gebhart/patrepeval huggingface dataset:
Molecular dynamics simulations of Ar+ and Cl+ impacts onto silicon surfaces: Distributions of reflected energies and angles (1998)

Previous profile evolution studies of plasma-assisted etch processes have shown that ions scattered from sidewalls can lead to microtrench formation on the bottom of an etched feature [see, for example, Dalton et al., J. Electrochem. Soc. 140, 2395 (1993)]. In these studies, the ions impacting feature surfaces with incident angles above a critical value were assumed to reflect specularly from the surfaces. In the present article, we describe the energy and angle distributions of reflected atoms obtained from molecular dynamics (MD) simulations. We simulated Ar+ and Cl+ ions impacting model silicon surfaces. The ion incident energies Ei were 20, 50, and 100 eV. We varied the ion incident angles θi from 0° to 85° from the surface normal. The model silicon surfaces had chlorine coverages of 0 monolayers (ML) of Cl, 1 ML Cl, and 2.3 ML Cl. We determined the Ar and Cl reflection probabilities, i.e., the fraction of Ar and Cl atoms scattered from the surfaces during the 1–2 ps MD trajectories. For θi⩾75°, we found that the reflection probabilities were greater than 90% in most cases. For these large incident angles, we describe the distributions of energies Er and angles (polar θr and azimuthal φr) for the Ar and Cl atoms reflected from the surfaces. The results of the MD simulations are compared with the assumption of specular scattering. In addition, we compare the average energies of the reflected atoms with the predictions of two simple models based on the binary collision approximation. We discuss the effects of incident ion species, Ei, θi, chlorine surface coverage, and surface roughness on these results.
Actin Concentration and Monomer-Polymer Ratio in Developing Chicken Skeletal Muscle1 (1986)

The actin concentration and monomer-polymer ratio in developing chicken skeletal muscle were determined by means of a DNase I inhibition assay. The concentration of G-actin in embryonic muscle was much higher than the critical concentration for polymerization of purified actin. As muscle development progressed, the amount of total actin remarkably increased, whereas the concentration of G-actin markedly decreased, and finally in adults reached the critical concentration for polymerization of purified actin. When the monomeric actin in the soluble fraction of embryonic muscle was purified, the critical concentration for polymerization of the embryonic actin decreased to the same value as that of adult skeletal muscle actin. On the other hand, there was no difference between the crude and purified actin in the type of actin. They consisted of alpha-, beta-, and gamma-actins; their amounts were in the order, beta greater than gamma greater than alpha. Furthermore, polymerization of the monomeric actin in the soluble fraction of embryonic muscle was induced by the addition of myosin or HMM. The large amount of monomeric actin in the embryonic skeletal muscle may be due to the presence of some factor(s) which inhibits actin polymerization and also to an insufficiency of myosin.
Effect of L-Arginine on Plasminogen-Activator Inhibitor in Hypertensive Patients with Hypercholesterolemia (1993)

To the Editor: Vascular endothelium converts L-arginine to nitric oxide. An increase in blood pressure after the inhibition of nitric oxide synthase suggests that a deficiency of nitric oxide may contribute to the pathogenesis of hypertension1. Indeed, exogenous L-arginine produces systemic hypotension in patients with essential hypertension2. Sodium nitroprusside (a nitric oxide donor) inhibits the release of plasminogen-activator inhibitor (PAI) from platelets and has fibrinolytic properties3. Plasma PAI activity is increased in patients with hypertension, venous thrombosis, and recurrent myocardial infarction4. L-Arginine hydrochloride (Boehringer-Mannheim), at a daily dose of 60 mmol given over a three-hour period, . . .
Design and Production of Active Cellulosome Chimeras (2001)

