gebhart/patrepeval huggingface dataset:
Immersion Vaccination of Sockeye Salmon (<i>Oncorhynchus nerka</i>) with Two Pathogenic Strains of <i>Vibrio anguillarum</i> (1979)

Sockeye salmon (Oncorhynchus nerka) were immersion-vaccinated in suspensions containing 5 × 10 7 , 5 × 10 6 , 5 × 10 5 , or 5 × 10 4 bacteria/mL of bivalent or monovalent, formalin-killed Vibrio anguillarum, Types I and II. The fish were split into two lots and held for 54 d. At that time one lot was challenged with living, virulent V. anguillarum, Type I, and one with living, virulent V. anguillarum, Type II. Immunization with bivalent bacterin effectively protected the fish from vibriosis, but monovalent vaccine was effective only against the homologous challenge. Immunization with the highest concentration of Type I monovalent bacterin resulted in 0% Type I and 58% Type II challenge mortality. Immunization with the highest concentration of Type II monovalent bacterin resulted in 41% Type I and 0% Type II challenge mortality. Immunization with the highest concentration of bivalent Type I/Type II bacterin resulted in 2% mortality in both challenges. Protective bacterins were effective at concentrations down to 5 × 10 5 bacteria/mL. Key words: immersion vaccination, bivalent vaccines, Vibrio anguillarum, vibriosis
Widespread distribution of prophage-encoded virulence factors in marine Vibrio communities (2018)

Prophages are known to encode important virulence factors in the human pathogen Vibrio cholerae. However, little is known about the occurrence and composition of prophage-encoded traits in environmental vibrios. A database of 5,674 prophage-like elements constructed from 1,874 Vibrio genome sequences, covering sixty-four species, revealed that prophage-like elements encoding possible properties such as virulence and antibiotic resistance are widely distributed among environmental vibrios, including strains classified as non-pathogenic. Moreover, we found that 45% of Vibrio species harbored a complete prophage-like element belonging to the Inoviridae family, which encode the zonula occludens toxin (Zot) previously described in the V. cholerae. Interestingly, these zot-encoding prophages were found in a variety of Vibrio strains covering both clinical and marine isolates, including strains from deep sea hydrothermal vents and deep subseafloor sediments. In addition, the observation that a spacer from the CRISPR locus in the marine fish pathogen V. anguillarum strain PF7 had 95% sequence identity with a zot gene from the Inoviridae prophage found in V. anguillarum strain PF4, suggests acquired resistance to inoviruses in this species. Altogether, our results contribute to the understanding of the role of prophages as drivers of evolution and virulence in the marine Vibrio bacteria.
Combining free energy calculations with tailored enzyme activity assays to elucidate substrate binding of a phospho-lysine phosphatase (2020)

Studying enzymes that are involved in the regulation of dynamic post-translational modifications (PTMs) is of key importance in proteomics research. Such investigations can be particularly challenging when the modification itself is intrinsically labile. In this article, we elucidate the enzymatic activity of <i>Phospholysine Phosphohistidine Inorganic Pyrophosphate Phosphatase</i> (LHPP) towards different <i>O</i>- and <i>N</i>-phosphorylated peptides by a combined experimental and computational approach. LHPP has been previously described to hydrolyze the phosphoramidate bonds in different small molecule substrates, including phosphorylated lysine (pLys). Taking the instability of the phosphoramidate bond into account, we conducted a carefully adjusted enzymatic assay with various pLys pentapeptides to confirm enzymatic phosphatase activity with LHPP. Molecular docking was employed to explore possible binding poses of the substrates in complex with the enzyme. Molecular dynamics based free energy calculations, which are unique in their accuracy and solid theoretical basis, were further applied to predict relative binding affinity of different substrates. Comparison of simulations with experiments clearly suggested a distinct binding motif of pLys peptides as well as a very narrow promiscuity of LHPP. We believe this integrated approach can be widely adopted to study the structure and interaction of poorly characterized enzyme-substrate complexes, in particular with synthetically challenging or labile substrates.
Methodologies for sub-1nm EOT TDDB evaluation (2011)

