gebhart/patrepeval huggingface dataset:
A Comparative Analysis of Novel Deep Learning and Ensemble Learning Models to Predict the Allergenicity of Food Proteins (2021)

Traditional food allergen identification mainly relies on in vivo and in vitro experiments, which often needs a long period and high cost. The artificial intelligence (AI)-driven rapid food allergen identification method has solved the above mentioned some drawbacks and is becoming an efficient auxiliary tool. Aiming to overcome the limitations of lower accuracy of traditional machine learning models in predicting the allergenicity of food proteins, this work proposed to introduce deep learning model-transformer with self-attention mechanism, ensemble learning models (representative as Light Gradient Boosting Machine (LightGBM) eXtreme Gradient Boosting (XGBoost)) to solve the problem. In order to highlight the superiority of the proposed novel method, the study also selected various commonly used machine learning models as the baseline classifiers. The results of 5-fold cross-validation showed that the area under the receiver operating characteristic curve (AUC) of the deep model was the highest (0.9578), which was better than the ensemble learning and baseline algorithms. But the deep model need to be pre-trained, and the training time is the longest. By comparing the characteristics of the transformer model and boosting models, it can be analyzed that, each model has its own advantage, which provides novel clues and inspiration for the rapid prediction of food allergens in the future.
Effects of the cap layer on the properties of AlN barrier HEMT grown on 6-inch Si(111) substrate (2020)

Abstract A series of AlN/GaN heterostructures were grown on 150 mm Si substrates by metal organic chemical vapor deposition (MOCVD). Different cap layer structures, including gallium nitride (GaN) and silicon nitride (SiN x ), were used to passivate the heterostructure surface. A 3.5 nm thick SiN x cap is able to maintain the two dimensional electron gas (2DEG) stability in a long period. An AlN/GaN heterostructure with a 4.5 nm thick AlN barrier exhibits the best 2DEG properties, in terms of sheet resistance, carrier mobility and stability. The carrier mobility of the 2DEG can be enhanced by a combination of SiNx and GaN cap layers to over 1400 cm 2 /Vs.
Discovery of a Series of 2,5-Diaminopyrimidine Covalent Irreversible Inhibitors of Bruton’s Tyrosine Kinase with in Vivo Antitumor Activity (2014)

Bruton's tyrosine kinase (Btk) is an attractive drug target for treating several B-cell lineage cancers. Ibrutinib is a first-in-class covalent irreversible Btk inhibitor and has demonstrated impressive effects in multiple clinical trials. Herein, we present a series of novel 2,5-diaminopyrimidine covalent irreversible inhibitors of Btk. Compared with ibrutinib, these inhibitors exhibited a different selectivity profile for the analyzed kinases as well as a dual-action mode of inhibition of both Btk activation and catalytic activity, which counteracts a negative regulation loop for Btk. Two compounds from this series, 31 and 38, showed potent antiproliferative activities toward multiple B-cell lymphoma cell lines, including germinal center B-cell-like diffuse large B cell lymphoma (GCB-DLBCL) cells. In addition, compound 31 significantly prevented tumor growth in a mouse xenograft model.
Optimization of the Aerodynamic Plasma Actuator as an Electrohydrodynamic (EHD) Electrical Device (2006)

Electrohydrodynamic plasma actuators have proven effective for flow attachment in internal and external aerodynamics, and for modification of the lift, drag, and stall angle of airfoils. The performance of plasma actuators has been studied with such classical aerodynamic tools as wind tunnels, drag balances, Pitot tubes, smoke flow visualization, and fluid dynamic modeling programs. However, the physical processes and power flows that occur in plasma actuators, before the plasma ions transfer their momentum to the neutral background gas, are those of an electrical device. Optimization of such actuators needs to include the methods of electrical engineering and plasma physics, including classical electrical discharge physics. To implement a program of optimization, we have conceptually divided the power flow through a plasma actuator into the following four sinks: 1.) Reactive power losses due to inadequate impedance matching of the power supply to the actuator; 2.) Dielectric heating of the actuator insulating materials; 3.) Power required to maintain the atmospheric pressure plasma; and 4.) Power coupled to the neutral gas flow by ion-neutral collisions. These four power flows can be, and usually are, of comparable magnitude. In this paper, we review our progress in understanding and minimizing the first three power flows, and maximizing the fourth by adjustment of the actuator geometry and materials, as well as such plasma parameters as the RF frequency and RMS voltage.
Mos oncogene product associates with kinetochores in mammalian somatic cells and disrupts mitotic progression. (1994)