Defined chimeric cellulosomes were produced in which selected enzymes were incorporated in specific locations within a multicomponent complex. The molecular building blocks of this approach are based on complementary protein modules from the cellulosomes of two clostridia, Clostridium thermocellum and Clostridium cellulolyticum, wherein cellulolytic enzymes are incorporated into the complexes by means of high-affinity species-specific cohesin-dockerin interactions. To construct the desired complexes, a series of chimeric scaffoldins was prepared by recombinant means. The scaffoldin chimeras were designed to include two cohesin modules from the different species, optionally connected to a cellulose-binding domain. The two divergent cohesins exhibited distinct specificities such that each recognized selectively and bound strongly to its dockerin counterpart. Using this strategy, appropriate dockerin-containing enzymes could be assembled precisely and by design into a desired complex. Compared with the mixture of free cellulases, the resultant cellulosome chimeras exhibited enhanced synergistic action on crystalline cellulose.
cataract surgical problem (2001)

Journal of Cataract & Refractive Surgery: October 2001 - Volume 27 - Issue 10 - p 1539 doi: 10.1016/S0886-3350(01)01136-1
A Rapid-Response, High-Sensitivity Nanophase Humidity Sensor for Respiratory Monitoring (2004)

An ionic-type humidity sensor based on a plasma-deposited nanophase Si thin film was developed. Detection of relative humidity cycles between 20% and 90% was possible in /spl les/0.2 s with /spl sim/5 orders of magnitude variation in conductance. Such superior performance is attributable to the unique arrayed column-void network structure and ultrafine thickness (e.g., 50 nm) of the Si film as well as to the lateral electrode configuration. Our sensor can be miniaturized, integrated with signal processing circuits, and fabricated on plastics. A crucial implementation, where our sensor would be very suitable and beneficial, is respiratory monitoring.
A new interface specification methodology and its application to transducer synthesis (1988)

In this dissertation, I present a new methodology for the abstract specification of digital circuit interfaces. An interface is the collection of signal wires that cross a circuit boundary and the constraints on the events on those wires. The specification methodology is based on a formalization of the timing diagrams commonly used by digital circuit designers. This mostly graphical method is not only familiar to its intended users but is also concise in its description. An interactive editor, called Waves, has been implemented to support this methodology and used to describe a wide range of circuit interfaces ranging from static memories, to microprocessors, to system busses. <p>Interface specification has a wide range of uses during the design and evaluation of a circuit. Waves diagrams and the constraints they capture form the basis for an entire new set of CAD tools that reason about interface design, synthesis, evaluation, and testing. One of these applications, the automatic synthesis of interface transducers, is highlighted in this dissertation. <p>An interface transducer is the collection of logic circuitry that connects two compatible circuit interfaces. In general, it includes both synchronous and asynchronous components and must satisfy the timing constraints of both interfaces. Interface transducers are required whenever a custom chip is integrated into a computer system or in general, whenever two circuit blocks need to be connected. Their automatic design can greatly reduce the time required to assemble systems or integrate new components into existing systems. <p>Janus uses a novel approach, based on a small set of templates, to synthesize mixed asynchronous and synchronous control logic. The synthesis algorithm, called Suture, first constructs a skeletal circuit and then locally modifies the design to meet interface timing constraints and eliminate internal race conditions. Optimizations of the resulting sequential logic yield transducers that are comparable in both size and performance to those generated by experienced designers. Three practical examples are used to demonstrate this result
Prospective Study of Type 1 and Type 2 Diabetes and Risk of Stroke Subtypes (2007)

Both type 1 and type 2 diabetes are associated with substantially increased risks of total and most subtypes of stroke.
Maize (<i>Zea mays</i>) genetic transformation by co‐cultivating germinating seeds with <i>Agrobacterium tumefaciens</i> (2006)

A novel plant genetic transformation method for maize (Zea mays) is reported. Using a scalpel, germinating seeds were wounded in the meristem and co-cultivated with an Agrobacterium tumefaciens strain harbouring a Ti plasmid. Seedlings produced from the treatment were screened by hygromycin selection. Fertile transgenic T(0) and T(1) plants were obtained. PCR amplification, PCR-Southern and Southern-blot analysis showed that the foreign gene had been introduced into the inbreds of maize. About 29% of T(0) seedlings examined were found to be transgenic, although the overall transformation was only 0.6% when total treated seeds were taken into account. The method circumvented tedious and prolonged tissue-culture steps, is simple and can be readily integrated into conventional plant breeding programs.
Multi-objective optimization of XBA sentinel antenna (2011)

