gebhart/patrepeval huggingface dataset:
Abstract 4728: Genome-wide analysis of genetic alterations in seminoma using high resolution single Nucleotide polymorphism (SNP) arrays (2010)

Abstract Testicular germ cell tumors (TGCT's) represent the most common malignancy among young males between the ages 15-40 years. Many genomic alterations have been observed in testicular cancer, however very few of these alterations have been associated with deregulation of gene function. The impact of CNVs on cancer susceptibility and tumor progression is only recently been explored in different cancer types. To our knowledge no comprehensive studies of testicular cancer using high-resolution SNP array have been performed, partially due to the rarity of this disease and low resolution of previous cytogenetic techniques. To identify new genomic alterations we performed a genome-wide analysis of copy-number changes and loss of heterozygosity (LOH) in 24 seminomas and validated our findings by a complementary approach. We have also confirmed the several previously reported genomic alterations in seminoma and discovered eight novel genomic alterations including amplifications and homozygous deletions. Moreover, a comparison of genomic alterations of early stage and late stage identified CNV that correlate with progression which included deletions in chromosome 4q, 5p, 9q, 13q and 20p and amplifications in chromosomes 9q and 13q. CNV aberrations for candidate genes within selected regions these regions were further validated using quantitative PCR (QPCR). 40-75% correlation was observed between CNV by SNP analysis and QPCR. In conclusion, SNP microarrays are a valuable tool to measure and identify genomic alterations in seminoma, and we identified several genomic alterations, which may help pinpoint cancer causing genes and strengthen our understanding the biology of seminoma. Note: This abstract was not presented at the AACR 101st Annual Meeting 2010 because the presenter was unable to attend. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 4728.
Matrix Isolation of Free Radicals from Carbohydrates (1985)

Photolytically produced H.-atoms in 6 mol dm-3 H2SO4/H2O glasses trapped at 77 K react upon annealing to 130 K with dissolved carbohydrates to form carbon-located free radicals by abstraction of carbon-bound protons. Analysis of electron spin resonance (e.s.r.) spectra at various annealing stages from alpha- and beta-D-glucose together with 6,6-d2-D-glucose, 6-deoxy-D-glucose, 2-deoxy-D-glucose, glucose-1-phosphate, D-xylose, D-allose and D-mannose indicates radical formation at all possible carbon sites with a strong preference for C1 and a somewhat enhanced contribution of C4 over the statistical expectation. The corresponding component spectra are analysed either by spectra isolation or simulation and their parameters are given. Intramolecular radical transformation at temperatures of 140-160 K is explained by acid-catalysed H2O-elimination. The findings are discussed in relation to the radiation-chemistry of aqueous glucose solutions. We thus show that the system of photolyzed Fe2+ in acidic glasses at low temperatures containing 10 mmol dm-3 carbohydrate is suitable for studying H(D.)-reactions by means of e.s.r. spectroscopy. Unlike previously used glasses containing carbohydrates, contributions of oxidation and reduction by direct effects or mixtures of direct and indirect effects and phase-effects due to incomplete glass formation are avoided.
Precision Tunable Silicon Compatible Microring Filters (2008)

Microring resonators can be used as passband filters for wavelength-division demultiplexing in electronic-photonic integrated circuits. For applications such as analog-to-digital converters, the resonant frequency of the filter has to be held at a certain value to allow minimum timing errors in the sampling of the signal. Thermal tuning is used to compensate for any fabrication errors or environmental temperature fluctuations that might lead to a shift in the resonant frequency. With an optimized heater design, we demonstrate efficient on-chip thermal tuning for a second-order silicon-rich silicon nitride microring resonator at 80 <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">mu</i> W/GHz. A closed-loop feedback circuit controls a resistive heater which is also used as a temperature sensor to maintain the resonant frequency within 280 MHz of the target value.
High-speed/high-bus system with optical analog of electrical high-impedance state (1993)

