gebhart/patrepeval huggingface dataset:
Smoking reduces klotho expression (2013)

Introduction Klotho (KL) is expressed as a hormone and a transmembrane protein. Mice low in KL develop sarcopenia and emphysema. Limited data exists in smokers, who may develop a similar phenotype. Aims 1) To compare serum KL levels (sKL) before and after attempted smoking cessation; 2) to evaluate the effect of smoking on muscle KL in an animal model. Methods We measured sKL in 13 smokers before and after attempted smoking cessation, 7 patients with COPD were studied 1 week apart as controls. Judged by exhaled carbon monoxide (CO) 8 patients quit. Gastrocnemius KL (mKL) was measured in mice exposed to 77 weeks of either smoke or sham air. KL levels were log transformed. Differences were assessed by t-test, relationships by Pearson’s and response to cessation by Wilcoxon. Results In successful quitters sKL rose from 2.80 (0.19) to 3.02 (0.14) pg/ml; p=0.04 but did not change in those continuing to smoke (p=0.81). There was no change in sKL measured 1 week apart in controls (p=0.84). Comparing the differences between repeat measurements in controls to those attempting smoking cessation, those successful in smoking cessation had a greater rise on repeat assessment (0.22 (0.25) v 0.00 (0.05) pg/ml; p=0.04), but those unsuccessful did not; p=0.34. Smoke-exposed mice (n=19) had lower mKL than the sham air group (n=9); p=0.001. Conclusions Muscle KL is reduced by smoking in mice. Successful smoking cessation is associated with a rise in sKL, while unsuccessful quit attempts yield an intermediate picture. We have shown that fat free mass improves with smoking cessation [Hopkinson, Resp Res 2007 (8):25], however, ongoing smoking abstinence is difficult. It is therefore of interest that smoking induces KL suppression, which may explain phenotypic features in COPD.
Binding Site Similarity Analysis for the Functional Classification of the Protein Kinase Family (2009)

Methods for analyzing complete gene families are becoming of increasing importance to the drug discovery process, because similarities and differences within a family are often the key to understanding functional differences that can be exploited in drug design. We undertake a large-scale structural comparison of protein kinase ATP-binding sites using a geometric hashing method. Subsequently, we propose a relevant classification of the protein kinase family based on the structural similarity of its binding sites. Our classification is not only able to reveal the great diversity of different protein kinases and therefore their different potential for inhibitor selectivity but it is also able to distinguish subtle differences within binding site conformation reflecting the protein activation state. Furthermore, using experimental inhibition profiling, we demonstrate that our classification can be used to identify protein kinase binding sites that are known experimentally to bind the same drug, demonstrating that it has potential as an inverse (protein) virtual screening tool, by identifying which other sites have the potential to bind a given drug. In this way the cross-reactivities of the anticancer drugs Tarceva and Gleevec are rationalized.
I/O-efficient spatial data structures for range queries (2012)

Range reporting is a one of the most fundamental topics in spatial databases and computational geometry. In this class of problems, the input consists of a set of geometric objects, such as points, line segments, rectangles etc. The goal is to preprocess the input set into a data structure, such that given a query range, one can efficiently report all input objects intersecting the range. The ranges most commonly considered are axis-parallel rectangles, halfspaces, points, simplices and balls.
Prostaglandin E2 Regulates Tumor Angiogenesis in Prostate Cancer (2008)