A multi-objective optimization approach has been applied to the synthesis problem of the geometrical structure of antenna with complex set of requirement specification. This methodology is a promising tool for new development and application for several kind of microwave structure.
Sub-picosecond optical pulse generation at 350 GHz in monolithic passive CPM MQW lasers (2002)

Subpicosecond optical pulses have been successfully generated using a novel monolithic passive colliding pulse mode-locked (CPM) semiconductor multiple quantum-well (MQW) laser. A transform-limited pulse width of 830 fs is achieved at a wavelength of 1.5 mu m and a repetition rate of 80 GHz. The measured time-bandwidth product is 0.31. A record high repetition rate of 350 GHz is also demonstrated with a 900 fs pulse width.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
A Robust Algorithm for Thickness Computation at Low Resolution and Its Application to <i>In Vivo </i> Trabecular Bone CT Imaging (2014)

Adult bone diseases, especially osteoporosis, lead to increased risk of fracture which in turn is associated with substantial morbidity, mortality, and financial costs. Clinically, osteoporosis is defined by low bone mineral density; however, increasing evidence suggests that the microarchitectural quality of trabecular bone (TB) is an important determinant of bone strength and fracture risk. Accurate measures of TB thickness and marrow spacing is of significant interest for early diagnosis of osteoporosis or treatment effects. Here, we present a new robust algorithm for computing TB thickness and marrow spacing at a low resolution achievable in vivo. The method uses a star-line tracing technique that effectively deals with partial voluming effects of in vivo imaging with voxel size comparable to TB thickness. Also, the method avoids the problem of digitization associated with conventional algorithms based on sampling distance transform along skeletons. Accuracy of the method was examined using computer-generated phantom images, while the robustness of the method was evaluated on human ankle specimens in terms of stability across a wide range of voxel sizes, repeat scan reproducibility under in vivo conditions, and correlation between thickness values computed at ex vivo and in vivo imaging resolutions. Also, the sensitivity of the method was examined by evaluating its ability to predict the bone strength of cadaveric specimens. Finally, the method was evaluated in a human study involving 40 healthy young-adult volunteers (age: 19-21 years; 20 males and 20 females) and ten athletes (age: 19-21 years; six males and four females). Across a wide range of voxel sizes, the new method is significantly more accurate and robust as compared to conventional methods. Both TB thickness and marrow spacing measures computed using the new method demonstrated strong associations (R2 ∈ [0.83, 0.87]) with bone strength. Also, the TB thickness and marrow spacing measures allowed discrimination between male and female volunteers (p ∈ [0.01, 0.04]) as well as between athletes and nonathletes (p ∈ [0.005, 0.03]).
A new assay for tRNA aminoacylation kinetics (1998)

An improved quantitative assay for tRNA aminoacylation is presented based on charging of a nicked tRNA followed by separation of an aminoacylated 3'-fragment on an acidic denaturing polyacrylamide gel. Kinetic parameters of tRNA aminoacylation by Escherichia coli AlaRS obtained by the new method are in excellent agreement with those measured by the conventional method. This assay provides several advantages over the traditional methods of measuring tRNA aminoacylation: (1) the fraction of aminoacyl-tRNA is measured directly; (2) data can be obtained at saturating amino acid concentrations; and (3) the assay is significantly more sensitive.
Experimental Analysis of the Water Absorption Effects on RF/mm-Wave Active/Passive Circuits Packaged in Multilayer Organic Substrates (2007)

