gebhart/patrepeval huggingface dataset:
Phenylalanine ammonia-lyase (PAL) from tobacco (<i>Nicotiana tabacum</i>): characterization of the four tobacco<i>PAL</i>genes and active heterotetrameric enzymes (2009)

PAL (L-phenylalanine ammonia-lyase), the first enzyme of phenylpropanoid biosynthesis, is often encoded by multigene families in plants. A PCR-based approach was used to isolate cDNA clones corresponding to the four PAL genes of tobacco (Nicotiana tabacum). By careful comparison of cDNA and genomic clones, a new PAL gene (PAL4) was defined. PCR amplification of PAL sequences from cDNA led to the generation of chimaeric clones between PAL1 and PAL4, and incorrect annotation of PAL4 ESTs (expressed sequence tags) as PAL1 in the EST database has given rise to a randomly shuffled tentative consensus sequence. The PAL2 previously described in the literature was shown, by domain swapping experiments with PAL1, to possess a single nucleotide substitution leading to an inactive enzyme. The altered amino acid resulting from this substitution maps to the base of the active site pocket in the three-dimensional structure of PAL. The inactive PAL2 allele could not be recovered from 13 different tobacco cultivars examined. PALs 1-4 were co-expressed in multiple plant organs, and were also co-induced following exposure of cell cultures to yeast elicitor or methyl jasmonate. All four tobacco PAL proteins expressed in Escherichia coli displayed normal Michaelis-Menten kinetics, with Km values between 36 and 60 muM. Co-expression of different PAL proteins in E. coli resulted in formation of heterotetramers, which possessed kinetic properties within the same range as those of the individual homotetramers. The potential physiological function of heterotetrameric PAL forms is discussed.
Techniques for improving the efficiency of heuristic search (1993)

Four techniques are presented which improve the efficiency of heuristic search algorithms: agenda data structures, island search, cycle checking and perimeter search. Both theoretical and experimental results are presented which show how these techniques improve the time complexity of heuristic search for certain problems.
The first step towards improving the efficiency of a heuristic search algorithm is to use the fastest possible data structure for storing unexplored nodes in the search space. Several candidate data structures are reviewed and a new type of data structure is presented which is both space and time efficient.
Islands are shown to be a generalization of subgoals. Two new algorithm are presented which make use of islands to improve search efficiency. Test results are presented which compare the performance of the island search algorithms to the performance of A$\sp*.$ The test results cover two problem domains, a grid search problem and a route planning problem. Island search is shown to be superior for these problems when island information is available.
A technique for improving the efficiency of depth-first search on graphs is presented. This technique is referred to as cycle checking since it prevents the generation of duplicate nodes caused by cycles in the search space. Two types of cycle checking are compared and test results are presented for the grid search and route planning problems. Simple guidelines are presented showing which type of cycle checking to use on a given problem.
Perimeter search can be viewed as a new type of bidirectional search. Unlike other bidirectional search algorithms, perimeter search avoids the pitfalls involved in trying to perform two simultaneous searches. Analytical and experimental results are presented to show how the perimeter search technique improves the time complexity of A$\sp*$ and IDA$\sp*$ on two types of problems. Also presented are near-optimal and parallel versions of the perimeter search algorithms.
Changes in membrane-microfilament interaction in intercellular adherens junctions upon removal of extracellular Ca2+ ions. (1986)

