gebhart/patrepeval huggingface dataset:
Transamidase kinetics. Amide formation in the enzymic reactions of thiol esters with amines (1975)

1. Beta-Phenylpropionylthiocholine and N-(5-aminopentyl)-5-dimethylaminonaphthalene-1-sulphonamide (dansylcadaverine) serve as a pair of water-soluble (pH7.5) model substrates for transamidating enzymes. Amide formation could be followed directly through fluorescence measurements by monitoring the continuous extraction of the water-soluble coupling product, N-(beta-phenylpropionyl)dansylcadaverine, into n-heptane. By this procedure, the steady-state kinetics of glutamine-lysine endo-gamma-glutamyltransferase from human plasma (fibrinoligase, thrombin- and Ca2+-activated blood coagulation Factor XII) and from guinea-pig liver (liver transglutaminase) were investigated at 25 degrees C. 2. With beta-phenylpropionylthiocholine as the varied substrate, Lineweaver-Burk plots with various concentrations of dansylcadaverine intercept on the horizontal axis, suggesting that formation of the acyl-enzyme is rate limiting. 3. On the basis of functional normality of active sites, kcat. values of 1.8 s(-1) and 0.9 s(-1) were obtained for the plasma and liver gamma-glutamyltransferase respectively. The two enzymes show identical affinities for the first substrate, beta-phenylpropionylthiocholine, with Ka 4 times 10(-4) M. 4. Utilization of the second substrate, dansylcadaverine, appears to be an order of magnitude more efficient with the liver enzyme. 5. N-(5-Amino-3-thiapentyl)-5-dimethylaminonaphthalene-1-sulphonamide (dansylthiacadaverine) could be used instead of dansylcadaverine in the fluorescent kinetic system. 6. Competitive inhibition by a non-fluorescent amine substrate histamine was also evaluated.
AIDS Researchers Negotiate Tricky Slopes of Science (1998)

PARK CITY, UTAH—Outdoors, the air was bracing, the powder fine, and the skiing sublime. Indoors, 500 AIDS researchers, fortified with coffee and hot cocoa, discussed and debated the latest research on HIV and SIV, the viruses that cause AIDS in humans and other primates. The recent Keystone meeting* at this well-known ski resort served as a reminder that, like the white mountain slopes, AIDS research has its share of both fast schusses and mogul fields.
Matching attack patterns to security vulnerabilities in software-intensive system designs (2005)

Fortifying software applications from attack is often an effort that occurs late in the software development process. Applying patches to fix vulnerable applications in the field is a common approach to securing applications. Abstract representations of attacks such as attack trees and attack nets can be used for identifying potential threats before a system is released. We have constructed attack patterns that can illuminate security vulnerabilities in a software-intensive system design. Matching our attack patterns to vulnerabilities in the design phase may stimulate security efforts to start early and to become integrated with the software process. The intent is that our attack patterns can be used to effectively encode software vulnerabilities in vulnerability databases. A case study of our approach with undergraduate students in a security course indicated that our attack patterns can provide general descriptions of vulnerabilities. The students were able to accurately map the patterns to vulnerabilities in a system design.
A Simple And Efficient FEM-Implementation Of The Modified Mohr-Coulomb Criterion (2006)

Summary This paper presents a conceptually simple finite element implementation of the combined elasto-plastic Mohr-Coulomb and Rankine material models, also known as Modified Mohr-Coulomb plasticity. The stress update is based on a return mapping scheme where all manipulations are carried out in principal stress space which simplifies the calculations. The model supports both associated and non-associated perfect plasticity.
Experimental Analysis of a Flyback Converter with Excellent Efficiency (2006)

Power conversion modules in consumer products are optimised for cost and not for efficiency. On the other side, efficiency has a value when using renewable energies such as photovoltaic. A bidirectional active-clamped flyback converter has been investigated to identify its maximum possible conversion efficiency for the principal use as maximum power point converter. A power train efficiency has been measured from a 200 W prototype that is above 91 % between 10 % and 100 % of the rated power and reaches a peak value of 96 %.
Cold-atom double-<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mi>Λ</mml:mi></mml:math>coherent population trapping clock (2013)

Miniature atomic clocks based on coherent population trapping (CPT) states in thermal atoms are an important component in many field applications, particularly where satellite frequency standards are not accessible. Cold-atom CPT clocks promise improved accuracy and stability over existing commercial technologies. Here we demonstrate a cold-atom CPT clock based on ${}^{87}$Rb using a high-contrast double-$\ensuremath{\Lambda}$ configuration. Doppler frequency shifts are explained using a simple model and canceled by interrogating the atoms with counterpropagating light beams. We realize a compact cold-atom CPT clock with a fractional frequency stability of $4\ifmmode\times\else\texttimes\fi{}{10}^{\ensuremath{-}11}{\ensuremath{\tau}}^{\ensuremath{-}1/2}$, thus demonstrating the potential of these devices. We also show that the long-term stability is currently limited by the second-order Zeeman shift to $2\ifmmode\times\else\texttimes\fi{}{10}^{\ensuremath{-}12}$ at 1000 s.
FBG-based large deflection shape sensing of a continuum manipulator: Manufacturing optimization (2016)

