gebhart/patrepeval huggingface dataset:
Identification and characterization of a functional, alternatively spliced Toll‐like receptor 7 (TLR7) and genomic disruption of TLR8 in chickens (2005)

Based upon the recognition of antiviral compounds and single stranded viral RNA the Toll-like receptors TLR7 and TLR8 are suggested to play a significant role in initiating antiviral immune responses. Here we report the molecular characterization of the chicken TLR7/8 loci which revealed an intact TLR7 gene and fragments of a TLR8-like gene with a 6-kilobase insertion containing chicken repeat 1 (CR1) retroviral-like insertion elements. The chicken TLR7 gene encodes a 1047-amino-acid protein with 62% identity to human TLR7 and a conserved pattern of predicted leucine-rich repeats. Highest levels of chicken TLR7 mRNA were detected in immune-related tissues and cells, especially the spleen, caecal, tonsil and splenic B cells. Alternative spliced forms of TLR7 mRNA were identified in chicken, mouse and human and expressed in similar tissues and cell types to the major form of chicken TLR7. The chicken TLR7+ HD11 cell line and fresh splenocytes produced elevated levels of interleukin-1beta (IL-1beta) mRNA after exposure to the agonists R848 and loxoribine. Interestingly, none of the TLR7 agonists stimulated increased type I interferon (IFN) mRNA whereas poly(I:C) (a TLR3 agonist) up-regulated both chicken IFN-alpha and chicken IFN-beta mRNA. In contrast, TLR7 agonists, particularly R848 and poly(U) stimulated up-regulation of chicken IL-1beta, and chicken IL-8 mRNAs more effectively than poly(I:C). Stimulation of chicken TLR7 with R848 was chloroquine sensitive, suggesting signalling within an endosomal compartment, as for mammalian TLR7. The deletion of TLR8 in galliforms, accompanied with the differential response after exposure to TLR7 agonists, offers insight into the evolution of vertebrate TLR function.
A performance, semantic and service quality-enhanced distributed search engine for improving geospatial resource discovery (2012)

Geospatial resource discovery is a critical step for developing geographic science applications. With the increasing number of geospatial resources available online, many Spatial Data Infrastructure (SDI) components (e.g. catalogues and portals) have been developed to help manage and discover geospatial resources. However, efficient and accurate geospatial resource discovery is still a big challenge because of the heterogeneity and complexity of decentralized network environments and interdisciplinary semantics. In this article, we report a search engine framework for efficient geospatial resource discovery, which reduces integration costs by leveraging existing Geospatial Cyberinfrastructure (GCI) components. Specifically, (1) the framework provides integration capability and flexibility by adopting the brokering approach, implementing a ‘plug-in’-based framework for metadata processing and proposing a dynamically configurable search workflow; (2) the asynchronous messaging and batch processing-based metadata record retrieval mode enhances the search performance and user interactivity; (3) an embedded semantic support system improves the discovery recall level and precision by providing semantic-based search rule creation and result similarity evaluation functions and (4) the engine assists user decision-making by integrating a service quality monitoring and evaluation system, data/service visualization tools, multiple views and additional information. Experiments and a search example show that the proposed engine helps both scientists and general users search for more accurate results with enhanced performance and user experience through a user-friendly interface.
Texture based image recognition in microscopy images of diffuse gliomas with multi-class gentle boosting mechanism (2010)

The diagnosis of diffuse gliomas requires the careful inspection of large amounts of visual data. Identifying tissue regions that inform diagnosis is a cumbersome task for human reviewers and is a process prone to inter-reader variability. In this paper we present an automatic method for identifying critical diagnostic regions within whole-slide microscopy images of gliomas. We frame the problem of critical region identification as a texture-based content retrieval task in the sense that each image is represented by a set of texture features. Both linear and nonlinear dimensionality reduction techniques are utilized to explore the intrinsic dimensionality of the feature space where images are classified by classification and regression trees with performances improved by a newly extended multi-class gentle boosting (MCGB) mechanism. The proposed method is demonstrated on 1200 sample regions using a five-fold cross validation, achieving a 96.25% classification accuracy.
A Systematic Study on Knoevenagel Reaction and Nazarov Cyclization of Less Reactive Carbonyl Compounds Using Rare Earth Triflates and Its Applications (2011)

A systematic study of Knoevenagel reaction and Nazarov cyclization was made on variety of less reactive carbonyl compounds such as <TEX>${\beta}$</TEX>-ketoesters, 1,3-diketones and cyclic active methylene compounds using <TEX>$Yb(OTf)_3$</TEX> as the catalyst. Recycling study confirms reusability of the catalyst without much loss of activity.
Transesterification of Jatropha oil using immobilized Pseudomonas fluorescens (2007)

