gebhart/patrepeval huggingface dataset:
Principle and simulation of microresonating cantilever sensor based on third harmonic detection (2006)

Resonating cantilever-based microbiochemical sensors usually consist of a vibration actuating system and a vibration detecting system, which complicates the sensor design and fabrication. We present a new idea for testing the cantilever's vibration without an exclusive detector. The amplitude of vibration can be detected by measuring the third harmonic of the actuating current, and the cantilever's resonance frequency can be consequently obtained. The change of the resonance frequency provides information about the biochemical reaction, which alters the mass of the cantilever and its natural frequency. A system model based on the idea is established and an approximate solution is given. The relation between the vibration state and the third harmonic is discussed, and a corresponding simulation is performed. The system sensitivity is evaluated. Both theoretical and simulation results show that the amplitude of the third harmonic of the actuating current can be used as a criterion to determine the cantilever's vibration state. The idea promises a simpler mechanical structure, thus a cheaper sensor. Sensors based on this idea would also be robust to atrocious environments because the material of the cantilever can be chosen from a wide range.
Conditions for self-collimation in three-dimensional photonic crystals (2005)

We introduce the theoretical criterion for achieving three-dimensional self-collimation of light in a photonic crystal. Based on this criterion, we numerically demonstrate a body-center-cubic structure that supports wide-angle self-collimation and is directly compatible with the recently developed holographic fabrication technique. We further show that both bends and beam splitters can be introduced into this structure by the use of interfaces.
On moment of velocity for signal analysis (2019)

The instantaneous frequency (IF) of a signal is a well-defined quantity that is widely used for analysing non-stationary signals. However, often in practice, IF as a function of time can possess large spikes and negative values. Moreover, IF is very sensitive to noise, limiting its range of practical application. Due to these deficiencies, we introduce the concept of moment of velocity (MoV) for signal analysis. As a case study, we compare the performance of MoV to a standard Hilbert transform-based approach for R-wave identification in human electrocardiogram signals, demonstrating that our approach is more robust to noise. We examine characteristic heartbeats obtained from the MIT-BIH Arrhythmia database. A detection error rate of 0.07%, a positive predictive value of 99.97%, and a sensitivity of 99.95% are achieved against analysis results from the database.
Generation of ring-shaped optical vortices in dissipative media by inhomogeneous effective diffusion (2018)

By means of systematic simulations we demonstrate generation of a variety of ring-shaped optical vortices (OVs) from a two-dimensional input with embedded vorticity, in a dissipative medium modeled by the cubic-quintic complex Ginzburg-Landau equation with an inhomogeneous effective diffusion (spatial-filtering) term, which is anisotropic in the transverse plane and periodically modulated in the longitudinal direction. We show the generation of stable square- and gear-shaped OVs, as well as tilted oval-shaped vortex rings, and string-shaped bound states built of a central fundamental soliton and two vortex satellites, or of three fundamental solitons. Their shape can be adjusted by tuning the strength and modulation period of the inhomogeneous diffusion. Stability domains of the generated OVs are identified by varying the vorticity of the input and parameters of the inhomogeneous diffusion. The results suggest a method to generate new types of ring-shaped OVs with applications to the work with structured light.
Dynamics of the generation of magnetic‐field‐aligned electric fields by drift currents (1994)

A study is made of the process of generation and evolution of parallel electric fields on closed geomagnetic field lines. Charge separation that is due to the different character of the drift of energetic electrons and protons of inhomogeneous magnetospheric plasma in the geomagnetic field is considered to be the factor responsible for the generation of the electric field. In a magnetic flux tube that drifts together with the cold plasma, this separation of charges is manifested as the injection of energetic electrons or protons. A numerical self‐consistent calculation of the evolution of the distribution functions of particles and of the parallel electric field is carried out for the injection of energetic electrons into the geomagnetic flux tube. An analytical investigation of the macroscopic and microscopic processes accompanying such injection is carried out. The calculations take into account cold ionospheric particles and energetic magnetospheric protons and electrons. It was found that an intense parallel electric field is produced in the form of two collisionless rarefaction shock waves that separate from the equatorial plane in the northward and southward directions. Below the front of each shock wave, there is mainly the ionospheric plasma, while behind the front there are the upward accelerated ionospheric ions and the hot magnetospheric plasma. Microscopic structure behind the shock front is formed by electrostatic oscillations of a large amplitude. Generation conditions for intense longitudinal fields are formulated: The difference in densities of injected energetic electrons and protons near the equatorial plane must exceed the initial density of cold particles, and the current‐associated velocity of cold electrons must be larger than the ion sound velocity. It is shown that these conditions can be satisfied, owing to a drift mechanism of charge separation. A rarefaction shock wave is excited with substantially smaller field‐aligned currents as compared with anomalous resistance or double layers. The observed manifestations of the rarefaction shock waves are auroral plasma cavities.
Determining Nanocapillary Geometry from Electrochemical Impedance Spectroscopy Using a Variable Topology Network Circuit Model (2010)

