gebhart/patrepeval huggingface dataset:
Requirement for BDNF in Activity-Dependent Survival of Cortical Neurons (1994)

Cultured embryonic cortical neurons from rats were used to explore mechanisms of activity-dependent neuronal survival. Cell survival was increased by the activation of voltage-sensitive calcium channels (VSCCs) but not by activation of N-methyl-D-aspartate receptors. These effects correlated with the expression of brain-derived neurotrophic factor (BDNF) induced by these two classes of calcium channels. Antibodies to BDNF (which block intracellular signaling by BDNF, but not by nerve growth factor, NT3, or NT4/5) reduced the survival of cortical neurons and reversed the VSCC-mediated increase in survival. Thus, endogenous BDNF is a trophic factor for cortical neurons whose expression is VSCC-regulated and that functions in the VSCC-dependent survival of these neurons.
Solid-immersion micromirror with enhanced angular deflection for silicon-based planar lightwave circuits (2006)

We report on a MEMS-based on-chip solid-immersion micromirror (SIM), which provides enhanced angular deflection and reduced diffraction loss. The SIM is driven by rotary comb-drive actuators. Maximum mechanical scan angle of 8 degree is achieved
Bimodal spatial distribution of pores in anodically oxidized aluminum thin films (2000)

Though porous anodic aluminum oxide has been the subject of considerable research since the 1950s, little attention has been devoted to the characterization of the self-organization of the pore structures, and fewer of these studies have focused on anodization of thin films. The degree to which these structures self-organize, however, could play a vital role in future applications of porous anodic aluminum oxide. In this study a model is developed to describe pore ordering in thin anodized aluminum films. The model is based on a radial distribution function approach to describe the interpore spacings. Idealized one-dimensional and two-dimensional (2D) radial distribution functions are combined by linear superposition to approximate experimental radial distribution functions. Using these radial distribution functions, an order parameter is developed and an improved definition of pore spacing is constructed. This method confirms that the oxide initially forms with a highly frustrated porous structure and reorganizes toward greater 2D order as the oxide grows into the film.
A deep learning approach to the classification of 3D CAD models (2014)

Model classification is essential to the management and reuse of 3D CAD models. Manual model classification is laborious and error prone. At the same time, the automatic classification methods are scarce due to the intrinsic complexity of 3D CAD models. In this paper, we propose an automatic 3D CAD model classification approach based on deep neural networks. According to prior knowledge of the CAD domain, features are selected and extracted from 3D CAD models first, and then preprocessed as high dimensional input vectors for category recognition. By analogy with the thinking process of engineers, a deep neural network classifier for 3D CAD models is constructed with the aid of deep learning techniques. To obtain an optimal solution, multiple strategies are appropriately chosen and applied in the training phase, which makes our classifier achieve better performance. We demonstrate the efficiency and effectiveness of our approach through experiments on 3D CAD model datasets.
Ultrashort Nacelles for Low Fan Pressure Ratio Propulsors (2014)

As the propulsor fan pressure ratio (FPR) is decreased for improved fuel burn, reduced emissions and noise, the fan diameter grows and innovative nacelle concepts with short inlets are required to reduce their weight and drag. This paper addresses the uncharted inlet and nacelle design space for low-FPR propulsors where fan and nacelle are more closely coupled than in current turbofan engines. The paper presents an integrated fan–nacelle design framework, combining a spline-based inlet design tool with a fast and reliable body-force-based approach for the fan rotor and stator blade rows to capture the inlet–fan and fan–exhaust interactions and flow distortion at the fan face. The new capability enables parametric studies of characteristic inlet and nacelle design parameters with a short turn-around time. The interaction of the rotor with a region of high streamwise Mach number at the fan face is identified as the key mechanism limiting the design of short inlets. The local increase in Mach number is due to flow acceleration along the inlet internal surface coupled with a reduction in effective flow area. For a candidate short-inlet design with length over diameter ratio L/D = 0.19, the streamwise Mach number at the fan face near the shroud increases by up to 0.16 at cruise and by up to 0.36 at off-design conditions relative to a long-inlet propulsor with L/D = 0.5. As a consequence, the rotor locally operates close to choke resulting in fan efficiency penalties of up to 1.6% at cruise and 3.9% at off-design. For inlets with L/D < 0.25, the benefit from reduced nacelle drag is offset by the reduction in fan efficiency, resulting in propulsive efficiency penalties. Based on a parametric inlet study, the recommended inlet L/D is suggested to be between 0.25 and 0.4. The performance of a candidate short inlet with L/D = 0.25 was assessed using full-annulus unsteady Reynolds-averaged Navier–Stokes (RANS) simulations at critical design and off-design operating conditions. The candidate design maintains the propulsive efficiency of the baseline case and fuel burn benefits are conjectured due to reductions in nacelle weight and drag compared to an aircraft powered by the baseline propulsor.
Suppression of Damping-Off Disease in Host Plants by the Rhizoplane Bacterium <i>Lysobacter</i> sp. Strain SB-K88 Is Linked to Plant Colonization and Antibiosis against Soilborne Peronosporomycetes (2005)

