gebhart/patrepeval huggingface dataset:
Plant evolution driven by interactions with symbiotic and pathogenic microbes (2021)

During 450 million years of diversification on land, plants and microbes have evolved together. This is reflected in today's continuum of associations, ranging from parasitism to mutualism. Through phylogenetics, cell biology, and reverse genetics extending beyond flowering plants into bryophytes, scientists have started to unravel the genetic basis and evolutionary trajectories of plant-microbe associations. Protection against pathogens and support of beneficial, symbiotic, microorganisms are sustained by a blend of conserved and clade-specific plant mechanisms evolving at different speeds. We propose that symbiosis consistently emerges from the co-option of protection mechanisms and general cell biology principles. Exploring and harnessing the diversity of molecular mechanisms used in nonflowering plant-microbe interactions may extend the possibilities for engineering symbiosis-competent and pathogen-resilient crops.
Large-eddy simulation of turbulent flow inside a sudden-expansion cylindrical chamber (2002)

A large-eddy simulation (LES) is performed for turbulent flow inside a combustion device. The combustion device is simplified as a cylinder with sudden expansion. To promote turbulent mixing and to accommodate flame stability, a flame holder is attached inside the combustion chamber. Emphasis is placed on the flow details with different geometries of the flame holder. The Smagorinsky model and the Lagrangian dynamic subgrid-scale model are applied and tested. The simulation code is constructed using a general coordinate system based on the physical contravariant velocity components. The calculated Reynolds numbers are 5000 and 50 000 based on the bulk velocity and the diameter of the inlet pipe. The predicted turbulent statistics are evaluated by comparing with the experimental data, which are obtained by laser Doppler velocimetry. The agreement of the LES with the experimental data is shown to be satisfactory.
RESULTS OF SHOULDER ARTHROPLASTY FOR HEAD NECROSIS AFTER FRACTURE OF THE PROXIMAL HUMERUS (2004)

Purpose: Collapse or necrosis of the head of the humerus after fracture of the proximal humerus can be an indication for shoulder arthroplasty. The poor results classically reported have led to a search for factors predictive of the anatomic and functional outcome after arthroplasty for fracture sequelae. Material and methods: Among the 221 Aequalis prostheses implanted for the treatment of sequelae after fracture of the proximal humerus, 137 (62%) developed post-traumatic avascular osteonecrosis of the humeral head with a deformed callus of the tuberosity. Head tilt was in a valgus position in 83 shoulders and in a varus position in 54. Mean age was 61.49 years. The initial fractures were subtuberosity fractures in 20% of the cases, three-fragment fractures in 32%, and cephalobituberosity fractures with four fragments in 48% of the cases.Twenty-five percent of the patients had undergone initial osteosynthesis. The rotator cuff was repaired in 4.5%, and two osteotomies of the less tuberosity and four osteotomies of the greater tuberosity were performed at implantation. Pre- and postoperative clinical and functional outcomes were assessed with the Constant score and a function index composed of eleven usual movements. Results: Mean follow-up was 44 months (24–104), with a mean 42° gain in anterior elevation and a 29° gain in external rotation. The gain in the Constant score was +32 points (mean score 61), and +43% with the weighted score. The four subscores (pain, motion, activity, force) improved two-fold. Analysis of the eleven usual movements demonstrated recovery in 88% of the patients. The subjective satisfaction index was 86%. The mean Constant score improved significantly more after total arthroplasty (67 points) than after humerus prosthesis (55 points). Complications (per- or postoperative mechanical problem, infection, neurological disorder) or the need for revision were unfavourable elements. Discussion: Deformation and deviation of the tuberosities, especially the greater tuberosity, often leads to osteotomy during the implantation procedure. In this series, osteotomies were exceptional and functional outcomes showed that deviated tuberosities could be preserved without having an unfavourable effect on functional prognosis. Much on the contrary, the absence of a tuberosity osteotomy simplified the operative procedure and produced much better functional outcome than observed in earlier studies. The rate of complication for secondary prosthetic implantation is not negligible (15%) and a simplified procedure without osteotomy is a useful criterion. Furthermore, rehabilitation may be started earlier after implantation when it is not retarded by osteotomy bone healing, found to be an unfavourable factor. Conclusion: Implantation of a shoulder prosthesis after collapse or necrosis of the head of the humerus after proximal fracture with varus or valgus impaction has provided good functional outcome without tuberosity osteotomy since the deformation of the tuberosity is generally well tolerated.
Analysis and variability of TGFbeta measurements in cancer patients with skeletal metastases. (2008)

