gebhart/patrepeval huggingface dataset:
Numerical Simulation of a Slit Resonator in a Grazing Flow (2006)

It is known experimentally that a grazing flow has significant influence on the performance of a resonant acoustic liner. As yet, detailed understanding of the effect in fluid dynamics or acoustics terms is not available. One principal reason for this is the smallness of the openings of the resonators of present day acoustic liners. The smallness of the holes makes in-depth experimental observation and mapping of the fluid flow field around the opening of a resonator in the presence of a grazing flow extremely difficult. As a result, there is a genuine lack of data leading directly to a lack of understanding. In this study, numerical simulations of the flow field around a slit resonator in the presence of a grazing flow under acoustic forcing are carried out. It is observed that at high sound pressure level, vortices are shed from the corners of the resonator opening. Some of these vortices merge together. Others are absorbed by the wall boundary layer. The simulated results indicate that a strong merged vortex is convected downstream by the grazing flow and persists for a long distance. This suggests possible fluid mechanical interaction between neighboring resonators of an acoustic liner when there is a grazing flow. This possible interaction, as far as is known, has not been included in any theoretical or semi-empirical model of acoustic liners. Detailed formulation of the computational model, as well as computational algorithm, are provided. The computation code is verified by comparing computed results with an exact linear solution and validated by comparing with measurements of a companion experiment. It is shown that the computation code is of high quality and accuracy.
Simple low-drift heating stage for scanning probe microscopes (1999)

A simple low-cost heating stage for scanning probe microscopes has been developed. The goal of this design is to minimize the drift due to thermal expansion of the sample and of the heater itself both in the vertical and the in-plane directions. It is composed of materials with different thermal expansion coefficients. The key point is to adjust the relative length of the different elements in such a way that the sample surface’s position is fixed when temperature changes. It has been proven to drift laterally less than 60 nm per degree and vertically less than 42 nm per degree. It allows one to access temperatures up to 150 °C. This stage can be adapted to most commercial microscopes and does not require modifications of the microscope itself. The design of the heating stage is presented with calibration results providing the good thermal stability of the design.
Suppressive effect of dietary raffinose on T-helper 2 cell-mediated immunity (2002)

The effects of the dietary oligosaccharide raffinose on immune responses, with special reference to its anti-allergic functions, were examined in vivo. First, feeding a diet supplemented with 50 g raffinose/kg to BALB/c mice significantly (P<0.05) increased interleukin (IL) 12 secretion from isolated Peyer's patch (PP) cells in vitro compared with feeding control diet. When isolated PP cells were used as antigen-presenting cells (APC) for CD4+ T-splenocytes isolated from ovalbumin (OVA)-specific T-cell receptor transgenic (Tg) mice in the presence of OVA as antigen, significantly (P<0.05) higher levels of interferon-gamma were observed in the cultures using APC from raffinose-fed mice than those cultures using APC from control mice. Second, the diet containing 50 g raffinose/kg or control diet was fed to OVA Tg mice, and subsequently, OVA was added to each diet to prime T cells in vivo. CD4+ T-cells from the mesenteric lymph nodes of the raffinose-fed mice secreted significantly (P<0.05) higher levels of IL-2 and significantly (P<0.05) lower levels of IL-4 following in vitro antigenic stimulation compared with those of the control mice. These present results suggest that feeding raffinose may suppress differentiation of naïve T-helper (Th) cells into Th2 cells in the mesenteric lymphoid nodes. Last, feeding raffinose suppressed rises of serum immunoglobulin E levels in the Tg mice treated with long-term ingestion of OVA. In conclusion, it is suggested that dietary raffinose suppresses serum immunoglobulin E response through suppression of Th2-type immune response against oral antigen in the lymphoid organs located in or near the intestine.
Winner of the Student Award in the Hospital Intern Category, 10th World Biomaterials Congress, May 17-22, 2016, Montreal QC, Canada: Peptide biomaterials raising adaptive immune responses in wound healing contexts (2016)

