Science.gov

Sample records for additional structural features

  1. The Purification of the Chlamydomonas reinhardtii chloroplast ClpP complex: additional subunits and structural features

    PubMed Central

    Derrien, Benoît; Majeran, Wojciech; Effantin, Grégory; Ebenezer, Joseph; Friso, Giulia; van Wijk, Klaas J.; Steven, Alasdair C.; Maurizi, Michael R.; Vallon, Olivier

    2012-01-01

    The ClpP peptidase is a major constituent of the proteolytic machinery of bacteria and organelles. The chloroplast ClpP complex is unusual, in that it associates a large number of subunits, one of which (ClpP1) is encoded in the chloroplast, the others in the nucleus. The complexity of these large hetero-oligomeric complexes has been a major difficulty in their overproduction and biochemical characterization. In this paper, we describe the purification of native chloroplast ClpP complex from the green alga Chlamydomonas reinhardtii, using a strain that carries the Strep-tag II at the C-terminus of the ClpP1 subunit. Similar to land plants, the algal complex comprises active and inactive subunits (3 ClpP and 5 ClpR, respectively). Evidence is presented that a sub-complex can be produced by dissociation, comprising ClpP1 and ClpR1, 2, 3 and 4, similar to the ClpR-ring described in land plants. Our Chlamydomonas ClpP preparation also contains two ClpT subunits, ClpT3 and ClpT4, which like the land plant ClpT1 and ClpT2 show 2 Clp-N domains. ClpTs are believed to function in substrate binding and/or assembly of the two heptameric rings. Phylogenetic analysis indicates that ClpT subunits have appeared independently in Chlorophycean algae, in land plants and in dispersed cyanobacterial genomes. Negative staining electron microscopy shows that the Chlamydomonas complex retains the barrel-like shape of homo-oligomeric ClpPs, with 4 additional peripheral masses that we speculate represent either the additional IS1 domain of ClpP1 (a feature unique to algae) or ClpTs or extensions of ClpR subunits PMID:22772861

  2. The purification of the Chlamydomonas reinhardtii chloroplast ClpP complex: additional subunits and structural features.

    PubMed

    Derrien, Benoît; Majeran, Wojciech; Effantin, Grégory; Ebenezer, Joseph; Friso, Giulia; van Wijk, Klaas J; Steven, Alasdair C; Maurizi, Michael R; Vallon, Olivier

    2012-09-01

    The ClpP peptidase is a major constituent of the proteolytic machinery of bacteria and organelles. The chloroplast ClpP complex is unusual, in that it associates a large number of subunits, one of which (ClpP1) is encoded in the chloroplast, the others in the nucleus. The complexity of these large hetero-oligomeric complexes has been a major difficulty in their overproduction and biochemical characterization. In this paper, we describe the purification of native chloroplast ClpP complex from the green alga Chlamydomonas reinhardtii, using a strain that carries the Strep-tag II at the C-terminus of the ClpP1 subunit. Similar to land plants, the algal complex comprises active and inactive subunits (3 ClpP and 5 ClpR, respectively). Evidence is presented that a sub-complex can be produced by dissociation, comprising ClpP1 and ClpR1, 2, 3 and 4, similar to the ClpR-ring described in land plants. Our Chlamydomonas ClpP preparation also contains two ClpT subunits, ClpT3 and ClpT4, which like the land plant ClpT1 and ClpT2 show 2 Clp-N domains. ClpTs are believed to function in substrate binding and/or assembly of the two heptameric rings. Phylogenetic analysis indicates that ClpT subunits have appeared independently in Chlorophycean algae, in land plants and in dispersed cyanobacterial genomes. Negative staining electron microscopy shows that the Chlamydomonas complex retains the barrel-like shape of homo-oligomeric ClpPs, with 4 additional peripheral masses that we speculate represent either the additional IS1 domain of ClpP1 (a feature unique to algae) or ClpTs or extensions of ClpR subunits.

  3. ProFold: Protein Fold Classification with Additional Structural Features and a Novel Ensemble Classifier

    PubMed Central

    2016-01-01

    Protein fold classification plays an important role in both protein functional analysis and drug design. The number of proteins in PDB is very large, but only a very small part is categorized and stored in the SCOPe database. Therefore, it is necessary to develop an efficient method for protein fold classification. In recent years, a variety of classification methods have been used in many protein fold classification studies. In this study, we propose a novel classification method called proFold. We import protein tertiary structure in the period of feature extraction and employ a novel ensemble strategy in the period of classifier training. Compared with existing similar ensemble classifiers using the same widely used dataset (DD-dataset), proFold achieves 76.2% overall accuracy. Another two commonly used datasets, EDD-dataset and TG-dataset, are also tested, of which the accuracies are 93.2% and 94.3%, higher than the existing methods. ProFold is available to the public as a web-server.

  4. ProFold: Protein Fold Classification with Additional Structural Features and a Novel Ensemble Classifier

    PubMed Central

    2016-01-01

    Protein fold classification plays an important role in both protein functional analysis and drug design. The number of proteins in PDB is very large, but only a very small part is categorized and stored in the SCOPe database. Therefore, it is necessary to develop an efficient method for protein fold classification. In recent years, a variety of classification methods have been used in many protein fold classification studies. In this study, we propose a novel classification method called proFold. We import protein tertiary structure in the period of feature extraction and employ a novel ensemble strategy in the period of classifier training. Compared with existing similar ensemble classifiers using the same widely used dataset (DD-dataset), proFold achieves 76.2% overall accuracy. Another two commonly used datasets, EDD-dataset and TG-dataset, are also tested, of which the accuracies are 93.2% and 94.3%, higher than the existing methods. ProFold is available to the public as a web-server. PMID:27660761

  5. Ciliate telomerase RNA structural features.

    PubMed Central

    McCormick-Graham, M; Romero, D P

    1995-01-01

    Telomerase RNA is an integral part of telomerase, the ribonucleoprotein enzyme that catalyzes the synthesis of telomeric DNA. The RNA moiety contains a templating domain that directs the synthesis of a species-specific telomeric repeat and may also be important for enzyme structure and/or catalysis. Phylogenetic comparisons of telomerase RNA sequences from various Tetrahymena spp. and hypotrich ciliates have revealed two conserved secondary structure models that share many features. We have cloned and sequenced the telomerase RNA genes from an additional six Tetrahymena spp. (T. vorax, T. borealis, T. australis, T. silvana, T. capricornis and T. paravorax). Inclusion of these sequences, most notably that from T. paravorax, in a phylogenetic comparative analysis allowed us to more narrowly define structural elements that may be necessary for a minimal telomerase RNA. A primary sequence element, positioned 5' of the template and conserved between all previously known ciliate telomerase RNAs, has been reduced from 5'-(C)UGUCA-3' to the 4 nt sequence 5'-GUCA-3'. Conserved secondary structural features and the impact they have on the general organization of ciliate telomerase RNAs is discussed. PMID:7739888

  6. Is adermatoglyphia an additional feature of Kindler Syndrome?*

    PubMed Central

    de Almeida Jr, Hiram Larangeira; Goetze, Fernanda Mendes; Fong, Kenneth; Lai-Cheong, Joey; McGrath, John

    2015-01-01

    A typical feature of Kindler Syndrome is skin fragility; this condition in currently classified as a form of epidermolysis bullosa. We describe a rarely reported feature of two cases, one sporadic and one familial; both patients noticed acquired adermatoglyphia. The loss of dermatoglyphics could be an additional feature of this syndrome. PMID:26375235

  7. Is adermatoglyphia an additional feature of Kindler Syndrome?

    PubMed

    Almeida, Hiram Larangeira de; Goetze, Fernanda Mendes; Fong, Kenneth; Lai-Cheong, Joey; McGrath, John

    2015-01-01

    A typical feature of Kindler Syndrome is skin fragility; this condition in currently classified as a form of epidermolysis bullosa. We describe a rarely reported feature of two cases, one sporadic and one familial; both patients noticed acquired adermatoglyphia. The loss of dermatoglyphics could be an additional feature of this syndrome.

  8. Effective face recognition using bag of features with additive kernels

    NASA Astrophysics Data System (ADS)

    Yang, Shicai; Bebis, George; Chu, Yongjie; Zhao, Lindu

    2016-01-01

    In past decades, many techniques have been used to improve face recognition performance. The most common and well-studied ways are to use the whole face image to build a subspace based on the reduction of dimensionality. Differing from methods above, we consider face recognition as an image classification problem. The face images of the same person are considered to fall into the same category. Each category and each face image could be both represented by a simple pyramid histogram. Spatial dense scale-invariant feature transform features and bag of features method are used to build categories and face representations. In an effort to make the method more efficient, a linear support vector machine solver, Pegasos, is used for the classification in the kernel space with additive kernels instead of nonlinear SVMs. Our experimental results demonstrate that the proposed method can achieve very high recognition accuracy on the ORL, YALE, and FERET databases.

  9. Structural features of lignohumic acids

    NASA Astrophysics Data System (ADS)

    Novák, František; Šestauberová, Martina; Hrabal, Richard

    2015-08-01

    The composition and structure of humic acids isolated from lignohumate, which is produced by hydrolytic-oxidative conversion of technical lignosulfonates, were characterized by chemical and spectral methods (UV/VIS, FTIR, and 13C NMR spectroscopy). As comparative samples, humic acids (HA) were isolated also from lignite and organic horizon of mountain spruce forest soil. When compared with other HA studied, the lignohumate humic acids (LHHA) contained relatively few carboxyl groups, whose role is partly fulfilled by sulfonic acid groups. Distinctive 13C NMR signal of methoxyl group carbons, typical for lignin and related humic substances, was found at the shift of 55.9 ppm. Other alkoxy carbons were present in limited quantity, like the aliphatic carbons. Due to the low content of these carbon types, the LHHA has high aromaticity of 60.6%. Comparison with the natural HA has shown that lignohumate obtained by thermal processing of technical lignosulfonate can be regarded as an industrially produced analog of natural humic substances. Based on the chemical and spectral data evaluation, structural features of lignohumate humic acids were clarified and their hypothetical chemical structure proposed, which described typical "average" properties of the isolated fraction.

  10. The suitability of concentration addition for predicting the effects of multi-component mixtures of up to 17 anti-androgens with varied structural features in an in vitro AR antagonist assay

    SciTech Connect

    Ermler, Sibylle; Scholze, Martin; Kortenkamp, Andreas

    2011-12-15

    The risks associated with human exposures to chemicals capable of antagonising the effects of endogenous androgens have attracted considerable recent interest. Exposure is typically to large numbers of chemicals with androgen receptor (AR) antagonist activity, yet there is limited evidence of the combined effects of multi-component mixtures of these chemicals. A few in vitro studies with mixtures of up to six AR antagonists suggest that the concept of concentration addition (CA) provides good approximations of experimentally observed mixture effects, but studies with larger numbers of anti-androgens, and with more varied structural features, are missing. Here we show that the mixture effects of up to 17 AR antagonists, comprising compounds as diverse as UV-filter substances, parabens, perfluorinated compounds, bisphenol-A, benzo({alpha})pyrene, synthetic musks, antioxidants and polybrominated biphenyls, can be predicted well on the basis of the anti-androgenicity of the single components using the concept of CA. We tested these mixtures in an in vitro AR-dependent luciferase reporter gene assay, based on MDA-kb2 cells. The effects of further mixtures, composed of four and six anti-androgens, could be predicted accurately by CA. However, there was a shortfall from expected additivity with a ten-component mixture at two different mixture ratios, but attempts to attribute these deviations to differential expression of hormone-metabolising CYP isoforms did not produce conclusive results. CA provides good approximations of in vitro mixture effects of anti-androgens with varying structural features. -- Highlights: Black-Right-Pointing-Pointer Humans are exposed to a large number of androgen receptor antagonists. Black-Right-Pointing-Pointer There is limited evidence of the combined effects of anti-androgenic chemicals. Black-Right-Pointing-Pointer We modelled the predictability of combined effects of up to 17 anti-androgens. Black-Right-Pointing-Pointer We tested the

  11. Structural features offshore northern Taiwan

    NASA Astrophysics Data System (ADS)

    Yicheng Yang, Eason; Liu, Char-Shine; Chang, Jih-Hsin; Chiu, Chien-Hsuan

    2016-04-01

    The area offshore northern Taiwan is the place where East China Sea Shelf extends into the Southern Okinawa Trough, and where pre-Pleistocene arc-continental collision had occurred. Comparison between fault distribution in the area with previously published results suggests that the fault distribution and regional structural framework are still controversial. Using marine multichannel seismic reflection data collected in 3 marine geophysical survey cruises, we remapped the fault distribution in the northern offshore area of Taiwan. By analyzing all the seismic profiles using the KINGDOM suite (a seismic interpretation software), a new fault distribution map is presented, and a subsurface unconformity PRSB (Pliocene reflection sequence boundary) is identified. Six major NE-SW trending high-angle normal faults cut the PRSB can be traced to the fault systems on land northernmost Taiwan. These normal faults are located between the Southern Okinawa Trough and the East China Sea continental shelf basin, and have been suggested to be reactivated from pre-existing reverse faults. The offsets of fault ramps in PRSB increase toward southeast. The isopach map of the study area compiled shows that sediment strata overlying PRSB thin toward northwest.

  12. Feature extraction for structural dynamics model validation

    SciTech Connect

    Hemez, Francois; Farrar, Charles; Park, Gyuhae; Nishio, Mayuko; Worden, Keith; Takeda, Nobuo

    2010-11-08

    This study focuses on defining and comparing response features that can be used for structural dynamics model validation studies. Features extracted from dynamic responses obtained analytically or experimentally, such as basic signal statistics, frequency spectra, and estimated time-series models, can be used to compare characteristics of structural system dynamics. By comparing those response features extracted from experimental data and numerical outputs, validation and uncertainty quantification of numerical model containing uncertain parameters can be realized. In this study, the applicability of some response features to model validation is first discussed using measured data from a simple test-bed structure and the associated numerical simulations of these experiments. issues that must be considered were sensitivity, dimensionality, type of response, and presence or absence of measurement noise in the response. Furthermore, we illustrate a comparison method of multivariate feature vectors for statistical model validation. Results show that the outlier detection technique using the Mahalanobis distance metric can be used as an effective and quantifiable technique for selecting appropriate model parameters. However, in this process, one must not only consider the sensitivity of the features being used, but also correlation of the parameters being compared.

  13. Feature based Weld-Deposition for Additive Manufacturing of Complex Shapes

    NASA Astrophysics Data System (ADS)

    Panchagnula, Jayaprakash Sharma; Simhambhatla, Suryakumar

    2016-08-01

    Fabricating functional metal parts using Additive Manufacturing (AM) is a leading trend. However, realizing overhanging features has been a challenge due to the lack of support mechanism for metals. Powder-bed fusion techniques like, Selective Laser Sintering (SLS) employ easily-breakable-scaffolds made of the same material to realize the overhangs. However, the same approach is not extendible to deposition processes like laser or arc based direct energy deposition processes. Although it is possible to realize small overhangs by exploiting the inherent overhanging capability of the process or by blinding some small features like holes, the same cannot be extended for more complex geometries. The current work presents a novel approach for realizing complex overhanging features without the need of support structures. This is possible by using higher order kinematics and suitably aligning the overhang with the deposition direction. Feature based non-uniform slicing and non-uniform area-filling are some vital concepts required in realizing the same and are briefly discussed here. This method can be used to fabricate and/or repair fully dense and functional components for various engineering applications. Although this approach has been implemented for weld-deposition based system, the same can be extended to any other direct energy deposition processes also.

  14. Structural features of algebraic quantum notations

    NASA Astrophysics Data System (ADS)

    Gire, Elizabeth; Price, Edward

    2015-12-01

    [This paper is part of the Focused Collection on Upper Division Physics Courses.] The formalism of quantum mechanics includes a rich collection of representations for describing quantum systems, including functions, graphs, matrices, histograms of probabilities, and Dirac notation. The varied features of these representations affect how computations are performed. For example, identifying probabilities of measurement outcomes for a state described in Dirac notation may involve identifying expansion coefficients by inspection, but if the state is described as a function, identifying those expansion coefficients often involves performing integrals. In this study, we focus on three notational systems: Dirac notation, algebraic wave-function notation, and matrix notation. These quantum notations must include information about basis states and their associated complex probability amplitudes. In this theory paper, we identify four structural features of quantum notations, which we term individuation, degree of externalization, compactness, and symbolic support for computational rules. We illustrate how student reasoning interacts with these structural features with episodes from interviews with advanced undergraduate physics majors reasoning about a superposition state of an infinite square well system. We find evidence of the students coordinating different notations through the use of Dirac notation, using an expression in Dirac notation to guide their work in another notation. These uses are supported by the high degree of individuation, compactness, and symbolic support for computation and the moderate degree of externalization provided by Dirac notation.

  15. Structure Property Studies for Additively Manufactured Parts

    SciTech Connect

    Milenski, Helen M; Schmalzer, Andrew Michael; Kelly, Daniel

    2015-08-17

    Since the invention of modern Additive Manufacturing (AM) processes engineers and designers have worked hard to capitalize on the unique building capabilities that AM allows. By being able to customize the interior fill of parts it is now possible to design components with a controlled density and customized internal structure. The creation of new polymers and polymer composites allow for even greater control over the mechanical properties of AM parts. One of the key reasons to explore AM, is to bring about a new paradigm in part design, where materials can be strategically optimized in a way that conventional subtractive methods cannot achieve. The two processes investigated in my research were the Fused Deposition Modeling (FDM) process and the Direct Ink Write (DIW) process. The objectives of the research were to determine the impact of in-fill density and morphology on the mechanical properties of FDM parts, and to determine if DIW printed samples could be produced where the filament diameter was varied while the overall density remained constant.

  16. Automated detection of glaucoma using structural and non structural features.

    PubMed

    Salam, Anum A; Khalil, Tehmina; Akram, M Usman; Jameel, Amina; Basit, Imran

    2016-01-01

    Glaucoma is a chronic disease often called "silent thief of sight" as it has no symptoms and if not detected at an early stage it may cause permanent blindness. Glaucoma progression precedes some structural changes in the retina which aid ophthalmologists to detect glaucoma at an early stage and stop its progression. Fundoscopy is among one of the biomedical imaging techniques to analyze the internal structure of retina. Our proposed technique provides a novel algorithm to detect glaucoma from digital fundus image using a hybrid feature set. This paper proposes a novel combination of structural (cup to disc ratio) and non-structural (texture and intensity) features to improve the accuracy of automated diagnosis of glaucoma. The proposed method introduces a suspect class in automated diagnosis in case of any conflict in decision from structural and non-structural features. The evaluation of proposed algorithm is performed using a local database containing fundus images from 100 patients. This system is designed to refer glaucoma cases from rural areas to specialists and the motivation behind introducing suspect class is to ensure high sensitivity of proposed system. The average sensitivity and specificity of proposed system are 100 and 87 % respectively. PMID:27652092

  17. Quantifying Wrinkle Features of Thin Membrane Structures

    NASA Technical Reports Server (NTRS)

    Jacobson, Mindy B.; Iwasa, Takashi; Naton, M. C.

    2004-01-01

    For future micro-systems utilizing membrane based structures, quantified predictions of wrinkling behavior in terms of amplitude, angle and wavelength are needed to optimize the efficiency and integrity of such structures, as well as their associated control systems. For numerical analyses performed in the past, limitations on the accuracy of membrane distortion simulations have often been related to the assumptions made. This work demonstrates that critical assumptions include: effects of gravity, supposed initial or boundary conditions, and the type of element used to model the membrane. In this work, a 0.2 m x 02 m membrane is treated as a structural material with non-negligible bending stiffness. Finite element modeling is used to simulate wrinkling behavior due to a constant applied in-plane shear load. Membrane thickness, gravity effects, and initial imperfections with respect to flatness were varied in numerous nonlinear analysis cases. Significant findings include notable variations in wrinkle modes for thickness in the range of 50 microns to 1000 microns, which also depend on the presence of an applied gravity field. However, it is revealed that relationships between overall strain energy density and thickness for cases with differing initial conditions are independent of assumed initial conditions. In addition, analysis results indicate that the relationship between wrinkle amplitude scale (W/t) and structural scale (L/t) is independent of the nonlinear relationship between thickness and stiffness.

  18. Structural Features of the Glutamate Transporter Family

    PubMed Central

    Slotboom, Dirk Jan; Konings, Wil N.; Lolkema, Juke S.

    1999-01-01

    transporters but may resemble loop-pores found in ion channels. A second distinctive structural feature is the presence of a highly amphipathic membrane-spanning helix that provides a hydrophilic path through the membrane. Recent data from analysis of site-directed mutants and studies on the mechanism and pharmacology of the transporters are discussed in relation to the structural model. PMID:10357852

  19. In situ formation of the first proteinogenically functionalized [TeW6O24O2(Glu)]7– structure reveals unprecedented chemical and geometrical features of the Anderson-type cluster† †Electronic supplementary information (ESI) available: Full experimental details and additional figures are provided. See DOI: 10.1039/c6cc07004c Click here for additional data file. Click here for additional data file. Click here for additional data file.

    PubMed Central

    Molitor, Christian; Bijelic, Aleksandar

    2016-01-01

    The chemistry of polyoxometalates (POMs) in a protein environment is an almost unexplored but highly relevant research field as important biological and pharmacological attributes of certain POMs are based on their interactions with proteins. We report on the A-type Anderson–Evans polyoxotungstate, [TeW6O24]6– (TEW), mediated crystallization of Coreopsis grandiflora aurone synthase (cgAUS1) using ∼0.24 mM protein and 1.0 mM TEW. The 1.78 Å crystal structure reveals the covalent binding of TEW to the protein under the formation of an unprecedented polyoxotungstate cluster, [TeW6O24O2(Glu)]7– (GluTEW). The polyoxotungstate–protein complex exhibits the first covalent bond between a protein and the A-type Anderson–Evans cluster, an archetype where up to now no hybrid structures exist. The polyoxotungstate is modified at two of its six addenda tungsten atoms, which covalently bind to the carboxylic oxygen atoms of glutamic acid (Glu157), leading to W–O distances of ∼2.35 Å. This ligand substitution reaction is accompanied by a reduction of the coordination number of two μ3 polyoxotungstate oxygen atoms. This is so far unique since all known hybridizations of the Anderson–Evans POM with organic units have been obtained via the functionalization of the B-type Anderson–Evans structure through its bridging oxygen atoms. The structure reported here proves the reactivity of this POM archetype's addenda atoms as it has been administered into the protein solution as a pre-assembled cluster. Moreover, the novel cluster [TeW6O24O2(Glu)]7– displays the great versatility of the Anderson–Evans POM class. PMID:27722437

  20. Structural features of plastic deformation in bulk metallic glasses

    SciTech Connect

    Scudino, S. Shakur Shahabi, H.; Stoica, M.; Kühn, U.; Kaban, I.; Escher, B.; Eckert, J.; Vaughan, G. B. M.

    2015-01-19

    Spatially resolved strain maps of a plastically deformed bulk metallic glass (BMG) have been created by using high-energy X-ray diffraction. The results reveal that plastic deformation creates a spatially heterogeneous atomic arrangement, consisting of strong compressive and tensile strain fields. In addition, significant shear strain is introduced in the samples. The analysis of the eigenvalues and eigenvectors of the strain tensor indicates that considerable structural anisotropy occurs in both the magnitude and direction of the strain. These features are in contrast to the behavior observed in elastically deformed BMGs and represent a distinctive structural sign of plastic deformation in metallic glasses.

  1. Additivity of Feature-Based and Symmetry-Based Grouping Effects in Multiple Object Tracking

    PubMed Central

    Wang, Chundi; Zhang, Xuemin; Li, Yongna; Lyu, Chuang

    2016-01-01

    Multiple object tracking (MOT) is an attentional process wherein people track several moving targets among several distractors. Symmetry, an important indicator of regularity, is a general spatial pattern observed in natural and artificial scenes. According to the “laws of perceptual organization” proposed by Gestalt psychologists, regularity is a principle of perceptual grouping, such as similarity and closure. A great deal of research reported that feature-based similarity grouping (e.g., grouping based on color, size, or shape) among targets in MOT tasks can improve tracking performance. However, no additive feature-based grouping effects have been reported where the tracking objects had two or more features. “Additive effect” refers to a greater grouping effect produced by grouping based on multiple cues instead of one cue. Can spatial symmetry produce a similar grouping effect similar to that of feature similarity in MOT tasks? Are the grouping effects based on symmetry and feature similarity additive? This study includes four experiments to address these questions. The results of Experiments 1 and 2 demonstrated the automatic symmetry-based grouping effects. More importantly, an additive grouping effect of symmetry and feature similarity was observed in Experiments 3 and 4. Our findings indicate that symmetry can produce an enhanced grouping effect in MOT and facilitate the grouping effect based on color or shape similarity. The “where” and “what” pathways might have played an important role in the additive grouping effect. PMID:27199875

  2. Additivity of Feature-Based and Symmetry-Based Grouping Effects in Multiple Object Tracking.

    PubMed

    Wang, Chundi; Zhang, Xuemin; Li, Yongna; Lyu, Chuang

    2016-01-01

    Multiple object tracking (MOT) is an attentional process wherein people track several moving targets among several distractors. Symmetry, an important indicator of regularity, is a general spatial pattern observed in natural and artificial scenes. According to the "laws of perceptual organization" proposed by Gestalt psychologists, regularity is a principle of perceptual grouping, such as similarity and closure. A great deal of research reported that feature-based similarity grouping (e.g., grouping based on color, size, or shape) among targets in MOT tasks can improve tracking performance. However, no additive feature-based grouping effects have been reported where the tracking objects had two or more features. "Additive effect" refers to a greater grouping effect produced by grouping based on multiple cues instead of one cue. Can spatial symmetry produce a similar grouping effect similar to that of feature similarity in MOT tasks? Are the grouping effects based on symmetry and feature similarity additive? This study includes four experiments to address these questions. The results of Experiments 1 and 2 demonstrated the automatic symmetry-based grouping effects. More importantly, an additive grouping effect of symmetry and feature similarity was observed in Experiments 3 and 4. Our findings indicate that symmetry can produce an enhanced grouping effect in MOT and facilitate the grouping effect based on color or shape similarity. The "where" and "what" pathways might have played an important role in the additive grouping effect.

  3. Automated analysis of fundamental features of brain structures.

    PubMed

    Lancaster, Jack L; McKay, D Reese; Cykowski, Matthew D; Martinez, Michael J; Tan, Xi; Valaparla, Sunil; Zhang, Yi; Fox, Peter T

    2011-12-01

    Automated image analysis of the brain should include measures of fundamental structural features such as size and shape. We used principal axes (P-A) measurements to measure overall size and shape of brain structures segmented from MR brain images. The rationale was that quantitative volumetric studies of brain structures would benefit from shape standardization as had been shown for whole brain studies. P-A analysis software was extended to include controls for variability in position and orientation to support individual structure spatial normalization (ISSN). The rationale was that ISSN would provide a bias-free means to remove elementary sources of a structure's spatial variability in preparation for more detailed analyses. We studied nine brain structures (whole brain, cerebral hemispheres, cerebellum, brainstem, caudate, putamen, hippocampus, inferior frontal gyrus, and precuneus) from the 40-brain LPBA40 atlas. This paper provides the first report of anatomical positions and principal axes orientations within a standard reference frame, in addition to "shape/size related" principal axes measures, for the nine brain structures from the LPBA40 atlas. Analysis showed that overall size (mean volume) for internal brain structures was preserved using shape standardization while variance was reduced by more than 50%. Shape standardization provides increased statistical power for between-group volumetric studies of brain structures compared to volumetric studies that control only for whole brain size. To test ISSN's ability to control for spatial variability of brain structures we evaluated the overlap of 40 regions of interest (ROIs) in a standard reference frame for the nine different brain structures before and after processing. Standardizations of orientation or shape were ineffective when not combined with position standardization. The greatest reduction in spatial variability was seen for combined standardizations of position, orientation and shape. These

  4. Bioinspired Cellular Structures: Additive Manufacturing and Mechanical Properties

    NASA Astrophysics Data System (ADS)

    Stampfl, J.; Pettermann, H. E.; Liska, R.

    Biological materials (e.g., wood, trabecular bone, marine skeletons) rely heavily on the use of cellular architecture, which provides several advantages. (1) The resulting structures can bear the variety of "real life" load spectra using a minimum of a given bulk material, featuring engineering lightweight design principles. (2) The inside of the structures is accessible to body fluids which deliver the required nutrients. (3) Furthermore, cellular architectures can grow organically by adding or removing individual struts or by changing the shape of the constituting elements. All these facts make the use of cellular architectures a reasonable choice for nature. Using additive manufacturing technologies (AMT), it is now possible to fabricate such structures for applications in engineering and biomedicine. In this chapter, we present methods that allow the 3D computational analysis of the mechanical properties of cellular structures with open porosity. Various different cellular architectures including disorder are studied. In order to quantify the influence of architecture, the apparent density is always kept constant. Furthermore, it is shown that how new advanced photopolymers can be used to tailor the mechanical and functional properties of the fabricated structures.

  5. Origin of additional spectral features in modulated reflectance spectra of 2-dimensional semiconductor systems

    SciTech Connect

    Mukherjee, Amlan; Ghosh, Sandip

    2014-03-28

    High resolution photoreflectance (PR) spectroscopy study on a single GaAs/AlGaAs quantum well representing a two-dimensional (2D) system, shows additional distinct spectral features on the high energy side of the first confined heavy-hole and light-hole exciton transitions. The PR experiments involved a special dual detection technique which significantly improved the measurement sensitivity. Photoluminescence excitation spectroscopy data on the sample showed broadened step-like features around these energies. A detailed lineshape analysis, including first principles simulations, was performed to understand the origins of these additional PR spectral features. They are shown to arise primarily from inhomogeneously broadened first excited state transition of the excitons, rather than from a change in the joint density of states at the exciton continuum edge. The analysis suggests that such features are more likely in the case of 2D excitons as compared to 3D excitons in bulk material. Apart from its significance for post-growth characterization, identification of these additional PR features enables direct estimation of the exciton binding energy.

  6. Structural properties of prokaryotic promoter regions correlate with functional features.

    PubMed

    Meysman, Pieter; Collado-Vides, Julio; Morett, Enrique; Viola, Roberto; Engelen, Kristof; Laukens, Kris

    2014-01-01

    The structural properties of the DNA molecule are known to play a critical role in transcription. In this paper, the structural profiles of promoter regions were studied within the context of their diversity and their function for eleven prokaryotic species; Escherichia coli, Klebsiella pneumoniae, Salmonella Typhimurium, Pseudomonas auroginosa, Geobacter sulfurreducens Helicobacter pylori, Chlamydophila pneumoniae, Synechocystis sp., Synechoccocus elongates, Bacillus anthracis, and the archaea Sulfolobus solfataricus. The main anchor point for these promoter regions were transcription start sites identified through high-throughput experiments or collected within large curated databases. Prokaryotic promoter regions were found to be less stable and less flexible than the genomic mean across all studied species. However, direct comparison between species revealed differences in their structural profiles that can not solely be explained by the difference in genomic GC content. In addition, comparison with functional data revealed that there are patterns in the promoter structural profiles that can be linked to specific functional loci, such as sigma factor regulation or transcription factor binding. Interestingly, a novel structural element clearly visible near the transcription start site was found in genes associated with essential cellular functions and growth in several species. Our analyses reveals the great diversity in promoter structural profiles both between and within prokaryotic species. We observed relationships between structural diversity and functional features that are interesting prospects for further research to yet uncharacterized functional loci defined by DNA structural properties.

  7. Structure damage detection based on random forest recursive feature elimination

    NASA Astrophysics Data System (ADS)

    Zhou, Qifeng; Zhou, Hao; Zhou, Qingqing; Yang, Fan; Luo, Linkai

    2014-05-01

    Feature extraction is a key former step in structural damage detection. In this paper, a structural damage detection method based on wavelet packet decomposition (WPD) and random forest recursive feature elimination (RF-RFE) is proposed. In order to gain the most effective feature subset and to improve the identification accuracy a two-stage feature selection method is adopted after WPD. First, the damage features are sorted according to original random forest variable importance analysis. Second, using RF-RFE to eliminate the least important feature and reorder the feature list each time, then get the new feature importance sequence. Finally, k-nearest neighbor (KNN) algorithm, as a benchmark classifier, is used to evaluate the extracted feature subset. A four-storey steel shear building model is chosen as an example in method verification. The experimental results show that using the fewer features got from proposed method can achieve higher identification accuracy and reduce the detection time cost.

  8. Structural Features of Algebraic Quantum Notations

    ERIC Educational Resources Information Center

    Gire, Elizabeth; Price, Edward

    2015-01-01

    The formalism of quantum mechanics includes a rich collection of representations for describing quantum systems, including functions, graphs, matrices, histograms of probabilities, and Dirac notation. The varied features of these representations affect how computations are performed. For example, identifying probabilities of measurement outcomes…

  9. 1. Building #3, original structure and first addition, north side, ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    1. Building #3, original structure and first addition, north side, looking south. Photo shows (from left) the original 1911 structure, the 1939 infill addition, and the 1934 structure. - S. W. Shattuck Chemical Company, Incorporated, Building No. 3, 1805 South Bannock Street, Denver, Denver County, CO

  10. Comparison of additive image fusion vs. feature-level image fusion techniques for enhanced night driving

    NASA Astrophysics Data System (ADS)

    Bender, Edward J.; Reese, Colin E.; Van Der Wal, Gooitzen S.

    2003-02-01

    The Night Vision & Electronic Sensors Directorate (NVESD) has conducted a series of image fusion evaluations under the Head-Tracked Vision System (HTVS) program. The HTVS is a driving system for both wheeled and tracked military vehicles, wherein dual-waveband sensors are directed in a more natural head-slewed imaging mode. The HTVS consists of thermal and image-intensified TV sensors, a high-speed gimbal, a head-mounted display, and a head tracker. A series of NVESD field tests over the past two years has investigated the degree to which additive (A+B) image fusion of these sensors enhances overall driving performance. Additive fusion employs a single (but user adjustable) fractional weighting for all the features of each sensor's image. More recently, NVESD and Sarnoff Corporation have begun a cooperative effort to evaluate and refine Sarnoff's "feature-level" multi-resolution (pyramid) algorithms for image fusion. This approach employs digital processing techniques to select at each image point only the sensor with the strongest features, and to utilize only those features to reconstruct the fused video image. This selection process is performed simultaneously at multiple scales of the image, which are combined to form the reconstructed fused image. All image fusion techniques attempt to combine the "best of both sensors" in a single image. Typically, thermal sensors are better for detecting military threats and targets, while image-intensified sensors provide more natural scene cues and detect cultural lighting. This investigation will address the differences between additive fusion and feature-level image fusion techniques for enhancing the driver's overall situational awareness.

  11. The Wavelet Element Method. Part 2; Realization and Additional Features in 2D and 3D

    NASA Technical Reports Server (NTRS)

    Canuto, Claudio; Tabacco, Anita; Urban, Karsten

    1998-01-01

    The Wavelet Element Method (WEM) provides a construction of multiresolution systems and biorthogonal wavelets on fairly general domains. These are split into subdomains that are mapped to a single reference hypercube. Tensor products of scaling functions and wavelets defined on the unit interval are used on the reference domain. By introducing appropriate matching conditions across the interelement boundaries, a globally continuous biorthogonal wavelet basis on the general domain is obtained. This construction does not uniquely define the basis functions but rather leaves some freedom for fulfilling additional features. In this paper we detail the general construction principle of the WEM to the 1D, 2D and 3D cases. We address additional features such as symmetry, vanishing moments and minimal support of the wavelet functions in each particular dimension. The construction is illustrated by using biorthogonal spline wavelets on the interval.

  12. Structural correlations between dermoscopic and histopathological features of juvenile xanthogranuloma.

    PubMed

    Song, M; Kim, S-H; Jung, D-S; Ko, H-C; Kwon, K-S; Kim, M-B

    2011-03-01

    Juvenile xanthogranuloma(JXG) is the variant of non-Langerhans' cell histiocytosis. The orange-yellow background coloration with clouds of paler yellow deposits is the most characteristic dermoscopic finding of JXG. Other dermoscopic features include erythematous border, subtle pigment network and white linear streak. The objective of this study was to present the structural correlation between dermoscopic features and histopathological findings of JXG and to find the different dermoscopic features in various stages of JXG. Eleven patients with histologically proven JXG were examined with polarized light dermoscopy. Histopathological findings were assessed and dermoscopic features including setting sun appearance, clouds of paler yellow globules, whitish streak, and branched and linear vessels were evaluated. Among 11 patients, five patients were in early evolutionary stage, four patients in fully developed stage and two in late regressive stage. The setting sun appearance was found in all patients in different stages except one in late regressive stage (90.9%). The clouds of paler yellow globules were present in nine patients (81.8%) and were constant features in fully developed stage and late regressive stage. The whitish streak was present in four patients (36.4%) and telangiectasia in 10 patients (81.8%). The setting sun appearance may hold diagnostic value in early evolutionary stage to fully developed stage, but not in late regressive stage. The clouds of paler yellow globules are more predominant in fully developed stage and late regressive stage. In addition to the use of dermoscopy as an accurate diagnostic tool for differential diagnosis, it could be applied in evaluation of histopathological maturation of JXG.

  13. Feature and Statistical Model Development in Structural Health Monitoring

    NASA Astrophysics Data System (ADS)

    Kim, Inho

    All structures suffer wear and tear because of impact, excessive load, fatigue, corrosion, etc. in addition to inherent defects during their manufacturing processes and their exposure to various environmental effects. These structural degradations are often imperceptible, but they can severely affect the structural performance of a component, thereby severely decreasing its service life. Although previous studies of Structural Health Monitoring (SHM) have revealed extensive prior knowledge on the parts of SHM processes, such as the operational evaluation, data processing, and feature extraction, few studies have been conducted from a systematical perspective, the statistical model development. The first part of this dissertation, the characteristics of inverse scattering problems, such as ill-posedness and nonlinearity, reviews ultrasonic guided wave-based structural health monitoring problems. The distinctive features and the selection of the domain analysis are investigated by analytically searching the conditions of the uniqueness solutions for ill-posedness and are validated experimentally. Based on the distinctive features, a novel wave packet tracing (WPT) method for damage localization and size quantification is presented. This method involves creating time-space representations of the guided Lamb waves (GLWs), collected at a series of locations, with a spatially dense distribution along paths at pre-selected angles with respect to the direction, normal to the direction of wave propagation. The fringe patterns due to wave dispersion, which depends on the phase velocity, are selected as the primary features that carry information, regarding the wave propagation and scattering. The following part of this dissertation presents a novel damage-localization framework, using a fully automated process. In order to construct the statistical model for autonomous damage localization deep-learning techniques, such as restricted Boltzmann machine and deep belief network

  14. Structural features determining thermal adaptation of esterases.

    PubMed

    Kovacic, Filip; Mandrysch, Agathe; Poojari, Chetan; Strodel, Birgit; Jaeger, Karl-Erich

    2016-02-01

    The adaptation of microorganisms to extreme living temperatures requires the evolution of enzymes with a high catalytic efficiency under these conditions. Such extremophilic enzymes represent valuable tools to study the relationship between protein stability, dynamics and function. Nevertheless, the multiple effects of temperature on the structure and function of enzymes are still poorly understood at the molecular level. Our analysis of four homologous esterases isolated from bacteria living at temperatures ranging from 10°C to 70°C suggested an adaptation route for the modulation of protein thermal properties through the optimization of local flexibility at the protein surface. While the biochemical properties of the recombinant esterases are conserved, their thermal properties have evolved to resemble those of the respective bacterial habitats. Molecular dynamics simulations at temperatures around the optimal temperatures for enzyme catalysis revealed temperature-dependent flexibility of four surface-exposed loops. While the flexibility of some loops increased with raising the temperature and decreased with lowering the temperature, as expected for those loops contributing to the protein stability, other loops showed an increment of flexibility upon lowering and raising the temperature. Preserved flexibility in these regions seems to be important for proper enzyme function. The structural differences of these four loops, distant from the active site, are substantially larger than for the overall protein structure, indicating that amino acid exchanges within these loops occurred more frequently thereby allowing the bacteria to tune atomic interactions for different temperature requirements without interfering with the overall enzyme function.

  15. Structural features of reconstituted wheat wax films

    PubMed Central

    Pambou, Elias; Li, Zongyi; Campana, Mario; Hughes, Arwel; Clifton, Luke; Gutfreund, Philipp; Foundling, Jill

    2016-01-01

    Cuticular waxes are essential for the well-being of all plants, from controlling the transport of water and nutrients across the plant surface to protecting them against external environmental attacks. Despite their significance, our current understanding regarding the structure and function of the wax film is limited. In this work, we have formed representative reconstituted wax film models of controlled thicknesses that facilitated an ex vivo study of plant cuticular wax film properties by neutron reflection (NR). Triticum aestivum L. (wheat) waxes were extracted from two different wheat straw samples, using two distinct extraction methods. Waxes extracted from harvested field-grown wheat straw using supercritical CO2 are compared with waxes extracted from laboratory-grown wheat straw via wax dissolution by chloroform rinsing. Wax films were produced by spin-coating the two extracts onto silicon substrates. Atomic force microscopy and cryo-scanning electron microscopy imaging revealed that the two reconstituted wax film models are ultrathin and porous with characteristic nanoscale extrusions on the outer surface, mimicking the structure of epicuticular waxes found upon adaxial wheat leaf surfaces. On the basis of solid–liquid and solid–air NR and ellipsometric measurements, these wax films could be modelled into two representative layers, with the diffuse underlying layer fitted with thicknesses ranging from approximately 65 to 70 Å, whereas the surface extrusion region reached heights exceeding 200 Å. Moisture-controlled NR measurements indicated that water penetrated extensively into the wax films measured under saturated humidity and under water, causing them to hydrate and swell significantly. These studies have thus provided a useful structural basis that underlies the function of the epicuticular waxes in controlling the water transport of crops. PMID:27466439

  16. Structural features of reconstituted wheat wax films.

    PubMed

    Pambou, Elias; Li, Zongyi; Campana, Mario; Hughes, Arwel; Clifton, Luke; Gutfreund, Philipp; Foundling, Jill; Bell, Gordon; Lu, Jian R

    2016-07-01

    Cuticular waxes are essential for the well-being of all plants, from controlling the transport of water and nutrients across the plant surface to protecting them against external environmental attacks. Despite their significance, our current understanding regarding the structure and function of the wax film is limited. In this work, we have formed representative reconstituted wax film models of controlled thicknesses that facilitated an ex vivo study of plant cuticular wax film properties by neutron reflection (NR). Triticum aestivum L. (wheat) waxes were extracted from two different wheat straw samples, using two distinct extraction methods. Waxes extracted from harvested field-grown wheat straw using supercritical CO2 are compared with waxes extracted from laboratory-grown wheat straw via wax dissolution by chloroform rinsing. Wax films were produced by spin-coating the two extracts onto silicon substrates. Atomic force microscopy and cryo-scanning electron microscopy imaging revealed that the two reconstituted wax film models are ultrathin and porous with characteristic nanoscale extrusions on the outer surface, mimicking the structure of epicuticular waxes found upon adaxial wheat leaf surfaces. On the basis of solid-liquid and solid-air NR and ellipsometric measurements, these wax films could be modelled into two representative layers, with the diffuse underlying layer fitted with thicknesses ranging from approximately 65 to 70 Å, whereas the surface extrusion region reached heights exceeding 200 Å. Moisture-controlled NR measurements indicated that water penetrated extensively into the wax films measured under saturated humidity and under water, causing them to hydrate and swell significantly. These studies have thus provided a useful structural basis that underlies the function of the epicuticular waxes in controlling the water transport of crops. PMID:27466439

  17. Structural features of reconstituted wheat wax films.

    PubMed

    Pambou, Elias; Li, Zongyi; Campana, Mario; Hughes, Arwel; Clifton, Luke; Gutfreund, Philipp; Foundling, Jill; Bell, Gordon; Lu, Jian R

    2016-07-01

    Cuticular waxes are essential for the well-being of all plants, from controlling the transport of water and nutrients across the plant surface to protecting them against external environmental attacks. Despite their significance, our current understanding regarding the structure and function of the wax film is limited. In this work, we have formed representative reconstituted wax film models of controlled thicknesses that facilitated an ex vivo study of plant cuticular wax film properties by neutron reflection (NR). Triticum aestivum L. (wheat) waxes were extracted from two different wheat straw samples, using two distinct extraction methods. Waxes extracted from harvested field-grown wheat straw using supercritical CO2 are compared with waxes extracted from laboratory-grown wheat straw via wax dissolution by chloroform rinsing. Wax films were produced by spin-coating the two extracts onto silicon substrates. Atomic force microscopy and cryo-scanning electron microscopy imaging revealed that the two reconstituted wax film models are ultrathin and porous with characteristic nanoscale extrusions on the outer surface, mimicking the structure of epicuticular waxes found upon adaxial wheat leaf surfaces. On the basis of solid-liquid and solid-air NR and ellipsometric measurements, these wax films could be modelled into two representative layers, with the diffuse underlying layer fitted with thicknesses ranging from approximately 65 to 70 Å, whereas the surface extrusion region reached heights exceeding 200 Å. Moisture-controlled NR measurements indicated that water penetrated extensively into the wax films measured under saturated humidity and under water, causing them to hydrate and swell significantly. These studies have thus provided a useful structural basis that underlies the function of the epicuticular waxes in controlling the water transport of crops.

  18. Structural features of sequential weak measurements

    NASA Astrophysics Data System (ADS)

    Diósi, Lajos

    2016-07-01

    We discuss the abstract structure of sequential weak measurement (WM) of general observables. In all orders, the sequential WM correlations without postselection yield the corresponding correlations of the Wigner function, offering direct quantum tomography through the moments of the canonical variables. Correlations in spin-1/2 sequential weak measurements coincide with those in strong measurements, they are constrained kinematically, and they are equivalent with single measurements. In sequential WMs with postselection, an anomaly occurs, different from the weak value anomaly of single WMs. In particular, the spread of polarization σ ̂ as measured in double WMs of σ ̂ will diverge for certain orthogonal pre- and postselected states.

  19. An Indian boy with additional features in Pallister-Killian syndrome.

    PubMed

    Shah, Krati; George, Renu; Balla, Evangelynn Singh; Oommen, Samuel P; Padankatti, Caroline S; Srivastava, Vivi M; Danda, Sumita

    2012-09-01

    Pallister-Killian syndrome (PKS; OMIM: # 601803) is a rare sporadic genetic disorder characterized by pigmentary skin changes, distinctive dysmorphology, developmental delay, and mosaicism for tetrasomy of chromosome 12p. The authors report a case of PKS in a 2-y-old boy. He had pigmentary skin changes, characteristic facial features, developmental delay and hearing loss. He had sacral and post-auricular pits in addition, which has not yet been reported. A diagnosis of PKS was suspected on the basis of the patient's clinical features. Skin fibroblast culture was done which showed mosaic tetrasomy of isochromosome 12p consistent with Pallister-Killian syndrome. This case highlights the importance of dysmorphology as a diagnostic tool for recognition and accurate genetic counseling in genetic syndromes. PMID:22012142

  20. Biobased extreme pressure additives: Structure-property considerations

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Extreme pressure additives are widely used in lubricant formulations for engine oils, hydraulic fluids, gear oils, metalworking fluids, and many others. Extreme pressure additives contain selected elements such as sulfur, phosphorus, and halogens in their structures. These elements, under extreme tr...

  1. Coding of odor stimulus features among secondary olfactory structures.

    PubMed

    Xia, Christina Z; Adjei, Stacey; Wesson, Daniel W

    2015-07-01

    Sensory systems must represent stimuli in manners dependent upon a wealth of factors, including stimulus intensity and duration. One way the brain might handle these complex functions is to assign the tasks throughout distributed nodes, each contributing to information processing. We sought to explore this important aspect of sensory network function in the mammalian olfactory system, wherein the intensity and duration of odor exposure are critical contributors to odor perception. This is a quintessential model for exploring processing schemes given the distribution of odor information by olfactory bulb mitral and tufted cells into several anatomically distinct secondary processing stages, including the piriform cortex (PCX) and olfactory tubercle (OT), whose unique contributions to odor coding are unresolved. We explored the coding of PCX and OT neuron responses to odor intensity and duration. We found that both structures similarly partake in representing descending intensities of odors by reduced recruitment and modulation of neurons. Additionally, while neurons in the OT adapt to odor exposure, they display reduced capacity to adapt to either repeated presentations of odor or a single prolonged odor presentation compared with neurons in the PCX. These results provide insights into manners whereby secondary olfactory structures may, at least in some cases, uniquely represent stimulus features. PMID:26041832

  2. Coding of odor stimulus features among secondary olfactory structures

    PubMed Central

    Xia, Christina Z.; Adjei, Stacey

    2015-01-01

    Sensory systems must represent stimuli in manners dependent upon a wealth of factors, including stimulus intensity and duration. One way the brain might handle these complex functions is to assign the tasks throughout distributed nodes, each contributing to information processing. We sought to explore this important aspect of sensory network function in the mammalian olfactory system, wherein the intensity and duration of odor exposure are critical contributors to odor perception. This is a quintessential model for exploring processing schemes given the distribution of odor information by olfactory bulb mitral and tufted cells into several anatomically distinct secondary processing stages, including the piriform cortex (PCX) and olfactory tubercle (OT), whose unique contributions to odor coding are unresolved. We explored the coding of PCX and OT neuron responses to odor intensity and duration. We found that both structures similarly partake in representing descending intensities of odors by reduced recruitment and modulation of neurons. Additionally, while neurons in the OT adapt to odor exposure, they display reduced capacity to adapt to either repeated presentations of odor or a single prolonged odor presentation compared with neurons in the PCX. These results provide insights into manners whereby secondary olfactory structures may, at least in some cases, uniquely represent stimulus features. PMID:26041832

  3. Structural transformation features in titanium crystallite under mechanical loading

    SciTech Connect

    Kryzhevich, Dmitrij S.

    2015-10-27

    The features of defect structure generation and development in titanium crystallites were studied on the basis of molecular dynamics method. Interatomic interaction was described using many-body potentials calculated in the approximation of the embedded atom method. It is shown that local structural changes begin to occur in the crystallite at the achievement of a threshold strain value, which is accompanied by a dramatic decrease of potential energy. The features of the formation of local structural changes, which are precursors of classical stacking faults, were studied.

  4. Structural health monitoring feature design by genetic programming

    NASA Astrophysics Data System (ADS)

    Harvey, Dustin Y.; Todd, Michael D.

    2014-09-01

    Structural health monitoring (SHM) systems provide real-time damage and performance information for civil, aerospace, and other high-capital or life-safety critical structures. Conventional data processing involves pre-processing and extraction of low-dimensional features from in situ time series measurements. The features are then input to a statistical pattern recognition algorithm to perform the relevant classification or regression task necessary to facilitate decisions by the SHM system. Traditional design of signal processing and feature extraction algorithms can be an expensive and time-consuming process requiring extensive system knowledge and domain expertise. Genetic programming, a heuristic program search method from evolutionary computation, was recently adapted by the authors to perform automated, data-driven design of signal processing and feature extraction algorithms for statistical pattern recognition applications. The proposed method, called Autofead, is particularly suitable to handle the challenges inherent in algorithm design for SHM problems where the manifestation of damage in structural response measurements is often unclear or unknown. Autofead mines a training database of response measurements to discover information-rich features specific to the problem at hand. This study provides experimental validation on three SHM applications including ultrasonic damage detection, bearing damage classification for rotating machinery, and vibration-based structural health monitoring. Performance comparisons with common feature choices for each problem area are provided demonstrating the versatility of Autofead to produce significant algorithm improvements on a wide range of problems.

  5. Artificial-neural-network-based classification of mammographic microcalcifications using image structure features

    NASA Astrophysics Data System (ADS)

    Dhawan, Atam P.; Chitre, Yateen S.; Moskowitz, Myron

    1993-07-01

    Mammography associated with clinical breast examination and self-breast examination is the only effective and viable method for mass breast screening. It is however, difficult to distinguish between benign and malignant microcalcifications associated with breast cancer. Most of the techniques used in the computerized analysis of mammographic microcalcifications segment the digitized gray-level image into regions representing microcalcifications. We present a second-order gray-level histogram based feature extraction approach to extract microcalcification features. These features, called image structure features, are computed from the second-order gray-level histogram statistics, and do not require segmentation of the original image into binary regions. Several image structure features were computed for 100 cases of `difficult to diagnose' microcalcification cases with known biopsy results. These features were analyzed in a correlation study which provided a set of five best image structure features. A feedforward backpropagation neural network was used to classify mammographic microcalcifications using the image structure features. The network was trained on 10 cases of mammographic microcalcifications and tested on additional 85 `difficult-to-diagnose' microcalcifications cases using the selected image structure features. The trained network yielded good results for classification of `difficult-to- diagnose' microcalcifications into benign and malignant categories.

