Different Types Of Domains Research Articles

Efficient production and purification of extracellular domain of human FGFR-Fc fusion proteins from Chinese hamster ovary cells

The family of fibroblast growth factor receptors (FGFRs) plays an important role in cell growth, survival, differentiation and angiogenesis. The three immunoglobulin-like extracellular domains of FGFR (D1, D2, and D3) are critical for ligand binding and specificity towards fibroblast growth factor and heparan sulfate. Fibroblast growth factor receptors are overexpressed in a wide variety of tumors, such as breast, bladder, and prostate cancer, and therefore they are attractive targets for different types of anticancer therapies. In this study, we have cloned, expressed in CHO cells and purified Fc-fused extracellular domains of different types of FGFRs (ECD_FGFR1a-Fc, ECD_FGFR1b-Fc, ECD_FGFR2a-Fc, ECD_FGFR2b-Fc, ECD_FGFR3a-Fc, ECD_FGFR3b-Fc, ECD_FGFR4a-Fc, ECD_FGFR4b-Fc), which could be used as molecular targets for the selection of specific antibodies. The fusion proteins were analyzed using gel electrophoresis, Western blotting and mass spectrometry. To facilitate their full characterization, the fusion proteins were deglycosylated using PNGase F enzyme. With an optimized transient transfection protocol and purification procedure we were able to express the proteins at a high level and purify them to homogeneity.

Generation of disk-like domains with nanometer scale thickness in merocyanine dye LB film induced by hydrothermal treatment

We have characterized the binary LB films of merocyanine dye (MS) and arachidic acid (C20) before and after hydrothermal treatment (HTT), which is defined as a heat treatment under relative humidity of 100%, focusing on the morphology studied by bright field (BF) microscopy and fluorescence (FL) microscopy. BF microscopy observation has revealed that the as-deposited MS-C20 binary LB film is found to emit intense red fluorescence over the whole film area by 540-nm excitation. Since the surface image is almost featureless, it is considered that the crystallite sizes of J-aggregate are less than 10 μm. Interestingly, after HTT, round-shaped domains are observed in the LB systems, and the sizes are reaching 100 μm in diameter. Crystallites of J-aggregate, which are bluish in color and emit intense red fluorescence, tend to be in the round domains. We have observed two different types of domains, i.e., blue-rimmed domains and white-rimmed domains, which are postulated to be confined in the inner layers and located at the outermost layer, respectively. The thickness of the domains is equal to or less than that of the double layer of the MS-C20 mixed LB film, which is ca. 5.52 nm. The molecular order of MS in the J-aggregate is improved by the HTT process leading to the significant sharpening of the band shape together with the further red shift of the band (from 590 to 594 nm up to 597 to 599 nm). The reorganized J-band is considered to be ‘apparently’ isotropic owing to the random growth of the J-aggregate in the film plane. We consider that the lubrication effect by the presence of water molecules predominates in the HTT process.

Automatic Music Genre Classification of Audio Signals with Machine Learning Approaches

AbstractMusical genre classification is put into context by explaining about the structures in music and how it is analyzed and perceived by humans. The increase of the music databases on the personal collection and the Internet has brought a great demand for music information retrieval, and especially automatic musical genre classification. In this research we focused on combining information from the audio signal than different sources. This paper presents a comprehensive machine learning approach to the problem of automatic musical genre classification using the audio signal. The proposed approach uses two feature vectors, Support vector machine classifier with polynomial kernel function and machine learning algorithms. More specifically, two feature sets for representing frequency domain, temporal domain, cepstral domain and modulation frequency domain audio features are proposed. Using our proposed features SVM act as strong base learner in AdaBoost, so its performance of the SVM classifier cannot improve using boosting method. The final genre classification is obtained from the set of individual results according to a weighting combination late fusion method and it outperformed the trained fusion method. Music genre classification accuracy of 78% and 81% is reported on the GTZAN dataset over the ten musical genres and the ISMIR2004 genre dataset over the six musical genres, respectively. We observed higher classification accuracies with the ensembles, than with the individual classifiers and improvements of the performances on the GTZAN and ISMIR2004 genre datasets are three percent on average. This ensemble approach show that it is possible to improve the classification accuracy by using different types of domain based audio features.

