gebhart/patrepeval huggingface dataset:
Abstract 4161: Development of a real-time multiplex PCR assay for the detection of FGFR3 mutations in urine (2011)

Abstract Background: We have recently reported the development of a Multi-Analyte Diagnostic Readout (MADR) non-invasive assay using urinary Matrix Metalloproteinases (MMPs) and FGFR3 as triage monitors in high-risk bladder cancer populations. This concept combines the marker performance characteristics of protein and DNA biomarkers into one assay for optimal performance. Eight common FGFR3 mutations in 3 exons have been associated with bladder cancer. Analysis of mutational status for each single mutation required 8 amplification steps, which were costly and time consuming. We have now developed a real-time multiplexed FGFR3 assay, generating a cost-effective, clinically applicable assay for the detection of FGFR3 mutations in urine. Methods: Our approach involves a two-step PCR amplification process. The initial round generates exon specific PCR products, which are then used as template for real-time PCR mutation detection utilizing locked nucleic acid (LNA) oligonucleotides. These LNA suppress wild-type DNA amplification. To convert our existing FGFR3 assay to a multiplex format, primary amplifications of exons 7, 10, and 15 were combined into a single real-time PCR assay for exon specific amplification and DNA quantitation. The LNA-mediated mutation detection was then converted from 4 reactions to 2 duplex amplifications. All multiplex assays were carried out on the Roche LC 480 real-time PCR platform. Results: To validate the new the multiplex format, FGFR3 multiplex analysis was performed on DNA isolated from 50 Ta stage bladder tumors. FGFR3 mutations were detected in 90% (48/50) of the tumors. To directly compare performance with single mutation analysis, 40 urine samples previously analyzed using the singleplex format were again tested using the multiplex FGFR3 assay. 100% concordance was seen between the two assay formats. Conclusions: By multiplexing the FGFR3 mutation analysis we reduced the number of amplification steps, improving assay turnaround time and throughput, without compromising assay performance. The FGFR3 multiplex analysis provides a robust, cost-effective DNA assay that in combination with MMP protein analysis delivers a clinically applicable assay with optimal performance. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 4161. doi:10.1158/1538-7445.AM2011-4161
Selective Crystal Growth and Structural, Optical, and Electronic Studies of Mn3Ta2O8 (2015)

Mn3Ta2O8, a stable targeted material with an unusual and complex cation topology in the complicated Mn-Ta-O phase space, has been grown as a ≈3-cm-long single crystal via the optical floating-zone technique. Single-crystal absorbance studies determine the band gap as 1.89 eV, which agrees with the value obtained from density functional theory electronic-band-structure calculations. The valence band consists of the hybridized Mn d-O p states, whereas the bottom of the conduction band is formed by the Ta d states. Furthermore, out of the three crystallographically distinct Mn atoms that are four-, seven-, or eight-coordinate, only the former two contribute their states near the top of the valence band and hence govern the electronic transitions across the band gap.
Structure-based design of inhibitors of purine nucleoside phosphorylase. 3. 9-Arylmethyl derivatives of 9-deazaguanine substituted on the arylmethyl group. [Erratum to document cited in CA119(25):271601v] (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleStructure-based design of inhibitors of purine nucleoside phosphorylase. 3. 9-Arylmethyl derivatives of 9-deazaguanine substituted on the arylmethyl group. [Erratum to document cited in CA119(25):271601v]Mark D. Erion, Shri Niwas, Jerry D. Rose, Subramaniam Ananthan, Mark Allen, John A. Secrist III, Y. Sudhakar Babu, Charles E. Bugg, Wayne C. Guida, and Cite this: J. Med. Chem. 1994, 37, 7, 1034Publication Date (Print):April 1, 1994Publication History Published online1 May 2002Published inissue 1 April 1994https://pubs.acs.org/doi/10.1021/jm00033a022https://doi.org/10.1021/jm00033a022research-articleACS PublicationsRequest reuse permissionsArticle Views49Altmetric-Citations2LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Analytical investigation of the switching frequency harmonic characteristic for common mode reduction modulator (2005)