  6. Structure of continental rifts: Role of older features and magmatism

    SciTech Connect

    Keller, G.R.

    1996-12-31

    Recent geological and geophysical studies in several continental rifts have begun to shed light on the details of the processes which govern the structural evolution of these important exploration targets. In Kenya and Tanzania, the classic East African rift has been the object of several investigations which reveal that its location follows the boundary (suture ?) between the Tanzanian craton (Archean) and Mozambiquan belt (Proterozoic), The Baikal rift also follows a similar boundary, and the Mid-continent rift of North America appears to do the same. Rifts themselves often act as zones of weakness which are reactivated by younger tectonic regimes. The classic North American example of this effect is the Eocambrian Southern Oklahoma aulacogen which was deformed to create the Anadarko basin and Wichita uplift in the late Paleozoic. The Central basin platform has a similar history although the original rift formed at {approximately}1,100Ma. Integration of geophysical data with petrologic and geochemical data from several rift zones has also provided a new picture of the nature and extent of magmatic modification of the crust. An interesting contradiction is that Phanerozoic rifts, except the Afar region, show little evidence for major magmatic modification of the crust whereas, at least in North America, many Precambrian rifts are associated with very large mafic bodies in the crust. The Kenya rift displays evidence for modification of the lower crust in a two-phase magmatic history, but upper crustal magmatic features are limited to local intrusions associated with volcanoes. In this rift, complex basement structure plays a much more important role than previously realized, and the geophysical signatures of basement structure and magmatism are easy to confuse. If this is also the case in other rifts, additional rift basins remain to be discovered.

  7. Structure of continental rifts: Role of older features and magmatism

    SciTech Connect

    Keller, G.R. )

    1996-01-01

    Recent geological and geophysical studies in several continental rifts have begun to shed light on the details of the processes which govern the structural evolution of these important exploration targets. In Kenya and Tanzania, the classic East African rift has been the object of several investigations which reveal that its location follows the boundary (suture ) between the Tanzanian craton (Archean) and Mozambiquan belt (Proterozoic), The Baikal rift also follows a similar boundary, and the Mid-continent rift of North America appears to do the same. Rifts themselves often act as zones of weakness which are reactivated by younger tectonic regimes. The classic North American example of this effect is the Eocambrian Southern Oklahoma aulacogen which was deformed to create the Anadarko basin and Wichita uplift in the late Paleozoic. The Central basin platform has a similar history although the original rift formed at [approximately]1,100Ma. Integration of geophysical data with petrologic and geochemical data from several rift zones has also provided a new picture of the nature and extent of magmatic modification of the crust. An interesting contradiction is that Phanerozoic rifts, except the Afar region, show little evidence for major magmatic modification of the crust whereas, at least in North America, many Precambrian rifts are associated with very large mafic bodies in the crust. The Kenya rift displays evidence for modification of the lower crust in a two-phase magmatic history, but upper crustal magmatic features are limited to local intrusions associated with volcanoes. In this rift, complex basement structure plays a much more important role than previously realized, and the geophysical signatures of basement structure and magmatism are easy to confuse. If this is also the case in other rifts, additional rift basins remain to be discovered.

  8. Additives

    NASA Technical Reports Server (NTRS)

    Smalheer, C. V.

    1973-01-01

    The chemistry of lubricant additives is discussed to show what the additives are chemically and what functions they perform in the lubrication of various kinds of equipment. Current theories regarding the mode of action of lubricant additives are presented. The additive groups discussed include the following: (1) detergents and dispersants, (2) corrosion inhibitors, (3) antioxidants, (4) viscosity index improvers, (5) pour point depressants, and (6) antifouling agents.

  9. Effects of anodizing parameters and heat treatment on nanotopographical features, bioactivity, and cell culture response of additively manufactured porous titanium.

    PubMed

    Amin Yavari, S; Chai, Y C; Böttger, A J; Wauthle, R; Schrooten, J; Weinans, H; Zadpoor, A A

    2015-06-01

    Anodizing could be used for bio-functionalization of the surfaces of titanium alloys. In this study, we use anodizing for creating nanotubes on the surface of porous titanium alloy bone substitutes manufactured using selective laser melting. Different sets of anodizing parameters (voltage: 10 or 20V anodizing time: 30min to 3h) are used for anodizing porous titanium structures that were later heat treated at 500°C. The nanotopographical features are examined using electron microscopy while the bioactivity of anodized surfaces is measured using immersion tests in the simulated body fluid (SBF). Moreover, the effects of anodizing and heat treatment on the performance of one representative anodized porous titanium structures are evaluated using in vitro cell culture assays using human periosteum-derived cells (hPDCs). It has been shown that while anodizing with different anodizing parameters results in very different nanotopographical features, i.e. nanotubes in the range of 20 to 55nm, anodized surfaces have limited apatite-forming ability regardless of the applied anodizing parameters. The results of in vitro cell culture show that both anodizing, and thus generation of regular nanotopographical feature, and heat treatment improve the cell culture response of porous titanium. In particular, cell proliferation measured using metabolic activity and DNA content was improved for anodized and heat treated as well as for anodized but not heat-treated specimens. Heat treatment additionally improved the cell attachment of porous titanium surfaces and upregulated expression of osteogenic markers. Anodized but not heat-treated specimens showed some limited signs of upregulated expression of osteogenic markers. In conclusion, while varying the anodizing parameters creates different nanotube structure, it does not improve apatite-forming ability of porous titanium. However, both anodizing and heat treatment at 500°C improve the cell culture response of porous titanium.

  10. Effects of anodizing parameters and heat treatment on nanotopographical features, bioactivity, and cell culture response of additively manufactured porous titanium.

    PubMed

    Amin Yavari, S; Chai, Y C; Böttger, A J; Wauthle, R; Schrooten, J; Weinans, H; Zadpoor, A A

    2015-06-01

    Anodizing could be used for bio-functionalization of the surfaces of titanium alloys. In this study, we use anodizing for creating nanotubes on the surface of porous titanium alloy bone substitutes manufactured using selective laser melting. Different sets of anodizing parameters (voltage: 10 or 20V anodizing time: 30min to 3h) are used for anodizing porous titanium structures that were later heat treated at 500°C. The nanotopographical features are examined using electron microscopy while the bioactivity of anodized surfaces is measured using immersion tests in the simulated body fluid (SBF). Moreover, the effects of anodizing and heat treatment on the performance of one representative anodized porous titanium structures are evaluated using in vitro cell culture assays using human periosteum-derived cells (hPDCs). It has been shown that while anodizing with different anodizing parameters results in very different nanotopographical features, i.e. nanotubes in the range of 20 to 55nm, anodized surfaces have limited apatite-forming ability regardless of the applied anodizing parameters. The results of in vitro cell culture show that both anodizing, and thus generation of regular nanotopographical feature, and heat treatment improve the cell culture response of porous titanium. In particular, cell proliferation measured using metabolic activity and DNA content was improved for anodized and heat treated as well as for anodized but not heat-treated specimens. Heat treatment additionally improved the cell attachment of porous titanium surfaces and upregulated expression of osteogenic markers. Anodized but not heat-treated specimens showed some limited signs of upregulated expression of osteogenic markers. In conclusion, while varying the anodizing parameters creates different nanotube structure, it does not improve apatite-forming ability of porous titanium. However, both anodizing and heat treatment at 500°C improve the cell culture response of porous titanium. PMID

  11. Quantifying sequence and structural features of protein-RNA interactions.

    PubMed

    Li, Songling; Yamashita, Kazuo; Amada, Karlou Mar; Standley, Daron M

    2014-09-01

    Increasing awareness of the importance of protein-RNA interactions has motivated many approaches to predict residue-level RNA binding sites in proteins based on sequence or structural characteristics. Sequence-based predictors are usually high in sensitivity but low in specificity; conversely structure-based predictors tend to have high specificity, but lower sensitivity. Here we quantified the contribution of both sequence- and structure-based features as indicators of RNA-binding propensity using a machine-learning approach. In order to capture structural information for proteins without a known structure, we used homology modeling to extract the relevant structural features. Several novel and modified features enhanced the accuracy of residue-level RNA-binding propensity beyond what has been reported previously, including by meta-prediction servers. These features include: hidden Markov model-based evolutionary conservation, surface deformations based on the Laplacian norm formalism, and relative solvent accessibility partitioned into backbone and side chain contributions. We constructed a web server called aaRNA that implements the proposed method and demonstrate its use in identifying putative RNA binding sites. PMID:25063293

  12. Structuring Numbers 1 to 20: Developing Facile Addition and Subtraction

    ERIC Educational Resources Information Center

    Ellemor-Collins, David; Wright, Robert

    2009-01-01

    The Numeracy Intervention Research Project (NIRP) aims to develop assessment and instructional tools for use with low-attaining 3rd- and 4th-graders. The NIRP approach to instruction in addition and subtraction in the range 1 to 20 is described. The approach is based on a notion of structuring numbers, which draws on the work of Freudenthal and…

  13. A neighboring structure reconstructed matching algorithm based on LARK features

    NASA Astrophysics Data System (ADS)

    Xue, Taobei; Han, Jing; Zhang, Yi; Bai, Lianfa

    2015-11-01

    Aimed at the low contrast ratio and high noise of infrared images, and the randomness and ambient occlusion of its objects, this paper presents a neighboring structure reconstructed matching (NSRM) algorithm based on LARK features. The neighboring structure relationships of local window are considered based on a non-negative linear reconstruction method to build a neighboring structure relationship matrix. Then the LARK feature matrix and the NSRM matrix are processed separately to get two different similarity images. By fusing and analyzing the two similarity images, those infrared objects are detected and marked by the non-maximum suppression. The NSRM approach is extended to detect infrared objects with incompact structure. High performance is demonstrated on infrared body set, indicating a lower false detecting rate than conventional methods in complex natural scenes.

  14. Features and characterization needs of rubber composite structures

    NASA Technical Reports Server (NTRS)

    Tabaddor, Farhad

    1989-01-01

    Some of the major unique features of rubber composite structures are outlined. The features covered are those related to the material properties, but the analytical features are also briefly discussed. It is essential to recognize these features at the planning stage of any long-range analytical, experimental, or application program. The development of a general and comprehensive program which fully accounts for all the important characteristics of tires, under all the relevant modes of operation, may present a prohibitively expensive and impractical task at the near future. There is therefore a need to develop application methodologies which can utilize the less general models, beyond their theoretical limitations and yet with reasonable reliability, by proper mix of analytical, experimental, and testing activities.

  15. The design of impact absorbing structures for additive manufacture

    NASA Astrophysics Data System (ADS)

    Brennan-Craddock, J.; Brackett, D.; Wildman, R.; Hague, R.

    2012-08-01

    Additive manufacturing (AM) is increasingly becoming a viable manufacturing process due to dramatic advantages that it facilitates in the area of design complexity. This paper investigates the potential of additively manufactured lattice structures for the application of tailored impact absorption specifically for conformal body protection. It explores lattice cell types based on foam microstructures and assesses their suitability for impact absorption. The effect of varying the cell strut edge design is also investigated. The implications of scaling these cells up for AM are discussed as well as the design issues regarding the handling of geometric complexity and the requirement for body conformity. The suitability of AM materials for this application is also discussed.

  16. 113. Stage level floor structure. In addition to the movable ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    113. Stage level floor structure. In addition to the movable sections, there were hinged slots that could be opened in the stage floor (see sheet 4 of 9, note 4; sheet 5 of 9, note 2; and sheet 7 of 9, note 1). A remaining cast iron bracket is visible in the left foreground of the photograph. The actual structure for a hinged section is visible in the background, to the right of center. The hydraulic ram (type D) visible below the floor level is the south ram in the middle row; the view is facing north. - Auditorium Building, 430 South Michigan Avenue, Chicago, Cook County, IL

  17. Integrated visual analysis of protein structures, sequences, and feature data

    PubMed Central

    2015-01-01

    Background To understand the molecular mechanisms that give rise to a protein's function, biologists often need to (i) find and access all related atomic-resolution 3D structures, and (ii) map sequence-based features (e.g., domains, single-nucleotide polymorphisms, post-translational modifications) onto these structures. Results To streamline these processes we recently developed Aquaria, a resource offering unprecedented access to protein structure information based on an all-against-all comparison of SwissProt and PDB sequences. In this work, we provide a requirements analysis for several frequently occuring tasks in molecular biology and describe how design choices in Aquaria meet these requirements. Finally, we show how the interface can be used to explore features of a protein and gain biologically meaningful insights in two case studies conducted by domain experts. Conclusions The user interface design of Aquaria enables biologists to gain unprecedented access to molecular structures and simplifies the generation of insight. The tasks involved in mapping sequence features onto structures can be conducted easier and faster using Aquaria. PMID:26329268

  18. Oxygen additions in serial femtosecond crystallographic protein structures.

    PubMed

    Wang, Jimin

    2016-10-01

    In principle, serial femtosecond crystallography (SFX) could yield data sets that are completely free of the effects caused by slow, radiation-induced chemical reactions, for example, oxygen additions, responsible for radiation damage. However, experimental evidence is presented here that SFX data sets obtained by techniques that expose different parts of the same specimen to single pulses of radiation do not have this property, even if the specimen in question is frozen. The diffraction image of each such crystal obtained with the first pulse of radiation is certain to represent the structure of a protein that has not been modified chemically, but all of the images obtained subsequently from the same crystal will represent structures that have been modified to a lesser or greater extent by oxygen additions because of the rapid diffusion of oxygenic free radicals through the specimen. The higher the level of oxygen additions a crystal suffers during data collection, the poorer the statistical quality of data set obtained from it will, and the higher the free R-factors of the resulting structural model. PMID:27438534

  19. Lithospheric structure on Venus from tectonic modelling of compressional features

    NASA Technical Reports Server (NTRS)

    Banerdt, W. B.; Golombek, M. P.

    1987-01-01

    In previous studies, extensional models were used that incorporated realistic rheologies in order to constrain lithospheric structure. Lithospheric modelling is considered herein from the standpoint of compressional deformation. Features of presumed compressional tectonic origin are reviewed and a model for compressional folding based on lithospheric strength envelopes are presented that include the effects of both brittle and ductile yielding as well as finite elastic strength. Model predictions are then compared with the widths and spacings of observed tectonic features and it is concluded that the results are consistent with a thin crust overlying a relatively stronger mantle, with thermal gradients probably in the range of 10 to 15 deg/km.

  20. Mechanical features of the shuttle rotating service structure

    NASA Technical Reports Server (NTRS)

    Crump, J. M.

    1985-01-01

    With the development of the space shuttle launching facilities, it became mandatory to develop a shuttle rotating service structure to provide for the insertion and/or removal of payloads at the launch pads. The rotating service structure is a welded tubular steel space frame 189 feet high, 65 feet wide, and weighing 2100 tons. At the pivot column the structure is supported on a 30 inch diameter hemispherical bearing. At the opposite terminus the structure is supported on two truck assemblies each having eight 36 inch diameter double flanged wheels. The following features of the rotating service structure are discussed: (1) thermal expansion and contraction; (2) hurricane tie downs; (3) payload changeout room; (4) payload ground handling mechanism; (5) payload and orbiter access platforms; and (6) orbiter cargo bay access.

  1. New features in the structure of the classical Kuiper Belt

    NASA Astrophysics Data System (ADS)

    Gladman, Brett; Bannister, Michele T.; Alexandersen, Mike; Chen, Ying-Tung; Gwyn, Stephen; Kavelaars, J. J.; Petit, Jean-Marc; Volk, Kathryn; OSSOS collaboration

    2016-10-01

    We report fascinating new dynamical structures emerging from a higher precision view of the classical Kuiper belt (the plentiful non-resonant orbits with semimajor axes in roughly the a=35-60 au range). The classical Kuiper Belt divides into multiple sub-populations: an 'inner' classical belt (a small group of non-resonant objects with a<39.4 au where the 3:2 resonance is located), an abundant 'main' classical belt (between the 3:2 and the 2:1 at a=47.4 au), and a difficult to study outer classical belt beyond the 2:1. We examine the dynamical structure, as precisely revealed in the detections from OSSOS (the Outer Solar System Origin's Survey); the data set is of superb quality in terms of orbital element and numbers of detections (Kavelaars et al, this meeting).The previous CFEPS survey showed that the main classical belt requires a complex dynamical substructure that goes beyond a simple 'hot versus cold' division based primarily on orbital inclination; the 'cold' inclination component requires two sub-components in the semimajor axis and perihelion distance q space (Petit et al 2011). CFEPS modelled this as a 'stirred' component present at all a=40-47 AU semimajor axes, with a dense superposed 'kernel' near a=44 AU at low eccentricity; the first OSSOS data release remained consistent with this (Bannister et al 2016). As with the main asteroid belt, as statistics and orbital quality improve we see additional significant substructure emerging in the classical belt's orbital distribution.OSSOS continues to add evidence that the cold stirred component extends smoothly beyond the 2:1 (Bannister et al 2016). Unexpectedly, the data also reveal the clear existence of a paucity of orbits just beyond the outer edge of the kernel; there are significantly fewer TNOs in the narrow semimajor axis band from a=44.5-45.0 AU. This may be related to the kernel population's creation, or it may be an independent feature created by planet migration as resonances moved in the

  2. Common DNA structural features exhibited by eukaryotic ribosomal gene promoters.

    PubMed Central

    Marilley, M; Pasero, P

    1996-01-01

    Nucleotide sequences of DNA regions containing eukaryotic ribosomal promoters were analysed using strategies designed to reveal sequence-directed structural features. DNA curvature, duplex stability and pattern of twist angle variation were studied by computer modelling. Although ribosomal promoters are known to lack sequence homology (unless very closely related species are considered), investigation of these structural characteristics uncovered striking homologies in all the taxonomic groups examined so far. This wide conservation of DNA structures, while DNA sequence is not conserved, suggests that the determined structures are fundamental for ribosomal promoter function. Moreover, this result agrees well with the recent observations showing that RNA polymerase I transcription factors have not evolved as intensively as previously suspected. PMID:8710487

  3. Structure of ternary additive hard-sphere fluid mixtures

    NASA Astrophysics Data System (ADS)

    Malijevský, Alexander; Malijevský, Anatol; Yuste, Santos B.; Santos, Andrés; López de Haro, Mariano

    2002-12-01

    Monte Carlo simulations on the structural properties of ternary fluid mixtures of additive hard spheres are reported. The results are compared with those obtained from a recent analytical approximation [S. B. Yuste, A. Santos, and M. López de Haro, J. Chem. Phys. 108, 3683 (1998)] to the radial distribution functions of hard-sphere mixtures and with the results derived from the solution of the Ornstein-Zernike integral equation with both the Martynov-Sarkisov and the Percus-Yevick closures. Very good agreement between the results of the first two approaches and simulation is observed, with a noticeable improvement over the Percus-Yevick predictions especially near contact.

  4. Additive manufacturing of ceramic structures by laser engineered net shaping

    NASA Astrophysics Data System (ADS)

    Niu, Fangyong; Wu, Dongjiang; Ma, Guangyi; Zhang, Bi

    2015-11-01

    Ceramic is an important material with outstanding physical properties whereas impurities and porosities generated by traditional manufacturing methods limits its further industrial applications. In order to solve this problem, direct fabrication of Al2O3 ceramic structures is conducted by laser engineered net shaping system and pure ceramic powders. Grain refinement strengthening method by doping ZrO2 and dispersion strengthening method by doping SiC are proposed to suppress cracks in fabricating Al2O3 structure. Phase compositions, microstructures as well as mechanical properties of fabricated specimens are then analyzed. The results show that the proposed two methods are effective in suppressing cracks and structures of single-bead wall, arc and cylinder ring are successfully deposited. Stable phase of α-Al2O3 and t-ZrO2 are obtained in the fabricated specimens. Micro-hardness higher than 1700 HV are also achieved for both Al2O3 and Al2O3/ZrO2, which are resulted from fine directional crystals generated by the melting-solidification process. Results presented indicate that additive manufacturing is a very attractive technique for the production of high-performance ceramic structures in a single step.

  5. Weighted Feature Significance: A Simple, Interpretable Model of Compound Toxicity Based on the Statistical Enrichment of Structural Features

    PubMed Central

    Huang, Ruili; Southall, Noel; Xia, Menghang; Cho, Ming-Hsuang; Jadhav, Ajit; Nguyen, Dac-Trung; Inglese, James; Tice, Raymond R.; Austin, Christopher P.

    2009-01-01

    In support of the U.S. Tox21 program, we have developed a simple and chemically intuitive model we call weighted feature significance (WFS) to predict the toxicological activity of compounds, based on the statistical enrichment of structural features in toxic compounds. We trained and tested the model on the following: (1) data from quantitative high–throughput screening cytotoxicity and caspase activation assays conducted at the National Institutes of Health Chemical Genomics Center, (2) data from Salmonella typhimurium reverse mutagenicity assays conducted by the U.S. National Toxicology Program, and (3) hepatotoxicity data published in the Registry of Toxic Effects of Chemical Substances. Enrichments of structural features in toxic compounds are evaluated for their statistical significance and compiled into a simple additive model of toxicity and then used to score new compounds for potential toxicity. The predictive power of the model for cytotoxicity was validated using an independent set of compounds from the U.S. Environmental Protection Agency tested also at the National Institutes of Health Chemical Genomics Center. We compared the performance of our WFS approach with classical classification methods such as Naive Bayesian clustering and support vector machines. In most test cases, WFS showed similar or slightly better predictive power, especially in the prediction of hepatotoxic compounds, where WFS appeared to have the best performance among the three methods. The new algorithm has the important advantages of simplicity, power, interpretability, and ease of implementation. PMID:19805409

  6. Nanoscale structural features determined by AFM for single virus particles.

    PubMed

    Chen, Shu-wen W; Odorico, Michael; Meillan, Matthieu; Vellutini, Luc; Teulon, Jean-Marie; Parot, Pierre; Bennetau, Bernard; Pellequer, Jean-Luc

    2013-11-21

    In this work, we propose "single-image analysis", as opposed to multi-image averaging, for extracting valuable information from AFM images of single bio-particles. This approach allows us to study molecular systems imaged by AFM under general circumstances without restrictions on their structural forms. As feature exhibition is a resolution correlation, we have performed AFM imaging on surfaces of tobacco mosaic virus (TMV) to demonstrate variations of structural patterns with probing resolution. Two AFM images were acquired with the same tip at different probing resolutions in terms of pixel width, i.e., 1.95 and 0.49 nm per pixel. For assessment, we have constructed an in silico topograph based on the three-dimensional crystal structure of TMV as a reference. The prominent artifacts observed in the AFM-determined shape of TMV were attributed to tip convolutions. The width of TMV rod was systematically overestimated by ~10 nm at both probing resolutions of AFM. Nevertheless, the effects of tip convolution were less severe in vertical orientation so that the estimated height of TMV by AFM imaging was in close agreement with the in silico X-ray topograph. Using dedicated image processing algorithms, we found that at low resolution (i.e., 1.95 nm per pixel), the extracted surface features of TMV can be interpreted as a partial or full helical repeat (three complete turns with ~7.0 nm in length), while individual protein subunits (~2.5 nm) were perceivable only at high resolution. The present study shows that the scales of revealed structural features in AFM images are subject to both probing resolution and processing algorithms for image analysis. PMID:24056758

  7. Tuning structure and mobility of solvation shells surrounding tracer additives

    SciTech Connect

    Carmer, James; Jain, Avni; Bollinger, Jonathan A.; Truskett, Thomas M.; Swol, Frank van

    2015-03-28

    Molecular dynamics simulations and a stochastic Fokker-Planck equation based approach are used to illuminate how position-dependent solvent mobility near one or more tracer particle(s) is affected when tracer-solvent interactions are rationally modified to affect corresponding solvation structure. For tracers in a dense hard-sphere fluid, we compare two types of tracer-solvent interactions: (1) a hard-sphere-like interaction, and (2) a soft repulsion extending beyond the hard core designed via statistical mechanical theory to enhance tracer mobility at infinite dilution by suppressing coordination-shell structure [Carmer et al., Soft Matter 8, 4083–4089 (2012)]. For the latter case, we show that the mobility of surrounding solvent particles is also increased by addition of the soft repulsive interaction, which helps to rationalize the mechanism underlying the tracer’s enhanced diffusivity. However, if multiple tracer surfaces are in closer proximity (as at higher tracer concentrations), similar interactions that disrupt local solvation structure instead suppress the position-dependent solvent dynamics.

  8. Tuning structure and mobility of solvation shells surrounding tracer additives

    NASA Astrophysics Data System (ADS)

    Carmer, James; Jain, Avni; Bollinger, Jonathan A.; van Swol, Frank; Truskett, Thomas M.

    2015-03-01

    Molecular dynamics simulations and a stochastic Fokker-Planck equation based approach are used to illuminate how position-dependent solvent mobility near one or more tracer particle(s) is affected when tracer-solvent interactions are rationally modified to affect corresponding solvation structure. For tracers in a dense hard-sphere fluid, we compare two types of tracer-solvent interactions: (1) a hard-sphere-like interaction, and (2) a soft repulsion extending beyond the hard core designed via statistical mechanical theory to enhance tracer mobility at infinite dilution by suppressing coordination-shell structure [Carmer et al., Soft Matter 8, 4083-4089 (2012)]. For the latter case, we show that the mobility of surrounding solvent particles is also increased by addition of the soft repulsive interaction, which helps to rationalize the mechanism underlying the tracer's enhanced diffusivity. However, if multiple tracer surfaces are in closer proximity (as at higher tracer concentrations), similar interactions that disrupt local solvation structure instead suppress the position-dependent solvent dynamics.

  9. Towards improved NDE and SHM methodologies incorporating nonlinear structural features

    NASA Astrophysics Data System (ADS)

    Chillara, Vamshi Krishna

    Ultrasound is widely employed in Nondestructive Evaluation (NDE) and Structural Health Monitoring (SHM) applications to detect and characterize damage/defects in materials. In particular, ultrasonic guided waves are considered a foremost candidate for in-situ monitoring applications. Conventional ultrasonic techniques rely on changes/discontinuities in linear elastic material properties, namely the Young's modulus and shear modulus to detect damage. On the other hand, nonlinear ultrasonic techniques that rely on micro-scale nonlinear material/structural behavior are proven to be sensitive to damage induced microstructural changes that precede macro-scale damage and are hence capable of early damage detection. The goal of this thesis is to investigate the capabilities of nonlinear guided waves --- a fusion of nonlinear ultrasonic techniques with the guided wave methodologies for early damage detection. To that end, the thesis focuses on two important aspects of the problem: 1. Wavemechanics - deals with ultrasonic guided wave propagation in nonlinear waveguides; 2. Micromechanics - deals with correlating ultrasonic response with micro-scale nonlinear material behavior. For the development of efficient NDE and SHM methodologies that incorporate nonlinear structural features, a detailed understanding of the above aspects is indispensable. In this thesis, the wavemechanics aspect of the problem is dealt with from both theoretical and numerical standpoints. A generalized theoretical framework is developed to study higher harmonic guided waves in plates. This was employed to study second harmonic guided waves in pipes using a large-radius asymptotic approximation. Second harmonic guided waves in plates are studied from a numerical standpoint. Theoretical predictions are validated and some key aspects of higher harmonic generation in waveguides are outlined. Finally, second harmonic guided waves in plates with inhomogeneous and localized nonlinearities are studied and

  10. Landscape Features Shape Genetic Structure in Threatened Northern Spotted Owls

    USGS Publications Warehouse

    Funk, W. Chris; Forsman, Eric D.; Mullins, Thomas D.; Haig, Susan M.

    2008-01-01

    Several recent studies have shown that landscape features can strongly affect spatial patterns of gene flow and genetic variation. Understanding landscape effects on genetic variation is important in conservation for defining management units and understanding movement patterns. The landscape may have little effect on gene flow, however, in highly mobile species such as birds. We tested for genetic breaks associated with landscape features in the northern spotted owl (Strix occidentalis caurina), a threatened subspecies associated with old forests in the U.S. Pacific Northwest and extreme southwestern Canada. We found little evidence for distinct genetic breaks in northern spotted owls using a large microsatellite dataset (352 individuals from across the subspecies' range genotyped at 10 loci). Nonetheless, dry low-elevation valleys and the Cascade and Olympic Mountains restrict gene flow, while the Oregon Coast Range facilitates it. The wide Columbia River is not a barrier to gene flow. In addition, inter-individual genetic distance and latitude were negatively related, likely reflecting northward colonization following Pleistocene glacial recession. Our study shows that landscape features may play an important role in shaping patterns of genetic variation in highly vagile taxa such as birds.

  11. Faxing Structures to the Moon: Freeform Additive Construction System (FACS)

    NASA Technical Reports Server (NTRS)

    Howe, A. Scott; Wilcox, Brian; McQuin, Christopher; Townsend, Julie; Rieber, Richard; Barmatz, Martin; Leichty, John

    2013-01-01

    Using the highly articulated All-Terrain Hex-Limbed Extra-Terrestrial Explorer (ATHLETE) robotic mobility system as a precision positioning tool, a variety of print head technologies can be used to 3D print large-scale in-situ structures on planetary surfaces such as the moon or Mars. In effect, in the same way CAD models can be printed in a 3D printer, large-scale structures such as walls, vaults, domes, berms, paving, trench walls, and other insitu derived elements can be FAXed to the planetary surface and built in advance of the arrival of crews, supplementing equipment and materials brought from earth. This paper discusses the ATHLETE system as a mobility / positioning platform, and presents several options for large-scale additive print head technologies, including tunable microwave "sinterator" approaches and in-situ concrete deposition. The paper also discusses potential applications, such as sintered-in-place habitat shells, radiation shielding, road paving, modular bricks, and prefabricated construction components.

  12. Aspartylglucosaminuria in a Puerto Rican family: additional features of a panethnic disorder.

    PubMed

    Chitayat, D; Nakagawa, S; Marion, R W; Sachs, G S; Hahm, S Y; Goldman, H S

    1988-11-01

    We report on 3 Puerto Rican brothers with the clinical and laboratory findings of aspartylglucosaminuria (AGU). Their parents were first cousins. The affected sibs have the "cardinal" manifestations of AGU, including developmental disabilities, progressive "coarsening" of the face, and early onset of hepatosplenomegaly. Biochemical studies showed elevated levels of urinary aspartylglucosamine and very low activity of aspartylglucosaminidase(AGA) in cultured fibroblasts. With long term follow-up, previously undescribed manifestations were noted, including radiographic evidence of spondylolysis and spondylolisthesis in early childhood and development of macro-orchidism during puberty. This family shows that AGU is not limited to individuals of Finnish background, but that the gene is panethnic in distribution and that additional changes, not previously noted, may present with advancing age. PMID:3228136

  13. Hemipteran Mitochondrial Genomes: Features, Structures and Implications for Phylogeny

    PubMed Central

    Wang, Yuan; Chen, Jing; Jiang, Li-Yun; Qiao, Ge-Xia

    2015-01-01

    The study of Hemipteran mitochondrial genomes (mitogenomes) began with the Chagas disease vector, Triatoma dimidiata, in 2001. At present, 90 complete Hemipteran mitogenomes have been sequenced and annotated. This review examines the history of Hemipteran mitogenomes research and summarizes the main features of them including genome organization, nucleotide composition, protein-coding genes, tRNAs and rRNAs, and non-coding regions. Special attention is given to the comparative analysis of repeat regions. Gene rearrangements are an additional data type for a few families, and most mitogenomes are arranged in the same order to the proposed ancestral insect. We also discuss and provide insights on the phylogenetic analyses of a variety of taxonomic levels. This review is expected to further expand our understanding of research in this field and serve as a valuable reference resource. PMID:26039239

  14. A deep learning framework for modeling structural features of RNA-binding protein targets

    PubMed Central

    Zhang, Sai; Zhou, Jingtian; Hu, Hailin; Gong, Haipeng; Chen, Ligong; Cheng, Chao; Zeng, Jianyang

    2016-01-01

    RNA-binding proteins (RBPs) play important roles in the post-transcriptional control of RNAs. Identifying RBP binding sites and characterizing RBP binding preferences are key steps toward understanding the basic mechanisms of the post-transcriptional gene regulation. Though numerous computational methods have been developed for modeling RBP binding preferences, discovering a complete structural representation of the RBP targets by integrating their available structural features in all three dimensions is still a challenging task. In this paper, we develop a general and flexible deep learning framework for modeling structural binding preferences and predicting binding sites of RBPs, which takes (predicted) RNA tertiary structural information into account for the first time. Our framework constructs a unified representation that characterizes the structural specificities of RBP targets in all three dimensions, which can be further used to predict novel candidate binding sites and discover potential binding motifs. Through testing on the real CLIP-seq datasets, we have demonstrated that our deep learning framework can automatically extract effective hidden structural features from the encoded raw sequence and structural profiles, and predict accurate RBP binding sites. In addition, we have conducted the first study to show that integrating the additional RNA tertiary structural features can improve the model performance in predicting RBP binding sites, especially for the polypyrimidine tract-binding protein (PTB), which also provides a new evidence to support the view that RBPs may own specific tertiary structural binding preferences. In particular, the tests on the internal ribosome entry site (IRES) segments yield satisfiable results with experimental support from the literature and further demonstrate the necessity of incorporating RNA tertiary structural information into the prediction model. The source code of our approach can be found in https

  15. Features of quasistable laminar flows of He II and an additional dissipative process

    NASA Astrophysics Data System (ADS)

    Gritsenko, I. A.; Klokol, K. A.; Sokolov, S. S.; Sheshin, G. A.

    2016-03-01

    Quasistable laminar flow of He II at a temperature of 140 mK is studied experimentally. The liquid flow was excited by a vibrating quartz tuning fork with a resonance frequency of about 24 kHz. It was found that for velocities of the tuning fork oscillations from 0.046 to 0.16 m/s, the He II flow can be both quasistable laminar and turbulent. Transitions between these flow regimes were observed. When the velocity of the tuning fork oscillations increases more rapidly, the velocity at which the quasistable flow becomes unstable and undergoes a transition to a turbulent flow is higher. Mechanisms for the dissipation of the energy of the oscillating tines of the tuning fork in the quasistable laminar flow regime are analyzed. It is found that there is an additional mechanism for dissipation of the energy of the oscillating tuning fork beyond internal friction in the quartz. This mechanism is associated with mutual friction owing to scattering of thermal excitations of He II on quantized vortices and leads to a cubic dependence of the exciting force on the fluid velocity.

  16. Unique structural features of red kidney bean purple acid phosphatase.

    PubMed

    Cashikar, A G; Rao, M N

    1995-06-01

    Purple acid phosphatase from red kidney beans (Phaseolus vulgaris) has been purified to homogeneity and characterized. The enzyme is a homodimer of 60 kDa subunits each containing one atom of zinc and iron in the active site. Circular dichroism spectral studies on the purified enzyme reveals that a large portion of the peptide backbone is in the unordered and beta-turn conformation. A unique feature of the red kidney bean acid phosphatase, which we have found, is that one of the two cysteines of each subunit is involved in the formation of an inter-subunit disulphide. The thiol group of the other cysteine is not necessary for the activity of the enzyme. Western blot analysis with antibodies raised against kidney bean acid phosphatase could not recognize acid phosphatases from other sources except from potato. This paper emphasizes the fact that acid phosphatases are functionally, but not structurally, conserved enzymes. PMID:7590853

  17. Automatic classification of hepatocellular carcinoma images based on nuclear and structural features

    NASA Astrophysics Data System (ADS)

    Kiyuna, Tomoharu; Saito, Akira; Marugame, Atsushi; Yamashita, Yoshiko; Ogura, Maki; Cosatto, Eric; Abe, Tokiya; Hashiguchi, Akinori; Sakamoto, Michiie

    2013-03-01

    Diagnosis of hepatocellular carcinoma (HCC) on the basis of digital images is a challenging problem because, unlike gastrointestinal carcinoma, strong structural and morphological features are limited and sometimes absent from HCC images. In this study, we describe the classification of HCC images using statistical distributions of features obtained from image analysis of cell nuclei and hepatic trabeculae. Images of 130 hematoxylin-eosin (HE) stained histologic slides were captured at 20X by a slide scanner (Nanozoomer, Hamamatsu Photonics, Japan) and 1112 regions of interest (ROI) images were extracted for classification (551 negatives and 561 positives, including 113 well-differentiated positives). For a single nucleus, the following features were computed: area, perimeter, circularity, ellipticity, long and short axes of elliptic fit, contour complexity and gray level cooccurrence matrix (GLCM) texture features (angular second moment, contrast, homogeneity and entropy). In addition, distributions of nuclear density and hepatic trabecula thickness within an ROI were also extracted. To represent an ROI, statistical distributions (mean, standard deviation and percentiles) of these features were used. In total, 78 features were extracted for each ROI and a support vector machine (SVM) was trained to classify negative and positive ROIs. Experimental results using 5-fold cross validation show 90% sensitivity for an 87.8% specificity. The use of statistical distributions over a relatively large area makes the HCC classifier robust to occasional failures in the extraction of nuclear or hepatic trabecula features, thus providing stability to the system.

  18. Orientale and Caloris. [lunar basins with similar structural features

    NASA Technical Reports Server (NTRS)

    Mccauley, J. F.

    1977-01-01

    Based on revised stratigraphy, structural interpretation, explosion-crater data, and a genetic model for Orientale, it is suggested that Orientale and Caloris have much in common. It is noted that: (1) although the basin fill in Caloris is different from that seen in Orientale, the materials between the most prominent scarp and the weakly-developed outer scarp may be degraded equivalents of the massifs and knobs associated with the Montes Rook, (2) the Montes Rook and the main Caloris scarp have similar stratigraphic and structural features, (3) the lineated ejecta derived from shallower horizons are found near and beyond the weakly-developed outer Caloris scarp which is the counterpart of the Orientale scarp, (4) a well developed field of secondary craters is observed beyond 1 basin diameter at Caloris, (5) the observed textural differences between the material around the main Caloris scarp and the lineated material beyond suggest that Mercury is layered and that Caloris crater excavated coherent materials from one or more of these layers at depth, and (6) the difference in spacing between the Caloris rings is not related to internal layering effects.

  19. Structural origin for low-temperature relaxation features in magnetic nanoparticles

    NASA Astrophysics Data System (ADS)

    Laha, S. S.; Regmi, R.; Lawes, G.

    2013-08-01

    In addition to superparamagnetic relaxation associated with coherent spin reversal, magnetic nanoparticles often also exhibit additional relaxation features in the magnetic dissipation at low temperatures. Our studies show that the incorporation of boron, gadolinium and lanthanum into iron oxide (Fe3O4) nanoparticles substantially enhances these low-temperature magnetic relaxation properties. The structural and morphological studies of these nanoparticles were conducted using x-ray diffraction, transmission electron microscopy and Raman spectroscopy. The doped samples have retained the crystal structure of the parent Fe3O4 nanoparticles, although the shape and size of some of the nanoparticle samples have changed. Using ac magnetic susceptibility measurements, we parameterized the low-temperature magnetic features, with the amplitude of the associated magnetic relaxation showing a dramatic increase for certain dopants. The enhanced frequency-dependent magnetic relaxation features can be attributed to structural, rather than magnetic, defects in these doped Fe3O4 nanoparticles. These results strongly suggest that the low-temperature magnetic relaxation typically observed in magnetic nanoparticles is a single-particle effect produced by structural defects and is not significantly influenced by interparticle interactions.

  20. Aeromagnetic map of Korea; Magnetic patterns and structural features

    NASA Astrophysics Data System (ADS)

    Park, Yeong-Sue; Rim, Hyoungrea; Lim, Mutaek; Shin, Young Hong

    2014-05-01

    Regional airborne magnetic survey is very cost-effective mapping tool. Magnetic anomaly maps have abundant information, which are an important tool for understanding the geological evolution and mineral exploration. The pattern of magnetic anomaly map is a powerful indicator of geologic structure and rock formation. Magnetic anomaly patterns primarily reflect the distribution and structural setting of magnetized material within the crust. These features including amplitude and orientation of individual anomalies or the texture of anomalous regions can provide useful constraints for geological interpretation. KIGAM has conducted airborne magnetic mapping programme since 1982, and has coverage of almost whole the country. The latest version of airborne magnetic anomaly map was published by compiling data acquired from 1982 to 2012. The helicopter-borne surveys were flown by a line spacing 1~2 km with control lines of 5~8 km. The flight altitude was tried to keep 100~150 m above ground surface with sampling distance of 30m. The data were continued to the reference level of 300 m above ground level, and regional field was reduced by 11th generation IGRF. This paper introduced the latest version of magnetic anomaly map of Korea, and briefly examined the magnetic characteristics, with geologic characteristics and structural features of tectonic zones. Furthermore, magnetic patterns were quantitatively analyzed by using skeletonization technique. Korea, southern part of the Korean peninsula, could be divided in 5 tectonic provinces, such as, Gyeonggi massif, Okcheon fold belt, Sobaeksan massif, Gyeongsang basin, and circum-Pacific alkali volcanic zone. Magnetic anomalies in Gyeonggi massif zone are broadly distributed with moderately high amplitude, and the dominant trend is NE, but not strong. Okcheon fold belt can be magnetically characterized as strong dominant NE trend (Sinian direction) and linear positive anomalies of high amplitude. Sobaeksan massif is magnetically

  1. Time series analysis and feature extraction techniques for structural health monitoring applications

    NASA Astrophysics Data System (ADS)

    Overbey, Lucas A.

    Recently, advances in sensing and sensing methodologies have led to the deployment of multiple sensor arrays on structures for structural health monitoring (SHM) applications. Appropriate feature extraction, detection, and classification methods based on measurements obtained from these sensor networks are vital to the SHM paradigm. This dissertation focuses on a multi-input/multi-output approach to novel data processing procedures to produce detailed information about the integrity of a structure in near real-time. The studies employ nonlinear time series analysis techniques to extract three different types of features for damage diagnostics: namely, nonlinear prediction error, transfer entropy, and the generalized interdependence. These features form reliable measures of generalized correlations between multiple measurements to capture aspects of the dynamics related to the presence of damage. Several analyses are conducted on each of these features. Specifically, variations of nonlinear prediction error are introduced, analyzed, and validated, including the use of a stochastic excitation to augment generality, introduction of local state-space models for sensitivity enhancement, and the employment of comparisons between multiple measurements for localization capability. A modification and enhancement to transfer entropy is created and validated for improved sensitivity. In addition, a thorough analysis of the effects of variability to transfer entropy estimation is made. The generalized interdependence is introduced into the literature and validated as an effective measure of damage presence, extent, and location. These features are validated on a multi-degree-of-freedom dynamic oscillator and several different frame experiments. The evaluated features are then fed into four different classification schemes to obtain a concurrent set of outputs that categorize the integrity of the structure, e.g. the presence, extent, location, and type of damage, taking

  2. Nonlocal sparse model with adaptive structural clustering for feature extraction of aero-engine bearings

    NASA Astrophysics Data System (ADS)

    Zhang, Han; Chen, Xuefeng; Du, Zhaohui; Li, Xiang; Yan, Ruqiang

    2016-04-01

    Fault information of aero-engine bearings presents two particular phenomena, i.e., waveform distortion and impulsive feature frequency band dispersion, which leads to a challenging problem for current techniques of bearing fault diagnosis. Moreover, although many progresses of sparse representation theory have been made in feature extraction of fault information, the theory also confronts inevitable performance degradation due to the fact that relatively weak fault information has not sufficiently prominent and sparse representations. Therefore, a novel nonlocal sparse model (coined NLSM) and its algorithm framework has been proposed in this paper, which goes beyond simple sparsity by introducing more intrinsic structures of feature information. This work adequately exploits the underlying prior information that feature information exhibits nonlocal self-similarity through clustering similar signal fragments and stacking them together into groups. Within this framework, the prior information is transformed into a regularization term and a sparse optimization problem, which could be solved through block coordinate descent method (BCD), is formulated. Additionally, the adaptive structural clustering sparse dictionary learning technique, which utilizes k-Nearest-Neighbor (kNN) clustering and principal component analysis (PCA) learning, is adopted to further enable sufficient sparsity of feature information. Moreover, the selection rule of regularization parameter and computational complexity are described in detail. The performance of the proposed framework is evaluated through numerical experiment and its superiority with respect to the state-of-the-art method in the field is demonstrated through the vibration signals of experimental rig of aircraft engine bearings.

  3. Morphological change tracking of dendritic spines based on structural features.

    PubMed

    Son, J; Song, S; Lee, S; Chang, S; Kim, M

    2011-03-01

    Identification and tracking of dendritic spine morphology from two-dimensional time-lapsed images plays an important role in neurobiological research. Such analysis can enable us to derive a correlation between morphological characteristics and molecular mechanism of dendritic spine development and remodelling. Moreover, Neuronal morphology of hippocampal Cornu Ammonis 1 region is critical for understanding the Alzheimer's disease. Therefore, we need to extract and trace the dendritic spines accurately for examining their development and remodelling processes, which are related to functions of hippocampal Cornu Ammonis 1. There are some problems to be solved in related researches. Noise due to the properties of optical microscopes makes it difficult to identify and trace dendritic spines accurately. To solve these problems, in this paper we present a local spine detection technique minimizing noise influence in two-dimensional optical microscopy images. Also, we suggest an efficient mapping method for tracking the dynamics of dendritic spines to measure their morphological changes quantitatively. First, to utilize structural feature of spines, which are small protrusions of tree-like dendrites, we extract the tips of each dendritic branch and use this position as an initial contour position for a deformable model-based segmentation. We then use a geodesic active contour model to detect the spines accurately. Secondly, we apply an optical flow method, which takes into account both structure and movement of objects, to map every time-series image frame. Proposed method provides accurate measurements of dendritic spine length, volume, shape classification for time-lapse images of dendrites of hippocampal neurons. We compared the proposed spine detection algorithm with manual method performed by biologists and noncommercial software NeuronIQ. In particular, this method is able to segment dendritic spines better than existing methods with high sensitivity in adjacent

  4. Structural features of the exocellular polysaccharides of Mycobacterium tuberculosis.

    PubMed Central

    Lemassu, A; Daffé, M

    1994-01-01

    The cell envelope which surrounds pathogenic mycobacteria is postulated to be a defence barrier against phagocytic cells and its outermost constituents have a tendency to accumulate in the culture medium. The present work demonstrates that the exocellular material of Mycobacterium tuberculosis contains large amounts of polysaccharides with only traces, if any at all, of lipids. Three types of polysaccharides were purified by anion-exchange and gel-filtration chromatography; all were found to be neutral compounds devoid of acyl substituents. They consisted of D-glucan, D-arabino-D-mannan and D-mannan, which were eluted from gel-filtration columns in positions corresponding to molecular masses of 123, 13 and 4 kDa respectively. Their predominant structural features were determined by the characterization of the per-O-methyl derivatives of enzymic, acetolysis and Smith-degradation products and by 1H- and 13C-n.m.r. spectroscopy of the purified polysaccharides, using mono- and two-dimensional homonuclear chemical-shift correlated spectroscopy and two-dimensional heteronuclear (1H/13C) spectroscopy. The glucan which represented up to 90% of the polysaccharides was composed of repeating units of five or six-->4-alpha-D-Glcp-1--> residues and a -->4-alpha-D-Glcp substituted at position 6 with an alpha-D-Glcp, indicating a glycogen-like highly branched structure not related to the so-called polysaccharide-II previously identified in tuberculin. The arabinomannan consisted of a mannan segment composed of a -->6-alpha-D-Man-1--> core substituted at some positions 2 with an alpha-D-Manp. The arabinan termini of the arabinomannan were found to be extensively capped with mannosyl residues. The possibility that these polysaccharides contribute to the persistence of the tubercle bacillus in the macrophage by molecular mimicry is discussed. PMID:8297342

  5. Structural changes in gluten protein structure after addition of emulsifier. A Raman spectroscopy study

    NASA Astrophysics Data System (ADS)

    Ferrer, Evelina G.; Gómez, Analía V.; Añón, María C.; Puppo, María C.

    2011-06-01

    Food protein product, gluten protein, was chemically modified by varying levels of sodium stearoyl lactylate (SSL); and the extent of modifications (secondary and tertiary structures) of this protein was analyzed by using Raman spectroscopy. Analysis of the Amide I band showed an increase in its intensity mainly after the addition of the 0.25% of SSL to wheat flour to produced modified gluten protein, pointing the formation of a more ordered structure. Side chain vibrations also confirmed the observed changes.

  6. Potential applications of ferrocene as a structural feature in antioxidants.

    PubMed

    Liu, Zai-Qun

    2011-04-01

    Comparing with the wide usage of ferrocene in novel materials, ferrocene was unusually applied to be a structural feature in designing drugs even though some researchers pointed out that ferrocene and its derivatives possessed potential pharmacological applications. This was due to that low polarity limited bioavailability of ferrocene in vivo. Since ferrocene was inert to the oxidation at atmosphere, it was deduced that synthetic derivatives of ferrocene may be a novel kind of antioxidant, in which other organic groups may enhance the bioavailability of ferrocene, or large conjugated system formed among ferrocenyl and other organic groups may increase the antioxidant effectiveness. Thus, synthetic derivatives of ferrocene were divided into nonconjugated and conjugated ones in this review. For nonconjugated ferrocenyl derivatives, carbon chain or simple group attached one or two cyclopentadienyl rings in ferrocene to form a novel molecule with ferrocenyl group. The aim of synthesis of nonconjugated ferrocenyl compounds was to increase the bioavailability of ferrocene in vivo. On the other hand, the conjugated ferrocenyl derivatives referred to introduce other group to form a conjugated system with the cyclopentadienyl ring in ferrocene. The large conjugated system was beneficial for the single electron to dispense among the whole molecule while forming radicals, and enhanced the antioxidant capacity of the whole molecule. This review summarized the potential usage of ferrocene in antioxidants.

  7. Structural features of DNA interaction with caffeine and theophylline

    NASA Astrophysics Data System (ADS)

    Nafisi, Shohreh; Manouchehri, Firouzeh; Tajmir-Riahi, Heidar-Ali; Varavipour, Maryam

    2008-03-01

    Caffeine and theophylline are strong antioxidants that prevent DNA damage. The anticancer and antiviral activities of these natural products are implicated in their mechanism of actions. However, there has been no information on the interactions of these xanthine derivatives with individual DNA at molecular level. The aim of this study was to examine the stability and structural features of calf-thymus DNA complexes with caffeine and theophylline in aqueous solution, using constant DNA concentration (6.25 mM) and various caffeine or theophylline/DNA(P) ratios of 1/80, 1/40, 1/20, 1/10, 1/5, 1/2 and 1/1. FTIR, UV-visible spectroscopic methods were used to determine the ligand external binding modes, the binding constant and the stability of caffeine, theophylline-DNA complexes in aqueous solution. Spectroscopic evidence showed that the complexation of caffeine and theophylline with DNA occurred via G-C and A-T and PO 2 group with overall binding constants of K(caffeine-DNA) = 9.7 × 10 3 M -1 and K(theophylline-DNA) = 1.7 × 10 4 M -1. The affinity of ligand-DNA binding is in the order of theophylline > caffeine. A partial B to A-DNA transition occurs upon caffeine and theophylline complexation.

  8. Size control and structure features of spherical calcium carbonate particles

    NASA Astrophysics Data System (ADS)

    Trushina, D. B.; Sulyanov, S. N.; Bukreeva, T. V.; Kovalchuk, M. V.

    2015-07-01

    The size of porous spherical calcium carbonate particles obtained by precipitation from a supersaturated solution has been controlled using bovine serum albumin as an organic additive and ethylene glycol and glycerol as cosolvents of the reaction mixture. The structural aspects of the formation of these particles, which affect the possibility of controlling their sizes, are considered. Highly porous vaterite particles with an average size of about 500 nm have been obtained by adding ethylene glycol and glycerol to the reaction mixture and agitation for no less than 30 min. It is shown that particles are formed as a result of the attachment of vaterite nanocrystallites, the shape of which is anisotropic and can be described by a biaxial ellipsoid.

  9. Automated discovery of structural features of the optic nerve head on the basis of image and genetic data

    NASA Astrophysics Data System (ADS)

    Christopher, Mark; Tang, Li; Fingert, John H.; Scheetz, Todd E.; Abramoff, Michael D.