Measuring and understanding TDDB reliability in sub-1nm EOT dielectrics is both a practical and scientific challenge. We present three different methods for the experimental determination of the SBD and wearout parameters needed to construct an all-in-one TDDB reliability prediction consisting of a SBD-free region, a leakage current-dominated region and a HBD-limited region. We demonstrate these methods on several sub-1nm EOT high-k/metal gate nMOS and pMOS devices and evaluate their advantage and disadvantages. We also discuss the validity and interpretation of the SBD/wearout model, confronting it with experiments that demonstrate how SBD paths can be annealed by reversing the stress polarity.
Leguminous Cover Crop Astragalus sinicus Enhances Grain Yields and Nitrogen Use Efficiency through Increased Tillering in an Intensive Double-Cropping Rice System in Southern China (2019)

Chinese milk vetch (Astragalus sinicus L., vetch), a leguminous winter cover crop, has been widely adopted by farmers in southern China to boost yield of the succeeding rice crop. However, the effects of vetch on rice grain yield and nitrogen (N) use efficiency have not yet been well studied in the intensive double-cropped rice cropping systems. To fill this gap, we conducted a three-year field experiment to evaluate the impacts of the vetch crop on yields and N use efficiency in the subsequent early and late rice seasons. With moderate N input (100 kg N ha−1 for each rice crop), vetch cover significantly increased grain yields by 7.3–13.4% for early rice, by 8.2–10.4% for late rice, and by 8.6–11.5% for total annual rice production when compared with winter fallow. When rice crops received an N input of 200 kg N ha−1, vetch cover increased grain yields by 5.9–18.4% for early rice, by 3.8–10.1% for late rice, and by 6.2–11.3% for annual rice production. Moreover, comparable grain yields (11.9 vs. 12.0 Mg ha−1 for annual rice production) were observed between vetch cover with moderate N and fallow with added N fertilizer. Yield components analysis indicated that the increased tillering number was the main factor for the enhanced grain yields by vetch cover. Vetch cover with moderate and higher N input resulted in higher agronomic N use efficiency and applied N recovery efficiency compared with the fallow treatments. Here, our results showed that vetch as a winter cover crop can be combined with reduced N fertilizer input while maintaining high grain yields, thus gaining a more sustainable rice production system.
Mobile Face Capture for Virtual Face Videos (2005)

Minimally obtrusive face capture is essential for applications in tele-conferencing, collaborative work, and mobile applications. Acquiring and coding video for such applications is a challenging problem, particularly for a mobile user. A pilot head-mounted display system (HMD) is shown that captures two side views of the face and generates in real-time a quality frontal video of the wearer. The face is captured with little obstruction of the users field of view. The frontal views are generated by warping and blending the side views after a calibration step. In tests of a bench prototype, the generated virtual videos compared well with real video based on both objective and qualitative criteria. With success of the pilot work, we are continuing development of the mobile HMD system.
Design of a magnetron sputter source with soft x-ray monitoring capabilities (1996)

First Page
Tumor Inhibition by Metallocene Dihalides of Early Transition Metals (1983)

Metallocene dihalides, (η5-C5H5)2MX2, represent the first organometallic antitumor agents. Their antitumor activity has been established in vitro and in vivo, e.g. against the Ehrlich ascites tumor, the lymphoid leukemia L1210, or the lymphocytic leukemia P388. Considering the structure-activity relation three statements can be made: (i) There exists a strong dependence of the cytostatic activity of the metallocene dichlorides (C5H5)2MCl2 upon the central metal atom M. (ii) Within the titanocene dihalide system (C5H5)2TiX2 the Cl ligands can be replaced by other halide or pseudohalide ligands without reduction of the tumor-inhibiting potency, (iii) Chemical modification of the cyclopentadienyl rings, e.g. mono- or 1,1′-disubstitution with organic residues, leads to a diminution of the cytostatic activity in dependence on the degree of substitution. With regard to the mechanism of action of the metallocene dihalides, precursor incorporation studies indicate an attack within the nucleic acid metabolism. This is confirmed by cytokinetic and by microanalytical (electron energy loss-spectroscopic) investigations as well as by the light-microscopic and ultrastructural alteration patterns of treated tumor cells.
Introduction to Structural Mechanics (2015)

