gebhart/patrepeval huggingface dataset:
Abstract 2569: Lyc-O-Mato causes cell cycle arrest and apoptosis in human bladder transitional carcinoma cells (2012)

Abstract Approximately two thirds of new bladder cancer cases in the United States are superficial papillary transitional cell carcinoma (TCC), the majority of which are low-grade neoplasms. Data suggest that bladder carcinogenesis is a multi-step, multi-focal (field effect) process, possibly involving the spread of pre-malignant clones-all of which are prerequisites for effective preventive and/or interventional approaches. Epidemiological data suggests an inverse relationship between serum levels of carotenoids and risk of bladder cancer which has encouraged further investigation. In this study, we evaluated the effect of Lyc-O-Mato® (a crude tomato extract containing 10% lycopene and other tomato phytonutrients viz. tocopherols, phytoene, phytofluene, beta-carotene, phospholipids and phytosterols) on human bladder cancer cell growth, cell cycle modulation, induction of apoptosis, and associated molecular alterations. Treatment of bladder cancer cell lines (T-24, high-grade TCC and TCC-SUP, high-grade invasive tumor) with Lyc-O-Mato® at doses of 1-60µM resulted in inhibition of cell growth along with a G1 arrest in T24 cells and G2/M arrest in TCCSUP cells at 24 h post-treatment. In other studies, Lyc-O-Mato® treatment strongly induced the expression of p21/waf1 and p27/kip1, and resulted in a decrease in cyclin-dependent kinases (CDKs) and cyclins involved in G1 and G2/M progression in T24 and TCC SUP cells. Lyc-O-Mato® exposure to these cells showed an increased interaction between cyclin dependent kinase inhibitors (CDKIs)-cyclin-dependent kinases (CDKs) and decrease in the interaction of cyclins and CDKs with their respective stages of the cell cycle. Furthermore, Lyc-O-Mato® treatment significantly reduced the phosphorylation of Retinoblastoma at Serine780, although no significant changes were observed in the total levels of this protein. In additional studies, Lyc-O-Mato® showed a dose- and time-dependent apoptotic death in both T24 and TCC SUP cells which was associated with significant downregulation of survivin along with the enhancement of pro-apoptotic protein, Bax. These observations provide a strong rationale for further evaluating preventive and/or intervention strategies for Lyc-O-Mato® in pre-clinical models of bladder cancer. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 2569. doi:1538-7445.AM2012-2569
Identification of novel secreted proteases during extracellular proteolysis by dermatophytes at acidic pH (2011)

The dermatophytes are a group of closely related fungi which are responsible for the great majority of superficial mycoses in humans and animals. Among various potential virulence factors, their secreted proteolytic activity attracts a lot of attention. Most dermatophyte-secreted proteases which have so far been isolated in vitro are neutral or alkaline enzymes. However, inspection of the recently decoded dermatophyte genomes revealed many other hypothetical secreted proteases, in particular acidic proteases similar to those characterized in Aspergillus spp. The validation of such genome predictions instigated the present study on two dermatophyte species, Microsporum canis and Arthroderma benhamiae. Both fungi were found to grow well in a protein medium at acidic pH, accompanied by extracellular proteolysis. Shotgun MS analysis of secreted protein revealed fundamentally different protease profiles during fungal growth in acidic versus neutral pH conditions. Most notably, novel dermatophyte-secreted proteases were identified at acidic pH such as pepsins, sedolisins and acidic carboxypeptidases. Therefore, our results not only support genome predictions, but demonstrate for the first time the secretion of acidic proteases by dermatophytes. Our findings also suggest the existence of different pathways of protein degradation into amino acids and short peptides in these highly specialized pathogenic fungi.
Biaxial Constitutive Model of Active Coronary Media Based on Microstructural Information (2013)