The mos protooncogene has opposing effects on cell cycle progression. It is required for reinitiation of meiotic maturation and for meiotic progression through metaphase II, yet it is an active component of cytostatic factor. mos is a potent oncogene in fibroblasts, but high levels of expression are lethal. The lethality of mos gene expression in mammalian cells could be a consequence of a blockage induced by its cytostatic factor-related activity, which may appear at high dosage in mitotic cells. We have directly tested whether expression of the Mos protein can block mitosis in mammalian cells by microinjecting a fusion protein between Escherichia coli maltose-binding protein and Xenopus c-Mos into PtK1 epithelial cells and analyzing the cells by video time-lapse and immunofluorescence microscopy. Time-course analyses showed that Mos blocked mitosis by preventing progression to a normal metaphase. Chromosomes frequently failed to attain a bipolar orientation and were found near one pole. Injection of a kinase-deficient mutant Mos had no effect on mitosis, indicating that the blockage of mitotic progression required Mos kinase activity. Antitubulin immunostaining of cells blocked by Mos showed that microtubules were present but that spindle morphology was abnormal. Immunostaining for the Mos fusion protein showed that both wild-type and kinase mutant proteins localized at the kinetochores. Our results suggest that mitotic blockage by Mos may result from an action of the Mos kinase on the kinetochores, thus increasing chromosome instability and preventing normal congression.
Identification and Management of Pediculosis (1994)

Currently, pediculosis affects 6-12 million persons in the United States each year, and this number continues to rise. Social stigma and persistent misconceptions complicate the implementation of appropriate management strategies. Diagnosis is made on the basis of finding nits (i.e., silvery-white eggs firmly attached to the hair shaft), concentrated on the crown, behind the ears, and at the nape of the neck. Transmission occurs by direct contact with an infested person or indirectly by contact with clothing, personal grooming articles, bedding, or upholstered furniture containing viable nits or lice. Although three chemical agents are currently available, permethrin 1.0% (Nix Creme Rinse) is the treatment of choice. Environmental treatment is also necessary for the eradication of the infestation. Health care personnel who come into contact with this population need to be well informed of the facts in order to disseminate accurate information for diagnosis and management.
Focusing properties of arbitrary optical fields combining spiral phase and cylindrically symmetric state of polarization (2018)

The tight focusing properties of optical fields combining a spiral phase and cylindrically symmetric state of polarization are presented. First, we theoretically analyze the mathematical characterization, Stokes parameters, and Poincaré sphere representations of arbitrary cylindrical vector (CV) vortex beams. Then, based on the vector diffraction theory, we derive and build an integrated analytical model to calculate the electromagnetic field and Poynting vector distributions of the input CV vortex beams. The calculations reveal that a generalized CV vortex beam can generate a sharper focal spot than that of a radially polarized (RP) plane beam in the focal plane. Besides, the focal size decrease accompanies its elongation along the optical axis. Hence, it seems that there is a trade-off between the transverse and axial resolutions. In addition, under the precondition that the absolute values between polarization order and topological charge are equal, a higher-order CV vortex can also achieve a smaller focal size than an RP plane beam. Further, the intensity for the sidelobe admits a significant suppression. To give a deep understanding of the peculiar focusing properties, the magnetic field and Poynting vector distributions are also demonstrated in detail. These properties may be helpful in applications such as optical trapping and manipulation of particles and superresolution microscopy imaging.
Antimicrobial resistance of Streptococcus pneumoniae recovered from outpatients in the United States during the winter months of 1994 to 1995: results of a 30-center national surveillance study (1996)