Hodge decomposition and solution formulas for some first-order time-dependent parabolic operators with non-constant coefficients

In this paper, we present a Hodge decomposition for the \(L_p\)-space of some parabolic first-order partial differential operators with non-constant coefficients. This is done over different types of domains in Euclidean space \(\mathbb{R }^n\) and on some conformally flat cylinders and the \(n\)-torus associated with different spinor bundles. Initially, we apply a regularization procedure in order to control the non-removable singularities over the hyperplane \(t=0\). Using the setting of Clifford algebras combined with a Witt basis, we introduce some specific integral and projection operators. We present an \(L_p\)-decomposition where one of the components is the kernel of the regularized parabolic Dirac operator with non-constant coefficients. After that, we study the behavior of the solutions and the validity of our results when the regularization parameter tends to zero. To round off, we give some analytic solution formulas for the special context of domains on cylinders and \(n\)-tori.

Combining psychological models with machine learning to better predict people’s decisions

Creating agents that proficiently interact with people is critical for many applications. Towards creating these agents, models are needed that effectively predict people’s decisions in a variety of problems. To date, two approaches have been suggested to generally describe people’s decision behavior. One approach creates a-priori predictions about people’s behavior, either based on theoretical rational behavior or based on psychological models, including bounded rationality. A second type of approach focuses on creating models based exclusively on observations of people’s behavior. At the forefront of these types of methods are various machine learning algorithms.This paper explores how these two approaches can be compared and combined in different types of domains. In relatively simple domains, both psychological models and machine learning yield clear prediction models with nearly identical results. In more complex domains, the exact action predicted by psychological models is not even clear, and machine learning models are even less accurate. Nonetheless, we present a novel approach of creating hybrid methods that incorporate features from psychological models in conjunction with machine learning in order to create significantly improved models for predicting people’s decisions. To demonstrate these claims, we present an overview of previous and new results, taken from representative domains ranging from a relatively simple optimization problem and complex domains such as negotiation and coordination without communication.

Novel domain combinations in proteins encoded by chimeric transcripts

Motivation: Chimeric RNA transcripts are generated by different mechanisms including pre-mRNA trans-splicing, chromosomal translocations and/or gene fusions. It was shown recently that at least some of chimeric transcripts can be translated into functional chimeric proteins.Results: To gain a better understanding of the design principles underlying chimeric proteins, we have analyzed 7,424 chimeric RNAs from humans. We focused on the specific domains present in these proteins, comparing their permutations with those of known human proteins. Our method uses genomic alignments of the chimeras, identification of the gene–gene junction sites and prediction of the protein domains. We found that chimeras contain complete protein domains significantly more often than in random data sets. Specifically, we show that eight different types of domains are over-represented among all chimeras as well as in those chimeras confirmed by RNA-seq experiments. Moreover, we discovered that some chimeras potentially encode proteins with novel and unique domain combinations. Given the observed prevalence of entire protein domains in chimeras, we predict that certain putative chimeras that lack activation domains may actively compete with their parental proteins, thereby exerting dominant negative effects. More generally, the production of chimeric transcripts enables a combinatorial increase in the number of protein products available, which may disturb the function of parental genes and influence their protein–protein interaction network.Availability: our scripts are available upon request.Contact: avalencia@cnio.esSupplementary information: Supplementary data are available at Bioinformatics online.

A Generic Framework for Distributed Multirobot Cooperation

DEMiR-CF is a generic framework designed for a multirobot team to efficiently allocate tasks among themselves and achieve an overall mission. In the design of DEMiR-CF, the following issues were particularly investigated as the design criteria: efficient and realistic representation of missions, efficient allocation of tasks to cooperatively achieve a global goal, maintenance of the system coherence and consistency by the team members, detection of the contingencies and recover from various failures that may arise during runtime, efficient reallocation of tasks (if necessary) and reorganization of team members (if necessary). DEMiR-CF is designed to address different types of missions from the simplest to more complex ones, including missions with interrelated tasks and multi-resource (robot) requirements. Efficiency of the framework is validated through experiments in three different types of domains.

