) based on a sensitive cell-to-cell fusion assay. A proprietary vector was constructed containing a near-full-length HIV-1 genome with the yeast uracil biosynthesis (URA3) gene replacing the HIV-1 env coding sequence. Patient-derived HIV-1 PCR products were introduced by homologous recombination using an innovative yeast-based cloning strategy. The env-expressing vectors were then used in a cell-to-cell fusion assay to determine the presence of R5 and/or non-R5 HIV-1 variants within the viral population. Results were compared with (i) the original version of Trofile (Monogram Biosciences, San Francisco, CA), (ii) population sequencing, and (iii) 454 pyrosequencing, with the genotypic data analyzed using several bioinformatics tools, i.e., the 11/24/25 rule, Geno2Pheno (2% to 5.75%, 3.5%, or 10% false-positive rate [FPR]), and webPSSM. VERITROP consistently detected minority non-R5 variants from clinical specimens, with an analytical sensitivity of 0.3%, with viral loads of ≥1,000 copies/ml, and from B and non-B subtypes. In a pilot study, a 73.7% (56/76) concordance was observed with the original Trofile assay, with 19 of the 20 discordant results corresponding to non-R5 variants detected using VERITROP and not by the original Trofile assay. The degree of concordance of VERITROP and Trofile with population and deep sequencing results depended on the algorithm used to determine HIV-1 coreceptor tropism. Overall, VERITROP showed better concordance with deep sequencing/Geno2Pheno at a 0.3% detection threshold (67%), whereas Trofile matched better with population sequencing (79%). However, 454 sequencing using Geno2Pheno at a 10% FPR and 0.3% threshold and VERITROP more accurately predicted the success of a maraviroc-based regimen. In conclusion, VERITROP may promote the development of new HIV coreceptor antagonists and aid in the treatment and management of HIV-infected individuals prior to and/or during treatment with this class of drugs.
Noise Analysis of Time-to-Digital Converter in All-Digital PLLs (2006)

In an all-digital PLL architecture the conventional phase-frequency detector is replaced in part by a time-to-digital converter. This paper presents an exact analysis of the mechanism by which reference clock jitter and/or supply/substrate noise are converted into TDC noise that is injected into the ADPLL loop. The cases of white and sinusoidal noise are considered and the analytical results are compared with simulations
The influence of eliminating the fixed electrode from an air-coupled, dual deflectable membrane, capacitive micromachined ultrasonic transducer (2014)

Multiple moving membrane, capacitive micromachined ultrasonic transducers (M <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> -CMUTs) benefit from a multiple vibrating membrane configuration that enhances the transducer properties. In this work, further improvement in the device displacement amplitude is achieved through eliminating the transducer fixed electrode. Two M <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> -CMUT devices have been fabricated and their electrical impedances are compared. It is demonstrated that the 50 μm radius transducer without the fixed electrode shows a 70% increase in the membrane displacement amplitude at a DC voltage of 20 V compared with the M <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> -CMUT with a fixed bottom electrode of the same dimension.
Tomographie optique par une technique d'holographie numérique en faible cohérence Optical tomography by means of a numerical low-coherence holographic technique (1997)

Digital holograms are recorded by a CCD camera and are numerically reconstructed, in intensity and phase, by means of an algorithm which calculates their discrete Fresnel transform. By using a low-coherence source, the tomography of a 3D scene can be performed without lateral scanning with a depth resolution equal to the coherence length and a lateral resolution equal to the diffraction limit of the microscope objective used
Synthesis of an Anti-Methicillin-Resistant <i>Staphylococcus aureus </i>(MRSA) Carbapenem via Stannatrane-Mediated Stille Coupling (2000)

A short synthesis of carbapenem 1 is described. The key step involves the cross-coupling of an enol triflate with an amino-substituted sp3 carbon. This cross-couping, which allows the introduction of the complete side chain in one step, utilizes a stannatrane as the heteroalkyl transfer reagent.
Terrain topography measurement using multipass polarimetric synthetic aperture radar data (2000)