Detailed morphological data of vascular smooth muscle cells (VSMC) of coronary arteries were limited. The present study was to quantify dimensions and orientation of swine coronary VSMC and to develop a micro-structural constitutive model of active media. It was found that geometrical parameters of VSMC (length, width, spatial aspect ratio, and orientation) follow normal distributions, and VSMCs orientate towards the circumferential direction of vessels with oblique and symmetrical angles. A micro-structural model of media layer was developed to accurately predict biaxial active responses of coronary arterial media, based on experimental measurements. The present morphological data base and micro-structural model lead to a better understanding of biomechanics of muscular vessels.
LANDSAT-4 TM image data quality analysis for energy-related applications (1983)

This project represents a no-cost agreement between National Aeronautic Space Administration Goddard Space Flight Center (NASA GSFC) and the Pacific Northwest Laboratory (PNL). PNL is a Department of Energy (DOE) national laboratory operted by Battelle Memorial Institute at its Pacific Northwest Laboratories in Richland, Washington. The objective of this investigation is to evaluate LANDSAT's thematic mapper (TM) data quality and utility characteristics from an energy research and technological perspective. Of main interest is the extent to which repetitive TM data might support DOE efforts relating to siting, developing, and monitoring energy-related facilities, and to basic geoscientific research. The investigation utilizes existing staff and facility capabilities, and ongoing programmatic activities at PNL and other DOE national laboratories to cooperatively assess the potential usefulness of the improved experimental TM data. The investigation involves: (1) both LANDSAT 4 and 5 TM data, (2) qualitative and quantitative use consideration, and 3) NASA P (corrected) and A (uncorrected) CCT analysis for a variety of sites of DOE interest. Initial results were presented at the LANDSAT Investigator's Workshops and at specialized LANDSAT TM sessions at various conferences.
A Theoretical Analysis of the Conditions for Unambiguous Node Localization in Sensor Networks (2004)

In this paper we provide a theoretical foundation for the problem of network localization in which some nodes know their locations and other nodes determine their locations by measuring distances or bearings to their neighbors. Distance information is the separation between two nodes connected by a sensing/communication link. Bearing is the angle between a sensing/communication link and the x-axis of a node's local coordinate system. We construct grounded graphs to model network localization and apply graph rigidity theory and parallel drawings to test the conditions for unique localizability and to construct uniquely localizable networks. We further investigate partially localizable networks.
Abstract 16810: Identification of a New Class of Small Molecule Antagonists for Protease Proprotein Convertase Subtilisin-Like Kexin Type 9 (2017)

Intervention with drugs to reduce low density lipoprotein-cholesterol (LDL-C) has proven to decrease mortality. Here, we report the development of small molecules that lower LDL-C by targeting the ...
Fabrication of open stencil masks with asymmetric void ratio for the ion projection lithography space charge experiment (2000)

For the ion projection lithography space charge experiment [P.W.H. de Jager et al., J. Vac. Sci. Technol. B 17, 3098 (1999)] a suitable stencil test mask has been realized and used. This article addresses the stress engineering and fabrication process of this specific test mask with openings in the range of some few 100 nm up to some 100 μm. This large difference in stencil pattern dimensions causes reactive ion etching (RIE) lag (dependence of the etch rate on feature size and pattern density) during the fabrication process and considerable stress variations across the membrane field. The solution to these problems was by (i) implementing novel doping technologies to create variable thickness areas on the membrane serving as reinforcement and stress relief structures, and (ii) adjusting the design to feature sizes and pattern densities to the same order of magnitude for the e-beam lithography and RIE processing steps. The etching of the openings through the 3 μm thick Si membrane was done by inductively coupled plasma etching with gas chopping techniques. These methods as devoloped for this specific test mask can be used to improve the stencil mask technology in general.
Analysis of RNA nearest neighbor parameters reveals interdependencies and quantifies the uncertainty in RNA secondary structure prediction (2018)