Bi-axial magnetic orientation in a twinnedErBa2Cu3Oy superconductor by controlling grain size

Bi-axial magnetic orientation inErBa2Cu3Oy (Er123) superconductor with a twinned microstructure was demonstrated.A ball-milling process effectively improved the degree of the in-plane andc-axis orientation of Er123 powder samples oriented in a modulated rotating magnetic fieldof 10 T. From the relationship between the particle size and the degree of orientation, it isconcluded that pulverization induced the appearance of the in-plane magnetic anisotropy ofEr123 grains through inhomogenization of two different types of domains in their grains.The present study presents a production technique of RE123 bulk magnets and coatedconductors without epitaxy technology.

Solvation of hydrophobes in water and simple liquids

The solvation of nonpolar molecules in water and that in simple liquids are compared and contrasted. First, solvation thermodynamics is reviewed in a way that focuses on how the enthalpy and entropy of solvation depend on the choice of microscopic volume change v in the solvation process--including special choices v being zero (fixed-volume condition) and v being the partial molecular volume of a solute molecule (fixed-pressure condition)--and how the solvation quantities are related with temperature derivatives of the solvation free energy. Second, the solvation free energy and the solvation enthalpy of a Lennard-Jones (LJ) atom in model water are calculated in the parameter space representing the solute size and the strength of the solute-solvent interaction, and the results are compared with those for an LJ atom in the LJ solvent. The solvation diagrams showing domains of different types of solvation in the parameter space are obtained both for the constant-volume condition and for the constant-pressure condition. Similarities between water and the simple liquid are found when the constant-volume solvation is considered while a significant difference manifests itself in the fixed-pressure solvation. The domain of solvation of hydrophobic character in the parameter space is large in the constant-volume solvation both for water and for the simple liquid. When switched to the constant-pressure condition accompanying a microscopic volume change, the hydrophobic domain remains large in water but it becomes significantly small in the simple liquid. The contrasting results are due to the smallness of the thermal pressure coefficient of water at low temperatures.

Gendered gambling domains and changes in Sweden

The study examines two Swedish replication prevalence studies (n = 10,000 and n = 15,000) with the aim of exploring evidence for a feminization of gambling in Sweden between 1997/1998 and 2008/2009. Gambling domains were classified based on the games' basic orientation towards strategy and chance, as well as on each game's setting in either a public place or a home environment. The criterion for a domain was that the respondent had gambled at least twice a month in any mode of gambling within the domain. Logistic regression analysis showed no signs of a feminization. Instead, the gender order in gambling seems to be reinforced. Preferences for the different types of domains were still highly gendered, despite the fact that men in 2008/2009 tended to gamble more on games of chance, especially in public places. The implications of the findings in relation to gender equality and constraints on women's leisure activities are further discussed.

Microstructure, surface composition and chemical stability of partly ordered LaTiO 2N

LaTiO 2N was synthesized in a thermal ammonolysis process of crystalline La 2Ti 2O 7 prepared by conventional solid state reaction or by ammonolysis of a homogeneous amorphous precursor obtained from a soft-chemistry approach. At room temperature slowly cooled LaTiO 2N prepared from either precursor crystallizes in space group I 1 ¯ and shows a partially ordered anionic arrangement, in contrast to a quenched reference sample. The material possesses a complex microstructure represented by twin domains of different types and orientations, as well as incommensurately modulated fragments. The presence of minor C- and N-containing phases such as carbonates, cyanides and nitrates as well as a small amount of a reoxidation intermediate was detected by infrared and Raman spectroscopy. These small amounts of secondary phases can generally influence the results of the O/N content determination of oxynitride compounds when using thermal analysis methods. The formation of such unwanted secondary phases can be avoided by quenching the oxynitride sample or by cooling in inert atmosphere.