EGTA-induced depletion of Ca2+ ions from the culture medium of Madin-Darby bovine kidney epithelial cells results in rapid splitting of adherens-type junctions and the detachment of the vinculin- and actin-containing filament bundle from the cytoplasmic faces of the plasma membrane of the zonula adhaerens. This process was monitored by phase-contrast microscopy, combined with electron microscopy and immunofluorescent localization of the two proteins. It is shown that shortly after extracellular free Ca2+ concentration is lowered to the micromolar range, the actin-containing, junction-associated belt of microfilaments, together with the vinculin-rich junctional plaque material, is irreversibly detached as one structural unit from the plasma membrane, contracts, and is displaced towards the perinuclear cytoplasm where it gradually disintegrates. Other actin- and vinculin-containing structures present in the same cells, notably the focal contacts at the substratum, are not similarly affected by the Ca2+ depletion and retain both the adhesion to the external surface and the association with the plaque and microfilament components. Electron microscopic examination has shown that the membrane domain of the zonulae adhaerentes, unlike that of desmosomes, is not endocytosed after Ca2+ removal and that the displaced actin- and vinculin-containing plaque and filament belt are not associated with a particular membrane. It is further shown that upon restoration of normal Ca2+ levels in the culture medium, new intercellular contacts are established gradually by accretion of both vinculin and actin into new belt-like plaque- and microfilament-containing structures.
Balanced allocations (extended abstract) (1994)

Article Balanced allocations (extended abstract) Share on Authors: Yossi Azar Tel Aviv University, Israel Tel Aviv University, IsraelView Profile , Andrei Z. Broder Digital Systems Research Center, 130 Lytton Avenue, Palo Alto, CA Digital Systems Research Center, 130 Lytton Avenue, Palo Alto, CAView Profile , Anna R. Karlin Digital Systems Research Center, 130 Lytton Avenue, Palo Alto, CA Digital Systems Research Center, 130 Lytton Avenue, Palo Alto, CAView Profile , Eli Upfal IBM Almaden Research Center, San Jose, CA and Department of Applied Mathematics, The Weizmann Institute of Science, Rehovot, Israel IBM Almaden Research Center, San Jose, CA and Department of Applied Mathematics, The Weizmann Institute of Science, Rehovot, IsraelView Profile Authors Info & Claims STOC '94: Proceedings of the twenty-sixth annual ACM symposium on Theory of ComputingMay 1994 Pages 593–602https://doi.org/10.1145/195058.195412Online:23 May 1994Publication History 82citation901DownloadsMetricsTotal Citations82Total Downloads901Last 12 Months122Last 6 weeks9 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access
Ozone: Efficient Execution with Zero Timing Leakage for Modern Microarchitectures (2017)

Time variation during program execution can leak sensitive information. Time variations due to program control flow and hardware resource contention have been used to steal encryption keys in cipher implementations such as AES and RSA. A number of approaches to mitigate timing-based side-channel attacks have been proposed including cache partitioning, control-flow obfuscation and injecting timing noise into the outputs of code. While these techniques make timing-based side-channel attacks more difficult, they do not eliminate the risks. Prior techniques are either too specific or too expensive, and all leave remnants of the original timing side channel for later attackers to attempt to exploit. In this work, we show that the state-of-the-art techniques in timing side-channel protection, which limit timing leakage but do not eliminate it, still have significant vulnerabilities to timing-based side-channel attacks. To provide a means for total protection from timing-based side-channel attacks, we develop Ozone, the first zero timing leakage execution resource for a modern microarchitecture. Code in Ozone execute under a special hardware thread that gains exclusive access to a single core's resources for a fixed (and limited) number of cycles during which it cannot be interrupted. Memory access under Ozone thread execution is limited to a fixed size uncached scratchpad memory, and all Ozone threads begin execution with a known fixed microarchitectural state. We evaluate Ozone using a number of security sensitive kernels that have previously been targets of timing side-channel attacks, and show that Ozone eliminates timing leakage with minimal performance overhead.
The Capsule and S-Layer: Two Independent and Yet Compatible Macromolecular Structures in <i>Bacillus anthracis</i> (1998)

