gebhart/patrepeval huggingface dataset:
Atopic Dermatitis‐Like Skin Lesions Reduced by Topical Application and Intraperitoneal Injection of Hirsutenone in NC/Nga Mice (2010)

Atopic dermatitis (AD) is a common inflammatory skin disease. The increasing prevalence and severity of AD have prompted the developments of safer, more effective drugs. Although topical corticosteroids have been used as first line therapy for AD, their potential side effects limit their clinical applications. To investigate the effect of hirsutenone (HIR), a diarylheptanoid compound, on AD-like skin lesions and other factors related to immune response is the aim of this paper Th2-related cytokines (IL-4, IL-5, IL-13), eosinophil, IgE inflammatory factors (COX-2, iNOS) levels were reduced in blood, lymphocytes, and tissue after HIR treatment. These results suggest that HIR might be an effective treatment for AD.
Ligand-Guided Selection of Target-Specific Aptamers: A Screening Technology for Identifying Specific Aptamers Against Cell-Surface Proteins (2016)

We report on a new strategy for identifying highly specific aptamers against a predetermined epitope of a target. Termed “ligand-guided selection” (LIGS), this method uniquely exploits the selection step, the core of SELEX (Systematic Evolution Exponential enrichment). LIGS uses a naturally occurring stronger and highly specific bivalent binder, an antibody (Ab) interacting with its cognate antigen to outcompete specific aptamers from a partially enriched SELEX pool, as a strategy. We demonstrate the hypothesis of LIGS by utilizing an Ab binding to membrane-bound Immunoglobulin M (mIgM) to selectively elute aptamers that are specific for mIgM from a SELEX pool that is partially enriched toward mIgM expressing Ramos cells. The selected aptamers show specificity toward Ramos cells. We identified three aptamer candidates utilizing LIGS that could be outcompeted by mIgM Ab, demonstrating that LIGS can be successfully applied to select aptamers from a partially evolved cell-SELEX library, against predetermined receptor proteins using a cognate ligand. This proof-of-concept study introduces a new biochemical-screening platform that exploits the binding of a secondary stronger molecular entity to its target as a partition step, to identify highly specific artificial nucleic acid ligands.
Production ray tracing of feature lines (2018)

Automated feature line drawing of virtual 3D objects helps artists depict shapes and allows for creating stylistic rendering effects. High-fidelity drawing of lines that are very thin or have varying thickness and color, or lines of recursively reflected and refracted objects, is a challenging task. In this paper we describe an image-based feature detection and line drawing method that integrates naturally into a ray tracing renderer and runs as a post-process, after the pixel sampling stage. Our method supports arbitrary camera projections and surface shaders, and its performance does not dependent on the geometric complexity of the scene but on the pixel sampling rate. By leveraging various attributes stored in every pixel sample, which are typically available in production renderers, e.g. for arbitrary output variables (AOVs), feature lines of reflected and refracted objects can be obtained with relative ease. The color and width of the lines can be driven by the surface shaders, which allows for achieving a wide variety of artistic styles.
Sparse stimuli for cochlear implants (2008)

The aim of the present research is to explore the applica-tion of sparse coding principles to the processing within a cochlear implant. These principles would determine what information in noisy speech should be extracted and used to excite the electrode array within the cochlea. The hypothe-sis is that reducing redundancy in the signal, making it more sparse, would improve speech recognition scores in noise. The proposed sparse coding strategy was based on a combination of ICA (independent component analysis) and PCA (principal component analysis), both operating on the spectrotemporal envelope of the speech signal. The algo-rithm is tested for speech in quiet and modulated babble noise conditions (signal-to-noise ratios, SNR=15 dB, 10 dB, 5 dB). Results show that the algorithm is beneficial, partic-ularly when baseline performance of listeners is poor. This approach is applicable both to acoustical hearing aids and cochlear implants. 1.
Nondestructive mapping of carrier concentration and dislocation density in <i>n</i>+-type GaAs (1994)