    2014-03-01

    Evaluation of optic nerve head (ONH) structure is a commonly used clinical technique for both diagnosis and monitoring of glaucoma. Glaucoma is associated with characteristic changes in the structure of the ONH. We present a method for computationally identifying ONH structural features using both imaging and genetic data from a large cohort of participants at risk for primary open angle glaucoma (POAG). Using 1054 participants from the Ocular Hypertension Treatment Study, ONH structure was measured by application of a stereo correspondence algorithm to stereo fundus images. In addition, the genotypes of several known POAG genetic risk factors were considered for each participant. ONH structural features were discovered using both a principal component analysis approach to identify the major modes of variance within structural measurements and a linear discriminant analysis approach to capture the relationship between genetic risk factors and ONH structure. The identified ONH structural features were evaluated based on the strength of their associations with genotype and development of POAG by the end of the OHTS study. ONH structural features with strong associations with genotype were identified for each of the genetic loci considered. Several identified ONH structural features were significantly associated (p < 0.05) with the development of POAG after Bonferroni correction. Further, incorporation of genetic risk status was found to substantially increase performance of early POAG prediction. These results suggest incorporating both imaging and genetic data into ONH structural modeling significantly improves the ability to explain POAG-related changes to ONH structure.

  10. A set of structural features defines the cis-regulatory modules of antenna-expressed genes in Drosophila melanogaster.

    PubMed

    López, Yosvany; Vandenbon, Alexis; Nakai, Kenta

    2014-01-01

    Unraveling the biological information within the regulatory region (RR) of genes has become one of the major focuses of current genomic research. It has been hypothesized that RRs of co-expressed genes share similar architecture, but to the best of our knowledge, no studies have simultaneously examined multiple structural features, such as positioning of cis-regulatory elements relative to transcription start sites and to each other, and the order and orientation of regulatory motifs, to accurately describe overall cis-regulatory structure. In our work we present an improved computational method that builds a feature collection based on all of these structural features. We demonstrate the utility of this approach by modeling the cis-regulatory modules of antenna-expressed genes in Drosophila melanogaster. Six potential antenna-related motifs were predicted initially, including three that appeared to be novel. A feature set was created with the predicted motifs, where a correlation-based filter was used to remove irrelevant features, and a genetic algorithm was designed to optimize the feature set. Finally, a set of eight highly informative structural features was obtained for the RRs of antenna-expressed genes, achieving an area under the curve of 0.841. We used these features to score all D. melanogaster RRs for potentially unknown antenna-expressed genes sharing a similar regulatory structure. Validation of our predictions with an independent RNA sequencing dataset showed that 76.7% of genes with high scoring RRs were expressed in antenna. In addition, we found that the structural features we identified are highly conserved in RRs of orthologs in other Drosophila sibling species. This approach to identify tissue-specific regulatory structures showed comparable performance to previous approaches, but also uncovered additional interesting features because it also considered the order and orientation of motifs.

  11. Teachers' Personal Agency: Making Sense of Slope through Additive Structures

    ERIC Educational Resources Information Center

    Walter, Janet G.; Gerson, Hope

    2007-01-01

    In the context of a three-year professional development program in mathematics, practicing elementary teachers persistently engaged in collaborative inquiry and reflection to build connected meanings for slope. One teacher invented a compelling representation for slope as a process of repeated addition, using Cuisenaire rods, based on teachers'…

  12. Identifying Cross-Domain Distinguishing Features of Cognitive Structure

    ERIC Educational Resources Information Center

    Ifenthaler, Dirk

    2011-01-01

    Our research aims to identify domain-specific similarities and differences of externalized cognitive structures. Cognitive structure, also known as knowledge structure or structural knowledge, is conceived as the manner in which an individual organizes the relationships of concepts in memory. By diagnosing these structures precisely, even…

  13. Conductivity and structure of bilinear organic addition compounds

    PubMed Central

    Phillips, J. C.

    1976-01-01

    The relationship between crystal structures and metallic conductivities of linear organic materials such as tetrathiafulvalene-tetracyanoquinodimethane is explained in terms of strong lateral elastic interactions between chains. A microdomain model is presented in which at high temperatures there are, in general, two coexisting phases on each stacked molecular chain. The ordering of (in general, four) phases on two interacting chains leads to a variety of phase transitions at low temperatures. By examining temperature-dependent electrical conductivities and magnetic susceptibilities one can establish the character of each such transition. PMID:16592359

  14. Generic eukaryotic core promoter prediction using structural features of DNA.

    PubMed

    Abeel, Thomas; Saeys, Yvan; Bonnet, Eric; Rouzé, Pierre; Van de Peer, Yves

    2008-02-01

    Despite many recent efforts, in silico identification of promoter regions is still in its infancy. However, the accurate identification and delineation of promoter regions is important for several reasons, such as improving genome annotation and devising experiments to study and understand transcriptional regulation. Current methods to identify the core region of promoters require large amounts of high-quality training data and often behave like black box models that output predictions that are difficult to interpret. Here, we present a novel approach for predicting promoters in whole-genome sequences by using large-scale structural properties of DNA. Our technique requires no training, is applicable to many eukaryotic genomes, and performs extremely well in comparison with the best available promoter prediction programs. Moreover, it is fast, simple in design, and has no size constraints, and the results are easily interpretable. We compared our approach with 14 current state-of-the-art implementations using human gene and transcription start site data and analyzed the ENCODE region in more detail. We also validated our method on 12 additional eukaryotic genomes, including vertebrates, invertebrates, plants, fungi, and protists.

  15. Crystal structure of advanced lithium titanate with lithium oxide additives

    NASA Astrophysics Data System (ADS)

    Hoshino, Tsuyoshi; Sasaki, Kazuya; Tsuchiya, Kunihiko; Hayashi, Kimio; Suzuki, Akihiro; Hashimoto, Takuya; Terai, Takayuki

    2009-04-01

    Li 2TiO 3 is one of the most promising candidates among solid breeder materials proposed for fusion reactors. However, the mass of Li 2TiO 3 was found to decrease with time in the sweep gas mixed with hydrogen. This mass change indicates that the oxygen content of the sample decreased, suggesting the change from Ti 4+ to Ti 3+. In the present paper, the crystal structure and the non-stoichiometry of Li 2TiO 3 added with Li 2O have been extensively investigated by means of X-ray diffraction (XRD) and thermogravimetry. In the case of the Li 2TiO 3 samples used in the present study, LiO-C 2H 5 or LiO-i-C 3H 7 and Ti(O-i-C 3H 7) 4 were mixed in the proportion corresponding to the molar ratio Li 2O/TiO 2 of either 2.00 or 1.00. In thermogravimetry, the mass of this sample decreased with time due to lithium deficiency, where no presence of oxygen deficiency was indicated.

  16. An Eye-Tracking Study of Multiple Feature Value Category Structure Learning: The Role of Unique Features

    PubMed Central

    Liu, Zhiya; Song, Xiaohong; Seger, Carol A.

    2015-01-01

    We examined whether the degree to which a feature is uniquely characteristic of a category can affect categorization above and beyond the typicality of the feature. We developed a multiple feature value category structure with different dimensions within which feature uniqueness and typicality could be manipulated independently. Using eye tracking, we found that the highest attentional weighting (operationalized as number of fixations, mean fixation time, and the first fixation of the trial) was given to a dimension that included a feature that was both unique and highly typical of the category. Dimensions that included features that were highly typical but not unique, or were unique but not highly typical, received less attention. A dimension with neither a unique nor a highly typical feature received least attention. On the basis of these results we hypothesized that subjects categorized via a rule learning procedure in which they performed an ordered evaluation of dimensions, beginning with unique and strongly typical dimensions, and in which earlier dimensions received higher weighting in the decision. This hypothesis accounted for performance on transfer stimuli better than simple implementations of two other common theories of category learning, exemplar models and prototype models, in which all dimensions were evaluated in parallel and received equal weighting. PMID:26274332

  17. Robust feature tracking for endoscopic pose estimation and structure recovery

    NASA Astrophysics Data System (ADS)

    Speidel, S.; Krappe, S.; Röhl, S.; Bodenstedt, S.; Müller-Stich, B.; Dillmann, R.

    2013-03-01

    Minimally invasive surgery is a highly complex medical discipline with several difficulties for the surgeon. To alleviate these difficulties, augmented reality can be used for intraoperative assistance. For visualization, the endoscope pose must be known which can be acquired with a SLAM (Simultaneous Localization and Mapping) approach using the endoscopic images. In this paper we focus on feature tracking for SLAM in minimally invasive surgery. Robust feature tracking and minimization of false correspondences is crucial for localizing the endoscope. As sensory input we use a stereo endoscope and evaluate different feature types in a developed SLAM framework. The accuracy of the endoscope pose estimation is validated with synthetic and ex vivo data. Furthermore we test the approach with in vivo image sequences from da Vinci interventions.

  18. Process Features in Writing: Internal Structure and Incremental Value over Product Features. Research Report. ETS RR-15-27

    ERIC Educational Resources Information Center

    Zhang, Mo; Deane, Paul

    2015-01-01

    In educational measurement contexts, essays have been evaluated and formative feedback has been given based on the end product. In this study, we used a large sample collected from middle school students in the United States to investigate the factor structure of the writing process features gathered from keystroke logs and the association of that…

  19. An identification method for enclosed voids restriction in manufacturability design for additive manufacturing structures

    NASA Astrophysics Data System (ADS)

    Liu, Shutian; Li, Quhao; Chen, Wenjiong; Tong, Liyong; Cheng, Gengdong

    2015-06-01

    Additive manufacturing (AM) technologies, such as selective laser sintering (SLS) and fused deposition modeling (FDM), have become the powerful tools for direct manufacturing of complex parts. This breakthrough in manufacturing technology makes the fabrication of new geometrical features and multiple materials possible. Past researches on designs and design methods often focused on how to obtain desired functional performance of the structures or parts, specific manufacturing capabilities as well as manufacturing constraints of AM were neglected. However, the inherent constraints in AM processes should be taken into account in design process. In this paper, the enclosed voids, one type of manufacturing constraints of AM, are investigated. In mathematics, enclosed voids restriction expressed as the solid structure is simplyconnected. We propose an equivalent description of simply-connected constraint for avoiding enclosed voids in structures, named as virtual temperature method (VTM). In this method, suppose that the voids in structure are filled with a virtual heating material with high heat conductivity and solid areas are filled with another virtual material with low heat conductivity. Once the enclosed voids exist in structure, the maximum temperature value of structure will be very high. Based upon this method, the simplyconnected constraint is equivalent to maximum temperature constraint. And this method can be easily used to formulate the simply-connected constraint in topology optimization. The effectiveness of this description method is illustrated by several examples. Based upon topology optimization, an example of 3D cantilever beam is used to illustrate the trade-off between manufacturability and functionality. Moreover, the three optimized structures are fabricated by FDM technology to indicate further the necessity of considering the simply-connected constraint in design phase for AM.

  20. Protein subcellular localization prediction based on compartment-specific features and structure conservation

    PubMed Central

    Su, Emily Chia-Yu; Chiu, Hua-Sheng; Lo, Allan; Hwang, Jenn-Kang; Sung, Ting-Yi; Hsu, Wen-Lian

    2007-01-01

    Background Protein subcellular localization is crucial for genome annotation, protein function prediction, and drug discovery. Determination of subcellular localization using experimental approaches is time-consuming; thus, computational approaches become highly desirable. Extensive studies of localization prediction have led to the development of several methods including composition-based and homology-based methods. However, their performance might be significantly degraded if homologous sequences are not detected. Moreover, methods that integrate various features could suffer from the problem of low coverage in high-throughput proteomic analyses due to the lack of information to characterize unknown proteins. Results We propose a hybrid prediction method for Gram-negative bacteria that combines a one-versus-one support vector machines (SVM) model and a structural homology approach. The SVM model comprises a number of binary classifiers, in which biological features derived from Gram-negative bacteria translocation pathways are incorporated. In the structural homology approach, we employ secondary structure alignment for structural similarity comparison and assign the known localization of the top-ranked protein as the predicted localization of a query protein. The hybrid method achieves overall accuracy of 93.7% and 93.2% using ten-fold cross-validation on the benchmark data sets. In the assessment of the evaluation data sets, our method also attains accurate prediction accuracy of 84.0%, especially when testing on sequences with a low level of homology to the training data. A three-way data split procedure is also incorporated to prevent overestimation of the predictive performance. In addition, we show that the prediction accuracy should be approximately 85% for non-redundant data sets of sequence identity less than 30%. Conclusion Our results demonstrate that biological features derived from Gram-negative bacteria translocation pathways yield a significant

  1. Influence of ecological and geological features on rangewide patterns of genetic structure in a widespread passerine

    PubMed Central

    Adams, R V; Burg, T M

    2015-01-01

    Geological and ecological features restrict dispersal and gene flow, leading to isolated populations. Dispersal barriers can be obvious physical structures in the landscape; however microgeographic differences can also lead to genetic isolation. Our study examined dispersal barriers at both macro- and micro-geographical scales in the black-capped chickadee, a resident North American songbird. Although birds have high dispersal potential, evidence suggests dispersal is restricted by barriers. The chickadee's range encompasses a number of physiological features which may impede movement and lead to divergence. Analyses of 913 individuals from 34 sampling sites across the entire range using 11 microsatellite loci revealed as many as 13 genetic clusters. Populations in the east were largely panmictic whereas populations in the western portion of the range showed significant genetic structure, which often coincided with large mountain ranges, such as the Cascade and Rocky Mountains, as well as areas of unsuitable habitat. Unlike populations in the central and southern Rockies, populations on either side of the northern Rockies were not genetically distinct. Furthermore, Northeast Oregon represents a forested island within the Great Basin; genetically isolated from all other populations. Substructuring at the microgeographical scale was also evident within the Fraser Plateau of central British Columbia, and in the southeast Rockies where no obvious physical barriers are present, suggesting additional factors may be impeding dispersal and gene flow. Dispersal barriers are therefore not restricted to large physical structures, although mountain ranges and large water bodies do play a large role in structuring populations in this study. PMID:25074576

  2. Blurred face recognition by fusing blur-invariant texture and structure features

    NASA Astrophysics Data System (ADS)

    Zhu, Mengyu; Cao, Zhiguo; Xiao, Yang; Xie, Xiaokang

    2015-10-01

    Blurred face recognition is still remaining as a challenge task, but with wide applications. Image blur can largely affect recognition performance. The local phase quantization (LPQ) was proposed to extract the blur-invariant texture information. It was used for blurred face recognition and achieved good performance. However, LPQ considers only the phase blur-invariant texture information, which is not sufficient. In addition, LPQ is extracted holistically, which cannot fully explore its discriminative power on local spatial properties. In this paper, we propose a novel method for blurred face recognition. The texture and structure blur-invariant features are extracted and fused to generate a more complete description on blurred image. For texture blur-invariant feature, LPQ is extracted in a densely sampled way and vector of locally aggregated descriptors (VLAD) is employed to enhance its performance. For structure blur-invariant feature, the histogram of oriented gradient (HOG) is used. To further enhance its blur invariance, we improve HOG by eliminating weak gradient magnitude which is more sensitive to image blur than the strong gradient. The improved HOG is then fused with the original HOG by canonical correlation analysis (CCA). At last, we fuse them together by CCA to form the final blur-invariant representation of the face image. The experiments are performed on three face datasets. The results demonstrate that our improvements and our proposition can have a good performance in blurred face recognition.

  3. Influence of landscape features on the microgeographic genetic structure of a resident songbird.

    PubMed

    Adams, R V; Lazerte, S E; Otter, K A; Burg, T M

    2016-08-01

    Landscape features influence individual dispersal and as a result can affect both gene flow and genetic variation within and between populations. The landscape of British Columbia, Canada, is already highly heterogeneous because of natural ecological and geological transitions, but disturbance from human-mediated processes has further fragmented continuous habitat, particularly in the central plateau region. In this study, we evaluated the effects of landscape heterogeneity on the genetic structure of a common resident songbird, the black-capped chickadee (Poecile atricapillus). Previous work revealed significant population structuring in British Columbia that could not be explained by physical barriers, so our aim was to assess the pattern of genetic structure at a microgeographic scale and determine the effect of different landscape features on genetic differentiation. A total of 399 individuals from 15 populations were genotyped for fourteen microsatellite loci revealing significant population structuring in this species. Individual- and population-based analyses revealed as many as nine genetic clusters with isolation in the north, the central plateau and the south. Moreover, a mixed modelling approach that accounted for non-independence of pairwise distance values revealed a significant effect of land cover and elevation resistance on genetic differentiation. These results suggest that barriers in the landscape influence dispersal which has led to the unexpectedly high levels of population isolation. Our study demonstrates the importance of incorporating landscape features when interpreting patterns of population differentiation. Despite taking a microgeographic approach, our results have opened up additional questions concerning the processes influencing dispersal and gene flow at the local scale.

  4. Influence of landscape features on the microgeographic genetic structure of a resident songbird.

    PubMed

    Adams, R V; Lazerte, S E; Otter, K A; Burg, T M

    2016-08-01

    Landscape features influence individual dispersal and as a result can affect both gene flow and genetic variation within and between populations. The landscape of British Columbia, Canada, is already highly heterogeneous because of natural ecological and geological transitions, but disturbance from human-mediated processes has further fragmented continuous habitat, particularly in the central plateau region. In this study, we evaluated the effects of landscape heterogeneity on the genetic structure of a common resident songbird, the black-capped chickadee (Poecile atricapillus). Previous work revealed significant population structuring in British Columbia that could not be explained by physical barriers, so our aim was to assess the pattern of genetic structure at a microgeographic scale and determine the effect of different landscape features on genetic differentiation. A total of 399 individuals from 15 populations were genotyped for fourteen microsatellite loci revealing significant population structuring in this species. Individual- and population-based analyses revealed as many as nine genetic clusters with isolation in the north, the central plateau and the south. Moreover, a mixed modelling approach that accounted for non-independence of pairwise distance values revealed a significant effect of land cover and elevation resistance on genetic differentiation. These results suggest that barriers in the landscape influence dispersal which has led to the unexpectedly high levels of population isolation. Our study demonstrates the importance of incorporating landscape features when interpreting patterns of population differentiation. Despite taking a microgeographic approach, our results have opened up additional questions concerning the processes influencing dispersal and gene flow at the local scale. PMID:26905462

  5. Structural Features for Functional Selectivity at Serotonin Receptors

    PubMed Central

    Wacker, Daniel; Wang, Chong; Katritch, Vsevolod; Han, Gye Won; Huang, Xi-Ping; Vardy, Eyal; McCorvy, John D.; Jiang, Yi; Chu, Meihua; Siu, Fai Yiu; Liu, Wei; Xu, H. Eric; Cherezov, Vadim; Roth, Bryan L.; Stevens, Raymond C.

    2013-01-01

    Drugs active at G protein-coupled receptors (GPCRs) can differentially modulate either canonical or non-canonical signaling pathways via a phenomenon known as functional selectivity or biased signaling. We report biochemical studies that show that the hallucinogen lysergic acid diethylamide (LSD), its precursor ergotamine (ERG) and related ergolines display strong functional selectivity for β-arrestin signaling at the 5-hydroxytryptamine (5-HT) receptor 5-HT2B, while being relatively unbiased at the 5-HT1B receptor. To investigate the structural basis for biased signaling, we determined the crystal structure of the human 5-HT2B receptor bound to ERG, and compared it with the 5-HT1B/ERG structure. Given the relatively poor understanding of GPCR structure-function to date, insight into different GPCR signaling pathways are important to better understand both adverse and favorable therapeutic activities. PMID:23519215

  6. Molecular Modeling of Mechanosensory Ion Channel Structural and Functional Features

    PubMed Central

    Gessmann, Renate; Kourtis, Nikos; Petratos, Kyriacos; Tavernarakis, Nektarios

    2010-01-01

    The DEG/ENaC (Degenerin/Epithelial Sodium Channel) protein family comprises related ion channel subunits from all metazoans, including humans. Members of this protein family play roles in several important biological processes such as transduction of mechanical stimuli, sodium re-absorption and blood pressure regulation. Several blocks of amino acid sequence are conserved in DEG/ENaC proteins, but structure/function relations in this channel class are poorly understood. Given the considerable experimental limitations associated with the crystallization of integral membrane proteins, knowledge-based modeling is often the only route towards obtaining reliable structural information. To gain insight into the structural characteristics of DEG/ENaC ion channels, we derived three-dimensional models of MEC-4 and UNC-8, based on the available crystal structures of ASIC1 (Acid Sensing Ion Channel 1). MEC-4 and UNC-8 are two DEG/ENaC family members involved in mechanosensation and proprioception respectively, in the nematode Caenorhabditis elegans. We used these models to examine the structural effects of specific mutations that alter channel function in vivo. The trimeric MEC-4 model provides insight into the mechanism by which gain-of-function mutations cause structural alterations that result in increased channel permeability, which trigger cell degeneration. Our analysis provides an introductory framework to further investigate the multimeric organization of the DEG/ENaC ion channel complex. PMID:20877470

  7. Molecular modeling of mechanosensory ion channel structural and functional features.

    PubMed

    Gessmann, Renate; Kourtis, Nikos; Petratos, Kyriacos; Tavernarakis, Nektarios

    2010-09-16

    The DEG/ENaC (Degenerin/Epithelial Sodium Channel) protein family comprises related ion channel subunits from all metazoans, including humans. Members of this protein family play roles in several important biological processes such as transduction of mechanical stimuli, sodium re-absorption and blood pressure regulation. Several blocks of amino acid sequence are conserved in DEG/ENaC proteins, but structure/function relations in this channel class are poorly understood. Given the considerable experimental limitations associated with the crystallization of integral membrane proteins, knowledge-based modeling is often the only route towards obtaining reliable structural information. To gain insight into the structural characteristics of DEG/ENaC ion channels, we derived three-dimensional models of MEC-4 and UNC-8, based on the available crystal structures of ASIC1 (Acid Sensing Ion Channel 1). MEC-4 and UNC-8 are two DEG/ENaC family members involved in mechanosensation and proprioception respectively, in the nematode Caenorhabditis elegans. We used these models to examine the structural effects of specific mutations that alter channel function in vivo. The trimeric MEC-4 model provides insight into the mechanism by which gain-of-function mutations cause structural alterations that result in increased channel permeability, which trigger cell degeneration. Our analysis provides an introductory framework to further investigate the multimeric organization of the DEG/ENaC ion channel complex.

  8. Learning about the internal structure of categories through classification and feature inference.

    PubMed

    Jee, Benjamin D; Wiley, Jennifer

    2014-01-01

    Previous research on category learning has found that classification tasks produce representations that are skewed toward diagnostic feature dimensions, whereas feature inference tasks lead to richer representations of within-category structure. Yet, prior studies often measure category knowledge through tasks that involve identifying only the typical features of a category. This neglects an important aspect of a category's internal structure: how typical and atypical features are distributed within a category. The present experiments tested the hypothesis that inference learning results in richer knowledge of internal category structure than classification learning. We introduced several new measures to probe learners' representations of within-category structure. Experiment 1 found that participants in the inference condition learned and used a wider range of feature dimensions than classification learners. Classification learners, however, were more sensitive to the presence of atypical features within categories. Experiment 2 provided converging evidence that classification learners were more likely to incorporate atypical features into their representations. Inference learners were less likely to encode atypical category features, even in a "partial inference" condition that focused learners' attention on the feature dimensions relevant to classification. Overall, these results are contrary to the hypothesis that inference learning produces superior knowledge of within-category structure. Although inference learning promoted representations that included a broad range of category-typical features, classification learning promoted greater sensitivity to the distribution of typical and atypical features within categories.

  9. Structural features of cholesteryl ester transfer protein: a molecular dynamics simulation study.

    PubMed

    Lei, Dongsheng; Zhang, Xing; Jiang, Shengbo; Cai, Zhaodi; Rames, Matthew J; Zhang, Lei; Ren, Gang; Zhang, Shengli

    2013-03-01

    Cholesteryl ester transfer protein (CETP) mediates the net transfer of cholesteryl esters (CEs) from atheroprotective high-density lipoproteins (HDLs) to atherogenic low-density lipoproteins (LDLs) or very-low-density lipoproteins (VLDLs). Inhibition of CETP raises HDL cholesterol (good cholesterol) levels and reduces LDL cholesterol (bad cholesterol) levels, making it a promising drug target for the prevention and treatment of coronary heart disease. Although the crystal structure of CETP has been determined, the molecular mechanism mediating CEs transfer is still unknown, even the structural features of CETP in a physiological environment remain elusive. We performed molecular dynamics simulations to explore the structural features of CETP in an aqueous solution. Results show that the distal portion flexibility of N-terminal β-barrel domain is considerably greater in solution than in crystal; conversely, the flexibility of helix X is slightly less. During the simulations the distal end of C-terminal β-barrel domain expanded while the hydrophilic surface increasing more than the hydrophobic surface. In addition, a new surface pore was generated in this domain. This surface pore and all cavities in CETP are stable. These results suggest that the formation of a continuous tunnel within CETP by connecting cavities is permitted in solution. PMID:23042613

  10. Altered Structural and Functional Feature of Striato-Cortical Circuit in Benign Epilepsy with Centrotemporal Spikes.

    PubMed

    Luo, Cheng; Zhang, Yaodan; Cao, Weifang; Huang, Yue; Yang, Fei; Wang, Jianjun; Tu, Shipeng; Wang, Xiaoming; Yao, Dezhong

    2015-09-01

    Benign epilepsy with centrotemporal spikes (BECT) is the most common form of childhood idiopathic focal epilepsy syndrome. We investigated quantitative evidence regarding brain morphology and functional connectivity features to provide insight into the neuroanatomical foundation of this disorder, using high resolution T1-weighted magnetic resonance imaging (MRI) and resting state functional MRI in 21 patients with BECT and in 20 healthy children. The functional connectivity analysis, seeded at the regions with altered gray-matter (GM) volume in voxel-based morphometry (VBM) analysis, was further performed. Then, the observed structural and functional alteration were investigated for their association with the clinical and behavior manifestations. The increased GM volume in the striatum and fronto-temporo-parietal cortex (striato-cortical circuit) was observed in BECT. The decreased connections were found among the motor network and frontostriatal loop, and between the default mode network (DMN) and language regions. Additionally, the GM of striatum was negatively correlated with age at epilepsy onset. The current observations may contribute to the understanding of the altered structural and functional feature of striato-cortical circuit in patients with BECT. The findings also implied alterations of the motor network and DMN, which were associated with the epileptic activity in patients with BECT. This further suggested that the onset of BECT might have enduring structural and functional effects on brain maturation.

  11. An automated approach to network features of protein structure ensembles.

    PubMed

    Bhattacharyya, Moitrayee; Bhat, Chanda R; Vishveshwara, Saraswathi

    2013-10-01

    Network theory applied to protein structures provides insights into numerous problems of biological relevance. The explosion in structural data available from PDB and simulations establishes a need to introduce a standalone-efficient program that assembles network concepts/parameters under one hood in an automated manner. Herein, we discuss the development/application of an exhaustive, user-friendly, standalone program package named PSN-Ensemble, which can handle structural ensembles generated through molecular dynamics (MD) simulation/NMR studies or from multiple X-ray structures. The novelty in network construction lies in the explicit consideration of side-chain interactions among amino acids. The program evaluates network parameters dealing with topological organization and long-range allosteric communication. The introduction of a flexible weighing scheme in terms of residue pairwise cross-correlation/interaction energy in PSN-Ensemble brings in dynamical/chemical knowledge into the network representation. Also, the results are mapped on a graphical display of the structure, allowing an easy access of network analysis to a general biological community. The potential of PSN-Ensemble toward examining structural ensemble is exemplified using MD trajectories of an ubiquitin-conjugating enzyme (UbcH5b). Furthermore, insights derived from network parameters evaluated using PSN-Ensemble for single-static structures of active/inactive states of β2-adrenergic receptor and the ternary tRNA complexes of tyrosyl tRNA synthetases (from organisms across kingdoms) are discussed. PSN-Ensemble is freely available from http://vishgraph.mbu.iisc.ernet.in/PSN-Ensemble/psn_index.html.

  12. Coherent quantum transport features in carbon superlattice structures

    PubMed Central

    McIntosh, R.; Henley, S. J.; Silva, S. R. P.; Bhattacharyya, S.

    2016-01-01

    Whilst resonant transmission is well understood and can be fully harnessed for crystalline superlattices, a complete picture has not yet emerged for disordered superlattices. It has proven difficult to tune resonant transmission in disordered diamond-like carbon (DLC) superlattices as conventional models are not equipped to incorporate significant structural disorder. In this work, we present concurrent experimental and theoretical analysis which addresses resonant transmission in DLC superlattices. Devices were fabricated by growing alternate layers of DLC with different percentages of sp3 hybridized carbon.Coherent quantum transport effects were demonstrated in these structurally disordered DLC superlattices through distinct current modulation with negative differential resistance (NDR) in the current-voltage (I-V) measurements. A model was developed using tight-binding calculations assuming a random variation of the hopping integral to simulate structural (bond-length) disorder. Calculations of the I-V characteristics compliment the interpretation of the measurements and illustrate that while DLC superlattice structures are unlike their classical counterparts, the near-field structural order will help with the confinement of quantised states. The present model provides an empirical guide for tailoring the properties of future devices, giving rise to much hope that carbon electronics operating at high frequencies over large areas can now be developed. PMID:27759047

  13. Unusual Features of Crystal Structures of Some Simple Copper Compounds

    ERIC Educational Resources Information Center

    Douglas, Bodie

    2009-01-01

    Some simple copper compounds have unusual crystal structures. Cu[subscript 3]N is cubic with N atoms at centers of octahedra formed by 6 Cu atoms. Cu[subscript 2]O (cuprite) is also cubic; O atoms are in tetrahedra formed by 4 Cu atoms. These tetrahedra are linked by sharing vertices forming two independent networks without linkages between them.…

  14. Novel features of the rotary catalytic mechanism revealed in the structure of yeast F1 ATPase

    SciTech Connect

    Kabaleeswaran, Venkataraman; Puri, Neeti; Walker, John E.; Leslie, Andrew G.W.; Mueller, David M.

    2010-03-08

    The crystal structure of yeast mitochondrial F{sub 1} ATPase contains three independent copies of the complex, two of which have similar conformations while the third differs in the position of the central stalk relative to the {alpha}{sub 3}{beta}{sub 3} sub-assembly. All three copies display very similar asymmetric features to those observed for the bovine enzyme, but the yeast F{sub 1} ATPase structures provide novel information. In particular, the active site that binds ADP in bovine F{sub 1} ATPase has an ATP analog bound and therefore this structure does not represent the ADP-inhibited form. In addition, one of the complexes binds phosphate in the nucleotide-free catalytic site, and comparison with other structures provides a picture of the movement of the phosphate group during initial binding and subsequent catalysis. The shifts in position of the central stalk between two of the three copies of yeast F{sub 1} ATPase and when these structures are compared to those of the bovine enzyme give new insight into the conformational changes that take place during rotational catalysis.

  15. Structural features of the kx-1 region of turbulent pipe flow at Reτ = 3008

    NASA Astrophysics Data System (ADS)

    Ahn, Junsun; Sung, Hyung Jin

    2015-11-01

    Structural features of a turbulent pipe flow were explored by using the direct numerical simulation data at Reτ = 3008 (Ahn et al. 2015). Based on the pre-multiplied streamwise energy spectra of the streamwise velocity fluctuations, three spectral regions were classified: the inner site, the outer site and kx- 1 region. The inner site was created by the self-sustaining near-wall cycle with λx+ ~ 1000, where λx is the streamwise wavelength. The outer site was made due to very-large-scale motions with λx/R ~10, which were generated by the streamwise pseudo-alignment of the adjacent large-scale motions. Between the inner and outer sites, the kx- 1 region appeared at y+ = 90-300, where λx >= 20 y and λx/R <=5. By using the conditional averaging, self-similar structures of the streamwise velocity fluctuations structures in the kx- 1 region were retained, which were considered as the attached eddies proposed by Townsend (1976). In addition, the vortical structures in the kx- 1 region were examined by two-point correlation of the velocity components and the vortices in order to find the dominant behavior of the structures. This work was supported by the Creative Research Initiatives (No. 2015-001828) program of the National Research Foundation of Korea (MSIP).

  16. Strong Nonadditivity as a Key Structure–Activity Relationship Feature: Distinguishing Structural Changes from Assay Artifacts

    PubMed Central

    2015-01-01

    Nonadditivity in protein–ligand affinity data represents highly instructive structure–activity relationship (SAR) features that indicate structural changes and have the potential to guide rational drug design. At the same time, nonadditivity is a challenge for both basic SAR analysis as well as many ligand-based data analysis techniques such as Free-Wilson Analysis and Matched Molecular Pair analysis, since linear substituent contribution models inherently assume additivity and thus do not work in such cases. While structural causes for nonadditivity have been analyzed anecdotally, no systematic approaches to interpret and use nonadditivity prospectively have been developed yet. In this contribution, we lay the statistical framework for systematic analysis of nonadditivity in a SAR series. First, we develop a general metric to quantify nonadditivity. Then, we demonstrate the non-negligible impact of experimental uncertainty that creates apparent nonadditivity, and we introduce techniques to handle experimental uncertainty. Finally, we analyze public SAR data sets for strong nonadditivity and use recourse to the original publications and available X-ray structures to find structural explanations for the nonadditivity observed. We find that all cases of strong nonadditivity (ΔΔpKi and ΔΔpIC50 > 2.0 log units) with sufficient structural information to generate reasonable hypothesis involve changes in binding mode. With the appropriate statistical basis, nonadditivity analysis offers a variety of new attempts for various areas in computer-aided drug design, including the validation of scoring functions and free energy perturbation approaches, binding pocket classification, and novel features in SAR analysis tools. PMID:25760829

  17. Hysterosalpingographic features of cervical abnormalities: acquired structural anomalies

    PubMed Central

    Zafarani, F; Shahrzad, G

    2015-01-01

    Cervical abnormalities may be congenital or acquired. Congenital cervical structural anomalies are relatively uncommon, whereas acquired cervical abnormalities are commonly seen in gynaecology clinics. Acquired abnormalities of the cervix can cause cervical factor infertility and recurrent spontaneous abortion. Various imaging tools have been used for evaluation of the uterine cavity and fallopian tubes. Hysterosalpingography (HSG) is a quick and minimally invasive tool for evaluation of infertility that facilitates visualization of the inner surfaces of the uterine cavity and fallopian tubes, as well as the cervical canal and isthmus. The lesions of the uterine cervix show various imaging manifestations on HSG such as narrowing, dilatation, filling defects, irregularities and diverticular projections. This pictorial review describes and illustrates the hysterosalpingographic appearances of normal variants and acquired structural abnormalities of the cervix. Accurate diagnosis of such cases is considered essential for optimal treatment. The pathological findings and radiopathological correlation will be briefly discussed. PMID:26111269

  18. Kuparuk pipeline system features unique river crossing structure

    SciTech Connect

    Smyth, R.E.

    1982-09-01

    Oil is delivered to the Trans Alaskan Pipeline System (TAPS) by utilizing a unique support structure designed to cross a one mile wide area of the Kuparuk River. Arctic permafrost conditions require that the pipeline be entirely above ground. Consisting of a bent supported by 2 vertical supports and cross bracing designed to withstand 100-year flood conditions during spring breakup, the Kuparuk river crossing was initially planned to be buried but massive ice was encountered during core sampling.

  19. Novel RNA structural features of an alternatively splicing group II intron from Clostridium tetani.

    PubMed

    McNeil, Bonnie A; Zimmerly, Steven

    2014-06-01

    Group II introns are ribozymes in bacterial and organellar genomes that function as self-splicing introns and as retroelements. Previously, we reported that the group II intron C.te.I1 of Clostridium tetani alternatively splices in vivo to produce five distinct coding mRNAs. Accurate fusion of upstream and downstream reading frames requires a shifted 5' splice site located 8 nt upstream of the usual 5' GUGYG motif. This site is specified by the ribozyme through an altered intron/exon-binding site 1 (IBS1-EBS1) pairing. Here we use mutagenesis and self-splicing assays to investigate in more detail the significance of the structural features of the C.te.I1 ribozyme. The shifted 5' splice site is shown to be affected by structures in addition to IBS1-EBS1, and unlike other group II introns, C.te.I1 appears to require a spacer between IBS1 and the GUGYG motif. In addition, the mechanism of 3' exon recognition is modified from the ancestral IIB mechanism to a IIA-like mechanism that appears to be longer than the typical single base-pair interaction and may extend up to 4 bp. The novel ribozyme properties that have evolved for C.te.I1 illustrate the plasticity of group II introns in adapting new structural and catalytic properties that can be utilized to affect gene expression.

  20. Structural damage localisation for a frame structure from changes in curvature of approximate entropy feature vectors

    NASA Astrophysics Data System (ADS)

    An, Y. H.; Ou, J. P.

    2014-01-01

    At present, accurate vibration-based damage localisation cannot be achieved very well in mechanical and civil engineering fields due to high noise in the measurements and low accuracy in finite element (FE) model of the measured structures. To address these issues, a method for damage detection is proposed in this work, i.e. the mean curvature difference method of approximate entropy (ApEn) feature vectors, based on the ApEn theory and curvature method. Simulation results of both single and multiple damage cases under pulse excitation indicate that the proposed method can be utilised to determine whether the damage is present in the structure or not and to locate the damage accurately, and the method exhibits strong anti-noise ability: it is feasible for damage with 5% stiffness reduction even if the noise level is up to 25%. Moreover, the proposed method does not require a structural FE model. Experimental results of a six-storey shear frame model also validated the proposed method. All of these lay a good foundation for its application in shear frame structures.

  1. Structural Features Facilitating Tumor Cell Targeting and Internalization by Bleomycin and Its Disaccharide

    PubMed Central

    2016-01-01

    We have shown previously that the bleomycin (BLM) carbohydrate moiety can recapitulate the tumor cell targeting effects of the entire BLM molecule, that BLM itself is modular in nature consisting of a DNA-cleaving aglycone which is delivered selectively to the interior of tumor cells by its carbohydrate moiety, and that there are disaccharides structurally related to the BLM disaccharide which are more efficient than the natural disaccharide at tumor cell targeting/uptake. Because BLM sugars can deliver molecular cargoes selectively to tumor cells, and thus potentially form the basis for a novel antitumor strategy, it seemed important to consider additional structural features capable of affecting the efficiency of tumor cell recognition and delivery. These included the effects of sugar polyvalency and net charge (at physiological pH) on tumor cell recognition, internalization, and trafficking. Since these parameters have been shown to affect cell surface recognition, internalization, and distribution in other contexts, this study has sought to define the effects of these structural features on tumor cell recognition by bleomycin and its disaccharide. We demonstrate that both can have a significant effect on tumor cell binding/internalization, and present data which suggests that the metal ions normally bound by bleomycin following clinical administration may significantly contribute to the efficiency of tumor cell uptake, in addition to their characterized function in DNA cleavage. A BLM disaccharide-Cy5** conjugate incorporating the positively charged dipeptide d-Lys-d-Lys was found to associate with both the mitochondria and the nuclear envelope of DU145 cells, suggesting possible cellular targets for BLM disaccharide–cytotoxin conjugates. PMID:25905565

  2. Biocompatibility and Structural Features of Biodegradable Polymer Scaffolds.

    PubMed

    Nasonova, M V; Glushkova, T V; Borisov, V V; Velikanova, E A; Burago, A Yu; Kudryavtseva, Yu A

    2015-11-01

    We performed a comparative analysis of physicochemical properties and biocompatibility of scaffolds of different composition on the basis of biodegradable polymers fabricated by casting and electrospinning methods. For production of polyhydroxyalkanoate-based scaffolds by electrospinning method, the optimal concentration of the polymer was 8-10%. Fiber diameter and properties of the scaffold produced by electrospinning method depended on polymer composition. Addition of polycaprolactone increased elasticity of the scaffolds. Bio- and hemocompatibility of the scaffolds largely depended on the composition formulation and method of scaffold fabrication. Polylactide introduced into the composition of polyhydroxybutyrate-oxyvalerate scaffolds accelerated degradation and increased adhesive properties of the scaffolds. PMID:26608377

  3. Features of structural response of mechanically loaded crystallites to irradiation

    SciTech Connect

    Korchuganov, Aleksandr V.

    2015-10-27

    A molecular dynamics method is employed to investigate the origin and evolution of plastic deformation in elastically deformed iron and vanadium crystallites due to atomic displacement cascades. Elastic stress states of crystallites result from different degrees of specimen deformation. Crystallites are deformed under constant-volume conditions. Atomic displacement cascades with the primary knock-on atom energy up to 50 keV are generated in loaded specimens. It is shown that irradiation may cause not only the Frenkel pair formation but also large-scale structural rearrangements outside the irradiated area, which prove to be similar to rearrangements proceeding by the twinning mechanism in mechanically loaded specimens.

  4. Structurally-modified subphthalocyanines: molecular design towards realization of expected properties from the electronic structure and structural features of subphthalocyanine.

    PubMed

    Shimizu, Soji; Kobayashi, Nagao

    2014-07-01

    This feature article summarizes recent contributions of the authors in the synthesis of structurally-modified subphthalocyanines. The structural modification covers (1) modification of the conjugated system of subphthalocyanines to create novel conjugated systems comprising three pyrroles or pyrrole-like subunits, (2) core-modification by expansion of the inner pyrrolic five-membered ring to larger six- and seven-membered ring units, and (3) exterior-modification by annulation of functional units to subphthalocyanines. These modifications in the structure of subphthalocyanines have been performed with the aim of demonstrating unique properties originating from the bowl-shaped C3v-symmetric structure as well as the electronic structure delineated by the 14π-electron conjugated system on the curved molecular surface. The possible structural modifications surveyed in this feature article and their concomitant properties will provide important future guidelines to the design of subphthalocyanine-based functional molecules, considering the fact that subphthalocyanines have recently been attracting considerable attention as potential candidates in the field of optoelectronics and molecular electronics. PMID:24710280

  5. Automated measurement of CT noise in patient images with a novel structure coherence feature

    NASA Astrophysics Data System (ADS)

    Chun, Minsoo; Choi, Young Hun; Hyo Kim, Jong

    2015-12-01

    While the assessment of CT noise constitutes an important task for the optimization of scan protocols in clinical routine, the majority of noise measurements in practice still rely on manual operation, hence limiting their efficiency and reliability. This study presents an algorithm for the automated measurement of CT noise in patient images with a novel structure coherence feature. The proposed algorithm consists of a four-step procedure including subcutaneous fat tissue selection, the calculation of structure coherence feature, the determination of homogeneous ROIs, and the estimation of the average noise level. In an evaluation with 94 CT scans (16 517 images) of pediatric and adult patients along with the participation of two radiologists, ROIs were placed on a homogeneous fat region at 99.46% accuracy, and the agreement of the automated noise measurements with the radiologists’ reference noise measurements (PCC  =  0.86) was substantially higher than the within and between-rater agreements of noise measurements (PCCwithin  =  0.75, PCCbetween  =  0.70). In addition, the absolute noise level measurements matched closely the theoretical noise levels generated by a reduced-dose simulation technique. Our proposed algorithm has the potential to be used for examining the appropriateness of radiation dose and the image quality of CT protocols for research purposes as well as clinical routine.

  6. CFD simulation of flow features and vorticity structures in tuna-like swimming

    NASA Astrophysics Data System (ADS)

    Yang, Liang; Su, Yu-Min

    2011-03-01

    The theoretical research on the propulsive principle of aquatic animal becomes more important and attracted more researchers to make efforts on it. In the present study, a computational fluid dynamic (CFD) simulation of a three-dimensional traveling-wave undulations body of tuna has been developed to investigate the fluid flow features and vorticity structures around this body when moving in a straight line. The undulation only takes place in the posterior half of the fish, and the tuna-tail is considered as a lunate fin oscillating with the mode combined swaying with yawing. A Reynolds-averaged Navier-Stokes (RANS) equation is developed, employing a control-volume method and a k-omega SST turbulent model; meanwhile an unstructured tetrahedral grid, which is generated for the three-dimensional geometry, is used based on the deformation of the hind parts of the body and corresponding movement of the tail. We calculated the hydrodynamic performance of tuna-like body when a tuna swims in a uniform velocity, and compared the input power coefficient, output power coefficient and propulsive efficiency of the oscillating tuna-tail with or without body vortex shedding. Additionally, the load distribution on the body, flow features and vorticity structures around the body were demonstrated. The effect of interaction between the body-generated vortices and the tail-generated vorticity on the hydrodynamic performance can be obtained.

  7. Features of transport in ultrathin gold nanowire structures.

    PubMed

    Pud, Sergii; Kisner, Alexandre; Heggen, Marc; Belaineh, Dagmawi; Temirov, Ruslan; Simon, Ulrich; Offenhäusser, Andreas; Mourzina, Yulia; Vitusevich, Svetlana

    2013-03-25

    The origin of the interface formation appearing due to the realization of contacts to ultrathin gold nanowire devices is revealed. Such interfaces play an important role in transport mechanisms in nanowire structures and can determine the electrical and operating parameters of a nanodevice. Based on experimental results, the specific electrical properties of bundles of ultrathin gold nanowires fabricated by wet chemical synthesis and subsequently assembled and contacted with gold electrodes are reported. It is demonstrated that these properties are strongly affected by the monolayers of organic molecules inevitably present on the surface of the nanowires due to synthetic conditions. In particular, such layers form a potential barrier to tunneling of the electrons from contacts to the nanowires. The electric transport behavior of the investigated nanowire structures in the temperature range from 500 mK to 300 K obeys the model of thermal fluctuation-induced tunneling conduction through the nanowire-metal electrode molecular junction. Application of this model allows calculation of the parameters of the molecular potential barrier. The formation of such a molecular barrier is verified by scanning tunneling microscope (STM) and transmission electron microscope (TEM) measurements performed using a supporting graphene layer. These findings are important for designing novel nanodevices for molecular electronics on the basis of ultrathin nanowires.

  8. Electrooptical properties and structural features of amorphous ITO

    SciTech Connect

    Amosova, L. P.

    2015-03-15

    Thin indium-tin oxide (ITO) films are deposited onto cold substrates by magnetron-assisted sputtering. The dependences of the structural, electrical, and optical properties of the films on the oxygen content in the atmosphere of sputtering and the growth rate are studied. It is shown that, if the substrate temperature is no higher than the ITO crystallization temperature and the conditions of growth deviate from the optimal relationship between the oxygen pressure and the growth rate, the resistance of the layers can be six or seven orders of magnitude higher than the resistance of conducting amorphous layers and reach hundreds of megaohms. At the same time, the optical properties of insulating layers in the visible spectral region are completely identical to the properties of the conducing amorphous modification. A conceptual model of defects responsible for the insulating properties of amorphous ITO is proposed.

  9. Thermodynamic Features of Structural Motifs Formed by β-L-RNA.

    PubMed

    Szabat, Marta; Gudanis, Dorota; Kotkowiak, Weronika; Gdaniec, Zofia; Kierzek, Ryszard; Pasternak, Anna

    2016-01-01

    This is the first report to provide comprehensive thermodynamic and structural data concerning duplex, hairpin, quadruplex and i-motif structures in β-L-RNA series. Herein we confirm that, within the limits of experimental error, the thermodynamic stability of enantiomeric structural motifs is the same as that of naturally occurring D-RNA counterparts. In addition, formation of D-RNA/L-RNA heterochiral duplexes is also observed; however, their thermodynamic stability is significantly reduced in reference to homochiral D-RNA duplexes. The presence of three locked nucleic acid (LNA) residues within the D-RNA strand diminishes the negative effect of the enantiomeric, complementary L-RNA strand in the formation of heterochiral RNA duplexes. Similar behavior is also observed for heterochiral LNA-2'-O-methyl-D-RNA/L-RNA duplexes. The formation of heterochiral duplexes was confirmed by 1H NMR spectroscopy. The CD curves of homochiral L-RNA structural motifs are always reversed, whereas CD curves of heterochiral duplexes present individual features dependent on the composition of chiral strands.

  10. Structural features of the extracellular portion of membrane-anchoring peptides on membrane-bound immunoglobulins.

    PubMed

    Major, J G; Davis, F M; Liou, R S; Chang, T W

    1996-02-01

    Membrane-bound immunoglobulins, mIgs, are displayed as transmembrane proteins on the surface of B cells, where they serve as antigen receptors. The mIgs are anchored to the membrane through a carboxy-terminal extension of the immunoglobulin heavy chain. Three distinct structural regions of these membrane-anchor peptides, of mouse and human mIgs, have been delineated: (1) a central conserved stretch of 25 hydrophobic, unchanged amino acid residues, which spans the membrane lipid bilayer; (2) a C-terminal hydrophilic region of 3-28 amino acids, which is intracytoplasmic; and (3) an N-terminal extracellular hydrophilic region of 13-67 amino acids, which is isotype-specific. Here we report predicted secondary and tertiary structures of the third structural region of the membrane anchoring peptide along with corroborating experimental evidence. The predictions of secondary and tertiary structure indicate that most of these regions can assume an chi-helical conformation. Circular dichroism spectroscopy of corresponding synthetic peptide confirms this essential feature. The choice of solvent and pH have dramatic effects on peptide helicity; solvent conditions consistent with a membrane-proximal environment promote helicity. Additional studies suggest that the two adjacent extracellular peptides may be stabilized through coiled-coil interactions similar to those described for some other transmembrane proteins.

  11. Functional and structural features of cholangiocytes in health and disease

    PubMed Central

    Maroni, Luca; Haibo, Bai; Ray, Debolina; Zhou, Tianhao; Wan, Ying; Meng, Fanyin; Marzioni, Marco; Alpini, Gianfranco

    2015-01-01

    Cholangiocytes are the epithelial cells that line the bile ducts. Along the biliary tree, two different kinds of cholangiocytes exist; small and large cholangiocytes. Each type has important differences in their biological role in physiological and pathological conditions. In response to injury, cholangiocytes become reactive and acquire a neuroendocrine-like phenotype with the secretion of a number of peptides. These molecules act in an autocrine/paracrine fashion to modulate cholangiocyte biology and determine the evolution of biliary damage. The failure of such mechanisms is believed to influence the progression of cholangiopathies, a group of diseases that selectively target biliary cells. Therefore, the understanding of mechanisms regulating cholangiocyte response to injury is expected to foster the development of new therapeutic options to treat biliary diseases. In the present review, we will discuss the most recent findings in the mechanisms driving cholangiocyte adaptation to damage, with particular emphasis on molecular pathways that are susceptible of therapeutic intervention. Morphogenic pathways (Hippo, Notch, Hedgehog), which have been recently shown to regulate biliary ontogenesis and response to injury, will also be reviewed. In addition, the results of ongoing clinical trials evaluating new drugs for the treatment of cholangiopathies will be discussed. PMID:26273695

  12. Chaotic features of nuclear structure and dynamics: selected topics

    NASA Astrophysics Data System (ADS)

    Zelevinsky, Vladimir; Volya, Alexander

    2016-03-01

    Quantum chaos has become an important element of our knowledge about physics of complex systems. In typical mesoscopic systems of interacting particles the dynamics invariably become chaotic when the level density, growing by combinatorial reasons, leads to the increasing probability of mixing simple mean-field (particle-hole) configurations. The resulting stationary states have exceedingly complicated structures that are comparable to those in random matrix theory. We discuss the main properties of mesoscopic quantum chaos and show that it can serve as a justification for application of statistical mechanics to mesoscopic systems. We show that quantum chaos becomes a powerful instrument for experimental, theoretical and computational work. The generalization to open systems and effects in the continuum are discussed with the help of the effective non-Hermitian Hamiltonian; it is shown how to formulate this approach for numerous problems of quantum signal transmission. The artificially introduced randomness can also be helpful for a deeper understanding of physics. We indicate the problems that require more investigation so as to be understood further.

  13. Structural and functional features of central nervous system lymphatic vessels.

    PubMed

    Louveau, Antoine; Smirnov, Igor; Keyes, Timothy J; Eccles, Jacob D; Rouhani, Sherin J; Peske, J David; Derecki, Noel C; Castle, David; Mandell, James W; Lee, Kevin S; Harris, Tajie H; Kipnis, Jonathan

    2015-07-16

    One of the characteristics of the central nervous system is the lack of a classical lymphatic drainage system. Although it is now accepted that the central nervous system undergoes constant immune surveillance that takes place within the meningeal compartment, the mechanisms governing the entrance and exit of immune cells from the central nervous system remain poorly understood. In searching for T-cell gateways into and out of the meninges, we discovered functional lymphatic vessels lining the dural sinuses. These structures express all of the molecular hallmarks of lymphatic endothelial cells, are able to carry both fluid and immune cells from the cerebrospinal fluid, and are connected to the deep cervical lymph nodes. The unique location of these vessels may have impeded their discovery to date, thereby contributing to the long-held concept of the absence of lymphatic vasculature in the central nervous system. The discovery of the central nervous system lymphatic system may call for a reassessment of basic assumptions in neuroimmunology and sheds new light on the aetiology of neuroinflammatory and neurodegenerative diseases associated with immune system dysfunction.

