gebhart/patrepeval huggingface dataset:
Detection of <i>Mycobacterium avium</i> subsp. <i>paratuberculosis</i> by a Sonicate Immunoassay Based on Surface-Enhanced Raman Scattering (2007)

A sandwich immunoassay for the rapid, low-level detection of Mycobacterium avium subsp. paratuberculosis has been developed. M. avium subsp. paratuberculosis is the causative agent of Johne's disease in cattle, and one of the major obstacles in controlling the spread of this disease is the inability to rapidly detect small amounts of bacteria or other diagnostic markers shed during the subclinical stage of infection. This paper details the development and performance of an assay for sonicated M. avium subsp. paratuberculosis lysate that is based on surface-enhanced Raman scattering (SERS). There are two key components of the assay: (i) an immobilized layer of monoclonal antibodies that target a surface protein on the microorganism; and (ii) extrinsic Raman labels (ERLs) that are designed to selectively bind to captured proteins and produce large SERS signals. By correlating the number of M. avium subsp. paratuberculosis bacilli present prior to sonication to the amount of total protein in the resulting sonicate, the detection limit determined for total protein can be translated to the microorganism concentration. These findings yield detection limits of 100 and 200 ng/ml (estimated to be 500 and 1,000 M. avium subsp. paratuberculosis bacilli/ml) for sonicate spiked in phosphate buffer and sonicate spiked in whole milk, respectively. Moreover, the time required to complete the assay, which includes sample preparation, antigen extraction, ERL incubation, and readout, is less than 24 h. The potential for incorporation of this novel assay into diagnostic laboratories is also briefly discussed.
A cool approach to reducing electrode-induced trauma: Localized therapeutic hypothermia conserves residual hearing in cochlear implantation (2016)

Collectively, these results suggest that therapeutic hypothermia during cochlear implantation may reduce traumatic effects of electrode insertion and improve conservation of residual hearing.
Synthesis and Characterization of Metal–Organic Framework-74 Containing 2, 4, 6, 8, and 10 Different Metals (2014)

Metal-organic frameworks (MOFs) containing more than two kinds of metal ions mixed in one secondary building unit are rare because the synthesis often yields mixed MOF phases rather than a pure phase of a mixed-metal MOF (MM-MOF). In this study, we use a one-pot reaction to make microcrystalline MOF-74 [M2(DOT); DOT = dioxidoterephthalate] with 2 (Mg and Co), 4 (Mg, Co, Ni, and Zn), 6 (Mg, Sr, Mn, Co, Ni, and Zn), 8 (Mg, Ca, Sr, Mn, Fe, Co, Ni, and Zn), and 10 (Mg, Ca, Sr, Ba, Mn, Fe, Co, Ni, Zn, and Cd) different kinds of divalent metals. The powder X-ray diffraction patterns of MM-MOF-74 were identical with those of single-metal MOF-74, and no amorphous phases were found by scanning electron microscopy. The successful preparation of guest-free MM-MOF-74 samples was confirmed by N2 adsorption measurements. Elemental analysis data also support the fact that all metal ions used in the MOF synthesis are incorporated within the same MOF-74 structure. Energy-dispersive X-ray spectroscopies indicate that metal ions are heterogeneously distributed within each of the crystalline particles. This approach is also employed to incorporate metal ions (i.e., Ca, Sr, Ba, and Cd) from which the parent MOF structure could not be made as a single-metal-containing MOF.
Optimal trade-off between sampling rate and quantization precision in A/D conversion (2015)

The jointly optimized sampling rate and quantization precision in A/D conversion is studied. In particular, we consider a basic pulse code modulation A/D scheme in which a stationary process is sampled and quantized by a scalar quantizer. We derive an expression for the minimal mean squared error under linear estimation of the analog input from the digital output, which is also valid under sub-Nyquist sampling. This expression allows for the computation of the sampling rate that minimizes the error under a fixed bitrate at the output, which is the result of an interplay between the number of bits allocated to each sample and the distortion resulting from sampling. We illustrate the results for several examples, which demonstrate the optimality of sub-Nyquist sampling in certain cases.
Cartesian Versus Joint Space Command Shaping for a Ship Boom Crane (2000)