Transmission mappings (500 μm×500 μm resolution) at wavelengths of 0.9–1.5 μm on 3 in., n+-GaAs wafers (n≂1–2×1018 cm−3) correlate well with carrier concentration n, measured by the Hall effect, and dislocation density, as confirmed by KOH etch-pit patterns. The absorption for λ≳1.0 μm (below band edge) varies directly with n via free-carrier interconduction-band transitions, while the absorption for λ≲0.95 μm (near band edge) varies inversely with n because of band-filling effects. Both phenomena are highly useful for n+-GaAs wafer characterization.
Iterative generation of attenuation maps in TOF-PET/MR using consistency conditions (2009)

2013 Objectives A novel method improving the estimation of the attenuation map for future PET/MR systems using the anatomical reference from MRI and gamma attenuation from PET emission data is presented. Besides the unique benefits of this new hybrid modality, MRI unfortunately does not provide a direct measurement of attenuation coefficients for 511keV photons as CT, which is one of the key prerequisites for quantitative PET. Thus, several research groups are addressing this topic with segmentation, atlas-based registration and computer learning techniques using data bases with MR and corresponding CT images. Methods We propose a new iterative reconstruction approach to simultaneously compute the activity and the attenuation distribution using the segmented MR image as geometrical reference. The main advantage over other mentioned approaches is the use of the true physical attenuation of the 511keV photons provided by the PET list mode data. The novel approach uses a discrete consistency condition from which a maximum likelihood estimation of the activity and attenuation is derived. Results First results from simulated and measured clinical data, compared to reference data achieved using CT attenuation maps, indicate an excellent agreement between both correction techniques. High impact of scattered and accidental coincidences is discussed in detail. Moreover, it was observed that performing TOF reconstruction and previous region segmentation minimizes inherent crosstalk between the activity and attenuation estimation. Conclusions The proposed hybrid method using PET and MR data leads to more robust and accurate attenuation correction which is a significant step towards quantitative PET/MR.
Joint myocardial T<sub>1</sub> and T<sub>2</sub> mapping using a combination of saturation recovery and T<sub>2</sub>‐preparation (2015)

The proposed sequence allows joint estimation of accurate and coregistered quantitative myocardial T1 and T2 maps in a single breath-hold. Magn Reson Med 76:888-896, 2016. © 2015 Wiley Periodicals, Inc.
Design of a loaded monopole having hemispherical coverage using a genetic algorithm (1997)

A genetic algorithm is used to design a monopole loaded with a modified folded dipole so that it radiates uniform power over the hemisphere. Each of the wires that make up the antenna are given a range of possible lengths. The genetic algorithm randomly selects a sample population of possible antenna configurations from the total population of all configurations. The radiation pattern of each sample configuration is computed using the numerical electromagnetics code (NEC). The solutions are compared with the desired pattern and ranked in terms of performance. The best solutions are retained and mated with one another and the process is repeated until an optimal solution is obtained. The genetic algorithm quickly produced an antenna that has a nearly uniform power over the hemisphere. Although the antenna was designed to operate at a frequency of 1.6 GHz, it performed satisfactorily over the frequency range from 1.4 to 1.8 GHz. The antenna was fabricated and the computational results were verified experimentally. We have shown that the genetic algorithm is a very powerful tool for designing wire antennas; it is expected that this process can be used to design any antenna that can be analyzed using an electromagnetic code.
Design of Efficient ARQ Schemes with Anti-Jamming Coding for Cognitive Radios (2009)

We introduce simple yet efficient ARQ protocols in conjunction with two types of anti-jamming coding techniques - rateless coding and piecewise coding - for cognitive radios. For piecewise coding, we propose to employ systematic codes to facilitate efficient selected retransmissions and design short codes to maximize secondary user throughput. For rateless coding, we consider a protocol that transmits new parity packets during retransmission and show that this scheme is stable if the jamming rate of the system is within a certain range. For both anti-jamming coding schemes, the corresponding simple ARQ protocols provide significant improvement in secondary user throughput. Moreover, the piecewise coding together with its ARQ protocol offers similar or better throughput performance compared with the rateless coding counterpart, without incurring the stability issue.
Calcitonin stimulates the secretion of urokinase‐type plasminogen activator from prostate cancer cells: Its possible implications on tumor cell invasion (2005)

