gebhart/patrepeval huggingface dataset:
Basic molecular dynamics (2004)

This chapter provides the introductory appetizer and aims to leave the reader new to MD with a feeling for what the subject is all about. Later chapters will address the techniques in detail; here the goal is to demonstrate a working example with a minimum of fuss and so convince the beginner that MD is not only straightforward but also that it works successfully. Of course, the technique for evaluating the forces discussed here is not particularly efficient from a computational point of view and the model is about the simplest there is. Such matters will be rectified later. The general program organization and stylistic conventions used in case studies throughout the book are also introduced.
Engineering Approaches to Biomanipulation (2007)

This article presents a review on the existing techniques for manipulating biological cells. Because biomanipulation involves a wide range of disciplines, from biology to engineering, we concentrate on some of the key methodologies that would result in an efficient biomanipulation system. Some of the key methodologies discussed in this article for cell manipulation relate to the use of magnetics, microelectromechanical systems (MEMS)-based approaches, optics, electric field, and mechanical techniques. Recent advances in engineering have allowed researchers worldwide to address the problems arising from conventional manipulation techniques. This paper assimilates significance and limitations of biomanipulation techniques described in the literature.
Low frequency passive noise control of a piston structure with a weak radiating cell (1999)

The concept of a weak sound radiating cell is proposed to reduce the low-frequency radiated noise from structures. The cell consists of two mechanically coupled surfaces such that, when placed on a vibrating structure, the response of the two surfaces are nearly out-of-phase and nearly of the same strength over a wide frequency range. This structure response leads the cell to behave as an acoustic dipole and thus a poor sound-radiating source. The control of low-frequency structurally radiated noise is then achieved by covering the structure with an array of these weak radiating cells, i.e., surface treatment. Thus the surface treatment essentially transforms the response of the structure to that of a distributed array of dipoles yielding a low sound radiating structure. A theoretical model of a single weak radiating cell applied to a simple piston structure was developed and experimental verification was performed. Overall sound power level reductions of over 6 dB were experimentally achieved between 400 and 1600 Hz with maximum reductions of over 30 dB at discrete frequencies.
Synthesis of Novel 3,5-Dichloro-2-arylpyridines by Palladium Acetate-Catalyzed Ligand-Free Suzuki Reactions in Aqueous Media (2009)

A highly efficient palladium acetate-catalyzed ligand-free Suzuki reaction of 2,3,5-trichloropyridine with arylboronic acids in aqueous phase was developed. High yields of 3,5-dichloro-2-arylpyridines, a simple Pd source, absence of ligands, and environmentally benign as well as mild reaction conditions are important features of this method.
Halftoning with error diffusion on an image-adaptive raster (1994)

We present a modified halftoning algorithm. The basic idea is to use error diffusion not on a fixed raster, but to adapt the raster to the properties of the original gray-tone image, e.g., the local intensity. The choice of a coarser raster in the high- and low-level input regions leads to the suppression of wormilke textures and to a decrease in calculation effort. The advantages and problems of this approach are discussed and examples are shown.
Homogeneous 1,4-addition of hydrogen catalyzed by tricarbonyl(arene)chromium complexes (1968)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTHomogeneous 1,4-addition of hydrogen catalyzed by tricarbonyl(arene)chromium complexesE. N. Frankel, E. Selke, and C. A. GlassCite this: J. Am. Chem. Soc. 1968, 90, 9, 2446–2448Publication Date (Print):April 1, 1968Publication History Published online1 May 2002Published inissue 1 April 1968https://doi.org/10.1021/ja01011a058RIGHTS & PERMISSIONSArticle Views387Altmetric-Citations50LEARN 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 (388 KB) Get e-Alerts Get e-Alerts
Methodology for Combined TMS and EEG (2009)

The combination of transcranial magnetic stimulation (TMS) with simultaneous electroencephalography (EEG) provides us the possibility to non-invasively probe the brain's excitability, time-resolved connectivity and instantaneous state. Early attempts to combine TMS and EEG suffered from the huge electromagnetic artifacts seen in EEG as a result of the electric field induced by the stimulus pulses. To deal with this problem, TMS-compatible EEG systems have been developed. However, even with amplifiers that are either immune to or recover quickly from the pulse, great challenges remain. Artifacts may arise from the movement of electrodes, from muscles activated by the pulse, from eye movements, from electrode polarization, or from brain responses evoked by the coil click. With careful precautions, many of these problems can be avoided. The remaining artifacts can be usually reduced by filtering, but control experiments are often needed to make sure that the measured signals actually originate in the brain. Several studies have shown the power of TMS-EEG by giving us valuable information about the excitability or connectivity of the brain.
Cyclooxygenases 1 and 2 contribute to peroxynitrite‐mediated inflammatory pain hypersensitivity (2008)