A total of 1,527 clinically significant outpatient isolates of Streptococcus pneumoniae were prospectively collected in 30 different U.S. medical centers between November 1994 and April 1995. Overall, 23.6% of strains were not susceptible to penicillin, with 14.1% intermediate and 9.5% high-level resistant. The frequencies of recovery of intermediate and high-level resistant strains varied considerably between different medical centers and in different geographic areas. In general, intermediate and high-level penicillin resistance was most common with isolates of S. pneumoniae recovered from pediatric patients. The in vitro activities of 22 other antimicrobial agents were assessed against this collection of isolates. Ampicillin was consistently 1 twofold dilution less active than penicillin. Amoxicillin and amoxicillin-clavulanate were essentially equivalent to penicillin in activity. The rank order of activity for cephalosporins was cefotaxime = ceftriaxone > or = cefpodoxime > or = cefuroxime > cefprozil > or = cefixime > cefaclor = loracarbef > cefadroxil = cephalexin. The National Committee for Clinical Laboratory Standards [Performance Standards for Antimicrobial Susceptibility Testing, Sixth Information Supplement (M100-S6), 1995] has established MIC breakpoints for resistance (i.e., > or = 2 micrograms/ml) with three cephalosporins versus S. pneumoniae, namely, cefotaxime, ceftriaxone, and cefuroxime. The overall percentages of strains resistant to these three antimicrobial agents were 3, 5, and 12, respectively. The overall frequency of resistance was 10% with all three macrolides examined in this study, clarithromycin, erythromycin, and azithromycin. The overall percentages of chloramphenicol, tetracycline, and trimethoprim-sulfamethoxazole resistance were 4.3, 7.5, and 18, respectively. The resistance percentages among the cephalosporins, macrolides, chloramphenicol, tetracycline, and trimethoprim-sulfamethoxazole were consistently higher among penicillin-intermediate strains than among susceptible isolates and even higher still among organisms expressing high-level penicillin resistance. Multiply resistant strains represented 9.1% of the organisms examined in this study. Finally, rifampin resistance was uncommon (i.e., 0.5%), and vancomycin resistance was not detected. The quinopristin-dalfopristin combination was consistently active at concentrations of 0.25 to 4 micrograms/ml, but rates of resistance could not be determined in the absence of established interpretive criteria for MIC results.
Optimization of attenuated phase-shift mask for contact hole printing (1999)

The goal of this study is to characterize the process latitude of an attenuated phase gift mask on contact hole printing. The parameters chosen to examine the effect on process windows are numerical aperture (NA) and partial coherence. In addition to these, another important element we would like to determine from this test is the appropriate mask to wafer CD bias. The range of numerical aperture is from 0.5 to 0.63 and the range of partial coherence ins from 0.32 to 0.67. Within the ranges of study, it is found that the DOF increases with decreasing partial coherence for iso contacts, but decreases with decreasing partial coherence for dense ones. DOF increases with decreasing numerical aperture for both iso and dense contact holes as expected. The best DOF of 2.1 micron was obtained with 0.5 NA and 0.4 partial coherence. In general, the required energy to open contact holes increases with decreasing numerical aperture, while the impact of partial coherence on best dosage is not as predominant as NA does. The effect of pre-treatment delays the side lobe formation for iso contact holes while seems to have no effect on dense ones.
Selective Enhancement of Nucleases by Polyvalent DNA-Functionalized Gold Nanoparticles (2011)

We demonstrate that polyvalent DNA-functionalized gold nanoparticles (DNA-Au NPs) selectively enhance ribonuclease H (RNase H) activity while inhibiting most biologically relevant nucleases. This combination of properties is particularly interesting in the context of gene regulation, since high RNase H activity results in rapid mRNA degradation and general nuclease inhibition results in high biological stability. We have investigated the mechanism of selective RNase H activation and found that the high DNA density of DNA-Au NPs is responsible for this unusual behavior. This work adds to our understanding of polyvalent DNA-Au NPs as gene regulation agents and suggests a new model for selectively controlling protein-nanoparticle interactions.
The Genome Portal of the Department of Energy Joint Genome Institute (2011)