RNA secondary structure prediction is often used to develop hypotheses about structure-function relationships for newly discovered RNA sequences, to identify unknown functional RNAs, and to design sequences. Secondary structure prediction methods typically use a thermodynamic model that estimates the free energy change of possible structures based on a set of nearest neighbor parameters. These parameters were derived from optical melting experiments of small model oligonucleotides. This work aims to better understand the precision of structure prediction. Here, the experimental errors in optical melting experiments were propagated to errors in the derived nearest neighbor parameter values and then to errors in RNA secondary structure prediction. To perform this analysis, the optical melting experimental values were systematically perturbed within the estimates of experimental error and alternative sets of nearest neighbor parameters were then derived from these error-bounded values. Secondary structure predictions using either the perturbed or reference parameter sets were then compared. This work demonstrated that the precision of RNA secondary structure prediction is more robust than suggested by previous work based on perturbation of the nearest neighbor parameters. This robustness is due to correlations between parameters. Additionally, this work identified weaknesses in the parameter derivation that makes accurate assessment of parameter uncertainty difficult. Considerations for experimental design are provided to mitigate these weaknesses are provided.
Multiblock Copolymers Based upon Increased Hydrophobicity Bisphenol A Moieties for Proton Exchange Membranes (2014)

Increasing hydrophobicity multiblock copolymers were synthesized by altering the copolymer composition of the hydrophobic segments. A series of nitrile-containing hydrophobic oligomers consisting of bisphenol A (Bis A), dimethylbisphenol A (DMBPA), and tetramethylbisphenol A (TMBPA) moieties were reacted with a disulfonated poly (arylene ether sulfone) hydrophilic segment to form the multiblock copolymer series. 1H and 19F NMR spectroscopy were used to monitor the progress of the copolymerization reactions and confirm the desired compositions. Membranes cast from the resultant multiblock copolymers had high molecular weight as measured by size-exclusion chromatography (SEC), and showed strong mechanical properties. As the hydrophobicity of the polymers increased from the Bis A, to the DMBPA, and to the TMBPA systems, the membranes showed a corresponding decrease in water uptake. The reduced water uptake and limited fluorine content produced membranes with significantly reduced methanol permeabilities over that of Nafion or other similar multiblock copolymer membranes. Electrochemical testing showed that the more hydrophobic TMBPA systems showed improved performance at higher methanol concentrations.
Pulse transmission coefficient: A nonhyperemic index for physiologic assessment of procedural success following percutaneous coronary interventions (2003)

Intracoronary pressure measurements and the determination of fractional flow reserve (FFR) after percutaneous coronary intervention (PCI) predict adverse events. Coronary lesions may impair the transmission of pressure waves across a stenosis, potentially acting as a high-frequency filter. The pulse transmission coefficient (PTC) is a nonhyperemic parameter that calculates the transmission of high-frequency components of the pressure signal through a stenosis. It was shown recently that PTC is highly correlated with FFR. This study was designed to examine the change of PTC as compared to FFR following PCI. Pressure signals were obtained by pressure guidewire in 27 lesions pre- and post-PCI and were analyzed with an algorithm that identifies the high-frequency component in the pressure signal. The PTC was calculated at baseline as the ratio between distal and proximal high-frequency components of the pressure waveform across the lesion. FFR measurements were assessed with intracoronary adenosine. There was a significant increase in PTC following PCI (0.15 +/- 0.17 at baseline vs. 0.84 +/- 0.11 post-PCI; P < 0.001). Comparable changes were observed for FFR (0.58 +/- 0.12 at baseline vs. 0.91 +/- 0.05 post-PCI; P < 0.001). PTC is a nonhyperemic parameter for physiologic assessment of coronary artery stenoses. Similar to FFR, PTC is significantly increased following PCI. Thus, it may serve as an adjunct index for the functional assessment of procedural success following PCI.
Synthesis and skeletal isomerization of the phosphinidene acetylide cluster complexes [Ru4(CO)10(μ4-PPh)(CCPh){WL(CO)}] where L = C5Me5 or C5H5 (1998)