Future generation, high throughput data processing applications, such as nuclear data acquisition, the determination of bi-molecular structures using synchrotron rotation, superconducting supercollider (SSC) research, aircraft data acquisition, and weather prediction will require systems capable of handling this increase in throughput.
Triazacyclohexane complexes of chromium as highly active homogeneous model systems for the Phillips catalyst (2000)

MAO activated 1,3,5-triazacyclohexane complexes of chromium(III) are highly active ethene polymerisation catalysts that resemble the Phillips catalyst in many important properties and may represent the first good homogeneous model system.
Stapled, Long-Acting Glucagon-like Peptide 2 Analog with Efficacy in Dextran Sodium Sulfate Induced Mouse Colitis Models (2018)

Glucagon-like peptide 2 (GLP-2) is a hormone that has been shown to stimulate intestinal growth and attenuate intestinal inflammation. Despite being efficacious in a variety of animal models of disease, its therapeutic potential is hampered by the short half-life in vivo. We now describe a highly potent, stapled long-acting GLP-2 analog, peptide 10, that has a more than 10-fold longer half-life than teduglutide and improved intestinotrophic and anti-inflammatory effects in mouse models of DSS-induced colitis.
BER sensitivity to timing offset in ultra wideband communications (2003)

This paper investigates the timing tolerances of ultra wideband communications (UWB). We quantify the BER sensitivity to timing offsets under various operating conditions and system setups, including AWGN and frequency flat channels, dense multipath fading channels, and different receiver types such as a sliding correlator and RAKE receivers. Through analyses, we illustrate that the reception quality of a UWB system is highly sensitive to both acquisition and tracking errors. In particular, direct-path channels exhibit little tolerance to the tracking error, while for dense multipath channels, the energy capture capability of a RAKE combiner can be severely compromised by mis-timing.
Paired Box 5 Methylation Detection by Droplet Digital PCR for Ultra-Sensitive Deep Surgical Margins Analysis of Head and Neck Squamous Cell Carcinoma (2015)

Molecular deep surgical margin analysis has been shown to predict locoregional recurrences of head and neck squamous cell carcinoma (HNSCC). To improve the accuracy and versatility of the analysis, we used a highly tumor-specific methylation marker and highly sensitive detection technology to test DNA from surgical margins. Histologically cancer-negative deep surgical margin samples were prospectively collected from 82 eligible HNSCC surgeries by an imprinting procedure (n = 75) and primary tissue collection (n = 70). Bisulfite-treated DNA from each sample was analyzed by both conventional quantitative methylation-specific PCR (QMSP) and QMSP by droplet digital PCR (ddQMSP) targeting Paired box 5 (PAX5) gene promoter methylation. The association between the presence of PAX5 methylation and locoregional recurrence-free survival (LRFS) was evaluated. PAX5 methylation was found in 68.0% (51 of 75) of tumors in the imprint samples and 71.4% (50 of 70) in the primary tissue samples. Among cases that did not have postoperative radiation (n = 31 in imprint samples, n = 29 in tissue samples), both conventional QMSP and ddQMSP revealed that PAX5 methylation-positive margins was significantly associated with poor LRFS by univariate analysis. In particular, ddQMSP increased detection of the PAX5 marker from 29% to 71% in the nonradiated imprint cases. Also, PAX5 methylated imprint margins were an excellent predictor of poor LRFS [HR, 3.89; 95% confidence interval (CI), 1.19-17.52; P = 0.023] by multivariate analysis. PAX5 methylation appears to be an excellent tumor-specific marker for molecular deep surgical margin analysis of HNSCC. Moreover, the ddQMSP assay displays increased sensitivity for methylation marker detection.
Tuning of a cholesteric filter having a negative dielectric anisotropy (2007)