  14. New structural features of Acacia tortuosa gum exudate.

    PubMed

    Martínez, Maritza; Beltrán, Olga; Rincón, Fernando; León de Pinto, Gladys; Igartuburu, José Manuel

    2015-09-01

    Acacia tortuosa produces a clear gum, very soluble in water. Previous reports showed that it was constituted by four fractions, one of them an arabinogalactan-protein complex. The elucidation of the A. tortuosa gum structure by the combination of classical chemical methods, size exclusion chromatography and NMR spectroscopy, was the objective of this investigation. The data obtained show that the heteropolysaccharide is an arabinogalactan type II, highly ramified, with lateral chains at C-2 as well as at C-6 of the galactose 3-O residues; mono-O-substituted galactoses were not detected. There are residues of mannose, the arabinose, pyranose predominantly, is terminal and 2-O-linked. The abundance of the 4-O-methyl-α-d-glucuronic acid was not previously reported. The proteic fraction is probably represented by an arabinogalactan-protein complex that binds poorly with β-glucosyl Yariv reagent, and two glycoproteins. The NMR spectra suggest that the carbohydrate links to hydroxyproline through the galactose (galactosylation).

  15. Chinese wine classification system based on micrograph using combination of shape and structure features

    NASA Astrophysics Data System (ADS)

    Wan, Yi

    2011-06-01

    Chinese wines can be classification or graded by the micrographs. Micrographs of Chinese wines show floccules, stick and granule of variant shape and size. Different wines have variant microstructure and micrographs, we study the classification of Chinese wines based on the micrographs. Shape and structure of wines' particles in microstructure is the most important feature for recognition and classification of wines. So we introduce a feature extraction method which can describe the structure and region shape of micrograph efficiently. First, the micrographs are enhanced using total variation denoising, and segmented using a modified Otsu's method based on the Rayleigh Distribution. Then features are extracted using proposed method in the paper based on area, perimeter and traditional shape feature. Eight kinds total 26 features are selected. Finally, Chinese wine classification system based on micrograph using combination of shape and structure features and BP neural network have been presented. We compare the recognition results for different choices of features (traditional shape features or proposed features). The experimental results show that the better classification rate have been achieved using the combinational features proposed in this paper.

  16. Structural features for α-galactomannan binding to galectin-1

    PubMed Central

    Miller, Michelle C; Klyosov, Anatole A; Mayo, Kevin H

    2012-01-01

    Galectins have a highly conserved carbohydrate-binding domain to which a variety of galactose-containing saccharides, both β- and α-galactosides, can interact with varying degrees of affinity. Recently, we demonstrated that the relatively large α(1 → 6)-d-galacto-β(1 → 4)-d-mannan (Davanat) binds galectin-1 (gal-1) primarily at an alternative carbohydrate-binding domain. Here, we used a series of α-galactomannans (GMs) that vary in their mannose-to-galactose ratios for insight into an optimal structural signature for GM binding to gal-1. Heteronuclear single-quantum coherence nuclear magnetic resonance spectroscopy with 15N-labeled gal-1 and statistical modeling suggest that the optimal signature consists of α-d-galactopyranosyl doublets surrounded by regions of about four or more “naked” mannose residues. These relatively large and complex GMs all appear to interact with varying degrees at essentially the same binding surface on gal-1 that includes the Davanat alternative binding site and elements of the canonical β-galactoside-binding region. The use of two small, well-defined GMs [61-α(1 → 6)-d-galactosyl-β-d-mannotriaose and 63,64-di-α(1 → 6)-d-galactosyl-β-d-mannopentaose] helped characterize how GMs, in general, interact in part with the canonical site. Overall, our findings contribute to better understanding interactions of gal-1 with larger, complex polysaccharides and to the development of GM-based therapeutics for clinical use. PMID:22156919

  17. Structural features underlying raloxifene's biophysical interaction with bone matrix.

    PubMed

    Bivi, Nicoletta; Hu, Haitao; Chavali, Balagopalakrishna; Chalmers, Michael J; Reutter, Christopher T; Durst, Gregory L; Riley, Anna; Sato, Masahiko; Allen, Matthew R; Burr, David D; Dodge, Jeffrey A

    2016-02-15

    Raloxifene, a selective estrogen receptor modulator (SERM), reduces fracture risk at least in part by improving the mechanical properties of bone in a cell- and estrogen receptor-independent manner. In this study, we determined that raloxifene directly interacts with the bone tissue. Through the use of multiple and complementary biophysical techniques including nuclear magnetic resonance (NMR) and Fourier transform infrared spectroscopy (FTIR), we show that raloxifene interacts specifically with the organic component or the organic/mineral composite, and not with hydroxyapatite. Structure-activity studies reveal that the basic side chain of raloxifene is an instrumental determinant in the interaction with bone. Thus, truncation of portions of the side chain reduces bone binding and also diminishes the increase in mechanical properties. Our results support a model wherein the piperidine interacts with bone matrix through electrostatic interactions with the piperidine nitrogen and through hydrophobic interactions (van der Waals) with the aliphatic groups in the side chain and the benzothiophene core. Furthermore, in silico prediction of the potential binding sites on the surface of collagen revealed the presence of a groove with sufficient space to accommodate raloxifene analogs. The hydroxyl groups on the benzothiophene nucleus, which are necessary for binding of SERMs to the estrogen receptor, are not required for binding to the bone surface, but mediate a more robust binding of the compound to the bone powder. In conclusion, we report herein a novel property of raloxifene analogs that allows them to interact with the bone tissue through potential contacts with the organic matrix and in particular collagen. PMID:26795112

  18. Structural features underlying raloxifene's biophysical interaction with bone matrix.

    PubMed

    Bivi, Nicoletta; Hu, Haitao; Chavali, Balagopalakrishna; Chalmers, Michael J; Reutter, Christopher T; Durst, Gregory L; Riley, Anna; Sato, Masahiko; Allen, Matthew R; Burr, David D; Dodge, Jeffrey A

    2016-02-15

    Raloxifene, a selective estrogen receptor modulator (SERM), reduces fracture risk at least in part by improving the mechanical properties of bone in a cell- and estrogen receptor-independent manner. In this study, we determined that raloxifene directly interacts with the bone tissue. Through the use of multiple and complementary biophysical techniques including nuclear magnetic resonance (NMR) and Fourier transform infrared spectroscopy (FTIR), we show that raloxifene interacts specifically with the organic component or the organic/mineral composite, and not with hydroxyapatite. Structure-activity studies reveal that the basic side chain of raloxifene is an instrumental determinant in the interaction with bone. Thus, truncation of portions of the side chain reduces bone binding and also diminishes the increase in mechanical properties. Our results support a model wherein the piperidine interacts with bone matrix through electrostatic interactions with the piperidine nitrogen and through hydrophobic interactions (van der Waals) with the aliphatic groups in the side chain and the benzothiophene core. Furthermore, in silico prediction of the potential binding sites on the surface of collagen revealed the presence of a groove with sufficient space to accommodate raloxifene analogs. The hydroxyl groups on the benzothiophene nucleus, which are necessary for binding of SERMs to the estrogen receptor, are not required for binding to the bone surface, but mediate a more robust binding of the compound to the bone powder. In conclusion, we report herein a novel property of raloxifene analogs that allows them to interact with the bone tissue through potential contacts with the organic matrix and in particular collagen.

  19. Structural features of conducting quasi-one-dimensional organic halides and pseudohalides

    NASA Technical Reports Server (NTRS)

    Williams, R.; Lowe-Ma, C.; Samson, S.

    1982-01-01

    The physical properties of quasi-one-dimensional conductors are profoundly influenced by slight changes in structure. The unusual structural features of this class of materials include only short range order of the anions and structure modulation. The nature of disorder and structure modulation can affect the character of the metal-to-insulator transition at low temperature, and may allow us to make some predictions of low temperature behavior based on room temperature structural properties.

  20. Structural Features of the Telomerase RNA Gene in the Naked Mole Rat Heterocephalus glaber

    PubMed Central

    Evfratov, S. A.; Smekalova, E. M.; Golovin, A. V.; Logvina, N. A.; Zvereva, M. I.; Dontsova, O. A.

    2014-01-01

    Telomere length, an important feature of life span control, is dependent on the activity of telomerase (a key enzyme of the telomere-length-maintaining system). Telomerase RNA is a component of telomerase and, thus, is crucial for its activity. The structures of telomerase RNA genes and their promoter regions were compared for the long-living naked mole rat and different organisms. Two rare polymorphisms in Heterocephalus glaber telomerase RNA (hgTER) were identified: A→G in the first loop of pseudoknot P2b-p3 (an equivalent of 111nt in hTR) and G→A in the scaRNA domain CR7-p8b (an equivalent of 421nt in hTR). Analysis of TER promoter regions allowed us to identify two new transcription factor binding sites. The first one is the ETS family site, which was found to be a conserved element for all the analyzed TER promoters. The second site is unique for the promoter region of TER of the naked mole rat and is a binding site for the SOX17 transcription factor. The absence of one Sp1 site in the TER promoter region of the naked small rat is an additional specific feature of the promoter area of hgTER. Such variation in the hgTER transcription regulation region and hgTER itself could provide increased telomerase activity in stem cells and an extended lifespan to H. glaber. PMID:25093110

  1. Three new crystal structures in the Na-Pb system: solving structures without additional experimental input.

    PubMed

    Ward, Logan; Michel, Kyle; Wolverton, Chris

    2015-09-01

    The structures of three Na-Pb compounds, γ, δ and δ', have remained incompletely solved for nearly 60 years. The space group, lattice parameters and positions of the Pb atoms of these three structures have been determined, but the positions of the Na atoms are still unknown. In this work, the First-Principles Assisted Structure Solution (FPASS) method [Meredig & Wolverton (2013). Nat. Mater. 12, 123-127] has been used to complete the description of these three structures using only experimental information available from the literature as input. The paper also discusses the relative advantages of constrained crystal structure prediction tools, like FPASS, in comparison to conventional crystal structure prediction methods in reference to their abilities to complete the solution of other unsolved structures. PMID:26317197

  2. Adaptive cellular structures and devices with internal features for enhanced structural performance

    NASA Astrophysics Data System (ADS)

    Pontecorvo, Michael Eugene

    and force inputs are contrasted in relation to these metrics. The key innovation to the early structural elements presented here is the combination of the VMT with the pin-jointed hexagonal cell. Chapter 3 explores several prototypes of repeatable structural elements for simultaneous load-carrying capability and energy dissipation that are based on this innovation. The final demonstration prototype presented in this chapter is a column-like element that is based on a hexagonal cell containing two horizontal springs and one vertical damper. The unit is enclosed by a pair of buckling plates that serve to give the prototype a high initial stiffness and load carrying capability. The prototype is tested in both displacement and force input and its behavior is compared to simulation. Chapter 4 builds on the conceptual designs of Chapter 3 with the introduction of a plate-like element, that contains two compact VMTs connected by a horizontally oriented damper. Pre-loaded springs are used in the prototype to perform the same load carrying function as the buckling plates in the column-like prototype with increased predictability. The plate-like prototype is studied under impact to demonstrate its effectiveness as a protective layer. It is shown to reduce peak impact loads transmitted to the base of the device by over 60%. In most cases, the prototype compares well with a conventional protective rubber layer, and in cases of extreme impact loads, it exceeds the performance of the rubber layer. In addition to impact testing, the prototype is also experimentally tested under harmonic displacement input, and is simulated under both harmonic displacement and force input. The experiments illustrate that while the VMT parameters of a single layer can be optimized to a particular harmonic load amplitude, having two layers with softer and stiffer VMTs allows the system to show good energy dissipation characteristics at different harmonic load amplitude levels. Chapter 5 examines using

  3. Therapeutic approaches against common structural features of toxic oligomers shared by multiple amyloidogenic proteins.

    PubMed

    Guerrero-Muñoz, Marcos J; Castillo-Carranza, Diana L; Kayed, Rakez

    2014-04-15

    Impaired proteostasis is one of the main features of all amyloid diseases, which are associated with the formation of insoluble aggregates from amyloidogenic proteins. The aggregation process can be caused by overproduction or poor clearance of these proteins. However, numerous reports suggest that amyloid oligomers are the most toxic species, rather than insoluble fibrillar material, in Alzheimer's, Parkinson's, and Prion diseases, among others. Although the exact protein that aggregates varies between amyloid disorders, they all share common structural features that can be used as therapeutic targets. In this review, we focus on therapeutic approaches against shared features of toxic oligomeric structures and future directions.

  4. Comparison study of feature extraction methods in structural damage pattern recognition

    NASA Astrophysics Data System (ADS)

    Liu, Wenjia; Chen, Bo; Swartz, R. Andrew

    2011-04-01

    This paper compares the performance of various feature extraction methods applied to structural sensor measurements acquired in-situ, from a decommissioned bridge under realistic damage scenarios. Three feature extraction methods are applied to sensor data to generate feature vectors for normal and damaged structure data patterns. The investigated feature extraction methods include identification of both time domain methods as well as frequency domain methods. The evaluation of the feature extraction methods is performed by examining distance values among different patterns, distance values among feature vectors in the same pattern, and pattern recognition success rate. The test data used in the comparison study are from the System Identification to Monitor Civil Engineering Structures (SIMCES) Z24 Bridge damage detection tests, a rigorous instrumentation campaign that recorded the dynamic performance of a concrete box-girder bridge under progressively increasing damage scenarios. A number of progressive damage test case data sets, including undamaged cases and pier settlement cases (different depths), are used to test the separation of feature vectors among different patterns and the pattern recognition success rate for different feature extraction methods is reported.

  5. An atomic view of additive mutational effects in a protein structure

    SciTech Connect

    Skinner, M.M.; Terwilliger, T.C.

    1996-04-01

    Substitution of a single amino acid in a protein will often lead to substantial changes in properties. If these properties could be altered in a rational way then proteins could be readily generated with functions tailored to specific uses. When amino acid substitutions are made at well-separated locations in a single protein, their effects are generally additive. Additivity of effects of amino acid substitutions is very useful because the properties of proteins with any combination of substitutions can be inferred directly from those of the proteins with single changes. It would therefore be of considerable interest to have a means of knowing whether substitutions at a particular pair of sites in a protein are likely to lead to additive effects. The structural basis for additivity of effects of mutations on protein function was examined by determining crystal structures of single and double mutants in the hydrophobic core of gene V protein. Structural effects of mutations were found to be cumulative when two mutations were made in a single protein. Additivity occurs in this case because the regions structurally affected by mutations at the two sites do not overlap even though the sites are separated by only 9 {angstrom}. Structural distortions induced by mutations in gene V protein decrease rapidly, but not isotropically, with distance from the site of mutation. It is anticipated that cases where structural and functional effects of mutations will be additive could be identified simply by examining whether the regions structurally affected by each component mutation overlap.

  6. Features of the electronic structure of the active center of an HbS molecule

    NASA Astrophysics Data System (ADS)

    Novoselov, D. Yu.; Korotin, Dm. M.; Anisimov, V. I.

    2016-01-01

    Features of the electronic structure of the nonprotein part of the mutant form of the human hemoglobin molecule, HbS, are studied along with the magnetic state of the iron ion that is the "nucleus" of the active center of the molecule. It is found that the mutant form of the HbS molecule differs from a normal hemoglobin molecule by the distortion of the local environment of the iron ion, which changes the energy level splitting by a crystal field. As a result of ab initio calculations, the magnetic transition in the iron atom from the high-spin state to the low-spin state upon the addition of molecular oxygen to hemoglobin molecule is reproduced. It is established for the first time that a change in the crystal and electronic structure of the active center as a result of a mutation can lead to a substantial change in the energy of the bond between the active center of the hemoglobin molecule and an oxygen molecule.

  7. Structural Features of a 3′ Splice Site in Influenza A

    PubMed Central

    2015-01-01

    Influenza A is an RNA virus with a genome of eight negative sense segments. Segment 7 mRNA contains a 3′ splice site for alternative splicing to encode the essential M2 protein. On the basis of sequence alignment and chemical mapping experiments, the secondary structure surrounding the 3′ splice site has an internal loop, adenine bulge, and hairpin loop when it is in the hairpin conformation that exposes the 3′ splice site. We report structural features of a three-dimensional model of the hairpin derived from nuclear magnetic resonance spectra and simulated annealing with restrained molecular dynamics. Additional insight was provided by modeling based on 1H chemical shifts. The internal loop containing the 3′ splice site has a dynamic guanosine and a stable imino (cis Watson–Crick/Watson–Crick) GA pair. The adenine bulge also appears to be dynamic with the A either stacked in the stem or forming a base triple with a Watson–Crick GC pair. The hairpin loop is a GAAA tetraloop closed by an AC pair. PMID:25909229

  8. Structural and Organisational Features of Sensorimotor Intelligence among Retarded Infants and Toddlers.

    ERIC Educational Resources Information Center

    Dunst, C. J.; And Others

    1981-01-01

    The structural features of sensorimotor intelligence were assessed among three groups of retarded infants and toddlers. Hierarchical cluster analysis (HCA) was performed on two measures of relationship (stage congruence and intercorrelations). The potential utility of HCA for studying Piaget's "structure d'ensemble" stage criteria is illustrated.…

  9. Prediction of structural features and application to outer membrane protein identification

    NASA Astrophysics Data System (ADS)

    Yan, Renxiang; Wang, Xiaofeng; Huang, Lanqing; Yan, Feidi; Xue, Xiaoyu; Cai, Weiwen

    2015-06-01

    Protein three-dimensional (3D) structures provide insightful information in many fields of biology. One-dimensional properties derived from 3D structures such as secondary structure, residue solvent accessibility, residue depth and backbone torsion angles are helpful to protein function prediction, fold recognition and ab initio folding. Here, we predict various structural features with the assistance of neural network learning. Based on an independent test dataset, protein secondary structure prediction generates an overall Q3 accuracy of ~80%. Meanwhile, the prediction of relative solvent accessibility obtains the highest mean absolute error of 0.164, and prediction of residue depth achieves the lowest mean absolute error of 0.062. We further improve the outer membrane protein identification by including the predicted structural features in a scoring function using a simple profile-to-profile alignment. The results demonstrate that the accuracy of outer membrane protein identification can be improved by ~3% at a 1% false positive level when structural features are incorporated. Finally, our methods are available as two convenient and easy-to-use programs. One is PSSM-2-Features for predicting secondary structure, relative solvent accessibility, residue depth and backbone torsion angles, the other is PPA-OMP for identifying outer membrane proteins from proteomes.

  10. Influence of major structural features of cellulose on rate of enzymatic hydrolysis

    SciTech Connect

    Fan, L.T.; Lee, Y.H.; Beardmore, D.R.

    1981-02-01

    The rate of enzymatic hydrolysis of cellulose is profoundly affected by the structural features of cellulose, especially by the degree of crystallinity and the specific surface area. This is a report on the results of experiments conducted on cellulosic samples to examine the relationship among their rates of hydrolysis and the two structural parameters.

  11. FeatureMap3D--a tool to map protein features and sequence conservation onto homologous structures in the PDB.

    PubMed

    Wernersson, Rasmus; Rapacki, Kristoffer; Staerfeldt, Hans-Henrik; Sackett, Peter Wad; Mølgaard, Anne

    2006-07-01

    FeatureMap3D is a web-based tool that maps protein features onto 3D structures. The user provides sequences annotated with any feature of interest, such as post-translational modifications, protease cleavage sites or exonic structure and FeatureMap3D will then search the Protein Data Bank (PDB) for structures of homologous proteins. The results are displayed both as an annotated sequence alignment, where the user-provided annotations as well as the sequence conservation between the query and the target sequence are displayed, and also as a publication-quality image of the 3D protein structure with the selected features and sequence conservation enhanced. The results are also returned in a readily parsable text format as well as a PyMol (http://pymol.sourceforge.net/) script file, which allows the user to easily modify the protein structure image to suit a specific purpose. FeatureMap3D can also be used without sequence annotation, to evaluate the quality of the alignment of the input sequences to the most homologous structures in the PDB, through the sequence conservation colored 3D structure visualization tool. FeatureMap3D is available at: http://www.cbs.dtu.dk/services/FeatureMap3D/. PMID:16845115

  12. Estimation of Position Specific Energy as a Feature of Protein Residues from Sequence Alone for Structural Classification.

    PubMed

    Iqbal, Sumaiya; Hoque, Md Tamjidul

    2016-01-01

    A set of features computed from the primary amino acid sequence of proteins, is crucial in the process of inducing a machine learning model that is capable of accurately predicting three-dimensional protein structures. Solutions for existing protein structure prediction problems are in need of features that can capture the complexity of molecular level interactions. With a view to this, we propose a novel approach to estimate position specific estimated energy (PSEE) of a residue using contact energy and predicted relative solvent accessibility (RSA). Furthermore, we demonstrate PSEE can be reasonably estimated based on sequence information alone. PSEE is useful in identifying the structured as well as unstructured or, intrinsically disordered region of a protein by computing favorable and unfavorable energy respectively, characterized by appropriate threshold. The most intriguing finding, verified empirically, is the indication that the PSEE feature can effectively classify disorder versus ordered residues and can segregate different secondary structure type residues by computing the constituent energies. PSEE values for each amino acid strongly correlate with the hydrophobicity value of the corresponding amino acid. Further, PSEE can be used to detect the existence of critical binding regions that essentially undergo disorder-to-order transitions to perform crucial biological functions. Towards an application of disorder prediction using the PSEE feature, we have rigorously tested and found that a support vector machine model informed by a set of features including PSEE consistently outperforms a model with an identical set of features with PSEE removed. In addition, the new disorder predictor, DisPredict2, shows competitive performance in predicting protein disorder when compared with six existing disordered protein predictors. PMID:27588752

  13. Estimation of Position Specific Energy as a Feature of Protein Residues from Sequence Alone for Structural Classification

    PubMed Central

    Iqbal, Sumaiya; Hoque, Md Tamjidul

    2016-01-01

    A set of features computed from the primary amino acid sequence of proteins, is crucial in the process of inducing a machine learning model that is capable of accurately predicting three-dimensional protein structures. Solutions for existing protein structure prediction problems are in need of features that can capture the complexity of molecular level interactions. With a view to this, we propose a novel approach to estimate position specific estimated energy (PSEE) of a residue using contact energy and predicted relative solvent accessibility (RSA). Furthermore, we demonstrate PSEE can be reasonably estimated based on sequence information alone. PSEE is useful in identifying the structured as well as unstructured or, intrinsically disordered region of a protein by computing favorable and unfavorable energy respectively, characterized by appropriate threshold. The most intriguing finding, verified empirically, is the indication that the PSEE feature can effectively classify disorder versus ordered residues and can segregate different secondary structure type residues by computing the constituent energies. PSEE values for each amino acid strongly correlate with the hydrophobicity value of the corresponding amino acid. Further, PSEE can be used to detect the existence of critical binding regions that essentially undergo disorder-to-order transitions to perform crucial biological functions. Towards an application of disorder prediction using the PSEE feature, we have rigorously tested and found that a support vector machine model informed by a set of features including PSEE consistently outperforms a model with an identical set of features with PSEE removed. In addition, the new disorder predictor, DisPredict2, shows competitive performance in predicting protein disorder when compared with six existing disordered protein predictors. PMID:27588752

  14. The performance improvement of automatic classification among obstructive lung diseases on the basis of the features of shape analysis, in addition to texture analysis at HRCT

    NASA Astrophysics Data System (ADS)

    Lee, Youngjoo; Kim, Namkug; Seo, Joon Beom; Lee, JuneGoo; Kang, Suk Ho

    2007-03-01

    In this paper, we proposed novel shape features to improve classification performance of differentiating obstructive lung diseases, based on HRCT (High Resolution Computerized Tomography) images. The images were selected from HRCT images, obtained from 82 subjects. For each image, two experienced radiologists selected rectangular ROIs with various sizes (16x16, 32x32, and 64x64 pixels), representing each disease or normal lung parenchyma. Besides thirteen textural features, we employed additional seven shape features; cluster shape features, and Top-hat transform features. To evaluate the contribution of shape features for differentiation of obstructive lung diseases, several experiments were conducted with two different types of classifiers and various ROI sizes. For automated classification, the Bayesian classifier and support vector machine (SVM) were implemented. To assess the performance and cross-validation of the system, 5-folding method was used. In comparison to employing only textural features, adding shape features yields significant enhancement of overall sensitivity(5.9, 5.4, 4.4% in the Bayesian and 9.0, 7.3, 5.3% in the SVM), in the order of ROI size 16x16, 32x32, 64x64 pixels, respectively (t-test, p<0.01). Moreover, this enhancement was largely due to the improvement on class-specific sensitivity of mild centrilobular emphysema and bronchiolitis obliterans which are most hard to differentiate for radiologists. According to these experimental results, adding shape features to conventional texture features is much useful to improve classification performance of obstructive lung diseases in both Bayesian and SVM classifiers.

  15. The Use of Additive Manufacturing for Fabrication of Multi-Function Small Satellite Structures

    SciTech Connect

    Horais, Brian J; Love, Lonnie J; Dehoff, Ryan R

    2013-01-01

    The use of small satellites in constellations is limited only by the growing functionality of smallsats themselves. Additive manufacturing provides exciting new design opportunities for development of multifunction CubeSat structures that integrate such functions as propulsion and thermal control into the satellite structures themselves. Manufacturing of these complex multifunction structures is now possible in lightweight, high strength, materials such as titanium by using existing electron beam melting additive manufacturing processes. However, the use of today's additive manufacturing capabilities is often cost-prohibitive for small companies due to the large capital investments required. To alleviate this impediment the U.S. Department of Energy has established a Manufacturing Demonstration Facility (MDF) at their Oak Ridge National Laboratory (ORNL) in Tennessee that provides industry access to a broad range of energy-efficient additive manufacturing equipment for collaborative use by both small and large organizations. This paper presents a notional CubeSat multifunction design that integrates the propulsion system into a three-unit (3U) CubeSat structure. The full-scale structure has been designed and fabricated at the ORNL MDF. The use of additive manufacturing for spacecraft fabrication is opening up many new possibilities in design and fabrication capabilities for what had previously been impossible structures to fabricate.

  16. Specific features of the motion of neutrons in a medium with a helical magnetic structure

    SciTech Connect

    Fraerman, A. A. Udalov, O. G.

    2007-02-15

    The specific features of the motion of neutrons in a noncoplanar magnetic field are considered by an example of the magnetization distribution in the form of a conical helix. The reflection coefficients of neutrons from holmium crystals are calculated. It is shown that, for a noncoplanar distribution of a magnetic field in a crystal, the reflection coefficient of neutrons with spin flip exhibits an additional feature.

  17. Elusive Structural, Functional, and Immunological Features of Act d 5, the Green Kiwifruit Kiwellin.

    PubMed

    Offermann, Lesa R; Giangrieco, Ivana; Perdue, Makenzie L; Zuzzi, Sara; Santoro, Mario; Tamburrini, Maurizio; Cosgrove, Daniel J; Mari, Adriano; Ciardiello, Maria Antonietta; Chruszcz, Maksymilian

    2015-07-29

    Kiwellin (Act d 5) is an allergenic protein contained in kiwifruit pulp in high amounts. The aim of this study was to investigate the three-dimensional structure of the natural molecule from green kiwifruit and its possible function. Kiwellin was crystallized, and its structure, including post-translational modifications, was elucidated. The molecular weight and structural features, in solution, were analyzed by gel filtration and circular dichroism, respectively. Although structurally similar to expansin, kiwellin lacks expansin activity and carbohydrate binding. A specific algorithm was applied to investigate any possible IgE reactivity correlation between kiwellin and a panel of 102 allergens, including expansins and other carbohydrate-binding allergens. The available data suggest a strong dependence of the kiwellin structure on the environmental/experimental conditions. This dependence therefore poses challenges in detecting the correlations between structural, functional, and immunological features of this protein.

  18. Elusive Structural, Functional, and Immunological Features of Act d 5, the Green Kiwifruit Kiwellin.

    PubMed

    Offermann, Lesa R; Giangrieco, Ivana; Perdue, Makenzie L; Zuzzi, Sara; Santoro, Mario; Tamburrini, Maurizio; Cosgrove, Daniel J; Mari, Adriano; Ciardiello, Maria Antonietta; Chruszcz, Maksymilian

    2015-07-29

    Kiwellin (Act d 5) is an allergenic protein contained in kiwifruit pulp in high amounts. The aim of this study was to investigate the three-dimensional structure of the natural molecule from green kiwifruit and its possible function. Kiwellin was crystallized, and its structure, including post-translational modifications, was elucidated. The molecular weight and structural features, in solution, were analyzed by gel filtration and circular dichroism, respectively. Although structurally similar to expansin, kiwellin lacks expansin activity and carbohydrate binding. A specific algorithm was applied to investigate any possible IgE reactivity correlation between kiwellin and a panel of 102 allergens, including expansins and other carbohydrate-binding allergens. The available data suggest a strong dependence of the kiwellin structure on the environmental/experimental conditions. This dependence therefore poses challenges in detecting the correlations between structural, functional, and immunological features of this protein. PMID:26146952

  19. Adaptive cellular structures and devices with internal features for enhanced structural performance

    NASA Astrophysics Data System (ADS)

    Pontecorvo, Michael Eugene

    and force inputs are contrasted in relation to these metrics. The key innovation to the early structural elements presented here is the combination of the VMT with the pin-jointed hexagonal cell. Chapter 3 explores several prototypes of repeatable structural elements for simultaneous load-carrying capability and energy dissipation that are based on this innovation. The final demonstration prototype presented in this chapter is a column-like element that is based on a hexagonal cell containing two horizontal springs and one vertical damper. The unit is enclosed by a pair of buckling plates that serve to give the prototype a high initial stiffness and load carrying capability. The prototype is tested in both displacement and force input and its behavior is compared to simulation. Chapter 4 builds on the conceptual designs of Chapter 3 with the introduction of a plate-like element, that contains two compact VMTs connected by a horizontally oriented damper. Pre-loaded springs are used in the prototype to perform the same load carrying function as the buckling plates in the column-like prototype with increased predictability. The plate-like prototype is studied under impact to demonstrate its effectiveness as a protective layer. It is shown to reduce peak impact loads transmitted to the base of the device by over 60%. In most cases, the prototype compares well with a conventional protective rubber layer, and in cases of extreme impact loads, it exceeds the performance of the rubber layer. In addition to impact testing, the prototype is also experimentally tested under harmonic displacement input, and is simulated under both harmonic displacement and force input. The experiments illustrate that while the VMT parameters of a single layer can be optimized to a particular harmonic load amplitude, having two layers with softer and stiffer VMTs allows the system to show good energy dissipation characteristics at different harmonic load amplitude levels. Chapter 5 examines using

  20. Development of Additive Construction Technologies for Application to Development of Lunar/Martian Surface Structures Using In-Situ Materials

    NASA Technical Reports Server (NTRS)

    Werkheiser, Niki J.; Fiske, Michael R.; Edmunson, Jennifer E.; Khoshnevis, Berokh

    2015-01-01

    For long-duration missions on other planetary bodies, the use of in situ materials will become increasingly critical. As human presence on these bodies expands, so must the breadth of the structures required to accommodate them including habitats, laboratories, berms, radiation shielding for natural radiation and surface reactors, garages, solar storm shelters, greenhouses, etc. Planetary surface structure manufacturing and assembly technologies that incorporate in situ resources provide options for autonomous, affordable, pre-positioned environments with radiation shielding features and protection from micrometeorites, exhaust plume debris, and other hazards. The ability to use in-situ materials to construct these structures will provide a benefit in the reduction of up-mass that would otherwise make long-term Moon or Mars structures cost prohibitive. The ability to fabricate structures in situ brings with it the ability to repair these structures, which allows for the self-sufficiency and sustainability necessary for long-duration habitation. Previously, under the auspices of the MSFC In-Situ Fabrication and Repair (ISFR) project and more recently, under the jointly-managed MSFC/KSC Additive Construction with Mobile Emplacement (ACME) project, the MSFC Surface Structures Group has been developing materials and construction technologies to support future planetary habitats with in-situ resources. One such additive construction technology is known as Contour Crafting. This paper presents the results to date of these efforts, including development of novel nozzle concepts for advanced layer deposition using this process. Conceived initially for rapid development of cementitious structures on Earth, it also lends itself exceptionally well to the automated fabrication of planetary surface structures using minimally processed regolith as aggregate, and binders developed from in situ materials as well. This process has been used successfully in the fabrication of

  1. Jackpot Structural Features: Rollover Effect and Goal-Gradient Effect in EGM Gambling.

    PubMed

    Li, En; Rockloff, Matthew J; Browne, Matthew; Donaldson, Phillip

    2016-06-01

    Relatively little research has been undertaken on the influence of jackpot structural features on electronic gaming machine (EGM) gambling behavior. This study considered two common features of EGM jackpots: progressive (i.e., the jackpot incrementally growing in value as players make additional bets), and deterministic (i.e., a guaranteed jackpot after a fixed number of bets, which is determined in advance and at random). Their joint influences on player betting behavior and the moderating role of jackpot size were investigated in a crossed-design experiment. Using real money, players gambled on a computer simulated EGM with real jackpot prizes of either $500 (i.e., small jackpot) or $25,000 (i.e., large jackpot). The results revealed three important findings. Firstly, players placed the largest bets (20.3 % higher than the average) on large jackpot EGMs that were represented to be deterministic and non-progressive. This finding was supportive of a hypothesized 'goal-gradient effect', whereby players might have felt subjectively close to an inevitable payoff for a high-value prize. Secondly, large jackpots that were non-deterministic and progressive also promoted high bet sizes (17.8 % higher than the average), resembling the 'rollover effect' demonstrated in lottery betting, whereby players might imagine that their large bets could be later recouped through a big win. Lastly, neither the hypothesized goal-gradient effect nor the rollover effect was evident among players betting on small jackpot machines. These findings suggest that certain high-value jackpot configurations may have intensifying effects on player behavior. PMID:26063627

  2. Nematode.net update 2011: addition of data sets and tools featuring next-generation sequencing data.

    PubMed

    Martin, John; Abubucker, Sahar; Heizer, Esley; Taylor, Christina M; Mitreva, Makedonka

    2012-01-01

    Nematode.net (http://nematode.net) has been a publicly available resource for studying nematodes for over a decade. In the past 3 years, we reorganized Nematode.net to provide more user-friendly navigation through the site, a necessity due to the explosion of data from next-generation sequencing platforms. Organism-centric portals containing dynamically generated data are available for over 56 different nematode species. Next-generation data has been added to the various data-mining portals hosted, including NemaBLAST and NemaBrowse. The NemaPath metabolic pathway viewer builds associations using KOs, rather than ECs to provide more accurate and fine-grained descriptions of proteins. Two new features for data analysis and comparative genomics have been added to the site. NemaSNP enables the user to perform population genetics studies in various nematode populations using next-generation sequencing data. HelmCoP (Helminth Control and Prevention) as an independent component of Nematode.net provides an integrated resource for storage, annotation and comparative genomics of helminth genomes to aid in learning more about nematode genomes, as well as drug, pesticide, vaccine and drug target discovery. With this update, Nematode.net will continue to realize its original goal to disseminate diverse bioinformatic data sets and provide analysis tools to the broad scientific community in a useful and user-friendly manner.

  3. Influence of culture medium growth variables on Ganoderma lucidum exopolysaccharides structural features.

    PubMed

    Fraga, Irene; Coutinho, João; Bezerra, Rui M; Dias, Albino A; Marques, Guilhermina; Nunes, Fernando M

    2014-10-13

    In this work the effect of carbon and nitrogen levels and initial pH of the wheat extract culture medium of submerged culture of Ganoderma lucidum on the amount, purity and structural features of exopolysaccharides (EPS) were studied. A low peptone level (1.65 g L(-1)) favored mycelium biomass, EPS purity, but a higher supply of peptone (4.80 g L(-1)) is needed for maximum EPS production. The carbohydrate composition of the EPS and structural features also changed significantly according to the different growing conditions, being observed significant differences in the (1 → 3)/(1 → 4)-Glcp ratio and also on the branching degree of EPS. As the biological activities of EPS are highly dependent on the polysaccharide structural features, this variability can have implications on the EPS biological activities, but can also be used advantageously to produce tailor made polysaccharides with specific applications.

  4. Effect of stabilizing additives on the structure and hydration of proteins: a study involving monoclinic lysozyme.

    PubMed

    Saraswathi, N T; Sankaranarayanan, R; Vijayan, M

    2002-07-01

    In pursuance of a long-range programme on the hydration, mobility and action of proteins, the structural basis of the stabilizing effect of sugars and polyols is being investigated. With two crystallographically independent molecules with slightly different packing environments in the crystal, monoclinic lysozyme constitutes an ideal system for exploring the problem. The differences in the structure and hydration of the two molecules provide a framework for examining the changes caused by stabilizing additives. Monoclinic crystals were grown under native conditions and also in the presence of 10% sucrose, 15% trehalose, 10% trehalose, 10% sorbitol and 5% glycerol. The crystal structures were refined at resolutions ranging from 1.8 to 2.1 A. The average B values, and hence the mobility of the structure, are lower in the presence of additives than in the native crystals. However, a comparison of the structures indicates that the effect of the additives on the structure and the hydration shell around the protein molecule is considerably less than that caused by differences in packing. It is also less than that caused by the replacement of NaNO(3) by NaCl as the precipitant in the crystallization experiments. This result is not in conformity with the commonly held belief that additives exert their stabilizing effect through the reorganization of the hydration shell, at least as far as the ordered water molecules are concerned.

  5. A spectral-structural bag-of-features scene classifier for very high spatial resolution remote sensing imagery

    NASA Astrophysics Data System (ADS)

    Zhao, Bei; Zhong, Yanfei; Zhang, Liangpei

    2016-06-01

    results show that the whole image as the scope of the pooling operator performs better than the scope generated by SP. In addition, SSBFC codes and pools the spectral and structural features separately to avoid mutual interruption between the spectral and structural features. The coding vectors of spectral and structural features are then concatenated into a final coding vector. Finally, SSBFC classifies the final coding vector by support vector machine (SVM) with a histogram intersection kernel (HIK). Compared with the latest scene classification methods, the experimental results with three VHSR datasets demonstrate that the proposed SSBFC performs better than the other classification methods for VHSR image scenes.

  6. Terrestrial exposure of oilfield flowline additives diminish soil structural stability and remediative microbial function.

    PubMed

    George, S J; Sherbone, J; Hinz, C; Tibbett, M

    2011-10-01

    Onshore oil production pipelines are major installations in the petroleum industry, stretching many thousands of kilometres worldwide which also contain flowline additives. The current study focuses on the effect of the flowline additives on soil physico-chemical and biological properties and quantified the impact using resilience and resistance indices. Our findings are the first to highlight deleterious effect of flowline additives by altering some fundamental soil properties, including a complete loss of structural integrity of the impacted soil and a reduced capacity to degrade hydrocarbons mainly due to: (i) phosphonate salts (in scale inhibitor) prevented accumulation of scale in pipelines but also disrupted soil physical structure; (ii) glutaraldehyde (in biocides) which repressed microbial activity in the pipeline and reduced hydrocarbon degradation in soil upon environmental exposure; (iii) the combinatory effects of these two chemicals synergistically caused severe soil structural collapse and disruption of microbial degradation of petroleum hydrocarbons.

  7. Key structural features of cis-cinnamic acid as an allelochemical.

    PubMed

    Abe, Masato; Nishikawa, Keisuke; Fukuda, Hiroshi; Nakanishi, Kazunari; Tazawa, Yuta; Taniguchi, Tomoya; Park, So-Young; Hiradate, Syuntaro; Fujii, Yoshiharu; Okuda, Katsuhiro; Shindo, Mitsuru

    2012-12-01

    1-O-cis-cinnamoyl-β-D-glucopyranose is one of the most potent allelochemicals isolated from Spiraea thunbergii Sieb. It is suggested that it derives its strong inhibitory activity from cis-cinnamic acid, which is crucial for phytotoxicity. It was synthesized to confirm its structure and bioactivity, and also a series of cis-cinnamic acid analogues were prepared to elucidate the key features of cis-cinnamic acid for lettuce root growth inhibition. The cis-cyclopropyl analogue showed potent inhibitory activity while the saturated and alkyne analogues proved to be inactive, demonstrating the importance of the cis-double bond. Moreover, the aromatic ring could not be replaced with a saturated ring. However, the 1,3-dienylcyclohexene analogue showed strong activity. These results suggest that the geometry of the C-C double bond between the carboxyl group and the aromatic ring is essential for potent inhibitory activity. In addition, using several light sources, the photostability of the cinnamic acid derivatives and the role of the C-C double bond were also investigated.

  8. Assessing Diversity of DNA Structure-Related Sequence Features in Prokaryotic Genomes

    PubMed Central

    Huang, Yongjie; Mrázek, Jan

    2014-01-01

    Prokaryotic genomes are diverse in terms of their nucleotide and oligonucleotide composition as well as presence of various sequence features that can affect physical properties of the DNA molecule. We present a survey of local sequence patterns which have a potential to promote non-canonical DNA conformations (i.e. different from standard B-DNA double helix) and interpret the results in terms of relationships with organisms' habitats, phylogenetic classifications, and other characteristics. Our present work differs from earlier similar surveys not only by investigating a wider range of sequence patterns in a large number of genomes but also by using a more realistic null model to assess significant deviations. Our results show that simple sequence repeats and Z-DNA-promoting patterns are generally suppressed in prokaryotic genomes, whereas palindromes and inverted repeats are over-represented. Representation of patterns that promote Z-DNA and intrinsic DNA curvature increases with increasing optimal growth temperature (OGT), and decreases with increasing oxygen requirement. Additionally, representations of close direct repeats, palindromes and inverted repeats exhibit clear negative trends with increasing OGT. The observed relationships with environmental characteristics, particularly OGT, suggest possible evolutionary scenarios of structural adaptation of DNA to particular environmental niches. PMID:24408877

  9. Contrasted structuring effects of mesoscale features on the seabird community in the Mozambique Channel

    NASA Astrophysics Data System (ADS)

    Jaquemet, S.; Ternon, J. F.; Kaehler, S.; Thiebot, J. B.; Dyer, B.; Bemanaja, E.; Marteau, C.; Le Corre, M.

    2014-02-01

    of mescoscale features in structuring the tropical seabird community in the Mozambique Channel, in addition to segregating tropical and non-tropical species. The mechanisms underlying the segregation of tropical seabirds seem to partially differ from that of other tropical regions, and this may be a consequence of the strong local mesoscale activity, affecting prey size and availability schemes. Beyond characterising the foraging habitats of the seabird community of the Mozambique Channel, this study highlights the importance of this region as a hot spot for seabirds; especially the southern part, where several endangered sub-Antarctic species over-winter.

  10. The effect of additional exposure to the unique features in a perceptual learning task can be attributed to a location bias.

    PubMed

    Recio, Sergio A; Iliescu, Adela F; Bergés, Germán D; Gil, Marta; de Brugada, Isabel

    2016-04-01

    It has been suggested that human perceptual learning could be explained in terms of a better memory encoding of the unique features during intermixed exposure. However, it is possible that a location bias could play a relevant role in explaining previous results of perceptual learning studies using complex visual stimuli. If this were the case, the only relevant feature would be the location, rather than the content, of the unique features. To further explore this possibility, we attempted to replicate the results of Lavis, Kadib, Mitchell, and Hall (2011, Experiment 2), which showed that additional exposure to the unique elements resulted in better discrimination than simple intermixed exposure. We manipulated the location of the unique elements during the additional exposure. In one experiment, they were located in the same position as that when presented together with the common element. In another experiment, the unique elements were located in the center of the screen, regardless of where they were located together with the common element. Our results showed that additional exposure only improved discrimination when the unique elements were presented in the same position as when they were presented together with the common element. The results reported here do not provide support for the explanation of the effects of additional exposure of the unique elements in terms of a better memory encoding and instead suggest an explanation in terms of location bias. PMID:26881901

  11. The effect of additional exposure to the unique features in a perceptual learning task can be attributed to a location bias.

    PubMed

    Recio, Sergio A; Iliescu, Adela F; Bergés, Germán D; Gil, Marta; de Brugada, Isabel

    2016-04-01

    It has been suggested that human perceptual learning could be explained in terms of a better memory encoding of the unique features during intermixed exposure. However, it is possible that a location bias could play a relevant role in explaining previous results of perceptual learning studies using complex visual stimuli. If this were the case, the only relevant feature would be the location, rather than the content, of the unique features. To further explore this possibility, we attempted to replicate the results of Lavis, Kadib, Mitchell, and Hall (2011, Experiment 2), which showed that additional exposure to the unique elements resulted in better discrimination than simple intermixed exposure. We manipulated the location of the unique elements during the additional exposure. In one experiment, they were located in the same position as that when presented together with the common element. In another experiment, the unique elements were located in the center of the screen, regardless of where they were located together with the common element. Our results showed that additional exposure only improved discrimination when the unique elements were presented in the same position as when they were presented together with the common element. The results reported here do not provide support for the explanation of the effects of additional exposure of the unique elements in terms of a better memory encoding and instead suggest an explanation in terms of location bias.

  12. What common structural features and variations of mammalian P450s are known to date?

    PubMed

    Otyepka, Michal; Skopalík, Josef; Anzenbacherová, Eva; Anzenbacher, Pavel

    2007-03-01

    Sufficient structural information on mammalian cytochromes P450 has now been published (including seventeen X-ray structures of these enzymes by June 2006) to allow characteristic features of these enzymes to be identified, including: (i) the presence of a common fold, typical of all P450s, (ii) similarities in the positioning of the heme cofactor, (iii) the spatial arrangement of certain structural elements, and (iv) the access/egress paths for substrates and products, (v) probably common orientation in the membrane, (vi) characteristic properties of the active sites with networks of water molecules, (vii) mode of interaction with redox partners and (viii) a certain degree of flexibility of the structure and active site determining the ease with which the enzyme may bind the substrates. As well as facilitating the identification of common features, comparison of the available structures allows differences among the structures to be identified, including variations in: (i) preferred access/egress paths to/from the active site, (ii) the active site volume and (iii) flexible regions. The availability of crystal structures provides opportunities for molecular dynamic simulations, providing data that are apparently complementary to experimental findings but also allow the dynamic behavior of access/egress paths and other dynamic features of the enzymes to be explored. PMID:17069978

  13. Structural Mapping of Paterae and Mountains on Io: Implications for Crustal Stresses and Feature Evolution

    NASA Astrophysics Data System (ADS)

    Ahern, A.; Radebaugh, J.; Christiansen, E. H.; Harris, R. A.

    2015-12-01

    Paterae and mountains are some of the most distinguishing and well-distributed surface features on Io, and they reveal the role of tectonism in Io's crust. Paterae, similar to calderas, are volcano-tectonic collapse features that often have straight margins. Io's mountains are some of the highest in the solar system and contain linear features that reveal crustal stresses. Paterae and mountains are often found adjacent to one another, suggesting possible genetic relationships. We have produced twelve detailed regional structural maps from high-resolution images of relevant features, where available, as well as a global structural map from the Io Global Color Mosaic. The regional structural maps identify features such as fractures, lineations, folds, faults, and mass wasting scarps, which are then interpreted in the context of global and regional stress regimes. A total of 1048 structural lineations have been identified globally. Preliminary analyses of major thrust and normal fault orientations are dominantly 90° offset from each other, suggesting the maximum contractional stresses leading to large mountain formation are not a direct result of tidal extension. Rather, these results corroborate the model of volcanic loading of the crust and global shortening, leading to thrust faulting and uplift of coherent crustal blocks. Several paterae, such as Hi'iaka and Tohil, are found adjacent to mountains inside extensional basins where lava has migrated up normal faults to erupt onto patera floors. Over time, mass wasting and volcanic resurfacing can change mountains from young, steep, and angular peaks to older, gentler, and more rounded hills. Mass wasting scarps make up 53% of all features identified. The structural maps highlight the significant effect of mass wasting on Io's surface, the evolution of mountains through time, the role of tectonics in the formation of paterae, and the formation of mountains through global contraction due to volcanism.

  14. Atomic structural features of dopant segregated grain boundary complexions in alumina by EXAFS

    NASA Astrophysics Data System (ADS)

    Behera, Shantanu Kumar

    The primary objective of this undertaking was to characterize the atomic structural features of dopant-segregated interfaces in a (pseudo) single phase microstructure and relate the same to atomic diffusion in the grain boundaries. Alumina was chosen as a model host system based on prior observations of grain boundary complexions in this system by electron microscopy. Two types of dopant chemistry were selected that are known to produce dramatically different microstructural behavior in alumina. These were, (i) rare earth element doping (Y) and (ii) Y-Si co-doping in alumina. In Y-doped alumina microstructures, different Gibbsian excess of the segregated dopant has been known to produce two distinct types of interface complexions. On the other hand, three distinct types of disordered grain boundary complexions have been observed in Y-Si codoped alumina. A quantitative grain growth study was performed in dense microstructures of these materials and different kinetic regimes of boundary mobility were identified. Subsequently, samples annealed at various temperatures were quenched to preserve the grain boundary structure and characterized using synchrotron extended X-ray absorption fine structure spectroscopy (EXAFS) at the Y K-edge. Distinct local structural features of the dopant segregation induced interface phases were observed and were used to distinguish between each of the complexion types. Computation of EXAFS spectra of theoretical clusters by ab initio methods and fitting the same with experimental data identified several types of interface complexions including: (i) sub-monolayer adsorption, where oversized isovalent dopants (Y) occupy substitutional cation sites at the grain boundary core and reduce the interface energy, (ii) saturation of dopants at the interface leading to bilayer adsorption, where dopants (Y) substitute host cations on both sides of the boundary interpolating into the crystals, (iii) multilayered adsorption, where a pseudo

  15. Ultra-low-molecular-weight heparins: precise structural features impacting specific anticoagulant activities.

    PubMed

    Lima, Marcelo A; Viskov, Christian; Herman, Frederic; Gray, Angel L; de Farias, Eduardo H C; Cavalheiro, Renan P; Sassaki, Guilherme L; Hoppensteadt, Debra; Fareed, Jawed; Nader, Helena B

    2013-03-01

    Ultra-low-molecular-weight heparins (ULMWHs) with better efficacy and safety ratios are under development; however, there are few structural data available. The main structural features and molecular weight of ULMWHs were studied and compared to enoxaparin. Their monosaccharide composition and average molecular weights were determined and preparations studied by nuclear magnetic resonance spectroscopy, scanning ultraviolet spectroscopy, circular dichroism and gel permeation chromatography. In general, ULMWHs presented higher 3-O-sulphated glucosamine and unsaturated uronic acid residues, the latter being comparable with their higher degree of depolymerisation. The analysis showed that ULMWHs are structurally related to LMWHs; however, their monosaccharide/oligosaccharide compositions and average molecular weights differed considerably explaining their different anticoagulant activities. The results relate structural features to activity, assisting the development of new and improved therapeutic agents, based on depolymerised heparin, for the prophylaxis and treatment of thrombotic disorders.

  16. An Ensemble-of-Classifiers Based Approach for Early Diagnosis of Alzheimer's Disease: Classification Using Structural Features of Brain Images

    PubMed Central

    Farhan, Saima; Tauseef, Huma

    2014-01-01

    Structural brain imaging is playing a vital role in identification of changes that occur in brain associated with Alzheimer's disease. This paper proposes an automated image processing based approach for the identification of AD from MRI of the brain. The proposed approach is novel in a sense that it has higher specificity/accuracy values despite the use of smaller feature set as compared to existing approaches. Moreover, the proposed approach is capable of identifying AD patients in early stages. The dataset selected consists of 85 age and gender matched individuals from OASIS database. The features selected are volume of GM, WM, and CSF and size of hippocampus. Three different classification models (SVM, MLP, and J48) are used for identification of patients and controls. In addition, an ensemble of classifiers, based on majority voting, is adopted to overcome the error caused by an independent base classifier. Ten-fold cross validation strategy is applied for the evaluation of our scheme. Moreover, to evaluate the performance of proposed approach, individual features and combination of features are fed to individual classifiers and ensemble based classifier. Using size of left hippocampus as feature, the accuracy achieved with ensemble of classifiers is 93.75%, with 100% specificity and 87.5% sensitivity. PMID:25276224

  17. Template Matching Method Based on Visual Feature Constraint and Structure Constraint

    NASA Astrophysics Data System (ADS)

    Li, Zhu; Tomotsune, Kojiro; Tomioka, Yoichi; Kitazawa, Hitoshi

    Template matching for image sequences captured with a moving camera is very important for several applications such as Robot Vision, SLAM, ITS, and video surveillance systems. However, it is difficult to realize accurate template matching using only visual feature information such as HSV histograms, edge histograms, HOG histograms, and SIFT features, because it is affected by several phenomena such as illumination change, viewpoint change, size change, and noise. In order to realize robust tracking, structure information such as the relative position of each part of the object should be considered. In this paper, we propose a method that considers both visual feature information and structure information. Experiments show that the proposed method realizes robust tracking and determine the relationships between object parts in the scenes and those in the template.

