gebhart/patrepeval huggingface dataset:
In vitro properties of phytases from various microbial origins (2002)

Abstract For the evaluation of the effectiveness of phytase preparations as feed additive, in vitro properties like temperature optimum, temperature stability, pH optimum and pH profile or proteolytic stability are of utmost importance. Although at present all commercial phytase preparations authorized as feed additives in the EU are produced by recombinant filamentous fungi and have similar in vitro properties (acidic pH optimum, narrow pH range, low thermostability) the diversity of microbial phytases is great. Microbial sources for phytases span from fungi and yeasts to bacteria. Some of the naturally occurring phytases were identified to have high thermostability and a broad pH range (e.g. Aspergillus fumigatus phytase). The bacterial Bacillus phytases generally differ from other phytases, having a pH optimum from 7.0 to 8.0, being Ca2+ dependent and highly specific for phytate. Thermostability can considerably be increased by protein engineering. A so-called Consensus phytase encoded by a synthetic gene was found to be stable in aqueous solutions at 70 °C and in feed at pelleting temperatures of 80–90 °C. The rate and site of inactivation of feed enzymes in the digestive tract are determined by their susceptibility to proteolytic enzymes. Highest residual activities after incubation in the presence of pepsin or in supernatants of stomach digesta was observed for Escherichia coli and Consensus phytases, while the Bacillus phytase was found to be most resistant to pancreatin. Comparative studies on in vitro properties of enzymes intended for use as feed additives provide valuable information for prediction of in vivo effectiveness.
The Functional Display of Interleukin-2 on Filamentous Phage (1997)

We report the novel display of interleukin-2 (IL-2) and an IL-2 analog, D126, on the surface of filamentous bacteriophage using a phagemid vector system. A synthetic human IL-2 gene and its D126 analog were fused to the carboxyl-terminal domain of the gene III minor phage coat protein. Expression of IL-2 and D126 was verified by their reactivity with an IL-2-specific antibody. Biological response of IL-2 phage on murine CTLL-2 cells was comparable to that of recombinant soluble IL-2, while the D126 phage displayed a reduced biological response similar to that previously measured by soluble D126 protein. Biosensor surface plasmon resonance was employed to verify binding of the IL-2 and D126 phage to the IL-2 alpha beta cc receptor complex. A 41-fold enrichment of IL-2 phage over R408 helper phage was demonstrated in biopanning affinity selection studies employing biotinylated alpha beta cc receptor complex. These biopanning studies are the first reports of affinity selection of IL-2 phage and demonstrate a novel use for the alpha beta cc receptor complex. Together, these studies confirm that the structural integrity of IL-2 and D126 is maintained when they are displayed as a gIIIp fusion protein on phage particles and provide the foundation for further selection studies employing IL-2 analog phage libraries.
Behavior of High-Performance Concrete under Uniaxial and Biaxial Loading (2008)

The American Concrete Institute (ACI) is a leading authority and resource worldwide for the development and distribution of consensus-based standards, technical resources, educational programs, certification programs, and proven expertise for individuals and organizations involved in concrete design, construction, and materials, who share a commitment to pursuing the best use of concrete.
Single-mode fibre fractional wave devices and polarisation controllers (1980)

We describe new single-mode fibre optic devices which are completely equivalent to fractional wave plates of classical optics. They employ a very simple configuration which uses the stress birefringence induced by bending the fibre. Several devices can be combined to control the polarisation inside any single-mode fibre.
Suppression of the SUGAR‐DEPENDENT1 triacylglycerol lipase family during seed development enhances oil yield in oilseed rape (Brassica napus L.) (2012)

Increasing the productivity of oilseed crops is an important challenge for plant breeders and biotechnologists. To date, attempts to increase oil production in seeds via metabolic pathway engineering have focused on boosting synthetic capacity. However, in the tissues of many organisms, it is well established that oil levels are determined by both anabolism and catabolism. Indeed, the oil content of rapeseed (Brassica napus L.) has been reported to decline by approximately 10% in the final stage of development, as the seeds desiccate. Here, we show that RNAi suppression of the SUGAR-DEPENDENT1 triacylglycerol lipase gene family during seed development results in up to an 8% gain in oil yield on either a seed, plant or unit area basis in the greenhouse, with very little adverse impact on seed vigour. Suppression of lipolysis could therefore constitute a new method for enhancing oil yield in oilseed crops.
Long‐term implantation of a system of electrical stimulation of paralyzed laryngeal muscles in dogs (1988)