Abstract This paper presents a command shaping control method for suppressing operator induced payload swing in rotary, ship-based, boom cranes. The crane configuration studied consists of a payload mass that swings on the end of a spherical pendulum of varying lift-line length (hoisting). The lift-line is attached to a boom capable of elevation (luffing). The boom can rotate about an axis perpendicular to the ship’s deck (slewing). Positioning of the payload is accomplished through luff, slew, and hoist commands issued in real-time by an operator. A Cartesian space command shaping method is developed and compared to a previously documented joint space approach. Although both methods are appropriate for low rate crane maneuvers, the Cartesian method provides better performance under the tested operating conditions. Simulation results are presented to compare their performance.
Noise Figure Reduction in Erbium-Doped Fiber Amplifiers Using Loop Mirror Filter (2001)

Noise figure reduction of an erbium-doped fiber amplifier using loop mirror filter is demonstrated. Approximately 0.5-dB noise figure reduction is achieved at input signal power level below - 30dBm. Transferring energy from the amplifier spontaneous emission to the input signal compensates for the insertion loss of the loop mirror filter device. The insertion loss of the device approximately 1 dB.
Sputter deposition of a spongelike morphology in metal coatings (2003)

Metallic films are grown with a “spongelike” morphology in the as-deposited condition using planar magnetron sputtering. The morphology of the deposit is characterized by metallic continuity in three dimensions with continuous and open porosity on the submicron scale. The stabilization of the spongelike morphology is found over a limited range of the sputter deposition parameters, that is, of working gas pressure and substrate temperature. This spongelike morphology is an extension of the features as generally represented in the classic zone models of growth for physical vapor deposits. Nickel coatings are deposited with working gas pressures up to 4 Pa and for substrate temperatures up to 1100 K. The morphology of the deposits is examined in plan and in cross section views with scanning electron microscopy. The parametric range of gas pressure and substrate temperature (relative to absolute melt point) under which the spongelike metal deposits are produced appear universal for other metals including gold, silver, and aluminum.
Impedance Spectroscopy of Teeth with and without Approximal Caries Lesions-an in vitro Study (1996)

Caries diagnosis by the measurement of electrical resistance is hampered by polarization effects when dc or single-low-frequency ac currents are used. Electrical impedance spectroscopy, measuring impedance over a large range of frequencies, will provide more detailed information about the electrical characteristics of teeth. It was the aim of this study (a) to characterize the complex impedance behavior of whole extracted teeth, measured at the approximal surface, and (b) to identify parameters of the complex impedance behavior of the teeth which would be useful in distinguishing between degrees of carious involvement. Thirty-nine extracted premolar teeth with 59 unrestored and undamaged (excepting caries) approximal surfaces were selected. The tooth surfaces were divided into three groups according to their macroscopic appearance: sound (group S, n = 16), white- or brown-spot lesion present (group L, n = 33), or cavitated (group C, n = 10). The teeth were inserted into a jig which allowed for counter-electrode contact via a conducting gel. The working electrode consisted of a carbonated fiber material. Electrical impedance measurements were performed over a maximum range of about 1 MHz to 0.1 Hz. We analyzed electrical impedance data by fitting equivalent circuits. Fit was evaluated numerically and visually. The complex impedance spectra divided naturally into three groups which corresponded almost perfectly with the classifications of S,L, and C. The groups differed most in the dc resistance (Rdc), as calculated from the impedance parameters. Mean Rdc for groups S, L, and C were 68 M omega, 5.9 M omega, and 321 k omega, respectively. These means were significantly different from each other (log-transformed data, ANOVA, p < 0.001; Tukey multiple comparisons, p < 0.001). It is concluded that the in vitro performance of electrical impedance spectroscopy in differentiating among sound, non-cavitated carious, and cavitated approximal tooth surfaces is excellent.
In-pavement wireless sensor network for vehicle classification (2011)