Foreign visitors discovering a new country usually start by looking at a map of the place; they identify its regions and their characteristics; they try to acquire a mental chart of the new country. Naturally, they have to choose a city or cities in which they are going to spend long stays. Only in those specific places, the visitors will try to learn about the specifics: street names, places of interests, public transportation network, convenience stores, and so on. In this chapter, a general map of the structural mechanics (the “country” in which the reader of this book is going to “reside”) is first presented. Next, the theory of frames (the “city” that the reader of the book is going to know very well) is placed in this general context. After reading the chapter, the reader will slowly improve his/her knowledge of the specific topic until becoming an expert in the theme. It is fair to say that the theory of frames is equivalent to a Rio de Janeiro in Brazil or a Paris in France or a Saint Petersburg in Russia.
Task dependence, veridicality, and preattentive vision: taking advantage of perceptually rich computer environments (1992)

This paper examines the mapping of data onto perceptual dimensions to create a visualization. The choice of perceptual variables depends critically on the goals of the visualization, and this task-dependency has implications for (1) the veridicality of the representation, (2) the mapping of data onto 'preattentive' features, and (3) the use of multiple senses to represent the data.
An Application of a Gradient Theory With Dissipative Boundary Conditions to Fully Developed Turbulent Flows (2006)

The paper presents a complete gradient theory of grade two, including new dissipative boundary conditions based on an axiomatic conception of a nonlocal continuum theory for materials of grade n. The total stress tensor of rank two in the equation of linear momentum contains two higher stress tensors of rank two and three. In the case of isotropic materials, both the tensors of rank two and three are tensor valued functions of the second order strain rate tensor and its first gradient. So the vector valued differential equation of motion is of order four, where the necessary dissipative boundary conditions are generated by using porosity tensors. An application to hydrodynamic turbulence by a linear theory is shown, whereby fully developed steady turbulent channel flows with fixed walls and one moving wall are also examined. The velocity distribution parameters are identified by a numerical optimization algorithm, using experimental data of velocity profiles of channel flow with fixed walls from the literature. These profiles were compared with others given in the literature. With these derived parameters, the predicted velocity gradient of a channel flow agrees well with data from the literature. In addition all simulations were successfully carried out using the finite difference method.
Mycoplasmas. Molecular Biology, Pathogenicity and strategies for control (2005)

International audience
Vitreous Bi–Se Layers as Near-Infrared Photodetectors (1968)

The infrared photodetecting properties of new vitreous Bi–Se films are described. Such films are prepared by coevaporation and vapor quenching. A room-temperature D* value of 2×1011 cm/W·sec1/2 was measured at the peak sensitivity wavelength (∼1 μ) for an optimum composition film. Response times range between 0.3 and 3 msec. In addition, measurements were made of D* as a function of sample composition, incident photon flux, and temperature.
Deposition of Coatings from Live Yeast Cells and Large Particles by “Convective-Sedimentation” Assembly (2009)

Convective assembly at high volume fraction was used for the rapid deposition of uniform, close-packed coatings of Saccharomyces cerevisiae yeast cells onto glass slides. A computational model was developed to calculate the thickness profiles of such coatings for different set of conditions. Both the experiments and the numerical simulations demonstrated that the deposition process is strongly affected by the presence of sedimentation. The deposition device was inclined to increase the uniformity of the coatings by causing the cells to sediment toward the three-phase contact line. In accordance with the simulation, the experiments showed that both increasing the angle of the device and decreasing the angle between the slides increased the uniformity of the deposited coatings. Finally, the "convective-sedimentation" assembly method was used to deposit mixed layers of live cells and large latex particles as an example of immobilized biologically active composite coatings.
Computational study of effect of transient fluid force on composite structures submerged in water (2014)