Solid-state nanopores and nanocapillaries find increasing use in a variety of applications including DNA sequencing, synthetic nanopores, next-generation membranes for water purification, and other nanofluidic structures. This paper develops the use of electrochemical impedance spectroscopy to determine the geometry of nanocapillaries. A network equivalent circuit element is derived to include the effects of the capacitive double layer inside the nanocapillaries as well as the influence of varying nanocapillary radius. This variable topology function is similar to the finite Warburg impedance in certain limits. Analytical expressions for several different nanocapillary shapes are derived. The functions are evaluated to determine how the impedance signals will change with different nanocapillary aspect ratios and different degrees of constriction or inflation at the capillary center. Next, the complex impedance spectrum of a nanocapillary array membrane is measured at varying concentrations of electrolyte to separate the effects of nanocapillary double layer capacitance from those of nanocapillary geometry. The variable topology equivalent circuit element model of the nanocapillary is used in an equivalent circuit model that included contributions from the membrane and the measurement apparatus. The resulting values are consistent with the manufacturer's specified tolerances of the nanocapillary geometry. It is demonstrated that electrochemical impedance spectroscopy can be used as a tool for in situ determination of the geometry of nanocapillaries.
Work In Progress: Knowledge Integration to Understand Why (2018)

Abstract This work in progress describes how a multifaceted faculty team in the Department of Electrical and Computer Engineering (ECE) is redefining teaching and learning in the junior year of the undergraduate degree program. Also known as the rigorous "technical core," it is well known that students struggle to grasp, and see the relevance of, extremely abstract and mathematically intense concepts introduced in the middle two years of the curriculum. With the goals of increasing overall understanding and reversing the alarming ECE national retention trend, the team is emphasizing knowledge integration – which builds on the concept of "nanocourses" – to help students connect the dots between topics and understand why they are learning material. In 2015, the ECE department received a five-year RED (Revolutionizing Engineering Departments) grant from the National Science Foundation to perform research that leads to scalable and sustainable change in engineering and computer science education for the nation. This paper describes how the department is, in effect, throwing away courses to overcome the challenges of the current educational system. Because the new pedagogical and organizational approach calls for a holistic view of the undergraduate degree, faculty members are thinking beyond the walls of their own classrooms to ensure students gain a big picture understanding of the discipline. This paper outlines the detailed process that allowed the faculty to step out of their traditional roles to prepare for revolutionary change and lay the groundwork for knowledge integration by dissecting, rearranging, and synchronizing content from seven ECE courses in the junior year. This paper also explores the motivation and process for implementing and assessing a series of knowledge integration (KI) activities, which serve as vehicles for helping students grasp the commonality and correlations between core concepts across the curriculum. In an environment conducive to dialogue, inquiry, and problem-solving, KI activities bring together into one room all the faculty members and students from the technical core for hands-on, group exercises. In addition to showing students firsthand how problems can be approached from multiple perspectives, KI activities illustrate societal relevance by demonstrating how anchoring concepts are integrated to form the building blocks of familiar applications such as the smart phone. After months of preparing for change, the team is energized by their early successes, but the idea that people are resistant to change has been affirmed. This paper shares the challenges the team has faced, and the steps they have taken to gracefully address student opposition and anxieties. As the department prepares for the next phase of the project, it seeks feedback and lessons learned from the engineering community to improve the project and extend the work to institutions across the country.
The Application of EPR Techniques to the Study of DNA (2018)

Kamzolova and Postnikova review the application of spin labels to the study of DNA. Spectra obtained from spin-labeled nucleic acids are characterized by dynamics that are faster than 1 nsec. Such fast times indicate weakly immobilized labels. Despite the problems associated with nonspecific labeling of nucleic acids, EPR may be used to obtain physical characteristics of DNA function. They cite examples from studies on the effects of conformational changes, radiation damage, binding with polymerase, and low melting regions detected by EPR spectra. The study of DNA flexibility began in 1970 when Wahl et al. examined the decay of the fluorescence polarization anisotropy (FPA) of the fluorescence dye, ethium, when intercalated in isolated DNA in solution. Hurley et al. examined the mode of binding of spin-labeled ethidium to chromatin and characterized the dynamics of the probe under a variety of conditions. SL-Ethidium binds to the regions of DNA which are not bound to the histones.
[West Nile virus: a migrating arbovirus of current interest]. (1999)