In cancer management, the cyclooxygenase (COX)-targeted approach has shown great promise in anticancer therapeutics. However, the use of COX-2 inhibitors has side effects and health hazards; thus, targeting its major metabolite prostaglandin E(2) (PGE(2))-mediated signaling pathway might be a rational approach for the next generation of cancer management. Recent studies on several in vitro and in vivo models have revealed that elevated expression of COX-2 correlates with prostate tumor growth and angiogenesis. In this study, we have shown the in-depth molecular mechanism and the PGE(2) activation of the epidermal growth factor receptor and beta3 integrin through E prostanoid 2 (EP2)-mediated and EP4-mediated pathways, which lead to activator protein-1 (AP-1) activation. Moreover, PGE(2) also induces activating transcription factor-4 (ATF-4) activation and stimulates cross-talk between ATF-4 and AP-1, which is unidirectional toward AP-1, which leads to the increased expressions of urokinase-type plasminogen activator and vascular endothelial growth factor and, eventually, regulates prostate tumor cell motility. In vivo Matrigel angiogenesis assay data revealed that PGE(2) induces angiogenesis through EP2 and EP4. Human prostate cancer specimen analysis also supported our in vitro and in vivo studies. Our data suggest that targeting PGE(2) signaling pathway (i.e., blocking EP2 and EP4 receptors) might be a rational therapeutic approach for overcoming the side effects of COX-2 inhibitors and that this might be a novel strategy for the next generation of prostate cancer management.
Exhaled markers of oxidative stress in idiopathic pulmonary fibrosis (2006)

Our data suggest that H2O2 and 8-isoprostane are increased in the EBC of patients with IPF. H2O2 may be correlated with the severity of the disease in IPF.
Protein hydration in solution: Experimental observation by x-ray and neutron scattering (1998)

The structure of the protein-solvent interface is the subject of controversy in theoretical studies and requires direct experimental characterization. Three proteins with known atomic resolution crystal structure (lysozyme, Escherichia coli thioredoxin reductase, and protein R1 of E. coli ribonucleotide reductase) were investigated in parallel by x-ray and neutron scattering in H2O and D2O solutions. The analysis of the protein-solvent interface is based on the significantly different contrasts for the protein and for the hydration shell. The results point to the existence of a first hydration shell with an average density approximately 10% larger than that of the bulk solvent in the conditions studied. Comparisons with the results of other studies suggest that this may be a general property of aqueous interfaces.
Anatomy of protein pockets and cavities: Measurement of binding site geometry and implications for ligand design (1998)

Identification and size characterization of surface pockets and occluded cavities are initial steps in protein structure-based ligand design. A new program, CAST, for automatically locating and measuring protein pockets and cavities, is based on precise computational geometry methods, including alpha shape and discrete flow theory. CAST identifies and measures pockets and pocket mouth openings, as well as cavities. The program specifies the atoms lining pockets, pocket openings, and buried cavities; the volume and area of pockets and cavities; and the area and circumference of mouth openings. CAST analysis of over 100 proteins has been carried out; proteins examined include a set of 51 monomeric enzyme-ligand structures, several elastase-inhibitor complexes, the FK506 binding protein, 30 HIV-1 protease-inhibitor complexes, and a number of small and large protein inhibitors. Medium-sized globular proteins typically have 10-20 pockets/cavities. Most often, binding sites are pockets with 1-2 mouth openings; much less frequently they are cavities. Ligand binding pockets vary widely in size, most within the range 10(2)-10(3)A3. Statistical analysis reveals that the number of pockets and cavities is correlated with protein size, but there is no correlation between the size of the protein and the size of binding sites. Most frequently, the largest pocket/cavity is the active site, but there are a number of instructive exceptions. Ligand volume and binding site volume are somewhat correlated when binding site volume is < or =700 A3, but the ligand seldom occupies the entire site. Auxiliary pockets near the active site have been suggested as additional binding surface for designed ligands (Mattos C et al., 1994, Nat Struct Biol 1:55-58). Analysis of elastase-inhibitor complexes suggests that CAST can identify ancillary pockets suitable for recruitment in ligand design strategies. Analysis of the FK506 binding protein, and of compounds developed in SAR by NMR (Shuker SB et al., 1996, Science 274:1531-1534), indicates that CAST pocket computation may provide a priori identification of target proteins for linked-fragment design. CAST analysis of 30 HIV-1 protease-inhibitor complexes shows that the flexible active site pocket can vary over a range of 853-1,566 A3, and that there are two pockets near or adjoining the active site that may be recruited for ligand design.
A case study of icon-scenario based animated menu's concept development (2006)