Real-time large deflection sensing of continuum dexterous manipulators (CDM) is essential and challenging for many minimally invasive surgery (MIS) applications. To this end, the feasibility of using Fiber Bragg Grating (FBG) sensors to detect large CDM deflections was demonstrated. Previous studies by our group proposed attaching an FBG array along with two nitinol (NiTi) wires as substrates to form a triangular cross section capable of large deflection detection for a 35 mm CDM. The strenuous fabrication procedure, however, relies on trial and error to ensure accurate attachment of components. In this paper, we propose a novel design for assembling large deflection FBG sensors utilizing a custom-design three-lumen polycarbonate tube with circular cross section. The proposed design eliminates fabrication challenges by embedding the FBG array and NiTi wires inside the tube in a more robust, repeatable, time-efficient and cost-effective (compared to multicore fibers) manner. Calibration experiments of the sensor assembly alone and inside the CDM indicate consistent linear (R <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> ~0.99) wavelength-curvature relationship. Experimental results show 3.3% error in curvature detection.
Efficient Recruitment of Lymphocytes in Inflamed Brain Venules Requires Expression of Cutaneous Lymphocyte Antigen and Fucosyltransferase-VII (2005)

Lymphocyte migration into the brain represents a critical event in the pathogenesis of multiple sclerosis and its animal model, experimental autoimmune encephalomyelitis (EAE). However, the mechanisms controlling the recruitment of lymphocytes to the CNS via inflamed brain venules are poorly understood, and therapeutic approaches to inhibit this process are consequently few. In this study, we demonstrate for the first time that human and murine Th1 lymphocytes preferentially adhere to murine inflamed brain venules in an experimental model that mimics early inflammation during EAE. A virtually complete inhibition of rolling and arrest of Th1 cells in inflamed brain venules was observed with a blocking anti-P-selectin glycoprotein ligand 1 Ab and anti-E- and P-selectin Abs. Th1 lymphocytes produced from fucosyltransferase (FucT)-IV(-/-) mice efficiently tethered and rolled, whereas in contrast, primary adhesion of Th1 lymphocytes obtained from FucT-VII(-/-) or Fuc-VII(-/-)FucT-IV(-/-) mice was drastically reduced, indicating that FucT-VII is critical for the recruitment of Th1 cells in inflamed brain microcirculation. Importantly, we show that Abs directed against cutaneous lymphocyte Ag (CLA), a FucT-VII-dependent carbohydrate modification of P-selectin glycoprotein ligand 1, blocked rolling of Th1 cells. By exploiting a system that allowed us to obtain Th1 and Th2 cells with skin- vs gut-homing (CLA(+) vs integrin beta(7)(+)) phenotypes, we observed that induced expression of CLA on Th cells determined a striking increase of rolling efficiency in inflamed brain venules. These observations allow us to conclude that efficient recruitment of activated lymphocytes to the brain in the contexts mimicking EAE is controlled by FucT-VII and its cognate cell surface Ag CLA.
Radiation therapy‐associated toxicity: Etiology, management, and prevention (2021)

Radiation therapy (RT) is a curative treatment for many malignancies and provides effective palliation in patients with tumor-related symptoms. However, the biophysical effects of RT are not specific to tumor cells and may produce toxicity due to exposure of surrounding organs and tissues. In this article, the authors review the clinical context, pathophysiology, risk factors, presentation, and management of RT side effects in each human organ system. Ionizing radiation works by producing DNA damage leading to tumor death, but effects on normal tissue may result in acute and/or late toxicity. The manifestation of toxicity depends on both cellular characteristics and affected organs' anatomy and physiology. There is usually a direct relationship between the radiation dose and volume to normal tissues and the risk of toxicity, which has led to guidelines and recommended dose limits for most tissues. Side effects are multifactorial, with contributions from baseline patient characteristics and other oncologic treatments. Technological advances in recent decades have decreased RT toxicity by dramatically improving the ability to deliver RT that maximizes tumor dose and minimizes organ dose. Thus the study of RT-associated toxicity is a complex, core component of radiation oncology training that continues to evolve alongside advances in cancer management. Because RT is used in up to one-half of all patients with cancer, an understanding of its acute and late effects in different organ systems is clinically pertinent to both oncologists and nononcologists.
Integrating local agriculture into nutrition programs can benefit children's health (2013)

