gebhart/patrepeval huggingface dataset:
Mono-modal waveguides filled with a pair of parallel epsilon-negative (ENG) and mu-negative (MNG) metamaterial layers (2003)

Here we analyze guided wave propagation in a parallel-plate waveguide filled with a pair of parallel lossless slabs; one possessing negative real permittivity but positive real permeability, and the other with negative real permeability and positive real permittivity, in the range of frequency of interest. It is shown that such a waveguide can support only a single propagating mode, essentially independent of the total thickness of this structure. Furthermore, this waveguide can still possess a propagating mode even when its thickness is very small. Field distribution and dispersion relations in such a mono-modal waveguide are obtained and discussed with physical insights and intuitive description for the mathematical findings.
Investigation of sp<sup>2</sup>-Carbon Pattern Geometry in Boron-Doped Diamond Electrodes for the Electrochemical Quantification of Hypochlorite at High Concentrations (2020)

An electrochemical sensor that contains patterned regions of sp<sup>2</sup>-carbon in a boron-doped diamond (BDD) matrix is presented for the quantitative detection of hypochlorite (OCl<sup>-</sup>) at high concentrations in the alkaline, chemically oxidizing environment associated with bleach. As BDD itself is unresponsive to OCl<sup>-</sup> reduction within the solvent window, by using a laser micromachining process, it is possible to write robust electrochemically active regions of sp<sup>2</sup>-carbon into the electrochemically inert sp<sup>3</sup>-BDD electrode. In this work, four different laser patterned BDD electrodes are examined, and their response compared across a range of OCl<sup>-</sup> concentrations (0.02-1.50 M). A single macrospot (0.37 mm diameter disk) electrode and a closely spaced microspot (46 μm diameter disk) hexagonal array electrode, containing the same surface area of sp<sup>2</sup>-carbon, are shown to provide the most linear response toward OCl<sup>-</sup> reduction. Finite element modeling (FEM) is employed to better understand the electrochemical system, due to the complexity of the electrode geometry, as well as the need to include contributions from migration and Ohmic drop at these high concentrations. FEM data suggest that only a small percentage (∼1 × 10<sup>-3</sup>%) of the total laser-machined sp<sup>2</sup> area is active toward the OCl<sup>-</sup> reduction process and that this process is kinetically very sluggish (∼<i>k</i><sub>eff</sub> = 1 × 10<sup>-12</sup> cm s<sup>-1</sup>). The sensitivity at the array electrode (-0.127 ± 0.004 mA M<sup>-1</sup>; <i>R</i><sup>2</sup> = 0.992) is higher than that at the single-spot electrode (-0.075 ± 0.002 mA M<sup>-1</sup>; <i>R</i><sup>2</sup> = 0.996) due to the enhanced effect of transport to the edges of the microspots, shown via simulation. The electrodes returned a relatively stable response over a greater than 3 month period of use in the OCl<sup>-</sup> solutions, demonstrating these hybrid sp<sup>2</sup>-BDD electrodes show promise for long-term monitoring applications in the harsh environments associated with bleaching applications.
Structural Analysis of the Mechanism of Adenovirus Binding to Its Human Cellular Receptor, CAR (1999)

Binding of virus particles to specific host cell surface receptors is known to be an obligatory step in infection even though the molecular basis for these interactions is not well characterized. The crystal structure of the adenovirus fiber knob domain in complex with domain I of its human cellular receptor, coxsackie and adenovirus receptor (CAR), is presented here. Surface-exposed loops on knob contact one face of CAR, forming a high-affinity complex. Topology mismatches between interacting surfaces create interfacial solvent-filled cavities and channels that may be targets for antiviral drug therapy. The structure identifies key determinants of binding specificity, which may suggest ways to modify the tropism of adenovirus-based gene therapy vectors.
Voltammetric pH sensor based on electrochemically modified pseudo-graphite (2020)