Biomaterials used in the context of tissue engineering or wound repair are commonly designed to be "nonimmunogenic." However, previously it has been observed that self-assembled peptide nanofiber materials are noninflammatory despite their immunogenicity, suggesting that they may be appropriate for use in wound-healing contexts. To test this hypothesis, mice were immunized with epitope-containing peptide self-assemblies until they maintained high antibody titers against the material, then gels of the same peptide assemblies were applied within full-thickness dermal wounds. In three different murine dermal-wounding models with different baseline healing rates, even significantly immunogenic peptide assemblies did not delay healing. Conversely, adjuvanted peptide assemblies, while raising similar antibody titers to unadjuvanted assemblies, did delay wound healing. Analysis of the healing wounds indicated that compared to adjuvanted peptide assemblies, the unadjuvanted assemblies exhibited a progression of the dominant T-cell subset from CD4(+) to CD8(+) cells in the wound, and CD4(+) cell populations displayed a more Th2-slanted response. These findings illustrate an example of a significant antibiomaterial adaptive immune response that does not adversely affect wound healing despite ongoing antibody production. This material would thus be considered "immunologically compatible" in this specific context rather than "nonimmunogenic," a designation that is expected to apply to a range of other protein- and peptide-based biomaterials in wound-healing and tissue-engineering applications. © 2016 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 104A: 1853-1862, 2016.
EXPERIMENTAL INVESTIGATION OF THE STRUCTURE OF VORTICES IN SIMPLE CYLINDRICAL VORTEX CHAMBERS (1962)

Abstract : An experimental study of the character of vortices in simple cylindrical vortex chambers completely open at one end is presented. Special attention is given to the problem of the transition from one-celled to two-celled vortex chambers having length-to-diameter ratios in the range 0 < L/D < 5, the character of the flow is primarily dependent on the ratio of a characteristic tangential velocity to a characteristic radial velocity V/U. In addition, it is shown that the Reynolds number based on the radial flow, while a parameter of major importance in laminar vortices, plays but a minor role in turbulent vortex motion. Transition from one-celled to two-celled vortex structure started for all vortex configurations tested (0 < L/D < 5) when V/U exceeded approximately 3.
Applications of Synthetic Gene Networks (2015)

Synthetic gene networks have evolved from simple proof-of-concept circuits to complex therapy-oriented networks over the past 15 years. This advancement has greatly facilitated the expansion of the emerging field of synthetic biology. In this review, we highlight the main applications ofsynthetic gene networks in understanding biological design principles, developing biosensors for diagnosis, producing industrial and biomedical compounds, and treating human diseases. Finally, we outline current challenges and future prospects of synthetic gene networks for advancing practical applications.
The role of water molecules in formation of heterometallic palladium acetate complexes with cerium and neodymium (2011)

The reactions of palladium(II) acetate with neodymium(III) and cerium(III) acetates in acetic acid containing a specified amount of water have been studied. The following homo- and heterometallic complexes have been synthesized and characterized by X-ray diffraction: Nd2(μ-OOCMe)2(μ,η2-OOCMe)2(η2-OOCMe)2(HOOCMe)2(OH2)2 · 4HOOCMe, [Pd(μ-OOCMe)4Ce(OH2)2(μ,η2-OOCMe)]2 · 2HOOCMe · 6H2O, [Pd(μ-OOCMe)4Ce(OH2)2(μ,η2-OOCMe)]2 · 14H2O, [Pd(μ-OOCMe)4M(HOOCMe)2(OH2)2]+ [Pd(μ-OOCMe)4M(μ-OOCMe)4Pd]− · 2MeCOOH · 1.5H2O (M = Nd, Ce), and {[Pd(μ-OOCMe)4Ce(OOCMe)4]2 [Pd4(μ-OOCMe)4]2(μ4-O)8CePd4}(OH)3 · 27H2O. From kinetic and structural data and optical spectra of reaction solutions, the conclusion was drawn that hydrolytic processes play a decisive role in complexation reactions.
A RE‐EXAMINATION OF MUSCLE PROTEIN SOLUBILITY (1995)