West Nile (WN) virus is a common arbovirosis in sub-Saharian Africa. It has occasionally caused epidemics or epizootics in horses in Mediterranean regions and southern Europe. The virus is transmitted to humans by mosquitoes (primarily the Culex species) that are infected by biting viremic birds. Infections in humans are usually asymptomatic. Recently, however, a growing number of cases involving central nervous system manifestations and deaths have been reported in elderly people in Algeria and Romania. Deaths have also been recorded in migrating birds in zones where the virus is emerging. An outbreak of WN virus in an urban area of North America in 1999 underscored the ability of viruses to appear suddenly in unexpected places. Molecular biology techniques are required for positive identification of WN virus. Serological tests alone do not allow differentiation from other flavivirus in the encephalitis group including Japanese encephalitis in Asia and Saint Louis encephalitis in North America. Virological monitoring of sentinel birds should provide a better understanding of epidemiological factors and of the pathological potential of circulating strains.
Attenuation of noise by diffraction at a barrier edge (1981)

Traffic noise attenuated by a barrier alongside a highway was measured with microphones positioned above an asphalt surface 15 and 30 m behind the barrier. The sound levels were analyzed to obtain the average sound pressure levels per ⅓-octave band. An idealized experiment was also performed using a barrier 2.5 m high and 17 m long erected on a flat asphalt surface. Sound pressure levels from a point source were measured for various source and receiver positions. Certain features of these measurements were presented at the last meeting in Los Angeles where the effects of atmospheric turbulence were discussed. The same measurements will now be compared with two versions of classical Kirchhoff-Fresnel diffraction theory which is currently used to predict the attenuation of noise by barriers. This comparison shows that the sound levels behind the barrier are higher than widely used diffraction theories by 1 to 3 dB at all frequencies—and, surprisingly, by 2 to 10 dB when compared with a theory that should be more precise. The largest discrepancies occur at the shorter source to receiver distances. An alternative diffraction theory as well as an empirical correction to Kirchhoff-Fresnel theory are offered which show good agreement with all the results. [Work supported by NSERC grant to Carleton University.]
<title>Reactive ion etching of CVD diamond films for MEMS applications</title> (2000)

Reactive Ion Etching is an effective method for etching of diamond films, in this paper, the influences of maskant, system pressure and the composition of reactive gas on the etch rate and etched surface of diamond were studied. A gas mixture of O<SUB>2</SUB> and Ar was used as the reactive agent, the concentration of Ar in this mixture is in the range of 0 to 100% (V/V), and the etching result reveals that argon is not necessary. The system pressure plays the dominant effect on the etched surface and etched contours of diamond structures. The highest etch rate appears in the range of 60 - 100 Torr, very low and very high pressure both result in etch rate decreasing. The maskant plays an important role in etching process, it can be sputtered and re-deposited on the etched surface of diamond and act as a micro mask, results in rougher etched surface in some conditions. The optimum processing parameters were achieved, and combined this patterning process with conventional photolithography and sacrificial wet etching process, we have formed a new type of surface micromachining technique for fabrication of diamond MEMS structures. Typical MEMS structures such as cantilever beams, diamond micro hinge and diamond tips array have been fabricated successfully.
Faculty Opinions recommendation of Pseudomonas evades immune recognition of flagellin in both mammals and plants. (2011)

The building blocks of bacterial flagella, flagellin monomers, are potent stimulators of host innate immune systems. Recognition of flagellin monomers occurs by flagellin-specific pattern-recognition receptors, such as Toll-like receptor 5 (TLR5) in mammals and flagellin-sensitive 2 (FLS2) in plants. Activation of these immune systems via flagellin leads eventually to elimination of the bacterium from the host. In order to prevent immune activation and thus favor survival in the host, bacteria secrete many proteins that hamper such recognition. In our search for Toll like receptor (TLR) antagonists, we screened bacterial supernatants and identified alkaline protease (AprA) of Pseudomonas aeruginosa as a TLR5 signaling inhibitor as evidenced by a marked reduction in IL-8 production and NF-kB activation. AprA effectively degrades the TLR5 ligand monomeric flagellin, while polymeric flagellin (involved in bacterial motility) and TLR5 itself resist degradation. The natural occurring alkaline protease inhibitor AprI of P. aeruginosa blocked flagellin degradation by AprA. P. aeruginosa aprA mutants induced an over 100-fold enhanced activation of TLR5 signaling, because they fail to degrade excess monomeric flagellin in their environment. Interestingly, AprA also prevents flagellin-mediated immune responses (such as growth inhibition and callose deposition) in Arabidopsis thaliana plants. This was due to decreased activation of the receptor FLS2 and clearly demonstrated by delayed stomatal closure with live bacteria in plants. Thus, by degrading the ligand for TLR5 and FLS2, P. aeruginosa escapes recognition by the innate immune systems of both mammals and plants.
P‐50: Distinguished Poster Paper: Arrays of Large Si Grains Grown at Room Temperature for x‐Si TFTS (2004)