A method has been investigated for the measurement of topography using airborne fully polarimetric synthetic aperture radar (SAR) data. Terrain slopes in both the range and azimuthal directions have been estimated using multipass flight geometries. Using these slope values, the Poisson equation was then solved to create a Digital Elevation Model (DEM) of the terrain topography. The method measures polarimetric orientation angles which are then converted into terrain slopes in the azimuthal direction. The conversion of these orientation angles into terrain slopes requires additional knowledge of the radar look angle and the range direction terrain slopes. The solution for slopes is, therefore, a problem coupled between the range and azimuthal directions. For specialized multipass flight geometries these orthogonal terrain slopes are solved for, and maps of terrain slopes are produced. In particular, the processing of two‐pass orthogonal and two‐pass antiparallel (headings Θ and Θ+ 180°) NASA ‐ Jet Propulsion Laboratory airborne SAR data sets has been carried out for an area in central California. When orthogonal slopes are derived using either of these data sets, a digital elevation model may be generated. The L band, polarimetric SAR (POLSAR) DEM created by this solution is compared to a coregistered C band, interferometric SAR (IFSAR) DEM. Similar comparisons are made for terrain slopes in the azimuthal ‐ range directions which are generated by the POLSAR and IFSAR elevation data. The polarimetric SAR, operating from an aircraft, or satellite, in a strip‐mapping mode, is capable of measuring terrain topography for large areas provided that phase‐preserving fully polarimetric data are taken. Polarimetric SAR data are also widely used for studies of crop classification, surface roughness, biomass density, and soil moisture content. All of these studies are adversely affected by scattering changes attributable to topography. The technique investigated here potentially offers a means to correct for these effects by making simultaneous, coregistered estimates of local orthogonal terrain slopes.
Review article: the safety and efficacy of alosetron, a 5‐HT<sub>3</sub> receptor antagonist, in female irritable bowel syndrome patients (1999)

Irritable bowel syndrome (IBS) is one of the most common gastrointestinal-related conditions. In this review, the safety and efficacy of alosetron, a potent and selective 5-HT3 receptor antagonist, in the treatment of IBS are discussed. Alosetron has been shown to produce statistically significant improvements in abdominal pain, stool consistency, stool frequency and urgency in female IBS patients. By contrast, no consistent improvement has been seen in male IBS patients treated with alosetron. The only adverse event of note with alosetron was constipation, and this represents a class effect of 5-HT3 receptor antagonists. In conclusion, alosetron is a safe and effective treatment for female IBS patients.
An Efficient CVA-Based Decoding Algorithm for Tail-Biting Codes (2011)

Tail-biting convolutional codes (TBCC) provide an efficient method to eliminate the rate loss caused by the known-tail encoding. To simplify the decoder design, circular Viterbi algorithm (CVA) has been proposed by recording and repeating the received block of (soft) symbols beyond the block boundary and continuing Viterbi decoding. However, CVA does not converge in the presence of circular trap. A checking rule is proposed for detecting the circular trap in existing CVA. Based on this rule, an efficient CVA-based decoding algorithm is obtained for tail-biting codes, which exhibits near-optimal performance for both short and long tail-biting codes. This new scheme provides faster convergence speed than the conventional CVA without increasing in complexity and storage space.
A poled electrooptic fiber (1996)

A simple fabrication technique, readily extensible to volume manufacturing, is presented to produce an electrooptically active fiber segment that can be simply integrated into optoelectronic devices. The fabrication technique offers a dielectric isolation structure surrounding the fiber to allow high field poling, a pair of electrodes used both for poling and for inducing an electrooptic effect that can be lithographically defined for either velocity-matched, high speed RF modulation or quasiphasematched three-wave mixing interactions, and ends of the fiber unaffected by the fabrication and available for splicing with additional fiber sections. An electrooptic coefficient, including overlap between the nonlinearity and the fiber mode, as high as 0.3 pm/V was obtained by combined temperature/electric field poling.
Identification and Structure Characterization of a Cdk Inhibitory Peptide Derived from Neuronal-specific Cdk5 Activator (1999)

The activation of cyclin-dependent kinase 5 (Cdk5) depends on the binding of its neuronal specific activator Nck5a. The minimal activation domain of Nck5a is located in the region of amino acid residues 150 to 291 (Tang, D., Chun, A. C. S., Zhang, M., and Wang, J. H. (1997) J. Biol. Chem. 272, 12318-12327). In this work we show that a 29-residue peptide, denoted as the alphaN peptide, encompassing amino acid residues Gln145 to Asp173 of Nck5a is capable of binding Cdk5 to result in kinase inhibition. This peptide also inhibits an active phospho-Cdk2-cyclin A complex, with a similar potency. Direct competition experiments have shown that this inhibitory peptide does not compete with Nck5a or cyclin A for Cdk5 or Cdk2, respectively. Steady state kinetic analysis has indicated that the alphaN peptide acts as a non-competitive inhibitor of Cdk5. Nck5a complex with respect to the peptide substrate. To understand the molecular basis of kinase inhibition by the peptide, we determined the structure of the peptide in solution by circular dichroism and two-dimensional 1H NMR spectroscopy. The peptide adopts an amphipathic alpha-helical structure from residues Ser149 to Arg162 which can be further stabilized by the helix-stabilizing solvent trifluoroethanol. The hydrophobic face of the helix is likely to be the kinase binding surface.