A nanocrystalline graphite-like amorphous carbon (graphite from the University of Idaho thermolyzed asphalt reaction, GUITAR) shares morphological features with classical graphites, including basal and edge planes (BP, EP). However, unlike graphites and other sp2-hybridized carbons, GUITAR has fast heterogenous electron transfer (HET) across its basal planes, and resistance to corrosion similar to sp3-C and boron-doped diamond electrodes. In this contribution, quinoid modified BP-GUITAR (q-GUITAR) is examined as a sensor for pH determination. This modification is performed by applying 2.0 V (vs. Ag/AgCl) for 150 seconds followed by 15 cyclic voltammetric scans from -0.7 to 1.0 V at 50 mV s-1 in 1.0 M H2SO4. The quinoid surface coverage of q-GUITAR is 1.35 × 10-9 mol cm-2, as measured by cyclic voltammetry. X-ray photoelectron spectroscopy analysis also confirms the high surface coverage. The quinoid surface concentration ranks highest in literature when compared with other basal plane graphitic materials. This yields a sensor that responds through a square wave voltammetric reduction peak shift of 63.3 mV per pH over a pH range from 0 to 11. The response on q-GUITAR is stable for >20 measurements and no surface re-activation is required between the measurements. The common interferents, Na+, K+ and dissolved oxygen, have no effect on the response of the q-GUITAR-based pH sensor.
Multilevel Switched-Capacitor AC–DC Step-Down Rectifier for Wireless Charging With Reduced Conduction Loss and Harmonic Content (2022)

In this article, a wireless charging architecture employing a multilevel switched-capacitor (MSC) ac–dc rectifier is investigated. The proposed MSC rectifier features a multilevel design that is scalable to accommodate different power ratings and load ranges. The topology showcases advantages for wireless power transfer (WPT) systems in terms of compactness, efficiency, impedance tunability, and harmonic attenuation. The single-stage active topology is capable of varying its low-distortion staircase input voltage to tune the WPT system for high system-wide efficiency. A seven-level, 20-W prototype is used to verify the WPT loading and loss analysis. The prototype operates at 150 kHz with up to 3:1 step-down conversion ratio to an output voltage of 5.0 V. The experimental peak dc-to-dc efficiency is 93.8% and the rectifier peak efficiency is 98.3%. The rectifier demonstrates low waveform distortion and high efficiency across many WPT loading conditions, solidifying its place as a strong candidate for wireless power applications.
Ferroelectric Nonvolatile Memory Field-Effect Transistors Based on a Novel Buffer Layer Structure (2000)

We have proposed and developed a ferroelectric nonvolatile field-effect transistor that incorporates a thin MgO buffer layer between a ferroelectric film and an oxidized Si substrate. The use of an MgO/SiO2 buffer for a ferroelectric gate is based on the following findings. First, a thin MgO buffer serves well as a template layer allowing the growth of highly oriented ferroelectric films on amorphous substrates. Second, MgO works well as a diffusion barrier between a ferroelectric film and a substrate, protecting the silicon FET channel region from interdiffusion or reaction that may occur during device processing. Third, thermal oxidation of Si is known to be one of the best ways of passivating silicon surfaces, thus to reduce high quality FET channels. The fabricated devices show excellent performance in ferroelectric polarization switching, memory retention, and fatigue resistance. The devices also demonstrate scalability in device dimension and operating voltage, i.e., they are suitable for low voltage operation (3-5 V or below) showing a sufficient memory window (1-2 V).
Digital Compensation of Amplifier Nonlinearities in the Receiver of a Wireless System (2007)

In order to enable efficient implementation of wireless systems with high signal dynamics, this paper proposes an approach to estimate and correct for the amplitude and phase distortion caused by nonlinear power amplifiers. The approach comprises a preamble design, an estimation method and a digital compensation algorithm. Correction for the nonlinearities is applied in the receiver, which requires no additional hardware. Performance evaluation of a 60 GHz OFDM-based system shows that the proposed approach can successfully be applied with minimal performance degradation compared to non-impaired systems.
Capturing Signals from Fast-relaxing Spins with Frequency-Swept MRI: SWIFT (2012)

Sweep imaging with Fourier transformation, SWIFT, is a relatively new addition to the class of ultra-short T2-sensitive MRI sequences. It reverses the recent paradigm of pulsed NMR methodology by exploiting features of continuous-wave experiments from the early days of NMR. Images are produced by collecting projections of the object in a radial manner. Each projection is excited by a frequency sweep in the presence of a field gradient. MR signal is acquired in gaps in the frequency-swept pulse, in a time-shared manner. Signals are excited sequentially in time and space, leading to phase variation. Phase variation due to the frequency-swept excitation is removed by correlation of the received data with the pulse waveform. The result is equivalent to FID excitation using a short hard pulse. The phase evolution time of signal prior to acquisition is as low as a few microseconds for high bandwidth SWIFT, so signals from spins with extremely short T2s (tens of microseconds) are preserved. Here we describe the SWIFT sequence and signal processing procedures, along with some applications, including magnetization-prepared imaging of the human brain, in vitro imaging of bone and cartilage, in vitro dental imaging, and high-resolution phase imaging of in vitro rat brain.