Electrical stimulation of the posterior cricoarytenoid muscle, synchronized with inspiration, was achieved in dogs utilizing a radio frequency stimulus triggered by a chest wall expansion transducer. This system brings about abduction of the paralyzed vocal cord for the entire duration of inspiration, which allows a normal flow of air through the larynx. The implantable part of that system was tested successfully in chronic experiments (up to 11 months) in dogs with experimental paralysis of the recurrent laryngeal nerve. We feel that the system may be suitable for pacing the paralyzed human larynx.
Review of the available urethral bulking agents (2002)

If durable and safe, these minimally invasive bulking agents may prove useful for all types of stress urinary incontinence. The price of minimal invasiveness may be lower efficacy, but their use does not compromise further therapy, should it be needed.
Clinical Trial Substantiates the Predictive Value of O-6-Methylguanine-DNA Methyltransferase Promoter Methylation in Glioblastoma Patients Treated with Temozolomide (2004)

This prospective clinical trial identifies MGMT-methylation status as an independent predictor for glioblastoma patients treated with a methylating agent. The association of the epigenetic inactivation of the DNA repair gene MGMT with better outcome in this homogenous cohort may have important implications for the design of future trials and supports efforts to deplete MGMT by O-6-benzylguanine, a noncytotoxic substrate of this enzyme.
Protein Sequence Alignment Techniques (1998)

The basic algorithms for alignment of two or more protein sequences are explained. Alternative methods for scoring substitutions and gaps (insertions and deletions) are described, as are global and local alignment methods. Multiple alignment techniques are explained, including methods for profile comparison. A summary is given of programs for the alignment and analysis of protein sequences, either from sequence alone, or from three-dimensional structure.
Mathematical Analysis of Copy Number Variation in a DNA Sample Using Digital PCR on a Nanofluidic Device (2008)

Copy Number Variations (CNVs) of regions of the human genome have been associated with multiple diseases. We present an algorithm which is mathematically sound and computationally efficient to accurately analyze CNV in a DNA sample utilizing a nanofluidic device, known as the digital array. This numerical algorithm is utilized to compute copy number variation and the associated statistical confidence interval and is based on results from probability theory and statistics. We also provide formulas which can be used as close approximations.
Adhesives from Renewable Resources (1989)

The wood products industry has a long and successful history of utilizing adhesives based on renewable resources. Their performance was adequate to see us through World War II and beyond. But the tremendous postwar expansion in the petrochemical industry provided compounds for synthetic resin adhesives so inexpensively, they steadily displaced natural adhesives. When embargo threatened key petrochemicals in 1973, their availability dropped and prices increased abruptly. Industry reacted with an immediate partial return to natural adhesives. As oil's availability improved and prices became more competitive, synthetic resin adhesives again became the industry standard. With over 70% of all wood products now bonded, industry is concerned about future sources of adhesives in the event that oil supplies are again disrupted by world events. There is strong support for research into adhesives based on renewable resources with emphasis on: 1) Phenol, methanol, urea, and resorcinol-acting compounds; 2) copolymeric adhesives involving synthetic resins and natural polymers; 3) new adhesive mechanisms and substrate treatments; 4) greater exterior durability for animal and vegetable protein adhesives.
Three-dimensional Structure of the EphB2 Receptor in Complex with an Antagonistic Peptide Reveals a Novel Mode of Inhibition (2007)