Peroxynitrite (ONOO(-)), the reaction product of the interaction between superoxide (O(2)(*-)) and nitric oxide (*NO), is a potent proinflammatory and cytotoxic nitrooxidative species. Its role as a mediator of hyperalgesia (clinically defined as an augmented sensitivity to painful stimuli) is not known. In light of the known proinflammatory properties of ONOO(-), our study addressed its potential involvement in the development of hyperalgesia associated with tissue damage and inflammation. Intraplantar injection in rats of the ONOO(-) precursor O(2)(*-) (1 microM) led to the development of thermal hyperalgesia associated with a profound localized inflammatory response. Both events were blocked by L-NAME (N(G)-nitro-L-arginine methyl ester, 3-30 mg/kg), a nitric oxide synthase inhibitor, or by FeTM-4-PyP(5+) [Fe(III)5,10,15,20-tetrakis(N-methylpyridinium-4-yl)porphyrin, 3-30 mg/kg], an ONOO(-) decomposition catalyst. These results suggested that locally synthesized ONOO(-) produced in situ by O(2)(*-) and *NO is key in the development of inflammatory hyperalgesia. The direct link between ONOO(-) and hyperalgesia was further supported by demonstrating that intraplantar injection of soluble ONOO(-) itself (1 microM) similarly led to inflammatory hyperalgesia. ONOO(-) generated by the interaction between exogenous administration of O(2)(*-) and endogenous *NO, or provided by direct injection of ONOO(-), activated the transcription factor NF-kappaB in paw tissues, enhancing expression of the inducible but not the constitutive cyclooxygenase enzyme (COX-2 and COX-1, respectively). ONOO(-)-mediated hyperalgesia was blocked in a dose-dependent manner by intraperitoneal injections of indomethacin (10 mg/kg), a nonselective COX-1/COX-2 inhibitor, or NS398 [N-(2-cyclohexyloxy-4-nitrophenyl)methanesulfonamide; 10 mg/kg] a selective COX-2 inhibitor, as well as by an anti-prostaglandin (PG) E(2) antibody (200 microg). In another established model of inflammation-related hyperalgesia by intraplantar injection of carrageenan in rats, inhibition of ONOO(-) with FeTM-4-PyP(5+) (3-30 mg/kg) inhibited the development of hyperalgesia and the release of PGE(2) in paw tissue exudates. Furthermore, FeTM-4-PyP(5+) synergized with indomethacin and NS397 (1-10 mg/kg) to block both hyperalgesia and edema. Taken together, these data show for the first time that ONOO(-) is a potent mediator of inflammation-derived hyperalgesia operating via the COX-to-PGE(2) pathway. These results provide a pharmacological rationale for the development of inhibitors of peroxynitrite biosynthesis as novel nonnarcotic analgesics. The broad implications of our study are that dual inhibition of both ONOO(-) formation and COX activity may provide an alternative therapeutic approach to the management of pain: effective analgesia with reduced side-effects typically associated with the use of COX inhibitors.
Accurate prediction of protein structures and interactions using a 3-track network (2021)

Abstract DeepMind presented remarkably accurate protein structure predictions at the CASP14 conference. We explored network architectures incorporating related ideas and obtained the best performance with a 3-track network in which information at the 1D sequence level, the 2D distance map level, and the 3D coordinate level is successively transformed and integrated. The 3-track network produces structure predictions with accuracies approaching those of DeepMind in CASP14, enables rapid solution of challenging X-ray crystallography and cryo-EM structure modeling problems, and provides insights into the functions of proteins of currently unknown structure. The network also enables rapid generation of accurate models of protein-protein complexes from sequence information alone, short circuiting traditional approaches which require modeling of individual subunits followed by docking. We make the method available to the scientific community to speed biological research. One-Sentence Summary Accurate protein structure modeling enables rapid solution of structure determination problems and provides insights into biological function.
Neither arginine nor histidine can carry out the function of lysine-295 in the ATP-binding site of p60src. (1986)

All 15 protein kinases whose amino acid sequence is known contain a lysine residue at a position homologous to that of lysine-295 in p60src, the transforming protein of Rous sarcoma virus. The ATP analog p-fluorosulfonyl 5'-benzoyl adenosine inactivates both p60src and the catalytic subunit of the cyclic AMP-dependent protein kinase by modification of this lysine. We used oligonucleotide-directed mutagenesis to examine the possible functions of this residue. Lysine-295 in p60src was replaced with a glutamic acid, an arginine, or a histidine residue, and mutant p60src proteins were characterized in chicken cells infected by mutant viruses. None of these three mutant p60src proteins had tyrosine protein kinase activity in vitro, and none induced morphological transformation of infected cells. Since neither a histidine nor an arginine residue can replace the function of lysine-295, we suggest that it carries out the specialized function of proton transfer in the phosphotransferase reaction. All three mutant viruses underwent reversion to wild type during passage in tissue culture. Because the rate with which this occurred differed significantly among the mutants, reversion appears to have resulted from errors in transcription, rather than from recombination with the cellular src gene.
Heat-resistant ceramics based on LAS-system non-metallic mineral and its thermal shock resistance (2010)