Transesterification of vegetable oils is an important reaction that produces fatty acid alkyl esters, methyl and ethyl esters which are excellent substitutes for diesel fuel. Biodiesel prepared by catalyzed mild transesterification has become of much current interest for alternative fuel production. In the present study the ability of a commercial immobilized Pseudomonas fluorescens MTCC 103 to catalyze the transesterification of Jatropha oil and methanol was investigated. The cell of P. fluorescens was easily immobilized within the sodium alginate during batch process. The important parameters like reaction temperature, pH, oil/methanol molar ratio, amount of beads and reaction time was studied. From the study it was found that maximum yield of biodiesel was obtained at the optimum conditions of at 40ºC, pH of 7.0 , molar ratio of  1:4, amount of beads of 3 g and reaction time of 48 h. The physical properties of the products were analyzed and the results were compared with conventional petroleum based diesel and it was found that the product can be used as an effective alternate fuel in existing diesel engine without any hardware engine modifications.   Key words: Transesterification, Biodiesel, Jatropha oil, Pseudomonas fluorescens.
A novel method of quadrature compensation in the butterfly resonator based on modal stiffness analysis (2018)

The butterfly gyroscope is simple to manufacture and it is considered as one kind of MEMS gyroscope with high sensitivity due to its unique structure. In reality, fabrication imperfections result in non-ideal geometries in the resonator, which in turn causes the quadrature error. The quadrature error has a great influence on the performance of the sensors in Micro and Nano scale, such as the zero-rate output (ZRO), the detection resolution and the dynamic range. However, the fact that the mechanical parameters of resonators are unknown (due to fabrication variation, fluctuations with temperature and aging) poses serious challenges. This paper presents a simple, yet effective method of quadrature compensation in butterfly resonator by electrostatic tuning. Theoretical calculation of quadrature error in butterfly gyroscope is carried out, establishing the mathematical model of quadrature compensation. Then, the simulation analysis is conducted to further analyze the mechanism of quadrature error and the method of quadrature compensation. Also, 5 butterfly gyroscopes fabricated on the same silicon wafer are selected for the experiment of quadrature compensation and the ZRO of the butterfly gyroscopes improves up to two orders of magnitude with quadrature cancellation, showing the feasibility of the proposed approach to quadrature compensation in the butterfly gyroscope. Finally, the way to decrease the direct current voltage VT required for suppressing the quadrature error is discussed. What is more, the method is not only suitable for the butterfly gyroscope, but also can be applied to other sensors in the Micro and Nanoscale.
Dynamic correlative VM placement for quality-assured cloud service (2013)

How to increase the utilization of data center networks (DCN) is a critical problem to ensure the quality of cloud services. Previous researches showed that the key is to increase the time-average utilization and decrease the overload ratio, and proposed many efficient virtual machine (VM) placement algorithms to achieve higher utilization. However, most of those works did not consider the quality assurance and statistical multiplexing methods, which can greatly improve the effectiveness of VM placement. In this paper, we propose a novel quality-assured VM placement scheme that dynamically places VMs to better multiplex time-varying resource demands. We firstly apply AutoRegressive Integrated Moving Average (ARIMA) and Generalized AutoRegressive Conditional Heteroskedasticity (GARCH model) to forecast the trend and volatility of the future demand, and then develop a Modern Portfolio Theory (MPT)-based method to enlarge DCN utilization and hedge the risk of server overloads. Extensive simulations and detailed analysis are conducted to validate the efficiency of our proposed scheme, which outperforms the previous works greatly.
Expression of renal cell protein markers is dependent on initial mechanical culture conditions (2002)

The rotating wall vessel is optimized for suspension culture, with laminar flow and adequate nutrient delivery, but minimal shear. However, higher shears may occur in vivo. During rotating wall vessel cultivation of human renal cells, size and density of glass-coated microcarrier beads were changed to modulate initial shear. Renal-specific proteins were assayed after 2 days. Flow cytometry antibody binding analysis of vitamin D receptor demonstrated peak expression at intermediate shears, with 30% reduction outside this range. Activity of cathepsin C showed the inverse pattern, lowest at midshear, with twofold increases at either extreme. Dipeptidyl-peptidase IV had no shear dependence, suggesting that the other results are specific, not universal, changes in membrane trafficking or protein synthesis. On addition of dextran, which changes medium density and viscosity but not shear, vitamin D receptor assay showed no differences from controls. Neither cell cycle, apoptosis/necrosis indexes, nor lactate dehydrogenase release varied between experiments, confirming that the changes are primary, not secondary to cell cycling or membrane damage. This study provides direct evidence that mechanical culture conditions modulate protein expression in suspension culture.
Variental difference in preference exhibited by western flower thrips <I>Flankliniella occidentalis</I> (Pergande) in <I>Eustoma russellianum</I> (2003)