The Eph family of receptor tyrosine kinases has been implicated in tumorigenesis as well as pathological forms of angiogenesis. Understanding how to modulate the interaction of Eph receptors with their ephrin ligands is therefore of critical interest for the development of therapeutics to treat cancer. Previous work identified a set of 12-mer peptides that displayed moderate binding affinity but high selectivity for the EphB2 receptor. The SNEW antagonistic peptide inhibited the interaction of EphB2 with ephrinB2, with an IC50 of approximately 15 microm. To gain a better molecular understanding of how to inhibit Eph/ephrin binding, we determined the crystal structure of the EphB2 receptor in complex with the SNEW peptide to 2.3-A resolution. The peptide binds in the hydrophobic ligand-binding cleft of the EphB2 receptor, thus competing with the ephrin ligand for receptor binding. However, the binding interactions of the SNEW peptide are markedly different from those described for the TNYL-RAW peptide, which binds to the ligand-binding cleft of EphB4, indicating a novel mode of antagonism. Nevertheless, we identified a conserved structural motif present in all known receptor/ligand interfaces, which may serve as a scaffold for the development of therapeutic leads. The EphB2-SNEW complex crystallized as a homodimer, and the residues involved in the dimerization interface are similar to those implicated in mediating tetramerization of EphB2-ephrinB2 complexes. The structure of EphB2 in complex with the SNEW peptide reveals novel binding determinants that could serve as starting points in the development of compounds that modulate Eph receptor/ephrin interactions and biological activities.
Suppression of interleukin 2-dependent human T cell growth in vitro by prostaglandin E (PGE) and their precursor fatty acids. Evidence for a PGE-independent mechanism of inhibition by the fatty acids. (1990)

PGE represent oxygenation products of polyunsaturated essential fatty acids and are important regulators of cell-mediated immune responses. Because oils enriched in such fatty acids reduce inflammation and tissue injury in vivo, we examined the effects of these PGE precursors on IL-2-driven growth of human T lymphocytes. Dihomogamma linoleic acid (DGLA), AA, and their metabolites (PGE1 and PGE2, respectively) strongly inhibited short- and long-term growth of IL-2-dependent T cell cultures; EPA was much less inhibitory and its product, PGE3, failed to suppress IL-2 responses. Short-term pretreatment of the cells with DGLA or AA and removal of the fatty acids before the proliferation assay resulted in a smaller reduction in [3H]TdR incorporation. PGE and fatty acids did not alter the number of high affinity IL-2 binding sites on the T cell cultures but reduced the percentage of cells expressing CD25 and HLA class II molecules. No PGE was detected in supernatants from the fatty acid-treated cultures. Moreover, indomethacin, a cyclooxygenase inhibitor, did not reverse the antiproliferative effects of the fatty acids. Together, these findings indicate that fatty acids can inhibit IL-2-driven T cell growth via a PGE-independent mechanism and might be relevant to inflammatory diseases associated with persistent T cell activation.
A design software tool for conceptual design of wind turbine gearboxes (2010)

The paper reports the development of a design software tool for wind turbine gearboxes. It facilitates the conceptual design of wind turbine gearboxes supporting designs with different combinations of epicyclic and parallel gear stages. Analyses of gear bending strength and pitting resistance are in accordance with the AGMA2001 standard. The calculations of the AGMA geometry factors and are verified in accordance with the AGMA 908 information sheets. A case study of a 2MW and three phase asynchronous generator with a nominal rotational speed around 1600 rpm has been tested to demonstrate the capabilities of the design software tool.
A genetically encoded fluorescent reporter reveals oscillatory phosphorylation by protein kinase C (2003)

Signals transduced by kinases depend on the extent and duration of substrate phosphorylation. We generated genetically encoded fluorescent reporters for PKC activity that reversibly respond to stimuli activating PKC. Specifically, phosphorylation of the reporter expressed in mammalian cells causes changes in fluorescence resonance energy transfer (FRET), allowing real time imaging of phosphorylation resulting from PKC activation. Targeting of the reporter to the plasma membrane, where PKC is activated, reveals oscillatory phosphorylation in HeLa cells in response to histamine. Each oscillation in substrate phosphorylation follows a calcium oscillation with a lag of approximately 10 s. Novel FRET-based reporters for PKC translocation, phosphoinositide bisphosphate conversion to IP3, and diacylglycerol show that in HeLa cells the oscillatory phosphorylations correlate with Ca2+-controlled translocation of conventional PKC to the membrane without oscillations of PLC activity or diacylglycerol. However, in MDCK cells stimulated with ATP, PLC and diacylglycerol fluctuate together with Ca2+ and phosphorylation. Thus, specificity of PKC signaling depends on the local second messenger-controlled equilibrium between kinase and phosphatase activities to result in strict calcium-controlled temporal regulation of substrate phosphorylation.
Polynomial length MDS codes with optimal repair in distributed storage (2011)