The Department of Energy (DOE) Joint Genome Institute (JGI) is a national user facility with massive-scale DNA sequencing and analysis capabilities dedicated to advancing genomics for bioenergy and environmental applications. Beyond generating tens of trillions of DNA bases annually, the Institute develops and maintains data management systems and specialized analytical capabilities to manage and interpret complex genomic data sets, and to enable an expanding community of users around the world to analyze these data in different contexts over the web. The JGI Genome Portal (http://genome.jgi.doe.gov) provides a unified access point to all JGI genomic databases and analytical tools. A user can find all DOE JGI sequencing projects and their status, search for and download assemblies and annotations of sequenced genomes, and interactively explore those genomes and compare them with other sequenced microbes, fungi, plants or metagenomes using specialized systems tailored to each particular class of organisms. We describe here the general organization of the Genome Portal and the most recent addition, MycoCosm (http://jgi.doe.gov/fungi), a new integrated fungal genomics resource.
Telomere dysfunction in human diseases: the long and short of it! (2009)

It has been over one hundred years since the first reported case of dyskeratosis congenita (DC) and over twenty since the discovery of telomerase, an enzyme that adds telomeric DNA repeats to chromosome ends. Emerging evidence suggests that telomere dysfunction plays an important role in the pathogenesis of DC and other human disorders involving tissues that require rapid repair and renewal capacities. Yet we still do not fully understand how mutations in telomere maintenance genes contribute to disease development in affected individuals. In this review, we provide an up-to-date summary of the topic by discussing the results from genetic screens of patients, in vitro mutational analysis of involved molecules, and genetically engineered mouse models. While these data shed important light on the mechanisms underlying disease development, further investigation, particularly in an in vivo setting, is needed.
Velocity retrieval of moving object from a single channel high resolution SAR data (2011)

Two-dimensional velocity retrieval methods from a single channel high resolution SAR data through a joint time-frequency analysis and a fractional Fourier transform (FrFT) are presented. Two-dimensional velocity can be measured by estimation of the Doppler center frequency and Doppler frequency rate for the range and azimuth velocity component, respectively. The Doppler spectrum along a Doppler phase history line in the time-frequency domain was reconstructed and projected onto the frequency and time dimension. The peak of the frequency-axis projected spectrum corresponds to the Doppler center frequency, while that of the time-axis indicates an azimuth time of closest approach. The Doppler frequency rate is also measured by the slope deviation of the Doppler spectrum. Simulation using TerraSAR-X parameters indicated that the velocity errors were less than 1 m/sec or 5% for moving objects with a velocity higher than 3 m/sec. While the measurement of Doppler center frequency was reliable over the entire velocity range, errors in Doppler frequency rate became large if the velocity was lower than 3 m/sec. An experiment using TerraSAR-X and truck-mounted corner reflectors validated the measurement accuracy of the approach. Absolute and percent errors of the range velocity were 1.4 km/h and 2.8%, respectively, while the azimuth velocity measurement was comparatively accurate under an assumption of zero acceleration. To apply the method to single-look complex data, the full Doppler bandwidth must be preserved. Application of a fractional Fourier transform (FrFT) to the same data is also presented. The FrFT approach significantly improves computational efficiency and is superior to the WVD approach in estimation of Doppler frequency rate.
Binding of Human Cytomegalovirus US2 to Major Histocompatibility Complex Class I and II Proteins Is Not Sufficient for Their Degradation (2002)

ABSTRACT Human cytomegalovirus (HCMV) glycoprotein US2 causes degradation of major histocompatibility complex (MHC) class I heavy-chain (HC), class II DR-α and DM-α proteins, and HFE, a nonclassical MHC protein. In US2-expressing cells, MHC proteins present in the endoplasmic reticulum (ER) are degraded by cytosolic proteasomes. It appears that US2 binding triggers a normal cellular pathway by which misfolded or aberrant proteins are translocated from the ER to cytoplasmic proteasomes. To better understand how US2 binds MHC proteins and causes their degradation, we constructed a panel of US2 mutants. Mutants truncated from the N terminus as far as residue 40 or from the C terminus to amino acid 140 could bind to class I and class II proteins. Nevertheless, mutants lacking just the cytosolic tail (residues 187 to 199) were unable to cause degradation of both class I and II proteins. Chimeric proteins were constructed in which US2 sequences were replaced with homologous sequences from US3, an HCMV glycoprotein that can also bind to class I and II proteins. One of these US2/US3 chimeras bound to class II but not to class I, and a second bound class I HC better than wild-type US2. Therefore, US2 residues involved in the binding to MHC class I differ subtly from those involved in binding to class II proteins. Moreover, our results demonstrate that the binding of US2 to class I and II proteins is not sufficient to cause degradation of MHC proteins. The cytosolic tail of US2 and certain US2 lumenal sequences, which are not involved in binding to MHC proteins, are required for degradation. Our results are consistent with the hypothesis that US2 couples MHC proteins to components of the ER degradation pathway, enormously increasing the rate of degradation of MHC proteins.
Strong and Stiff Aramid Nanofiber/Carbon Nanotube Nanocomposites (2015)