ABSTRACT Muscle proteins are conveniently characterized by their solubility properties. Sarcoplasmic proteins are defined as those soluble when muscle is extracted with water or solutions of low ionic strength, i.e., physiological or less. Myofibrillar proteins are generally thought to be soluble at elevated ionic strengths (> 0.3). Close examination of the extractability and solubility properties of these two groups of proteins, indicates that their solubility properties are not as different as is generally believed. With both groups of proteins, distinctions must be made between extractability and solubility. Our research results have revealed that the proteins of eight different white muscles are essentially completely soluble in solutions of physiological ionic strength or less and neutral pH. Six of these muscles were from white fleshed fish, and one each was from a fatty fish and chicken breast muscle. There were differences among the muscles of the various species. In mackerel and chicken breast muscle, it appeared that certain proteins had to be removed before the remaining myofibrillar proteins could be solubilized in water.
Measurement of High-Energy Neutron Spectra with a Bonner Sphere Extension System (2009)

Above 20 MeV the standard spheres of a Bonner sphere spectrometer (BSS) have similar responses, both in shape and sensitivity. The responses of the standard set also exhibit strongly diminishing sensitivities above 20 MeV. In the current work the Monte Carlo N-Particle eXtended (MCNPX) code was used to investigate different design modifications to increase the high-energy neutron response of a BSS. The cost-effective system expands upon the design of an existing, commercially available BSS system by adding concentric shells of copper, tungsten, and lead. These shells are used in various combinations with the existing spheres. The design, referred to as the Bonner sphere extension (BSE), incorporates both passive and active detection techniques including activation foils and the standard 6LiI(Eu) scintillator. Detailed models in MCNPX were used to create fine-group neutron responses from thermal to 1000 MeV. Measurements were performed with the BSE at Los Alamos Neutron Science Center, and the data were unfolded using the MXD-FC33 code and the calculated BSE response matrix. The resulting spectrum demonstrated the BSE system provided improvement in the measurement of the neutron spectra in the energy regions above 20 MeV when compared to the standard Bonner sphere system. The BSE system extends the sensitivity of the system to more than ten decades in energy while maintaining a nearly isotropic angular response.
3D reverse-time migration using the acoustic wave equation: An experience with the SEG/EAGE data set (2003)

Kirchhoff is the most commonly used 3D prestack migration algorithm because of its speed and other economic advantages, but it uses a high-frequency ray approximation to the wave equation and, therefore, has difficulties in imaging complex geologic structures where multipathing occurs (e.g., beneath rugose horizons such as faulted salt domes where traveltime calculations become difficult).
Catalytic Asymmetric Hydroalkenylation of Vinylarenes: Electronic Effects of Substrates and Chiral N‐Heterocyclic Carbene Ligands (2015)

An asymmetric tail-to-tail cross-hydroalkenylation of vinylarenes with terminal olefins was achieved by catalysis with NiH complexes bearing chiral N-heterocyclic carbenes (NHCs). The reaction provides branched gem-disubstituted olefins with high enantioselectivity (up to 94 % ee) and chemoselectivity (cross/homo product ratio: up to 99:1). Electronic effects of the substituents on the vinylarenes and on the N-aryl groups of the NHC ligands, but not a π,π-stacking mechanism, assist the steric effect and influence the outcome of the cross-hydroalkenylation.
Profiling-as-a-Service in Multi-tenant Cloud Computing Environments (2012)

Cloud computing integrates data, applications, users and servers on a vast scale and enables a global optimization of computing resources. However, due to security threats from both outside and inside the cloud, security remains as a significant challenge and obstacle in the wide adoptions of cloud computing paradigms. To enhance the security of networks, applications and data in the cloud, this position paper proposes to develop a profiling-as-a-service architecture to characterize, understand and profile network traffic at multiple layers in the multi-tenant cloud computing environment: network routers, hyper visors, virtual instances and applications. The proposed architecture will not only provide an in-depth understanding on traffic patterns of cloud tenants, but also enhance the security of cloud computing by collaboratively detecting and filtering unwanted traffic towards cloud instances.
Materials Characterization and Growth Mechanisms of ZnO, ZrO2, and HfO2 Deposited by Atomic Layer Deposition (2014)