This study investigated the effect of the initial transient hydrodynamic loading on dynamic responses of composite structures which move under water from the rest condition to a steady-state velocity for a given time duration with different acceleration profiles. Numerical analyses were conducted including the fluid-structure interaction. The computational model was validated against an experimental data, and various cases were examined numerically. The cases include various transient velocities of the structure, fluid boundary conditions, structural geometric configurations and material properties. The results showed that the peak fluid pressure and the resultant stresses in the composite structures are dependent on most of those parameters significantly. The maximum stresses under transient hydrodynamic loading could be an order of magnitude larger than those stresses under the final steady-state loading. A lighter composite structure experienced greater stresses and strains while the fluid pressure did not have any noticeable change under the same flow condition.
Persistence of insecticidal activities of crude essential oils of three aromatic plants towards four major stored product insect pests (2007)

Essential oils of aromatic plants with insecticidal properties are more and more considered as alternative insecticides to protect stored products. Many banned insecticides have high persistence which allow them to occur at several levels of trophic chains. The aim of the present work is to analyse the persistence of insecticidal activity of crude essential oil of three most used local aromatic plants : Annona senegalensis Pers. (Annonaceae), Hyptis spicigera L. (Lamiaceae) and Lippia rugosa L. (Verbenaceae) towards the four majors stored product insect pests: Sitophilus zeamais Motsch., Sitophilus oryzae L., Callosobruchus maculatus Fab. and Tribolium castaneum Herbst. This research revealed that H. spicigera essential oil was the most active towards S. oryzae with a LD50 = 20.18ppm. T. castaneum was the less sensitive insect to the three essential oils tested. During a period of 24 hours L. rugosa essential oil was the most persistent, showing mortalities for S. zeamais of 80%, S. oryzae more than 60%, C. maculatus 100% and T. castaneum_50%. The two other oils tested were not as persistent as L. rugosa. This important persistence of the essential oil of L. rugosa could be explained by its high content of oxygenated compounds compared to that of the other oils. This most interesting essential oil is therefore a suitable one for popularisation in strategies of pest management in storage.
Alterations of hippocampal postsynaptic densities following transient ischemia (2000)

A transient interruption in cerebral blood flow can lead to delayed neuronal death in certain vulnerable cell populations several days after blood flow is restored. Among the most vulnerable cell populations in the forebrain are hippocampal CA1 pyramidal neurons, which die between 48-72 h after the ischemic insult. Neurons in the dentate gyrus and area CA3 are relatively resistant, and will recover from the same insult. Uncovering the factors that render some neuronal populations vulnerable to transient ischemia is key to understanding mechanisms leading to cell death and to developing therapeutic interventions. By applying selective staining and three-dimensional (3D) imaging with electron tomography, we uncovered dramatic structural modifications in postsynaptic densities in the postischemic brain. Postsynaptic densities in the postischemic brain appeared both thicker and less condensed than those from sham-operated controls. Although the class of synapse could not be determined with the methods used, most are likely to be glutamatergic synapses onto dendritic spines, because the majority of synapses in the region examined belong to this class. Further analysis using electron tomography to examine the 3D structure of postsynaptic densities revealed degenerative changes, as evidenced by an overall loosening of the normally compact structure. Synaptic modifications were particularly severe and persistent in hippocampal area CA1 compared to the dentate gyrus. These structural modifications correlate well with biochemical and physiological studies indicating that alterations in synaptic transmission occur in the postischemic brain. The combination of selective staining and 3D reconstruction provides a valuable tool for revealing aspects of synaptic morphology not apparent from standard electron microscopic evaluation.
Control mechanisms in blood fluidity: role of adenosine triphosphate (1963)