Bacillus anthracis, the etiological agent of anthrax, is a gram-positive spore-forming bacterium. Fully virulent bacilli are toxinogenic and capsulated. Two abundant surface proteins, including the major antigen, are components of the B. anthracis surface layer (S-layer). The B. anthracis paracrystalline S-layer has previously only been found in noncapsulated vegetative cells. Here we report that the S-layer proteins are also synthesized under conditions where the poly-gamma-D-glutamic acid capsule is present. Structural and immunological analyses show that the capsule is exterior to and completely covers the S-layer proteins. Nevertheless, analysis of single and double S-layer protein mutants shows that the presence of these proteins is not required for normal capsulation of the bacilli. Similarly, the S-layer proteins assemble as a two-dimensional crystal, even in the presence of the capsule. Thus, both structures are compatible, and yet neither is required for the correct formation of the other.
Spontaneous subdural hematoma associated to Duret hemorrhage (2014)

Subdural hematoma (SH) is a neurosurgical emergency, usually caused by head trauma. Non-traumatic causes include aneurysm or arterial–venous malformation rupture, coagulopathy and others. We report the case of a 66 year-old man who developed apparently unprovoked signs of increased intracranial pressure. Brain computed tomography scan showed an acute spontaneous SH, surgically treated. Throughout surgery, a ruptured cortical artery with intensive bleeding appeared and was cauterized. After surgery, patient remained comatose and a new CT demonstrated Duret hemorrhage at the brainstem. Acute spontaneous SH of arterial origin is rare and highly lethal, in which a good prognosis relies on early diagnosis and treatment.
The impact of nurse prescribing on the role of the district nurse (2005)

This article details the results of a small qualitative research study which was conducted to explore the experiences of nurse prescribing by a group of district nurses working within one of the UK pilot sites. Semi-structured interviews were undertaken with seven (n=7) district nurses, who had a range of prescribing experience. The focus of the study was to evaluate changes in their roles as a result of being able to prescribe. Although the participants in the study identified many positive aspects of nurse prescribing in relation to their roles as district nurses, evidence presented indicates an overwhelming inconsistency among the participants, in terms of how each actually prescribed.
Verification of asynchronous circuits using time Petri net unfolding (1996)

Article Free Access Share on Verification of asynchronous circuits using time Petri net unfolding Authors: Alexei Semenov Department of Computing Science, University of Newcastle, Newcastle upon Tyne NE1 7RU, England Department of Computing Science, University of Newcastle, Newcastle upon Tyne NE1 7RU, EnglandView Profile , Alexandre Yakovlev Department of Computing Science, University of Newcastle, Newcastle upon Tyne NE1 7RU, England Department of Computing Science, University of Newcastle, Newcastle upon Tyne NE1 7RU, EnglandView Profile Authors Info & Claims DAC '96: Proceedings of the 33rd annual Design Automation ConferenceJune 1996 Pages 59–62https://doi.org/10.1145/240518.240530Published:01 June 1996Publication History 24citation370DownloadsMetricsTotal Citations24Total Downloads370Last 12 Months8Last 6 weeks0 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF
Polychlorotrifluoroethylene (PCTFE) Oligomer Pharmacokinetics in Fischer 344 Rats: Development of a Physiologically Based Model (1992)

The hydraulic fluid oil polychiorotrifluoroethylene (PCTFE) is hepato- and nephrotoxic in the rat. Male Fischer 344 rats were exposed to PCTFE either for a single 6-hr exposure (0.5 or 0.25 mg&sol;liter) or daily 5 days&sol;week, 6 hr&sol;day, for 13 weeks (0.5, 0.25, or 0.01 mg&sol;liter). Blood, tissue, and urinary PCTFE concentrations measured postexposure were used to develop a physiologically based pharmacokinetic (PB-PK) model. The PCTFE hydraulic fluid used was a mixture of trimeric and tetrameric oligomers with minor amounts of other chain lengths. The PB-PK model was designed to describe the behavior, not of individual oligomers, but of total mass for the trimer and tetramer in each tissue. Partition coefficients were estimated using the model to optimize tissue&sol;blood concentration ratios measured at the end of the 13-week exposure. First-order metabolic rate constants for both trimeric (2.0 hr−1) and tetrameric (1.0 hr−1) portions were estimated by optimization against urinary fluoride data assuming release of 0.77 mole fluoride per mole trimer and 0.844 mole fluoride per mole tetramer metabolized. To obtain accurate simulation of pharmacokinetic data it was necessary to hypothesize two fat compartments with diffusion-limited exchange of PCTFE oligomer with the blood. Relative concentrations of trimer and tetramer in venous blood, liver, and fat after a single 6-hr exposure were proportional to inhaled concentrations. Tetramer accumulated preferentially with multiple exposure. Components of PCTFE were metabolized to carboxylic acids with release of fluoride. Due to their persistence tetrameric oligomers appear to be more important than trimeric oligomers as causative agents of PCTFE hepato and nephrotoxicity in the rat.
Electron impact mass spectrometry of some 2‐(<i>p</i>‐bromophenyl)‐4,4‐disubstituted‐5(4<i>H</i>)‐oxazolones (1988)