Vehicle classification data, especially for trucks, is of considerable use to agencies involved in almost all aspects of transportation and pavement engineering. Current technologies for classification involve expensive installation and calibration procedures. A wireless sensor network (WSN) for vehicle classification based on axle count and spacing was designed, calibrated, tested, and deployed near a weigh station in Sunol, California. The WSN includes: vibration sensors which report pavement acceleration; vehicle detection sensors which report vehicle's time of arrival and departure; and an Access Point (AP) that logs the data collected from all these sensors. Both sensors are packaged for durability, occupy minimal space, have long lifetimes, and are embedded inside the pavement. The vibration sensors are capable of over-the-air software programming and are designed to be immune to sound. Vibration and classification ground truth data for 53 different trucks exiting the weigh station were collected. The vibration data collected at 512 Hz had an accuracy of 400 μg. A novel algorithm for estimating axle count and spacing has been developed. The combination of bandwidth-aware smoothing filter and peak detector that we use in this algorithm could be useful in many other applications. The algorithm successfully classified all 53 trucks.
Reliable discrimination of mortar launch/impact events using acoustics (2006)

Feature extraction methods based on the discrete wavelet transform and multiresolution analysis facilitate the development of a robust classification algorithm that reliably discriminates between launch and impact mortar events via acoustic signals produced during these events. Distinct characteristics arise within the different explosive events because impact events emphasize concussive and shrapnel effects, while launch events result from blasts that expel and propel a mortar round from a gun. The ensuing blast waves are readily characterized by variations in the corresponding peak pressure and rise time of the waveform, differences in the ratio of positive pressure amplitude to the negative amplitude, variations in the prominent frequencies associated with the varying blast events and variations in the overall duration of the resulting waveform. Unique attributes can also be identified that depend upon the properties of the gun tube, projectile speed at the muzzle, and the explosive/concussive properties associated with the events. In this work, the discrete wavelet transform is used to extract the predominant components of these characteristics from the acoustic signatures of the event at ranges of 1km. Highly reliable discrimination is achieved with a feedforward neural network classifier trained on a feature space derived from the distribution of wavelet coefficients and higher frequency details found within different levels of the multiresolution decomposition. We show that the algorithms provide a reliable discrimination (>97%) between launch and impact events using data collecting during several separate field test experiments.
Selective Light-Triggered Release of DNA from Gold Nanorods Switches Blood Clotting On and Off (2013)

Blood clotting is a precise cascade engineered to form a clot with temporal and spatial control. Current control of blood clotting is achieved predominantly by anticoagulants and thus inherently one-sided. Here we use a pair of nanorods (NRs) to provide a two-way switch for the blood clotting cascade by utilizing their ability to selectively release species on their surface under two different laser excitations. We selectively trigger release of a thrombin binding aptamer from one nanorod, inhibiting blood clotting and resulting in increased clotting time. We then release the complementary DNA as an antidote from the other NR, reversing the effect of the aptamer and restoring blood clotting. Thus, the nanorod pair acts as an on/off switch. One challenge for nanobiotechnology is the bio-nano interface, where coronas of weakly adsorbed proteins can obscure biomolecular function. We exploit these adsorbed proteins to increase aptamer and antidote loading on the nanorods.
Reduction of bound‐state and nonradiative defect densities in nonpolar (11&2macr;0) AlGaN/GaN quantum wells by the use of lateral epitaxial overgrowth technique (2005)

Reduction in bound-state and nonradiative defect densities was shown in nonpolar (11-20) AlxGa1–xN/GaN multiple quantum wells (MQWs) grown on GaN templates prepared by lateral epitaxial overgrowth (LEO-GaN), in terms of the appearance of correct in-plane light polarization and improved internal quantum efficiency. The (11-20) LEO-GaN grown by halide vapor phase epitaxy exhibited a fairly long photoluminescence (PL) lifetime (τPL=530 ps) at 300 K. Structural advantages of using nonpolar orientations were confirmed by a moderate shift of the PL peak energy and negligible change in low-temperature τPL with decreasing GaN well width, both of which are the results of eliminating quantum-confined Stark effects due to the spontaneous and piezoelectric polarization which exists in polar (0001) MQWs. (© 2005 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)
Insulin-like Growth Factor-I Receptor Blockade Improves Outcome in Mouse Model of Lung Injury (2008)