  18. Can artificial reefs mimic natural reef communities? The roles of structural features and age.

    PubMed

    Perkol-Finkel, S; Shashar, N; Benayahu, Y

    2006-03-01

    In light of the deteriorating state of coral reefs worldwide, the need to rehabilitate marine environments has greatly increased. Artificial reefs (ARs) have been suggested as a tool for reef conservation and rehabilitation. Although successions of AR communities have been thoroughly studied, current understanding of the interactions between artificial and natural reefs (NRs) is poor and a fundamental question still to be answered is that of whether AR communities can mimic adjacent NR communities. We suggest three alternative hypotheses: Neighboring ARs and NRs will (1) achieve a similar community structure given sufficient time; (2) be similar only if they possess similar structural features; (3) always differ, regardless of age or structural features. We examined these hypotheses by comparing the community structure on a 119-year old shipwreck to a neighboring NR. Fouling organisms, including stony and soft corals, sponges, tunicates, sea anemones and hydrozoans were recorded and measured along belt transects. The ahermatypic stony coral Tubastrea micrantha dominated vertical AR regions while the soft corals Nephthea sp. and Xenia sp. dominated both artificial and natural horizontal surfaces. Our results support the second hypothesis, indicating that even after a century an AR will mimic its adjacent NR communities only if it possesses structural features similar to those of the natural surroundings. However, if the two differ structurally, their communities will remain distinct.

  19. Can artificial reefs mimic natural reef communities? The roles of structural features and age.

    PubMed

    Perkol-Finkel, S; Shashar, N; Benayahu, Y

    2006-03-01

    In light of the deteriorating state of coral reefs worldwide, the need to rehabilitate marine environments has greatly increased. Artificial reefs (ARs) have been suggested as a tool for reef conservation and rehabilitation. Although successions of AR communities have been thoroughly studied, current understanding of the interactions between artificial and natural reefs (NRs) is poor and a fundamental question still to be answered is that of whether AR communities can mimic adjacent NR communities. We suggest three alternative hypotheses: Neighboring ARs and NRs will (1) achieve a similar community structure given sufficient time; (2) be similar only if they possess similar structural features; (3) always differ, regardless of age or structural features. We examined these hypotheses by comparing the community structure on a 119-year old shipwreck to a neighboring NR. Fouling organisms, including stony and soft corals, sponges, tunicates, sea anemones and hydrozoans were recorded and measured along belt transects. The ahermatypic stony coral Tubastrea micrantha dominated vertical AR regions while the soft corals Nephthea sp. and Xenia sp. dominated both artificial and natural horizontal surfaces. Our results support the second hypothesis, indicating that even after a century an AR will mimic its adjacent NR communities only if it possesses structural features similar to those of the natural surroundings. However, if the two differ structurally, their communities will remain distinct. PMID:16198411

  20. [Experience in simulating the structural and dynamic features of small proteins using table supercomputers].

    PubMed

    Kondrat'ev, M S; Kabanov, A V; Komarov, V M; Khechinashvili, N N; Samchenko, A A

    2011-01-01

    The results of theoretical studies of the structural and dynamic features of peptides and small proteins have been presented that were carried out by quantum chemical and molecular dynamics methods in high-performance graphic stations, "table supercomputers", using distributed calculations by the CUDA technology. PMID:22279747

  1. 1. VIEW OF THE DUGOUT STRUCTURE (FEATURE B16), FACING WEST. ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    1. VIEW OF THE DUGOUT STRUCTURE (FEATURE B-16), FACING WEST. FAMILY RESIDENCE (B-10) IS VISIBLE IN THE BACKGROUND ON THE UPPER RIGHT SIDE OF PHOTO. - Nevada Lucky Tiger Mill & Mine, Dugout, East slope of Buckskin Mountain, Paradise Valley, Humboldt County, NV

  2. A novel feature of structural variegation in leaves of the tropical plant Schismatoglottis calyptrata.

    PubMed

    Tsukaya, Hirokazu; Okada, Hiroshi; Mohamed, Maryati

    2004-12-01

    We report a novel feature of leaf variegation. As is often the case in tropical forest floor herbs, Schismatoglottis calyptrata leaves feature structural variegation. Examination of leaf anatomy in S. calyptrata revealed a novel feature of structural variegation, which was generated by variation in the spatial arrangement of the adaxial-most tip of the palisade cells. In fully green leaf parts, contact between the adaxial-most tip of the palisade cells and the cone-shaped base of the outer epidermis cells was tight, and palisade cells were arranged radially around each epidermal cell. In dull, grayish-green leaf parts, the contact was loose, and no particular spatial arrangement of palisade cells relative to epidermal cells was observed. This feature of structural variation could be disadvantageous for photosynthesis efficiency in view of the hypothesis that, for rainforest herbs, cone-shaped epidermal cells may function as lenses. However, the high frequency of leaf variegation of S. calyptrata in natural habits suggests that this structural variegation plays an unknown advantageous role.

  3. Combined imaging of oxidative stress and microscopic structure reveals new features in human atherosclerotic plaques

    NASA Astrophysics Data System (ADS)

    Lilledahl, Magnus B.; Gustafsson, Håkan; Ellingsen, Pål Gunnar; Zachrisson, Helene; Hallbeck, Martin; Hagen, Vegard Stenhjem; Kildemo, Morten; Lindgren, Mikael

    2015-02-01

    Human atherosclerotic samples collected by carotid endarterectomy were investigated using electronic paramagnetic resonance imaging (EPRI) for visualization of reactive oxygen species, and nonlinear optical microscopy (NLOM) to study structural features. Regions of strong EPRI signal, indicating a higher concentration of reactive oxygen species and increased inflammation, were found to colocalize with regions dense in cholesterol crystals as revealed by NLOM.

  4. [Experience in simulating the structural and dynamic features of small proteins using table supercomputers].

    PubMed

    Kondrat'ev, M S; Kabanov, A V; Komarov, V M; Khechinashvili, N N; Samchenko, A A

    2011-01-01

    The results of theoretical studies of the structural and dynamic features of peptides and small proteins have been presented that were carried out by quantum chemical and molecular dynamics methods in high-performance graphic stations, "table supercomputers", using distributed calculations by the CUDA technology.

  5. The Discourse Structure and Linguistic Features of Research Article Abstracts in English by Indonesian Academics

    ERIC Educational Resources Information Center

    Arsyad, Safnil

    2014-01-01

    To effectively teach university lecturers or students to write a good research article (RA) abstract for publication in international journals, instructors need to know the present characteristics of abstracts written published in such journals. This study examines the discourse structure and linguistic features of RA abstracts written in English…

  6. Structural evaluation of mixer pump installed in Tank 241-AN-107 for caustic addition project

    SciTech Connect

    Leshikar, G.A.

    1995-06-16

    This report documents the structural analysis and evaluation of a mixer pump and caustic addition system to be used in Tank 107-AN. This pump will be installed in the central pump pit of this double- shell tank for the purpose of bringing the hydroxide ion concentration into compliance with Tank Farm operating specifications.

  7. Recognizing clinical entities in hospital discharge summaries using Structural Support Vector Machines with word representation features

    PubMed Central

    2013-01-01

    Background Named entity recognition (NER) is an important task in clinical natural language processing (NLP) research. Machine learning (ML) based NER methods have shown good performance in recognizing entities in clinical text. Algorithms and features are two important factors that largely affect the performance of ML-based NER systems. Conditional Random Fields (CRFs), a sequential labelling algorithm, and Support Vector Machines (SVMs), which is based on large margin theory, are two typical machine learning algorithms that have been widely applied to clinical NER tasks. For features, syntactic and semantic information of context words has often been used in clinical NER systems. However, Structural Support Vector Machines (SSVMs), an algorithm that combines the advantages of both CRFs and SVMs, and word representation features, which contain word-level back-off information over large unlabelled corpus by unsupervised algorithms, have not been extensively investigated for clinical text processing. Therefore, the primary goal of this study is to evaluate the use of SSVMs and word representation features in clinical NER tasks. Methods In this study, we developed SSVMs-based NER systems to recognize clinical entities in hospital discharge summaries, using the data set from the concept extration task in the 2010 i2b2 NLP challenge. We compared the performance of CRFs and SSVMs-based NER classifiers with the same feature sets. Furthermore, we extracted two different types of word representation features (clustering-based representation features and distributional representation features) and integrated them with the SSVMs-based clinical NER system. We then reported the performance of SSVM-based NER systems with different types of word representation features. Results and discussion Using the same training (N = 27,837) and test (N = 45,009) sets in the challenge, our evaluation showed that the SSVMs-based NER systems achieved better performance than the CRFs

  8. Ten-Structure as Strategy of Addition 1-20 by Involving Spatial Structuring Ability for First Grade Students

    ERIC Educational Resources Information Center

    Salmah, Ummy; Putri, Ratu Ilma Indra; Somakim

    2015-01-01

    The aim of this study is to design learning activities that can support students to develop strategies for the addition of number 1 to 20 in the first grade by involving students' spatial structuring ability. This study was conducted in Indonesia by involving 27 students. In this paper, one of three activities is discussed namely ten-box activity.…

  9. Discriminative analysis of schizophrenia using support vector machine and recursive feature elimination on structural MRI images.

    PubMed

    Lu, Xiaobing; Yang, Yongzhe; Wu, Fengchun; Gao, Minjian; Xu, Yong; Zhang, Yue; Yao, Yongcheng; Du, Xin; Li, Chengwei; Wu, Lei; Zhong, Xiaomei; Zhou, Yanling; Fan, Ni; Zheng, Yingjun; Xiong, Dongsheng; Peng, Hongjun; Escudero, Javier; Huang, Biao; Li, Xiaobo; Ning, Yuping; Wu, Kai

    2016-07-01

    Structural abnormalities in schizophrenia (SZ) patients have been well documented with structural magnetic resonance imaging (MRI) data using voxel-based morphometry (VBM) and region of interest (ROI) analyses. However, these analyses can only detect group-wise differences and thus, have a poor predictive value for individuals. In the present study, we applied a machine learning method that combined support vector machine (SVM) with recursive feature elimination (RFE) to discriminate SZ patients from normal controls (NCs) using their structural MRI data. We first employed both VBM and ROI analyses to compare gray matter volume (GMV) and white matter volume (WMV) between 41 SZ patients and 42 age- and sex-matched NCs. The method of SVM combined with RFE was used to discriminate SZ patients from NCs using significant between-group differences in both GMV and WMV as input features. We found that SZ patients showed GM and WM abnormalities in several brain structures primarily involved in the emotion, memory, and visual systems. An SVM with a RFE classifier using the significant structural abnormalities identified by the VBM analysis as input features achieved the best performance (an accuracy of 88.4%, a sensitivity of 91.9%, and a specificity of 84.4%) in the discriminative analyses of SZ patients. These results suggested that distinct neuroanatomical profiles associated with SZ patients might provide a potential biomarker for disease diagnosis, and machine-learning methods can reveal neurobiological mechanisms in psychiatric diseases. PMID:27472673

  10. [MORPHOLOGICAL DIVERSITY OF FLEAS' STRUCTURES (SIPHONAPTERA) PART 3: GENERAL CHARACTERISTICS AND FEATURES OF THORACIC SETATION].

    PubMed

    Medvedev, S G

    2015-01-01

    The paper continues a series of publications (Medvedev, 2015a, b) devoted to the analysis of flea structural features. In the present publication, structural features of flea thoracic setation are analyzed for the first time. Six characters with 53 states in the structure of the chaetom of the pronotum, meso-, and metathoracic. segments are distinguished. The author analyzes the cases of the formation of similar states stipulated by processes of reduction or, by contrast, by strengthening of the chaetom in fleas of separate genera belonging to different superfamilies in relation to the type or peculiarities of parasitism in different flea species. In spite of the presence of strong variability in arrangement and number of thoracic setae, some examples of marking of groups in the range families and superfamilies by certain states of the chaetotaxy of the pronotum and metepimera are revealed.

  11. Structural systematic features of photoelectric effect in aromatic polymers with polymethine dyes

    SciTech Connect

    Aleksandrova, E. L.

    2007-12-15

    The structural systematic features of quantum-yield variation in charge-carrier photogeneration are investigated for polymer systems with molecules into which polymethine dyes of various structures had been introduced. The correlations between the quantum yields and the second-harmonic-generation efficiency in the media containing such dyes are revealed, and relations of the quantum yields to such dye-molecule structural parameters as the ionization potential of its donor fragment, the electron affinity of its acceptor fragment, and the electron-transfer distance between donor and acceptor fragments of the dye molecule are established.

  12. AFM and XPA data on structural features and properties of films and powders based on naphthalocyanines

    NASA Astrophysics Data System (ADS)

    Ramonova, A. G.; Nakusov, A. T.; Sozanov, V. G.; Bliev, A. P.; Magkoev, T. T.

    2015-06-01

    The template synthesis is used to produce powders and films based on naphthalocyanines and the corresponding metal complexes (Pc, CuPc, and NiPc). The atomic-force microscopy (AFM) and X-ray phase analysis (XPA) are employed in the study of structure and phase of fine powders and nanostructured films. The AFM data are used to determine the orientation and density of primary particles packed in the film. The XPA method is used to study the chemical composition and crystal structure of the synthesized samples. The regularities related to the structural features that affect the electrophysical properties of the films under study are revealed.

  13. New Features of Time Domain Electric-Field Structures in the Auroral Acceleration Region

    SciTech Connect

    Mozer, F.S.; Ergun, R.; Temerin, M.; Cattell, C.; Dombeck, J.; Wygant, J.

    1997-08-01

    The Polar Satellite carries the first three-axis electric field detector flown in the magnetosphere. Its direct measurement of electric field components perpendicular and parallel to the local magnetic field has revealed new classes and features of electric field structures associated with the plasma acceleration that produces discrete auroras and that populates the magnetosphere with plasma of ionospheric origin. These structures, associated with the hydrogen ion cyclotron mode, include very large solitary waves, spiky field structures, wave envelopes of parallel electric fields, and very large amplitude, nonlinear, coherent ion cyclotron waves. {copyright} {ital 1997} {ital The American Physical Society}

  14. Characterization of Effect of Support Structures in Laser Additive Manufacturing of Stainless Steel

    NASA Astrophysics Data System (ADS)

    Järvinen, Jukka-Pekka; Matilainen, Ville; Li, Xiaoyun; Piili, Heidi; Salminen, Antti; Mäkelä, Ismo; Nyrhilä, Olli

    Laser additive manufacturing (LAM) of stainless steel is a layer wisetechnology for fabricating 3D parts from metal powder via selectively melting powder with laser beam. Support structures play a significant role in LAM process as they help to remove heat away from the process and on the other hand hold the work piece in its place. A successful design of support structures can help to achievea building process fast and inexpensive with high quality. Aimof this study was to characterize the usability of two types of support structures: web and tube supports. Purpose of this studywas also to analyze how suitable they are in two industrial application cases: case for dental application and case for jewelry application. It was concluded that the removability of web supports was much better than tube supports. It was noticed that support structures are an important part of LAM process and they strongly affect the manufacturability and the end quality of the part.

  15. Structural features responsible for kinetic thermal stability of a carboxypeptidase from the archaebacterium Sulfolobus solfataricus.

    PubMed Central

    Villa, A; Zecca, L; Fusi, P; Colombo, S; Tedeschi, G; Tortora, P

    1993-01-01

    Investigations were performed on the structural features responsible for kinetic thermal stability of a thermostable carboxypeptidase from the thermoacidophilic archaebacterium Sulfolobus solfataricus which had been purified previously and identified as a zinc metalloprotease [Colombo, D'Auria, Fusi, Zecca, Raia and Tortora (1992) Eur. J. Biochem. 206, 349-357]. Removal of Zn2+ by dialysis led to reversible activity loss, which was promptly restored by addition of 80 microM ZnCl2 to the assay mixture. For the first-order irreversible thermal inactivation the metal-depleted enzyme showed an activation energy value of 205.6 kJ.mol-1, which is considerably lower than that of the holoenzyme (494.4 kJ.mol-1). The values of activation free energies, enthalpies and entropies also dropped with metal removal. Thermal inactivation of the apoenzyme was very quick at 80 degrees C, whereas the holoenzyme was stable at the same temperature. These findings suggest a major stabilizing role for the bivalent cation. Chaotropic salts strongly destabilized the holoenzyme, showing that hydrophobic interactions are involved in maintaining the native conformation of the enzyme. However, the inactivation rate was also increased by sodium sulphate, acetate and chloride, which are not chaotropes, indicating that one or more salt bridges concur in stabilizing the active enzyme. Furthermore, at the extremes of the pH-stability curve, NaCl did not affect the inactivation rate, confirming the stabilizing role of intramolecular ionic bonds, as a pH-dependent decrease in stability is likely to occur from breaking of salt bridges involved in maintaining the native conformation of the protein. PMID:8240298

  16. Structural features responsible for kinetic thermal stability of a carboxypeptidase from the archaebacterium Sulfolobus solfataricus.

    PubMed

    Villa, A; Zecca, L; Fusi, P; Colombo, S; Tedeschi, G; Tortora, P

    1993-11-01

    Investigations were performed on the structural features responsible for kinetic thermal stability of a thermostable carboxypeptidase from the thermoacidophilic archaebacterium Sulfolobus solfataricus which had been purified previously and identified as a zinc metalloprotease [Colombo, D'Auria, Fusi, Zecca, Raia and Tortora (1992) Eur. J. Biochem. 206, 349-357]. Removal of Zn2+ by dialysis led to reversible activity loss, which was promptly restored by addition of 80 microM ZnCl2 to the assay mixture. For the first-order irreversible thermal inactivation the metal-depleted enzyme showed an activation energy value of 205.6 kJ.mol-1, which is considerably lower than that of the holoenzyme (494.4 kJ.mol-1). The values of activation free energies, enthalpies and entropies also dropped with metal removal. Thermal inactivation of the apoenzyme was very quick at 80 degrees C, whereas the holoenzyme was stable at the same temperature. These findings suggest a major stabilizing role for the bivalent cation. Chaotropic salts strongly destabilized the holoenzyme, showing that hydrophobic interactions are involved in maintaining the native conformation of the enzyme. However, the inactivation rate was also increased by sodium sulphate, acetate and chloride, which are not chaotropes, indicating that one or more salt bridges concur in stabilizing the active enzyme. Furthermore, at the extremes of the pH-stability curve, NaCl did not affect the inactivation rate, confirming the stabilizing role of intramolecular ionic bonds, as a pH-dependent decrease in stability is likely to occur from breaking of salt bridges involved in maintaining the native conformation of the protein.

  17. Structural Features Affecting Trafficking, Processing, and Secretion of Trypanosoma cruzi Mucins*

    PubMed Central

    Cánepa, Gaspar E.; Mesías, Andrea C.; Yu, Hai; Chen, Xi; Buscaglia, Carlos A.

    2012-01-01

    Trypanosoma cruzi is wrapped by a dense coat of mucin-type molecules encoded by complex gene families termed TcSMUG and TcMUC, which are expressed in the insect- and mammal-dwelling forms of the parasite, respectively. Here, we dissect the contribution of distinct post-translational modifications on the trafficking of these glycoconjugates. In vivo tracing and characterization of tagged-variants expressed by transfected epimastigotes indicate that although the N-terminal signal peptide is responsible for targeting TcSMUG products to the endoplasmic reticulum (ER), the glycosyl phosphatidylinositol (GPI)-anchor likely functions as a forward transport signal for their timely progression along the secretory pathway. GPI-minus variants accumulate in the ER, with only a minor fraction being ultimately released to the medium as anchorless products. Secreted products, but not ER-accumulated ones, display several diagnostic features of mature mucin-type molecules including extensive O-type glycosylation, Galf-based epitopes recognized by monoclonal antibodies, and terminal Galp residues that become readily sialylated upon addition of parasite trans-sialidases. Processing of N-glycosylation site(s) is dispensable for the overall TcSMUG mucin-type maturation and secretion. Despite undergoing different O-glycosylation elaboration, TcMUC reporters yielded quite similar results, thus indicating that (i) molecular trafficking signals are structurally and functionally conserved between mucin families, and (ii) TcMUC and TcSMUG products are recognized and processed by a distinct repertoire of stage-specific glycosyltransferases. Thus, using the fidelity of a homologous expression system, we have defined some biosynthetic aspects of T. cruzi mucins, key molecules involved in parasite protection and virulence. PMID:22707724

  18. Addition of three-dimensional isoparametric elements to NASA structural analysis program (NASTRAN)

    NASA Technical Reports Server (NTRS)

    Field, E. I.; Johnson, S. E.

    1973-01-01

    Implementation is made of the three-dimensional family of linear, quadratic and cubic isoparametric solid elements into the NASA Structural Analysis program, NASTRAN. This work included program development, installation, testing, and documentation. The addition of these elements to NASTRAN provides a significant increase in modeling capability particularly for structures requiring specification of temperatures, material properties, displacements, and stresses which vary throughout each individual element. Complete program documentation is presented in the form of new sections and updates for direct insertion to the three NASTRAN manuals. The results of demonstration test problems are summarized. Excellent results are obtained with the isoparametric elements for static, normal mode, and buckling analyses.

  19. The role of emotion in musical improvisation: an analysis of structural features.

    PubMed

    McPherson, Malinda J; Lopez-Gonzalez, Monica; Rankin, Summer K; Limb, Charles J

    2014-01-01

    One of the primary functions of music is to convey emotion, yet how music accomplishes this task remains unclear. For example, simple correlations between mode (major vs. minor) and emotion (happy vs. sad) do not adequately explain the enormous range, subtlety or complexity of musically induced emotions. In this study, we examined the structural features of unconstrained musical improvisations generated by jazz pianists in response to emotional cues. We hypothesized that musicians would not utilize any universal rules to convey emotions, but would instead combine heterogeneous musical elements together in order to depict positive and negative emotions. Our findings demonstrate a lack of simple correspondence between emotions and musical features of spontaneous musical improvisation. While improvisations in response to positive emotional cues were more likely to be in major keys, have faster tempos, faster key press velocities and more staccato notes when compared to negative improvisations, there was a wide distribution for each emotion with components that directly violated these primary associations. The finding that musicians often combine disparate features together in order to convey emotion during improvisation suggests that structural diversity may be an essential feature of the ability of music to express a wide range of emotion.

  20. Hyperhomocysteinemia disrupts retinal pigment epithelial structure and function with features of age-related macular degeneration.

    PubMed

    Ibrahim, Ahmed S; Mander, Suchreet; Hussein, Khaled A; Elsherbiny, Nehal M; Smith, Sylvia B; Al-Shabrawey, Mohamed; Tawfik, Amany

    2016-02-23

    The disruption of retinal pigment epithelial (RPE) function and the degeneration of photoreceptors are cardinal features of age related macular degeneration (AMD); however there are still gaps in our understanding of underlying biological processes. Excess homocysteine (Hcy) has been reported to be elevated in plasma of patients with AMD. This study aimed to evaluate the direct effect of hyperhomocysteinemia (HHcy) on structure and function of RPE. Initial studies in a mouse model of HHcy, in which cystathionine-β-synthase (cbs) was deficient, revealed abnormal RPE cell morphology with features similar to that of AMD upon optical coherence tomography (OCT), fluorescein angiography (FA), histological, and electron microscopic examinations. These features include atrophy, vacuolization, hypopigmentation, thickened basal laminar membrane, hyporeflective lucency, choroidal neovascularization (CNV), and disturbed RPE-photoreceptor relationship. Furthermore, intravitreal injection of Hcy per se in normal wild type (WT) mice resulted in diffuse hyper-fluorescence, albumin leakage, and CNV in the area of RPE. In vitro experiments on ARPE-19 showed that Hcy dose-dependently reduced tight junction protein expression, increased FITC dextran leakage, decreased transcellular electrical resistance, and impaired phagocytic activity. Collectively, our results demonstrated unreported effects of excess Hcy levels on RPE structure and function that lead to the development of AMD-like features.

  1. Hyperhomocysteinemia disrupts retinal pigment epithelial structure and function with features of age-related macular degeneration

    PubMed Central

    Ibrahim, Ahmed S.; Mander, Suchreet; Hussein, Khaled A.; Elsherbiny, Nehal M.; Smith, Sylvia B.; Al-Shabrawey, Mohamed; Tawfik, Amany

    2016-01-01

    The disruption of retinal pigment epithelial (RPE) function and the degeneration of photoreceptors are cardinal features of age related macular degeneration (AMD); however there are still gaps in our understanding of underlying biological processes. Excess homocysteine (Hcy) has been reported to be elevated in plasma of patients with AMD. This study aimed to evaluate the direct effect of hyperhomocysteinemia (HHcy) on structure and function of RPE. Initial studies in a mouse model of HHcy, in which cystathionine-β-synthase (cbs) was deficient, revealed abnormal RPE cell morphology with features similar to that of AMD upon optical coherence tomography (OCT), fluorescein angiography (FA), histological, and electron microscopic examinations. These features include atrophy, vacuolization, hypopigmentation, thickened basal laminar membrane, hyporeflective lucency, choroidal neovascularization (CNV), and disturbed RPE–photoreceptor relationship. Furthermore, intravitreal injection of Hcy per se in normal wild type (WT) mice resulted in diffuse hyper-fluorescence, albumin leakage, and CNV in the area of RPE. In vitro experiments on ARPE-19 showed that Hcy dose-dependently reduced tight junction protein expression, increased FITC dextran leakage, decreased transcellular electrical resistance, and impaired phagocytic activity. Collectively, our results demonstrated unreported effects of excess Hcy levels on RPE structure and function that lead to the development of AMD-like features. PMID:26885895

  2. Discriminant features and temporal structure of nonmanuals in American Sign Language.

    PubMed

    Benitez-Quiroz, C Fabian; Gökgöz, Kadir; Wilbur, Ronnie B; Martinez, Aleix M

    2014-01-01

    To fully define the grammar of American Sign Language (ASL), a linguistic model of its nonmanuals needs to be constructed. While significant progress has been made to understand the features defining ASL manuals, after years of research, much still needs to be done to uncover the discriminant nonmanual components. The major barrier to achieving this goal is the difficulty in correlating facial features and linguistic features, especially since these correlations may be temporally defined. For example, a facial feature (e.g., head moves down) occurring at the end of the movement of another facial feature (e.g., brows moves up), may specify a Hypothetical conditional, but only if this time relationship is maintained. In other instances, the single occurrence of a movement (e.g., brows move up) can be indicative of the same grammatical construction. In the present paper, we introduce a linguistic-computational approach to efficiently carry out this analysis. First, a linguistic model of the face is used to manually annotate a very large set of 2,347 videos of ASL nonmanuals (including tens of thousands of frames). Second, a computational approach is used to determine which features of the linguistic model are more informative of the grammatical rules under study. We used the proposed approach to study five types of sentences--Hypothetical conditionals, Yes/no questions, Wh-questions, Wh-questions postposed, and Assertions--plus their polarities--positive and negative. Our results verify several components of the standard model of ASL nonmanuals and, most importantly, identify several previously unreported features and their temporal relationship. Notably, our results uncovered a complex interaction between head position and mouth shape. These findings define some temporal structures of ASL nonmanuals not previously detected by other approaches. PMID:24516528

  3. Addition of lipid to the photosynthetic membrane: effects on membrane structure and energy transfer

    PubMed Central

    1981-01-01

    We have carried out a series of experiments in which the lipid composition of the photosynthetic membrane has been altered by the addition of lipid from a defined source under experimental conditions. Liposomes prepared by sonication are mixed with purified photosynthetic membranes obtained from spinach chloroplasts and are taken through cycles of freezing and thawing. Several lines of evidence, including gel electrophoresis and freeze-fracture electron microscopy, indicate that an actual addition of lipid has taken place. Structural analysis by freeze-fracture shows that intramembrane particles are widely separated after the addition of large amounts of lipid, with one exception: large hexagonal lattices of particles appear in some regions of the membrane. These lattices are identical in appearance with lattices formed from a single purified component of the membrane known as chlorophyll-protein complex II. The suggestion that the presence of such lattices in lipid-enriched membranes reflects a profound rearrangement of photosynthetic structures has been confirmed by analysis of the fluorescence emission spectra of natural and lipid- enriched membranes. Specifically, lipid addition in each of the cases we have studied results in the apparent detachment of chlorophyll- protein complex II from photosynthetic reaction centers. It is concluded that specific arrangements of components in the photosynthetic membrane, necessary for the normal functioning of the membrane in the light reaction of photosynthesis, can be regulated to a large extent by the lipid content of the membrane. PMID:7298712

  4. Impact ignition of aluminum-teflon based energetic materials impregnated with nano-structured carbon additives

    NASA Astrophysics Data System (ADS)

    Kappagantula, Keerti; Pantoya, Michelle L.; Hunt, Emily M.

    2012-07-01

    The inclusion of graphene into composite energetic materials to enhance their performance is a new area of interest. Studies have shown that the addition of graphene significantly enhances the thermal transport properties of an energetic composite, but how graphene influences the composite's ignition sensitivity has not been studied. The objective of this study is to examine the influence of carbon additives in composite energetic material composed of aluminum and polytetrafluoroethylene (Teflon™) on ignition sensitivity due to low velocity, drop weight impact. Specifically, three forms of carbon additives were investigated and selected based on different physical and structural properties: spherically shaped amorphous nano particles of carbon, cylindrically shaped multi walled carbon nanotubes, and sheet like graphene flakes. Results show an interesting trend: composites consisting of carbon nanotubes are significantly more sensitive to impact ignition and require the lowest ignition energy. In contrast, graphene is least sensitive to ignition exhibiting negligible reduction in ignition energy with low concentrations of graphene additive. While graphene does not significantly sensitize the energetic composite to ignition, graphene does, however, result in greater overall reactivity as observed through images of the reaction. The enhanced thermal transport properties of graphene containing composites may promote greater energy transport once ignited, but those properties do not also increase ignition sensitivity. These results and the understanding of the structural arrangement of particles within a composite as a key parameter affecting impact ignition sensitivity will have an impact on the safe handling and use of composite energetic materials.

  5. The Influence of Structural Features of Particles on their Light Scattering Properties

    NASA Astrophysics Data System (ADS)

    Theilheim, K. O.

    The theory of the scattering of light by ensembles of particles with ir regular shape is of interest in the context of interstellar and interplanetary dust grains and particles associated with comets or observed in aerosols and hydrosols. The scattering properties of homogeneous particles are determined by both geometrical features and chemical composition as represented by the complex frequency dependent index of refraction. We have performed a systematic investigation on the former aspect, namely the influence of structural features of the surface of large dielectric particles on their light scattering properties. The geometrical surface structure will be discussed in terms of macro roughness and micro roughness as two limiting cases of a more general type of roughness. Some results will also be presented for composite roughness models. Finally I will discuss preliminary results of a scattering theory applicable to ensembles of particles with irregular shape and arbitrary size based on the method of perturbed boundary conditions.

  6. Large-scale oscillation of structure-related DNA sequence features in human chromosome 21

    NASA Astrophysics Data System (ADS)

    Li, Wentian; Miramontes, Pedro

    2006-08-01

    Human chromosome 21 is the only chromosome in the human genome that exhibits oscillation of the (G+C) content of a cycle length of hundreds kilobases (kb) ( 500kb near the right telomere). We aim at establishing the existence of a similar periodicity in structure-related sequence features in order to relate this (G+C)% oscillation to other biological phenomena. The following quantities are shown to oscillate with the same 500kb periodicity in human chromosome 21: binding energy calculated by two sets of dinucleotide-based thermodynamic parameters, AA/TT and AAA/TTT bi- and tri-nucleotide density, 5'-TA-3' dinucleotide density, and signal for 10- or 11-base periodicity of AA/TT or AAA/TTT. These intrinsic quantities are related to structural features of the double helix of DNA molecules, such as base-pair binding, untwisting or unwinding, stiffness, and a putative tendency for nucleosome formation.

  7. Image automatic-recognition scheme for dice game using structure features technique

    NASA Astrophysics Data System (ADS)

    Chen, Wen-Yuan; Chung, Chin-Ho

    2011-08-01

    In dice recognition, there are several situations that may cause dice image identification problems, including the color of background being the same as the dice, the shape of the dice being round, or the dice touching each other. Especially when the camera zooms in or out, the pip sizes become irregular. We analyze the dice structure features to develop an intelligent memorized least-distance search method (IMLDSM) that can achieve accurate dice detection. Compared to other schemes, our method has two major advantages: (i) Unlike other schemes using complicated classification methods to segment the dice, we adopt a novel, simple, and effective method to analyze dice structure features to achieve more accurate recognition results and (ii) the IMLDSM solves the problems of image zooming in and out, which other methods cannot. After over 250 test images that include different shapes, styles, sizes, and colors used in simulations, this scheme is proven to achieve 100% dice image identification.

  8. Evaluation of Waveform Structure Features on Time Domain Target Recognition under Cross Polarization

    NASA Astrophysics Data System (ADS)

    Selver, M. A.; Seçmen, M.; Zoral, E. Y.

    2016-08-01

    Classification of aircraft targets from scattered electromagnetic waves is a challenging application, which suffers from aspect angle dependency. In order to eliminate the adverse effects of aspect angle, various strategies were developed including the techniques that rely on extraction of several features and design of suitable classification systems to process them. Recently, a hierarchical method, which uses features that take advantage of waveform structure of the scattered signals, is introduced and shown to have effective results. However, this approach has been applied to the special cases that consider only a single planar component of electric field that cause no-cross polarization at the observation point. In this study, two small scale aircraft models, Boeing-747 and DC-10, are selected as the targets and various polarizations are used to analyse the cross-polarization effects on system performance of the aforementioned method. The results reveal the advantages and the shortcomings of using waveform structures in time-domain target identification.

  9. Structural Features in Heat Transfer Modeling of PEM Fuel Cell Materials

    NASA Astrophysics Data System (ADS)

    Botelho, Steven Joseph

    In this thesis, the impact of incorporating high resolution structural features into the thermal modeling of the polymer electrolyte membrane (PEM) fuel cell gas diffusion layer (GDL) and microporous layer (MPL) is studied. Atomic force microscopy (AFM) has been used to image the surfaces of untreated Toray GDL fibres, and the nano-sized particles within Sigracet MPL. The validity of the GDL smooth fibre assumption commonly employed in literature is studied using a thermal resistance network approach. The MPL, which has been found to show structural variability between manufacturers, was also analyzed using AFM to obtain distributions for the particle size and filling radius. The equivalent thermal resistance between MPL particles was computed using the Gauss-Seidel iterative method, and was found to be sensitive to the particle separation distance and filling radius. Finally, unit-cell analysis is presented as a methodology for incorporating MPL nano-features into modeling of the MPL bulk regions.

  10. Cryoelectron microscopy reveals new features in the three-dimensional structure of phosphorylase kinase.

    PubMed

    Nadeau, Owen W; Gogol, Edward P; Carlson, Gerald M

    2005-04-01

    Phosphorylase kinase (PhK), a regulatory enzyme in the cascade activation of glycogenolysis, is a 1.3-MDa hexadecameric complex, (alphabetagammadelta)(4). PhK comprises two arched octameric (alphabetagammadelta)(2) lobes that are oriented back-to-back with overall D(2) symmetry and connected by small bridges. These interlobal bridges, arguably the most questionable structural component of PhK, are one of several structural features that potentially are artifactually generated or altered by conventional sample preparation techniques for electron microscopy (EM). To minimize such artifacts, we have solved by cryoEM the first three-dimensional (3D) structure of nonactivated PhK from images of frozen hydrated molecules of the kinase. Minimal dose electron micrographs of PhK in vitreous ice revealed particles in a multitude of orientations. A simple model was used to orient the individual images for 3D reconstruction, followed by multiple rounds of refinement. Three-dimensional reconstruction of nonactivated PhK from approximately 5000 particles revealed a bridged, bilobal molecule with a resolution estimated by Fourier shell correlation analysis at 25 A. This new structure suggests that several prominent features observed in the structure of PhK derived from negatively stained particles arise as artifacts of specimen preparation. In comparison to the structure from negative staining, the cryoEM structure shows three important differences: (1) a dihedral angle between the two lobes of approximately 90 degrees instead of 68 degrees, (2) a compact rather than extended structure for the lobes, and (3) the presence of four, rather than two, connecting bridges, which provides the first direct evidence for these components as authentic elements of the kinase solution structure. PMID:15741332

  11. Phosphate addition and plant species alters microbial community structure in acidic upland grassland soil.

    PubMed

    Rooney, Deirdre C; Clipson, Nicholas J W

    2009-01-01

    Agricultural improvement (addition of fertilizers, liming) of seminatural acidic grasslands across Ireland and the UK has resulted in significant shifts in floristic composition, soil chemistry, and microbial community structure. Although several factors have been proposed as responsible for driving shifts in microbial communities, the exact causes of such changes are not well defined. Phosphate was added to grassland microcosms to investigate the effect on fungal and bacterial communities. Plant species typical of unimproved grasslands (Agrostis capillaris, Festuca ovina) and agriculturally improved grasslands (Lolium perenne) were grown, and phosphate was added 25 days after seed germination, with harvesting after a further 50 days. Phosphate addition significantly increased root biomass (p < 0.001) and shoot biomass (p < 0.05), soil pH (by 0.1 U), and microbial activity (by 5.33 mg triphenylformazan [TPF] g(-1) soil; p < 0.001). A slight decrease (by 0.257 mg biomass-C g(-1) soil; p < 0.05) in microbial biomass after phosphate addition was found. The presence of plant species significantly decreased soil pH (p < 0.05; by up to 0.2 U) and increased microbial activity (by up to 6.02 mg TPF g(-1) soil) but had no significant effect on microbial biomass. Microbial communities were profiled using automated ribosomal intergenic spacer analysis. Multidimensional scaling plots and canonical correspondence analysis revealed that phosphate addition and its interactions with upland grassland plant species resulted in considerable changes in the fungal and bacterial communities of upland soil. The fungal community structure was significantly affected by both phosphate (R = 0.948) and plant species (R = 0.857), and the bacterial community structure was also significantly affected by phosphate (R = 0.758) and plant species (R = 0.753). Differences in microbial community structure following P addition were also revealed by similarity percentage analysis. These data suggest

  12. Feature selection and the information content of Thematic Mapper simulator data for forest structural assessment

    NASA Technical Reports Server (NTRS)

    Spanner, M. A.; Brass, J. A.; Peterson, D. L.

    1984-01-01

    An assessment is made of the information content of Thematic Mapper Simulator (TMS) data for the case of a forested region, in order to determine the sensitivity of such data to forest crown closure and tree size class. Principal components analysis and Monte Carlo simulation indicated that channels 4, 7, 5 and 3 were optimal for four-channel forest structure analysis. As the number of channels supplied to the Monte Carlo feature selection routine increased, classification accuracy increased. The greatest sensitivity to the forest structural parameters, which included succession within clearcuts as well as crown closure and size class, was obtained from the 7-channel TMS data.

  13. Fabrication of small-scale structures with non-planar features

    SciTech Connect

    Burckel, David B.; Ten Eyck, Gregory A.

    2015-11-19

    The fabrication of small-scale structures is disclosed. A unit-cell of a small-scale structure with non-planar features is fabricated by forming a membrane on a suitable material. A pattern is formed in the membrane and a portion of the substrate underneath the membrane is removed to form a cavity. Resonators are then directionally deposited on the wall or sides of the cavity. The cavity may be rotated during deposition to form closed-loop resonators. The resonators may be non-planar. The unit-cells can be formed in a layer that includes an array of unit-cells.

  14. Crystal structure features in a new compound C4B25Mg1.42

    NASA Astrophysics Data System (ADS)

    Konovalikhin, S. V.; Ponomarev, V. I.

    2015-09-01

    The composition of C4B25Mg1.42 crystal obtained by self-propagating high-temperature synthesis was determined using X-ray diffraction. This is the first crystalline structure where all boron atoms in the В12 icosahedron occupy crystallographically independent positions; this circumstance allowed us to analyze the effect of substituents on bond lengths in the icosahedron. The crystal structure features, including the channels filled with disordered Mg atoms and the spread of В—В endo- and exo-bond lengths in the icosahedra, are described. A crystallochemical analysis of pair bonds has been performed for the first time.

  15. Incorporating temporal features of repeatedly measured covariates into tree-structured survival models.

    PubMed

    Wallace, Meredith L; Anderson, Stewart J; Mazumdar, Sati; Kong, Lan; Mulsant, Benoit H

    2012-03-01

    Tree-structured survival methods empirically identify a series of covariate-based binary split points, resulting in an algorithm that can be used to classify new patients into risk groups and subsequently guide clinical treatment decisions. Traditionally, only fixed-time (e.g. baseline) values are used in tree-structured models. However, this manuscript considers the scenario where temporal features of a repeated measures polynomial model, such as the slope and/or curvature, are useful for distinguishing risk groups to predict future outcomes. Both fixed- and random-effects methods for estimating individual temporal features are discussed, and methods for including these features in a tree model and classifying new cases are proposed. A simulation study is performed to empirically compare the predictive accuracies of the proposed methods in a wide variety of model settings. For illustration, a tree-structured survival model incorporating the linear rate of change of depressive symptomatology during the first four weeks of treatment for late-life depression is used to identify subgroups of older adults who may benefit from an early change in treatment strategy. PMID:22522377

  16. Characteristic structural features of indolicidin: effects of the cis-trans isomerism on its conformation.

    PubMed

    Leitgeb, Balázs

    2014-01-01

    Indolicidin is an antimicrobial peptide showing a broad spectrum of antibacterial and antifungal activities, and according to the cis-trans isomerism of three Xaa-Pro peptide bonds, eight different stereoisomers could be distinguished for this peptide. As the cis-trans isomerism about the Xaa-Pro peptide bonds was not considered in previous studies, the structural features of distinct stereoisomeric forms were not characterized in detail, so far. In this theoretical study, the influences of cis-trans isomerism on the conformation of indolicidin were investigated, as well as the typical structural properties of each stereoisomer were determined, focusing on the secondary structures and intramolecular interactions. Based on the results derived from the molecular dynamics simulations, it could be concluded that the eight different stereoisomeric forms of indolicidin adopted characteristic conformational features. Nevertheless, the appearance of various turn structures and intramolecular interactions proved to be dependent on the cis or trans nature of Xaa-Pro peptide bonds, indicating the relevant role of Pro amino acids in determining the three-dimensional structure of this peptide.

  17. A new approach to the structural features of the Aegean Sea: Cellular neural network

    NASA Astrophysics Data System (ADS)

    Aydogan, Davut; Elmas, Ali; Albora, A. Muhittin; Ucan, Osman N.

    2005-03-01

    In this study, structural features in the Aegean Sea were investigated by application of Cellular Neural Network (CNN) and Cross-Correlation methods to the gravity anomaly map. CNN is a stochastic image processing technique, which is based on template optimization using neighbourhood relationships of pixels, and probabilistic properties of two-Dimensional (2-D) input data. The performance of CNN can be evaluated by various interesting real applications in geophysics such as edge detection, data enhancement and separation of regional/residual potential anomaly maps. In this study, CNN is used in edge detection of geological bodies closer to the surface, which are masked by other structures with various depths and dimensions. CNN was first tested for (prismatic) synthetic examples and satisfactory results were obtained. Subsequently, CNN/Cross-Correlation maps and bathymetric features were evaluated together to obtain a new structural map for most of the Aegean Sea. In our structural map, the locations of the faults and basins are generally in accordance with the previous maps from restricted areas based on seismic data. In the southern and southeastern parts of the Aegean Sea, E-W trending faults cut NE-SW trending basins and faults, similar to on-shore Western Anatolia. Also, in the western, central and northern parts of the Aegean Sea, all of these structures are truncated by NE-trending faults.

  18. High-throughput screening for thermoelectric sulphides by using crystal structure features as descriptors

    NASA Astrophysics Data System (ADS)

    Zhang, Ruizhi; Du, Baoli; Chen, Kan; Reece, Mike; Materials Research Insititute Team

    With the increasing computational power and reliable databases, high-throughput screening is playing a more and more important role in the search of new thermoelectric materials. Rather than the well established density functional theory (DFT) calculation based methods, we propose an alternative approach to screen for new TE materials: using crystal structural features as 'descriptors'. We show that a non-distorted transition metal sulphide polyhedral network can be a good descriptor for high power factor according to crystal filed theory. By using Cu/S containing compounds as an example, 1600+ Cu/S containing entries in the Inorganic Crystal Structure Database (ICSD) were screened, and of those 84 phases are identified as promising thermoelectric materials. The screening results are validated by both electronic structure calculations and experimental results from the literature. We also fabricated some new compounds to test our screening results. Another advantage of using crystal structure features as descriptors is that we can easily establish structural relationships between the identified phases. Based on this, two material design approaches are discussed: 1) High-pressure synthesis of metastable phase; 2) In-situ 2-phase composites with coherent interface. This work was supported by a Marie Curie International Incoming Fellowship of the European Community Human Potential Program.

  19. Sequence-only evolutionary and predicted structural features for the prediction of stability changes in protein mutants

    PubMed Central

    2013-01-01

    Background Even a single amino acid substitution in a protein sequence may result in significant changes in protein stability, structure, and therefore in protein function as well. In the post-genomic era, computational methods for predicting stability changes from only the sequence of a protein are of importance. While evolutionary relationships of protein mutations can be extracted from large protein databases holding millions of protein sequences, relevant evolutionary features for the prediction of stability changes have not been proposed. Also, the use of predicted structural features in situations when a protein structure is not available has not been explored. Results We proposed a number of evolutionary and predicted structural features for the prediction of stability changes and analysed which of them capture the determinants of protein stability the best. We trained and evaluated our machine learning method on a non-redundant data set of experimentally measured stability changes. When only the direction of the stability change was predicted, we found that the best performance improvement can be achieved by the combination of the evolutionary features mutation likelihood and SIFTscore in conjunction with the predicted structural feature secondary structure. The same two evolutionary features in the combination with the predicted structural feature accessible surface area achieved the lowest error when the prediction of actual values of stability changes was assessed. Compared to similar studies, our method achieved improvements in prediction performance. Conclusion Although the strongest feature for the prediction of stability changes appears to be the vector of amino acid identities in the sequential neighbourhood of the mutation, the most relevant combination of evolutionary and predicted structural features further improves prediction performance. Even the predicted structural features, which did not perform well on their own, turn out to be beneficial

  20. Specific features of formation of radiation defects in the silicon layer in 'silicon-on-insulator' structures

    SciTech Connect

    Shcherbachev, K. D. Bublik, V. T.; Mordkovich, V. N.; Pazhin, D. M.

    2011-06-15

    Specific features of formation of radiation defects in thin silicon layer of silicon-on-insulator (SOI) structures have been studied. It is shown that there are differences between variations in the structural and electrical properties of the thin silicon layer and those in bulk silicon crystals (with similar electrical characteristics) subjected to the same radiation effect. It is established that the embedded insulator in the SOI structure represents a barrier for motion of radiation-induced intrinsic interstitial silicon atoms, which brings about an increase in the dose of bombarding ions, which leads to the loss of single-crystallinity of the silicon layer in a SOI structure. It is shown that {gamma}-ray irradiation with doses unaffecting the electrical conductivity of bulk silicon crystals appreciably affects the conductivity of the silicon layer in the SOI structures. In addition, variation in the conductivity of silicon layer is related to variation in the density of surface states at the interface between the silicon layer and the built-in insulator, rather than to generation of conventional radiation-induced structural defects in silicon.

  1. General features and master equations for structurization in complex dusty plasmas

    SciTech Connect

    Tsytovich, V. N.; Morfill, G. E.

    2012-02-15

    Dust structurization is considered to be typical for complex plasmas. Homogeneous dusty plasmas are shown to be universally unstable. The dusty plasma structurization instability is similar to the gravitational instability and can results in creation of different compact dust structures. A general approach for investigation of the nonlinear stage of structurization in dusty plasmas is proposed and master equations for the description of self-organized structures are formulated in the general form that can be used for any nonlinear model of dust screening. New effects due to the scattering of ions on the nonlinearly screened grains are calculated: nonlinear ion dust drag force and nonlinear ion diffusion. The physics of confinement of dust and plasma components in the equilibria of compact dust structures is presented and is supported by numerical calculations of master equations. The necessary conditions for the existence of equilibrium structures are found for an arbitrary nonlinearity in dust screening. Features of compact dust structures observed in recent experiments agree with the numerically calculated ones. Some proposals for future experiments in spherical chamber are given.

  2. Is the structural diversity of tripeptides sufficient for developing functional food additives with satisfactory multiple bioactivities?

    NASA Astrophysics Data System (ADS)

    Wang, Jian-Hui; Liu, Yong-Le; Ning, Jing-Heng; Yu, Jian; Li, Xiang-Hong; Wang, Fa-Xiang

    2013-05-01

    Multifunctional peptides have attracted increasing attention in the food science community because of their therapeutic potential, low toxicity and rapid intestinal absorption. However, previous study demonstrated that the limited structural variations make it difficult to optimize dipeptide molecules in a good balance between desirable and undesirable properties (F. Tian, P. Zhou, F. Lv, R. Song, Z. Li, J. Pept. Sci. 13 (2007) 549-566). In the present work, we attempt to answer whether the structural diversity is sufficient for a tripeptide to have satisfactory multiple bioactivities. Statistical test, structural examination and energetic analysis confirm that peptides of three amino acids long can bind tightly to human angiotensin converting enzyme (ACE) and thus exert significant antihypertensive efficacy. Further quantitative structure-activity relationship (QSAR) modeling and prediction of all 8000 possible tripeptides reveal that their ACE-inhibitory potency exhibits a good (positive) relationship to antioxidative activity, but has only a quite modest correlation with bitterness. This means that it is possible to find certain tripeptide entities possessing the optimal combination of strong ACE-inhibitory potency, high antioxidative activity and weak bitter taste, which are the promising candidates for developing multifunctional food additives with satisfactory multiple bioactivities. The marked difference between dipeptide and tripeptide can be attributed to the fact that the structural diversity of peptides increases dramatically with a slight change in sequence length.

  3. A role of BNLT compound addition on structure and properties of PZT ceramics

    NASA Astrophysics Data System (ADS)

    Jaita, P.; Watcharapasorn, A.; Jiansirisomboon, S.

    2010-09-01

    In this research, effects of lead-free bismuth sodium lanthanum titanate (BNLT) addition on structure and properties of lead zirconate titanate (PZT) ceramics were investigated. PZT ceramics with addition of 0.1-3.0 wt%BNLT were fabricated by a solid-state mixed oxide method and sintering at 1050-1200 °C for 2 h to obtain dense ceramics with at least 96% of theoretical density. X-ray diffraction indicated that complete solid solution occurred for all compositions. Phase identification showed both tetragonal and rhombohedral perovskite structure of PZT with no BNLT phase detected. Scanning electron micrographs of fractured PZT/BNLT ceramics showed equiaxed grain shape with both transgranular and intergranular fracture modes. Addition of BNLT was also found to reduce densification and effectively limited grain growth of PZT ceramic. Optimum Hv and KIC values were found to be 4.85 GPa and 1.56 MPa.m 1/2 for PZT/0.5 wt%BNLT sample. Among PZT/BNLT samples, room temperature dielectric constant seemed to be improved with increasing BNLT content. The maximum piezoelectric coefficient values were observed in pure PZT ceramic and were slightly decreased in BNLT-added samples. Small reduction of remanent polarization and coercive field in hysteresis loops was observed in BNLT-added samples, indicating a slightly suppressed ferroelectric interaction in this material system.