Keywords:

NMR;
MRI;
frequency modulation;
frequency sweep;
adiabatic pulses;
musculoskeletal imaging;
radial MRI
Field Validation of a Statistical-Based Bridge Damage-Detection Algorithm (2013)

This paper describes a field validation of a second-generation, statistical-based damage-detection algorithm and its ability to detect actual damage in bridges accurately. The algorithm had been theoretically validated previously. For the field tests, in lieu of introducing damage to a public bridge, two sacrificial specimens that simulated damage-sensitive locations of the bridge were mounted on the bridge, and different types and levels of damage in the form of cracks and simulated corrosion were induced in the specimens. Using strain data collected from sensors on the sacrificial specimens and on the bridge, the algorithm correctly identified the damage. Analysis of data from sensors far away from the damaged area revealed a relatively high false-positive rate.
Data from A Genetic Vaccine Encoding Shared Cancer Neoantigens to Treat Tumors with Microsatellite Instability (2023)

<div>Abstract<p>Tumors with microsatellite instability (MSI) are caused by a defective DNA mismatch repair system that leads to the accumulation of mutations within microsatellite regions. Indels in microsatellites of coding genes can result in the synthesis of frameshift peptides (FSP). FSPs are tumor-specific neoantigens shared across patients with MSI. In this study, we developed a neoantigen-based vaccine for the treatment of MSI tumors. Genetic sequences from 320 MSI tumor biopsies and matched healthy tissues in The Cancer Genome Atlas database were analyzed to select shared FSPs. Two hundred nine FSPs were selected and cloned into nonhuman Great Ape Adenoviral and Modified Vaccinia Ankara vectors to generate a viral-vectored vaccine, referred to as Nous-209. Sequencing tumor biopsies of 20 independent patients with MSI colorectal cancer revealed that a median number of 31 FSPs out of the 209 encoded by the vaccine was detected both in DNA and mRNA extracted from each tumor biopsy. A relevant number of peptides encoded by the vaccine were predicted to bind patient HLA haplotypes. Vaccine immunogenicity was demonstrated in mice with potent and broad induction of FSP-specific CD8 and CD4 T-cell responses. Moreover, a vaccine-encoded FSP was processed <i>in vitro</i> by human antigen-presenting cells and was subsequently able to activate human CD8 T cells. Nous-209 is an “off-the-shelf” cancer vaccine encoding many neoantigens shared across sporadic and hereditary MSI tumors. These results indicate that Nous-209 can induce the optimal breadth of immune responses that might achieve clinical benefit to treat and prevent MSI tumors.</p>Significance:<p>These findings demonstrate the feasibility of an “off-the-shelf” vaccine for treatment and prevention of tumors harboring frameshift mutations and neoantigenic peptides as a result of microsatellite instability.</p></div>
<i>HOXA11</i> DNA methylation—A novel prognostic biomarker in ovarian cancer (2008)

Epigenetic alterations play a major role in cancer. Recently we reported that stem cell Polycomb group targets (PcGTs) are up to 12-fold more likely to have cancer-specific promoter DNA hypermethylation than nontargets. To identify potential, prognostic DNA methylation markers in ovarian cancer we analyzed the DNA methylation at 71 different loci in 22 ovarian cancers and 18 non-neoplastic ovarian specimens by means of a quantitative, real-time PCR-based technique (MethyLight). We identified DNA methylation of HOXA10 and HOXA11, both of them PcGTs, to be the best discriminators between cancer and non-neoplastic tissue. In an independent set consisting of 92 ovarian cancer specimens further analysis demonstrated that HOXA11 DNA methylation is (i) strongly associated with the residual tumor after cytoreductive surgery and (ii) is a marker indicating poor prognosis. HOXA11 DNA methylation was independently associated with poor outcome [relative risk for death 3.4 (95% CI 1.2-9.9; p = 0.03)]. These findings support the view that the technical inability to optimally cytoreduce ovarian cancer is associated with particular molecular alterations in the tumor which per se define a subgroup of patients with poor outcome.
Nucleophilic Activation of Red Phosphorus for Controlled Synthesis of Polyphosphides (2020)