We previously demonstrated that xanthobaccin A from the rhizoplane bacterium Lysobacter sp. strain SB-K88 suppresses damping-off disease caused by Pythium sp. in sugar beet. In this study we focused on modes of Lysobacter sp. strain SB-K88 root colonization and antibiosis of the bacterium against Aphanomyces cochlioides, a pathogen of damping-off disease. Scanning electron microscopic analysis of 2-week-old sugar beet seedlings from seeds previously inoculated with SB-K88 revealed dense colonization on the root surfaces and a characteristic perpendicular pattern of Lysobacter colonization possibly generated via development of polar, brush-like fimbriae. In colonized regions a semitransparent film apparently enveloping the root and microcolonies were observed on the root surface. This Lysobacter strain also efficiently colonized the roots of several plants, including spinach, tomato, Arabidopsis thaliana, and Amaranthus gangeticus. Plants grown from both sugar beet and spinach seeds that were previously treated with Lysobacter sp. strain SB-K88 displayed significant resistance to the damping-off disease triggered by A. cochlioides. Interestingly, zoospores of A. cochlioides became immotile within 1 min after exposure to a SB-K88 cell suspension, a cell-free supernatant of SB-K88, or pure xanthobaccin A (MIC, 0.01 microg/ml). In all cases, lysis followed within 30 min in the presence of the inhibiting factor(s). Our data indicate that Lysobacter sp. strain SB-K88 has a direct inhibitory effect on A. cochlioides, suppressing damping-off disease. Furthermore, this inhibitory effect of Lysobacter sp. strain SB-K88 is likely due to a combination of antibiosis and characteristic biofilm formation at the rhizoplane of the host plant.
Reaction of spiro(4H-3,1-benzoxazine-4,4'-piperidin)-2(1H)-one derivatives and related compounds with phosphorus oxychloride. (1986)

Treatment of spiro[4H-3, 1-benzoxazine-4, 4'-piperidin]-2(1H)-one derivatives with POCl3 yielded 1, 2, 3, 4-tetrahydro-2, 9-diazaphenanthrene derivatives through a novel rearrangment. The reaction is suggested to processed via the formation of an isocyanate by dehydrative cleavage of the oxazinone ring with POCl3. It was also found that treatment of 4-(2-methoxycarbonylamino-phenyl)-1, 2, 5, 6-tetrahydropyridine derivatives with trichlorosilane/triethylamine gave the corresponding 10-oxo-1, 2, 3, 4, 9, 10-hexahydro-2, 9-diazaphenanthrene derivatives.
Star test: the theory and its applications (2000)

In this paper, we introduce a hierarchical test set structure called star test, derived from the experimental observation of the fault clustering phenomena. Based on the concept of star test, two applications are studied: one applied to built-in-self-test (BIST); the other to automatic test pattern generation (ATPG). First, a very high quality and low-cost BIST scheme, named STAR-BIST is proposed. Experimental results have demonstrated that a very high fault coverage can be obtained without any modification of the logic under test, no test data to store and very simple BIST hardware which does not depend on the size of the circuit. Second, an efficient test generator, named STAR-ATPG, is developed which speeds up the ATPG performance by a factor of up to five for large industrial circuits.
STRINGHALT IN HORSES: A DISTAL AXONOPATHY (1986)