Reactions of the phosphinidene cluster [Ru4(CO)13(µ3-PPh)] with tungsten acetylide complexes [WL(CO)3(CCPh)] (L = C5Me5 or C5H5) gave interconvertible isomers of formula [Ru4(CO)10(µ4-PPh)(CCPh){WL(CO)}]. The structures of the two C5Me5 derivatives were determined by X-ray diffraction, showing a novel WRu4P octahedral core arrangement, in which the acetylide ligand is co-ordinated to a WRu2 triangle with its C–C vector bridging the Ru–Ru edge. For one isomer the phosphinidene ligand is located at the position trans to the W atom, while in the second isomer it is at the cis position. Possible mechanisms for this rare example of skeletal isomerization are suggested.
A multiscale model of the electrohysterogram the BioModUE_PTL project (2013)

The electrohysterogram (EHG) is a promising means of monitoring pregnancy and of detecting a risk of preterm labor. To improve our understanding of the EHG as well as its relationship with the physiologic phenomena involved in uterine contractility, we plan to model these phenomena in terms of generation and propagation of uterine electrical activity. This activity can be realistically modeled by representing the principal ionic dynamics at the cell level, the propagation of electrical activity at the tissue level and then the way it is reflected on the skin surface through the intervening tissue. We present in this paper the different steps leading to the development and validation of a biophysics based multiscale model of the EHG, going from the cell to the electrical signal measured on the abdomen.
Elucidation of Transition Structures and Solvent Effects for the Mislow-Evans Rearrangement of Allylic Sulfoxides (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTElucidation of Transition Structures and Solvent Effects for the Mislow-Evans Rearrangement of Allylic SulfoxidesDeborah K. Jones-Hertzog and William L. JorgensenCite this: J. Am. Chem. Soc. 1995, 117, 35, 9077–9078Publication Date (Print):September 1, 1995Publication History Published online1 May 2002Published inissue 1 September 1995https://doi.org/10.1021/ja00140a029Request reuse permissionsArticle Views469Altmetric-Citations40LEARN 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 InReddit PDF (2 MB) Get e-AlertscloseSupporting Info (2)»Supporting Information Supporting Information Get e-Alerts
A highly parallel implementation of k-means for multithreaded architecture (2011)

We present a parallel implementation of the popular k-means clustering algorithm for massively multithreaded computer systems, as well as a parallelized version of the KKZ seed selection algorithm. We demonstrate that as system size increases, sequential seed selection can become a bottleneck. We also present an early attempt at parallelizing k-means that highlights critical performance issues when programming massively multithreaded systems. For our case studies, we used data collected from electric power simulations and run on the Cray XMT.
An Integrated Approach to the Generation of Environments from Formal Specifications (2000)

This paper describes an experiment in the use of a persistent object store to support the construction and execution of a software development environment. This development environment presents the user with language specific editors which provide access to incremental parsers. The editors and parsers are automatically generated from a formal language specification based on attribute grammars. This is facilitated through the persistent management of types and values and a dynamically callable compiler. We demonstrate that the provision of a persistent object store gives the system designer more freedom and that this leads to the construction of novel software architectures. 1 Introduction The majority of software engineering tools currently available tend to be large and do not integrate cleanly with one another. This lack of integration stems from the lack of integrated data storage abstractions provided by the platforms on which they are constructed. Usually, persi...
Purification, characterization, and molecular cloning of S-adenosyl-L-methionine: uroporphyrinogen III methyltransferase from Methanobacterium ivanovii (1991)

An S-adenosyl-L-methionine:uroporphyrinogen III methyltransferase (SUMT) activity has been identified in Methanobacterium ivanovii and was purified 4,500-fold to homogeneity with a 38% yield. The enzyme had an apparent molecular weight of 58,200 by gel filtration and consisted of two identical subunits of Mr 29,000, as estimated by gel electrophoresis under denaturing conditions. The Km value for uroporphyrinogen III was 52 nM. The enzyme catalyzed the two C-2 and C-7 methylation reactions converting uroporphyrinogen III into precorrin-2. Unlike Pseudomonas denitrificans SUMT, the only SUMT characterized to date (F. Blanche, L. Debussche, D. Thibaut, J. Crouzet and B. Cameron, J. Bacteriol. 171:4222-4231, 1989), M. ivanovii SUMT did not show substrate inhibition at uroporphyrinogen III concentrations of up to 20 microM. Oligonucleotide probes from limited peptide sequence information were used to clone the corresponding gene. The encoded polypeptide showed more than 40% strict homology with P. denitrificans SUMT. The M. ivanovii SUMT structural gene is likely to be, as is P. denitrificans cobA, involved in corrinoid synthesis.
Gas‐phase and liquid‐state properties of esters, nitriles, and nitro compounds with the OPLS‐AA force field (2001)