This paper reports on the implementation of the Icon-Scenario Based Animated Menu graphical user interface that is adopted across our latest 2G platform. We describe the concept development process of the phone's menu enhanced by the use of a captivating Icon-Scenario Based Animated Menu that takes usability into consideration and brings delight to users.
A combined normal- and transverse-displacement interferometer with an application to impact of <i>y</i>-cut quartz (1977)

A new transverse-displacement inteferometer (TDI) is described. This interferometer makes use of intensity variations of a beam obtained by superposition of two beams diffracted symmetrically from a diffraction grating copied onto a plane surface. The TDI is used to monitor the transverse motion of the rear surface of a y-cut quartz target plate in a plate-impact experiment. For this application, a 200-line/mm grating is copied onto the rear surface of the target plate. The normal motion of the rear surface is monitored by means of a standard Michelson interferometer in which the zeroth-order diffracted beam is used as the beam reflected from the moving mirror. The transverse motion is monitored simultaneously by means of a TDI employing the two fourth-order diffracted beams, with a resulting sensitivity of 0.625 μm per fringe. The recorded motion confirms the predicted features of two coupled elastic waves, each involving both normal and transverse motion.
Using offline bitstream analysis for power-aware video decoding in portable devices (2005)

Dynamic voltage/frequency scheduling algorithms for multimedia applications have recently been a subject of intensive research. Many of these algorithms use control-theoretic feedback techniques to predict the future execution demand of an application based on the demand in the recent past. Such techniques suffer from two major disadvantages: (i) they are computationally expensive, and (ii) it is difficult to give performance or quality-of-service guarantees based on these techniques (since the predictions can occasionally turn out to be incorrect). To address these shortcomings, in this paper we propose a completely new approach for dynamic voltage and frequency scaling. Our technique is based on an offline bitstream analysis of multimedia files. Based on this analysis, we insert metadata information describing the computational demand that will be generated when decoding the file. Such bitstream analysis and metadata insertion can be done when the multimedia file is being downloaded into a portable device from a desktop computer. In this paper we illustrate this technique using the MPEG-2 decoder application. We show that the amount of metadata that needs to be inserted is a very small fraction of the total size of the video clip and it can lead to significant energy savings. The metadata inserted will typically consist of the frequency value at which the processor needs to be run at different points in time during the decoding process. Lastly, in contrast to runtime prediction-based techniques, our scheme can be used to provide performance and quality-of-service guarantees and at the same time avoids any runtime computation overhead.
The <i>lba1</i> mutation of UPF1 RNA helicase involved in nonsense‐mediated mRNA decay causes pleiotropic phenotypic changes and altered sugar signalling in Arabidopsis (2006)

The low-beta-amylase1 (lba1) mutant of Arabidopsis thaliana has reduced sugar-induced expression of Atbeta-Amy and shows pleiotropic phenotypes such as early flowering; short day-sensitive growth; and seed germination that is hypersensitive to glucose and abscisic acid and resistant to mannose. lba1 was a missense mutation of UPF1 RNA helicase involved in nonsense-mediated mRNA decay (NMD), which eliminates mRNAs with premature termination codons (PTCs), and replaces highly conserved Gly851 of UPF1 with Glu. Expression of the wild-type UPF1 in lba1 rescued not only the reduced sugar-inducible gene expression, but also early flowering and altered seed-germination phenotypes. Sugar-inducible mRNAs were over-represented among transcripts decreased in sucrose-treated lba1 compared with Col plants, suggesting that UPF1 is involved in the expression of a subset of sugar-inducible genes. On the other hand, transcripts increased in lba1, which are likely to contain direct targets of NMD, included mRNAs for many transcription factors and metabolic enzymes that play diverse functions. Among these, the level of an alternatively spliced transcript of AtTFIIIA containing PTC was 17-fold higher in lba1 compared with Col plants, and it was reduced to the level in Col by expressing the wild-type UPF1. The lba1 mutant provides a good tool for studying NMD in plants.
Techniques for on-chip process voltage and temperature detection and compensation (2006)