A detailed investigation of the neuropathology of a horse affected with stringhalt was performed. Qualitative and quantitative light and electron microscopy, and single teased fibre preparations of peripheral nerve demonstrated predominantly axonal degeneration, the stage of which was appropriate for the duration of clinical signs. There was selective involvement of large myelinated nerve fibres. A proximal to distal increase in the severity of pathological changes was present in the peripheral nerves. The long left recurrent laryngeal nerve was the most severely affected, followed in order by its right counterpart, the hindlimb and forelimb nerves. Neurogenic atrophy of muscles innervated by affected peripheral nerves also showed a distally graded increase in severity. No lesions were observed in the central nervous system. It was concluded that this disease should be classified as a distal axonopathy.
Some galE mutants of Salmonella choleraesuis retain virulence (1986)

galE mutants were isolated from three mouse-virulent strains of Salmonella choleraesuis (of group C1, O antigen 6,7) by selection for resistance to 2-deoxygalactose. The galE derivative of strain 381 comprised two components: galactose sensitive, thought to be the original mutant; and galactose resistant, presumably by a second mutation reducing galK or galT function or both. The galactose-sensitive component had an intraperitoneal 50% lethal dose for BALB/c mice of ca. 4 X 10(6) CFU, whereas the galactose-resistant component was about as virulent as its gal+ parent, with a 50% lethal dose of ca. 100 CFU. The galE mutant of strain 110 was somewhat sensitive to galactose, as shown by retardation of growth; its 50% lethal dose, ca. 500 CFU, was not much greater than the ca. 200 CFU value for its parent. The galE mutant of strain 117 showed the same partial sensitivity to galactose as strain 110 galE, but was nonvirulent (50% lethal dose of ca. 10(6) CFU versus ca. 400 CFU for its parent). Growth on galactose-supplemented medium restored the smooth phenotype, as indicated by phage sensitivity to three of the four galE strains, but only partially so for the strain 117 galE mutant. The retention of parental virulence by galE mutants of S. choleraesuis which are galactose resistant or somewhat galactose sensitive contrasts with the greatly reduced virulence of galactose-resistant galE mutants of Salmonella typhimurium and Salmonella typhi; this difference may result from the absence of galactose from the O repeat unit in the lipopolysaccharide of group C1 salmonellae.
Sophorolipids: a yeast-derived glycolipid as greener structure directing agents for self-assembled nanomaterials (2010)

Sophorolipids, fully natural glycolipids, can form in water nanometre-size micelles of various geometries depending on their concentration as shown by small angle neutron scattering experiments. This property allows use of them, for the first time, as structure directing agents in the synthesis of nanostructured silica thin films via the evaporation induced self-assembly (EISA) process.
Extensive Intra-Kingdom Horizontal Gene Transfer Converging on a Fungal Fructose Transporter Gene (2013)

Comparative genomics revealed in the last decade a scenario of rampant horizontal gene transfer (HGT) among prokaryotes, but for fungi a clearly dominant pattern of vertical inheritance still stands, punctuated however by an increasing number of exceptions. In the present work, we studied the phylogenetic distribution and pattern of inheritance of a fungal gene encoding a fructose transporter (FSY1) with unique substrate selectivity. 109 FSY1 homologues were identified in two sub-phyla of the Ascomycota, in a survey that included 241 available fungal genomes. At least 10 independent inter-species instances of horizontal gene transfer (HGT) involving FSY1 were identified, supported by strong phylogenetic evidence and synteny analyses. The acquisition of FSY1 through HGT was sometimes suggestive of xenolog gene displacement, but several cases of pseudoparalogy were also uncovered. Moreover, evidence was found for successive HGT events, possibly including those responsible for transmission of the gene among yeast lineages. These occurrences do not seem to be driven by functional diversification of the Fsy1 proteins because Fsy1 homologues from widely distant lineages, including at least one acquired by HGT, appear to have similar biochemical properties. In summary, retracing the evolutionary path of the FSY1 gene brought to light an unparalleled number of independent HGT events involving a single fungal gene. We propose that the turbulent evolutionary history of the gene may be linked to the unique biochemical properties of the encoded transporter, whose predictable effect on fitness may be highly variable. In general, our results support the most recent views suggesting that inter-species HGT may have contributed much more substantially to shape fungal genomes than heretofore assumed.
Regulation of heterotopic ossification by monocytes in a mouse model of aberrant wound healing (2020)