Abstract Nonbonded and torsional parameters for carboxylate esters, nitriles, and nitro compounds have been developed for the OPLS‐AA force field. In addition, torsional parameters for alkanes have been updated. These parameters were fit to reproduce ab initio gas‐phase structures and conformational energetics, experimental condensed‐phase structural and thermodynamic properties, and experimental free energies of hydration. The computed densities, heats of vaporization, and heat capacities for fifteen liquids are in excellent agreement with experimental values. The new parameters permit accurate molecular modeling of compounds containing a wider variety of functional groups, which are common in organic molecules and drugs. © 2001 John Wiley &amp; Sons, Inc. J Comput Chem 22: 1340–1352, 2001
Continuous F0 in the source-excitation generation for HMM-based TTS: Do we need voiced/unvoiced classification? (2011)

Most HMM-based TTS systems use a hard voiced/unvoiced classification to produce a discontinuous F0 signal which is used for the generation of the source-excitation. When a mixed source excitation is used, this decision can be based on two different sources of information: the state-specific MSD-prior of the F0 models, and/or the frame-specific features generated by the aperiodicity model. This paper examines the meaning of these variables in the synthesis process, their interaction, and how they affect the perceived quality of the generated speech The results of several perceptual experiments show that when using mixed excitation, subjects consistently prefer samples with very few or no false unvoiced errors, whereas a reduction in the rate of false voiced errors does not produce any perceptual improvement. This suggests that rather than using any form of hard voiced/unvoiced classification, e.g., the MSD-prior, it is better for synthesis to use a continuous F0 signal and rely on the frame-level soft voiced/unvoiced decision of the aperiodicity model.
Multiple Roles of Hydrogen Treatments in Amorphous In–Ga–Zn–O Films (2017)

The roles of hydrogen introduced by post-deposition hydrogen treatments were investigated for amorphous In–Ga–Zn–O (a-IGZO) films using room-temperature hydrogen plasma (H-plasma) and high-temperature H2 annealing. It was found that these treatments cause different effects as confirmed by hard X-ray photoemission spectroscopy and difference spectrum analyses. The H-plasma treatment increased both the near-valence band maximum (near-VBM) states (observed just above VBM) and the –OH bonds (confirmed by O 1s core spectrum) if a-IGZO films were deposited under an optimum condition, leading to the conclusion that the room-temperature H treatment incorporates H to a-IGZO films as –OH bonds, and the increase in the relatively shallow near-VBM states (peaked at ∼1.0 eV, extended to ∼2.4 eV from VBM) is ascribed to the generated –OH bonds. On the other hand, high-temperature H2 annealing did not increase the O 1s –OH signal, and its difference spectrum showed a different peak centered at ∼0.7 eV. This difference spectrum is similar to that of H-less a-IGZO films deposited without O2 supply by ultra-high vacuum sputtering and assigned to oxygen deficiency. These results will contribute to control the operation characteristics and the instability issues of a-IGZO TFTs. Further, the deconvoluted difference spectra will be the standard fingerprints of these defects in a-IGZO.
On the Continuity of Achievable Rate Regions for Source Coding over Networks (2007)

The continuity property of achievable rate regions for source coding over networks is considered. We show rate- distortion regions are continuous with respect to distortion vectors. Then we focus on the continuity of lossless rate regions with respect to source distribution: First, the proof of continuity for general networks with independent sources is given; then, for the case of dependent sources, continuity is proven both in examples where one-letter characterizations are known and in examples where one-letter characterizations are not known; the proofs in the latter case rely on the concavity of the rate regions for those networks.