Common mode voltage (CMV) generated by two-level voltage source rectifier/inverter adjustable speed drive (ASD) system is troublesome and requires extra hardware fixes, which increase production costs and can lead to increased installation costs. The use of the common mode reduction modulator (CMRM) to control the common mode voltage has received some attention over the past few years. It is attractive for its software selectivity, no additional components, etc. From a product design viewpoint, there is a need to analytically analyze and quantify the switching frequency harmonic characteristics for the CMRM. A complete design-oriented analytical analysis of the switching frequency harmonic characteristic of CMRM for a two-level voltage source rectifier/inverter ASD system is presented in this paper. An analytical harmonic flux formula for CMRM is derived, followed by a per carrier cycle and per fundamental cycle calculation of the harmonic flux RMS value. The analytical solution has been verified against both the simulated and the experimental tested load current harmonic components.
Crystallization and preliminary x‐ray analysis of glucose‐fructose oxidoreductase from zymomonas mobilis (1994)

Glucose-fructose oxidoreductase (E.C. 1.1.99.-) from the ethanol-producing Gram-negative bacterium Zymomonas mobilis is a periplasmic, soluble enzyme that forms a homotetramer of 160 kDa with one NADP(H) cofactor per subunit that is tightly, but noncovalently, bound. The enzyme was crystallized by the hanging drop vapor diffusion method using sodium citrate as precipitant. The obtained crystals belong to the space group P2(1)2(1)2, with unit cell constants of 84.6 A, 94.1 A, and 117.0 A, consistent with two monomers in the asymmetric unit. They diffract to a resolution of about 2 A and are suitable for X-ray structure determination.
Heat Flux and Effectiveness in Bubble Colum Dehumidifiers for HDH Desalination (2013)

Humidification-dehumidification is a promising technology for decentralized, small-scale desalination, but high energy consumption and large dehumidifier size are disadvantages. Direct-contact dehumidification in bubble columns has previously been shown to decrease dehumidifier volume by an order of magnitude. In a bubble column dehumidifier, warm, moist air is bubbled though a column of fresh water cooled by heat exchange with seawater feed. The concentration gradient from the warm bubble center to the cool bubble surface drives radial mass diffusion, and water vapor condenses on the surface of the bubble. In this paper, a parallel-flow effectiveness is defined to complement heat flux when assessing the performance of a single-stage bubble column dehumidifier. A bubble column dehumidifier is tested using significantly smaller cooling coils than those tested in previous work. Experimental results are presented in terms of heat flux and effectiveness in order to better understand the factors influencing bubble column dehumidifier performance. It is found that the heat flux can be raised dramatically by reducing the coil area, but that this gain is accompanied by a loss of effectiveness. Increasing air temperature leads to increased heat flux but decreased effectiveness. Because the gas-side pressure drop increases with increasing column liquid height, significantly lower column liquid heights are tested than those used in previous work. The critical liquid height is found to be below 4 cm for the sparger and flow rate tested. Additional heat transfer in the air gap is explored, but found to be minimal for well-designed columns with low temperature pinch. These findings will inform the design of bubble column dehumidifiers for high heat recovery and low capital cost.
Development of a nomogram model using a very large sample of patients (pts) to predict the risk of 99mTc-bone scan (BS) positivity in pts receiving androgen deprivation therapy (ADT) for prostate cancer (PCa). (2012)