Childhood obesity has multiple interrelated causes and so should be addressed with multiple interventions, including innovative nutrition education programs that encourage healthy lifestyle choices in children. Research indicates that garden-based nutrition education increases fruit and vegetable preferences and consumption in children. Additionally, many reports on Farm to School programs indicate they promote both increased consumption of fruits and vegetables and participation in the National School Lunch Program. Within California, UC Agriculture and Natural Resources plays a leadership role in school garden and Farm to School programs. We provide a relevant literature review and assess the role of UC Cooperative Extension (UCCE) in program implementation and assessment, including results from a survey of UCCE advisors and directors. All respondents reported implementation of garden-based nutrition education and Farm to School programs; however, evaluation occurred much less frequently.
Discovery of a Novel Enzyme, Isonitrile Hydratase, Involved in Nitrogen-Carbon Triple Bond Cleavage (2001)

Isonitrile containing an N triple bond C triple bond was degraded by microorganism sp. N19-2, which was isolated from soil through a 2-month acclimatization culture in the presence of this compound. The isonitrile-degrading microorganism was identified as Pseudomonas putida. The microbial degradation was found to proceed through an enzymatic reaction, the isonitrile being hydrated to the corresponding N-substituted formamide. The enzyme, named isonitrile hydratase, was purified and characterized. The native enzyme had a molecular mass of about 59 kDa and consisted of two identical subunits. The enzyme stoichiometrically catalyzed the hydration of cyclohexyl isocyanide (an isonitrile) to N-cyclohexylformamide, but no formation of other compounds was detected. The apparent K(m) value for cyclohexyl isocyanide was 16.2 mm. Although the enzyme acted on various isonitriles, no nitriles or amides were accepted as substrates.
Evaluation of Atrial Conduction Time at Various Sites of Right Atrial Pacing and Influence on Atrioventricular Delay Optimization by Surface Electrocardiography (2004)

Cardiac function and electrical stability may be improved by programming of optimal AV delay in DDD pacing. This study tested the hypothesis if the global atrial conduction time at various pacing sites can be derived from the surface ECG to achieve an optimal electromechanical timing of the left heart. Data were obtained from 60 patients following dual chamber pacemaker implantation. Right atrial septal pacing was associated with significantly shorter atrial conduction time (P < 0.0005) and P wave duration (P < 0.005), compared to standard right atrial pacing sites at the right atrial appendage or at the right free wall. The last two pacing sites showed no significant difference. In a group of 31 patients with AV block, optimal AV delay was achieved by programming a delay of 100 ms from the end of the paced P wave to peak/nadir of the paced ventricular complex. Optimization of AV delay resulted in a relative increase of echocardiographic stroke volume (SV) (10.9 +/- 13.7%; 95% CI: 5.9-15.9%) when compared to nominal AV delay (170 ms). Optimized AV delay was highly variable (range 130-250 ms; mean 180 +/- 35 ms). The hemodynamic response was characterized by a weak significant relationship between SV increase and optimized AV delay (R2 = 0.196, R = 0.443, P = 0.047). The study validated that septal pacing is advantageous for atrial synchronization compared to conventional right atrial pacing. Tailoring the AV delay with respect to the surface ECG improved systolic function significantly and was superior to nominal AV delay settings in the majority of patients.
Polymeric particle formation through electrospraying at low atmospheric pressure (2008)

Electrospraying is a simple and versatile technique capable of producing polymeric particles. However, most investigations carried out thus far have been performed at ambient atmospheric pressure without studying the influences of pressure on the formation of polymeric particles. Here, we report our investigation on the effects of varying the pressure and the solution concentration on the microstructures of electrosprayed polymeric particles. Pressures are varied from ambient atmospheric pressure to 380 mmHg below ambient pressure, and solution concentrations are varied over a range of 3-7 w/v %. By varying these parameters, we manipulated the rate of solvent evaporation and the solidification of the electrosprayed particles. The results show that changes to the pressure had significant effects on the microstructure and morphology of poly(epsilon-caprolactone) (PCL) particles. The average particle size became larger as the chamber pressure decreased. At a solution concentration of 5 w/v % and a pressure 150 mmHg below ambient pressure, uniform and spherical PCL particles were generated. Electrospun fibers were formed when a solution concentration of 7 w/v % was used. The developed technique can be applied to prepare polymeric drug delivery carriers though a low-pressure-assisted spray-drying method, and is particularly suitable for fabricating delivery microspheres encapsulated with temperature-sensitive drugs and biomolecules.
DAE Tools: equation-based object-oriented modelling, simulation and optimisation software (2016)