Transforming growth factor beta (TGFbeta) plays an important role in cancer, but accurate measurement of circulating TGFbeta is complicated by the high TGFbeta content of platelets which can release TGFbeta ex vivo. We evaluated the use of citrate-theophylline-adenosine-dipyridamole (CTAD) tubes to reduce preanalytical variation in TGFbeta measurements caused by ex vivo platelet activation. CTAD substantially reduced ex vivo platelet activation relative to traditional plasma collections in normal donors, which correlated with a decrease in measured TGFbeta levels. We show that TGFbeta levels are elevated in the majority of cancer patients with skeletal metastases, and that within-patient variability of these levels is relatively low over several weeks. Patients with elevated TGFbeta could be subdivided into groups with or without evidence of platelet contribution to measured TGFbeta levels. The use of CTAD tubes allows a better determination of a patient's TGFbeta status, and may improve classification of patients with oncologic disease.
Terahertz Emission from Hybrid Perovskites Driven by Ultrafast Charge Separation and Strong Electron–Phonon Coupling (2018)

Unusual photophysical properties of organic-inorganic hybrid perovskites have not only enabled exceptional performance in optoelectronic devices, but also led to debates on the nature of charge carriers in these materials. This study makes the first observation of intense terahertz (THz) emission from the hybrid perovskite methylammonium lead iodide (CH<sub>3</sub> NH<sub>3</sub> PbI<sub>3</sub> ) following photoexcitation, enabling an ultrafast probe of charge separation, hot-carrier transport, and carrier-lattice coupling under 1-sun-equivalent illumination conditions. Using this approach, the initial charge separation/transport in the hybrid perovskites is shown to be driven by diffusion and not by surface fields or intrinsic ferroelectricity. Diffusivities of the hot and band-edge carriers along the surface normal direction are calculated by analyzing the emitted THz transients, with direct implications for hot-carrier device applications. Furthermore, photogenerated carriers are found to drive coherent terahertz-frequency lattice distortions, associated with reorganizations of the lead-iodide octahedra as well as coupled vibrations of the organic and inorganic sublattices. This strong and coherent carrier-lattice coupling is resolved on femtosecond timescales and found to be important both for resonant and far-above-gap photoexcitation. This study indicates that ultrafast lattice distortions play a key role in the initial processes associated with charge transport.
Specific contact resistivity of InGaAs/InP p -isotype heterojunctions (1992)

The specific contact resistivity of lattice matched InGaAs/InP p-isotype heterojunctions has been measured through the use of an interface transmission line model structure. The measured resistance values are comparable to or greater than those of the metal/semiconductor interface and depend heavily on the doping and the abrupt or graded nature of the interface.
High Power Blue-Violet Superluminescent Light Emitting Diodes with InGaN Quantum Wells (2010)

We report on the characteristics of blue superluminescent light emitting diodes based on the emission of InGaN quantum wells. Narrow ridge-waveguide devices realized by standard processing techniques and with extremely low facet reflectivity show single lateral mode emission and continuous-wave output powers &gt;35mW with a typical spectral bandwidth of 4-5 nm. Tuning the composition of the active region, superluminescent light emitting diodes spanning all the spectral range between 410 and 445 nm could be realized. The light output is highly directional and results in a coupling efficiency into single mode fibers &gt;50%. The device temperature behavior is also discussed. (C) 2010 The Japan Society of Applied Physics
Improves Symptoms and Urinary Biomarkers in Refractory Interstitial Cystitis/Bladder Pain Syndrome Patients Randomized to Extracorporeal Shock Wave Therapy Versus Placebo (2020)