Li2O-Al2O3-SiO2 (LAS) system-based ceramics have been prepared with petalite and kaolin and their thermal shock resistances investigated. Feed slurries in five combinations of petalite and kaolin composition between 40% and 60% were first prepared with 5, 15 and 35 μm fractions of petalite and slip casted into moulds. Then the casts were subjected to 2-stage sintering: in the first stage, at 850°C for 2 h and in the second stage, at 1200, 1250 and 1300°C for 2 h. Heating rate was 3°C per minute. The characteristics of sintering, microstructure, X-ray diffraction pattern and water absorption rate of the LAS ceramics produced were studied. Their thermal shock resistances were also measured by a directly flame contact method. Petalite was transformed into β-eucryptite and β-spodumene at temperatures higher than 1200°C. The LAS ceramics were found to have the highest thermal shock resistance at 1250°C. Even at the reduced addition of 45% petalite, the more the particle size of petalite increase, the better is thermal shock resistance of the LAS system ceramics.
Applications of Streamline Simulations to Reservoir Studies (2001)

Abstract Computer models of oil reservoirs have become increasingly more complex in order to represent geological reality and its impact on fluid flow. Memory and CPU time limitations by finite difference/volume simulators force a coarser resolution of reservoirs models through upscaling. Upscaling can lead to significant difficulties in reservoirs studies: (1) while the fine-scale geological model is build from petrophysical, log, and seismic data, its dynamic behaviour is never checked. As a result, a coarse-scale reservoir study can be linked to a fine-scale geological model but the two might be inconsistent in their dynamic behaviour. (2) Conversely, the upscaled model cannot be properly tested since the flow and production behaviour at the fine-scale level is not available. There is no reference solution for guiding important decisions for building a consistent upscaled model. (3) A large number of sector models are required in designing optimal well patterns. Streamlines simulation is now an attractive alternative to overcome some of these drawbacks since it offers substantial computational efficiency while minimising numerical diffusion and grid orientation effects. It allows the integration of fine-scale geological models into the reservoir engineering workflow. In this paper, we demonstrate the usefulness and efficiency of a streamline simulator (3DSL5) in the reservoir engineering workflow. We evaluate its speed, memory requirements and scalability using tracer and black oil test data sets on an SGI Origin 2000 (250 MHz MIPS). Our data are based on real fields and range from 200000 to 7 millions cells with cells as small as 30x30x0;5 meters. We examine problems with pre- and post-processing of large data sets and visualising such simulations. Streamlines allowed us to check the validity of a large geological model and to optimise wells patterns with more than 30 producers and injectors. Application of streamlines to the 10th SPE comparative solution project is also discussed. We demonstrate how streamline-based simulation has matured from a research tool to an industrial application providing real benefits to engineers as a complementary tool to existing conventional simulation technology based on finite volumes.
Resin development for electron microscopy and an analysis of embedding at low temperature* (1982)

SUMMARY We have tested a wide range of acrylate and methacrylate resin formulations and have concluded that embedding resins can be developed which are usable within a broad range of environmental conditions. To demonstrate this versatility, we have designed two highly‐cross‐linked resins, one polar and the other nonpolar, that are usable to temperatures from 243 to 223 K. Both of these resins formulations, which are now commercially available, show that systematic experiments can be easily done to study the effects of environmental parameters, such as water content, temperature, or resin polarity, on biological material during embedding. Using these resins and aldehyde‐fixed protein crystals, it can be shown that low temperature minimizes the loss of molecular structure to an extent that is not often obtainable with conventional methods of dehydration and embedding. Embedded crystals of aspartate aminotransferase still retained molecular order to 0·6 nm. Embedded crystals of catalase show X‐ray diffraction maxima out to 0·8 nm. When sectioned, catalase revealed stain‐limited electron and optical diffraction patterns to 2·5 nm. Nevertheless, our work clearly demonstrates that low temperature embedding procedures are superior and that versatile, general purpose resins can be designed to take advantage of this fact.
Melt-processable polypeptide/ionomer molecular composites (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMelt-processable polypeptide/ionomer molecular compositesR. A. Weiss, L. Shao, and R. D. LundbergCite this: Macromolecules 1992, 25, 23, 6370–6372Publication Date (Print):November 1, 1992Publication History Published online1 May 2002Published inissue 1 November 1992https://pubs.acs.org/doi/10.1021/ma00049a039https://doi.org/10.1021/ma00049a039research-articleACS PublicationsRequest reuse permissionsArticle Views82Altmetric-Citations34LEARN 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
System Design for the Measurement of Downhole Dynamic Rheology for Foam Fracturing Fluids (1991)