Imaging of Hybrid-Multiferroic and Translation Domains in a Spin-Spiral Ferroelectric

AbstractTwo fundamentally different types of domains were resolved in multiferroic MnWO4 by optical second harmonic generation (SHG). Hybrid-multiferroic (absolute) domains reflect the magnetic chirality coupled 1:1 to the spontaneous polarization because of the magnetic origin of the ferroelectric order. Magnetic translation (relative) domains reflect discontinuities in the progression of the magnetic spin spiral. SHG topography is the only experimental method so far allowing one to image both types of domains. The imaging procedure and the SHG contributions involved are therefore discussed in detail.

Effects of Co/Sm Composition on the Ordered Phase Formation in Sm-Co Thin Films Grown on Cu(111) Single-Crystal Underlayers

Sm-Co thin films were prepared on Cu(111) single-crystal underlayers by changing the Sm composition from 12 to 35 at.% and the effects of Co/Sm composition on the ordered phase formation were investigated. The epitaxial SmCo <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">5</sub> thin films were obtained for all samples. The SmCo <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">5</sub> epitaxial layer grown on Cu underlayer has two different types of domains whose orientations are rotated around film normal by 30 degrees to each other. Cu atoms substitute a part of the Co sites in the SmCo <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">5</sub> structure, and an alloy compound of Sm(Co,Cu) <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">5</sub> phase was formed for all samples. The Sm(Co,Cu) <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">5</sub> phase was more Cu enriched with increasing the Sm composition. The Cu atom diffusion into Sm-Co layer plays an important role in assisting the formation of Sm(Co,Cu) <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">5</sub> ordered phase.

Coordination of Sr and Mg in calcite and aragonite

AbstractStrontium and Mg in calcite and aragonite are widely used as proxies of temperature in palaeoenvironmental reconstructions. We use X-ray absorption fine structure (XAFS) to examine Sr and Mg substitution in calcite and aragonite. We have measured the K-edge X-ray absorption near-edge structure (XANES) and extended X-ray absorption fine structure (EXAFS) of Mg and Sr-bearing calcite and aragonite, plus the carbonates: strontianite, hydromagnesite, magnesite, dolomite and a suite of calcites with differing amounts of Mg. The Sr substitutes ideally for Ca in aragonite but causes a small (2%) dilation of the site. Strontium substitutes for octahedral Ca in calcite but with a 6.5% dilation and distortion. Magnesium in the calcites studied provides a variable XANES indicating that the Mg structural state in calcite is variable. Refinement of EXAFS gives Mg–O bond distances of ∼2.12 Å, which are much smaller than the Ca–O bond distance of 2.35 Å but consistent with published amounts of relaxation of the calcite structure. The XANES and EXAFS are consistent with a model whereby some calcites contain nanodomains, e.g. of dolomite and/or huntite structures. The variability in the XANES can be explained by domains of different types and/or sizes. Substitution of Mg into aragonite has 9-fold coordination but relatively short bond distances (2.08 Å) demonstrating either: (1) substantial distortion of the site; or (2) that Mg is accommodated in nanodomains of an unknown phase. Variability in the Mg structural state in calcite may be linked to the variety of temperature dependences observed, e.g. in foraminiferal calcite

An extremal metric approach to some problems on extremal decomposition

The paper presents a simple extremal metric approach to problems on extremal decomposition in families of systems of nonoverlapping domains of different types. The approach is based on using general properties of trajectories of the associated quadratic differentials for simpler extremal decomposition problems. Bibliography: 8 titles.

Evolutionary history and functional implications of protein domains and their combinations in eukaryotes

A rapid emergence of animal-specific domains was observed in animals, contributing to specific domain combinations and functional diversification, but no similar trends were observed in other clades of eukaryotes.

