gebhart/patrepeval huggingface dataset:
Impairment of d-alanine biosynthesis in Mycobacterium smegmatis determines decreased intracellular survival in human macrophages (2009)

d-Alanine is a structural component of mycobacterial peptidoglycan. The primary route of d-alanine biosynthesis in eubacteria is the enantiomeric conversion from l-alanine, a reaction catalysed by d-alanine racemase (Alr). Mycobacterium smegmatis alr insertion mutants are not dependent on d-alanine for growth and display a metabolic pattern consistent with an alternative pathway for d-alanine biosynthesis. In this study, we demonstrate that the M. smegmatis alr insertion mutant TAM23 can synthesize d-alanine at lower levels than the parental strain. The insertional inactivation of the alr gene also decreases the intracellular survival of mutant strains within primary human monocyte-derived macrophages. By complementation studies, we confirmed that the impairment of alr gene function is responsible for this reduced survival. Inhibition of superoxide anion and nitric oxide formation in macrophages suppresses the differential survival. In contrast, for bacteria grown in broth, both strains had approximately the same susceptibility to hydrogen peroxide, acidified sodium nitrite, low pH and polymyxin B. In contrast, TAM23 exhibited increased resistance to lysozyme. d-Alanine supplementation considerably increased TAM23 viability in nutritionally deficient media and within macrophages. These results suggest that nutrient deprivation in phagocytic cells combined with killing mediated by reactive intermediates underlies the decreased survival of alr mutants. This knowledge may be valuable in the construction of mycobacterial auxotrophic vaccine candidates.
Selection and amplification of modes of an optical frequency comb using a femtosecond laser injection-locking technique (2006)

The authors have demonstrated the selection and the amplification of the components of an optical frequency comb using a femtosecond laser injectionlocking technique. The author used a mode-locked femtosecond Ti:sapphire laser as the master laser and a single-mode diode laser as the slave laser. The femtosecond laser injection-locking technique was applied to a filter for mode selection of the optical frequency comb and an amplifier for amplification of the selected mode. The authors could obtain the laser source selected only the desired mode of the optical frequency comb and amplified the power of the selected modes several thousand times.
Production and Characterization of Monoclonal Antibodies Against Aflatoxin G <sub>1</sub> (2009)

Using semisolid methylcellulose HAT medium selection and non-competitive and competitive indirect enzyme-linked immunosorbent assay, three hybridomas that secreted antibodies for aflatoxin G(1) were selected after fusion of mouse SP2/0 myeloma cells with spleen cells isolated from BALB/c mice that had been immunized with the conjugate of aflatoxin G(1) (AFG(1)) and bovine serum albumin. The aflatoxin-modified protein used to immunize mice was produced chemically by activating aflatoxin G(1) to a 9,10-epoxide derivative, which then covalently bound to the protein. All of these antibodies were found to be specific to AFG(1), and reacted strongly with aflatoxin G(2). These antibodies were designated 1C8, 1C10, and DE7, and had affinities for AFG1 of 5.1 x 10(7), 2.7 x 10(8), and 1.1 x 10(8) liters mol(-1), respectively.
Hydrodearylation of Heavy Alkyl-Bridged Noncondensed Alkyl Aromatics to Recover High-Value Mono-Aromatics (2019)

A new refining process—hydrodearylation—that provides value creation to a refinery aromatic recovery complex is presented. An aromatic reject stream containing heavy alkyl-bridged noncondensed multi-aromatics from an aromatic recovery complex is processed over a zeolite-containing hydrocracking catalyst to recover high-value mono-aromatics including benzene, toluene, and xylenes (BTX). The use of the heavy aromatic bottom stream is limited as a gasoline blending component because of its high density, dark color, and high final boiling point. The hydrodearylation process upgrades the low-value stream containing bridged di-aromatics to significantly enhance high-value mono-aromatic content. Additionally, the process improves the color of the stream from a dark brown/reddish color to a light yellow color together with an observed 3.5% drop in density that improves volume swell. Two-dimensional gas chromatography confirms mono-aromatic formation as a result of di-aromatic conversion with a 15 wt % absolute increase in the mono-aromatic content (>5 wt % BTX) at optimum reaction conditions. Similarly, a 75% reduction in di-aromatics is observed. The mono-aromatics formed may be further processed downstream to add value by yielding additional BTX.
Microwave Noise Characterization of GaAs MESFET's: Evaluation by On-Wafer Low-Frequency Output Noise Current Measurement (1987)