  4. Structural features of northern Tarim basin: Implications for regional tectonics and petroleum traps

    SciTech Connect

    Dong Jia; Juafu Lu; Dongsheng Cai

    1998-01-01

    The rhombus-shaped Tarim basin in northwestern China is controlled mainly by two left-lateral strike-slip systems: the northeast-trending Altun fault zone along its southeastern side and the northeast-trending Aheqi fault zone along its northwestern side. In this paper, we discuss the northern Tarim basin`s structural features, which include three main tectonic units: the Kalpin uplift, the Kuqa depression, and the North Tarim uplift along the northern margin of the Tarim basin. Structural mapping in the Kalpin uplift shows that a series of imbricated thrust sheets have been overprinted by strike-slip faulting. The amount of strike-slip displacement is estimated to be 148 km by restoration of strike-slip structures in the uplift. The Kuqa depression is a Mesozoic-Cenozoic foredeep depression with well-developed flat-ramp structures and fault-related folds. The Baicheng basin, a Quaternary pull-apart basin, developed at the center of the Kuqa depression. Subsurface structures in the North Tarim uplift can be divided into the Mesozoic-Cenozoic and the Paleozoic lithotectonic sequences in seismic profiles. The Paleozoic litho-tectonic sequence exhibits the interference of earlier left-lateral and later right-lateral strike-slip structures. Many normal faults in the Mesozoic-Cenozoic litho-tectonic sequence form the negative flower structures in the North Tarim uplift; these structures commonly directly overlie the positive flower structures in the Paleozoic litho-tectonic sequence. The interference regions of the northwest-trending and northeast-trending folds in the Paleozoic tectonic sequence have been identified to have the best trap structures. Our structural analysis indicates that the Tarim basin is a transpressional foreland basin rejuvenated during the Cenozoic.

  5. Unique Structural Features and Sequence Motifs of Proline Utilization A (PutA)

    PubMed Central

    Singh, Ranjan K.; Tanner, John J.

    2013-01-01

    Proline utilization A proteins (PutAs) are bifunctional enzymes that catalyze the oxidation of proline to glutamate using spatially separated proline dehydrogenase and pyrroline-5-carboxylate dehydrogenase active sites. Here we use the crystal structure of the minimalist PutA from Bradyrhizobium japonicum (BjPutA) along with sequence analysis to identify unique structural features of PutAs. This analysis shows that PutAs have secondary structural elements and domains not found in the related monofunctional enzymes. Some of these extra features are predicted to be important for substrate channeling in BjPutA. Multiple sequence alignment analysis shows that some PutAs have a 17-residue conserved motif in the C-terminal 20–30 residues of the polypeptide chain. The BjPutA structure shows that this motif helps seal the internal substrate-channeling cavity from the bulk medium. Finally, it is shown that some PutAs have a 100–200 residue domain of unknown function in the C-terminus that is not found in minimalist PutAs. Remote homology detection suggests that this domain is homologous to the oligomerization beta-hairpin and Rossmann fold domain of BjPutA. PMID:22201760

  6. Unique structural features and sequence motifs of proline utilization A (PutA).

    PubMed

    Singh, Ranjan K; Tanner, John J

    2012-01-01

    Proline utilization A proteins (PutAs) are bifunctional enzymes that catalyze the oxidation of proline to glutamate using spatially separated proline dehydrogenase and pyrroline-5-carboxylate dehydrogenase active sites. Here we use the crystal structure of the minimalist PutA from Bradyrhizobium japonicum (BjPutA) along with sequence analysis to identify unique structural features of PutAs. This analysis shows that PutAs have secondary structural elements and domains not found in the related monofunctional enzymes. Some of these extra features are predicted to be important for substrate channeling in BjPutA. Multiple sequence alignment analysis shows that some PutAs have a 17-residue conserved motif in the C-terminal 20-30 residues of the polypeptide chain. The BjPutA structure shows that this motif helps seal the internal substrate-channeling cavity from the bulk medium. Finally, it is shown that some PutAs have a 100-200 residue domain of unknown function in the C-terminus that is not found in minimalist PutAs. Remote homology detection suggests that this domain is homologous to the oligomerization beta-hairpin and Rossmann fold domain of BjPutA. PMID:22201760

  7. Interactive effects between N addition and disturbance on boreal forest ecosystem structure and function

    NASA Astrophysics Data System (ADS)

    Nordin, Annika; Strengbom, Joachim; From, Fredrik

    2014-05-01

    In management of boreal forests, nitrogen (N) enrichment from atmospheric deposition or from forest fertilization can appear in combination with land-use related disturbances, i.e. tree harvesting by clear-felling. Long-term interactive effects between N enrichment and disturbance on boreal forest ecosystem structure and function are, however, poorly known. We investigated effects of N enrichment by forest fertilization done > 25 years ago on forest understory species composition in old-growth (undisturbed) forests, and in forests clear-felled 10 years ago (disturbed). In clear-felled forests we also investigated effects of the previous N addition on growth of tree saplings. The results show that the N enrichment effect on the understory species composition was strongly dependent on the disturbance caused by clear-felling. In undisturbed forests, there were small or no effects on understory species composition from N addition. In contrast, effects were large in forests first exposed to N addition and subsequently disturbed by clear-felling. Effects of N addition differed among functional groups of plants. Abundance of graminoids increased (+232%) and abundance of dwarf shrubs decreased (-44%) following disturbance in N fertilized forests. For vascular plants, the two perturbations had contrasting effects on α-(within forests) and β-diversity (among forests): in disturbed forests, N addition reduced, or had no effect on α-diversity, while β-diversity increased. For bryophytes, negative effects of disturbance on α-diversity were smaller in N fertilized forests than in forests not fertilized, while neither N addition nor disturbance had any effects on β-diversity. Moreover, sapling growth in forests clear-felled 10 years ago was significantly higher in previously N fertilized forests than in forests not fertilized. Our study show that effects of N addition on plant communities may appear small, short-lived, or even absent until exposed to a disturbance. This

  8. Inherent Structure-Based Multiview Learning With Multitemplate Feature Representation for Alzheimer's Disease Diagnosis.

    PubMed

    Liu, Mingxia; Zhang, Daoqiang; Adeli, Ehsan; Shen, Dinggang

    2016-07-01

    Multitemplate-based brain morphometric pattern analysis using magnetic resonance imaging has been recently proposed for automatic diagnosis of Alzheimer's disease (AD) and its prodromal stage (i.e., mild cognitive impairment or MCI). In such methods, multiview morphological patterns generated from multiple templates are used as feature representation for brain images. However, existing multitemplate-based methods often simply assume that each class is represented by a specific type of data distribution (i.e., a single cluster), while in reality, the underlying data distribution is actually not preknown. In this paper, we propose an inherent structure-based multiview leaning method using multiple templates for AD/MCI classification. Specifically, we first extract multiview feature representations for subjects using multiple selected templates and then cluster subjects within a specific class into several subclasses (i.e., clusters) in each view space. Then, we encode those subclasses with unique codes by considering both their original class information and their own distribution information, followed by a multitask feature selection model. Finally, we learn an ensemble of view-specific support vector machine classifiers based on their, respectively, selected features in each view and fuse their results to draw the final decision. Experimental results on the Alzheimer's Disease Neuroimaging Initiative database demonstrate that our method achieves promising results for AD/MCI classification, compared to the state-of-the-art multitemplate-based methods.

  9. Segmentation of vessel structures in serial whole slide sections using region-based context features

    NASA Astrophysics Data System (ADS)

    Schwier, Michael; Hahn, Horst K.; Dahmen, Uta; Dirsch, Olaf

    2016-03-01

    We present a method for the automatic segmentation of vascular structures in stacks of serial sections. It was initially motivated within the Virtual Liver Network research project that aims at creating a multi-scale virtual model of the liver. For this the vascular systems of several murine livers under different conditions need to be analyzed. To get highly detailed datasets, stacks of serial sections of the whole organs are prepared. Due to the huge amount of image data an automatic approach for segmenting the vessels is required. After registering the slides with an established method we use a set of Random Forest classifiers to distinguish vessels from tissue. Instead of a pixel-wise approach we perform the classification on small regions. This allows us to use more meaningful features. Besides basic intensity and texture features we introduce the concept of context features, which allow the classifiers to also consider the neighborhood of a region. Classification is performed in two stages. In the second stage the previous classification result of a region and its neighbors is used to refine the decision for a particular region. The context features and two stage classification process make our method very successful. It can handle different stainings and also detect vessels in which residue like blood cells remained. The specificity reaches 95%-99% for pure tissue, depending on staining and zoom level. Only in the direct vicinity of vessels the specificity declines to 88%-96%. The sensitivity rates reach between 89% and 98%.

  10. Inherent Structure-Based Multiview Learning With Multitemplate Feature Representation for Alzheimer's Disease Diagnosis.

    PubMed

    Liu, Mingxia; Zhang, Daoqiang; Adeli, Ehsan; Shen, Dinggang

    2016-07-01

    Multitemplate-based brain morphometric pattern analysis using magnetic resonance imaging has been recently proposed for automatic diagnosis of Alzheimer's disease (AD) and its prodromal stage (i.e., mild cognitive impairment or MCI). In such methods, multiview morphological patterns generated from multiple templates are used as feature representation for brain images. However, existing multitemplate-based methods often simply assume that each class is represented by a specific type of data distribution (i.e., a single cluster), while in reality, the underlying data distribution is actually not preknown. In this paper, we propose an inherent structure-based multiview leaning method using multiple templates for AD/MCI classification. Specifically, we first extract multiview feature representations for subjects using multiple selected templates and then cluster subjects within a specific class into several subclasses (i.e., clusters) in each view space. Then, we encode those subclasses with unique codes by considering both their original class information and their own distribution information, followed by a multitask feature selection model. Finally, we learn an ensemble of view-specific support vector machine classifiers based on their, respectively, selected features in each view and fuse their results to draw the final decision. Experimental results on the Alzheimer's Disease Neuroimaging Initiative database demonstrate that our method achieves promising results for AD/MCI classification, compared to the state-of-the-art multitemplate-based methods. PMID:26540666

  11. Effect of boron addition on the structure and magnetic properties of CoPt nanoparticles

    SciTech Connect

    Khemjeen, Yutthaya; Pinitsoontorn, Supree Chompoosor, Apiwat

    2015-05-07

    The effect of B addition on CoPt nanoparticles was investigated. The CoPt-B nanoparticles were synthesized by means of the polyol process. Transmission electron microscopy has shown that the as-synthesized particles have a spherical morphology with average size about 2–3 nm. The X-ray absorption spectroscopy and the X-ray diffraction technique showed the effect of B concentration on phase transformation. The addition of B at up to 60% promoted the formation of the L1{sub 0} phase when the nanoparticles were subjected to annealing at 600 °C. If the B content is higher than 60%, the phase transition is suppressed. The evidence of B addition on the structure of CoPt nanoparticles was further supported by the magnetic measurements. The results show that the coercivity of the annealed CoPt-B nanoparticles was enhanced by the B additions from 20% to 60%, with the maximum coercivity of 12 000 Oe for the CoPt-40%B sample.

  12. Response of bacterial community structure and function to experimental rainwater additions in a coastal eutrophic embayment

    NASA Astrophysics Data System (ADS)

    Teira, Eva; Hernando-Morales, Víctor; Martínez-García, Sandra; Figueiras, Francisco G.; Arbones, Belén; Álvarez-Salgado, Xosé Antón

    2013-03-01

    Although recognized as a potentially important source of both inorganic and organic nutrients, the impact of rainwater on microbial populations from marine planktonic systems has been poorly assessed. The effect of rainwater additions on bacterioplankton metabolism and community composition was evaluated in microcosm experiments enclosing natural marine plankton populations from the Ría de Vigo (NW Spain). The experiments were conducted during three different seasons (spring, autumn and winter) using rainwater collected at three different locations: marine, urban and rural sites. Bacterial abundance and production significantly increased up to 1.3 and 1.8-fold, respectively, after urban rainwater additions in spring, when ambient nutrient concentration was very low. Overall, the increments in bacterial production were higher than those in bacterial respiration, which implies that a higher proportion of carbon consumed by bacteria would be available to higher trophic levels. The response of the different bacterial groups to distinct rainwater types differed between seasons. The most responsive bacterial groups were Betaproteobacteria which significantly increased their abundance after urban (in spring and winter) and marine (in spring) rainwater additions, and Bacteroidetes which positively responded to all rainwater treatments in spring and to urban rainwater in autumn. Gammaproteobacteria and Roseobacter responded only to urban (in spring) and marine (in winter) rainwater treatment, respectively. The responses to rainwater additions were moderate and transient, and the resulting bacterial community structure was not importantly altered.

  13. Detection and analysis of unusual features in the structural model and structure-factor data of a birch pollen allergen.

    PubMed

    Rupp, Bernhard

    2012-04-01

    Physically improbable features in the model of the birch pollen structure Bet v 1d (PDB entry 3k78) are faithfully reproduced in electron density generated with the deposited structure factors, but these structure factors themselves exhibit properties that are characteristic of data calculated from a simple model and are inconsistent with the data and error model obtained through experimental measurements. The refinement of the 3k78 model against these structure factors leads to an isomorphous structure different from the deposited model with an implausibly small R value (0.019). The abnormal refinement is compared with normal refinement of an isomorphous variant structure of Bet v 1l (PDB entry 1fm4). A variety of analytical tools, including the application of Diederichs plots, Rσ plots and bulk-solvent analysis are discussed as promising aids in validation. The examination of the Bet v 1d structure also cautions against the practice of indicating poorly defined protein chain residues through zero occupancies. The recommendation to preserve diffraction images is amplified.

  14. Biomechanical and Structural Features of CS2 Fimbriae of Enterotoxigenic Escherichia coli

    PubMed Central

    Mortezaei, Narges; Singh, Bhupender; Zakrisson, Johan; Bullitt, Esther; Andersson, Magnus

    2015-01-01

    Enterotoxigenic Escherichia coli (ETEC) are a major cause of diarrhea worldwide, and infection of children in under-developed countries often leads to high mortality rates. Isolated ETEC expresses a plethora of colonization factors (fimbriae/pili), of which CFA/I and CFA/II, which are assembled via the alternate chaperone pathway (ACP), are among the most common. Fimbriae are filamentous structures whose shafts are primarily composed of helically arranged single pilin-protein subunits, with a unique biomechanical ability to unwind and rewind. A sustained ETEC infection, under adverse conditions of dynamic shear forces, is primarily attributed to this biomechanical feature of ETEC fimbriae. Recent understanding about the role of fimbriae as virulence factors points to an evolutionary adaptation of their structural and biomechanical features. In this work, we investigated the biophysical properties of CS2 fimbriae from the CFA/II group. Homology modeling of its major structural subunit, CotA, reveals structural clues related to the niche in which they are expressed. Using optical-tweezers force spectroscopy, we found that CS2 fimbriae unwind at a constant force of 10 pN and have a corner velocity (i.e., the velocity at which the force required for unwinding rises exponentially with increased speed) of 1300 nm/s. The biophysical properties of CS2 fimbriae assessed in this work classify them into a low-force unwinding group of fimbriae together with the CFA/I and CS20 fimbriae expressed by ETEC strains. The three fimbriae are expressed by ETEC, colonize in similar gut environments, and exhibit similar biophysical features, but differ in their biogenesis. Our observation suggests that the environment has a strong impact on the biophysical characteristics of fimbriae expressed by ETEC. PMID:26153701

  15. Biomechanical and structural features of CS2 fimbriae of enterotoxigenic Escherichia coli.

    PubMed

    Mortezaei, Narges; Singh, Bhupender; Zakrisson, Johan; Bullitt, Esther; Andersson, Magnus

    2015-07-01

    Enterotoxigenic Escherichia coli (ETEC) are a major cause of diarrhea worldwide, and infection of children in under-developed countries often leads to high mortality rates. Isolated ETEC expresses a plethora of colonization factors (fimbriae/pili), of which CFA/I and CFA/II, which are assembled via the alternate chaperone pathway (ACP), are among the most common. Fimbriae are filamentous structures whose shafts are primarily composed of helically arranged single pilin-protein subunits, with a unique biomechanical ability to unwind and rewind. A sustained ETEC infection, under adverse conditions of dynamic shear forces, is primarily attributed to this biomechanical feature of ETEC fimbriae. Recent understanding about the role of fimbriae as virulence factors points to an evolutionary adaptation of their structural and biomechanical features. In this work, we investigated the biophysical properties of CS2 fimbriae from the CFA/II group. Homology modeling of its major structural subunit, CotA, reveals structural clues related to the niche in which they are expressed. Using optical-tweezers force spectroscopy, we found that CS2 fimbriae unwind at a constant force of 10 pN and have a corner velocity (i.e., the velocity at which the force required for unwinding rises exponentially with increased speed) of 1300 nm/s. The biophysical properties of CS2 fimbriae assessed in this work classify them into a low-force unwinding group of fimbriae together with the CFA/I and CS20 fimbriae expressed by ETEC strains. The three fimbriae are expressed by ETEC, colonize in similar gut environments, and exhibit similar biophysical features, but differ in their biogenesis. Our observation suggests that the environment has a strong impact on the biophysical characteristics of fimbriae expressed by ETEC. PMID:26153701

  16. Hybrid Residual Flexibility/Mass-Additive Method for Structural Dynamic Testing

    NASA Technical Reports Server (NTRS)

    Tinker, M. L.

    2003-01-01

    A large fixture was designed and constructed for modal vibration testing of International Space Station elements. This fixed-base test fixture, which weighs thousands of pounds and is anchored to a massive concrete floor, initially utilized spherical bearings and pendulum mechanisms to simulate Shuttle orbiter boundary constraints for launch of the hardware. Many difficulties were encountered during a checkout test of the common module prototype structure, mainly due to undesirable friction and excessive clearances in the test-article-to-fixture interface bearings. Measured mode shapes and frequencies were not representative of orbiter-constrained modes due to the friction and clearance effects in the bearings. As a result, a major redesign effort for the interface mechanisms was undertaken. The total cost of the fixture design, construction and checkout, and redesign was over $2 million. Because of the problems experienced with fixed-base testing, alternative free-suspension methods were studied, including the residual flexibility and mass-additive approaches. Free-suspension structural dynamics test methods utilize soft elastic bungee cords and overhead frame suspension systems that are less complex and much less expensive than fixed-base systems. The cost of free-suspension fixturing is on the order of tens of thousands of dollars as opposed to millions, for large fixed-base fixturing. In addition, free-suspension test configurations are portable, allowing modal tests to be done at sites without modal test facilities. For example, a mass-additive modal test of the ASTRO-1 Shuttle payload was done at the Kennedy Space Center launch site. In this Technical Memorandum, the mass-additive and residual flexibility test methods are described in detail. A discussion of a hybrid approach that combines the best characteristics of each method follows and is the focus of the study.

  17. Influence of some structural features of a coal on its tendency to undergo reduction

    SciTech Connect

    Grigor'eva, E.A.; Bakirova, E.V.; Lesnikova, E.B.; Larina, N.K.; Zharova, M.N.; Dzhalyabova, L.V.

    1981-01-01

    Among the many factors determining the depth of conversion of a coal on hydrogenation, various structural features and, in particular, the nature and number of the labile oxygen-containing structures and bridge bonds, have an influence. There are statements that a direct relationship exists between the activity of a coal in destructive hydrogenation and the amount of oxygen in the ether/ester form, and also the nature of the bond of the mineral fraction of the coal with the organic constituents. The present paper is devoted to an investigation of the dependence of the tendancy of coal to undergo hydrogenation on the nature and number of the ether/ester and organomineral bonds in the structure of the coal. In experiments the researchers used the hydrolytic destruction of the coals and subsequent selective hydrogeneatin with sodium tetrahydroborate. 17 refs.

  18. Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function

    NASA Astrophysics Data System (ADS)

    Martin, O. C.; Krzywicki, A.; Zagorski, M.

    2016-07-01

    Living cells can maintain their internal states, react to changing environments, grow, differentiate, divide, etc. All these processes are tightly controlled by what can be called a regulatory program. The logic of the underlying control can sometimes be guessed at by examining the network of influences amongst genetic components. Some associated gene regulatory networks have been studied in prokaryotes and eukaryotes, unveiling various structural features ranging from broad distributions of out-degrees to recurrent "motifs", that is small subgraphs having a specific pattern of interactions. To understand what factors may be driving such structuring, a number of groups have introduced frameworks to model the dynamics of gene regulatory networks. In that context, we review here such in silico approaches and show how selection for phenotypes, i.e., network function, can shape network structure.

  19. Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function.

    PubMed

    Martin, O C; Krzywicki, A; Zagorski, M

    2016-07-01

    Living cells can maintain their internal states, react to changing environments, grow, differentiate, divide, etc. All these processes are tightly controlled by what can be called a regulatory program. The logic of the underlying control can sometimes be guessed at by examining the network of influences amongst genetic components. Some associated gene regulatory networks have been studied in prokaryotes and eukaryotes, unveiling various structural features ranging from broad distributions of out-degrees to recurrent "motifs", that is small subgraphs having a specific pattern of interactions. To understand what factors may be driving such structuring, a number of groups have introduced frameworks to model the dynamics of gene regulatory networks. In that context, we review here such in silico approaches and show how selection for phenotypes, i.e., network function, can shape network structure. PMID:27365153

  20. EBSD analysis of magnesium addition on inclusion formation in SS400 structural steel

    SciTech Connect

    Luo, Sin-Jie; Su, Yen-Hao Frank; Lu, Muh-Jung; Kuo, Jui-Chao

    2013-08-15

    In this study, the effect of magnesium addition on the inclusion formation in SS400 steel was investigated. The experimental specimens with and without Mg addition treatment were compared. The microstructure was observed using optical microscopy after etching with 3% nital. The morphology and chemical composition of the inclusions were analyzed via scanning electron microscopy and energy dispersive spectrometry. The lattice structure and orientation of the inclusions were identified by electron backscattering diffraction. The average size of inclusions in SS400 was between 0.67 and 0.75 μm, and between 0.65 and 0.68 μm in SS400 + Mg. The 2 ppm Mg addition resulted in the oxide formation change from Al{sub 2}O{sub 3} to MgO·Al{sub 2}O{sub 3} and in the inclusion formation change from Al{sub 2}O{sub 3}–MnS to MgO·Al{sub 2}O{sub 3}–MnS. Moreover, a simple-phase MnS with an average grain size of 1 μm to 2 μm was observed in rod-like, globular, and polyhedron forms. - Highlights: • The effect of magnesium addition was investigated for SS400 steel. • 2 ppm Mg addition changes the inclusion formation from Al2O3-MnS to MgO·Al2O3-MnS. • MnS observed in inclusions exhibits rod-like, globular, and polyhedron forms.

  1. Seismic expression of structural features on Landsat lineaments: an example from Denver basin

    SciTech Connect

    Shurr, G.W.; Jenkins, J.T. Jr.; Likarish, D.M.

    1985-02-01

    Lineaments interpreted from Landsat images mark the location and trend of basement faults observed on seismic lines in the eastern Denver basin. Linear features mapped as tone and texture patterns on multispectral scanner images in northeastern Colorado and southwestern Nebraska are used to interpret regional lineaments. Individual linear features up to 25 mi (40 km) long and visible on both bands 5 and 7 define a grid of regional lineaments trending northeast and northwest. Comparisons of lineaments with aeromagnetic and gravity maps and with interpretations of basement geology suggest that lineaments are the boundaries of basement blocks with areas of about 1000 mi/sup 2/ (2590 km/sup 2/). Constituent linear features within the lineament zone probably mark boundaries of smaller blocks of about 50 mi/sup 2/ (130 km/sup 2/). Seismic lines in northeastern Sedgwick County in extreme northeastern Colorado cross linear features that are components of a broad regional lineament that trends northeast and parallels the South Platte River. Seismic data consist of a grid of about 100 mi (160 km) of multifold Vibroseis lines. Basement faults, generally with offsets of less than 100 ft (30 m), are observed in seismic lines that cross some individual linear features. Monoclines and faults are present in Pennsylvanian to Tertiary strata that overlie basement. A time-structure map on the Precambrian and an isochron map of Wolfcamp (Lower Permian) to Precambrian show that the lineament is a 7-mi (11-km) wide zone of small, downdropped basement blocks. Thickening of Permian-Pennsylvanian strata on the downthrown side of faults suggests tectonic activity. Further tectonic activity is indicated by listric faulting in the Cretaceous Niobrara Formation.

  2. Endotoxin Structures in the Psychrophiles Psychromonas marina and Psychrobacter cryohalolentis Contain Distinctive Acyl Features

    PubMed Central

    Sweet, Charles R.; Alpuche, Giancarlo M.; Landis, Corinne A.; Sandman, Benjamin C.

    2014-01-01

    Lipid A is the essential component of endotoxin (Gram-negative lipopolysaccharide), a potent immunostimulatory compound. As the outer surface of the outer membrane, the details of lipid A structure are crucial not only to bacterial pathogenesis but also to membrane integrity. This work characterizes the structure of lipid A in two psychrophiles, Psychromonas marina and Psychrobacter cryohalolentis, and also two mesophiles to which they are related using MALDI-TOF MS and fatty acid methyl ester (FAME) GC-MS. P. marina lipid A is strikingly similar to that of Escherichia coli in organization and total acyl size, but incorporates an unusual doubly unsaturated tetradecadienoyl acyl residue. P. cryohalolentis also shows structural organization similar to a closely related mesophile, Acinetobacter baumannii, however it has generally shorter acyl constituents and shows many acyl variants differing by single methylene (-CH2-) units, a characteristic it shares with the one previously reported psychrotolerant lipid A structure. This work is the first detailed structural characterization of lipid A from an obligate psychrophile and the second from a psychrotolerant species. It reveals distinctive structural features of psychrophilic lipid A in comparison to that of related mesophiles which suggest constitutive adaptations to maintain outer membrane fluidity in cold environments. PMID:25010385

  3. Association between Culex quinquefasciatus (Diptera: Culicidae) oviposition and structural features of belowground stormwater treatment devices.

    PubMed

    Harbison, Justin E; Metzger, Marco E; Hu, Renjie

    2010-01-01

    Belowground stormwater treatment devices referred to as Best Management Practices (BMPs) can be persistent sources of Culex quinquefasciatus Say (Diptera: Culicidae) mosquitoes and in urban environments necessitate routine monitoring and insecticide treatment for control. The design of certain structural features of BMPs may discourage mosquito entry and oviposition, potentially reducing the need for control measures. From August 2007 to November 2008, 29 BMPs were intermittently monitored for the presence of mosquitoes and compared against selected structural features. A bucket ovitrap was developed to estimate entry of oviposition-site-seeking females into BMPs via egg raft counts. The number of egg rafts collected was positively associated with larger diameters and shorter lengths of conveyance pipe from the nearest inlet or outlet and with increasing number of pickholes in BMP manhole covers. In contrast, the number of days pickholes were sealed against adult mosquito entry was negatively associated with eggs rafts. Findings suggest that the design of belowground BMPs and their conveyance systems can influence mosquito oviposition inside these structures. Specific design criteria with the greatest potential to minimize mosquito production and provide safe access for monitoring and control activities are discussed. PMID:20180310

  4. Compression approach of street networks considering the structural and functional features of streets

    NASA Astrophysics Data System (ADS)

    Liu, Gang; He, Jing; Zhang, Xiping

    2015-10-01

    The compression of networks is an important aspect of complex networks and spatial generalization. Previous studies show that the dual graph for street-street relationships more accurately reflects the morphological features of street networks than the traditional methods. In this study, a dual graph for street-street relationship is constructed based on complex networks theory. We introduce the concept of m-order neighbors and take into account the factors of the node’s degree, closeness centrality, betweenness centrality, and distance within the dual graph. We also consider the importance contributions of the node itself and its 1- to m-order neighbors and define the evaluation model of node importance. We then propose a street compression process based on the evaluation of node importance for dual graph by considering the structural and functional features of streets. The degree distribution and topological similarity index are introduced to evaluate the level of maintaining the global structure and topological characteristics of the road network and to validate the efficiency of the proposed method. A real urban road network is used for the experiments. Results show that the proposed approach can be used in selecting important streets that can retain the global structural properties and topological connectivity of the street network.

  5. The RGD finger of Del-1 is a unique structural feature critical for integrin binding

    SciTech Connect

    Schürpf, Thomas; Chen, Qiang; Liu, Jin-huan; Wang, Rui; Springer, Timothy A.; Wang, Jia-huai

    2012-11-13

    Developmental endothelial cell locus-1 (Del-1) glycoprotein is secreted by endothelial cells and a subset of macrophages. Del-1 plays a regulatory role in vascular remodeling and functions in innate immunity through interaction with integrin {alpha}{sub V}{beta}{sub 3}. Del-1 contains 3 epidermal growth factor (EGF)-like repeats and 2 discoidin-like domains. An Arg-Gly-Asp (RGD) motif in the second EGF domain (EGF2) mediates adhesion by endothelial cells and phagocytes. We report the crystal structure of its 3 EGF domains. The RGD motif of EGF2 forms a type II' {beta} turn at the tip of a long protruding loop, dubbed the RGD finger. Whereas EGF2 and EGF3 constitute a rigid rod via an interdomain calcium ion binding site, the long linker between EGF1 and EGF2 lends considerable flexibility to EGF1. Two unique O-linked glycans and 1 N-linked glycan locate to the opposite side of EGF2 from the RGD motif. These structural features favor integrin binding of the RGD finger. Mutagenesis data confirm the importance of having the RGD motif at the tip of the RGD finger. A database search for EGF domain sequences shows that this RGD finger is likely an evolutionary insertion and unique to the EGF domain of Del-1 and its homologue milk fat globule-EGF 8. The RGD finger of Del-1 is a unique structural feature critical for integrin binding.

  6. Investigation of an investment casting method combined with additive manufacturing methods for manufacturing lattice structures

    NASA Astrophysics Data System (ADS)

    Kodira, Ganapathy D.

    Cellular metals exhibit combinations of mechanical, thermal and acoustic properties that provide opportunities for various implementations and applications; light weight aerospace and automobile structures, impact and noise absorption, heat dissipation, and heat exchange. Engineered cell topologies enable one to control mechanical, thermal, and acoustic properties of the gross cell structures. A possible way to manufacture complex 3D metallic cellular solids for mass production with a relatively low cost, the investment casting (IC) method may be used by combining the rapid prototyping (RP) of wax or injection molding. In spite of its potential to produce mass products of various 3D cellular metals, the method is known to have significant casting porosity as a consequence of the complex cellular topology which makes continuous fluid's access to the solidification interface difficult. The effects of temperature on the viscosity of the fluids were studied. A comparative cost analysis between AM-IC and additive manufacturing methods is carried out. In order to manufacture 3D cellular metals with various topologies for multi-functional applications, the casting porosity should be resolved. In this study, the relations between casting porosity and processing conditions of molten metals while interconnecting with complex cellular geometries are investigated. Temperature and pressure conditions on the rapid prototyping -- investment casting (RP-IC) method are reported, thermal stresses induced are also studied. The manufactured samples are compared with those made by additive manufacturing methods.

  7. Reversible intermolecular E-H oxidative addition to a geometrically deformed and structurally dynamic phosphorous triamide.

    PubMed

    Zhao, Wei; McCarthy, Sean M; Lai, Ting Yi; Yennawar, Hemant P; Radosevich, Alexander T

    2014-12-17

    The synthesis and reactivity of geometrically constrained tricoordinate phosphorus (σ(3)-P) compounds supported by tridentate triamide chelates (N[o-NR-C6H4]2(3-); R = Me or (i)Pr) are reported. Studies indicate that 2 (P{N[o-NMe-C6H4]2}) adopts a Cs-symmetric structure in the solid state. Variable-temperature NMR studies demonstrate a low-energy inversion at phosphorus in solution (ΔG(‡)(exptl)(298) = 10.7(5) kcal/mol), for which DFT calculations implicate an edge-inversion mechanism via a metastable C2-symmetric intermediate. In terms of reactivity, compound 2 exhibits poor nucleophilicity, but undergoes oxidative addition at ambient temperature of diverse O-H- and N-H-containing compounds (including alcohols, phenols, carboxylic acids, amines, and anilines). The resulting pentacoordinate adducts 2·[H][OR] and 2·[H][NHR] are characterized by multinuclear NMR spectroscopy and X-ray crystallography, and their structures (which span the pseudorotation coordinate between trigonal bipyramidal and square planar) are evaluated in terms of negative hyperconjugation. At elevated temperatures, the oxidative addition is shown to be reversible for volatile alcohols and amines.

  8. Structural and Ultra-Structural Features of the First Mandibular Molars of Young Rats Submitted to Pre and Postnatal Protein Deficiencies

    PubMed Central

    Gonçalves, L.A; Boldrini, S.C; Capote, T.S.O; Binotti, C.B; Azeredo, R.A; Martini, D.T; Rosenberg, B; Bautz, W.G; Liberti, E.A

    2009-01-01

    The effects of protein malnutrition, both in utero and prior to weaning, on formation of the first mandibular molars were evaluated by phase-contrast and electron microscopy in rats. The nourished group (GI) received a diet that included 20% casein, while the malnourished group (GII) received 5% casein. The first mandibular molars from GII exhibited low density of cells and odontoblasts, which lacked regular organization compared with molars from GI. In addition, a difference in collagen type was observed between the groups, with a prevalence of Type III collagen fibers detected in the dentin, periodontal ligament, and alveolar bone of GII, and a prevalence of Type I collagen fibers in GI. Finally, examination of surface area in molar sagittal sections indicated 30% less dentin in GII, compared with GI. Our results suggest that structural and ultra-structural features of the dentin-pulp complex and periodontal components of rat molars are affected by protein deficiency. PMID:19557153

  9. Soil microbial community structure and nitrogen cycling responses to agroecosystem management and carbon substrate addition

    NASA Astrophysics Data System (ADS)

    Berthrong, S. T.; Buckley, D. H.; Drinkwater, L. E.

    2011-12-01

    Fertilizer application in conventional agriculture leads to N saturation and decoupled soil C and N cycling, whereas organic practices, e.g. complex rotations and legume incorporation, often results in increased SOM and tightly coupled cycles of C and N. These legacy effects of management on soils likely affect microbial community composition and microbial process rates. This project tested if agricultural management practices led to distinct microbial communities and if those communities differed in ability to utilize labile plant carbon substrates and to produce more plant available N. We addressed several specific questions in this project. 1) Do organic and conventional management legacies on similar soils produce distinct soil bacterial and fungal community structures and abundances? 2) How do these microbial community structures change in response to carbon substrate addition? 3) How do the responses of the microbial communities influence N cycling? To address these questions we conducted a laboratory incubation of organically and conventionally managed soils. We added C-13 labelled glucose either in one large dose or several smaller pulses. We extracted genomic DNA from soils before and after incubation for TRFLP community fingerprinting. We measured C in soil pools and respiration and N in soil extracts and leachates. Management led to different compositions of bacteria and fungi driven by distinct components in organic soils. Biomass did not differ across treatments indicating that differences in cycling were due to composition rather than abundance. C substrate addition led to convergence in bacterial communities; however management still strongly influenced the difference in communities. Fungal communities were very distinct between managements and plots with substrate addition not altering this pattern. Organic soils respired 3 times more of the glucose in the first week than conventional soils (1.1% vs 0.4%). Organic soils produced twice as much

  10. Structural and ferromagnetic properties of an orthorhombic phase of MnBi stabilized with Rh additions

    DOE PAGES

    Taufour, Valentin; Thimmaiah, Srinivasa; March, Stephen; Saunders, Scott; Sun, Kewei; Lamichhane, Tej Nath; Kramer, Matthew J.; Bud’ko, Sergey L.; Canfield, Paul C.

    2015-07-28

    The article addresses the possibility of alloy elements in MnBi which may modify the thermodynamic stability of the NiAs-type structure without significantly degrading the magnetic properties. The addition of small amounts of Rh and Mn provides an improvement in the thermal stability with some degradation of the magnetic properties. The small amounts of Rh and Mn additions in MnBi stabilize an orthorhombic phase whose structural and magnetic properties are closely related to the ones of the previously reported high-temperature phase of MnBi (HT MnBi). The properties of the HT MnBi, which is stable between 613 and 719 K, have notmore » been studied in detail because of its transformation to the stable low-temperature MnBi (LT MnBi), making measurements near and below its Curie temperature difficult. The Rh-stabilized MnBi with chemical formula Mn1.0625–xRhxBi [x=0.02(1)] adopts a new superstructure of the NiAs/Ni2In structure family. It is ferromagnetic below a Curie temperature of 416 K. The critical exponents of the ferromagnetic transition are not of the mean-field type but are closer to those associated with the Ising model in three dimensions. The magnetic anisotropy is uniaxial; the anisotropy energy is rather large, and it does not increase when raising the temperature, contrary to what happens in LT MnBi. The saturation magnetization is approximately 3μB/f.u. at low temperatures. Thus, while this exact composition may not be application ready, it does show that alloying is a viable route to modifying the stability of this class of rare-earth-free magnet alloys.« less

  11. Structural and ferromagnetic properties of an orthorhombic phase of MnBi stabilized with Rh additions

    SciTech Connect

    Taufour, Valentin; Thimmaiah, Srinivasa; March, Stephen; Saunders, Scott; Sun, Kewei; Lamichhane, Tej Nath; Kramer, Matthew J.; Bud’ko, Sergey L.; Canfield, Paul C.

    2015-07-28

    The article addresses the possibility of alloy elements in MnBi which may modify the thermodynamic stability of the NiAs-type structure without significantly degrading the magnetic properties. The addition of small amounts of Rh and Mn provides an improvement in the thermal stability with some degradation of the magnetic properties. The small amounts of Rh and Mn additions in MnBi stabilize an orthorhombic phase whose structural and magnetic properties are closely related to the ones of the previously reported high-temperature phase of MnBi (HT MnBi). The properties of the HT MnBi, which is stable between 613 and 719 K, have not been studied in detail because of its transformation to the stable low-temperature MnBi (LT MnBi), making measurements near and below its Curie temperature difficult. The Rh-stabilized MnBi with chemical formula Mn1.0625–xRhxBi [x=0.02(1)] adopts a new superstructure of the NiAs/Ni2In structure family. It is ferromagnetic below a Curie temperature of 416 K. The critical exponents of the ferromagnetic transition are not of the mean-field type but are closer to those associated with the Ising model in three dimensions. The magnetic anisotropy is uniaxial; the anisotropy energy is rather large, and it does not increase when raising the temperature, contrary to what happens in LT MnBi. The saturation magnetization is approximately 3μB/f.u. at low temperatures. Thus, while this exact composition may not be application ready, it does show that alloying is a viable route to modifying the stability of this class of rare-earth-free magnet alloys.

  12. Structural features of mammalian histidine decarboxylase reveal the basis for specific inhibition

    PubMed Central

    Moya-García, AA; Pino-Ángeles, A; Gil-Redondo, R; Morreale, A; Sánchez-Jiménez, F

    2009-01-01

    For a long time the structural and molecular features of mammalian histidine decarboxylase (EC 4.1.1.22), the enzyme that produces histamine, have evaded characterization. We overcome the experimental problems for the study of this enzyme by using a computer-based modelling and simulation approach, and have now the conditions to use histidine decarboxylase as a target in histamine pharmacology. In this review, we present the recent (last 5 years) advances in the structure–function relationship of histidine decarboxylase and the strategy for the discovery of new drugs. PMID:19413567

  13. Features of the band structure for semiconducting iron, ruthenium, and osmium monosilicides

    SciTech Connect

    Shaposhnikov, V. L. Migas, D. B.; Borisenko, V. E.; Dorozhkin, N. N.

    2009-02-15

    The pseudopotential method has been used to optimize the crystal lattice and calculate the energy band spectra for iron, ruthenium and, osmium monosilicides. It is found that all these compounds are indirect-gap semiconductors with band gaps of 0.17, 0.22, and 0.50 eV (FeSi, RuSi, and OsSi, respectively). A distinctive feature of their band structure is the 'loop of extrema' both in the valence and conduction bands near the center of the cubic Brillouin zone.

  14. Learning a structured graphical model with boosted top-down features for ultrasound image segmentation.

    PubMed

    Hao, Zhihui; Wang, Qiang; Wang, Xiaotao; Kim, Jung Bae; Hwang, Youngkyoo; Cho, Baek Hwan; Guo, Ping; Lee, Won Ki

    2013-01-01

    A key problem for many medical image segmentation tasks is the combination of different-level knowledge. We propose a novel scheme of embedding detected regions into a superpixel based graphical model, by which we achieve a full leverage on various image cues for ultrasound lesion segmentation. Region features are mapped into a higher-dimensional space via a boosted model to become well controlled. Parameters for regions, superpixels and a new affinity term are learned simultaneously within the framework of structured learning. Experiments on a breast ultrasound image data set confirm the effectiveness of the proposed approach as well as our two novel modules.

  15. Biomechanical investigation into the structural design of porous additive manufactured cages using numerical and experimental approaches.

    PubMed

    Tsai, Pei-I; Hsu, Ching-Chi; Chen, San-Yuan; Wu, Tsung-Han; Huang, Chih-Chieh

    2016-09-01

    Traditional solid cages have been widely used in posterior lumbar interbody fusion (PLIF) surgery. However, solid cages significantly affect the loading mechanism of the human spine due to their extremely high structural stiffness. Previous studies proposed and investigated porous additive manufactured (AM) cages; however, their biomechanical performances were analyzed using oversimplified bone-implant numerical models. Thus, the aim of this study was to investigate the outer shape and inner porous structure of the AM cages. The outer shape of the AM cages was discovered using a simulation-based genetic algorithm; their inner porous structure was subsequently analyzed parametrically using T10-S1 multilevel spine models. Finally, six types of the AM cages, which were manufactured using selective laser melting, were tested to validate the numerical outcomes. The subsidence resistance of the optimum design was superior to the conventional cage designs. A porous AM cage with a pillar diameter of 0.4mm, a pillar angle of 40°, and a porosity of between 69% and 80% revealed better biomechanical performances. Both the numerical and experimental outcomes can help surgeons to understand the biomechanics of PLIF surgery combined with the use of AM cages. PMID:27392226

  16. Nuclear Magnetic Resonance Solution Structure of DNA Featuring Clustered 2'-Deoxyribonolactone and 8-Oxoguanine Lesions.

    PubMed

    Zálešák, Jan; Constant, Jean-François; Jourdan, Muriel

    2016-07-19

    Ionizing radiation, free radicals, and reactive oxygen species produce hundreds of different DNA lesions. Clustered lesions are typical for ionizing radiation. They compromise the efficiency of the base excision repair (BER) pathway, and as a consequence, they are much more toxic and mutagenic than isolated lesions. Despite their biological relevance, e.g., in cancer radiotherapy and accidental exposure, they are not very well studied from a structural point of view, and while insights provided by structural studies contribute to the understanding of the repair process, only three nuclear magnetic resonance (NMR) studies of DNA containing clusters of lesions were reported. Herein, we report the first NMR solution structure of two DNAs containing a bistranded cluster with the 2'-deoxyribonolactone and 8-oxoguanine lesions. Both DNA duplexes feature a 2'-deoxyribonolactone site in the middle of the sequence of one strand and differ by the relative position of the 8-oxoguanine, staggered 3' or 5' side on the complementary strand at a three-nucleotide distance. Depending on its relative position, the repair of the 8-oxoguanine lesion by the base excision repair protein Fpg is either almost complete or inhibited. We found that the structures of the two DNAs containing a bistranded cluster of two lesions are similar and do not deviate very much from the standard B-form. As no obvious structural deformations were observed between the two duplexes, we concluded that the differences in Fpg activity are not due to differences in their global conformation. PMID:27322640

  17. Structural and sequence features of two residue turns in beta-hairpins.

    PubMed

    Madan, Bharat; Seo, Sung Yong; Lee, Sun-Gu

    2014-09-01

    Beta-turns in beta-hairpins have been implicated as important sites in protein folding. In particular, two residue β-turns, the most abundant connecting elements in beta-hairpins, have been a major target for engineering protein stability and folding. In this study, we attempted to investigate and update the structural and sequence properties of two residue turns in beta-hairpins with a large data set. For this, 3977 beta-turns were extracted from 2394 nonhomologous protein chains and analyzed. First, the distribution, dihedral angles and twists of two residue turn types were determined, and compared with previous data. The trend of turn type occurrence and most structural features of the turn types were similar to previous results, but for the first time Type II turns in beta-hairpins were identified. Second, sequence motifs for the turn types were devised based on amino acid positional potentials of two-residue turns, and their distributions were examined. From this study, we could identify code-like sequence motifs for the two residue beta-turn types. Finally, structural and sequence properties of beta-strands in the beta-hairpins were analyzed, which revealed that the beta-strands showed no specific sequence and structural patterns for turn types. The analytical results in this study are expected to be a reference in the engineering or design of beta-hairpin turn structures and sequences.

  18. Weak conservation of structural features in the interfaces of homologous transient protein–protein complexes

    PubMed Central

    Sudha, Govindarajan; Singh, Prashant; Swapna, Lakshmipuram S; Srinivasan, Narayanaswamy

    2015-01-01

    Residue types at the interface of protein–protein complexes (PPCs) are known to be reasonably well conserved. However, we show, using a dataset of known 3-D structures of homologous transient PPCs, that the 3-D location of interfacial residues and their interaction patterns are only moderately and poorly conserved, respectively. Another surprising observation is that a residue at the interface that is conserved is not necessarily in the interface in the homolog. Such differences in homologous complexes are manifested by substitution of the residues that are spatially proximal to the conserved residue and structural differences at the interfaces as well as differences in spatial orientations of the interacting proteins. Conservation of interface location and the interaction pattern at the core of the interfaces is higher than at the periphery of the interface patch. Extents of variability of various structural features reported here for homologous transient PPCs are higher than the variation in homologous permanent homomers. Our findings suggest that straightforward extrapolation of interfacial nature and inter-residue interaction patterns from template to target could lead to serious errors in the modeled complex structure. Understanding the evolution of interfaces provides insights to improve comparative modeling of PPC structures. PMID:26311309

  19. Structural features of an arabinogalactan gum exudates from Spondias dulsis (Anacardiaceae).

    PubMed

    Martínez, Maritza; León de Pinto, Gladys; Sanabria, Lilian; Beltrán, Olga; Igartuburu, José M; Bahsas, Ali

    2003-03-28

    The tree Spondias dulcis, located in Venezuela, exudes a light-brown gum. The polysaccharide, isolated from the original gum, contains galactose, arabinose, mannose, rhamnose, glucuronic acid, and its 4-O-methyl derivative. Application of chemical methods, in combination with 1D and 2D NMR spectroscopy afforded interesting structural features of the gum polysaccharide. The unequivocal presence of rhamnose in the polymer structure was confirmed by chemical and spectral data [1H (1.03 ppm); 13C (16.92 ppm)]. Also confirmed was the existence of 3-O- and 6-O-substitutes galactose residues by the spectral data correlations observed in Heteronuclear Multiple Quantum Coherence (HMQC) and Heteronuclear Multiple Bond Correlation (HMBC). Also observed were unequivocal resonances for beta-D-glucuronic acid and its 4-O-methyl derivative, and the presence of 3-O-alpha-L-arabinofuranose and 3-O-beta-L-arabinopyranose residues.

  20. Novel structural features of the immunocompetent ceramide phospho-inositol glycan core from Trichomonas vaginalis.

    PubMed

    Heiss, Christian; Wang, Zhirui; Black, Ian; Azadi, Parastoo; Fichorova, Raina N; Singh, Bibhuti N

    2016-01-01

    The ceramide phosphoinositol glycan core (CPI-GC) of the lipophosphoglycan of Trichomonas vaginalis is a major virulent factor of this common genitourinary parasite. While its carbohydrate composition has been reported before, its structure has remained largely unknown. We isolated the glycan portions of CPI-GC by nitrous acid deamination and hydrofluoric acid treatment and investigated their structures by methylation analysis and 1- and 2-D NMR. We found that the α-anomer of galactose is a major constituent of CPI-GC. The β-anomer was found exclusively at the non-reducing end of CPI-GC side chains. Furthermore the data showed that the rhamnan backbone is more complex than previously thought and that the inositol residue at the reducing end is linked to a 4-linked α-glucuronic acid (GlcA) residue. This appears to be the most striking and novel feature of this GPI-anchor type molecule.

  1. Molybdenum nano emitters: the effect of the structural feature on oxygen damage immunity

    NASA Astrophysics Data System (ADS)

    Shen, Yan; Deng, Shaozhi; Xu, Ningsheng; Ye, Peng; Zhang, Yu; Liu, Fei; Chen, Jun; She, Juncong

    2016-04-01

    The structural feature of molybdenum (Mo) nano emitters has a significant effect on their field emission reliability in the oxidizing environment. Mo nanowalls have been studied to exhibit high oxygen damage immunity. The two-dimensional (2D) nanostructure has shown stable and recoverable field emission performance during oxygen exposure in the order of magnitude of 10‑4 Pa. By contrast, quasi 1D nanoscrews have more easily suffered irreversible emission degradation due to more serious oxygen molecule and ion erosion at a higher local electric field around the emitter surface. The 2D wall-like structure with a large emission edge has been proven to contribute to such strong immunity. The results indicate that the Mo nanowall emitter apparently could work properly in the vacuum environment with a certain amount of oxygen.

  2. The nop gene from Phanerochaete chrysosporium encodes a peroxidase with novel structural features.

    PubMed

    Larrondo, Luisf; Gonzalez, Angel; Perez Acle, Tomas; Cullen, Dan; Vicuña, Rafael

    2005-07-01

    Inspection of the genome of the ligninolytic basidiomycete Phanerochaete chrysosporium revealed an unusual peroxidase_like sequence. The corresponding full length cDNA was sequenced and an archetypal secretion signal predicted. The deduced mature protein (NoP, novel peroxidase) contains 295 aa residues and is therefore considerably shorter than other Class II (fungal) peroxidases, such as lignin peroxidases and manganese peroxidases. Comparative modeling of NoP was conducted using the crystal structures of Coprinus cinereus and Arthromyces ramosus peroxidases as templates. The model was validated by molecular dynamics and showed several novel structural features. In particular, NoP has only three disulfide bridges and tryptophan replaces the distal phenylalanine within the heme pocket.

  3. On the use of attractor dimension as a feature in structural health monitoring

    USGS Publications Warehouse

    Nichols, J.M.; Virgin, L.N.; Todd, M.D.; Nichols, J.D.

    2003-01-01

    Recent works in the vibration-based structural health monitoring community have emphasised the use of correlation dimension as a discriminating statistic in seperating a damaged from undamaged response. This paper explores the utility of attractor dimension as a 'feature' and offers some comparisons between different metrics reflecting dimension. This focus is on evaluating the performance of two different measures of dimension as damage indicators in a structural health monitoring context. Results indicate that the correlation dimension is probably a poor choice of statistic for the purpose of signal discrimination. Other measures of dimension may be used for the same purposes with a higher degree of statistical reliability. The question of competing methodologies is placed in a hypothesis testing framework and answered with experimental data taken from a cantilivered beam.

  4. Genomic-scale comparison of sequence- and structure-based methods of function prediction: Does structure provide additional insight?

    PubMed Central

    Fetrow, Jacquelyn S.; Siew, Naomi; Di Gennaro, Jeannine A.; Martinez-Yamout, Maria; Dyson, H. Jane; Skolnick, Jeffrey

    2001-01-01

    A function annotation method using the sequence-to-structure-to-function paradigm is applied to the identification of all disulfide oxidoreductases in the Saccharomyces cerevisiae genome. The method identifies 27 sequences as potential disulfide oxidoreductases. All previously known thioredoxins, glutaredoxins, and disulfide isomerases are correctly identified. Three of the 27 predictions are probable false-positives. Three novel predictions, which subsequently have been experimentally validated, are presented. Two additional novel predictions suggest a disulfide oxidoreductase regulatory mechanism for two subunits (OST3 and OST6) of the yeast oligosaccharyltransferase complex. Based on homology, this prediction can be extended to a potential tumor suppressor gene, N33, in humans, whose biochemical function was not previously known. Attempts to obtain a folded, active N33 construct to test the prediction were unsuccessful. The results show that structure prediction coupled with biochemically relevant structural motifs is a powerful method for the function annotation of genome sequences and can provide more detailed, robust predictions than function prediction methods that rely on sequence comparison alone. PMID:11316881

  5. Structural features affecting the enzymatic digestibility of pine wood pretreated with ionic liquids.

    PubMed

    Torr, Kirk M; Love, Karen T; Simmons, Blake A; Hill, Stefan J

    2016-03-01

    Pretreating lignocellulosic biomass with certain ionic liquids results in structural and chemical changes that make the biomass more digestible by enzymes. In this study, pine wood was pretreated with 1-ethyl-3-methylimidazolium chloride/acetate ([C2 mim]Cl and [C2 mim][OAc]) at different temperatures to investigate the relative importance of substrate features, such as accessible surface area, cellulose crystallinity, and lignin content, on enzymatic digestibility. The ionic liquid pretreatments resulted in glucan conversions ranging from 23% to 84% on saccharification of the substrates, with [C2 mim][OAc] being more effective than [C2 mim]Cl. The pretreatments resulted in no delignification of the wood, some loss of cellulose crystallinity under certain conditions, and varying levels of increased surface area. Enzymatic digestibility closely correlated with accessible surface area and porosity measurements obtained using Simons' staining and thermoporosimetry techniques. Increased accessible surface area was identified as the principal structural feature responsible for the improved enzymatic digestibility. PMID:26369903

  6. SoftSearch: Integration of Multiple Sequence Features to Identify Breakpoints of Structural Variations

    PubMed Central

    Hart, Steven N.; Sarangi, Vivekananda; Moore, Raymond; Baheti, Saurabh; Bhavsar, Jaysheel D.; Couch, Fergus J.; Kocher, Jean-Pierre A.