トルコギキョウの品種間で, ミカンキイロアザミウマによる葉の被害度が異なった.'ミッキーバイカラーローズ','ネイルマリンネオ','ネイルピーチネオ'は被害株率が高く, 一方,'クリアマリン','エクローサピンク','キングオブスノー','あずまの波','あずまの紫'など10品種では被害株率は30%以下と低く,'ティファニーピンク'など3品種の被害株率はその中間であった. 被害株率が低かった'あずまの紫'の葉片で幼虫を飼育すると, ほとんど1齢幼虫で死亡したが,'ミッキーバイカラーローズ'では幼虫の生存率は有意に高く, 葉での増殖が可能と考えられる. したがって, トルコギキョウの葉でみられる被害の品種間差異の一部はミカンキイロアザミウマの幼虫生存率の違いに起因すると考えられた. 一方, 花弁上では両品種とも幼虫の生存率は高く, 差は認められなかった.
Cell‐Cell Interactions and the Regulation of Testis Function (1991)

Regulatory interactions have been shown to occur between all the testicular cell types considered. The paracrine factors mediating these interactions generally influence either cellular growth or differentiation. The regulation of cellular growth is essential in the developing testis and is required for the maintenance of spermatogenesis in the adult testis. The rapid rate of germinal cell proliferation and the continuous but slowed growth of the peritubular cells and Leydig cells requires the presence of specific growth factors in the adult. Therefore, cell-cell interactions have evolved that involve growth factors such as IGF, TGF-alpha, TGF-beta and NGF. Other growth factors such as FGF or less characterized components like the seminiferous growth factor (SGF) also may be involved in the paracrine regulation of testis cell growth. An alternate cellular parameter to cell growth to consider is the regulation of cellular function and differentiation. A number of endocrine agents and locally produced paracrine factors have been shown to control and maintain testis cell function and differentiation. Cell-cell interactions mediated by factors such as androgens, POMC peptides, and PModS are all primarily directed at the regulation of cellular differentiation. Therefore, the agents which mediate cell-cell interactions in the testis can generally be categorized into factors that regulate cell growth or those which influence cellular differentiation. The specific cell-cell interactions identified will likely be the first of a large number of cellular interactions yet to be investigated. Although a number of potentially important cell-cell interactions have been identified, future research will require the elucidation of the in vivo physiological significance of these interactions. The existence of different cell types and potential cell-cell interactions in a tissue implies that the actions of an endocrine agent on a tissue will not simply involve a single hormone and single cell. The endocrine regulation of testis function will have effects on cell-cell interactions and be affected by local cell-cell interactions. The ability of LH to influence Leydig cell androgen production promotes a cascade of interactions mediated through several cell types to maintain the process of spermatogenesis. FSH actions on Sertoli cells also promote cell-cell interactions that influence germinal cell development, peritubular myoid cell differentiation and Leydig cell function. Therefore, elucidation of the endocrine regulation of testis function requires an understanding of the local cell-cell interactions in the testis.
Glutamate, Glutamate Receptors, and Downstream Signaling Pathways (2013)

Glutamate is a nonessential amino acid, a major bioenergetic substrate for proliferating normal and neoplastic cells, and an excitatory neurotransmitter that is actively involved in biosynthetic, bioenergetic, metabolic, and oncogenic signaling pathways. Glutamate signaling activates a family of receptors consisting of metabotropic glutamate receptors (mGluRs) and ionotropic glutamate receptors (iGluRs), both of which have been implicated in chronic disabling brain disorders such as Schizophrenia and neurodegenerative diseases like Alzheimer's, Parkinson's, and multiple sclerosis. In this review, we discuss the structural and functional relationship of mGluRs and iGluRs and their downstream signaling pathways. The three groups of mGluRs, the associated second messenger systems, and subsequent activation of PI3K/Akt, MAPK, NFkB, PLC, and Ca/CaM signaling systems will be discussed in detail. The current state of human mGluR1a as one of the most important isoforms of Group I-mGluRs will be highlighted. The lack of studies on the human orthologues of mGluRs family will be outlined. We conclude that upon further study, human glutamate-initiated signaling pathways may provide novel therapeutic opportunities for a variety of non-malignant and malignant human diseases.
Speech Analysis Technique for Speech Compression (2011)

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Ordered morphologies in binary blends of diblock copolymer and homopolymer and characterization of their intermaterial dividing surfaces (1991)