Abstract The mass spectrometric behaviour of four 2‐( p ‐bromophenyl)‐4,4‐disubstituted‐5(4 H )‐oxazolones has been investigated using linked scans, mass analyzed ion kinetic energy spectrometry, accurate mass measurements and collisional spectroscopy. The study shows the formation of similar ions in all cases, with the presence of skeletal rearrangements, leading to highly stable product ions.
Batch purification of ovomucoid and characterization of the purified product (1971)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTBatch purification of ovomucoid and characterization of the purified productJohn Gorton Davis, Carol J. Mapes, and John W. DonovanCite this: Biochemistry 1971, 10, 1, 39–42Publication Date (Print):January 5, 1971Publication History Published online1 May 2002Published inissue 5 January 1971https://pubs.acs.org/doi/10.1021/bi00777a006https://doi.org/10.1021/bi00777a006research-articleACS PublicationsRequest reuse permissionsArticle Views218Altmetric-Citations249LEARN 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
Offload Compiler Runtime for the Intel&#x00AE; Xeon Phi Coprocessor (2013)

The Intel® Xeon Phi coprocessor platform has a new software stack that enables new programming models. One such model is offload of computation from a host processor to a coprocessor that is a fully-capable Intel® Architecture CPU, namely, the Intel® Xeon Phi coprocessor. The purpose of that offload is to improve response time and/or throughput. This paper presents the compiler offload software runtime infrastructure for the Intel® Xeon Phi coprocessor, which includes a production C/C++ and Fortran compiler that enables offload to that coprocessor, and an underlying Intel® Many Integrated Core (Intel® MIC) platform software stack that enables offloading. The paper shares the insights that grow out of the experience of a multi-year, intensive development effort. It addresses end users' questions about offload with the compiler offload runtime, namely, why offload to a co-processor is useful, how it is specified, and what the conditions for the profitability of offload are. It also serves as a guide to potential third-party developers of offload runtimes, such as a gcc-based offload compiler, ports of existing commercial offloading compilers to Intel® Xeon Phi coprocessor such as CAPS®, and third-party offload library vendors that Intel is working with, such as NAG® and MAGMA®. It describes the software architecture and design of the offload compiler runtime. It enumerates the key performance features for this heterogeneous computing stack, related to initializa-tion, data movement and invocation. Finally, it evaluates the performance impact of those features for a set of directed micro-benchmarks and larger workloads.
A novel aqueous metronidazole 1% gel with hydrosolubilizing agents (HSA-3). (2006)