IGF-I regulated survival and migration of fibrogenic cells in the lung. Blockade of the IGF pathway increased fibroblast apoptosis and subsequent resolution of pulmonary fibrosis. Thus, IGF-IR may be a potential target for treatment of lung injury and fibrosis.
<title>History of one family of atmospheric radiative transfer codes</title> (1994)

Beginning in the early 1970's, the then Air Force Cambridge Research Laboratory initiated a program to develop computer-based atmospheric radiative transfer algorithms. The first attempts were translations of graphical procedures described in a 1970 report on The Optical Properties of the Atmosphere, based on empirical transmission functions and effective absorption coefficients derived primarily from controlled laboratory transmittance measurements. The fact that spectrally-averaged atmospheric transmittance (T) does not obey the Beer-Lambert Law (T equals exp(-(sigma) (DOT)(eta) ), where (sigma) is a species absorption cross section, independent of (eta) , the species column amount along the path) at any but the finest spectral resolution was already well known. Band models to describe this gross behavior were developed in the 1950's and 60's. Thus began LOWTRAN, the Low Resolution Transmittance Code, first released in 1972. This limited initial effort has how progressed to a set of codes and related algorithms (including line-of-sight spectral geometry, direct and scattered radiance and irradiance, non-local thermodynamic equilibrium, etc.) that contain thousands of coding lines, hundreds of subroutines, and improved accuracy, efficiency, and, ultimately, accessibility. This review will include LOWTRAN, HITRAN (atlas of high-resolution molecular spectroscopic data), FASCODE (Fast Atmospheric Signature Code), and MODTRAN (Moderate Resolution Transmittance Code), their permutations, validations, and applications, particularly as related to passive remote sensing and energy deposition.
Laser frequency stabilization using regenerative spectral hole burning (2000)

Summary form only given. We introduce laser frequency stabilization using continuously regenerated transient spectral holes in an inhomogeneously broadened resonance of a solid. Narrow spectral holes provide extreme frequency stabilization for time scales appropriate for spectroscopy, signal processing, laser ranging, and interferometry. This technique thus will have significant applications beyond the field of spectral hole burning.
Development of targeted therapy for a broad spectrum of solid tumors mediated by a double promoter plasmid expressing diphtheria toxin under the control of IGF2-P4 and IGF2-P3 regulatory sequences. (2013)

Our findings suggest that administration of P4-DTA-P3-DTA has the potential to reach and eradicate tumor cells and thus may help reduce tumor burden, improve the quality of life of the patients; and prolong their life span.
High-speed fluorescence lifetime measurement for investigation of dynamic phenomena (2009)

We present a novel method for high-speed measurements of fluorescence lifetime, in which fluorescence signal for precise lifetime determination is acquired in a short time on the order of microseconds. Our method is based on analog signal that contains a number of fluorescence photons in a pulse, on the contrary to the conventional time-correlated single-photon counting in which only a single photon is permitted for a fluorescence pulse. Because this method does not have any problem of photon counting pile-up, the measurement speed is not limited by the single-photon constraint and can increase up to the excitation repetition rate. In order to extract the accurate lifetime information from the analog signal contaminated by the slow instrumental response function (IRF), we have developed a new signal processing method, in which the lifetime is determined by difference between mean arrival time of the analog photo-electronic pulse of fluorescence signal and one of IRF signal. By both experimental and theoretical studies, we have verified that the measurement accuracy and precision are nearly independent of the width of the IRF so that inexpensive narrowbandwidth photo-detectors and low-speed electronics can be used for this method. Excellent accuracy and precision have been obtained experimentally for high-speed measurements completed in a few microseconds. These results suggest that our method can be well applied to measurement of fast dynamic phenomena and real time fluorescence lifetime imaging microscope with low cost.
Coupled Luminescent Methods in Drug Discovery: 3‐Min Assays for Cytotoxicity and Phosphatase Activity (2005)

This chapter contains sections titled: Introduction The DeathTRAK 3-Min Cytotoxicity Assay PhosTRAK: A Very Rapid, Homogeneous General Phosphatase Assay Coupled Luminescent Assays in Practice: Specifications and Limitations Summary and Conclusions Formulations References
Application of Adaptive Nulling to Electromagnetic Hyperthermia for Improved Thermal Dose Distribution in Cancer Therapy (1991)