Abstract Extracorporeal shock wave therapy (ESWT) has been shown to improve symptoms in patients with interstitial cystitis/bladder pain syndrome (IC/BPS); however, there is a lack of objective evidence. We measured change of urinary biomarker levels in 25 patients with IC/BPS received ESWT or placebo once a week for 4 weeks. Urines were collected from participants at baseline, 4 and 12 weeks post treatment. A representative 41 inflammatory growth factors, cytokines, and chemokines in urine were measured using a MILLIPLEX immunoassay kit. Symptom bother was assessed by O’Leary-Sant symptom scores (OSS), and visual analog scale (VAS) for pain.The ESWT group exhibited a significant reduction in the OSS and VAS compared to the placebo group 4 weeks post-treatment (p &lt; 0.05), and the effects were persistent at 12 weeks. The difference in urinary markers change in ESWT vs placebo was p= 0.054 for IL4, p=0.013 for VEGF, and p= 0.039 for IL9 at 4 weeks. The change of urine biomarker was not significant in other biomarkers or all the measured proteins at 12 weeks. The current data suggest that IL4, IL9, and VEGF mediation may be involved in its pathophysiologic mechanisms and response to LESW treatment.
Development of non-invasive vascular elastography for carotid artery plaque assessment (2006)

Only a minority of patients with carotid artery disease will experience warning symptoms since the majority of strokes are caused by previously asymptomatic lesions. Since morbidity and mortality after acute stroke are unacceptably high, patients should be diagnosed and treated before they develop any symptoms. Recently, a new method was proposed to non- invasively assess vascular elasticity maps (or elastograms). In this context, we propose the non-invasive vascular elastography (NIVE) method to study the mechanical properties of suspected unstable carotid artery plaques. A new implementation of the Lagrangian speckle model estimator that considers local echogenicity variations was used to assess the strain tensor from either cross-sectional or longitudinal ultrasound scans of carotid blood vessels. The feasibility was first assessed in a flow phantom with PolyVinyl Alcohol Cryogel (PVA-C) vessels simulating normal and stenosed carotids. Scanning of normal subjects and of a patient with severe carotid stenoses was also performed to further validate the method. Von Mises elastograms and stress- strain modulus 2D distributions were computed from the estimated axial and shear strains. The in vitro study showed a good reproducibility of the elastograms from which segmentation of regions with different mechanical properties was possible. Elasticity distributions of healthy carotid walls were in agreement with the literature. For the patient with a calcified internal carotid artery, axial and shear strains gave pertinent information about plaque size, tissue composition and mechanical interaction between the tissue biomaterials. symptomatic patients with carotid stenosis higher than 70%. However, asymptomatic patients with carotid stenosis higher than 50%, who can still undergo strokes, are not selected for surgery. Consequently, it would be important to early recognized disease formation in order to guide patients towards suitable treatment. In this context, we propose to predict the mechanical configuration of plaques and surrounding tissues with NIVE. This imaging modality was previously introduced in (3, 4). In this paper, a new implementation of the Lagrangian speckle model estimator (LSME) that considers local echogenicity variations was used to assess 2-D elastograms. The feasibility was first assessed on vascular phantoms, then ultrasound images were analysed in vivo to map the strain and shear distributions of healthy and pathological carotids.
<title>Photonic- bandgap interaction between surface plasma waves and dielectric grating</title> (2002)

Photonic band gap interaction between surface plasmon (SP) and dielectric gratings is calculated by rigorous coupled wave analysis (RCWA). Results from the RCWA show that the reflectance goes down near to 0%, and the diffraction efficiency increases above 50% even though the modulation depth of the grating layer is less than 100nm. If the grating vector is twice of the wave vector of SP, on the other hand, the reflectance surprisingly increases up to 90% even though the resonance condition of the SP is satisfied. This photonic band gap effect at the SP resonance can be completely analyzed by the RCWA, and verified by experiment.
Water Splitting over Graphene-Based Catalysts: Ab Initio Calculations (2014)

We present first-principles modeling of water oxidation over various graphene systems, such as nitrogen-doped graphene; graphene monolayers on iron, nickel, and copper surfaces; and bi- and trilayer graphene on copper surfaces. It is shown that nitrogen-doped graphene and graphene over copper are better for this reaction than those over platinum at temperatures below 100 °C. Bi- and trilayer graphene on copper have catalytic properties similar to those of a monolayer on copper.
Reduction of hepatocarcinogenesis by ursodeoxycholic acid in rats (2002)