Small but strong carbon nanotubes (CNTs) are fillers of choice for composite reinforcement owing to their extraordinary modulus and strength. However, the mechanical properties of the nanocomposites are still much below those for mechanical parameters of individual nanotubes. The gap between the expectation and experimental results arises not only from imperfect dispersion and poor load transfer but also from the unavailability of strong polymers that can be effectively utilized within the composites of nanotubes. Aramid nanofibers (ANFs) with analogous morphological features to nanotubes represent a potential choice to complement nanotubes given their intrinsic high mechanical performance and the dispersible nature, which enables solvent-based processing methods. In this work, we showed that composite films made from ANFs and multiwalled CNTs (MWCNTs) by vacuum-assisted flocculation and vacuum-assisted layer-by-layer assembly exhibited high ultimate strength of up to 383 MPa and Young's modulus (stiffness) of up to 35 GPa, which represent the highest values among all the reported random CNT nanocomposites. Detailed studies using different imaging and spectroscopic characterizations suggested that the multiple interfacial interactions between nanotubes and ANFs including hydrogen bonding and π-π stacking are likely the key parameters responsible for the observed mechanical improvement. Importantly, our studies further revealed the attractive thermomechanical characteristics of these nanocomposites with high thermal stability (up to 520 °C) and ultralow coefficients of thermal expansion (2-6 ppm·K(-1)). Our results indicated that ANFs are promising nanoscale building blocks for functional ultrastrong and stiff materials potentially extendable to nanocomposites based on other nanoscale fillers.
Renal effects of nitric oxide scavenging during hyperdynamic sepsis (1997)

Nitric oxide (NO) synthase inhibition aggravates renal failure in non-septic rats [1]. In a previous study it has been shown, that NO scavenging with modified haemoglobin reverses the haemodynamic changes seen with hyperdynamic sepsis [2]. Infusion of free haemoglobin can also effect renal function [3]. Therefore the effects of modified haemoglobin on renal function during ovine sepsis by measuring creatinine clearance and regional blood-flow in the kidney were investigated. Four days after surgical preparation for chronic study, sheep (n=14) received an infusion of live Ps. aeruginosa bacteria for 48 h. After 24 h of sepsis the animals were assigned to either a control (n=7, saline), or a treatment group (n=7, 100 mg Pyridoxalated Haemoglobin Polyoxyethylene Conjugate (PHP) kg−1). Creatinine clearance was determined every 12 h during the experiment. Regional blood flow to the kidney was measured with fluorescent microspheres. Statistic: Fisher's LSD with Bonferroni correction. Data are given as percent of base-line (mean±SEM). After 24 h all sheep had developed a hyperdynamic sepsis. PHP-infusion normalized the haemodynamic parameters. Effects of PHP-infusion on renal function and blood-flow are shown in Fig. 1.Fig. 1. (abstract 6).PHP-infusion during hyperdynamic sepsis caused a significant increase in creatinine clearance and no change in blood-flow to the kidney was observed after PHP-infusion. Renal side effects do not limit the use of modified haemoglobin in the treatment of septic shock.
Factor V and VIII activation "in vivo" during bleeding. Evidence of thrombin formation at the early stage of hemostasis. (1976)

Factor V and VIII activity was measured by a one-stage assay on capillary blood issuing from a skin cut. This activity increases during bleeding. The phenomenon is suppressed by a previous injection of a low dose of heparin. These data give evidence of a very early local formation of thrombin during hemostasis. The study of this activation process in patients with congenital deficiency of blood clotting factor allows to investigate the mechanism of thrombin formation in vivo. This demonstrates the preeminence of the tissue factor pathway and the need of factor VIII for factor X activation in the extrinsic system.