Adaptive nulling is applied to the problem of generating a therapeutic thermal dose distribution in electromagnetic hyperthermia treatment of cancer. A system design concept for implementing adaptive hyperthermia is introduced. With the proposed design concept, it may be possible to maximize the applied electric field at a tumor position in th target body and simultaneously minimize or reduce the electric field at target positions where undesired high temperature regions (hot spots) occur. In a clinical situation, either a gradient search algorithm or sample matrix inversion algorithm would be used to rapidly form the adaptive null (or nulls) prior to any significant tissue heating. Analysis of an annular phased array antenna embedded in an infinite homogeneous medium shows the potential merit of combining adaptive nulling with conventional near-field focusing used in hyperthermia. The analysis is based on a well-known moment-method theory for conducting thin wire antennas in a homogeneous conducting medium. The theory and software used to compute the moment-method received voltage at a short-dipole probe due to a transmitting dipole array are documented. Computer simulations show that adaptive nulling can prevent undesired high-temperature regions from occurring while simultaneously heating a deep-seated tumor site.
Strategies to support human oocyte development in vitro (2012)

Many young cancer patients are now being given the option to store ovarian cortical biopsies before undergoing potentially damaging chemo- or radiotherapy. This tissue mainly contains large numbers of immature primordial follicles. Currently the only option to restore fertility using this tissue is by transplantation which may not be a viable option for all patients. Greater options to realise the potential of this tissue to restore fertility could be achieved by the development of in vitro systems that support oocyte development. The ability to develop human oocytes from the most immature stages of follicles (primordial) through to maturation and fertilisation in vitro would revolutionise fertility preservation practice. This has been achieved in mouse where in vitro grown (IVG) oocytes from primordial follicles have resulted in the production of live offspring. However, developing IVG systems to support complete development of human oocytes has been more difficult because of differences in scale of timing and size. Our lab has been working on a multi-step culture system to support growth and development of bo-vine and human oocytes from primordial through to fully grown, using fresh and cryopreserved ovarian cortical tissue. This review outlines the approaches being taken to obtain complete in vitro development of human oocytes and strategies for assessing the health and viability of IVG oocytes.
Effects of N-Terminal Residues on the Assembly of Constrained β-Hairpin Peptides Derived from Aβ (2020)

This paper describes the synthesis, solution-phase biophysical studies, and X-ray crystallographic structures of hexamers formed by macrocyclic β-hairpin peptides derived from the central and C-terminal regions of Aβ, which bear "tails" derived from the N-terminus of Aβ. Soluble oligomers of the β-amyloid peptide, Aβ, are thought to be the synaptotoxic species responsible for neurodegeneration in Alzheimer's disease. Over the last 20 years, evidence has accumulated that implicates the N-terminus of Aβ as a region that may initiate the formation of damaging oligomeric species. We previously studied, in our laboratory, macrocyclic β-hairpin peptides derived from Aβ<sub>16-22</sub> and Aβ<sub>30-36</sub>, capable of forming hexamers that can be observed by X-ray crystallography and SDS-PAGE. To better mimic oligomers of full length Aβ, we use an orthogonal protecting group strategy during the synthesis to append residues from Aβ<sub>1-14</sub> to the parent macrocyclic β-hairpin peptide <b>1</b>, which comprises Aβ<sub>16-22</sub> and Aβ<sub>30-36</sub>. The N-terminally extended peptides <b>N+1</b>, <b>N+2</b>, <b>N+4</b>, <b>N+6</b>, <b>N+8</b>, <b>N+10</b>, <b>N+12</b>, and <b>N+14</b> assemble to form dimers, trimers, and hexamers in solution-phase studies. X-ray crystallography reveals that peptide <b>N+1</b> assembles to form a hexamer that is composed of dimers and trimers. These observations are consistent with a model in which the assembly of Aβ oligomers is driven by hydrogen bonding and hydrophobic packing of the residues from the central and C-terminal regions, with the N-terminus of Aβ accommodated by the oligomers as an unstructured tail.