Binary blends of a lamellar poly(styrene-b-isoprene) diblock copolymer and homopolystyrenes of various molecular weights self-assembled into highly ordered morphologies upon solvent evaporation. The equilibrium blend morphologies were studied by transmission electron microscopy and small angle x-ray scattering. The type of ordered morphology (lamellae, the ordered bicontinuous double diamond morphology, cylinders on a hexagonal lattice, and spheres on a cubic lattice) observed in each blend was generally dictated by the overall polystyrene volume fraction in the blend, i.e., the homopolymer concentration. The blend morphology also depended on the homopolymer molecular weight at a single fixed composition. The intermaterial dividing surface between the polystyrene and the polyisoprene microdomains was characterized by the interfacial mean curvature (H) and the average area per copolymer junction (σj). H and σj increased as the homopolymer concentration increased and/or as the homopolymer molecular weight decreased. These trends were generally obeyed both between and within ordered morphology types. The size of the microdomains was readily controlled by the homopolymer molecular weight.
DNA-Inspired Electrostatics (2000)

Under “physiological” conditions (a 0.1 molar solution of NaCl), a DNA molecule takes on the form of a disordered coil with a radius of gyration of several micrometers; if any lengths of the molecule come within 1 nm of one other, they strongly repel. But under different conditions—in a highly dilute aqueous solution that also contains a small concentration of polyvalent cations—the same DNA molecule condenses into a tightly packed, circumferentially wound torus. Figure 1a shows just such a DNA torus. Its average radius is about 50 nm, and the distance between the axes of neighboring, parallel portions of the molecule is only slightly larger than its diameter.
Generation and characterization of a human single-chain fragment variable (scFv) antibody against cytosine deaminase from Yeast (2008)

The construction of libraries of recombinant antibody fragments that are displayed on the surface of filamentous phage, and the selection of phage antibodies against target antigens, have become an important biotechnological tool in generating new monoclonal antibodies for research and clinical applications. The scFvH5 generated by this method is the first human antibody which is able to detect yCD in routinary laboratory techniques without interfering with its enzymatic function.
Visual Orientation in a Mirror World Tilted 90° (2005)

Previously, we showed that many supine observers in a furnished room tilted 90 degrees perceive themselves and the room as upright. We called this the "levitation illusion" because the arms feel weightless when held out from the body. We now report that a familiar scene viewed by supine observers through a mirror at 45 degrees appears vertical when, optically, it is horizontal and above the head. However, the body feels pitched upright only partially. This visual-righting effect, like the levitation illusion, is due to the polarity axis of the scene being accepted as vertical even in the presence of conflicting information from the gravity sense organs. In experiment 1 we tested the potency of objects containing either intrinsic polarity (due to familiar tops and bottoms) or extrinsic polarity (due to support relationships) to generate a visual-righting illusion. To almost all observers, a blank surface seen in the mirror appeared like a ceiling. A scene containing an object with intrinsic polarity, such as a chair or person, seen in the mirror appeared vertical to almost all observers. A scene containing a pair of objects with only extrinsic polarity, such as a ball on a shelf (but not a ball under a shelf), also appeared vertical to most observers. In experiment 2 we found that a polarised scene was more likely to produce a visual-righting illusion when it was arranged as a view through a window rather than as a picture inside a room.
Electronic and transport properties of nanotubes (2007)

This article reviews the electronic and transport properties of carbon nanotubes. The focus is mainly theoretical, but when appropriate the relation with experimental results is mentioned. While simple band-folding arguments will be invoked to rationalize how the metallic or semiconducting character of nanotubes is inferred from their topological structure, more sophisticated tight-binding and ab initio treatments will be introduced to discuss more subtle physical effects, such as those induced by curvature, tube-tube interactions, or topological defects. The same approach will be followed for transport properties. The fundamental aspects of conduction regimes and transport length scales will be presented using simple models of disorder, with the derivation of a few analytic results concerning specific situations of short- and long-range static perturbations. Further, the latest developments in semiempirical or ab initio simulations aimed at exploring the effect of realistic static scatterers (chemical impurities, adsorbed molecules, etc.) or inelastic electron-phonon interactions will be emphasized. Finally, specific issues, going beyond the noninteracting electron model, will be addressed, including excitonic effects in optical experiments, the Coulomb-blockade regime, and the Luttinger liquid, charge density waves, or superconducting transition.
Improved method for quantitating and obtaining the unsaponifiable matter of fats and oils (1988)

Abstract A quantitative method for saponifying and isolating the unsaponifiable matter (UM) from fats and oils is detailed. The method, which is a modification of a previously described procedure, is faster, uses about half the solvent, and is easier to execute. The minimum time needed to completely saponify a large number of fats and oils is established and conditions for removing contaminating soap from the extracted UM are described. Evidence presented shows some fats and oils to be incompletely saponified using previously indicated time‐temperature conditions. The method compares favorably with the AOAC method, but is not applicable to the analysis of marine oils.