An (n, k) maximum distance separable (MDS) code can be used to store data in n storage nodes, such that the system can tolerate the failure of any (n-k) storage nodes. Recently, MDS codes have been constructed which satisfy an additional optimal repair property as follows: the failure of a single storage node can be repaired by downloading a fraction of 1/(n - k) of the data stored in every surviving storage node. In previous constructions satisfying this optimal repair property, the size of the code is polynomial in k for the high-redundancy regime of k/n ≤ 1/2, but the codes have an exponential size (w.r.t. k) for the practically important low-redundancy regime of k/n >; 1/2. In this paper, we construct a class of polynomial size codes in this low redundancy regime.
Strain relaxation kinetics in Si1−xGex/Si heterostructures (1991)

A semiempirical kinetic model is presented which maps out the thermal budget for processing of strained layer devices through epitaxial growth and postgrowth anneals. Misfit strain relaxation in Si1−xGex/Si heterostructures by the injection and propagation of a/2 〈110〉 60°-type misfit dislocations has been studied for a range of geometries and dimensions. Strained layer superlattices, Si1−xGex alloy layers, 0&amp;lt;x&amp;lt;0.3, and alloy layers with unstrained Si capping layers of thickness 0 to 400 nm were grown by molecular-beam epitaxy on (100) Si substrates and subjected to post-growth thermal cycles. Velocity and nucleation rate data from Nomarski interference microscopy of defect-etched surfaces were correlated with electron beam induced current microscopy transmission electron microscopy and x-ray diffraction results to define Arrhenius relationships for misfit dislocation injection rates and propagation velocities. A unified kinetic model for misfit strain relaxation that incorporates both nucleation and propagation is then developed, which is applicable for all heterostructures and thermal cycles in the low dislocation density regime &amp;lt;103 mm−1. Nonuniform strain distribution in graded device heterostructures is considered by defining the effective stress acting on misfit dislocations for an arbitrary geometry. The effective stress was varied from 0 to 750 MPa in Si1−xGex/Si heterostructures by varying both layer dimensions and Ge concentration. Misfit dislocation nucleation rates varied from 10−3 to 103 mm−2 s−1 and misfit extension velocities of 25 nm s−1 to 2 mm s−1 were obtained over the temperature range 450–1000 °C for anneals of duration 5–2000 s. Activation energies, stress exponents, and prefactors in the Arrhenius relations were found to be independent of Ge concentration, effective stress, and heterostructure geometry allowing a comprehensive model to be developed. The onset of strain relaxation during epitaxial growth cycles (the ‘‘apparent critical thickness’’ or metastability limit) characteristic of molecular-beam epitaxy and chemical vapor deposition was measured and correlated with the simulation of misfit dislocation injection and propagation in typical growth sequences. The kinetic model is also used to define the maximum time-temperature envelope, or thermal budget (t, T), for the misfit dislocation-free processing of Si1−xGex/Si heterostructures subjected to post-growth thermal treatme
[Epidemiology of cervical papillomavirus infections. Recent knowledge]. (2001)

GENERAL DATA: There is now considerable evidence that high risk human papillomaviruses (HPV), such as HPV 16, are closely associated with cancer of the cervix. HPVs that are primarily transmitted through sexual contact, are found in over 99% of the cases of invasive cervical cancer. Although most women can be infected during their sexual life, a small minority is at risk for developing cancer. The long latency period between primary infection and cancer emergence suggests that additional factors are involved in the process of tumor development: sexual behavior, immune status, genetic predispositions, nutritional status, tobacco use, socio-economical level. NATURAL HISTORY: HPVs infect epithelial cells of the transformation zone of the cervix. As with other sexually transmitted diseases, the incidence of HPV infection is highest among young women. However, this viral infection is more often than not transient, because most individuals develop an effective type-specific immune response. Approximately 1% of the population has genital warts and 4% of women have cervical precancerous lesions: low grade squamous intraepithelial lesion (LGSIL) or high grade SIL. These last lesions preferentially observed in women aged 35-40 yrs are at high risk of progression towards an invasive cancer. ONCOGENIC POTENTIAL OF HPV: Pre-malignant and malignant cells arise as a result of HPV DNA integration in the host cellular genome, and overexpression of the viral E6 and E7 oncogenes. Cells acquire a proliferative advantage by escaping growth control exerted by p53 and p 105Rb. Both cellular proteins are indeed inactivated respectively by E6 and E7 proteins. Aneuploidy and karyotypic abnormalities are also key events in the tumor progression. A PREVENTABLE DISEASE: Cervical cancer is more than ever a preventable disease. While waiting for clinically applicable vaccination programs, strategies to prevent cervical cancer include 1) improved screening covering the widest possible population and using HPV testing, 2) close management and follow-up of women with precancerous lesions.
Gestion et mondialisation (2009)