A simplified noise equivalent circuit is presented for submicron-gate-length MESFET's in the common-source configuration, consisting of five linear circuit elements: the gate-to source capacitance C/sub gs/, the total input resistance R/sub T/, the transconductance g/sub m/, the output resistance R/sub 0/, and a noise current source of spectral density S/sub io/ at the output port. All of these elements can be determined by on-wafer measurements, and the noise current can be measured at a low frequency. The minimum noise figure of the device calculated from this model, as well as the bias and frequency dependence of the noise figure, is shown to be in agreement with microwave noise figure measurements. Thus a technique has been established for determination of the minimum noise figure of a device solely by on-wafer measurements rather than by the usual microwave measurements. The proposed technique can be employed rapidly, conveniently, without the need for tuning, and at the wafer stage of device fabrication.
A method to keep the excitation light sheet in focus in selective plane illumination microscopy (2017)

Abstract Keeping the excitation light sheet in focus is critical in selective plane illumination microscopy (SPIM) to ensure its 3D imaging ability. Unfortunately, an effective method that can be used in SPIM on general biological specimens to find the axial position of the excitation light sheet and keep it in focus is barely available. Here, we present a method to solve the problem. We investigate its mechanism and demonstrate its performance on a lattice light sheet microscope.
Pt–Cu nanoctahedra: synthesis and comparative study with nanocubes on their electrochemical catalytic performance (2012)

Pt–Cu nanoctahedra were successfully synthesized through a simultaneous reduction of platinum(II) acetylacetonate and copper(I)/(II) chloride in the presence of tungsten hexacarbonyl, oleylamine and oleic acid at high temperature. Comparative studies of electrocatalysis on Pt nanocubes, the {111}-terminated Pt–Cu nanoctahedra and {100}-bounded Pt–Cu nanocubes with similar composition and size indicate that the activity of Pt–Cu nanocrystals towards formic acid oxidation is shape-dependent, and is higher than that of Pt nanocubes.
Design of a compact quarter wave coaxial cavity resonator for plasma ignition applications (2011)

Atmospheric and higher pressure RF and microwave plasma sources have numerous applications including material processing and spectroscopy. More recently, advantages in using such discharges for combustion ignition are being investigated. A particularly simple and compact microwave discharge generating device is the quarter wave coaxial cavity resonator (QWCCR). This paper presents a new, compacted design of such a device. A simple approximate analysis of the quality factor, Q, which is a measure of the resonant electromagnetic potential step-up capability is given, and compared to experimentally measured quality factors showing reasonable agreement. Analytic results indicate that the foreshortened folded cavity quality factors are comparable to tapered coaxial cavity designs.
Antenna design for underwater radio communications (2016)

In this paper we assess the influence of the conductivity of the medium on the radiation characteristics and input impedance of a loop antenna designed for underwater communications. The initial study is based on simulation of the antenna characteristics using FEKO electromagnetic (EM) software. Additionally, an equivalent circuit model of the antenna is also obtained and simulation of the input impedance on ADS software shows good agreement with the EM simulator. It is found that the radiation pattern, of the loop antenna changes significantly with the conductivity of the medium, from freshwater to seawater. The loop antennas were built with baluns and tested in freshwater, where the insertion loss between two identical antennas and the radiation pattern of one of them were also measured. The results show good agreement with the simulations.
Sonoluminescence (1991)