    2013-01-01

    Background Structural variation (SV) represents a significant, yet poorly understood contribution to an individual’s genetic makeup. Advanced next-generation sequencing technologies are widely used to discover such variations, but there is no single detection tool that is considered a community standard. In an attempt to fulfil this need, we developed an algorithm, SoftSearch, for discovering structural variant breakpoints in Illumina paired-end next-generation sequencing data. SoftSearch combines multiple strategies for detecting SV including split-read, discordant read-pair, and unmated pairs. Co-localized split-reads and discordant read pairs are used to refine the breakpoints. Results We developed and validated SoftSearch using real and synthetic datasets. SoftSearch’s key features are 1) not requiring secondary (or exhaustive primary) alignment, 2) portability into established sequencing workflows, and 3) is applicable to any DNA-sequencing experiment (e.g. whole genome, exome, custom capture, etc.). SoftSearch identifies breakpoints from a small number of soft-clipped bases from split reads and a few discordant read-pairs which on their own would not be sufficient to make an SV call. Conclusions We show that SoftSearch can identify more true SVs by combining multiple sequence features. SoftSearch was able to call clinically relevant SVs in the BRCA2 gene not reported by other tools while offering significantly improved overall performance. PMID:24358278

  7. Site-Specific DNA Structural and Dynamic Features Revealed by Nucleotide-Independent Nitroxide Probes†

    PubMed Central

    Popova, Anna M.; Kálai, Tamás; Hideg, Kálmán; Qin, Peter Z.

    2009-01-01

    In site-directed spin labeling, a covalently attached nitroxide probe containing a chemically inert unpaired electron is utilized to obtain information on the local environment of the parent macromolecule. Studies presented here examine the feasibility of probing local DNA structural and dynamic features using a class of nitroxide probes that are linked to chemically substituted phosphorothioate positions at the DNA backbone. Two members of this family, designated as R5 and R5a, were attached to eight different sites of a dodecameric DNA duplex without severely perturbing the native B-form conformation. Measured X-band electron paramagnetic resonance (EPR) spectra, which report on nitroxide rotational motions, were found to vary depending on the location of the label (e.g., duplex center vs termini) and the surrounding DNA sequence. This indicates that R5 and R5a can provide information on the DNA local environment at the level of an individual nucleotide. As these probes can be attached to arbitrary nucleotides within a nucleic acid sequence, they may provide a means to “scan” a given DNA molecule in order to interrogate its local structural and dynamic features. PMID:19650666

  8. Specific features of the nonradiative relaxation of Er{sup 3+} ions in epitaxial Si structures

    SciTech Connect

    Kudryavtsev, K. E. Kryzhkov, D. I.; Antonov, A. V.; Shengurov, D. V.; Shmagin, V. B.; Krasilnik, Z. F.

    2014-12-15

    The specific features of the nonradiative relaxation of Er{sup 3+} ions in Si:Er layers grown by sublimation molecular-beam epitaxy (SMBE) are studied. In Si:Er/Si diode structures containing precipitation-type emitting centers, a resonance photoresponse at the wavelength λ ≈ 1.5 μm is observed, which is indicative of the nonradiative relaxation of Er3+ ions via the energy back-transfer mechanism. Saturation of the erbium-related photocurrent is for the first time observed at high temperatures. This allows estimation of the concentration of Er centers that undergo relaxation via the above-mentioned back-transfer mechanism (N{sub 0} ≈ 5 × 10{sup 16} cm{sup −3}). In terms of order of magnitude, the estimated concentration N{sub 0} corresponds to the concentration of optically active Er ions upon excitation of the Si:Er layers by means of the recombination mechanism. The features of the nonradiative relaxation of Er{sup 3+} ions in Si:Er/Si structures with different types of emitting centers are analyzed.

  9. Site-Specific DNA Structural and Dynamic Features Revealed by Nucleotide-Independent Nitroxide Probes

    SciTech Connect

    Popova, Anna; Kalai, Tamas; Hideg, Kalman; Qin, Peter Z.

    2009-09-15

    In site-directed spin labeling, a covalently attached nitroxide probe containing a chemically inert unpaired electron is utilized to obtain information on the local environment of the parent macromolecule. Studies presented here examine the feasibility of probing local DNA structural and dynamic features using a class of nitroxide probes that are linked to chemically substituted phosphorothioate positions at the DNA backbone. Two members of this family, designated as R5 and R5a, were attached to eight different sites of a dodecameric DNA duplex without severely perturbing the native B-form conformation. Measured X-band electron paramagnetic resonance (EPR) spectra, which report on nitroxide rotational motions, were found to vary depending on the location of the label (e.g., duplex center vs termini) and the surrounding DNA sequence. This indicates that R5 and R5a can provide information on the DNA local environment at the level of an individual nucleotide. As these probes can be attached to arbitrary nucleotides within a nucleic acid sequence, they may provide a means to “scan” a given DNA molecule in order to interrogate its local structural and dynamic features.

  10. Structural and ultrastructural features of the agouti tongue (Dasyprocta aguti Linnaeus, 1766)

    PubMed Central

    Ciena, Adriano Polican; Bolina, Cristina de Sousa; de Almeida, Sonia Regina Yokomizo; Rici, Rose Eli Grassi; de Oliveira, Moacir Franco; da da Silva, Marcelo Cavenaghi Pereira; Miglino, Maria Angélica; Watanabe, Ii-sei

    2013-01-01

    The agouti (Dasyprocta aguti Linnaeus, 1766) is a wild rodent belonging to the family Dasyproctidae that is found throughout Brazil and feeds on fruits and seeds. The aim of the present study was to describe the following features of the tongue of agouti: its morphological structures, the three-dimensional characteristics of the lingual papillae surface, the connective tissue cores (CTCs) and the epithelial cell ultrastructure. Four types of papillae were observed on the dorsal surface of the tongue with a triangular shape: filiform, fungiform, foliate and vallate. Filiform papillae were distributed throughout the tongue surface, and removal of the epithelial surface revealed conical CTCs and multifilaments. Fungiform papillae were observed in the rostral and middle regions, whereas foliate papillae developed in pairs on the lateral margin of the caudal region. Removal of the epithelium in these regions revealed CTCs with parallel laminar conformation. Vallate papillae were arranged in a V-shape in the caudal region, and their CTCs ranged in shape from elongate to ovoid. The ultrastructural components of the dorsal epithelium were the basal, spinous, granular and keratinised layers. A broad area with cytoplasmic projections was identified in the interface region between the lamina propria and the basal layer. Flattened cells with intermediate filaments were observed in the transitional region between spinous and granular layers. The keratinised layer was composed of superimposed epithelial cells where desmosomes and cell-surface microridges were observed. These structural features, including the three-dimensional aspects of the lingual papillae, the CTCs and the epithelial ultrastructure, indicate that when compared with other animals, particularly other rodent species, the morphological features of the tongue of agouti are relatively well developed, especially regarding foliate and vallate papillae. PMID:23701183

  11. Properties of Inconel 625 Mesh Structures Grown by Electron Beam Additive Manufacturing

    SciTech Connect

    List III, Frederick Alyious; Dehoff, Ryan R; Lowe, Larry E; Sames, William J

    2014-01-01

    Relationships between electron beam parameters (beam current, beam speed, and beam focus) and physical properties (mass, diameter, elastic modulus, and yield strength) have been investigated for Inconel 625 mesh cubes fabricated using an additive manufacturing technology based on electron beam melting. The elastic modulus and yield strength of the mesh cubes have been systematically varied by approximately a factor of ten by changing the electron beam parameters. Simple models have been used to understand better these relationships. Structural anisotropies of the mesh associated with the layered build architecture have been observed and may contribute, along with microstructural anisotropies, to the anisotropic mechanical properties of the mesh. Knowledge of this kind is likely applicable to other metal and alloy systems and is essential to rapidly realize the full potential of this burgeoning technology.

  12. Application and testing of additive manufacturing for mirrors and precision structures

    NASA Astrophysics Data System (ADS)

    Sweeney, Michael; Acreman, Martyn; Vettese, Tom; Myatt, Ray; Thompson, Mike

    2015-09-01

    Additive Manufacturing (aka AM, and 3-D printing) is widely touted in the media as the foundation for the next industrial revolution. Beneath the hype, AM does indeed offer profound advantages in lead-time, dramatically reduced consumption of expensive raw materials, while enabling new and innovative design forms that cannot be produced by other means. General Dynamics and their industry partners have begun to embrace this technology for mirrors and precision structures used in the aerospace, defense, and precision optical instrumentation industries. Aggressively lightweighted, open and closed back test mirror designs, 75-150 mm in size, were first produced by AM from several different materials. Subsequent optical finishing and test experiments have exceeded expectations for density, surface finish, dimensional stability and isotropy of thermal expansion on the optical scale of measurement. Materials currently under examination include aluminum, titanium, beryllium, aluminum beryllium, Inconel 625, stainless steel/bronze, and PEKK polymer.

  13. Structural and biocompatibility properties of dextran from Weissella cibaria JAG8 as food additive.

    PubMed

    Tingirikari, Jagan Mohan Rao; Kothari, Damini; Shukla, Rishikesh; Goyal, Arun

    2014-09-01

    Dextran produced from Weissella cibaria JAG8 was purified and characterized. The molecular mass of dextran as determined by the gel filtration and copper bicinchoninate method was approximately, 800 kDa. Monosaccharide analysis revealed that the polysaccharide comprised only glucose units. Dynamic light scattering study confirmed the mono-disperse nature of dextran with hydrodynamic radius of 900 nm. Surface morphology study of dextran by scanning electron microscopy showed the porous web like structure. Cytotoxicity studies on human cervical cancer (HeLa) cell line showed non-toxic and biocompatible nature of dextran. The relative browning for dextran from W. cibaria JAG8 was similar to commercial prebiotic Nutraflora P-95 and 3-fold lower than Raftilose P-95. Synthesis of dextran by dextransucrase treated, sucrose-supplemented skimmed milk revealed the promising potential of dextran as a food additive.

  14. Structure-property relationships in ABA copolymer gels with A homopolymer additions

    NASA Astrophysics Data System (ADS)

    Seitz, Michelle; Rottsolk, Rebecca; Page, Kirt; Shull, Kenneth

    2009-03-01

    ABA acrylic triblock copolymers with poly(methyl methacrylate) endblocks and poly(butyl acrylate) midblocks transition from free flowing liquids to elastic solids with decreasing temperature in alcohol solvents. Homopolymer PMMA chains can be solubilized in the micelle cores if they are shorter than the endblocks. Indentation and compression tests were used to determine gel's modulus and large strain behavior. Gels with volume fractions of PMMA less than ˜0.2 are highly elastic and have moduli dictated by stretching of bridging midblocks. At higher PMMA contents, gels exhibit greater permanent deformation and moduli over an order of magnitude larger than would be expected from rubber elasticity alone. Small angle X-ray and neutron scattering and mean field simulations were used to correlate changes in gel structure and micelle morphology with the addition of homopolymer.

  15. Tailoring of Boehmite-Derived Aluminosilicate Aerogel Structure and Properties: Influence of Ti Addition

    NASA Technical Reports Server (NTRS)

    Hurwitz, Frances I.; Guo, Haiquan; Sheets, Erik J.; Miller, Derek R.; Newlin, Katy N.

    2010-01-01

    Aluminosilicate aerogels offer potential for extremely low thermal conductivities at temperatures greater than 900 C, beyond where silica aerogels reach their upper temperature limits. Aerogels have been synthesized at various Al:Si ratios, including mullite compositions, using Boehmite (AlOOH) as the Al source, and tetraethoxy orthosilicate as the Si precursor. The Boehmite-derived aerogels are found to form by a self-assembly process of AlOOH crystallites, with Si-O groups on the surface of an alumina skeleton. Morphology, surface area and pore size varies with the crystallite size of the starting Boehmite powder, as well as with synthesis parameters. Ternary systems, including Al-Si-Ti aerogels incorporating a soluble Ti precursor, are possible with careful control of pH. The addition of Ti influences sol viscosity, gelation time pore structure and pore size distribution, as well as phase formation on heat treatment.

  16. Special Feature: Liquids and Structural Glasses Special Feature: Glass rheology: From mode-coupling theory to a dynamical yield criterion

    NASA Astrophysics Data System (ADS)

    Brader, Joseph M.; Voigtmann, Thomas; Fuchs, Matthias; Larson, Ronald G.; Cates, Michael E.

    2009-09-01

    The mode coupling theory (MCT) of glasses, while offering an incomplete description of glass transition physics, represents the only established route to first-principles prediction of rheological behavior in nonergodic materials such as colloidal glasses. However, the constitutive equations derivable from MCT are somewhat intractable, hindering their practical use and also their interpretation. Here, we present a schematic (single-mode) MCT model which incorporates the tensorial structure of the full theory. Using it, we calculate the dynamic yield surface for a large class of flows.

  17. Raman spectroscopic evaluation of meat batter structural changes induced by thermal treatment and salt addition.

    PubMed

    Herrero, A M; Carmona, P; López-López, I; Jiménez-Colmenero, F

    2008-08-27

    Raman spectroscopy, texture, proximate composition, and water binding analysis were carried out to evaluate the effect of thermal treatment and/or salt addition to meat batter. For this purpose, different meat batters were elaborated: control meat batter (no salt) and meat batters with low (1.0%) and high (2.5%) NaCl content with and without thermal treatment (70 degrees C/30 min). Increase (P < 0.05) in penetration force and hardness upon heating was observed. Results also showed hardness increasing (P < 0.05) as a function of salt addition in heated meat batter. Raman spectroscopy analysis revealed a significant (P < 0.05) decrease in alpha-helix content accompanied by an increase (P < 0.05) in beta-sheets resulting from heating. Significant (P < 0.05) correlations were found between these secondary structural changes in meat proteins and water binding and textural properties of meat batter. In this way, a significant correlation was found between beta-sheets, salt content, hardness, and chewiness in heated samples.

  18. Essential Structural Requirements and Additive Effects for Flavonoids to Scavenge Methylglyoxal.

    PubMed

    Shao, Xi; Chen, Huadong; Zhu, Yingdong; Sedighi, Rashin; Ho, Chi-Tang; Sang, Shengmin

    2014-04-01

    Reactive dicarbonyl species, such as methylglyoxal (MGO), are considered as the major precursors of advanced glycation end products (AGEs), which are believed to be one of the physiological causes of diabetes and its complications. Scavenging of reactive dicarbonyl species using naturally occurring flavonoids has been proposed as an effective way to prevent diabetic complications. To elucidate the structural requirements of flavonoids in scavenging MGO, seven flavonoids (quercetin, luteolin, epicatechin, genistein, daidzein, apigenin, and phloretin) and five sub-components of the flavonoids (gallic acid, phloroglucinol, pyrogallol, pyrocatechol, and resorcinol) were examined in this study. Our results showed the following: (1) 1,2,3-trihydroxybenzene (pyrogallol) has higher MGO scavenging activity than 1,3,5-trihydroxybenzene and 1,2- and 1,3-dihydroxybenzene, and substitution at position 5 of pyrogallol diminished the scavenging activity, indicating that position 5 is the active site of pyrogallol; (2) the A ring is the active site of flavonoids in contributing the MGO-trapping efficacy, and the hydroxyl group at C-5 on the A ring enhances the trapping efficacy; (3) the double bond between C-2 and C-3 on the C ring could facilitate the trapping efficacy; and (4) the number of hydroxyl groups on the B ring does not significantly influence the trapping efficacy. In addition, we found there is an additive effect in MGO trapping by two common flavonoids, quercetin and phloretin, indicating that flavonoid-enriched foods and beverages hold great promise to prevent the development of diabetic complications.

  19. Topological features in crystal structures: a quotient graph assisted analysis of underlying nets and their embeddings.

    PubMed

    Eon, Jean Guillaume

    2016-05-01

    Topological properties of crystal structures may be analysed at different levels, depending on the representation and the topology that has been assigned to the crystal. Considered here is the combinatorial or bond topology of the structure, which is independent of its realization in space. Periodic nets representing one-dimensional complexes, or the associated graphs, characterize the skeleton of chemical bonds within the crystal. Since periodic nets can be faithfully represented by their labelled quotient graphs, it may be inferred that their topological features can be recovered by a direct analysis of the labelled quotient graph. Evidence is given for ring analysis and structure decomposition into building units and building networks. An algebraic treatment is developed for ring analysis and thoroughly applied to a description of coesite. Building units can be finite or infinite, corresponding to 1-, 2- or even 3-periodic subnets. The list of infinite units includes linear chains or sheets of corner- or edge-sharing polyhedra. Decomposing periodic nets into their building units relies on graph-theoretical methods classified as surgery techniques. The most relevant operations are edge subdivision, vertex identification, edge contraction and decoration. Instead, these operations can be performed on labelled quotient graphs, evidencing in almost a mechanical way the nature and connection mode of building units in the derived net. Various examples are discussed, ranging from finite building blocks to 3-periodic subnets. Among others, the structures of strontium oxychloride, spinel, lithiophilite and garnet are addressed. PMID:27126104

  20. Structural features of a potential gas hydrate area in the Pointer Ridge off southwest Taiwan

    NASA Astrophysics Data System (ADS)

    Wang, Hsueh-Fen; Hsu, Shu-Kun; Tsai, Ching-Hui; Chen, Song-Chuen; Liu, Char-Shine; Lin, Hsiao-Shan

    2015-04-01

    The offshore area of the southwest Taiwan is located in the oblique convergence zone between the northern continental margin of South China Sea and the Manila accretionary wedge. To the west of the deformation front offshore southwestern Taiwan, the Pointer Ridge is located in the passive South China Sea continental margin. The continental margin is compose of extensional horst-and-graben structures. There are numerous submarine channels and linear ridge, formed due to the submarine erosion across the continental slope region. According to geophysical research off SW Taiwan, abundant gas hydrate may exist. In this study, our purpose is to understand the relationship between the near-seafloor structures of the Pointer Ridge and the gas hydrate formation off SW Taiwan. The data we used include multi-beam echo sounder (MBES), side-scan sonar (SSS), sub-bottom profiler (SBP) and the multi-channel reflection seismic (MCS) data. Our results show the pockmark and gas seepage structures mainly appear in the place where the gradient of the BSR thickness is maximum. Those sites contain authigenic carbonate signature shown in the sub-bottom profiler. We also observe several folds and faults structures in this extensional background; however, these compressional features need further studies.

  1. The Structure of Neurexin 1[alpha] Reveals Features Promoting a Role as Synaptic Organizer

    SciTech Connect

    Chen, Fang; Venugopal, Vandavasi; Murray, Beverly; Rudenko, Gabby

    2014-10-02

    {alpha}-Neurexins are essential synaptic adhesion molecules implicated in autism spectrum disorder and schizophrenia. The {alpha}-neurexin extracellular domain consists of six LNS domains interspersed by three EGF-like repeats and interacts with many different proteins in the synaptic cleft. To understand how {alpha}-neurexins might function as synaptic organizers, we solved the structure of the neurexin 1{alpha} extracellular domain (n1{alpha}) to 2.65 {angstrom}. The L-shaped molecule can be divided into a flexible repeat I (LNS1-EGF-A-LNS2), a rigid horseshoe-shaped repeat II (LNS3-EGF-B-LNS4) with structural similarity to so-called reelin repeats, and an extended repeat III (LNS5-EGF-B-LNS6) with controlled flexibility. A 2.95 {angstrom} structure of n1{alpha} carrying splice insert SS3 in LNS4 reveals that SS3 protrudes as a loop and does not alter the rigid arrangement of repeat II. The global architecture imposed by conserved structural features enables {alpha}-neurexins to recruit and organize proteins in distinct and variable ways, influenced by splicing, thereby promoting synaptic function.

  2. CDK1 structures reveal conserved and unique features of the essential cell cycle CDK

    PubMed Central

    Brown, Nicholas R.; Korolchuk, Svitlana; Martin, Mathew P.; Stanley, Will; Moukhametzianov, Rouslan; Noble, Martin E.M.; Endicott, Jane A.

    2015-01-01

    CDK1 is the only essential cell cycle CDK in human cells and is required for successful completion of M-phase. It is the founding member of the CDK family and is conserved across all eukaryotes. Here we report the crystal structures of complexes of CDK1–Cks1 and CDK1–cyclin B–Cks2. These structures confirm the conserved nature of the inactive monomeric CDK fold and its ability to be remodeled by cyclin binding. Relative to CDK2–cyclin A, CDK1–cyclin B is less thermally stable, has a smaller interfacial surface, is more susceptible to activation segment dephosphorylation, and shows differences in the substrate sequence features that determine activity. Both CDK1 and CDK2 are potential cancer targets for which selective compounds are required. We also describe the first structure of CDK1 bound to a potent ATP-competitive inhibitor and identify aspects of CDK1 structure and plasticity that might be exploited to develop CDK1-selective inhibitors. PMID:25864384

  3. Oxide-ion and proton conducting electrolyte materials for clean energy applications: structural and mechanistic features.

    PubMed

    Malavasi, Lorenzo; Fisher, Craig A J; Islam, M Saiful

    2010-11-01

    This critical review presents an overview of the various classes of oxide materials exhibiting fast oxide-ion or proton conductivity for use as solid electrolytes in clean energy applications such as solid oxide fuel cells. Emphasis is placed on the relationship between structural and mechanistic features of the crystalline materials and their ion conduction properties. After describing well-established classes such as fluorite- and perovskite-based oxides, new materials and structure-types are presented. These include a variety of molybdate, gallate, apatite silicate/germanate and niobate systems, many of which contain flexible structural networks, and exhibit different defect properties and transport mechanisms to the conventional materials. It is concluded that the rich chemistry of these important systems provides diverse possibilities for developing superior ionic conductors for use as solid electrolytes in fuel cells and related applications. In most cases, a greater atomic-level understanding of the structures, defects and conduction mechanisms is achieved through a combination of experimental and computational techniques (217 references). PMID:20848015

  4. Oxide-ion and proton conducting electrolyte materials for clean energy applications: structural and mechanistic features.

    PubMed

    Malavasi, Lorenzo; Fisher, Craig A J; Islam, M Saiful

    2010-11-01

    This critical review presents an overview of the various classes of oxide materials exhibiting fast oxide-ion or proton conductivity for use as solid electrolytes in clean energy applications such as solid oxide fuel cells. Emphasis is placed on the relationship between structural and mechanistic features of the crystalline materials and their ion conduction properties. After describing well-established classes such as fluorite- and perovskite-based oxides, new materials and structure-types are presented. These include a variety of molybdate, gallate, apatite silicate/germanate and niobate systems, many of which contain flexible structural networks, and exhibit different defect properties and transport mechanisms to the conventional materials. It is concluded that the rich chemistry of these important systems provides diverse possibilities for developing superior ionic conductors for use as solid electrolytes in fuel cells and related applications. In most cases, a greater atomic-level understanding of the structures, defects and conduction mechanisms is achieved through a combination of experimental and computational techniques (217 references).

  5. Structural features of endocrine active chemicals--A comparison of in vivo and in vitro data.

    PubMed

    Lewin, Geertje; Escher, Sylvia E; van der Burg, Bart; Simetska, Nelly; Mangelsdorf, Inge

    2015-08-01

    Studies on reproductive toxicity need high numbers of test animals. Therefore, we investigated whether chemical structural features (SF) in combination with in vitro data on specific adverse outcome pathways (AOPs) may be used for predicting reproductive toxicity of untested chemicals. Using the OECD Toolbox and expert judgment, we identified 89 structure groups for 275 chemicals for which the results of prenatal developmental toxicity or multigeneration studies were present in the Fraunhofer database on Fertility and Developmental Toxicity in experimental animals (FeDTex) database. Likewise, we evaluated 220 chemicals which had been tested in reporter gene assays on endocrine ((anti)estrogenic and (anti)androgenic) properties in the CALUX(®) test battery. There was a large spread of effect levels for substances within the chemical structure groups for both, in vivo and in vitro results. The groups of highest concern (diphenyl derivatives, planar conjugated systems with fused rings, phenols and organophosphates) correlated quite well, however, between the in vivo and in vitro data on estrogenic activity. For the 56 chemicals represented in both databases, lowest effect doses in vivo correlated well with the estrogenic activity in vitro. These results suggest that a panel of assays covering relevant AOPs and data on metabolism and toxicokinetics may allow prediction of relative reproductive or development toxicity potency within the identified chemical structure groups.

  6. Synchrotron X-Ray Microdiffraction Reveals Intrinsic Structural Features of Amyloid Deposits In Situ

    PubMed Central

    Briki, Fatma; Vérine, Jérôme; Doucet, Jean; Bénas, Philippe; Fayard, Barbara; Delpech, Marc; Grateau, Gilles; Riès-Kautt, Madeleine

    2011-01-01

    Amyloidoses are increasingly recognized as a major public health concern in Western countries. All amyloidoses share common morphological, structural, and tinctorial properties. These consist of staining by specific dyes, a fibrillar aspect in electron microscopy and a typical cross-β folding in x-ray diffraction patterns. Most studies that aim at deciphering the amyloid structure rely on fibers generated in vitro or extracted from tissues using protocols that may modify their intrinsic structure. Therefore, the fine details of the in situ architecture of the deposits remain unknown. Here, we present to our knowledge the first data obtained on ex vivo human renal tissue sections using x-ray microdiffraction. The typical cross-β features from fixed paraffin-embedded samples are similar to those formed in vitro or extracted from tissues. Moreover, the fiber orientation maps obtained across glomerular sections reveal an intrinsic texture that is correlated with the glomerulus morphology. These results are of the highest importance to understanding the formation of amyloid deposits and are thus expected to trigger new incentives for tissue investigation. Moreover, the access to intrinsic structural parameters such as fiber size and orientation using synchrotron x-ray microdiffraction, could provide valuable information concerning in situ mechanisms and deposit formation with potential benefits for diagnostic and therapeutic purposes. PMID:21767502

  7. CDK1 structures reveal conserved and unique features of the essential cell cycle CDK

    NASA Astrophysics Data System (ADS)

    Brown, Nicholas R.; Korolchuk, Svitlana; Martin, Mathew P.; Stanley, Will A.; Moukhametzianov, Rouslan; Noble, Martin E. M.; Endicott, Jane A.

    2015-04-01

    CDK1 is the only essential cell cycle CDK in human cells and is required for successful completion of M-phase. It is the founding member of the CDK family and is conserved across all eukaryotes. Here we report the crystal structures of complexes of CDK1-Cks1 and CDK1-cyclin B-Cks2. These structures confirm the conserved nature of the inactive monomeric CDK fold and its ability to be remodelled by cyclin binding. Relative to CDK2-cyclin A, CDK1-cyclin B is less thermally stable, has a smaller interfacial surface, is more susceptible to activation segment dephosphorylation and shows differences in the substrate sequence features that determine activity. Both CDK1 and CDK2 are potential cancer targets for which selective compounds are required. We also describe the first structure of CDK1 bound to a potent ATP-competitive inhibitor and identify aspects of CDK1 structure and plasticity that might be exploited to develop CDK1-selective inhibitors.

  8. Structural and superconducting features of Tl-1223 prepared at ambient pressure

    DOE PAGES

    Shipra, Fnu; Idrobo Tapia, Juan Carlos; Sefat, Athena Safa

    2015-09-25

    This study provides an account of the bulk preparation of TlBa2Ca2Cu3O9-δ (Tl-1223) superconductor at ambient pressure, and the Tc features under thermal-annealing conditions. The ‘as-prepared’ Tl-1223 (Tc =106 K) presents a significantly higher Tc = 125 K after annealing the polycrystalline material in either flowing Ar+4% H2, or N2 gases. In order to understand the fundamental reasons for a particular Tc, we refined the average bulk structures using powder X-ray diffraction data. Although Ar+4%H2 annealed Tl- 1223 shows an increased ‘c’ lattice parameter, it shrinks by 0.03% (approximately unchanged) upon N2 anneal. Due to such indeterminate conclusions on the averagemore » structural changes, local structures were investigated at using aberration-corrected scanning-transmission electron microscopy technique. Similar compositional changes in the atomic arrangements of both annealed-samples of Tl-1223 were detected in which the plane containing Ca atomic layer gives a non-uniform contrast, due to substitution of some heavier Tl. In this report, extensive bulk properties are summarized through temperature-dependent resistivity, and shielding and Meissner fractions of magnetic susceptibility results; the bulk and local structures are investigated to correlate to properties.« less

  9. Structural and superconducting features of Tl-1223 prepared at ambient pressure

    SciTech Connect

    Shipra, Fnu; Idrobo Tapia, Juan Carlos; Sefat, Athena Safa

    2015-09-25

    This study provides an account of the bulk preparation of TlBa2Ca2Cu3O9-δ (Tl-1223) superconductor at ambient pressure, and the Tc features under thermal-annealing conditions. The ‘as-prepared’ Tl-1223 (Tc =106 K) presents a significantly higher Tc = 125 K after annealing the polycrystalline material in either flowing Ar+4% H2, or N2 gases. In order to understand the fundamental reasons for a particular Tc, we refined the average bulk structures using powder X-ray diffraction data. Although Ar+4%H2 annealed Tl- 1223 shows an increased ‘c’ lattice parameter, it shrinks by 0.03% (approximately unchanged) upon N2 anneal. Due to such indeterminate conclusions on the average structural changes, local structures were investigated at using aberration-corrected scanning-transmission electron microscopy technique. Similar compositional changes in the atomic arrangements of both annealed-samples of Tl-1223 were detected in which the plane containing Ca atomic layer gives a non-uniform contrast, due to substitution of some heavier Tl. In this report, extensive bulk properties are summarized through temperature-dependent resistivity, and shielding and Meissner fractions of magnetic susceptibility results; the bulk and local structures are investigated to correlate to properties.

  10. Grapevine yellow speckle viroid: structural features of a new viroid group.

    PubMed Central

    Koltunow, A M; Rezaian, M A

    1988-01-01

    A single stranded circular RNA was isolated from grapevines infected with yellow speckle disease. The RNA which we have called grapevine yellow speckle viroid (GYSV), contains 367 nucleotide residues and has the potential to form the rod-like secondary structure characteristic of viroids. GYSV has 37% sequence homology with the recently described apple scar skin viroid (ASSV; 330 residues) and has some sequence homology with the viroids in the potato spindle tuber viroid (PSTV) group. The sequence of GYSV has characteristics which fit the structural domains described for the PSTV group. However, GYSV lacks the PSTV central conserved sequence. Instead, there is a conserved sequence in the central region of GYSV and ASSV which has the potential to form a stem loop configuration and a stable palindromic structure as does the central conserved region of the PSTV group. These structural features suggest there is a different central conserved region for GYSV and ASSV. The results support the viroid nature of GYSV and its inclusion into a separate viroid group which we suggest should be represented by ASSV. Images PMID:3344221

  11. Inhalation TTC values: A new integrative grouping approach considering structural, toxicological and mechanistic features.

    PubMed

    Tluczkiewicz, I; Kühne, R; Ebert, R-U; Batke, M; Schüürmann, G; Mangelsdorf, I; Escher, S E

    2016-07-01

    The present publication describes an integrative grouping concept to derive threshold values for inhalation exposure. The classification scheme starts with differences in toxicological potency and develops criteria to group compounds into two potency classes, namely toxic (T-group) or low toxic (L-group). The TTC concept for inhalation exposure is based on the TTC RepDose data set, consisting of 296 organic compounds with 608 repeated-dose inhalation studies. Initially, 21 structural features (SFs) were identified as being characteristic for compounds of either high or low NOEC values (Schüürmann et al., 2016). In subsequent analyses these SF groups were further refined by taking into account structural homogeneity, type of toxicological effect observed, differences in absorption, metabolism and mechanism of action (MoA), to better define their structural and toxicological boundaries. Differentiation of a local or systemic mode of action did not improve the classification scheme. Finally, 28 groups were discriminated: 19 T-groups and 9 L-groups. Clearly distinct thresholds were derived for the T- and L-toxicity groups, being 2 × 10(-5) ppm (2 μg/person/day) and 0.05 ppm (4260 μg/person/day), respectively. The derived thresholds and the classification are compared to the initial mainly structure driven grouping (Schüürmann et al., 2016) and to the Cramer classification. PMID:27041393

  12. Children's Understanding of the Additive Composition of Number and of the Decimal Structure: What Is the Relationship?

    ERIC Educational Resources Information Center

    Krebs, Georgina; Squire, Sarah; Bryant, Peter

    2003-01-01

    Nunes and Bryant (Children doing mathematics, Blackwell, Oxford, 1996) proposed that an understanding of the additive composition of number could be a precursor to an understanding of the decimal structure. If this is so, children should achieve an understanding of additive composition before they can handle the decimal structure. The aim of our…

  13. Multiple Eyewall Structure and its Wind Features in 2012 Typhoon Bolaven

    NASA Astrophysics Data System (ADS)

    Origuchi, S.

    2015-12-01

    Typhoon 'Bolaven' passed the Okinawa Main Island at about 1200 UTC 26 August 2012, while moving northwestward. The radar images showed that 'Bolaven' had the multiple eyewall structure. The surface observation data at Nago of Okinawa showed that the precipitation and surface wind velocity in the typhoon's central region were weaker than those of the Japan Meteorological Agency (JMA)'s operational forecast. Cloud-resolving ensemble simulations were performed to investigate the relations between the multiple eyewall structure and the wind features in the typhoon's central regions. The ensemble simulations reproduced double eyewall structures in several members. To evaluate the reproducibility of multiple eyewall structures, the multi-eye index (MEI) was defined in this study. Compared with the members in which the typhoon had the spiral rainband structures, the pressure gradients in the typhoon's central region of the small MEI (multiple eyewall) members were weak. The precipitation and surface wind velocity were also weaker than those of the typhoons with spiral rainbands. In case of the multiple eyewall typhoon, the gentle pressure gradients and the associated weaker surface inflows suppressed convections in the inner eyewall. The statistical analysis was performed based on the ensemble prediction. A clear positive correlation was indicated between the MEI and the wind velocity (tangential wind and inward radial wind) in the typhoon's central region. This result explains the reason why the actual wind velocity was weaker than that of the original JMA's forecast. The relationship between the atmospheric environmental factors around the typhoon (e.g., level of free convection and convective available potential energy) and MEI was investigated from the outputs of ensemble simulations. The results indicated that there were no strong relations between them. This suggests that the formation of the multiple eyewall structures is not simply determined by the atmospheric

  14. Synthesis, structure and luminescence properties of lanthanide complex with a new tetrapodal ligand featuring salicylamide arms

    SciTech Connect

    Song Xueqin; Wen Xiaoguang; Liu Weisheng; Wang Daqi

    2010-01-15

    A new tetrapodal ligand 1,1,1-tetrakis{l_brace}[(2'-(2-furfurylaminoformyl))phenoxyl]methyl{r_brace}methane (L) has been prepared and their coordination chemistry with Ln{sup III} ions has been investigated. The structure of {l_brace}[Ln{sub 4}L{sub 3}(NO{sub 3}){sub 12}].H{sub 2}O{r_brace}{sub i}nfinity (Ln=Nd, Eu)] shows the binodal 4,3-connected three-dimensional interpenetration coordination polymers with topology of a (8{sup 6}){sub 3}(8{sup 3}){sub 4} notation. [DyL(NO{sub 3}){sub 3}(H{sub 2}O){sub 2}].0.5CH{sub 3}OH and [ErL(NO{sub 3}){sub 3}(H{sub 2}O) (CH{sub 3}OH)].CH{sub 3}COCH{sub 3} is a 1:1 mononuclear complex with interesting supramolecular features. The structure of [NdL(H{sub 2}O){sub 6}].3ClO{sub 4}.3H{sub 2}O is a 2:1 mononuclear complex which further self-assembled through hydrogen bond to form a three-dimensional supramolecular structures. The result presented here indicates that both subtle variation of the terminal group and counter anions can be applied in the modulation of the overall molecular structures of lanthanide complex of salicylamide derivatives due to the structure specialties of this type of ligand. The luminescence properties of the Eu{sup III} complex are also studied in detail. - Grapical Abstract: We present here a series of zero- to three-dimensional lanthanide coordination structures and luminescence properties of Eu(III) complex of a new tetrapodal ligand.

  15. effect of hydrogen addition and burner diameter on the stability and structure of lean, premixed flames

    NASA Astrophysics Data System (ADS)

    Kaufman, Kelsey Leigh

    Low swirl burners (LSBs) have gained popularity in heating and gas power generation industries, in part due to their proven capacity for reducing the production of NOx, which in addition to reacting to form smog and acid rain, plays a central role in the formation of the tropospheric ozone layer. With lean operating conditions, LSBs are susceptible to combustion instability, which can result in flame extinction or equipment failure. Extensive work has been performed to understand the nature of LSB combustion, but scaling trends between laboratory- and industrial-sized burners have not been established. Using hydrogen addition as the primary method of flame stabilization, the current work presents results for a 2.54 cm LSB to investigate potential effects of burner outlet diameter on the nature of flame stability, with focus on flashback and lean blowout conditions. In the lean regime, the onset of instability and flame extinction have been shown to occur at similar equivalence ratios for both the 2.54 cm and a 3.81 cm LSB and depend on the resolution of equivalence ratios incremented. Investigations into flame structures are also performed. Discussion begins with a derivation for properties in a multicomponent gas mixture used to determine the Reynolds number (Re) to develop a condition for turbulent intensity similarity in differently-sized LSBs. Based on this requirement, operating conditions are chosen such that the global Reynolds number for the 2.54 cm LSB is within 2% of the Re for the 3.81 cm burner. With similarity obtained, flame structure investigations focus on flame front curvature and flame surface density (FSD). As flame structure results of the current 2.54 cm LSB work are compared to results for the 3.81 cm LSB, no apparent relationship is shown to exist between burner diameter and the distribution of flame surface density. However, burner diameter is shown to have a definite effect on the flame front curvature. In corresponding flow conditions, a

  16. Gram-Negative Marine Bacteria: Structural Features of Lipopolysaccharides and Their Relevance for Economically Important Diseases

    PubMed Central

    Anwar, Muhammad Ayaz; Choi, Sangdun

    2014-01-01

    Gram-negative marine bacteria can thrive in harsh oceanic conditions, partly because of the structural diversity of the cell wall and its components, particularly lipopolysaccharide (LPS). LPS is composed of three main parts, an O-antigen, lipid A, and a core region, all of which display immense structural variations among different bacterial species. These components not only provide cell integrity but also elicit an immune response in the host, which ranges from other marine organisms to humans. Toll-like receptor 4 and its homologs are the dedicated receptors that detect LPS and trigger the immune system to respond, often causing a wide variety of inflammatory diseases and even death. This review describes the structural organization of selected LPSes and their association with economically important diseases in marine organisms. In addition, the potential therapeutic use of LPS as an immune adjuvant in different diseases is highlighted. PMID:24796306

  17. Robust Classification and Segmentation of Planar and Linear Features for Construction Site Progress Monitoring and Structural Dimension Compliance Control

    NASA Astrophysics Data System (ADS)

    Maalek, R.; Lichti, D. D.; Ruwanpura, J.

    2015-08-01

    The application of terrestrial laser scanners (TLSs) on construction sites for automating construction progress monitoring and controlling structural dimension compliance is growing markedly. However, current research in construction management relies on the planned building information model (BIM) to assign the accumulated point clouds to their corresponding structural elements, which may not be reliable in cases where the dimensions of the as-built structure differ from those of the planned model and/or the planned model is not available with sufficient detail. In addition outliers exist in construction site datasets due to data artefacts caused by moving objects, occlusions and dust. In order to overcome the aforementioned limitations, a novel method for robust classification and segmentation of planar and linear features is proposed to reduce the effects of outliers present in the LiDAR data collected from construction sites. First, coplanar and collinear points are classified through a robust principal components analysis procedure. The classified points are then grouped using a robust clustering method. A method is also proposed to robustly extract the points belonging to the flat-slab floors and/or ceilings without performing the aforementioned stages in order to preserve computational efficiency. The applicability of the proposed method is investigated in two scenarios, namely, a laboratory with 30 million points and an actual construction site with over 150 million points. The results obtained by the two experiments validate the suitability of the proposed method for robust segmentation of planar and linear features in contaminated datasets, such as those collected from construction sites.

  18. Total System Performance Assessment-License Application Design Selection (LADS) Phase 1 Analysis of Surface Modification Consisting of Addition of Alluvium (Feature 23a)

    SciTech Connect

    N. Erb

    1999-06-11

    The objective of this report is to document the analysis that was conducted to evaluate the effect of a potential change to the TSPA-VA base case design that could improve long-term repository performance. The design feature evaluated in this report is a modification of the topographic surface of Yucca Mountain. The modification consists of covering the land surface immediately above the repository foot-print with a thick layer of unconsolidated material utilizing rip-rap and plants to mitigate erosion. This surface modification is designated as Feature 23a or simply abbreviated as F23a. The fundamental aim of F23a is to reduce the net infiltration into the unsaturated zone by enhancing the potential for evapotranspiratiration at the surface; such a change would, in turn, reduce the seepage flux and the rate of radionuclide releases from the repository. Field and modeling studies of water movement in the unsaturated zone have indicated that shallow infiltration at the surface is almost negligible in locations where the bedrock is covered by a sufficiently thick soil layer. In addition to providing storage for meteoric water, a thick soil layer would slow the downward movement of soil moisture to such an extent that evaporation and transpiration could easily transfer most of the soil-water back to the atmosphere. Generic requirements for the effectiveness of this design feature are two-fold. First, the soil layer above the repository foot-print must be thick enough to provide sufficient storage of meteoric water (from episodic precipitation events) and accommodate plant roots. Second, the added soil layer must be engineered so as to mitigate thinning by erosional processes and have sufficient thickness to accommodate the roots of common desert plants. Under these two conditions, it is reasonable to expect that modification would be effective for a significant time period and the net infiltration and deep percolation flux would be reduced by orders of magnitude lower

  19. Ancestral multipartite units in light-responsive plant promoters have structural features correlating with specific phototransduction pathways.

    PubMed Central

    Argüello-Astorga, G R; Herrera-Estrella, L R

    1996-01-01

    Regulation of plant gene transcription by light is mediated by multipartite cis-regulatory units. Previous attempts to identify structural features that are common to all light-responsive elements (LREs) have been unsuccessful. To address the question of what is needed to confer photoresponsiveness to a promoter, the upstream sequences from more than 110 light-regulated plant genes were analyzed by a new, phylogenetic-structural method. As a result, 30 distinct conserved DNA module arrays (CMAs) associated with light-responsive promoter regions were identified. Several of these CMAs have remained invariant throughout the evolutionary radiation of angiosperms and are conserved between homologous genes as well as between members of different gene families. The identified CMAs share a gene superfamily-specific core that correlates with the particular phytochrome-dependent transduction pathway that controls their expression, i.e. ACCTA(A/C)C(A/C) for the cGMP-dependent phenylpropanoid metabolism-associated genes, and GATA(A/T)GR for the Ca2+/calmodulin-dependent photosynthesis-associated nuclear genes. In addition to suggesting a general model for the functional and structural organization of LREs, the data obtained in this study indicate that angiosperm LREs probably evolved from complex cis-acting elements involved in regulatory processes other than photoregulation in gymnosperms. PMID:8938415

  20. Catalogue of the morphological features in the Spitzer Survey of Stellar Structure in Galaxies (S4G)

    NASA Astrophysics Data System (ADS)

    Herrera-Endoqui, M.; Díaz-García, S.; Laurikainen, E.; Salo, H.

    2015-10-01

    Context. A catalogue of the features for the complete Spitzer Survey of Stellar Structure in Galaxies (S4G), including 2352 nearby galaxies, is presented. The measurements are made using 3.6 μm images, largely tracing the old stellar population; at this wavelength the effects of dust are also minimal. The measured features are the sizes, ellipticities, and orientations of bars, rings, ringlenses, and lenses. Measured in a similar manner are also barlenses (lens-like structures embedded in the bars), which are not lenses in the usual sense, being rather the more face-on counterparts of the boxy/peanut structures in the edge-on view. In addition, pitch angles of spiral arm segments are measured for those galaxies where they can be reliably traced. More than one pitch angle may appear for a single galaxy. All measurements are made in a human-supervised manner so that attention is paid to each galaxy. Aims: We create a catalogue of morphological features in the complete S4G. Methods: We used isophotal analysis, unsharp masking, and fitting ellipses to measured structures. Results: We find that the sizes of the inner rings and lenses normalized to barlength correlate with the galaxy mass: the normalized sizes increase toward the less massive galaxies; it has been suggested that this is related to the larger dark matter content in the bar region in these systems. Bars in the low mass galaxies are also less concentrated, likely to be connected to the mass cut-off in the appearance of the nuclear rings and lenses. We also show observational evidence that barlenses indeed form part of the bar, and that a large fraction of the inner lenses in the non-barred galaxies could be former barlenses in which the thin outer bar component has dissolved. Full Tables 2 and 3 are only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (ftp://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/582/A86

  1. Novel Features of Eukaryotic Photosystem II Revealed by Its Crystal Structure Analysis from a Red Alga.

    PubMed

    Ago, Hideo; Adachi, Hideyuki; Umena, Yasufumi; Tashiro, Takayoshi; Kawakami, Keisuke; Kamiya, Nobuo; Tian, Lirong; Han, Guangye; Kuang, Tingyun; Liu, Zheyi; Wang, Fangjun; Zou, Hanfa; Enami, Isao; Miyano, Masashi; Shen, Jian-Ren

    2016-03-11

    Photosystem II (PSII) catalyzes light-induced water splitting, leading to the evolution of molecular oxygen indispensible for life on the earth. The crystal structure of PSII from cyanobacteria has been solved at an atomic level, but the structure of eukaryotic PSII has not been analyzed. Because eukaryotic PSII possesses additional subunits not found in cyanobacterial PSII, it is important to solve the structure of eukaryotic PSII to elucidate their detailed functions, as well as evolutionary relationships. Here we report the structure of PSII from a red alga Cyanidium caldarium at 2.76 Å resolution, which revealed the structure and interaction sites of PsbQ', a unique, fourth extrinsic protein required for stabilizing the oxygen-evolving complex in the lumenal surface of PSII. The PsbQ' subunit was found to be located underneath CP43 in the vicinity of PsbV, and its structure is characterized by a bundle of four up-down helices arranged in a similar way to those of cyanobacterial and higher plant PsbQ, although helices I and II of PsbQ' were kinked relative to its higher plant counterpart because of its interactions with CP43. Furthermore, two novel transmembrane helices were found in the red algal PSII that are not present in cyanobacterial PSII; one of these helices may correspond to PsbW found only in eukaryotic PSII. The present results represent the first crystal structure of PSII from eukaryotic oxygenic organisms, which were discussed in comparison with the structure of cyanobacterial PSII.

  2. Structural and dynamic features of cold-shock proteins of Listeria monocytogenes, a psychrophilic bacterium.

    PubMed

    Lee, Juho; Jeong, Ki-Woong; Jin, Bonghwan; Ryu, Kyoung-Seok; Kim, Eun-Hee; Ahn, Joong-Hoon; Kim, Yangmee

    2013-04-01

    Cold-shock proteins (Csps), proteins expressed when the ambient temperature drops below the growth-supporting temperature, bind to single-stranded nucleic acids and act as RNA chaperones to regulate translation. Listeria monocytogenes is a psychrophilic food-borne pathogen that is problematic for the food industry. Structures of Csps from psychrophilic bacteria have not yet been studied. Despite dramatic differences in the thermostability of Csps of various thermophilic microorganisms, these proteins share a high degree of primary sequence homology and a high degree of three-dimensional structural similarity. Here, we investigated the structural and dynamic features as well as the thermostability of L. monocytogenes CspA (Lm-CspA). Lm-CspA has a five-stranded β-barrel structure with hydrophobic core packing and two salt bridges. When heptathymidine (dT(7)) binds, values for the heteronuclear nuclear Overhauser effect and order parameters of residues in surface loop regions near nucleic acid binding sites increase dramatically. Moreover, Carr-Purcell-Meiboom-Gill experiments showed that slow motions observed for the nucleic acid binding residues K7, W8, F15, F27, and R56 disappeared in Lm-CspA-dT(7). Lm-CspA is less thermostable than mesophilic and thermophilic Csps, with a lower melting temperature (40 °C). The structural flexibility that accompanies longer surface loops and less hydrophobic core packing and a number of salt bridges and unfavorable electrostatic repulsion are likely key factors in the low thermostability of Lm-CspA. This implies that the large conformational flexibility of psychrophilic Lm-CspA, which more easily accommodates nucleic acids at low temperature, is required for RNA chaperone function under cold-shock conditions and for the cold adaptation of L. monocytogenes. PMID:23506337

  3. Structural and mechanical features of the order-disorder transition in experimental hard-sphere packings

    NASA Astrophysics Data System (ADS)

    Hanifpour, M.; Francois, N.; Robins, V.; Kingston, A.; Vaez Allaei, S. M.; Saadatfar, M.

    2015-06-01

    Here we present an experimental and numerical investigation on the grain-scale geometrical and mechanical properties of partially crystallized structures made of macroscopic frictional grains. Crystallization is inevitable in arrangements of monosized hard spheres with packing densities exceeding Bernal's limiting density ϕBernal≈0.64 . We study packings of monosized hard spheres whose density spans over a wide range (0.59 <ϕ <0.72 ) . These experiments harness x-ray computed tomography, three-dimensional image analysis, and numerical simulations to access precisely the geometry and the 3D structure of internal forces within the sphere packings. We show that clear geometrical transitions coincide with modifications of the mechanical backbone of the packing both at the grain and global scale. Notably, two transitions are identified at ϕBernal≈0.64 and ϕc≈0.68 . These results provide insights on how geometrical and mechanical features at the grain scale conspire to yield partially crystallized structures that are mechanically stable.

  4. PredictProtein—an open resource for online prediction of protein structural and functional features

    PubMed Central

    Yachdav, Guy; Kloppmann, Edda; Kajan, Laszlo; Hecht, Maximilian; Goldberg, Tatyana; Hamp, Tobias; Hönigschmid, Peter; Schafferhans, Andrea; Roos, Manfred; Bernhofer, Michael; Richter, Lothar; Ashkenazy, Haim; Punta, Marco; Schlessinger, Avner; Bromberg, Yana; Schneider, Reinhard; Vriend, Gerrit; Sander, Chris; Ben-Tal, Nir; Rost, Burkhard

    2014-01-01

    PredictProtein is a meta-service for sequence analysis that has been predicting structural and functional features of proteins since 1992. Queried with a protein sequence it returns: multiple sequence alignments, predicted aspects of structure (secondary structure, solvent accessibility, transmembrane helices (TMSEG) and strands, coiled-coil regions, disulfide bonds and disordered regions) and function. The service incorporates analysis methods for the identification of functional regions (ConSurf), homology-based inference of Gene Ontology terms (metastudent), comprehensive subcellular localization prediction (LocTree3), protein–protein binding sites (ISIS2), protein–polynucleotide binding sites (SomeNA) and predictions of the effect of point mutations (non-synonymous SNPs) on protein function (SNAP2). Our goal has always been to develop a system optimized to meet the demands of experimentalists not highly experienced in bioinformatics. To this end, the PredictProtein results are presented as both text and a series of intuitive, interactive and visually appealing figures. The web server and sources are available at http://ppopen.rostlab.org. PMID:24799431

  5. Structural features of phosphate accumulations in the Gantour basin - Morocco : Application of GIS

    NASA Astrophysics Data System (ADS)

    Mohamed, Laadraoui; El Hassane, Boumaggard; Essaid, Jourani

    2010-05-01

    The Moroccan Atlantic margin raises a lot of interest because of its potential resources in phosphates. It also holds in its Mesetien part one of the largest phosphatic deposit in the world. The authors present the results of their researches on structural environments of the phosphatic sedimentary sequences in the Gantour deposit in western Morocco. These investigations are mainly based on field data, data recorded from work done by the OCP (Office Chérifien des Phosphates) group, the interpretation of industrial seismic profiles and the application of GIS. Our aim are devoted to the apprehension of the geometry and the cinematic of these basins which are contemporaneous to the Central Atlantic Rifting, as well as the determination of the list of factors liable to the genesis of these phosphatic basins. Other data of field observations (cartography, study of structural features,...) permit to identify the general structure of the prospect. Sedimentation of phosphated deposits is strained by the presence of two wrench faulting systems oriented N20¬40E, N80¬120E and N140¬160E.