L’économie mondiale est en crise. Apparue dans la sphère financière globalisée, cette « crise » se serait propagée à l’économie réelle planétaire, laquelle, pour s’adapter, exige des élites politiques qu’elles interviennent et encouragent la mise en œuvre d’instruments de gestion portant sur l’emploi, l’organisation du travail ou les relations avec les différents marchés (clients et fournisseurs). Une telle vision, dominante, naturalise la production des dynamiques contemporaines. Elle présen...
Discrete-continuous optimization for large-scale structure from motion (2011)

Recent work in structure from motion (SfM) has successfully built 3D models from large unstructured collections of images downloaded from the Internet. Most approaches use incremental algorithms that solve progressively larger bundle adjustment problems. These incremental techniques scale poorly as the number of images grows, and can drift or fall into bad local minima. We present an alternative formulation for SfM based on finding a coarse initial solution using a hybrid discrete-continuous optimization, and then improving that solution using bundle adjustment. The initial optimization step uses a discrete Markov random field (MRF) formulation, coupled with a continuous Levenberg-Marquardt refinement. The formulation naturally incorporates various sources of information about both the cameras and the points, including noisy geotags and vanishing point estimates. We test our method on several large-scale photo collections, including one with measured camera positions, and show that it can produce models that are similar to or better than those produced with incremental bundle adjustment, but more robustly and in a fraction of the time.
Fused Piperidines as a Novel Class of Potent and Orally Available Transient Receptor Potential Melastatin Type 8 (TRPM8) Antagonists (2012)

The transient receptor potential melastatin type 8 (TRPM8) is a nonselective cation channel primarily expressed in a subpopulation of sensory neurons that can be activated by a wide range of stimuli, including menthol, icilin, and cold temperatures (<25 °C). Antagonism of TRPM8 is currently under investigation as a new approach for the treatment of pain. As a result of our screening efforts, we identified tetrahydrothienopyridine 4 as an inhibitor of icilin-induced calcium influx in CHO cells expressing recombinant rat TRPM8. Exploration of the structure-activity relationships of 4 led to the identification of a potent and orally bioavailable TRPM8 antagonist, tetrahydroisoquinoline 87. Compound 87 demonstrated target coverage in vivo after oral administration in a rat pharmacodynamic model measuring the prevention of icilin-induced wet-dog shakes (WDS).
An efficient multi-view rasterization architecture (2006)

TV have been designed and built. However, these displays have received relatively little attention in the context of real-time computer graphics. We present a novel rasterization architecture that rasterizes each triangle to multiple views simultaneously. When determining which tile in which view to rasterize next, we use an efficiency measure that estimates which tile is expected to get the most hits in the texture cache. Once that tile has been rasterized, the efficiency measure is updated, and a new tile and view are selected. Our traversal algorithm provides significant reductions in the amount of texture fetches, and bandwidth gains on the order of a magnitude have been observed. We also present an approximate rasterization algorithm that avoids pixel shader evaluations for a substantial amount (up to 95%) of fragments and still maintains high image quality.
Cigarette Smoke Suppresses Bik To Cause Epithelial Cell Hyperplasia and Mucous Cell Metaplasia (2011)

These studies show that CS suppresses Bik expression to block airway epithelia cell death and thereby increases epithelial cell hyperplasia in chronic bronchitis.