Gallium Nitride (GaN) is recognized as one of the best candidates for high-power high-frequency metal-oxide-semiconductor field-effect-transistors (MOSFETs). The critical component to enable this technology is the development of a robust oxide with low density of defects and preferential mobility properties that can produce an enhancement mode transistor rather than a depletion mode transistor. Zirconium oxide (ZrO2) and hafnium oxide (HfO2) are considered as two promising oxides for the gate oxide of the GaN MOSFETs. On the other hand, zinc oxide (ZnO) is an alternative wide bandgap semiconductor for GaN. ZnO has some advantages over GaN in optoelectronics due to its large exciton binding energy (~60 meV), and is widely used as the active channel in thin film transistors (TFTs). To control the electrical properties of the deposited thin films, a fundamental understanding of the nucleation and growth mechanisms is essential. In this dissertation, the material characterization and growth mechanisms of atomic layer deposition (ALD) of the three important oxides in semiconductor industry, ZnO, ZrO2, and HfO2, were investigated. The oxides were deposited using thermal and plasma-enhanced ALD on Si(100) substrate at various deposition temperatures. Different analytical techniques, including spectroscopic ellipsometry (SE), X-ray photoelectron spectroscopy (XPS), X-ray diffraction (XRD), atomic force microscopy (AFM), and transmission electron microscopy (TEM) were utilized to analyze the optical, chemical, and morphological characteristics of the oxide thin films. Based on the results, nucleation and growth mechanisms were proposed for thermal and plasma enhanced ALD of ZnO, ZrO2, and HfO2. The role of ALD parameters, as well as –OH reaction sites on the nucleation and growth mechanisms were described. Atomistic growth mechanisms of thermal ALD ZnO, ZrO2, and HfO2 were studied using a density functional theory (DFT) approach. The important role of formation of intermediate structures between surface reaction sites and the precursor molecules were emphasized. The results were found to be consistent with the variation of growth rate of the ALD oxides with the deposition temperature. Finally, it was found that PEALD ZrO2 offered the best properties for the gate oxide of the GaN MOSFETs with the lowest value of density of interface traps.
Thousand Cankers Disease is Widespread in Black Walnut in the Western United States (2011)

Thousand cankers disease of black walnut is caused by aggressive feeding by the walnut twig beetle and subsequent canker development around beetle galleries caused the fungus Geosmithia morbida. The authors We confirmed the presence of G. morbida from symptomatic black walnut or hybrids in California, Colorado, Idaho, New Mexico, Oregon, Utah, and Washington. Thousand cankers disease continues to cause extensive mortality to black walnut over a wide geographic region and is intensifying in the western United States. Accepted for publication 2 June 2011. Published 30 June 2011.
Fetal cholinergic anti-inflammatory pathway and necrotizing enterocolitis: the brain-gut connection begins in utero (2013)

Necrotizing enterocolitis (NEC) is an acute neonatal inflammatory disease that affects the intestine and may result in necrosis, systemic sepsis and multisystem organ failure. NEC affects 5-10% of all infants with birth weight ≤ 1500 g or gestational age less than 30 weeks. Chorioamnionitis (CA) is the main manifestation of pathological inflammation in the fetus and is strong associated with NEC. CA affects 20% of full-term pregnancies and upto 60% of preterm pregnancies and, notably, is often an occult finding. Intrauterine exposure to inflammatory stimuli may switch innate immunity cells such as macrophages to a reactive phenotype ("priming"). Confronted with renewed inflammatory stimuli during labour or postnatally, such sensitized cells can sustain a chronic or exaggerated production of proinflammatory cytokines associated with NEC (two-hit hypothesis). Via the cholinergic anti-inflammatory pathway, a neurally mediated innate anti-inflammatory mechanism, higher levels of vagal activity are associated with lower systemic levels of proinflammatory cytokines. This effect is mediated by the α7 subunit nicotinic acetylcholine receptor (α7nAChR) on macrophages. The gut is the most extensive organ innervated by the vagus nerve; it is also the primary site of innate immunity in the newborn. Here we review the mechanisms of possible neuroimmunological brain-gut interactions involved in the induction and control of antenatal intestinal inflammatory response and priming. We propose a neuroimmunological framework to (1) study the long-term effects of perinatal intestinal response to infection and (2) to uncover new targets for preventive and therapeutic intervention.
Thermodynamics of RNA Folding in a Conserved Ribosomal RNA Domain (1994)