4552 Background: Decisions to start imaging pts with PCa can be difficult due to the heterogeneous nature of the disease. Nomograms can combine information on multiple disease factors to improve predictive accuracy and are not influenced by subjective confounders that may affect clinical judgment. However, currently available nomograms for PCa predict current or future risk of positive BS in ADT-naive pts only. We have developed a new nomogram to predict current BS positivity in ADT-treated pts with PCa using a very large pt sample. Methods: All BS records from 1650 ADT-treated pts who received treatment at the Memorial Sloan-Kettering Cancer Center from 2000 to 2011 were analyzed. Pts were followed up from the start of ADT until the first positive BS or last hospital visit. Multivariate logistic regression analysis was used to model the variables that could be used for predicting likelihood of metastases and the variables were incorporated into the nomogram model. The current probability of bone metastasis was generated by the nomogram using the pt variables at each BS and the predictive accuracy was quantified by calculating the concordance index (C-index). Results: In total, 3949 BS records were analyzed and 950 pts had a positive scan. There was an average of 1.1 prior negative scans before a positive result was recorded. Median prostate-specific antigen (PSA) was 2.5 ng/mL and mean PSA doubling time (PSADT) was 7.8 months. At the same time of the positive scans, 49.4% of pts had a PSA &lt;10 ng/mL. Based on clinical relevance and data availability, 13 variables were included in the nomogram model: number of previous negative BSs, PSA, PSADT, prostatectomy, radiotherapy, brachytherapy, chemotherapy, immunotherapy, estrogen therapy, cryotherapy, clinical trial enrollment, and most recent primary and secondary Gleason grades. C-index for the nomogram was 0.76. Conclusions: This is the first nomogram to predict current BS positivity in pts with PCa following ADT. The nomogram was devised from a very large data set from a single center and provides high predictive accuracy.
Uncooled Tunable Transmitter 2.5GHz and 45kM SM Fiber Transmission Experimental Research for TWDM-PON (2014)

Three-section DBR laser temperature and current tuning performance have been investigated and temperature change causes laser wavelength shift can be compensated by DBR and phase section current tuning. 45kM fiber transmission results have been reported
Market Microstructure Design and Flash Crashes: A Simulation Approach (2013)

We study consequences of regulatory interventions in limit order markets that aim at stabilizing the market after an occurrence of a “flash crash”. We use a simulation platform that creates random arrivals of trade orders, that allows us to analyze subtle theoretical features of liquidity and price variability under various market structures. The simulations are performed under continuous double-auction microstructure, and under alternatives, including imposing minimum resting times, shutting off trading for a period of time, and switching to call auction mechanisms. We find that the latter is the most effective in restoring the liquidity of the book and recovery of the price level. However, one has to be cautious about possible consequences of the intervention on the traders' strategies, including an undesirable slowdown of a convergence to a new equilibrium after a change in fundamentals.
Modeling of Input Nonlinearity and Waveform Engineered High-Efficiency Class-F Power Amplifiers (2020)

A comprehensive time-domain modeling and a generalized design methodology for input and output waveform engineered Class-F power amplifiers (PAs) are presented in this article. A closed-form relationship between input nonlinearity and second harmonic source impedance (Z <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2S</sub> ) termination is presented from which efficiency and output power performance are predicted for Class-F PAs. The maximum, minimum, and safe Z <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2S</sub> design space for a Class-F PA are identified. Moreover, the derived design equations show that the typical fundamental load of a Class-F PA operation must be re-engineered in the presence of input nonlinearity in order to achieve optimum efficiency performance. The theoretical analyses are first validated with pulsed vector load-pull (VLP) measurements with a gallium nitride (GaN) 2 mm device. Then, high-power (210 W) GaN 24-mm devices with in-package Z <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2S</sub> terminations are implemented. Measurement results with the new source and load design space show efficiency improvement of 4.4% compared to the nominal Class-F PA.
Glycosides of Pyrido [2,3-

c

]-1,2,6-thiadiazine 2,2-Dioxides (1990)

Abstract The synthesis and characterization of ribo-furanosides and glucopyranosides of pyrido[2,3-c]-1,2,6-thiadiazine 2,2-dioxides are described. Conformational aspects related to the latter are discussed according to 2D-homonuclear H nmr data and dynamic H nmr spectral studies.
Distributed Overlay Virtual Ethernet (DOVE) integration with Openstack (2013)