CONTRIBUTIONS OF DOMAIN-RELATED PHENOMENA ON DIELECTRIC CONSTANT OF LEAD-BASED FERROELECTRIC CERAMICS UNDER UNIAXIAL COMPRESSIVE PRE-STRESS

The dielectric constant of lead-based ferroelectric ceramics in three different systems, i.e. BT-PZT, PMN-PT and PMN-PZT, was measured under uniaxial compressive pre-stress to investigate the contributions of different domain-phenomena. The dielectric constant was observed at room temperature under the compressive pre-stress up to 15 MPa, 22 MPa and 5 MPa for BT-PZT, PMN-PT and PMN-PZT, respectively, using a homebuilt uniaxial compressometer. Dielectric constant of the BT-PZT ceramics increased significantly with increasing applied stress. Larger changes in the dielectric constant with the applied stress were observed in the PZT-rich compositions. However, for PMN-PT and PMN-PZT ceramic systems, changes in the dielectric constant with the stress were found to depend significantly on the ceramic compositions. The experimental results could be explained by both intrinsic and extrinsic domain-related mechanisms involving domain wall motions, as well as the de-aging phenomenon from the application of the compressive pre-stress. Roles of different types of domains, i.e. micro-domains and nano-domains, were also discussed.

The conformal radius as a function and its gradient image

Let Ω be a domain in\(\bar {\mathbb{C}}\) with three or more boundary points in\(\bar {\mathbb{C}}\) andR(w, Ω) the conformal, resp. hyperbolic radius of Ω at the pointw e Ω/{∞}. We give a unified proof and some generalizations of a number of known theorems that are concerned with the geometry of the surface\(s_\Omega = \{ (w,h)|w \in \Omega ,h = R(w,\Omega )\} \) in the case that the Jacobian of ∇R(w, Ω), the gradient ofR, is nonegative on Ω. We discuss the function ∇R(w, Ω) in some detail, since it plays a central role in our considerations. In particular, we prove that ∇R(w, Ω) is a diffeomorphism of Ω for four different types of domains.

Two types of structural domains in Pb3(PO4)2

The conditions of the formation of suborientation states in multidomain and single-domain Pb3(PO4)2 crystals are analyzed. It is shown that suborientation states belong to sets of two structurally different types of domains differing in the angle sign and the orientation of the axis of rotation with respect to the coordinate system of the paraelastic phase. These structural differences are proposed to be described by the Gibbs vector. It is concluded that this macroscopic parameter corresponds to cooperative displacement of some groups of atoms with respect to other groups, with the crystal matrix being at rest. It is found that the modulus of the Gibbs vector is proportional to the spontaneous-strain components and depends linearly on the crystallographic parameter c in the ferroelastic phase.

Effect of Molecular Surface Packing on the Enzymatic Activity Modulation of an Anchored Protein on Phospholipid Langmuir Monolayers

The catalytic activity of a glycosylphosphatidylinositol (GPI)-anchored alkaline phosphatase has been studied in Langmuir phospholipid monolayers at different surface pressures. The enzyme substrate, p-nitrophenyl phosphate, was injected into the subphase of mixed enzyme/lipid Langmuir monolayers. Its hydrolysis product was followed by monitoring the absorbance at 410 nm in situ in the monolayer subphase of the Langmuir trough. Several surface pressures, corresponding to different molecular surface densities, were attained by lateral compression of the monolayers. The morphology of the monolayers, observed by fluorescence microscopy, showed three different types of domains owing to the heterogeneous partition of the enzyme within the mixed enzyme/lipid film. The catalytic activity was modulated by the enzyme surface density, and it increased until a pressure of 18 mN/m was reached, but it decreased significantly when the equilibrium in-plane elasticity (surface compressional modulus) increased more noticeably, resulting in alterations in the interface morphology. A model for the modulation of the enzyme orientation and catalytic activity by lipid/enzyme surface morphology and enzyme surface packing at the air/liquid interface is proposed. The results might have an important impact on the comprehension of the enzymatic activity regulation of GPI-anchored proteins in biomembranes.