Sonoluminescence (SL) is an extraordinary phenomenon in that a standing wave sound field with an energy of 10−12 eV per atom can focus to such an extent that photons are emitted with energies that can be greater than 1 eV. The phenomenon has been known for over 50 years and the long held picture that it is due to acoustic cavitation has been demonstrated beyond a shadow of a doubt by the recent work of Gaitan and Crum [J. Acoust. Soc. Am. Suppl. 1 87, S141 (1990)]. They measured the dynamic radius, light emission, and sound field of a single bubble. Here, their pioneering work is extended to determine the details of the individual photon bursts and it is found that they last less than 2 ns and incude about a million photons. From a more general perspective the issue is raised of: Do cooperative optical processes affect the bursts and what are the limits of amplification that can be achieved via the self-focusing effects which lead to SL? Calculations suggest that our current acousto-optic conversion efficiency of 10−5 can be increased by at least 3 orders of magnitude. [Work supported by the Dept. of Energy, Office of Basic Energy Sci.]
Vasculogenesis (1995)

Induction by fibroblast growth factors of mesoderm during gastrulation leads to blood-forming tissue, including angioblasts and hemopoietic cells, that together constitute the blood islands of the yolk sac. The differentiation of angioblasts from mesoderm and the formation of primitive blood vessels from angioblasts at or near the site of their origin are the two distinct steps during the onset of vascularization that are defined as vasculogenesis. Vascular endothelial growth factor and its high-affinity receptor tyrosine kinase flk-1 represent a paracrine signaling system crucial for the differentiation of endothelial cells and the development of the vascular system. Specified cell adhesion molecules such as VE-cadherin and PECAM-1 (CD-31), and transcription factors such as ets-1, as well as mechanical forces and vascular regression and remodeling are involved in the subsequent events of endothelial cell differentiation, apoptosis, and angiogenesis.
High average-power Yb:YAG end-pumped zig-zag slab laser (2001)

A diode-pumped Yb:YAG laser has been developed with a novel end-pumped zig-zag slab architecture. In cw operation the laser emitted 415 W multimode and 228 W with linear polarization and average M2 beam quality of 1.35.
Mathematical Modelling of Lamellar Aggregation of Dispersed Globular Nanoparticles nC<sub>60</sub> on the Interface Upon Sublimation of Water Molecules from Rapid Frozen Dispersion (2018)

The publication is focused on the problem of nanoparticle aggregation on the sublimation interface between vacuum and rapid frozen liquid dispersion. The main aims are simulation experiments of mathematical modelling of these processes. During lyophilization of rapid frozen liquid dispersion of nanoparticles, a self-organization of nanoparticles occurs. The resulting structure depends on setting the process parameters. According to the current knowledge, they include temperature, vacuum depth, and nanoparticle fraction in the dispersion liquid. On the free sublimation interface, a streamlined flow of dispersion liquid molecules, also referred to as sublimation wind, flows into the vacuum. Lamellar nanoparticle aggregates are formed on the interface surface in this mode, which are gradually torn by the pressure of the sublimation wind. Aggregated materials with very high specific surface area may be formed by these processes. Mathematical modelling of nanoparticle dynamics on two-dimensional sublimation layer is employed to deepen the understanding of basic mechanisms of these aggregation processes. The simulation results are in good agreement with the experimental results of lamellar nanostructure aggregation of bonded globular nanoparticles nC(60). Further refinements based on the simulation experiments will allow active control of the process and quality of aggregated nanostructures.
Learning constitutive equations of physical components with constraints discovery (2018)

We address the problem of learning constitutive equations of acausal physical components in partially known physical systems. The parameters of the constitutive equations satisfy a set of unknown constraints. We propose an iterative procedure for joint parameters and constraints learning and discuss practical aspects of its implementation. The procedure favors exploration during the first iterations. This enables learning a model for the constraints. As the constraints learning advances more weight is given to finding the constitutive equations. We test our method on a demonstrative example in which the model of a nonlinear resistor is learned.
Antigenic conservation of the 15,000-dalton outer membrane lipoprotein PCP of Haemophilus influenzae and biologic activity of anti-PCP antisera (1990)