Abstract Arrays of large Si grains have been grown by phase‐modulated excimer‐laser annealing at room temperature. Home‐plate‐ and square‐shaped grains could be grown over the whole irradiated substrate area. These results indicate that the fabrication of x‐Si TFTs on glass is a realistic development target.
Investigation of the Expression of Amnion Antigens by Spiral Arteries in Human Utero‐Placental Tissues (1987)

Two monoclonal antibodies raised against human amnion, GB3 and GB5, were used in an indirect immunoperoxidase method to investigate the expression of amnion antigens by spiral arteries in pregnant and nonpregnant uterine tissues. GB3 showed focal reactivity with occasional spiral arteries in the placental bed throughout pregnancy, but no GB3-staining was observed in nonpregnant endometrium. In contrast, GB5 showed bandlike circumferential reactivity with spiral arteries at all gestational ages examined. GB5-positivity showed no relation to the presence of endovascular or perivascular trophoblast. In nonpregnant endometrium, GB5 labeled rare spiral arteries. However, in a premenstrual specimen showing pseudodecidual change, there was circumferential reactivity with GB5 resembling that in pregnancy. The reaction patterns of GB3 or GB5 were not similar to those for two other basement-membrane components, fibronectin and type IV collagen. The results suggest that expression of the GB5 antigen may in part be regulated by hormones.
Enhanced stimulus-secretion coupling in polyamine-depleted rat insulinoma cells. An effect involving increased cytoplasmic Ca2+, inositol phosphate generation, and phorbol ester sensitivity. (1993)

To extend previous observations on the role of polyamines in insulin production, metabolism, and replication of insulin-secreting pancreatic beta cells, we have studied the role of polyamines in the regulation of the stimulus-secretion coupling of clonal rat insulinoma cells (RINm5F). For this purpose, RINm5F cells were partially depleted in their polyamine contents by use of the specific ornithine decarboxylase inhibitor difluoromethylornithine (DFMO), which led to an increase in cellular insulin and ATP contents. Analysis of different parts of the signal transduction pathway revealed that insulin secretion and the increase in cytoplasmic free Ca2+ concentration ([Ca2+]i) after K(+)-induced depolarization were markedly enhanced in DFMO-treated cells. These effects were paralleled by increased voltage-activated Ca2+ currents, as judged by whole-cell patch-clamp analysis, probably reflecting increased channel activity rather than elevated number of channels per cell. DFMO treatment also rendered phospholipase C in these cells more sensitive to the muscarinic receptor agonist carbamylcholine, as evidenced by enhanced generation of inositol phosphates, increase in [Ca2+]i and insulin secretion, despite an unaltered ligand binding to muscarinic receptors and lack of effect on protein kinase C activity. In addition, the tumor promoter 12-O-tetradecanoylphorbol 13-acetate, at concentrations suggested to be specific for protein kinase C activation, evoked an increased insulin output in polyamine-deprived cells compared to control cells. The stimulatory effects of glucose or the cyclic AMP raising agent theophylline on insulin release were not increased by DFMO treatment. In spite of increased binding of sulfonylurea in DFMO-treated cells, there was no secretory response or altered increase in [Ca2+]i in response to the drug in these cells. It is concluded that partial polyamine depletion sensitizes the stimulus-secretion coupling at multiple levels in the insulinoma cells, including increased voltage-dependent Ca2+ influx and enhanced responsiveness to activators of phospholipase C and protein kinase C. In their entirety, our present results indicate that the behavior of the stimulus-secretion coupling of polyamine-depleted RINm5F insulinoma cells changes towards that of native beta cells, thus improving the usefulness of this cell line for studies of beta cell insulin secretion.
An Intuitive Graphical Webserver for Multiple-Choice Protein Sequence\n Search (2013)

Every day tens of thousands of sequence searches and sequence alignment\nqueries are submitted to webservers. The capitalized word "BLAST" become a\nverb, describing the act of performing sequence search and alignment. However,\nif one needs to search for sequences that contain, for example, two hydrophobic\nand three polar residues at five given positions, the query formation on the\nmost frequently used webservers will be difficult. Some servers support the\nformation of queries with regular expressions, but most of the users are\nunfamiliar with their syntax. Here we present an intuitive, easily applicable\nwebserver, the Protein Sequence Analysis server, that allows the formation of\nmultiple choice queries by simply drawing the residues to their positions; if\nmore than one residue are drawn to the same position, then they will be nicely\nstacked on the user interface, indicating the multiple choice at he given\nposition. This computer-game like interface is natural and intuitive, and the\ncoloring of the residues makes possible to form queries requiring not just\ncertain amino acids in the given positions, but also small nonpolar, negatively\ncharged, hydrophobic, positively charged, or polar ones. The webserver is\navailable at http://psa.pitgroup.org.\n