We have studied the tunability of the reflection notch of a cholesteric filter containing a negative dielectric anisotropy LC in a planar alignment. For this purpose, we studied physical, optical and electro-optical characteristics of mixtures containing chiral dopant S811 and the negative dielectric anisotropy liquid crystal ZLI-2806. Interestingly, smectic A phases were seen at room temperature for S811 loadings >20% by weight of ZLI-2806. Polarized optical microscopy (POM) and differential scanning calorimetry (DSC) studies confirmed the formation of a cholesteric phase above room temperature. A phase diagram was constructed by varying S811from 9-50% by weight in the mixture. Reflection notchs were not seen at room temperature for compositions of S811 >20%. On heating, the selective reflection notch of the cholesteric phase appeared and blue shifted with temperature. Various methods of tuning the reflection notch were examined. Thermal tuning from 2200 nm to 450 nm was observed over the temperature range 23 to 55&deg; C. Application of a DC field led to electrical tuning (~50 nm) of the notch. The notch was also tuned (>500 nm) optically by exposing a dye doped cholesteric cell to laser lines at either 532 or 647 nm.
Identification of a Macromolecular Inhibitol of Glucocorticoid‐Receptor Complex Activation in Rat Liver Cytosol (1983)

We have identified an endogenous regulator of the glucocorticoid receptor following fractionation of dialyzed rat liver cytosol on DEAE-cellulose. The macromolecular regulator, purified approximately 20-fold as judged by Lowry-reactive material, inhibits activation of glucocorticoid-receptor complexes when assayed by DNA-cellulose binding and by chromatography on DEAE-cellulose minicolumns. In addition the active DEAE-cellulose fraction stabilizes the unoccupied glucocorticoid receptor against heat inactivation. Evidence is presented that the observed inhibition of activation by the active DEAE-cellulose fraction is not due to concentration of cytosolic proteases or RNA. The inhibitory molecule in the active fraction is not stable to heating at 90 degrees C (15 min) and is partially inactivated at 45 degrees C (15-60 min).
Rare copy number variations in congenital heart disease patients identify unique genes in left-right patterning (2011)

Dominant human genetic diseases that impair reproductive fitness and have high locus heterogeneity constitute a problem for gene discovery because the usual criterion of finding more mutations in specific genes than expected by chance may require extremely large populations. Heterotaxy (Htx), a congenital heart disease resulting from abnormalities in left-right (LR) body patterning, has features suggesting that many cases fall into this category. In this setting, appropriate model systems may provide a means to support implication of specific genes. By high-resolution genotyping of 262 Htx subjects and 991 controls, we identify a twofold excess of subjects with rare genic copy number variations in Htx (14.5% vs. 7.4%, P = 1.5 × 10(-4)). Although 7 of 45 Htx copy number variations were large chromosomal abnormalities, 38 smaller copy number variations altered a total of 61 genes, 22 of which had Xenopus orthologs. In situ hybridization identified 7 of these 22 genes with expression in the ciliated LR organizer (gastrocoel roof plate), a marked enrichment compared with 40 of 845 previously studied genes (sevenfold enrichment, P < 10(-6)). Morpholino knockdown in Xenopus of Htx candidates demonstrated that five (NEK2, ROCK2, TGFBR2, GALNT11, and NUP188) strongly disrupted both morphological LR development and expression of pitx2, a molecular marker of LR patterning. These effects were specific, because 0 of 13 control genes from rare Htx or control copy number variations produced significant LR abnormalities (P = 0.001). These findings identify genes not previously implicated in LR patterning.
Single and Double Polymerase Chain Reaction for Detection of Bovine Viral Diarrhea Virus in Tissue Culture and Sera (1993)

Bovine viral diarrhea virus (BVDV) is an ubiquitous pathogen of cattle and has been reported in other ruminants. It is also frequently present in laboratory and biological materials as an adventitious agent. This virus is difficult to detect in some specimens, especially in the presence of specific antibody and when the virus is present in low concentrations. In this paper, we describe a single polymerase chain reaction (PCR) to amplify virus sequences from infected cell culture and a nested double PCR to detect small concentrations of several virus strains in sera. Total cellular RNA was extracted from cell cultures infected with the cytopathic strain 72 and noncytopathic strain 2724 of BVDV. Ten different genomic sequences along the length of the viral RNA ranging in size from 397 to 1,016 base pairs (bp) were successfully amplified by PCR. A 404-bp probe made from amplified product from the 3' end hybridized specifically with the RNA of several BVDV strains blotted on nylon filters. Viral RNA was extracted from serum and amplified using 2 sets of degenerate nested primers designed from the 3' end of the viral genome in a double PCR protocol. Double amplification of the viral sequences greatly enhanced the sensitivity of the detection of many strains present in serum. Advantages of using double PCR over single PCR and virus isolation is discussed.
VORTEX HEAT TRANSFER ENHANCEMENT IN NARROW CHANNELS WITH A SINGLE OVAL-TRENCH DIMPLE ORIENTED AT DIFFERENT ANGLES TO THE FLOW (2018)