Calcitonin (CT) is synthesized and secreted in prostate epithelium, and its secretion from malignant prostates is several folds higher than that in benign prostates. CT receptor (CTR) is expressed in malignant prostate epithelium, and its activation increases invasiveness of prostate cancer (PC) cells via activation of protein kinase A. Since the role of urokinase-type plasminogen activator (uPA) in invasion of PC has been established, we tested the hypothesis that CT increases invasion of PC cells by stimulating uPA secretion from PC cells. Exogenously added CT stimulated the secretion of uPA from PC-3M cells in a dose-dependent manner, which was blocked by Rp.cAMP, a competitive inhibitor of protein kinase A. CT stimulated the secretion of MMP-2 and MMP-9 from PC-3M cells, and also increased their invasiveness. Both these actions of CT were blocked by uPA-neutralizing antibodies. Immunofluorescence studies with PC-3M cells suggest that CT stimulated redistribution of cellular uPA to focal adhesion sites, which was further confirmed by co-immunoprecipitation of uPA with focal adhesion kinase (FAK) in response to CT. These results suggest that CT increases invasiveness of PC cells by stimulating PKA-mediated uPA secretion and by redirecting the secreted uPA to focal adhesion sites. The results also suggest that uPA may, at least in part, mediate proinvasive actions of CT on PC cells by stimulating the secretion of gelatinases and degradation of focal adhesion sites.
Hyperhalogens: Discovery of a New Class of Highly Electronegative Species (2010)

Hyper trumps super: A central atom, typically a metal, surrounded by halogen or oxygen atoms is called a superhalogen. Theoretical calculations and experiments reveal that a new class of highly electronegative species can be created when the central metal atom is surrounded by superhalogen moieties. These hyperhalogens can have electron affinities even larger than those of their superhalogen building blocks.
Automated Irrigation Based on Threshold Canopy Temperature (1992)

An automated drip irrigation system was controlled by continuously measuring cotton canopy temperature and computing 15-minute averages in a three-year field study between 1988-1990. Irrigation was applied only when average canopy temperature exceeded predetermined threshold values. Threshold temperatures were tested in 2 C increments between 26 C and 32 C. The length of irrigation cycles was shortest and amount per irrigation event was highest for all threshold temperatures during the early growth stage because canopies were small and warm bare soil contributed to measured canopy temperature. The ratio of water use to reference evapotranspiration decreased as threshold canopy temperature increased from 26 C to 32 C, but water use efficiency increased. Average canopy temperature during the period DOY 198 to 273, while net radiation exceeded 300 W m-2 and air temperature at 2 m exceeded 28 C, increased as threshold canopy temperature increased. Lint yield was highest for the 28 C threshold temperature and decreased for higher or lower threshold temperatures. Threshold temperatures = 28 C restricted water application and created increasing levels of water stress. The 28 C threshold should provide maximum lint yield where water supply and season length do not limit production. Under limited production conditions a 30 C threshold may be preferable to a 28 C threshold because lint yield is only slightly reduced but water use efficiency is higher and cotton matures more rapidly. Maximum yields were produced by 28 C and 30 C threshold canopy temperatures in which total seasonal water use ranged between 64 and 84 cm.
Transmission response measurements of frequency-translating devices using a vector network analyzer (1996)

A new method for accurately determining the transmission response of frequency-translating devices (FTDs) is presented. The absolute amplitude and phase of the FTD under test is obtained using a vector network analyzer (VNA) and two test FTDs, where one FTD must have reciprocal frequency response characteristics. The characterization of single-sideband (SSB) FTDs is obtained in a straightforward manner by combining data from three VNA two-port swept measurements. The characterization of double-sideband (DSB) FTDs can be performed in the same manner as for SSB FTDs, or, more accurately, by combining data from six two-port swept baseband measurements. A complete analysis of the characterization method using low-pass equivalent (LPE) signals and systems is presented, along with the development of the appropriate data reduction procedures needed to arrive at the de-embedded LPE FTD transmission responses. The validation and accuracy of the method is demonstrated with results for both SSB and DSB FTDs operating at 20 GHz.
Adaptive Filtering for Video Coding with Focus Change (2007)