This paper presents techniques to detect process, voltage and temperature (PVT) variations in an integrated circuit chip and wafer. Conventional techniques are limited to detection of process variations in which the MOS devices (NMOS and PMOS) move in similar direction i.e. fast n-fast p or slow n-slow p. The presented techniques can be used to compensate skewed variations on the chip i.e. fast n-slow p or slow n-fast p thus increasing the utilization (yield) of the wafer. The proposed techniques can be implemented in any standard CMOS process and can easily be integrated with any circuit requiring PVT compensation. Major applications of these circuits are in I/O drivers and PVT sensitive analog circuits. For I/O drivers, simulation results show that the rise/fall time variation with PVT has been reduced to more than half using the proposed circuits.
Plant-based vaccines for animals and humans: recent advances in technology and clinical trials (2015)

It has been about 30 years since the first plant engineering technology was established. Although the concept of plant-based pharmaceuticals or vaccines motivates us to develop practicable commercial products using plant engineering, there are some difficulties in reaching the final goal: to manufacture an approved product. At present, the only plant-made vaccine approved by the United States Department of Agriculture is a Newcastle disease vaccine for poultry that is produced in suspension-cultured tobacco cells. The progress toward commercialization of plant-based vaccines takes much effort and time, but several candidate vaccines for use in humans and animals are in clinical trials. This review discusses plant engineering technologies and regulations relevant to the development of plant-based vaccines and provides an overview of human and animal vaccines currently under clinical trials.
Pre-Excitation, Catalytic Oxidation of Analytes over Hopcalite in Flame/Furnace Infrared Emission (FIRE) Spectrometry (1992)

Gas-phase infrared emission measurements made with the use of a new, specially designed, electrically heated furnace or a small hydrogen/air flame have shown that oxidation of a variety of carbon-based analytes to CO 2 over the catalyst hopcalite prior to vibrational excitation in the furnace or flame markedly improves the response of the FIRE radiometer. Calibration curves obtained with the use of the furnace alone were generally nonlinear, while those obtained with the flame alone had slopes that were compound dependent. By the use of hopcalite in conjunction with the furnace, conversion to CO 2 was significantly improved, and the FIRE response to pure acetone, benzene, dichloromethane, 1-chloro-2-methylpropane, heptane, methanol, and toluene became directly proportional to the number of moles of carbon introduced. In the case of the flame, as little as 0.1 g of hopcalite was sufficient to give a single, linear calibration curve (based on moles of carbon) for injection volumes of 0.2–1.0 μL of a test mixture composed of equal volumes of acetone, benzene, hexane, propanol, and tetrahydrofuran. With the use of hopcalite at its experimentally determined, optimum operating temperature of 380°C, an air flow rate of 45 mL min −1 , and a furnace temperature of 600°C, the detection limit for hexane was found to be 518 ng C s −1 . The use of hopcalite in conjunction with the flame (900°C) improved this detection limit by two orders of magnitude, due to the combined effects of an increase in excitation temperature and a decrease in source background noise. Injection of chlorinated compounds was found to temporarily poison the hopcalite, resulting in soot formation and loss of catalytic activity for periods of approximately ten minutes.
Santonin and Related Compounds. XV.<sup>1</sup> Preparation of trans- and cis-4,9-Dimethyl-Δ<sup>4</sup>-3-octalon-6-acetic Acids<sup>2</sup> (1958)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSantonin and Related Compounds. XV.1 Preparation of trans- and cis-4,9-Dimethyl-Δ4-3-octalon-6-acetic Acids2MASAITI YANAGITA, SEIITI INAYAMA, MINORU HIRAKURA, and FUJIO SEKICite this: J. Org. Chem. 1958, 23, 5, 690–699Publication Date (Print):May 1, 1958Publication History Published online1 May 2002Published inissue 1 May 1958https://pubs.acs.org/doi/10.1021/jo01099a014https://doi.org/10.1021/jo01099a014research-articleACS PublicationsRequest reuse permissionsArticle Views119Altmetric-Citations14LEARN 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
Transient grating measurements of film thickness in multilayer metal films (2001)