Ursodeoxycholic acid (UDCA) is used worldwide for treatment of primary biliary cirrhosis and chronic liver diseases. However, its action on hepatocarcinogenesis remains to be explored. To clarify its effect, in vivo and in vitro experiments were performed. Ninety Fisher 344 rats were fed a standard diet (Group 1, n = 30), a standard diet supplemented with 0.1% UDCA (Group 2, n = 30) and 0.3% UDCA (Group 3, n = 30). The rats were given an i.p. injection of diethylnitrosamine (DEN) weekly for 6 weeks. Fifteen additional rats were fed 0.3% UDCA supplemented diet without DEN treatment (Group 4). The rats were killed at 5, 10 and 18 weeks after the last injection of DEN. The number of liver tumor and percentage of the GST-P-positive hepatocytes were significantly reduced by UDCA treatment. The PCNA-positive cells were decreased by administration of UDCA at 18 weeks. The increased number of apoptotic cells was observed in the GST-P-negative area at 5, 10 and 18 weeks and in the GST-P-positive area at 18 weeks in the UDCA group. Expression of Bax in mitochondria and cytochrome c in cytosol was increased by UDCA treatment. Caspase 3 activity was also increased in the UDCA groups. The addition of UDCA into the culture of Huh7 and Fao hepatocellular carcinoma (HCC) cells induced apoptosis in a dose-dependent manner. The data of the present study suggest that UDCA treatment reduces hepatocarcinogenesis via inducing apoptosis of 'initiated hepatocytes' as well as inhibiting proliferation.
William Graeme Laver. 3 June 1929 — 26 September 2008 (2010)

Abstract A novel influenza virus of swine origin that emerged in Mexico in April 2009 has spread globally in humans and caused the first pandemic of influenza in the twenty-first century. Our options for controlling the pandemic include the use of anti-influenza drugs and vaccines against this novel influenza virus. William Graeme Laver contributed significantly to both of these strategies. The anti-influenza drugs (Relenza and Tamiflu) that target the viral enzyme were designed on the basis of the three-dimensional structure of the neuraminidase from crystals prepared by Graeme from influenza virus grown in chicken embryos. These drugs have been stockpiled in many countries and are the first option for the treatment of infected persons. The second option, and the preferred one for the control of influenza, is vaccination; Graeme Laver's structural studies on the disruption of influenza virus with mild detergent provided one of the first subunit vaccines, which remains the basis of the influenza vaccine currently prepared in Australia. Our knowledge about the origin of pandemic influenza viruses also comes from the pioneering field work of Graeme Laver. His Australian heritage of adventure in the great outdoors led to studies on influenza in wild migratory birds. These studies laid the foundation for the concept that the wild waterfowl of the world are the natural reservoirs of all influenza viruses. Although Graeme Laver's curiosity was to establish the fundamental properties of influenza viruses, his work translated into humanitarian endeavours relevant today in pandemic planning for influenza.
Microphysics of Neutron Star Outer Envelopes in the Periodized, Magnetic Thomas-Fermi Model (2014)

Static and dynamic properties of low density outer envelopes of neutron stars are calculated within the nonlinear magnetic Thomas-Fermi model, assuming degenerate electrons. A novel domain decomposition enables proper description of lattice symmetry and may be seen as a prototype for the general class of problems involving nonlinear charge screening of periodic, quasi-low-dimensionality structures, e.g. liquid crystals. We describe a scalable implementation of the method using Hypre. Phase velocity of long wavelength transverse phonons is found to be a factor of 5-7 larger than in the corresponding Coulomb crystal model, which could have implications for low temperature phonon-mediated thermal conductivity. Other findings include $c'&lt;0$ elastic instabilities for both bcc and fcc lattices, reminiscent of the situation in some light actinides, and suggestive of a symmetry-lowering transition to a tetragonal or orthorhombic lattice.
Selective enzyme impregnation of chips to reduce specific refining energy in alkaline peroxide mechanical pulping (2009)