We propose an adaptive filtering approach for coding video that exhibits localized camera focus changes, e.g., such that different portions of a video frame can undergo different blurriness/sharpness changes with respect to corresponding areas in frames used for prediction. First we obtain, for each macroblock, the filter that provides maximum reduction in residual energy, when applied to the reference macroblock before to motion compensation. Then, starting from the block-wise filter parameters, we divide the macroblocks into classes, by clustering macroblocks that have been assigned "similar" filters. Finally, for each class, a two-dimensional filter is designed to minimize the average residual energy for all macroblocks in the class. The resulting filters are applied to the reference frames to generate better matches for motion compensation. Simulation results shows that the proposed method provides up to 1 dB gain over current H.264 for certain sequences. As compared to H.264 with multiple reference frames, the coding gain is about 0.5 dB.
Prediction of Li-Ion Battery State of Charge Using Multilayer Perceptron and Long Short-Term Memory Models (2019)

Lithium-ion batteries are used in different applications such as electric vehicles and grid-scale energy storage. These applications rely greatly on the accurate measurement and prediction of state of charge (SOC) to ascertain the battery's available capacity. Although multiple methods exist in the literature to predict SOC and other battery parameters, they have low accuracy, make offline predictions, and do not consider enough battery parameters. The battery's nonlinear characteristics and time-variance have direct impacts on the applications connected to it, which make the prediction a complex but more necessary problem to solve. This paper bridges the gap by comparing the performance of two widely used data-driven learning models: long short-term memory (LSTM) and a multilayer perceptron (MLP), for predicting SOC using predictors such as cell current, cell voltage, elapsed time, and cell temperature. The models are run using mean squared error as the loss function, and different loss function optimizers. The models are also applied to datasets from different charging/discharging rates to demonstrate their efficacy. A recommendation is finally made on the model for SOC prediction subject to specific conditions considered in the paper, and the groups of optimizers that work better to minimize the loss function.
Folded multiple-capture: an architecture for high dynamic range disturbance-tolerant focal plane array (2004)

Earlier studies have shown that multiple capture can achieve high SNR, but cannot satisfy the high dynamic range (HDR) and high speed requirements of the Vertically-Integrated-Sensor-Array (VISA) project. Synchronous self-reset, on the other hand, can achieve these requirements, but suffers from poor SNR. Extended counting can achieve high dynamic range at high frame rate and with good SNR, but at the expense of high power consumption. The paper proposes a new HDR focal plane array architecture, denoted by folded-multiple capture (FMC), which by combining features of the synchronous self-reset and multiple capture schemes, can satisfy the VISA requirements at a fraction of the power dissipation and with more robustness to device variations than extended counting. The architecture is also capable of detecting subframe disturbances, e.g., due to laser jamming, and correcting for it.
Helmholtz equation–least-squares method for reconstructing acoustic pressure fields (1997)

A method using spherical wave expansion theory to reconstruct an acoustic pressure field from a vibrating object is developed. The radiated acoustic pressures are obtained by means of an expansion of independent functions generated by the Gram–Schmidt orthonormalization with respect to the particular solutions to the Helmholtz equation on the vibrating surface under consideration. The coefficients associated with these independent functions are determined by requiring the assumed form of the solution to satisfy the pressure boundary condition at the measurement points. The errors incurred in this process are minimized by the least-squares method. Once these coefficients are specified, the acoustic pressure at any point, including the source surface, is completely determined. In this paper, this method is used to reconstruct the surface acoustic pressures based on the measured acoustic pressure signals in the field. It is shown that this method can be applied to both separable and nonseparable geometries, and the solutions thus obtained are unique. However, the convergence may be worse for an elongated object subject to high-frequency excitations. [Work supported by the Institute for Manufacturing Research at Wayne State University.]
Simultaneous optical wavelength interchange with a two-dimensional second-order nonlinear photonic crystal (2000)