In this work, DAE Tools modelling, simulation and optimisation software, its programming paradigms and main features are presented. The current approaches to mathematical modelling such as the use of modelling languages and general-purpose programming languages are analysed. The common set of capabilities required by the typical simulation software are discussed, and the shortcomings of the current approaches recognised. A new hybrid approach is introduced, and the modelling languages and the hybrid approach are compared in terms of the grammar, compiler, parser and interpreter requirements, maintainability and portability. The most important characteristics of the new approach are discussed, such as: (1) support for the runtime model generation; (2) support for the runtime simulation set-up; (3) support for complex runtime operating procedures; (4) interoperability with the third party software packages (i.e. NumPy/SciPy); (5) suitability for embedding and use as a web application or software as a service; and (6) code-generation, model exchange and co-simulation capabilities. The benefits of an equation-based approach to modelling, implemented in a fourth generation object-oriented general purpose programming language such as Python are discussed. The architecture and the software implementation details as well as the type of problems that can be solved using DAE Tools software are described. Finally, some applications of the software at different levels of abstraction are presented, and its embedding capabilities and suitability for use as a software as a service is demonstrated.
Fast VM Startup by Cooperative Image Caching for Cloud Data Centers (2018)

Virtual machine (VM) management is one of the key problems in cloud data centers. Many efforts have been put on finding an (approximate) optimal placement of VMs at physical machines (PMs) to achieve high resource utility. In this paper, we consider to reduce the startup delay of VMs, which is a key issue for improving user experience and resource utility. The basic idea of our work is to cache VM images at PMs so as to reduce the time of VM image retrieval. By handling VM placement and image placement jointly and de-centrally, we design a joint placement algorithm and an associated layered transport VM selection algorithm, so as to start VMs quickly in the meanwhile save some calculation resources. The key point of our algorithms lies in how to accelerate the startup of VM with limited information in a distributed fat-tree network. The proposed algorithms are evaluated by extensive simulations using a distributed system simulator SimGrid. The results show that our algorithms just lost a little performance in most cases, compared with the centralized algorithm and a classical cache placement strategy.
Potassium ion-sensitive field effect transistor (1975)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPotassium ion-sensitive field effect transistorStanley D. Moss, Jiri. Janata, and Curtis C. JohnsonCite this: Anal. Chem. 1975, 47, 13, 2238–2243Publication Date (Print):November 1, 1975Publication History Published online1 May 2002Published inissue 1 November 1975https://pubs.acs.org/doi/10.1021/ac60363a005https://doi.org/10.1021/ac60363a005research-articleACS PublicationsRequest reuse permissionsArticle Views1302Altmetric-Citations212LEARN 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
Epitaxial lateral overgrowth of a-plane GaN by metalorganic chemical vapor deposition (2007)

We report on epitaxial lateral overgrowth (ELO) of (112¯0) a-plane GaN by metalorganic chemical vapor deposition. Different growth rates of Ga- and N-polar wings together with wing tilt create a major obstacle for achieving a smooth, fully coalesced surface in ELO a-plane GaN. To address this issue a two-step growth method was employed to provide a large aspect ratio of height to width in the first growth step followed by enhanced lateral growth in the second by controlling the growth temperature. By this method, the average ratio of Ga- to N-polar wing growth rate has been reduced from 4–6 to 1.5–2, which consequently reduced the wing-tilt induced height difference between the two approaching wings at the coalescence front, thereby making their coalescence much easier. Transmission electron microscopy showed that the threading dislocation density in the wing regions was 1.0×108 cm−2, more than two orders of magnitude lower than that in the window regions (4.2×1010 cm−2). However, a relatively high density of basal stacking faults of 1.2×104 cm−1 was still present in the wing regions as compared to c -plane GaN, where they are rarely observed away from the substrate. Atomic force microscopy (AFM) measurements showed two orders of magnitude higher density of surface pits in the window than in the wing regions, which were considered to be terminated by dislocations (partial ones related to stacking faults and full ones) on the surface. The existence of basal stacking faults was also revealed by AFM measurements on the a-plane ELO sample after wet chemical etching in hot H3PO4∕H2SO4 (1:1). The extensions of Ga-polar wings near the meeting fronts were almost free of stacking faults. The improvement of crystalline quality in the overgrown layer by ELO was also verified by near field scanning optical microscopy and time-resolved photoluminescence measurements; the former showing strongly enhanced luminescence from the wing regions, and the latter indicating longer decay times (0.25 ns) compared to a standard a-plane GaN template (40 ps).
Efficacy and safety of various repeat treatment dosing regimens of rituximab in patients with active rheumatoid arthritis: results of a Phase III randomized study (MIRROR) (2010)

RTX 2 x 500 and 2 x 1000 mg could not be clearly differentiated, although some efficacy outcomes suggest improved outcomes in the rituximab 2 x 1000 mg group. Retreatment from Week 24 resulted in a sustained suppression of disease activity through to Week 48.