Abstract To investigate the rheology of multi-phase fluids and especially foams under realistic field conditions a downhole flow loop has been constructed and tested. The interactions between gravitational, frictional and other (e.g. gas solubility) factors have been investigated and isolated in a series of experiments. Here the system design of the multi-phase fluid flow loop and the special considerations of the design and their justification are described. To evaluate the data a new two-phase flow equation and a methodology of interpretation are outlined. Applications of the methodology in the treatment of sample data are also presented. The choice of a vertical instead of a horizontal apparatus is justified from the fundamental treatment in this work. It shows that the presence of the gravitational effects magnifies the frictional effects, allowing their more accurate estimation.
A Nonrelational Data Warehouse for the Analysis of Field and Laboratory Data From Multiple Heterogeneous Photovoltaic Test Sites (2016)

A nonrelational, distributed computing, data warehouse, and analytics environment (Energy-CRADLE) was developed for the analysis of field and laboratory data from multiple heterogeneous photovoltaic (PV) test sites. This data informatics and analytics infrastructure was designed to process diverse formats of PV performance data and climatic telemetry time-series data collected from a PV outdoor test network, i.e., the Solar Durability and Lifetime Extension global SunFarm network, as well as point-in-time laboratory spectral and image measurements of PV material samples. Using Hadoop/HBase for the distributed data warehouse, Energy-CRADLE does not have a predefined data table schema, which enables ingestion of data in diverse and changing formats. For easy data ingestion and data retrieval, Energy-CRADLE utilizes Hadoop streaming to enable Python MapReduce and provides a graphical user interface, i.e., py-CRADLE. By developing the Hadoop distributed computing platform and the HBase NoSQL database schema for solar energy, Energy-CRADLE exemplifies an integrated, scalable, secure, and user-friendly data informatics and analytics system for PV researchers. An example of Energy-CRADLE enabled scalable, data-driven, analytics is presented, where machine learning is used for anomaly detection across 2.2 million real-world current-voltage (I-V) curves of PV modules in three distinct Köppen-Geiger climatic zones.
Montelukast and fluticasone compared with salmeterol and fluticasone in protecting against asthma exacerbation in adults: one year, double blind, randomised, comparative trial (2003)

The addition of montelukast in patients whose symptoms remain uncontrolled by inhaled fluticasone could provide equivalent clinical control to salmeterol.
A novel low temperature PVD planarized Al-Cu process for high aspect ratio sub-half micron interconnect (2002)

A novel low cost and low temperature PVD planarized Al-Cu:0.5% process for simultaneous high aspect ratio interconnect hole fill and metal layer planarization is reported. This is accomplished by using low pressure Al-Cu sputtering deposition with moderate heat applied to the wafers. The low pressure sputtering deposition reduces the amount of migrated Al atoms needed for hole fill and metal layer planarization. The low pressure also helps maintain a very clean environment for easy migration of Al atoms. These features result in excellent interconnect hole fill and metal layer planarization at low temperatures (<450/spl deg/C). Completely filled sub-half micron Al plugs of high aspect ratio (up to 4:1) have been fabricated. Low via resistance (<1.2 /spl Omega/ for 0.35 /spl mu/m vias), high via chain yield (/spl sim/100%), and good via reliability have been demonstrated by this PVD planarized process at a wafer temperature of 380/spl deg/C.
Direct evidence for enzyme persulfide and disulfide intermediates during 4-thiouridine biosynthesis (2006)

Two proposed mechanisms for 4-thiouridine generation share key cysteine persulfide and disulfide intermediates, and indirect evidence of their existence has been previously reported; chemical trapping and mass spectrometry have now provided direct and definitive evidence of these key intermediates.
Hot carrier effects in nMOSFETs in 0.1 μm CMOS technology (2003)

Recent studies show that, for a given technology, as the effective channel length is scaled down towards 0.1 /spl mu/m, the worst case hot carrier stress condition for nMOSFETs switches from I/sub b,/ /sub peak/ (peak substrate current bias condition) to V/sub g/=V/sub d/. In this paper, we demonstrate that the worst case stress condition is determined by the ratio of I/sub b/|/sub Ib,/ /sub peak/ to I/sub b/|/sub Vg=Vd/. Post-metallization anneal in deuterium similarly improves hot carrier lifetime under bias at I/sub b, peak/ and V/sub g/=V/sub d/.