Reactions between red phosphorus (P<sub>red</sub>) and potassium ethoxide in various organic solvents under reflux convert this rather inert form of the element to soluble polyphosphides. The activation is hypothesized to proceed via a nucleophilic attack by ethoxide on the polymeric structure of P<sub>red</sub>, leading to disproportionation of the latter, as judged from observation of P(OEt)<sub>3</sub> in the reaction products. A range of solvents has been probed, revealing that different polyphosphide anions (P<sub>7</sub><sup>3-</sup>, P<sub>16</sub><sup>2-</sup>, P<sub>21</sub><sup>3-</sup>, and P<sub>5</sub><sup>-</sup>) can be stabilized depending on the combination of the boiling point and dielectric constant (polarity) of the solvent. The effectiveness of activation also depends on the nature of nucleophile, with the rate of reaction between P<sub>red</sub> and KOR increasing in the order <i>t</i>-Bu < <i>n</i>-Hex < Et < Me, which is in agreement with the increasing order of nucleophilic strength. Thiolates and amides were also examined as potential activators, but the reaction with these nucleophiles were substantially slower; nonetheless, all reactions between P<sub>red</sub> and NaSR yielded exclusively P<sub>16</sub><sup>2-</sup> as a soluble polyphosphide product.
Thermal-mechanical-noise-based CMUT characterization and sensing (2012)

When capacitive micromachined ultrasonic transducers (CMUTs) are monolithically integrated with custom-designed low-noise electronics, the output noise of the system can be dominated by the CMUT thermal-mechanical noise both in air and in immersion even for devices with low capacitance. Because the thermal-mechanical noise can be related to the electrical admittance of the CMUTs, this provides an effective means of device characterization. This approach yields a novel method to test the functionality and uniformity of CMUT arrays and the integrated electronics when a direct connection to CMUT array element terminals is not available. Because these measurements can be performed in air at the wafer level, the approach is suitable for batch manufacturing and testing. We demonstrate this method on the elements of an 800-μm-diameter CMUT-on-CMOS array designed for intravascular imaging in the 10 to 20 MHz range. Noise measurements in air show the expected resonance behavior and spring softening effects. Noise measurements in immersion for the same array provide useful information on both the acoustic cross talk and radiation properties of the CMUT array elements. The good agreement between a CMUT model based on finite difference and boundary element methods and the noise measurements validates the model and indicates that the output noise is indeed dominated by thermal-mechanical noise. The measurement method can be exploited to implement CMUT-based passive sensors to measure immersion medium properties, or other parameters affecting the electro-mechanics of the CMUT structure.
Response of varactors containing DNA-conjugated polymer (2012)

We study the effect on the microwave S-parameters of adding a conjugated polymer layer to a deoxyribonucleic acid-based (DNA-based) biopolymer within a variable capacitor (varactor) using a capacitive test structure. The conjugated polymer we are using in this work is poly(3-hexylthiophene-2,5-diyl) (P3HT) and the DNA-based biopolymer is DNA-CTMA. The results are compared to both the baseline DNA-based biopolymer and the conjugated polymer layer added to a layer of polyvinyl alcohol. The addition of the conjugated polymer layer underneath the DNA-based biopolymer is found to most significantly improve the stability and dielectric tuning of the DNA-based biopolymer.
A novel self-routing address scheme for all-optical packet-switched networks with arbitrary topologies (2003)

Pure all-optical packet-switched networks in which both header processing and packet routing are carried out in the optical domain overcome the bandwidth bottlenecks of optoelectronic conversions and therefore are expected to meet the needs of next generation high speed networks. Due to the limited capabilities of available optical logic devices, realizations of pure all-optical packet-switched networks in the near future will likely employ routing schemes that minimize the complexity of routing control. In this paper, we propose a novel self-routing scheme that identifies the output ports of the nodes in a network instead of the nodes themselves. The proposed address scheme requires single bit processing only and is applicable to small to medium size pure all-optical packet-switched networks with arbitrary topologies. Unlike traditional self-routing schemes, multiple paths between two nodes can be defined. An hierarchical address structure can be used in the proposed routing scheme to shorten the address.
Multifocal multiphoton microscopy (MMM) at a frame rate beyond 600 Hz (2007)