In this demo we present IBM comprehensive SDN based network virtualization solution - DOVE (Distributed Overlay Virtual Ethernet network), providing multi tenant NaaS, and its integration with the cloud computing platform Openstack. The demo is based on the work “An Intent-based Approach for Network Virtualization” presented in IFIP/IEEE IM 2013 [1].
Endogenous modulators of glucocorticoid receptor function also regulate purified protein kinase C. (1991)

Modulator-1 and -2, proposed to be novel ether-linked aminophosphoglycerides, were originally identified as regulators of glucocorticoid receptor function (Bodine, P. V., and Litwack, G. (1990) J. Biol. Chem. 265, 9544-9554). We now demonstrate that these modulators are also potent new stimulators of protein kinase C activity in vitro. These endogenous biomolecules regulate purified protein kinase C activity in a biphasic and dose-dependent pattern, as determined by histone phosphorylation. Modulators, at concentrations within their apparent cellular range, stimulate protein kinase C-catalyzed histone phosphorylation 2-4-fold when added separately, or 10-12-fold when added together. This enhancement of kinase activity apparently is specific for protein kinase C, since neither protein kinase M, nor cAMP-dependent protein kinase A are stimulated by the modulators. The stimulation of purified protein kinase C occurs only when the enzyme has been initially activated by calcium, phosphatidylserine, and diacylglycerol, indicating that the modulators do not simply substitute for one of the enzyme cofactors. In addition, the modulators appear to interact directly with protein kinase C, perhaps with the regulatory domain of the enzyme, since these biomolecules inhibit the binding of phorbol ester to purified protein kinase C. Finally, time-course studies of protein kinase C-catalyzed histone phosphorylation indicate that the velocity of the enzyme reaction is increased by the modulators. Taken together, these results suggest that the modulators are a new class of regulators of protein kinase C.
Frequency Converter Based on Nanoscale MgO Magnetic Tunnel Junctions (2009)

We observe both dc voltage rectification and frequency conversion that occur when a reference microwave current is injected to a MgO based magnetic tunnel junction (MTJ). The rectification that is spin-transfer torque dependent is observed when the frequency of the input microwave current coincides with the resonance frequency of the magnetization of the active layer. In addition, we demonstrate that frequency conversion is the result of amplitude modulation between the reference signal and the resistance of the MTJ that is fluctuating at the resonance frequency of the magnetization of the active layer.
Bis(ethylenediseleno)tetraselenafulvalene (BEDSe-TSeF) (1983)

The title compound, synthesized from 4,5-ethylenediseleno-1,3-diselenol-2-one (5,6-dihydro-1,3,4,7-tetraselenainden-2-one)via trimethyl phosphite coupling, has been characterized and several charge-transfer salts of this new π-donor have been prepared.
Improving neural response to sound improves reading (2012)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
Tissue Engineered and Native Ovine Pulmonary Valves: A High Resolution Three-Dimensional Structural Characterization (2009)

Tissue engineered heart valves (TEHV) have received much attention as a potential pediatric valve replacement therapy, offering a variety of prospective long-term functional improvements over current options. Early in vivo and in vitro efforts have produced TEHV showing increasingly equivalent mechanical and structural properties compared to native valves [1]. Despite these advances, a significant gap in the literature exists regarding detailed 3D structural information of TEHV prior to implantation (in vitro) and after implantation (explants) as well as that of the native valve. The present work was performed to provide high resolution 3D structural data of implanted TEHV, the native pulmonary valve (PV), and pre-implant scaffold to develop an accurate understanding of developing tissue.
Structure and chemistry of passivated SiC/SiO2 interfaces (2016)