Heterotopic ossification (HO) is an aberrant regenerative process with ectopic bone induction in response to musculoskeletal trauma, in which mesenchymal stem cells (MSC) differentiate into osteochondrogenic cells instead of myocytes or tenocytes. Despite frequent cases of hospitalized musculoskeletal trauma, the inflammatory responses and cell population dynamics that regulate subsequent wound healing and tissue regeneration are still unclear. Here we examine, using a mouse model of trauma-induced HO, the local microenvironment of the initial post-injury inflammatory response. Single cell transcriptome analyses identify distinct monocyte/macrophage populations at the injury site, with their dynamic changes over time elucidated using trajectory analyses. Mechanistically, transforming growth factor beta-1 (TGFβ1)-producing monocytes/macrophages are associated with HO and aberrant chondrogenic progenitor cell differentiation, while CD47-activating peptides that reduce systemic macrophage TGFβ levels and help ameliorate HO. Our data thus implicate CD47 activation as a therapeutic approach for modulating monocyte/macrophage phenotypes, MSC differentiation and HO formation during wound healing.
Mechanisms of Action of New Antiepileptic Drugs (1989)

Our understanding of how new antiepileptic drugs work mirrors what we know about how currently marketed antiepileptic compounds exert their action--that information is scarce and elusive. The mechanism of action of antiepileptic drugs is nevertheless inextricably linked to epileptogenesis itself, and investigations of several promising new compounds are underway to establish the levels at which these drugs act. Compounds act on synapses and membranes as well as affecting receptors, neurotransmitters, and peptides. The most extensive data are available on drugs that inhibit the action of GABA or its receptors, including new benzodiazepine-like agents and barbituric-acid derivatives. The few drugs that act by inhibiting the effects of excitatory amino acids are reviewed. Finally, the maximal electroshock test is an empirical method to determine the antiepileptic properties of a drug; several agents under development have been effective in this screening technique.
Modeling β-Adrenergic Control of Cardiac Myocyte Contractility in Silico (2003)

The beta-adrenergic signaling pathway regulates cardiac myocyte contractility through a combination of feedforward and feedback mechanisms. We used systems analysis to investigate how the components and topology of this signaling network permit neurohormonal control of excitation-contraction coupling in the rat ventricular myocyte. A kinetic model integrating beta-adrenergic signaling with excitation-contraction coupling was formulated, and each subsystem was validated with independent biochemical and physiological measurements. Model analysis was used to investigate quantitatively the effects of specific molecular perturbations. 3-Fold overexpression of adenylyl cyclase in the model allowed an 85% higher rate of cyclic AMP synthesis than an equivalent overexpression of beta 1-adrenergic receptor, and manipulating the affinity of Gs alpha for adenylyl cyclase was a more potent regulator of cyclic AMP production. The model predicted that less than 40% of adenylyl cyclase molecules may be stimulated under maximal receptor activation, and an experimental protocol is suggested for validating this prediction. The model also predicted that the endogenous heat-stable protein kinase inhibitor may enhance basal cyclic AMP buffering by 68% and increasing the apparent Hill coefficient of protein kinase A activation from 1.0 to 2.0. Finally, phosphorylation of the L-type calcium channel and phospholamban were found sufficient to predict the dominant changes in myocyte contractility, including a 2.6x increase in systolic calcium (inotropy) and a 28% decrease in calcium half-relaxation time (lusitropy). By performing systems analysis, the consequences of molecular perturbations in the beta-adrenergic signaling network may be understood within the context of integrative cellular physiology.
Architecture Optimization Based on Incremental Approach for Airplane Digital Distributed Flight Control System (2008)