We introduce a multiphoton microscope for high-speed three-dimensional (3D) fluorescence imaging. The system combines parallel illumination by a multifocal multiphoton microscope (MMM) with parallel detection via a segmented high-sensitivity charge-couple device (CCD) camera. The instrument consists of a Ti-sapphire laser illuminating a microlens array that projects 36 foci onto the focal plane. The foci are scanned using a resonance scanner and imaged with a custom-made CCD camera. The MMM increases the imaging speed by parallelizing the illumination; the CCD camera can operate at a frame rate of 1428 Hz while maintaining a low read noise of 11 electrons per pixel by dividing its chip into 16 independent segments for parallelized readout. We image fluorescent specimens at a frame rate of 640 Hz. The calcium wave of fluo3 labeled cardiac myocytes is measured by imaging the spontaneous contraction of the cells in a 0.625 second sequence movie, consisting of 400 single images.
RIPENING CHANGES AND FLAVOR DEVELOPMENT IN MICROBIAL ENZYME TREATED CHEDDAR CHEESE SLURRIES (1979)

ABSTRACT Cheddar cheese slurries from salted curds were studied to determine an initial level of microbial protease and lipase that potentially might be incorporated optimally into Cheddar cheese to accelerate ripening without developing flavor defects. Soluble protein, free volatile fatty acids values and total bacteria counts of microbial enzyme treated slurries were considerably higher than in controls. Slurry pH decreased slightly during initial ripening but then rose gradually, with the rate of rise, particularly marked in microbial enzyme treated slurries. Electrophoretic illustrations indicated more degradation of ols, and p‐caseins in microbial enzyme treated slurries than in the control slurry. Bitter peptides formed in microbial enzyme treated slurries were transitory. Microbial enzymes used in slurries were inactivated at 80°C.
Transition-State Structure of <i>Neisseria meningitides</i> 5‘-Methylthioadenosine/<i>S</i>-Adenosylhomocysteine Nucleosidase (2007)

5‘-Methylthioadenosine/S-adenosylhomocysteine nucleosidase (MTAN) is a bacterial enzyme that is involved in quorum sensing pathways and a potential target for the design of antibiotics. Kinetic isotope effects (KIEs) and computer modeling using density functional theory were used to determine the transition state of N. meningitides MTAN. KIEs were measured for hydrolysis of 5‘- methylthioadenosine (MTA) and were corrected for forward commitment to catalysis to obtain intrinsic KIEs for [1‘-3H], [9-15N], [1‘-14C], [2‘-3H], [4‘-3H], [5‘-3H2], and [Me-3H3] MTAs. KIEs support an early SN1 transition state unlike the dissociative transition states of other MTANs. Computational modeling of intrinsic KIEs places the leaving group adenine at 1.68 Å from the anomeric carbon, a Pauling bond order of 0.50, and no participation of the hydroxide nucleophile. The N7 of adenine is protonated and the leaving group is cationic owing to the significant bond order to the C1‘−N9 bond at the transition state. The 3‘-OH is not strongly polarized or ionized at the transition state, unlike other MTANs. The early transition state of N. meningitides MTAN is supported by its inhibition with transition-state analogues.
<title>Development of surface micromachining technologies for microfluidics and bioMEMS</title> (2001)

In the last decade, examples of devices manufactured with SUMMiT(TM) technology have demonstrated the capabilities of polysilicon surface micromachining. Currently we are working on enhancements to this technology that utilize additional structural layers of silicon nitride to enable Microfluidics and BioMEMS applications. The addition of the silicon nitride layers allows the fabrication of microfluidic flow channels that are transparent (allowing observation of cellular motion) and insulating (allowing the placement of polysilicon electrodes at arbitrary locations in the flow channels). The goal of this technology development effort is to ultimately provide functionality that is not feasible with other microfabrication technologies. The enhancements build on the key features of surface micromachining: manufacturability and compatibility with CMOS processing, which allow us to leverage the investment already made in the microelectronics processing technology. In this paper we will present examples of devices fabricated using this new enhanced surface micromachining technology. These devices include pumps, valves, and a cell manipulator.© (2001) COPYRIGHT SPIE--The International Society for Optical Engineering. Downloading of the abstract is permitted for personal use only.