The feasibility of using near-hermetic organic materials for microwave and millimeter-wave packaging is investigated. The effects of moisture on both passive and active components on/inside the nonhermetic materials are tested. Microstrip patch antennas on three low moisture absorption substrates (0.1% or less) are subjected to immersion tests until saturated and the corresponding measured frequency shifts are found to be less than 0.25% for two of the three materials tested. The recovery time from saturation to normal operation is found to occur from natural evaporation at room temperature in 10 min or less. One of the three materials, a promising organic laminate material called liquid crystal polymer (LCP), showed no measurable change in weight or in antenna resonance frequency between the ambient (air) state and that after extended submersion in water. In addition, a novel laminated LCP package for a 13-25 GHz monolithic microwave integrated circuit (MMIC) formed from seven thin layers of laser-machined LCP is subjected to immersion testing. The seal for the embedded chip cavity (formed by the LCP conforming around the feeding transmission lines) is found to be robust for protecting the embedded chip. Standard hermetic materials are suggested to be a potentially unnecessary requirement for reliable, long-lifetime, high-performance RF systems.
Phosphorylation of human progesterone receptors at serine-294 by mitogen-activated protein kinase signals their degradation by the 26S proteasome (2000)

Ligand-dependent down-regulation that leads to rapid and extensive loss of protein is characteristic of several nuclear steroid receptors, including human progesterone receptors (PRs). In breast cancer cells, >95% of PRs are degraded 6 h after the start of progestin treatment. The mechanism for down-regulation is unknown. We examined the role of PR phosphorylation by mitogen-activated protein kinases (MAPKs) in this process. Lactacystin and calpain inhibitor I, specific inhibitors of the 26S proteasome, blocked progestin-induced down-regulation, and ubiquitinated conjugates of PR accumulated in cells. Ligand-dependent PR degradation was also blocked by specific inhibition of p42 and p44 MAPKs. To define the targets of phosphorylation by this kinase, two serine/proline MAPK consensus sites on PR were mutated. We demonstrate that mutation of PR serine-294 to alanine (S294A) specifically and completely prevents ligand-dependent receptor down-regulation. We also find that rapid, ligand-independent degradation of immature PR intermediates occurs by a proteasome-mediated pathway. These results demonstrate that PR destruction, by either of two alternate routes, is mediated by the 26S proteasome. Specifically, down-regulation of mature PRs occurs by a mechanism in which ligand binding activates PR phosphorylation by MAPKs at a unique serine residue, which then targets the receptors for degradation.
Elements of mathematical ecology (2002)

Preface Part I. Unstructured Population Models Section A. Single Species Models: 1. Exponential, logistic and Gompertz growth 2. Harvest models - bifurcations and breakpoints 3. Stochastic birth and death processes 4. Discrete-time models 5. Delay models 6. Branching processes Section B. Interacting Populations: 7. A classical predator-prey model 8. To cycle or not to cycle 9. Global bifurcations in predator-prey models 10. Chemosts models 11. Discrete-time predator-prey models 12. Competition models 13. Mutualism models Section C. Dynamics of Exploited Populations: 14. Harvest models and optimal control theory Part II. Structured Population Models Section D. Spatially-Structured Models: 15. Spatially-structured models 16. Spatial steady states: linear problems 17. Spatial steady states: nonlinear problems 18. Models of spread Section E. Age-Structured Models: 19. An overview of linear age-structured models 20. The Lokta integral equation 21. The difference equation 22. The Leslie matrix 23. The McKendrick-von Foerster PDE 24. Some simple nonlinear models Section F. Gender-Structured Models: 25. Two-sex models References Index.
Porous, Crystalline, Covalent Organic Frameworks (2006)

The preparation of highly porous, crystalline organic frameworks by polycondensation reactions of p-phenyleneboronic acid is described. Extensive characterization studies, complemented by computation, suggest that the resulting 2-D sheets stack in staggered (graphite-like) or eclipsed (like in boron nitride) arrangements, depending upon the building blocks used. These thermally stable materials display pore sizes of 7-27 Å, and surface areas comparable to those of porous zeolites.
T‐one insensitive steady state imaging: A framework for purely <i>T</i><sub>2</sub>‐weighted TrueFISP (2011)