Rosacea is a common chronic dermatosis that often is characterized by the presence of facial erythema, visible blood vessels, papules, and pustules. Because the face is the predominant site of involvement, rosacea may cause serious psychologic trauma and can significantly affect the quality of life of individuals with the condition. The first topical therapy approved for rosacea by the US Food and Drug Administration was metronidazole for the treatment of inflammatory lesions and erythema. A stable aqueous gel formulation of 1% metronidazole has been developed with the novel combination of hydrosolubilizing agents. Metronidazole 1% gel is a clear gel that exhibits advantageous qualities. Some features of the new product include being highly spreadable, easy to use, cosmetically friendly, ultramild, nondrying, and moisturizing. Data are presented from a 21-day cumulative irritation study, an assessment of skin barrier function, an in vitro skin penetration study, an absorption following maximal topical exposure study, and a skin hydration study.
MC<sup>2</sup>-RAM: An In-8T-SRAM Computing Macro Featuring Multi-Bit Charge-Domain Computing and ADC-Reduction Weight Encoding (2021)

In-memory computing (IMC) is a promising hardware architecture to circumvent the memory walls in data-intensive applications, like deep learning. Among various memory technologies, static random-access memory (SRAM) is promising thanks to its high computing accuracy, reliability, and scalability to advanced technology nodes. This paper presents a novel multi-bit capacitive convolution in-SRAM computing macro for high accuracy, high throughput and high efficiency deep learning inference. It realizes fully parallel charge-domain multiply-and-accumulate (MAC) within compact 8-transistor 1-capacitor (8T1C) SRAM arrays that is only 41% larger than the standard 6T cells. It performs MAC with multi-bit activations without conventional digital bit-serial shift-and-add schemes, leading to drastically improved throughput for high-precision CNN models. An ADC-reduction encoding scheme complements the compact sram design, by reducing the number of needed ADCs by half for energy and area savings. A $576 \times 130$ macro with 64 ADCs is evaluated in 65nm with post-layout simulations, showing 4.60 TOPS/mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> compute density and 59.7 TOPS/W energy efficiency with 4/4-bit activations/weights. The MC <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> - RAM also achieves excellent linearity with only 0.14 mV (4.5% of the LSB) standard deviation of the output voltage in Monte Carlo simulations.
Metal-Catalyzed and Metal-Free Intermolecular Amination of Light Alkanes and Benzenes (2016)

GRAPHICAL ABSTRACT
A nanoscale CMOS charge pump with near perfect current matching (2013)

A drain-switching charge pump (CP) design is presented with near perfect current matching and extended flat current response over a range of process, voltage, and temperature variations. Current mismatch is compensated dynamically without the need for a replica charge pump or extended digitally-assisted calibration routines. The self-regulated circuit uses several simple yet effective feedback mechanisms to overcome the basic shortcomings of nanometer devices and reduced power supplies. The circuit is designed in 90nm CMOS and simulated extensively using Monte Carlo analysis while sweeping the operating temperature to provide statistically relevant operating conditions. The proposed design achieves near perfect current matching at output voltages between 0.16V and 0.98V for temperatures ranging from -30 to 90 degrees Celsius and a power supply between 1.08V and 1.32V.
An electroacoustic surface‐wave convolver of fabricated from a thin piezoelectric film and a semiconductor (1992)

Abstract A surface acoustic wave convolver composed of ZnO with high piezoelectricity and GaAs with high mobility is thought to be a highly efficient active device, and considerable work and development has been carried out on this device. However, no theoretical analysis which takes into account every parameter such as the dependencies on ZnO film thickness and carriers in GaAs has been carried out. In this paper, the propagation characteristic of the surface acoustic wave in the ZnO/GaAs system was analyzed theoretically, taking into account the semiconductor carrier concentration in order to clarify the dependencies of the convolution efficiency of a ZnO/GaAs convolver on the ZnO film thickness, carrier density, and mobility. In addition, the dependencies of the convolution output on the surface acoustic wave oscillation characteristic in the ZnO/GaAs system and carrier density will be shown.
Application of Ultrasound in Medicine (2011)

Ultrasound device, essentially, consists of a transducer, transmitter pulse generator, compensating amplifiers, the control unit for focusing, digital processors and systems for display. It is used in cases of: abdominal, cardiac, maternity, gynecological, urological and cerebrovascular examination, breast examination, and small pieces of tissue as well as in pediatric and operational review.