A possible role for cellular energy metabolism in the control of the blood clotting mechanism has been shown. High-energy phosphate was found to strongly inhibit the recalcification time of plasma prepared with siliconized or glass surfaces. The nucleotide, adenosine triphosphate, in crystalline form and chromatographically pure, will inhibit or completely prevent coagulation in vitro. Reactivity is based primarily on the high-energy phosphate linkage and secondarily upon the nucleoside, adenosine. The principal site of action for ATP is on an unidentified precursor of thromboplastin. Available evidence indicates an important role for energy metabolism in the cellular mechanisms which effect a control over thromboplastin generation and its possible thrombotic and arteriosclerotic sequelae. cellular control mechanisms; blood fluidity; thrombosis arteriosclerosis; aging Submitted on July 1, 1963
Raloxifene-stimulated experimental breast cancer with the paradoxical actions of estrogen to promote or prevent tumor growth: A unifying concept in anti-hormone resistance (2010)

We have previously demonstrated that prolonged treatments with raloxifene (RAL) in vitro will result in phase II RAL resistance and RAL-induced tumor growth. Clinical interest prompted us to re-examine RAL resistance in vivo, particularly the effects of long-term treatments (a decade or more) on the evolution of RAL resistance. In this study, we have addressed the question of this being a reproducible phenomenon in wild-type estrogen receptor (ER)-positive human breast cell line MCF-7. MCF-7 cells cultured under estrogen-deprived conditions in the presence of 1 microM RAL for more than a year develop RAL resistance resulting in an independent cell line, MCF7-RAL. The MCF7-RAL cells grow in response to both estradiol E2 and RAL. Fulvestrant (FUL) blocks RAL and E2-mediated growth. Transplantation of MCF7-RAL cells into athymic ovariectomized mice and treatment with physiologic doses of E2 causes early E2-stimulated tumor growth. In contrast, continuous treatment of implanted animals with daily oral RAL (1.5 mg daily) causes growth of small tumors within 15 weeks. Continuous re-transplantation of the tumors growing in RAL-treated mice indicated that RAL stimulated tumor growth. Tumors in the untreated mice did not grow. Bi-transplantation of MCF7-E2 and MCF7-RAL tumors into the opposing mammary fat pads of the same ovariectomized animal demonstrated that MCF7-E2 grew with E2 stimulation and not with RAL. Conversely, MCF7-RAL tumors grew with RAL and not E2, a characteristic of phase II resistance. Established phase II resistance of MCF7-RAL tumors was confirmed following up to 7 years of serial transplantation in RAL-treated athymic mice. The ERalpha was retained in these tumors. The cyclical nature of RAL resistance was confirmed and extended during a 2-year evolution of the resistant phases of the MCF7-RAL tumors. The MCF7-RAL tumors that initially were inhibited by E2 grew in the presence of E2 and subsequently grew with either RAL or E2. RAL remained the major grow stimulus and RAL enhanced E2-stimulated growth. Subsequent transplantation of E2 stimulated tumors and evaluations of the actions of RAL, demonstrated robust E2-stimulated growth that was blocked by RAL. These are the characteristics of the anti-estrogenic actions of RAL on E2-stimulated breast cancer growth with a minor component of phase I RAL resistance. Continuous transplantation of the phase I RAL-stimulated tumors for >8 months causes reversion to phase II resistance. These data and literature reports of the cyclical nature of anti-androgen/androgen responsiveness of prostate cancer growth, illustrate the generality of the evolution of anti-hormonal resistance in sex steroid-sensitive target tissues.
Numerical Simulation and Analysis of Manipulated Transitional Flow over a Fence (1996)

A direct numerical simulation of flow over a fence was performed for a Reynoldsnumber of 250 (based on fence height and maximum inflow velocity). The free shear layer created at the sharp edge of the fence undergoes transition to turbulence before reattaching on the bottom plate behind the flow obstacle. This flow has been manipulated with ten stationary or oscillating wall jets located on a cross wind line before the separation in front of the fence. A 50 % reduction in the mean recirculating length (behind the fence) could be observed for the case with oscillating vertical wall jets (periodical blowing/suction). The disturbance frequency was selected to be close to the frequency of the KelvinHelmholtz instability mode. Eigenmode-decompositions of the flow fields showed that in the most successful manipulation with oscillating jets, a pair of two-dimensional spatial modes, together with the corresponding temporal modes (oscillating at the forcing frequency), are responsible for an accelerated increase of the vorticity thickness in the free shear layer and for the accelerated transition.