A transient grating technique has been used to measure film thicknesses in five multilayer film structures. Through-plane acoustic responses are observed through time-resolved diffraction that reveals their return to the free surface after partial reflections within the structure. Optical heterodyne detection with a controlled reference field amplitude permits optimization of the signal/noise ratio relative to detection of the signal against the far stronger incident probe field or against a dark background (homodyne detection). In-plane acoustic waves are also generated and observed.
Enhancing the Immune Response to Recombinant Plague Antigens (2004)

Abstract : The etiologic agent of plague is the Gram negative bacterium Yersinia pestis. Y. pestis is a concern as one of the microorganisms with potential for use against civilian or military populations as a biological warfare/ biological terrorism agent. In that case, the pneumonic form of plague would be the most likely outcome. This form of plague is particularly devastating because of the rapidity of onset, the high mortality, and the rapid spread of the disease. Immunization against aerosolized plague presents a particular challenge for vaccine developers. The studies reported herein explore the ability of a novel adjuvant, designated LT(R192G), to promote the rapid development of long-lasting, high titer antibodies against a recombinant plague antigen (F1-V) and protection in a murine model. Subsequent studies will be performed in non-human primates. Different routes of administration are examined to test the hypothesis that heterologous boosting will be more effective than homologous boosting at increasing the magnitude and/or duration of the antibody response.
Genetic variation in EEG activity during sleep in inbred mice (1998)

The genetic variation in spontaneous rhythmic electroencephalographic (EEG) activity was assessed by the quantitative analysis of the EEG in six inbred mice strains. Mean spectral EEG profiles (0-25 Hz) over 24 h were obtained for paradoxical sleep (PS), slow-wave sleep (SWS), and wakefulness. A highly significant genotype-specific variation was found for theta peak frequency during both PS and SWS, which strongly suggests the presence of a gene with a major effect. The strain distribution of theta peak frequency during exploratory behavior differed from that during sleep. In SWS, the relative contributions of delta (1-4 Hz) and sigma (11-15) power to the EEG varied with genotype and power in both frequency bands was negatively correlated. In addition, the EEG dynamics at state transitions were analyzed with a 4-s resolution. The onset of PS, but not that of wakefulness, was preceded by a pronounced peak in high-frequency (>11 Hz) power. These findings are discussed in terms of the neurophysiological mechanisms underlying rhythm generation and their control and modulation by the brain stem reticular-activating system.
On Computing Dominant Frequency From Bipolar Intracardiac Electrograms (2006)

Dominant frequency (DF) computed from action potentials is a key parameter for investigating atrial fibrillation in animal studies and computer models. A recent clinical trial reported consistent results computing DF from 30 Hz to 400 Hz bandpass filtered bipolar electrograms in humans. The DF (< 15 Hz and, thus, filtered out) was recovered by rectifying the signal, while the theoretical background of this approach was left uncommented. It is the focus of this paper to provide this background by a Fourier analysis. We demonstrate that it is mainly the timing of the narrow deflections (local activation at the catheter tip) which contribute to the DF peak in the frequency spectrum. Due to the typical signal morphology pronounced harmonic peaks occur in the spectrum. This is a disadvantage when computing the regularity index (RI) as a parameter for local organization and signal quality. It is demonstrated for synthetical and patient data that at low DF the RI is far below the optimal value one even for high underlying organization and good signal quality. The insight obtained promotes the development of better measures for organization. The finding that mainly timing of activation contributes to DF might promote the development of powerful realtime signal processing tools for computing DF.