There are many passive techniques of heat transfer enhancement; however, only a few of them are capable of providing a reliable increase in a heat transfer rate exceeding an increase in pressure losses. One of such successful techniques is the profiling of a heat transfer surface with a regular arrangement of dimples. Detailed numerical simulation of fluid flow and heat transfer has been performed in a dimpled narrow channel at a Reynolds number of 10,000. The orientation of oval-trench dimples on the heated surface has been evaluated numerically to establish the superior thermohydraulic performance over spherical dimples.
Mapping studies on a pericentric inversion (18) (P11.31 q21.1) in a family with both schizophrenia and learning disability (1999)

Chromosomal abnormalities that co-occur with psychiatric disorders can be useful direct pointers to the locus of susceptibility genes. Two families with pericentric inversions of chromosome 18, inv 18(p11.3 q21.1) and psychiatric illness have previously been described. We have fine mapped the chromosomal breakpoints of the rearrangement in a clinically well, inversion carrier from one of these families where other inversion carriers suffered from chronic schizophrenia or severe learning disability. Yeast artificial chromosomes (YACs) from the Whitehead/MIT physical maps of human chromosome 18 have been positioned relative to the chromosomal breakpoints and a number of YACs that span these breakpoints have been identified. Linkage and association studies have previously suggested these regions of chromosome 18q and 18p as candidate loci harbouring genes involved in bipolar disorder and schizophrenia.
Measurements of Transfer Inefficiency of 250-Element Undercut-Isolated Charge Coupled Devices (1973)

A 250-element charge coupled device is described in which the transfer electrodes are delineated and isolated using an undercut-etch technique. The device has metal electrodes on two thicknesses of oxide and is primarily intended to be operated in a two-phase manner. Measurements of transfer inefficiency as a function of frequency have been made on both n- and p-channel devices. Below 1 MHz, values of 4 × 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">−4</sup> per transfer independent of transfer frequency have been obtained. Above 1 MHz the transfer inefficiency progressively rises as the dynamics of charge motion limit the transfer of charge.
Impact of Perlite on the Properties and Stability of Water-Based Mud in Elevated-Temperature Applications (2020)

Barite settling is one of the common drilling fluid issues encountered while drilling deep wells. In this study, the effect of perlite on the properties and stability of water-based drilling fluid was investigated. Perlite is an inexpensive additive used in different industrial applications such as bricks, concrete, thermal insulators, sludge absorbents, fillers, tiles, ruminants, and poultry. Perlite additive was also introduced to the oil industry in drilling applications as an effective fluid loss control agent to reduce the drilling fluid invasion into the formations. Perlite was added to the drilling fluid in various concentrations, ranging between 0 and 3.0 lb/bbl. The sag test was performed to assess the drilling fluid's stability under dynamic and static conditions at a temperature of 120/250 °F. Then, the impact of perlite on the properties of drilling fluid was assessed by measuring the density and pH at room temperature. While the rheological, viscoelastic, and filtration properties were evaluated at 250 °F. This study showed that an increase in perlite concentration, from 0 to 3 lb/bbl, slightly reduced the pH of the drilling mud; however, all of the values were within the acceptable pH range (9-11). In contrast, this concentration of perlite had an immeasurable impact on drilling fluid density. Perlite enhanced the drilling fluid's homogeneity and stability by reducing the dynamic and static sag factors, and 3.0 lb/bbl perlite was adequate to eliminate barite sag at a temperature up to 250 °F. Perlite was found to be effective in improving the rheological and viscoelastic properties. A significant enhancement of filtration properties was observed by the reduction in filtrate volume and filter cake thickness by 64 and 31%, respectively.
Closed-form Solutions for Cohesive Zone Modeling (2015)