Abstract Eucalyptus wood chips were impregnated with various blends of fiber modifying enzymes prior to preconditioning refiner chemical-alkaline peroxide mechanical pulp processing. The process includes chemical pretreatment and two stages of refining. The energy consumption was compared at the same Canadian standard freeness level of 350 ml. Some enzyme treatments were found to reduce specific refining energy (SRE) by at least 24%. The enzyme hydrolysis within the cell wall was observed by transmission electron microscopy of impregnated chips with high spatial resolution. The enzyme blends that successfully reduced SRE requirements were found to selectively loosen the bonds between the S1 and S2 layers of the fiber wall. Enzymes which selectively attached the S2 layer did not impart any SRE reduction. All experiments for impregnation and pulp processing were conducted at the Andritz Pilot Plant in Springfield, OH.
An Analysis of Prompt Fission Gas Release from a Cladding Breach (1983)

An analytical model was developed to study the prompt escape of gaseous and volatile fission products present in the fuel-cladding gap of a light water reactor fuel rod following a cladding breach. Key questions include how fast fission gas is released and what mass fraction of the gap gas remains in the failed rod. Analysis shows that only a small mass fraction (∼0.17) of the total gas inventory initially present in the fuel-cladding gap escapes promptly following cladding rupture, regardless of the size of the rupture, when the rod is surrounded by liquid coolant at high pressure (∼6 to 15 MPa). However, during a loss-of-coolant type of accident, where the fuel rod is surrounded mainly by low pressure steam (∼0.1 MPa), a large mass fraction (∼0.95) of the gap gas is found to escape the rod shortly after cladding rupture due to the greater ratio of the initial rod pressure to the coolant pressure.
Towards Using Conversations with Spoken Dialogue Systems in the Automated Assessment of Non-Native Speakers of English (2016)

Diane Litman, Steve Young, Mark Gales, Kate Knill, Karen Ottewell, Rogier van Dalen, David Vandyke. Proceedings of the 17th Annual Meeting of the Special Interest Group on Discourse and Dialogue. 2016.
Demonstration of spin injection in a CW VECSEL at RT with a dynamic and accurate control of its polarization state (2017)

International audience
Influence of Grain Size on Yield Stress at Moderate Temperatures in Ferrite-Pearlite Steel (1987)

The influence of grain size on the yield strength at moderate temperature in ferrite-pearlite steels was studied with paying attention to the ky value in the Petch equation.The lower yield stress of a ferrite-pearlite steel has been considered to depend on the grain size, and is estimated by the Petch equation.The ky value in the Petch equation is considered as the value which ralates with the dislocation mobility and the Pierce-force.The ky value is reported to be constant as 2.2kgf/mm2/mm-1/2 below the room temperature.On the other hand, the investigation on ky above the room temperature has not been reported.The authors have verified that the ky value decreased with the increase in temperature above the room temperature.The temperature dependence of ky is clasified to four ranges between 25°C and 550°C.The dependence can be explained by the decrease in pinning force of dislocations by carbon and nitrogen, the active multification of dislocations, and I.S.(Interstitial-Substitutional) effect.The ky value becomes negative, when the grain boundary sliding occurs because of the creep phenomenon under the lower strain rate at relatively high temperatures.The ky value can not become negative without the creep phenomenon, but the ky value approaches to zero.
H~~ control design for a stationary fuel cell power plant (2006)

Control of fuel cell power plants is very challenging due to the transient nature of the loads and the preference towards simpler, integrated system design necessitated by cost reduction. We study here, the problem of coordinating the fuel and air flows into the fuel processor of a stationary PEMFC power plant based on the load requirement while ensuring proper regulation of the CPO (catalytic partial oxidation) reactor temperature and protecting the cell stack from hydrogen starvation. A linear model of the relevant dynamics is obtained from a nonlinear system level dynamic model. Model reduction is performed to obtain a linear model of tractable size. The open loop plant behavior is analyzed using relative gain array (RGA) and it is shown that loop interactions are significant away from DC. A multivariable Hinfin controller has been designed to optimize tracking and disturbance rejection performance. It is shown by simulations that the resulting controller adequately deals with loop interactions and improves transient performance. The order of the Hinfin controller is reduced without significant degradation in performance using controller order reduction methods