A new conceptual framework called T-one insensitive steady state imaging is proposed for fast generation of MR images with pure T(2) contrast. This is accomplished by imaging between nonequally spaced inversion pulses, with the magnetization vector alternatively residing in states parallel and antiparallel to B(0) for durations TP(i) and TA(i), respectively. With TP(i) and TA(i) adequately chosen, identical signal time evolution can be obtained for different T(1) values, i.e., T(1) contrast can efficiently be removed from resultant images. As a specific realization of this principle, T-one insensitive steady state imaging sequences are presented which use True free induction steady precession readout blocks between the inversion pulses. While the conventional True free induction steady precession signal time course would be determined by both T(2) and T(1), a pure T(2) dependence is realized with successfully suppressed influence of longitudinal relaxation, and images with essentially T(2) contrast alone are obtained. Analytical expressions are provided for the description of the ideal signal behavior, which help in creating pathways for sequence parameter optimization. The performance of the technique is analyzed with Bloch equation simulations. In vivo results obtained in healthy volunteers and brain tumor patients are presented.
A framework to quantify karyotype variation associated with CHO cell line instability at a single‐cell level (2016)

Chinese hamster ovary (CHO) cells, the major mammalian host cells for biomanufacturing of therapeutic proteins, have been extensively investigated to enhance productivity and product quality. However, cell line instability resulting in unexpected changes in productivity or product quality continues to be a challenge. Based on previous reports about causes and characteristics of production instability, we hypothesized that chromosomal rearrangements due to genomic instability are associated with production instability and that these events can be characterized. We developed a production instability model using secreted alkaline phosphatase (SEAP)-expressing CHO cells (CHO-SEAP) as well as a framework to quantify chromosomal rearrangements by karyotyping. In the absence of methotrexate (MTX), CHO-SEAP cells exhibited a slightly increased growth rate, a significantly decreased specific productivity, and changes in the chromosomal rearrangement ratio of seven chromosomes. In contrast, when MTX was re-introduced, the growth rate and SEAP productivity reversed to the initial values, demonstrating the reversibility of production instability in CHO-SEAP cells. Fluorescence in situ hybridization analysis identified that the SEAP genes were incorporated in the chromosomal rearrangement (insertion) part of the der(Z9) chromosome. Karyotype analysis indicated that the insertion ratio of the der(Z9) chromosome decreased in the CHO-SEAP cells grown without MTX, demonstrating a correlation between chromosomal rearrangement and production instability. Our results support a mechanism for production instability, wherein a randomly generated chromosomal rearrangement (or genotype) results in cells with a growth advantage that is also associated with non (or low)-producing traits. As a result, the non-producing cells grow faster and thereby outgrow the producing population. Biotechnol. Bioeng. 2017;114: 1045-1053. © 2016 Wiley Periodicals, Inc.
An evidence-based review of botulinum toxin (Botox) applications in non-cosmetic head and neck conditions (2013)

Botulinum toxin (Botox) is an exotoxin produced from Clostridium botulinum. It works by blocking the release of acetylcholine from the cholinergic nerve end plates leading to inactivity of the muscles or glands innervated. Botox is best known for its beneficial role in facial aesthetics but recent literature has highlighted its usage in multiple non-cosmetic medical and surgical conditions. This article reviews the current evidence pertaining to Botox use in the head and neck. A literature review was conducted using The Cochrane Controlled Trials Register, Medline and EMBASE databases limited to English Language articles published from 1980 to 2012. The findings suggest that there is level 1 evidence supporting the efficacy of Botox in the treatment of spasmodic dysphonia, essential voice tremor, headache, cervical dystonia, masticatory myalgia, sialorrhoea, temporomandibular joint disorders, bruxism, blepharospasm, hemifacial spasm and rhinitis. For chronic neck pain there is level 1 evidence to show that Botox is ineffective. Level 2 evidence exists for vocal tics, trigeminal neuralgia, dysphagia and post-laryngectomy oesophageal speech. For stuttering, 'first bite syndrome', facial nerve paresis, Frey's syndrome, oromandibular dystonia and palatal/stapedial myoclonus the evidence is level 4. Thus, the literature highlights a therapeutic role for Botox in a wide range of non-cosmetic conditions pertaining to the head and neck (mainly level 1 evidence). With ongoing research, the spectrum of clinical applications and number of people receiving Botox will no doubt increase. Botox appears to justify its title as 'the poison that heals'.