Here, we report on the chemistry and structure of 4H-SiC/SiO2 interfaces passivated either by nitric oxide annealing or Ba deposition. Using aberration corrected scanning transmission electron microscopy and spectroscopy, we find that Ba and N remain localized at SiC/SiO2 interface after processing. Further, we find that the passivating species can introduce significant changes to the near-interface atomic structure of SiC. Specifically, we quantify significant strain for nitric oxide annealed sample where Si dangling bonds are capped by N. In contrast, strain is not observed at the interface of the Ba treated samples. Finally, we place these results in the context of field effect mobility.
Quantitative strain analysis in AlGaAs-based devices (2003)

We present a strategy for quantitative spectroscopic analysis of packaging-induced strain using both finite element analysis and band-structure calculations. This approach holds for a wide class of AlGaAs-based, and related, devices, among them high-power “cm-bars.” The influence on the results of particular device structure properties, such as intrinsic strain and quantum-well geometry, is analyzed. We compare theoretical results based on a unaxial stress model with photocurrent data obtained from an externally strained cm-bar, and obtain better agreement than from alternative strain models. The general approach is also applicable to the analysis of all data that refer to changes of the electronic band structure, such as absorption and photoluminescence.
Peshawaraquinone a Novel Naphthoquinone and a New Indanone from the stem of Heterophragma adenophyllum Seem (2015)

Peshawaraquinone; a novel naphthoquinone (1) and a new indanone (2) were isolated from the stem heartwood of Heterophragma adenophyllum Seem. Their structures were elucidated using advance spectral techniques including X-ray crystallography for the compound 1.&#13;\n&#13;\n
Characterization of Protective Immune Responses Induced by Pneumococcal Surface Protein A in Fusion with Pneumolysin Derivatives (2013)

Pneumococcal surface protein A (PspA) and Pneumolysin derivatives (Pds) are important vaccine candidates, which can confer protection in different models of pneumococcal infection. Furthermore, the combination of these two proteins was able to increase protection against pneumococcal sepsis in mice. The present study investigated the potential of hybrid proteins generated by genetic fusion of PspA fragments to Pds to increase cross-protection against fatal pneumococcal infection. Pneumolisoids were fused to the N-terminus of clade 1 or clade 2 pspA gene fragments. Mouse immunization with the fusion proteins induced high levels of antibodies against PspA and Pds, able to bind to intact pneumococci expressing a homologous PspA with the same intensity as antibodies to rPspA alone or the co-administered proteins. However, when antibody binding to pneumococci with heterologous PspAs was examined, antisera to the PspA-Pds fusion molecules showed stronger antibody binding and C3 deposition than antisera to co-administered proteins. In agreement with these results, antisera against the hybrid proteins were more effective in promoting the phagocytosis of bacteria bearing heterologous PspAs in vitro, leading to a significant reduction in the number of bacteria when compared to co-administered proteins. The respective antisera were also capable of neutralizing the lytic activity of Pneumolysin on sheep red blood cells. Finally, mice immunized with fusion proteins were protected against fatal challenge with pneumococcal strains expressing heterologous PspAs. Taken together, the results suggest that PspA-Pd fusion proteins comprise a promising vaccine strategy, able to increase the immune response mediated by cross-reactive antibodies and complement deposition to heterologous strains, and to confer protection against fatal challenge.
Investigating the aging behavior of polysiloxane nanocomposites with degradative thermal analysis and broadband dielectric spectroscopy (2007)

This article provides an overview of traditional and contemporary management theories. Concerns, characteristics, and skills of effective managers are also presented. Further, a self-assessment (survey) of 7 highly effective health care managers in a South Georgia community was conducted to determine their ratings on 6 management indices. The assessment or Scale of Transformational Leadership uses a Likert-type scale to allow for the evaluation of managers. The scale contains 6 management elements for assessment: attention, meaning, trust, self, vision, and feeling. Individual ratings and group summary skills rating are presented. Findings revealed the order of managerial importance of the elements as follows (from highest to lowest): Management of Trust, Management of Attention, Management of Self, Management of Feeling, Management of Meaning, and Management of Risk. As a second tier, the final ratings are corroborated by health care management interns.