A gene from Haemophilus influenzae encoding an outer membrane lipoprotein of about 15,000 daltons and which comigrates with the peptidoglycan-associated lipoprotein (PAL) of H. influenzae on sodium dodecyl sulfate-polyacrylamide gel electrophoresis has been previously reported and designated pcp gene, and its product has been designated PCP. in order to obtain specific immunologic probes for the analysis of PCP expression, cellular location, and antigenic conservation in H. influenzae, pcp was fused to the lac polylinker region of plasmid pUC19 and the hybrid gene was expressed in Escherichia coli. PCP purified from these cells was used to generate rabbit and mouse polyclonal antisera and mouse monoclonal antibody against PCP. Western immunoblot analysis with anti-PCP monoclonal antibody demonstrated that PCP is present and antigenically conserved in 30 tested strains of H. influenzae, including 27 clinical nontypeable strains. Polyclonal antiserum against PCP killed 9 of 11 clinical H. influenzae strains in a complement-mediated bactericidal assay, and bactericidal activity was additive with bactericidal activity of antisera against PAL. These results indicate that PCP is a potentially valuable component for a subunit vaccine against nontypeable H. influenzae disease, especially in combination with PAL or other components.
A Tissue Homogenate Method To Prepare Gram-Scale Allium Thiosulfinates and Their Disulfide Conjugates with Cysteine and Glutathione (2013)

The health benefits of Allium vegetables are widely attributed to the enzyme-derived organosulfur compounds called thiosulfinates (TS). However, the lack of a suitable method to prepare TS in good yields has hampered the evaluation of their biological activities. This paper describe a simple enzymatic method using Allium tissue homogenates as a reaction system to prepare gram-scale TS, including those enriched in 1-propenyl groups, which are particularly difficult to obtain. This method is simple, easy to scale up, and requires no column purification step, making it suitable for practical large-scale production of Allium TS. The prepared TS were further utilized to prepare the disulfide conjugates with cysteine and glutathione (CySSR and GSSR, R = methyl, ethyl, propyl, 1-propenyl, and allyl), which are the presumptive metabolites of TS. Among all of the Allium CySSR and GSSR conjugates, the newly prepared glutathione conjugate with 1-propenyl TS, GSSPe, showed the most potent effect to induce quinone reductase (QR, a representative phase II enzyme) in murine hepatoma cells (Hepa 1c1c7) and inhibit nitric oxide (NO) production in lipopolysaccharide (LPS)-stimulated macrophage cells (RAW 264.7).
High Speed Two-Dimensional Protein Separation without Gel by Isoelectric Focusing−Asymmetrical Flow Field Flow Fractionation: Application to Urinary Proteome (2009)

An online multilane channel system for isoelectric focusing and asymmetrical flow field-flow fractionation (IEF-AF4) is utilized for the two-dimensional separation (2D: isoelectric point, pI, and hydrodynamic diameter, d(s)) of a human proteome sample followed by the shotgun proteomic analysis using nanoflow liquid chromatography-electrospray ionization-tandem mass spectrometry (nLC-ESI-MS-MS). IEF-AF4 was recently developed to carry out nongel-based high speed two-dimensional protein separation [ Kim , K. , et al. Anal. Chem. 2009, 81 , 1715 ]. In IEF-AF4, proteins are separated according to pI along an IEF channel located at the head of six AF4 channels, and then the fractionated protein bands are directed to multilane AF4 channels for size-based separation. In this report, the original IEF-AF4 system has been modified to avoid the possible adsorption of proteins onto the membrane wall of IEF segments during isoelectric focusing by isolating the IEF channel segments from the multilane AF4 channels. The performance of the modified IEF-AF4 system was tested with protein standards and was further applied for the 2D fractionation of the human urinary proteome sample under two ampholyte solutions with different pH ranges (pH 3-10 and 3-6). The entire 2D separation was achieved in less than 30 min. The collected protein fractions were digested for peptide analysis using nLC-ESI-MS-MS, resulting in the identification of 245 total urinary proteins, including 110 unique proteins that are not yet reported in literature. Our experiments also showed a higher efficiency in the identification of urine proteins using ampholyte solution in the narrower pH range.
Potent, Selective and Low-Calcemic Inhibitors of CYP24 Hydroxylase:  24-Sulfoximine Analogues of the Hormone 1α,25-Dihydroxyvitamin D<sub>3</sub> (2004)