Over the years, technical improvements, such as digital computer and digital communication, are drastically changing avionics architecture designs. Airplane performance and business pressures related to cost have been the main drivers to change the flight control systems (FCS) from mechanical to digital fly-by-wire designs. In this context, there exists a great motivation to change current FCS architecture to ldquomorerdquo distributed architectures, better optimized in terms of hardware redundancy for future generation aircraft. Analysis of existing FCS architectures of Airbus and Boeing airplanes, as well as future requirements (eco-efficiency), drive us to introduce a brief overview of an incremental methodology of architectural design process based on progressive requirements injection and distribution of systempsilas functionality.
Horizontal acceleration corrections in airborne gravimetry (1996)

Abstract The stabilized platforms used in marine and airborne gravimeters behave like damped long-period pendulums. When subjected to horizontal accelerations they tilt, resulting in gravimeter reading errors. The amount of tilt depends on the ratio of the period of the horizontal motion to that of the platform and is negligible if this ratio is less than about 0.1 (LaCoste, 1967). This condition can be achieved in straight and level flight using an auto pilot, provided the platform period is set to a sufficiently long period (Brozena and Peters, 1988). Course changes are sometimes unavoidable, however, resulting in lost data (Bell et al., 1991; Brozena, 1984). The aim of this paper is to show that such data loss is unnecessary since the tilt, and hence the gravimeter error, can be accurately modeled from the horizontal accelerations. Moreover the technique will improve data quality whenever long period horizontal accelerations occur. Measuring these accelerations is now straightforward with differential carrier phase GPS.
Field Dependence of Mobilities for Gas-Phase-Protonated Monomers and Proton-Bound Dimers of Ketones by Planar Field Asymmetric Waveform Ion Mobility Spectrometer (PFAIMS) (2002)

The dependence of the mobilities of gas-phase ions on electric fields from 0 to 90 Td at ambient pressure was determined for protonated monomers [(MH+(H2O)n] and proton bound dimers [M2H+(H2O)n] for a homologous series of normal ketones, from acetone to decanone (M=C3H6O to C10H20O). This dependence was measured as the normalized function of mobility alpha (E/N) using a planar field asymmetric waveform ion mobility spectrometer (PFAIMS) and the ions were mass-identified using a PFAIMS drift tube coupled to a tandem mass spectrometer. Methods are described to obtain alpha (E/N) from the measurements of compensation voltage versus amplitude of an asymmetric waveform of any shape. Slopes of alpha for MH+ versus E/N were monotonic from 0 to 90 Td for acetone, butanone, and pentanone. Plots for ketones from hexanone to octanone exhibited plateaus at high fields. Nonanone and decanone showed plots with an inversion of slope above 70 Td. Proton bound dimers for ketones with carbon numbers greater than five exhibited slopes for alpha versus E/N, which decreased continuously with increasing E/N. These findings are the first alpha values for ions from a homologous series under atmosphere pressure and are preliminary to explanations of alpha (E/N) with ion structure.
Polymerizable Biomimetic Vesicles with Controlled Local Presentation of Adhesive Functional DOPA Groups (2010)

Inspired by strong adhesive properties of mussel footprint proteins, which are largely governed by the presence of dihydroxy-phenylalanine (DOPA) amino acid moieties, we present a novel approach for presenting DOPA groups in a very defined way in order to modulate the adhesion between artificial interfaces. To this end, linear peptide amphiphiles are synthesized with attached DOPA functional groups and a polymerizable diacetylenic tail. The obtained amphiphiles can be coassembled with matrix amphiphiles into vesicles, which can be subsequently stabilized through UV-light-induced solid-state polymerization. Depending on the molar ratio of matrix and adhesive amphiphiles, the vesicles self-assemble into spherical, fibrilar, or planar nanostructures. The adhesive properties of the surface-adsorbed vesicles are evaluated by drop casting them onto a planar solid substrate and performing macroscopic shear tests in contact with a similar substrate. The shear forces are investigated as a function of substrate chemistry, vesicle polymerization conditions, vesicle concentration, and number of adhesive DOPA groups in the interface. Substrate adhesion is enhanced by surface-confined vesicles and greatly depends on the presentation of DOPA groups in the adhesive interface, either as a mono- or multilayer conformation. Because the adhesive structures can be transferred onto substrates from low-viscosity aqueous solution, they may serve as interesting nanoscale gluing pads in future applications, where the high viscosity of polymer-based glues renders the controlled formation of nanoscale adhesion pads difficult.