We present a theoretical analysis for simultaneous optical wavelength interchange and isolation of a pair of collinear input optical signals by use of two concurrent difference-frequency-generation processes in a two-dimensional second-order nonlinear photonic crystal. We have derived a set of relations, including a general nonlinear Bragg condition, that we use to determine the parameters of the nonlinear lattice, given the input wavelengths and desired exit angles of the wavelength-interchanged outputs.
Hydrogel droplet microarrays with trapped antibody-functionalized beads for multiplexed protein analysis (2010)

Antibody microarrays are a powerful tool for rapid, multiplexed profiling of proteins. 3D microarray substrates have been developed to improve binding capacity, assay sensitivity, and mass transport, however, they often rely on photopolymers which are difficult to manufacture and have a small pore size that limits mass transport and demands long incubation time. Here, we present a novel 3D antibody microarray format based on the entrapment of antibody-coated microbeads within alginate droplets that were spotted onto a glass slide using an inkjet. Owing to the low concentration of alginate used, the gels were highly porous to proteins, and together with the 3D architecture helped enhance mass transport during the assays. The spotting parameters were optimized for the attachment of the alginate to the substrate. Beads with 0.2 µm, 0.5 µm and 1 µm diameter were tested and 1 µm beads were selected based on their superior retention within the hydrogel. The beads were found to be distributed within the entire volume of the gel droplet using confocal microscopy. The assay time and the concentration of beads in the gels were investigated for maximal binding signal using one-step immunoassays. As a proof of concept, six proteins including cytokines (TNFα, IL-8 and MIP/CCL4), breast cancer biomarkers (CEA and HER2) and one cancer-related protein (ENG) were profiled in multiplex using sandwich assays down to pg mL(-1) concentrations with 1 h incubation without agitation in both buffer solutions and 10% serum. These results illustrate the potential of beads-in-gel microarrays for highly sensitive and multiplexed protein analysis.
The I-<i>Ceu</i>I endonuclease recognizes a sequence of 19 base pairs and preferentially cleaves the coding strand of the<i>Chlamydomonas moewusii</i>chloroplast large subunit rRNA gene (1992)

The I-CeuI endonuclease is a member of the growing family of homing endonucleases that catalyse mobility of group I introns by making a double-strand break at the homing site of these introns in cognate intronless alleles during genetic crosses. In a previous study, we have shown that a short DNA fragment of 26 bp, encompassing the homing site of the fifth intron in the Chlamydomonas eugametos chloroplast large subunit rRNA gene (Ce LSU.5), was sufficient for I-CeuI recognition and cleavage. Here, we report the recognition sequence of the I-CeuI endonuclease, as determined by random mutagenesis of nucleotide positions adjacent to the I-CeuI cleavage site. Single-base substitutions that completely abolish endonuclease activity delimit a 15-bp sequence whereas those that reduce the cleavage rate define a 19-bp sequence that extends from position -7 to position +12 with respect to the Ce LSU.5 intron insertion site. As the other homing endonucleases that have been studied so far, the I-CeuI endonuclease recognizes a non-symmetric degenerate sequence. The top strand of the recognition sequence is preferred for I-CeuI cleavage and the bottom strand most likely determines the rate of double-strand breaks.
High Temperature Transfer Molding Resins Based on 2,3,3',4'-Biphenyltetracarboxylic Dianhydride (2002)

As part of an ongoing effort to develop materials for resin transfer molding (RTM) processes to fabricate high performance/high temperature composite structures, phenylethynyl containing imides have been under investigation. New phenylethynyl containing imide compositions were prepared using 2,3,3',4'-biphenyltetracarboxylic dianhydride (a-BPDA) and evaluated for cured glass transition temperature (Tg), melt flow behavior, and for processability into flat composite panels via RTM. The a-BPDA imparts a unique combination of properties that are desirable for high temperature transfer molding resins. In comparison to its symmetrical counterpart (i.e. 3,3',4,4'-biphenyltetracarboxylic dianhydride), a-BPDA affords oligomers with lower melt viscosities and when cured, higher Tgs. Several candidates exhibited the appropriate combination of properties such as a low and stable melt viscosity required for RTM processes, high cured Tg, and moderate toughness. The chemistry, physical, and composite properties of select resins will be discussed.