A small, 58 nt domain of the large subunit ribosomal RNA (Escherichia coli sequence 1051 to 1108) is a highly conserved junction of three helices whose secondary structure has been established by phylogenetic comparisons. To detect any contributions of additional tertiary interactions, the thermal denaturation of the rRNA domain was followed by either UV hyperchromicity or calorimetry in buffers containing a wide range of Mg2+ concentrations. Several smaller fragments corresponding to two different hairpin stem-loop structures within the domain were also synthesized and melted for comparison with the larger molecule. A model of the secondary structure unfolding was devised, based on measured enthalpies and melting temperatures of the component hairpins and tabulated parameters of base-pair stacking and loop closure. The model closely simulates the observed melting data when three additional factors are included: two parameters to account for coaxial stackings within a junction of helices, and a set of undefined "tertiary" interactions that unfolds before the secondary structure and is preferentially stabilized by Mg2+. A critical feature of this model is a conserved pair, U1082/A1086, that is within the junction loop and hypothesized to stack with an adjacent helix. The model correctly predicts the effects of disrupting this pair in a U1086 sequence variant. Although the set of "tertiary" interactions contributes a significant fraction of the RNA unfolding enthalpy (delta H approximately 25 kcal/mol, out of 180 kcal/mol total), its overall stability is marginal at 37 degrees C.
Group Ratio Round-Robin: O(1) Proportional Share Scheduling for Uniprocessor and Multiprocessor Systems (2004)

Proportional share resource management provides a flexible and useful abstraction for multiplexing time-shared resources. We present Group Ratio Round-Robin (GR3), the first proportional share scheduler that combines accurate proportional fairness scheduling behavior with O(1) scheduling overhead on both uniprocessor and multiprocessor systems. GR3 uses a novel client grouping strategy to organize clients into groups of similar processor allocations which can be more easily scheduled. Using this grouping strategy, GR3 combines the benefits of low overhead round-robin execution with a novel ratio-based scheduling algorithm. GR3 can provide fairness within a constant factor of the ideal generalized processor sharing model for client weights with a fixed upper bound and preserves its fairness properties on multiprocessor systems. We have implemented GR3 in Linux and measured its performance against other schedulers commonly used in research and practice, including the standard Linux scheduler, Weighted Fair Queueing, Virtual-Time Round-Robin, and Smoothed Round-Robin. Our experimental results demonstrate that GR3 can provide much lower scheduling overhead and much better scheduling accuracy in practice than these other approaches.
Electron diffraction, X-ray powder diffraction and pair-distribution-function analyses to determine the crystal structures of Pigment Yellow 213, C<sub>23</sub>H<sub>21</sub>N<sub>5</sub>O<sub>9</sub> (2009)

The crystal structure of the nanocrystalline alpha phase of Pigment Yellow 213 (P.Y. 213) was solved by a combination of single-crystal electron diffraction and X-ray powder diffraction, despite the poor crystallinity of the material. The molecules form an efficient dense packing, which explains the observed insolubility and weather fastness of the pigment. The pair-distribution function (PDF) of the alpha phase is consistent with the determined crystal structure. The beta phase of P.Y. 213 shows even lower crystal quality, so extracting any structural information directly from the diffraction data is not possible. PDF analysis indicates the beta phase to have a columnar structure with a similar local structure as the alpha phase and a domain size in column direction of approximately 4 nm.