A dozen 24-sulfoximine analogues of the hormone 1alpha,25-dihydroxyvitamin D(3) were prepared, differing not only at the stereogenic sulfoximine stereocenter but also at the A-ring. Although these sulfoximines were not active transcriptionally and were only very weakly antiproliferative, some of them are powerful hydroxylase enzyme inhibitors. Specifically, 24-(S)-NH phenyl sulfoximine 3a is an extremely potent CYP24 inhibitor (IC(50) = 7.4 nM) having low calcemic activity. In addition, this compound shows high selectivity toward the CYP24 enzyme in comparison to CYP27A1 (IC(50) > 1000 nM) and CYP27B (IC(50) = 554 nM).
RRR: Rapid Ring Recovery Submillisecond Decentralized Recovery for Ethernet Ring (2010)

Ethernet is the indisputable de facto technology for local area networks due to its simplicity, low cost, and wide-scale adoption. In recent times, Ethernet has entered new networking areas, such as Metro Area Network (MAN) and Industrial Area Network (IAN), where specialized protocols dominate the market. In addition to the well known advantages, Ethernet acts as the common platform to integrate multiple protocols. However, Ethernet falls short of the stringent resilience requirements mandated by applications in MEN and IAN, despite progress made by the community on additional standardization. We describe a new approach for swift failure detection and recovery in Ethernet ring topologies called Rapid Ring Recovery (RRR). RRR is based on the novel usage of multiple virtual rings. Our implementation augmenting an off-the-shelf Ethernet switch shows that RRR reconverges after a fault in 294 microseconds while sustaining the loss of only eight large frames at 95 percent traffic load.
Traumatic Brain Injury Biomarkers: From Pipeline to Diagnostic Assay Development (2009)

In recent years, the term proteomics is often mentioned together with biomarker discovery, as proteomic studies have the capability of identifying unique and unobvious protein biomarkers from tissues or biofluids derived from animal models or human clinical samples inflicted with various diseases. Proteomics has yielded hundreds of potential biomarker candidates. However, biomarker discovery is only the beginning of a long road for generating a validated, clinically relevant, and FDA-approved biomarker assay. Many technical, financial, legal, and regulatory hurdles have to be overcome before the components can be commercially produced (1, 2). This chapter outlines in a condensed version the steps to successfully develop clinically acceptable biomarkers, given the marker of choice withstands the rigor of developmental challenges along the road.
Unified ZVS strategy for DAB with triple‐phase‐shift modulation in boost mode (2019)

In this study, the switching mode and working waveform of dual active bridge (DAB) converter under triple phase‐shift modulation scheme is analysed, and an ALL‐ZVS (zero voltage switching) control strategy of all devices for full‐power range with voltage transfer ratio M > 1 is proposed. First, a feasible control domain of ALL‐ZVS is derived by analysing the constraints of the control variables of ZVS for all switching devices under different operating modes. On this basis, an ALL‐ZVS control strategy of current RMS quasi‐optimisation under the condition of M > 1 is proposed with the existing inductor current RMS optimisation control algorithm. It can be concluded that the proposed control strategy not only eliminates the switching loss, but also reduces the conduction loss, greatly improves the efficiency of the DAB converter. Finally, an experimental platform is built, and the experimental results verify the correctness and effectiveness of the proposed control strategy.
Authentication of Swipe Fingerprint Scanners (2017)

Swipe fingerprint scanners (sensors) can be distinguished based on their scanner pattern-a sufficiently unique, persistent, and unalterable intrinsic characteristic even to scanners of the same technology, manufacturer, and model. We propose a method to extract the scanner pattern from a single image acquired by a widely-used capacitive swipe fingerprint scanner and compare it with a similarly extracted pattern from another image acquired by the same or by another scanner. The method is extremely simple and computationally efficient as it based on moving-average filtering, yet it is very accurate and achieves an equal error rate below 0.1% for 27 swipe fingerprint scanners of exactly the same model. We also show the receiver operating characteristic for different decision thresholds of two modes of the method. The method can enhance the security of a biometric system by detecting an attack on the scanner in which an image containing the fingerprint pattern of the legitimate user and acquired by the authentic fingerprint scanner has been replaced by another image that may still contain the fingerprint pattern of the legitimate user but has been acquired by another, unauthentic fingerprint scanner, i.e., for scanner authentication.