Closed-form solutions for cohesive zone modeling within the framework of classical lamination theory (CLT), for the popular mode I double cantilever beam (DCB) test and the mode II end notched flexure (ENF) test are provided in this paper. Zerothickness virtual multi-linear traction-separation laws are introduced to simulate the cohesive interactions between potential crack surfaces. The problem is formulated by solution forms corresponding to each segment of the cohesive laws and using appropriate boundary and continuity conditions. Detailed algorithms for each case is provided to clearly show the influence of the cohesive zone law on the ensuing crack growth. Comprehensive parametric studies are performed on the crack growth response and the process zone length, revealing their relations to the delamination length, cohesive parameters and the shape of the traction-separation laws. With applicability to general multilayered structures, and the capability to incorporate arbitrary, piecewise linear cohesive constitutive laws, the closed-form solutions can serve as a tool to determine the accuracy of numerical solutions used in conjunction with the finite element simulations.
Evaluation of combined bevacizumab plus irinotecan therapy in brain tumors using magnetic resonance imaging measures of relative cerebral blood volume (2011)

Frequently, bevacizumab is combined with chemotherapeutics such as irinotecan, motivated by studies showing improved clinical outcomes compared with historical controls. However, no systematic studies have been performed to determine if and how these drugs should be combined for optimal therapeutic response. The purpose of this study was to characterize the temporal combinations of bevacizumab and irinotecan by measuring the contrast-agent enhanced tumor volumes and relative cerebral blood volume using dynamic susceptibility contrast imaging. The studies, performed in the U87 brain tumor model, show a vascular normalization window with bevacizumab monotherapy and are consistent with clinical indications of no additional benefit in the addition of irinotecan to bevacizumab therapy.
Frequency- and time-domain analyses of nonuniform lossy coupled transmission lines with linear and nonlinear terminations (2000)

A new technique for the frequency- and time-domain characterization of nonuniform coupled transmission lines is presented in this paper. In the frequency domain, a method-of-moments-based approach is used to compute the 2N/spl times/2N scattering parameter matrix of the N-coupled lines using special frequency-dependent basis functions that give good accuracy over very large bandwidths. In the time domain, the structure's S-parameters are used as its Green's function and are combined with source and terminating load conditions to obtain its transient response. The proposed method can account for loss and is particularly suitable for wideband microwave component designs and ultrahigh-speed/large-bandwidth digital interconnects, including nonlinear terminating loads. A detailed formulation of both the frequency- and time-domain approaches is presented. Several examples of two- and three-line structures are analyzed and the results are compared to published results and other computer-aided-design simulations.
Interaction of deep-ultraviolet laser light with GaAs surfaces in aqueous solutions (1986)

We have investigated the surface oxidation of GaAs and subsequent oxide dissolution that is caused by ultraviolet laser light at 257 nm in an aqueous environment. This process has a chemistry distinct from the related process that uses visible light. Further, unique light-guided surface-relief structures result from the ultraviolet chemistry and the ultraviolet optical properties of the semiconductor surface.
An electronic spectroscopic study of iron coordination in hemerythrin (1980)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAn electronic spectroscopic study of iron coordination in hemerythrinJoann Sanders Loehr, Thomas M. Loehr, A. Grant Mauk, and Harry B. GrayCite this: J. Am. Chem. Soc. 1980, 102, 23, 6992–6996Publication Date (Print):November 5, 1980Publication History Published online1 May 2002Published inissue 5 November 1980https://pubs.acs.org/doi/10.1021/ja00543a015https://doi.org/10.1021/ja00543a015research-articleACS PublicationsRequest reuse permissionsArticle Views155Altmetric-Citations28LEARN 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