  6. Sublimation epitaxy of AlN on SiC: growth morphology and structural features

    NASA Astrophysics Data System (ADS)

    Kakanakova-Georgieva, A.; Persson, P. O. Å.; Yakimova, R.; Hultman, L.; Janzén, E.

    2004-12-01

    In order to study the development of individual AlN crystallites, sublimation epitaxy of AlN was performed on 4H-SiC, off-axis substrates in an inductively heated setup. Growth process variables like temperature, extrinsic nitrogen pressure and time were changed in an attempt to favor the lateral growth of individual AlN crystallites and thus open possibilities to prepare continuous patterns. Scanning and transmission electron microscopy and cathodoluminescence were used to obtain plan-view and cross-sectional images of the grown patterns and to study their morphology and structural features. The growth at 1900 °C/200 mbar results in AlN pattern consisting of individual single wurzite AlN crystallites with plate-like shape aligned along [ 1 1¯ 0 0] direction. The only defects these AlN crystallites contain are threading dislocations, some of which are terminated by forming half-loops. Because of the uniform distribution of the crystallites and their high structural perfection, this AlN pattern could represent interest as a template for bulk AlN growth. Alternative growth approaches to AlN crystallite formation are possible resulting in variation of the final AlN pattern structure. From a viewpoint of obtaining continuous patterns, the more favorable growth conditions involve applying of increased extrinsic gas pressure, 700 mbar in our case.

  7. Structural and mechanical features of the order-disorder transition in experimental hard-sphere packings.

    PubMed

    Hanifpour, M; Francois, N; Robins, V; Kingston, A; Allaei, S M Vaez; Saadatfar, M

    2015-06-01

    Here we present an experimental and numerical investigation on the grain-scale geometrical and mechanical properties of partially crystallized structures made of macroscopic frictional grains. Crystallization is inevitable in arrangements of monosized hard spheres with packing densities exceeding Bernal's limiting density ϕ(Bernal)≈0.64. We study packings of monosized hard spheres whose density spans over a wide range (0.59<ϕ<0.72). These experiments harness x-ray computed tomography, three-dimensional image analysis, and numerical simulations to access precisely the geometry and the 3D structure of internal forces within the sphere packings. We show that clear geometrical transitions coincide with modifications of the mechanical backbone of the packing both at the grain and global scale. Notably, two transitions are identified at ϕ(Bernal)≈0.64 and ϕ(c)≈0.68. These results provide insights on how geometrical and mechanical features at the grain scale conspire to yield partially crystallized structures that are mechanically stable. PMID:26172700

  8. Automatic registration of Iphone images to LASER point clouds of the urban structures using shape features

    NASA Astrophysics Data System (ADS)

    Sirmacek, B.; Lindenbergh, R. C.; Menenti, M.

    2013-10-01

    Fusion of 3D airborne laser (LIDAR) data and terrestrial optical imagery can be applied in 3D urban modeling and model up-dating. The most challenging aspect of the fusion procedure is registering the terrestrial optical images on the LIDAR point clouds. In this article, we propose an approach for registering these two different data from different sensor sources. As we use iPhone camera images which are taken in front of the interested urban structure by the application user and the high resolution LIDAR point clouds of the acquired by an airborne laser sensor. After finding the photo capturing position and orientation from the iPhone photograph metafile, we automatically select the area of interest in the point cloud and transform it into a range image which has only grayscale intensity levels according to the distance from the image acquisition position. We benefit from local features for registering the iPhone image to the generated range image. In this article, we have applied the registration process based on local feature extraction and graph matching. Finally, the registration result is used for facade texture mapping on the 3D building surface mesh which is generated from the LIDAR point cloud. Our experimental results indicate possible usage of the proposed algorithm framework for 3D urban map updating and enhancing purposes.

  9. Probabilistic uncertainty quantification of wavelet-transform-based structural health monitoring features

    NASA Astrophysics Data System (ADS)

    Sarrafi, Aral; Mao, Zhu

    2016-04-01

    In the application of Structural Health Monitoring (SHM), processing the online-acquired data plays a very important role, among which wavelet transform is an outstanding tool and compared to Fourier transform, it handles the nonstationary behaviors in the time series in an adaptive fashion. When dealing with time-variant data, there are uncertainties from numerous resources inherent to the feature estimation, such as measurement noise, operational and environmental variability, hardware limitation, etc. The corruption from uncertainty will make the data interpretation ambiguous and thereby dramatically degrades the decision quality with regard to the occurrence, location, severity, and extent of damages. This paper derives a probabilistic model to quantify analytically the uncertainty of wavelet transform feature as a random variable, and variance is derived analytically in this work. Considering central limit theorem, Gaussian probability density function characterizes the distribution and this has been validated via Monte Carlo testing. By fully characterizing the uncertainty, the damage detection implementations may be facilitated with a quantified false alarm rate and miss catch rate.

  10. Importance of ion bombardment during coverage of Au nanoparticles on their structural features and optical response

    SciTech Connect

    Resta, V.; Peláez, R. J.; Afonso, C. N.

    2014-03-28

    This work studies the changes in the optical response and morphological features of 6 ± 1 nm diameter Au nanoparticles (NPs) when covered by a layer of a-Al{sub 2}O{sub 3} by pulsed laser deposition (PLD). The laser fluence used for ablating the Al{sub 2}O{sub 3} target is varied in order to modify the kinetic energy (KE) of the species bombarding the NPs during their coverage. When the ion KE < 200 eV, the structural features and optical properties of the NPs are close to those of uncovered ones. Otherwise, a shift to the blue and a strong damping of the surface plasmon resonance is observed as fluence is increased. There are two processes responsible for these changes, both related to aluminum ions arriving to the substrate during the coverage process, i.e., sputtering of the metal and implantation of aluminum species in the metal. Both processes have been simulated using standard models for ion bombardment, the calculated effective implanted depths allow explaining the observed changes in the optical response, and the use of a size-dependent sputtering coefficient for the Au NPs predicts the experimental sputtering fractions. In spite of the work is based on PLD, the concepts investigated and conclusions can straightforwardly be extrapolated to other physical vapor deposition techniques or processes involving ion bombardment of metal NPs by ions having KE > 200 eV.

  11. Changes in bacterial diversity and community structure following pesticides addition to soil estimated by cultivation technique.

    PubMed

    Cycoń, Mariusz; Piotrowska-Seget, Zofia

    2009-07-01

    An experiment was conducted under laboratory conditions to investigate the effect of increasing concentrations of fenitrothion (2, 10 and 200 mg a.i./kg soil), diuron (1.5, 7.5 and 150 mg a.i./kg soil) and thiram (3.5, 17.5 and 350 mg a.i./kg soil) on soil respiration, bacterial counts and changes in culturable fraction of soil bacteria. To ascertain these changes, the community structure, bacterial biodiversity and process of colony formation, based on the r/K strategy concept, EP- and CD-indices and the FOR model, respectively, were determined. The results showed that the measured parameters were generally unaffected by the lowest dosages of pesticides, corresponding to the recommended field rates. The highest dosages of fenitrothion and thiram suppressed the peak SIR by 15-70% and 20-80%, respectively, while diuron increased respiration rate by 17-25% during the 28-day experiment. Also, the total numbers of bacteria increased in pesticide-treated soils. However, the reverse effect on day 1 and, in addition, in case of the highest dosages of insecticide on days 14 and 28, was observed. Analysis of the community structure revealed that in all soil treatments bacterial communities were generally dominated by K-strategists. Moreover, differences in the distribution of individual bacteria classes and the gradual domination of bacteria populations belonging to r-strategists during the experiment, as compared to control, was observed. However, on day 1, at the highest pesticide dosages, fast growing bacteria constituted only 1-10% of the total colonies number during 48 h of plate incubation, whereas in remaining samples they reached from 20 to 40% of total cfu. This effect, in case of fenitrothion, lasted till the end of the experiment. At the highest dosages of fenitrothion, diuron and at all dosages of thiram the decrease of biodiversity, as indicated by EP- and CD-indices on day 1, was found. At the next sampling time, no significant retarding or stimulating effect

  12. Additive Manufacturing of a Photo-Cross-Linkable Polymer via Direct Melt Electrospinning Writing for Producing High Strength Structures.

    PubMed

    Chen, Fei; Hochleitner, Gernot; Woodfield, Tim; Groll, Juergen; Dalton, Paul D; Amsden, Brian G

    2016-01-11

    Melt electrospinning writing (MEW) is an emerging additive manufacturing technique that enables the design and fabrication of micrometer-thin fibrous scaffolds made of biocompatible and biodegradable polymers. By using a computer-aided deposition process, a unique control over pore size and interconnectivity of the resulting scaffolds is achieved, features highly interesting for tissue engineering applications. However, MEW has been mainly used to process low melting point thermoplastics such as poly(ε-caprolactone). Since this polymer exhibits creep and a reduction in modulus upon hydration, we manufactured scaffolds of poly(L-lactide-co-ε-caprolactone-co-acryloyl carbonate) (poly(LLA-ε-CL-AC)), a photo-cross-linkable and biodegradable polymer, for the first time. We show that the stiffness of the scaffolds increases significantly (up to ∼10-fold) after cross-linking by UV irradiation at room temperature, compared with un-cross-linked microfiber scaffolds. The preservation of stiffness and high average fiber modulus (370 ± 166 MPa) within the cross-linked hydrated scaffolds upon repetitive loading (10% strain at 1 Hz up to 200,000 cycles) suggests that the prepared scaffolds may be of potential interest for soft connective tissue engineering applications. Moreover, the approach can be readily adapted through manipulation of polymer properties and scaffold geometry to prepare structures with mechanical properties suitable for other tissue engineering applications.

  13. Additive Manufacturing of a Photo-Cross-Linkable Polymer via Direct Melt Electrospinning Writing for Producing High Strength Structures.

    PubMed

    Chen, Fei; Hochleitner, Gernot; Woodfield, Tim; Groll, Juergen; Dalton, Paul D; Amsden, Brian G

    2016-01-11

    Melt electrospinning writing (MEW) is an emerging additive manufacturing technique that enables the design and fabrication of micrometer-thin fibrous scaffolds made of biocompatible and biodegradable polymers. By using a computer-aided deposition process, a unique control over pore size and interconnectivity of the resulting scaffolds is achieved, features highly interesting for tissue engineering applications. However, MEW has been mainly used to process low melting point thermoplastics such as poly(ε-caprolactone). Since this polymer exhibits creep and a reduction in modulus upon hydration, we manufactured scaffolds of poly(L-lactide-co-ε-caprolactone-co-acryloyl carbonate) (poly(LLA-ε-CL-AC)), a photo-cross-linkable and biodegradable polymer, for the first time. We show that the stiffness of the scaffolds increases significantly (up to ∼10-fold) after cross-linking by UV irradiation at room temperature, compared with un-cross-linked microfiber scaffolds. The preservation of stiffness and high average fiber modulus (370 ± 166 MPa) within the cross-linked hydrated scaffolds upon repetitive loading (10% strain at 1 Hz up to 200,000 cycles) suggests that the prepared scaffolds may be of potential interest for soft connective tissue engineering applications. Moreover, the approach can be readily adapted through manipulation of polymer properties and scaffold geometry to prepare structures with mechanical properties suitable for other tissue engineering applications. PMID:26620885

  14. Raman imaging to study structural and chemical features of the dentin enamel junction

    NASA Astrophysics Data System (ADS)

    Alebrahim, M. Anwar; Krafft, C.; Popp, J.

    2015-10-01

    The structure and chemical features of the human dentin enamel junction (DEJ) were characterized using Raman spectroscopic imaging. Slices were prepared from 10 German, and 10 Turkish teeth. Raman images were collected at 785 nm excitation and the average Raman spectra were calculated for analysis. Univariate and multivariate spectral analysis were applied for investigation. Raman images were obtained based on the intensity ratios of CH at 1450 cm-1 (matrix) to phosphate at 960 cm-1 (mineral), and carbonate to phosphate (1070/960) ratios. Different algorithms (HCA, K-means cluster and VCA) also used to study the DEJ. The obtained results showed that the width of DEJ is about 5 pm related to univariate method while it varies from 6 to 12 μm based on multivariate spectral technique. Both spectral analyses showed increasing in carbonate content inside the DEJ compared to the dentin, and the amide I (collagen) peak in dentin spectra is higher than DEJ spectra peak.

  15. Polymyxins and quinazolines are LSD1/KDM1A inhibitors with unusual structural features.

    PubMed

    Speranzini, Valentina; Rotili, Dante; Ciossani, Giuseppe; Pilotto, Simona; Marrocco, Biagina; Forgione, Mariantonietta; Lucidi, Alessia; Forneris, Federico; Mehdipour, Parinaz; Velankar, Sameer; Mai, Antonello; Mattevi, Andrea

    2016-09-01

    Because of its involvement in the progression of several malignant tumors, the histone lysine-specific demethylase 1 (LSD1) has become a prominent drug target in modern medicinal chemistry research. We report on the discovery of two classes of noncovalent inhibitors displaying unique structural features. The antibiotics polymyxins bind at the entrance of the substrate cleft, where their highly charged cyclic moiety interacts with a cluster of positively charged amino acids. The same site is occupied by quinazoline-based compounds, which were found to inhibit the enzyme through a most peculiar mode because they form a pile of five to seven molecules that obstruct access to the active center. These data significantly indicate unpredictable strategies for the development of epigenetic inhibitors. PMID:27626075

  16. [Topographic features of lingual nerve and its relationship with other anatomical structures in maxillolingual groove].

    PubMed

    Dyidyikin, S S; Syomkin, V A; Kuzin, A V; Sogacheva, V V

    2016-01-01

    By surgical interventions in maxillolingual groove area one should consider anatomical variations and topography of vessels, glands ducts and lingual nerve to prevent their injury. At the Department of Operative Surgery and Topographic Anatomy of the First Moscow State Medical University named after I.M. Sechenov we carried out anatomical study on cadavers (men and women, n=30).The study revealed topographical features of the lingual nerve and its relationship to other anatomical structures in the maxillolingual groove. It was found out that at the level of the second molar (96%) lingual nerve "crosses" duct of submandibular salivary gland, at the level of the third molar lingual nerve is located under the duct and lateral to it, closer to the inner surface of the body of the mandible. At the level of the first molar lingual nerve is located above and medial to Wharton duct and passes along sublingual-lingual muscles (m.hyoglossus).

  17. Complex structural rearrangement features suggesting chromoanagenesis mechanism in a case of 1p36 deletion syndrome.

    PubMed

    Zanardo, Évelin Aline; Piazzon, Flavia Balbo; Dutra, Roberta Lelis; Dias, Alexandre Torchio; Montenegro, Marília Moreira; Novo-Filho, Gil Monteiro; Costa, Thaís Virgínia Moura Machado; Nascimento, Amom Mendes; Kim, Chong Ae; Kulikowski, Leslie Domenici

    2014-12-01

    Genome rearrangements are caused by the erroneous repair of DNA double-strand breaks, leading to several alterations that result in loss or gain of the structural genomic of a dosage-sensitive genes. However, the mechanisms that promote the complexity of rearrangements of congenital or developmental defects in human disease are unclear. The investigation of complex genomic abnormalities could help to elucidate the mechanisms and causes for the formation and facilitate the understanding of congenital or developmental defects in human disease. We here report one case of a patient with atypical clinical features of the 1p36 syndrome and the use of cytogenomic techniques to characterize the genomic alterations. Analysis by multiplex ligation-dependent probe amplification and array revealed a complex rearrangement in the 1p36.3 region with deletions and duplication interspaced by normal sequences. We also suggest that chromoanagenesis could be a possible mechanism involved in the repair and stabilization of this rearrangement.

  18. Polymyxins and quinazolines are LSD1/KDM1A inhibitors with unusual structural features

    PubMed Central

    Speranzini, Valentina; Rotili, Dante; Ciossani, Giuseppe; Pilotto, Simona; Marrocco, Biagina; Forgione, Mariantonietta; Lucidi, Alessia; Forneris, Federico; Mehdipour, Parinaz; Velankar, Sameer; Mai, Antonello; Mattevi, Andrea

    2016-01-01

    Because of its involvement in the progression of several malignant tumors, the histone lysine-specific demethylase 1 (LSD1) has become a prominent drug target in modern medicinal chemistry research. We report on the discovery of two classes of noncovalent inhibitors displaying unique structural features. The antibiotics polymyxins bind at the entrance of the substrate cleft, where their highly charged cyclic moiety interacts with a cluster of positively charged amino acids. The same site is occupied by quinazoline-based compounds, which were found to inhibit the enzyme through a most peculiar mode because they form a pile of five to seven molecules that obstruct access to the active center. These data significantly indicate unpredictable strategies for the development of epigenetic inhibitors. PMID:27626075

  19. Structural Features and Biological Properties of Ellagitannins in Some Plant Families of the Order Myrtales

    PubMed Central

    Yoshida, Takashi; Amakura, Yoshiaki; Yoshimura, Morio

    2010-01-01

    Plant tannins, including hydrolysable and condensed varieties, are well known antioxidants in medicinal plants, foods, and edible fruits. Their diverse biological properties and potential for disease prevention have been demonstrated by various in vitro and in vivo assays. A number of ellagitannins, the largest group of hydrolysable tannins, have been isolated from dicotyledoneous angiosperms and characterized. This diverse class of tannins is sub-grouped into simple ellagitannins, C-glycosidic ellagitannins, complex tannins (condensates of C-glycosidic tannins with flavan-3-ol), and oligomers up to pentamers. This review outlines and describes the chemotaxonomic significance of structural features in various types of ellagitannins found in plants belonging to the Myrtaceae, Onagraceae, and Melastomataceae families, which are all included in the order Myrtales. Any biological activities that have been reported, including antitumor and antibacterial effects as well as enzyme inhibition, are also reviewed. PMID:20162003

  20. Two-prism crystal structures for far-field imaging of subwavelength features at terahertz frequencies

    NASA Astrophysics Data System (ADS)

    Barros, D. A.; Dumelow, T.

    2016-08-01

    We investigate how a system of two single crystals can be used for far field imaging of subwavelength features. We make use of the phonon response to induce canalization of narrow collimated beams in crystals with suitably high anisotropy at the appropriate transverse optical phonon frequency. By cutting the crystals into suitably designed prisms, we show that an magnified image can be obtained and projected into the far field by a two-prism structure, noting that a single prism does not give a faithful reproduction of the object and will usually result in total internal reflection of most of the radiation. We show simulations using triglycine sulphate, which is both highly anisotropic and has very low absorption, at low temperature.

  1. Polymyxins and quinazolines are LSD1/KDM1A inhibitors with unusual structural features

    PubMed Central

    Speranzini, Valentina; Rotili, Dante; Ciossani, Giuseppe; Pilotto, Simona; Marrocco, Biagina; Forgione, Mariantonietta; Lucidi, Alessia; Forneris, Federico; Mehdipour, Parinaz; Velankar, Sameer; Mai, Antonello; Mattevi, Andrea

    2016-01-01

    Because of its involvement in the progression of several malignant tumors, the histone lysine-specific demethylase 1 (LSD1) has become a prominent drug target in modern medicinal chemistry research. We report on the discovery of two classes of noncovalent inhibitors displaying unique structural features. The antibiotics polymyxins bind at the entrance of the substrate cleft, where their highly charged cyclic moiety interacts with a cluster of positively charged amino acids. The same site is occupied by quinazoline-based compounds, which were found to inhibit the enzyme through a most peculiar mode because they form a pile of five to seven molecules that obstruct access to the active center. These data significantly indicate unpredictable strategies for the development of epigenetic inhibitors.

  2. Critical review of the safety assessment of nano-structured silica additives in food.

    PubMed

    Winkler, Hans Christian; Suter, Mark; Naegeli, Hanspeter

    2016-01-01

    The development of nano-materials is viewed as one of the most important technological advances of the 21st century and new applications of nano-sized particles in the production, processing, packaging or storage of food are expected to emerge soon. This trend of growing commercialization of engineered nano-particles as part of modern diet will substantially increase oral exposure. Contrary to the proven benefits of nano-materials, however, possible adverse health effects have generally received less attention. This problem is very well illustrated by nano-structured synthetic amorphous silica (SAS), which is a common food additive since several decades although the relevant risk assessment has never been satisfactorily completed. A no observed adverse effect level of 2500 mg SAS particles/kg body weight per day was derived from the only available long-term administration study in rodents. However, extrapolation to a safe daily intake for humans is problematic due to limitations of this chronic animal study and knowledge gaps as to possible local intestinal effects of SAS particles, primarily on the gut-associated lymphoid system. This uncertainty is aggravated by digestion experiments indicating that dietary SAS particles preserve their nano-sized structure when reaching the intestinal lumen. An important aspect is whether food-borne particles like SAS alter the function of dendritic cells that, embedded in the intestinal mucosa, act as first-line sentinels of foreign materials. We conclude that nano-particles do not represent a completely new threat and that most potential risks can be assessed following procedures established for conventional chemical hazards. However, specific properties of food-borne nano-particles should be further examined and, for that purpose, in vitro tests with decision-making cells of the immune system are needed to complement existing in vivo studies. PMID:27287345

  3. Critical review of the safety assessment of nano-structured silica additives in food.

    PubMed

    Winkler, Hans Christian; Suter, Mark; Naegeli, Hanspeter

    2016-06-10

    The development of nano-materials is viewed as one of the most important technological advances of the 21st century and new applications of nano-sized particles in the production, processing, packaging or storage of food are expected to emerge soon. This trend of growing commercialization of engineered nano-particles as part of modern diet will substantially increase oral exposure. Contrary to the proven benefits of nano-materials, however, possible adverse health effects have generally received less attention. This problem is very well illustrated by nano-structured synthetic amorphous silica (SAS), which is a common food additive since several decades although the relevant risk assessment has never been satisfactorily completed. A no observed adverse effect level of 2500 mg SAS particles/kg body weight per day was derived from the only available long-term administration study in rodents. However, extrapolation to a safe daily intake for humans is problematic due to limitations of this chronic animal study and knowledge gaps as to possible local intestinal effects of SAS particles, primarily on the gut-associated lymphoid system. This uncertainty is aggravated by digestion experiments indicating that dietary SAS particles preserve their nano-sized structure when reaching the intestinal lumen. An important aspect is whether food-borne particles like SAS alter the function of dendritic cells that, embedded in the intestinal mucosa, act as first-line sentinels of foreign materials. We conclude that nano-particles do not represent a completely new threat and that most potential risks can be assessed following procedures established for conventional chemical hazards. However, specific properties of food-borne nano-particles should be further examined and, for that purpose, in vitro tests with decision-making cells of the immune system are needed to complement existing in vivo studies.

  4. Structure of the Spt16 Middle Domain Reveals Functional Features of the Histone Chaperone FACT*

    PubMed Central

    Kemble, David J.; Whitby, Frank G.; Robinson, Howard; McCullough, Laura L.; Formosa, Tim; Hill, Christopher P.

    2013-01-01

    The histone chaperone FACT is an essential and abundant heterodimer found in all eukaryotes. Here we report a crystal structure of the middle domain of the large subunit of FACT (Spt16-M) to reveal a double pleckstrin homology architecture. This structure was found previously in the Pob3-M domain of the small subunit of FACT and in the related histone chaperone Rtt106, although Spt16-M is distinguished from these structures by the presence of an extended α-helix and a C-terminal addition. Consistent with our finding that the double pleckstrin homology structure is common to these three histone chaperones and reports that Pob3 and Rtt106 double pleckstrin homology domains bind histones H3-H4, we also find that Spt16-M binds H3-H4 with low micromolar affinity. Our structure provides a framework for interpreting a large body of genetic data regarding the physiological functions of FACT, including the identification of potential interaction surfaces for binding histones or other proteins. PMID:23417676

  5. Structural features of Nigeria's coastal margin: an assessment based on age data from wells

    NASA Astrophysics Data System (ADS)

    Onuoha, K. Mosto

    1999-10-01

    Geological age data from 127 wells drilled for petroleum exploration and production purposes in both the onshore and offshore sections of the Nigerian coastal margin have been examined and correlated from well to well across the margin. By examining the variations in depth to selected key geological marker horizons, the positions of faults and fractures have been inferred between wells and along designated cross-sections. These faults extend across the margin from land to sea, and most of them trend northeast-southwest and north-south. Graben and horst structures dominate the western part of the Nigerian margin. The most prominent of these features on the western part of the margin is the Okitipupa structure, a basement ridge that separates the sediments of the Tertiary Niger Delta to the east from those of the Cretaceous Dahomey Embayment to the west. The Niger Delta basin and the major faults bounding it are the other important tectonic features on the Nigerian coastal margin. It appears that major fractures and transcurrent faults influenced sedimentation rates in different parts of the margin throughout the Tertiary period. A landward prolongation of two main oceanic fracture zones (Chain and Charcot) appears to merge well with some of the inferred faults, especially in the case of the Chain Fracture Zone. It is a well known fact that seismic activities are associated with oceanic fracture zones. The delineation of the extensions of these faults and fractures in the Nigerian continental interior can be regarded as an important basic step towards the assessment of the seismicity of the country's coastal margin. The next logical step would be to determine, through the deployment of a seismograph network, the level of activities associated with these faults.

  6. Tectonic activity and structural features of active intracontinental normal faults in the Weihe Graben, central China

    NASA Astrophysics Data System (ADS)

    Rao, Gang; Lin, Aiming; Yan, Bing; Jia, Dong; Wu, Xiaojun

    2014-12-01

    This study examines the tectonic activity and structural features of active normal faults in the Weihe Graben, central China. The Weihe Graben is an area with a high level of historic seismicity, and it is one of the intracontinental systems that developed since Tertiary in the extensional environment around the Ordos Block. Analysis of high-resolution remote-sensing imagery data, field observations, and radiocarbon dating results reveal the following: i) active normal faults are mainly developed within a zone < 500 m wide along the southern border of the eastern part of the Weihe Graben; ii) the active faults that have been identified are characterized by stepwise fault scarps dipping into the graben at angles of 40°-71°; iii) there are numerous discontinuous individual fault traces, ranging in length from a few tens of meters to 450 m (generally < 200 m); iv) fault zone structures, topographic features, and fault striations on the main fault planes indicate almost pure normal-slip; and v) late Pleistocene-Holocene terrace risers, loess, and alluvial deposits have been vertically offset by up to ~ 80 m, with a non-uniform dip-slip rate (throw-rates) ranging from ~ 2.1 to 5.7 mm/yr, mostly 2-3 mm/yr. Our results reveal that active normal faults have been developing in the Weihe Graben under an ongoing extensional environment, probably associated with the pre-existing graben and spreading of the continental crust, and this is in contrast with the Ordos Block and neighboring orogenic regions. These results provide new insights into the nature of extensional tectonic deformation in intracontinental graben systems.

  7. Atomic Structure of GRK5 Reveals Distinct Structural Features Novel for G Protein-coupled Receptor Kinases*♦

    PubMed Central

    Komolov, Konstantin E.; Bhardwaj, Anshul; Benovic, Jeffrey L.

    2015-01-01

    G protein-coupled receptor kinases (GRKs) are members of the protein kinase A, G, and C families (AGC) and play a central role in mediating G protein-coupled receptor phosphorylation and desensitization. One member of the family, GRK5, has been implicated in several human pathologies, including heart failure, hypertension, cancer, diabetes, and Alzheimer disease. To gain mechanistic insight into GRK5 function, we determined a crystal structure of full-length human GRK5 at 1.8 Å resolution. GRK5 in complex with the ATP analog 5′-adenylyl β,γ-imidodiphosphate or the nucleoside sangivamycin crystallized as a monomer. The C-terminal tail (C-tail) of AGC kinase domains is a highly conserved feature that is divided into three segments as follows: the C-lobe tether, the active-site tether (AST), and the N-lobe tether (NLT). This domain is fully resolved in GRK5 and reveals novel interactions with the nucleotide and N-lobe. Similar to other AGC kinases, the GRK5 AST is an integral part of the nucleotide-binding pocket, a feature not observed in other GRKs. The AST also mediates contact between the kinase N- and C-lobes facilitating closure of the kinase domain. The GRK5 NLT is largely displaced from its previously observed position in other GRKs. Moreover, although the autophosphorylation sites in the NLT are >20 Å away from the catalytic cleft, they are capable of rapid cis-autophosphorylation suggesting high mobility of this region. In summary, we provide a snapshot of GRK5 in a partially closed state, where structural elements of the kinase domain C-tail are aligned to form novel interactions to the nucleotide and N-lobe not previously observed in other GRKs. PMID:26032409

  8. Features of sound propagation in the ocean with fine-structure inhomogeneities

    NASA Astrophysics Data System (ADS)

    Gostev, V. S.; Mikryukov, A. V.; Popov, O. E.

    2016-09-01

    We analyze the results of an experiment using an explosive sound source in the tropical part of the Indian Ocean. We consider the time structure of sound signals in geometric shadow zones to a distance of 270 km and the scheme of how the sound field in the shadow zone is formed by rays reflected from horizontally extended fine-structured sound velocity layers. From the results of calculation using a wave program that realizes the method of psuedodifferential parabolic equations, we analyze the influence of signal scattering by fine-structure sound velocity inhomogeneities on the sound field distribution in a waveguide. We show that the field formed by spots of light in each of the shadow zones is generated by a regular field and propagates in parallel to it, taking energy from the regular zone in the near field and in each subsequent convergence zone. This mechanism causes an additional decrease in the field in illuminated zones, which can be interpreted as additional attenuation of the regular sound field.

  9. Additional Constraints on the Shallow Seismic Velocity Structure of the Atlantis Massif Oceanic Core Complex

    NASA Astrophysics Data System (ADS)

    Henig, A. S.; Blackman, D. K.; Harding, A. J.; Kent, G. M.; Canales, J. P.

    2008-12-01

    We investigate the detailed structure of the uppermost ~km of Atlantis Massif, an oceanic core complex at 30°N on the Mid Atlantic Ridge, using pre-existing multichannel seismic data. The Synthetic On- Bottom Experiment (SOBE) method that we employ downward continues both the shots and receivers to a depth just above the seafloor. This allows us to pick refracted arrivals recorded on the streamer at very-near offset, providing constraints from rays that are received within the 300-2000 m range that was unavailable to earlier studies where standard shot gathers had been analyzed. Thus, we can better model the upper few hundred meters of the section which, in turn, adds confidence for determining the deeper (400-1500 m) structure. New work on a ridge-parallel line has been added to last year's work on a cross-axis line over the Central Dome of the massif. Tomographic results are similar for these crossing lines: a thin (100-150 m) low velocity (< 3 km/s) layer caps the dome; high horizontal gradients (>1.25 s-1) occur in local (1-2 km wide) regions within these 6-8 km long subsections of the MCS lines analyzed to date; and very high vertical velocity gradients, greater than 3.75 s-1, occur within the km just below the exposed detachment in these areas. We obtain general agreement with Canales et al., 2008, results over the Central Dome but our models suggest a finer scale lateral heterogeneity. We have begun analysis of additional and extended MCS lines over the domal core of the massif and our priority for this presentation is to assess the detailed structure of the Southern Ridge. In at least some areas the thin, low velocity layer contrasts sufficiently with underlying material that a clear refracted arrival is visible in supergathers. We will determine whether the low velocity layer persists over the whole dome or if it is restricted to the Central Dome. An important question is whether its thickness on the Southern Ridge, if it exists there, differs from that

  10. ECG-Based Detection of Early Myocardial Ischemia in a Computational Model: Impact of Additional Electrodes, Optimal Placement, and a New Feature for ST Deviation

    PubMed Central

    Loewe, Axel; Schulze, Walther H. W.; Jiang, Yuan; Wilhelms, Mathias; Luik, Armin; Dössel, Olaf; Seemann, Gunnar

    2015-01-01

    In case of chest pain, immediate diagnosis of myocardial ischemia is required to respond with an appropriate treatment. The diagnostic capability of the electrocardiogram (ECG), however, is strongly limited for ischemic events that do not lead to ST elevation. This computational study investigates the potential of different electrode setups in detecting early ischemia at 10 minutes after onset: standard 3-channel and 12-lead ECG as well as body surface potential maps (BSPMs). Further, it was assessed if an additional ECG electrode with optimized position or the right-sided Wilson leads can improve sensitivity of the standard 12-lead ECG. To this end, a simulation study was performed for 765 different locations and sizes of ischemia in the left ventricle. Improvements by adding a single, subject specifically optimized electrode were similar to those of the BSPM: 2–11% increased detection rate depending on the desired specificity. Adding right-sided Wilson leads had negligible effect. Absence of ST deviation could not be related to specific locations of the ischemic region or its transmurality. As alternative to the ST time integral as a feature of ST deviation, the K point deviation was introduced: the baseline deviation at the minimum of the ST-segment envelope signal, which increased 12-lead detection rate by 7% for a reasonable threshold. PMID:26587538

  11. ECG-Based Detection of Early Myocardial Ischemia in a Computational Model: Impact of Additional Electrodes, Optimal Placement, and a New Feature for ST Deviation.

    PubMed

    Loewe, Axel; Schulze, Walther H W; Jiang, Yuan; Wilhelms, Mathias; Luik, Armin; Dössel, Olaf; Seemann, Gunnar

    2015-01-01

    In case of chest pain, immediate diagnosis of myocardial ischemia is required to respond with an appropriate treatment. The diagnostic capability of the electrocardiogram (ECG), however, is strongly limited for ischemic events that do not lead to ST elevation. This computational study investigates the potential of different electrode setups in detecting early ischemia at 10 minutes after onset: standard 3-channel and 12-lead ECG as well as body surface potential maps (BSPMs). Further, it was assessed if an additional ECG electrode with optimized position or the right-sided Wilson leads can improve sensitivity of the standard 12-lead ECG. To this end, a simulation study was performed for 765 different locations and sizes of ischemia in the left ventricle. Improvements by adding a single, subject specifically optimized electrode were similar to those of the BSPM: 2-11% increased detection rate depending on the desired specificity. Adding right-sided Wilson leads had negligible effect. Absence of ST deviation could not be related to specific locations of the ischemic region or its transmurality. As alternative to the ST time integral as a feature of ST deviation, the K point deviation was introduced: the baseline deviation at the minimum of the ST-segment envelope signal, which increased 12-lead detection rate by 7% for a reasonable threshold.

  12. An Individual with Blepharophimosis-Ptosis-Epicanthus Inversus Syndrome (BPES) and Additional Features Expands the Phenotype Associated with Mutations in KAT6B

    PubMed Central

    Yu, Hung-Chun; Geiger, Elizabeth A.; Medne, Livija; Zackai, Elaine H.; Shaikh, Tamim H.

    2015-01-01

    Blepharophimosis-Ptosis-Epicanthus Inversus Syndrome (BPES) is an autosomal dominant disorder caused by mutations in FOXL2. We identified an individual with BPES and additional phenotypic features who did not have a FOXL2 mutation. We used whole exome sequencing to identify a de novo mutation in KAT6B (lysine acetyltransferase 6B) in this individual. The mutation was a 2 bp insertion leading to a frameshift which resulted in a premature stop codon. The resulting truncated protein does not have the C-terminal serine/methionine transcription activation domain necessary for interaction with other transcriptional and epigenetic regulators. This mutation likely has a dominant-negative or gain-of-function effect, similar to those observed in other genetic disorders resulting from KAT6B mutations, including Say-Barber-Biesecker-Young-Simpson (SBBYSS) and Genitopatellar syndrome (GTPTS). Thus, our subject’s phenotype broadens the spectrum of clinical findings associated with mutations in KAT6B. Furthermore, our results suggest that individuals with BPES without a FOXL2 mutation should be tested for KAT6B mutations. The transcriptional and epigenetic regulation mediated by KAT6B appears crucial to early developmental processes, which when perturbed can lead to a wide spectrum of phenotypic outcomes. PMID:24458743

  13. Combinatorial reshaping of a lipase structure for thermostability: additive role of surface stabilizing single point mutations.

    PubMed

    Kumar, Rakesh; Singh, Ranvir; Kaur, Jagdeep

    2014-05-16

    Thermostable lipases are of high priority for industrial applications. In the present study, targeted improvement of the thermostability of a lipase from metagenomic origin was examined by using a combinatorial protein engineering approach exploring additive effects of single amino acid substitutions. A variant (LipR5) was generated after combination of two thermostabilizing mutations (R214C & N355K). Thermostability of the variant enzyme was analyzed by half-life measurement and circular dichroism (CD). To assess whether catalytic properties were affected by mutation, the optimal reaction conditions were determined. The protein LipR5, displayed optimum activity at 50°C and pH 8.0. It showed two fold enhancement in thermostability (at 60°C) as compared to LipR3 (R214C) and nearly 168 fold enhancement as compared to parent enzyme (LipR1). Circular dichroism and fluorescence study suggest that the protein structure had become more rigid and stable to denaturation. Study of 3D model suggested that Lys355 was involved in formation of a Hydrogen bond with OE1 of Glu284. Lys355 was also making salt bridge with OE2 of Glu284. PMID:24751523

  14. Influencing the structure of block copolymer micelles with small molecule additives

    NASA Astrophysics Data System (ADS)

    Robertson, Megan; Singh, Avantika; Cooksey, Tyler; Kidd, Bryce; Piemonte, Rachele; Wang, Shu; Mai Le, Kim; Madsen, Louis

    Amphiphilic block copolymer micelles in water are under broad exploration for drug delivery applications due to their high loading capacity and targeted drug delivery. We aim to understand the kinetic and thermodynamic processes that underlie the self-assembly of diblock copolymer micelle systems. The present work focuses on diblock copolymers containing poly(ethylene oxide) (a hydrophilic polymer) and polycaprolactone (a hydrophobic polymer), which spontaneously self-assemble into spherical micelles in water. Addition of a common good solvent (a co-solvent) for both of the constituting blocks, such as tetrahydrofuran (THF), reduces the interfacial tension at the core-corona interface. We are currently investigating the effect of this phenomenon on the micelle structural properties, using small-angle scattering and nuclear magnetic resonance. We have characterized the hydrodynamic radius, core radius, corona thickness, aggregation number, degree of swelling of the micelle core with the co-solvent, and unimer (free chain) concentration, as a function of the co-solvent concentration. Fundamental knowledge from these studies will inform design of drug delivery systems by allowing us to tailor micelle properties for optimal cargo loading.

  15. Use of Data Assimilation to Determine Features of Neuron Structure and Connectivity

    NASA Astrophysics Data System (ADS)

    Eldridge, Michael J.

    Neurons and the synaptic connections between them underlie the computational power of the brain. We present numerical models of neural behavior and show how to tune these models based on experimental evidence. Though the basic principles behind the creation and propagation of action potentials are understood, it is experimentally feasible to measure only a small number of the quantities that go into our models, substantially increasing the difficulty of making accurate predictions. Additionally, because biologically motivated models are very often nonlinear, we will focus on tools and techniques which do not require linearity. We present novel methods of using time series of measurements to determine the features of nonlinear systems and predict their future behavior. We show how time-delayed coordinates can substitute for additional measurements and provide us with a better estimation of the state and parameters of the underlying system. A general expression for our objective function as a path integral is derived from probabilistic considerations and methods for evaluating the expression are discussed. We demonstrate how the techniques developed can be used to determine properties of a biophysical system from a realistic set of limited measurements. We examine experimental electrophysiological recordings of zebra finch neurons and use them to hone the predictive powers of our models for single cells. Then, moving beyond the single cell level, we demonstrate how our approach can be used to determine changes in network connectivity due to synaptic plasticity in ways that direct experiment cannot.

  16. Assessment of the micro-structure and depletion potentials in two-dimensional binary mixtures of additive hard-disks

    NASA Astrophysics Data System (ADS)

    Perera-Burgos, Jorge Adrián; Méndez-Alcaraz, José Miguel; Pérez-Ángel, Gabriel; Castañeda-Priego, Ramón

    2016-09-01

    Depletion forces are a particular class of effective interactions that have been mainly investigated in binary mixtures of hard-spheres in bulk. Although there are a few contributions that point toward the effects of confinement on the depletion potential, little is known about such entropic potentials in two-dimensional colloidal systems. From theoretical point of view, the problem resides in the fact that there is no general formulation of depletion forces in arbitrary dimensions and, typically, any approach that works well in three dimensions has to be reformulated for lower dimensionality. However, we have proposed a theoretical framework, based on the formalism of contraction of the description within the integral equations theory of simple liquids, to account for effective interactions in colloidal liquids, whose main feature is that it does not need to be readapted to the problem under consideration. We have also shown that such an approach allows one to determine the depletion pair potential in three-dimensional colloidal mixtures even near to the demixing transition, provided the bridge functions are sufficiently accurate to correctly describe the spatial correlation between colloids [E. López-Sánchez et al., J. Chem. Phys. 139, 104908 (2013)]. We here report an extensive analysis of the structure and the entropic potentials in binary mixtures of additive hard-disks. In particular, we show that the same functional form of the modified-Verlet closure relation used in three dimensions can be straightforwardly employed to obtain an accurate solution for two-dimensional colloidal mixtures in a wide range of packing fractions, molar fractions, and size asymmetries. Our theoretical results are explicitly compared with the ones obtained by means of event-driven molecular dynamics simulations and recent experimental results. Furthermore, to assess the accuracy of our predictions, the depletion potentials are used in an effective one-component model to reproduce

  17. Assessment of the micro-structure and depletion potentials in two-dimensional binary mixtures of additive hard-disks.

    PubMed

    Perera-Burgos, Jorge Adrián; Méndez-Alcaraz, José Miguel; Pérez-Ángel, Gabriel; Castañeda-Priego, Ramón

    2016-09-14

    Depletion forces are a particular class of effective interactions that have been mainly investigated in binary mixtures of hard-spheres in bulk. Although there are a few contributions that point toward the effects of confinement on the depletion potential, little is known about such entropic potentials in two-dimensional colloidal systems. From theoretical point of view, the problem resides in the fact that there is no general formulation of depletion forces in arbitrary dimensions and, typically, any approach that works well in three dimensions has to be reformulated for lower dimensionality. However, we have proposed a theoretical framework, based on the formalism of contraction of the description within the integral equations theory of simple liquids, to account for effective interactions in colloidal liquids, whose main feature is that it does not need to be readapted to the problem under consideration. We have also shown that such an approach allows one to determine the depletion pair potential in three-dimensional colloidal mixtures even near to the demixing transition, provided the bridge functions are sufficiently accurate to correctly describe the spatial correlation between colloids [E. López-Sánchez et al., J. Chem. Phys. 139, 104908 (2013)]. We here report an extensive analysis of the structure and the entropic potentials in binary mixtures of additive hard-disks. In particular, we show that the same functional form of the modified-Verlet closure relation used in three dimensions can be straightforwardly employed to obtain an accurate solution for two-dimensional colloidal mixtures in a wide range of packing fractions, molar fractions, and size asymmetries. Our theoretical results are explicitly compared with the ones obtained by means of event-driven molecular dynamics simulations and recent experimental results. Furthermore, to assess the accuracy of our predictions, the depletion potentials are used in an effective one-component model to reproduce

  18. Structural Features of a Bacteroidetes-Affiliated Cellulase Linked with a Polysaccharide Utilization Locus.

    PubMed

    Naas, A E; MacKenzie, A K; Dalhus, B; Eijsink, V G H; Pope, P B

    2015-01-01

    Previous gene-centric analysis of a cow rumen metagenome revealed the first potentially cellulolytic polysaccharide utilization locus, of which the main catalytic enzyme (AC2aCel5A) was identified as a glycoside hydrolase (GH) family 5 endo-cellulase. Here we present the 1.8 Å three-dimensional structure of AC2aCel5A, and characterization of its enzymatic activities. The enzyme possesses the archetypical (β/α)8-barrel found throughout the GH5 family, and contains the two strictly conserved catalytic glutamates located at the C-terminal ends of β-strands 4 and 7. The enzyme is active on insoluble cellulose and acts exclusively on linear β-(1,4)-linked glucans. Co-crystallization of a catalytically inactive mutant with substrate yielded a 2.4 Å structure showing cellotriose bound in the -3 to -1 subsites. Additional electron density was observed between Trp178 and Trp254, two residues that form a hydrophobic "clamp", potentially interacting with sugars at the +1 and +2 subsites. The enzyme's active-site cleft was narrower compared to the closest structural relatives, which in contrast to AC2aCel5A, are also active on xylans, mannans and/or xyloglucans. Interestingly, the structure and function of this enzyme seem adapted to less-substituted substrates such as cellulose, presumably due to the insufficient space to accommodate the side-chains of branched glucans in the active-site cleft.

  19. Exploring polarization features in light reflection from beetles with structural colors

    NASA Astrophysics Data System (ADS)

    Arwin, Hans; Magnusson, Roger; Fernández del Río, Lía.; Landin, Jan; Mendoza-Galván, Arturo; Järrendahl, Kenneth

    2015-03-01

    A Mueller matrix of a sample can be used to determine the polarization of reflected light for incident light with arbitrary polarization. The polarization can be quantified in terms of ellipticity, polarization azimuth and degree of polarization. We apply spectroscopic Mueller-matrix ellipsometry at multiple angles of incidence to study the cuticle of beetles and derive polarization features for incident unpolarized light. In particular we address chiral phenomena in scarab beetles, the origin of their structural colors and the observed high degree of circular polarization is discussed. Results from beetles in Scarabaeidae subfamilies Cetoniinae and Rutelinae are presented including specimens with broad-band silver-or gold-like colors with metallic shine as well as specimens with narrow-band green or red reflectors. The variation of polarization with angle of incidence and occurrence of both left-handed and right-handed polarization from a single species are presented. We also use Mueller-matrix thicknesses and optical properties. Interference oscillations in the observed spectra are due to allowed optical modes and we show how to develop a structural model of a cuticle based on this effect. Sum decomposition of Mueller matrices measured on a depolarizing cuticle of a beetle is briefly discussed.

  20. Structural features and stability of an RNA triple helix in solution.

    PubMed Central

    Holland, J A; Hoffman, D W

    1996-01-01

    A 30 nt RNA with a sequence designed to form an intramolecular triple helix was analyzed by one-and two-dimensional NMR spectroscopy and UV absorption measurements. NMR data show that the RNA contains seven pyrimidine-purine-pyrimidine base triples stabilized by Watson-Crick and Hoogsteen interactions. The temperature dependence of the imino proton resonances, as well as UV absorption data, indicate that the triple helix is highly stable at acidic pH, melting in a single sharp transition centered at 62 degrees C at pH 4.3. The Watson-Crick and Hoogsteen pairings are disrupted simultaneously upon melting. The NMR data are consistent with a structural model where the Watson-Crick paired strands form an A-helix. Results of model building, guided by NMR data, suggest a possible hydrogen bond between the 2' hydroxyl proton of the Hoogsteen strand and a phosphate oxygen of the purine strand. The structural model is discussed in terms of its ability to account for some of the differences in stability reported for RNA and DNA triple helices and provides insight into features that are likely to be important in the design of RNA binding compounds. PMID:8759020

  1. Hsp60, a novel target for antitumor therapy: structure-function features and prospective drugs design.

    PubMed

    Pace, Andrea; Barone, Giampaolo; Lauria, Antonino; Martorana, Annamaria; Piccionello, Antonio Palumbo; Pierro, Paola; Terenzi, Alessio; Almerico, Anna Maria; Buscemi, Silvestre; Campanella, Claudia; Angileri, Francesca; Carini, Francesco; Zummo, Giovanni; de Macario, Everly Conway; Cappello, Francesco; Macario, Alberto J L

    2013-01-01

    Heat shock protein 60 kDa (Hsp60) is a chaperone classically believed to be involved in assisting the correct folding of other mitochondrial proteins. Hsp60 also plays a role in cytoprotection against cell stressors, displaying for example, antiapoptotic potential. Despite the plethora of studies devoted to the mechanism of Hsp60's function, especially in prokaryotes, fundamental issues still remain unexplored, including the definition of its role in cancer. Key questions still unanswered pertain to the differences in structure-function features that might exist between the well-studied prokaryotic GroEL and the largely unexplored eukaryotic Hsp60 proteins. In this article we discuss these differences in sequence, structure, and roles of Hsp60, focusing on the human ortholog with the view of devising compounds to block its ability to favour tumor-cell growth and survival. Compounds currently known to directly or indirectly affect Hsp60 functions, such as protein folding, HIF-1α accumulation, or Hsp60-induced cell proliferation, are discussed along with strategies that might prove effective for developing Hsp60-targeting drugs for anticancer therapy.

  2. Halokinesis and structural evolution of the major features in eastern and southern Tunisian Atlas

    NASA Astrophysics Data System (ADS)

    Hlaiem, Amor

    1999-05-01

    The eastern and southern Tunisian Atlas is marked by the presence of three major faults; the N-S Axis Fault, the NW-SE Gafsa Fault, and the E-W northern Chott Fault. Seismic lines crossing these structures show the existence of significant halokinetics that began in the Early Jurassic. The aim of this paper is to study and better understand the Triassic salt movements, which are mainly linked to periods when the major basement faults were reactivated resulting in extension, compression, transtension or/and transpression. Analysis of the seismic data allows us to conclude that the Triassic salt migration started in the Early Jurassic and continued during the Late Jurassic and the Early Cretaceous. Although these periods are characterized by an extensional tectonic regime, the synsedimentary halokinesis is accompanied by thickening and thinning of the overlying series. Salt remobilization was accentuated during the compressional deformation which occurred from the Late Tertiary to Quaternary and resulted in local diapiric extrusions along the major structural features.

  3. Crystallographic features of the structure of a martensite packet of the NiMn intermetallic compound

    NASA Astrophysics Data System (ADS)

    Khlebnikova, Yu. V.; Egorova, L. Yu.; Rodionov, D. P.; Belosludtseva, E. S.; Kazantsev, V. A.

    2016-06-01

    Optical microscopy, scanning electron microscopy, and X-ray diffraction are used to show that a pseudosingle crystal forms upon cooling of an alloy Ni49Mn51 single crystal below the temperature of the β→θ (bcc → fct) transformation. At room temperature, this pseudosingle crystal has the structure of tetragonal L10 martensite with parameters a = 0.3732 nm and c = 0.3537 nm and a tetragonality c/ a = 0.94775. The temperatures of the forward and reverse B2 → L10 transformations are determined. The crystallographic features of martensite packet formation are analyzed. As shown by EBSD, neighboring martensite packets always have three kinds of tetragonal martensite plates, which are in a twin position and have different tetragonality axis directions. Repeated heating and quenching of the pseudosingle crystal result in recrystallization with the formation of coarse grains. The packet structure of the tetragonal martensite is retained in this case, and the sizes of the packets formed within a grain decrease by a factor of 2-3 as compared to the initial pseudosingle crystal.

  4. Update of PROFEAT: a web server for computing structural and physicochemical features of proteins and peptides from amino acid sequence.

    PubMed

    Rao, H B; Zhu, F; Yang, G B; Li, Z R; Chen, Y Z

    2011-07-01

    Sequence-derived structural and physicochemical features have been extensively used for analyzing and predicting structural, functional, expression and interaction profiles of proteins and peptides. PROFEAT has been developed as a web server for computing commonly used features of proteins and peptides from amino acid sequence. To facilitate more extensive studies of protein and peptides, numerous improvements and updates have been made to PROFEAT. We added new functions for computing descriptors of protein-protein and protein-small molecule interactions, segment descriptors for local properties of protein sequences, topological descriptors for peptide sequences and small molecule structures. We also added new feature groups for proteins and peptides (pseudo-amino acid composition, amphiphilic pseudo-amino acid composition, total amino acid properties and atomic-level topological descriptors) as well as for small molecules (atomic-level topological descriptors). Overall, PROFEAT computes 11 feature groups of descriptors for proteins and peptides, and a feature group of more than 400 descriptors for small molecules plus the derived features for protein-protein and protein-small molecule interactions. Our computational algorithms have been extensively tested and used in a number of published works for predicting proteins of specific structural or functional classes, protein-protein interactions, peptides of specific functions and quantitative structure activity relationships of small molecules. PROFEAT is accessible free of charge at http://bidd.cz3.nus.edu.sg/cgi-bin/prof/protein/profnew.cgi.

  5. Using intramolecular disulfide bonds in tau protein to deduce structural features of aggregation-resistant conformations.

    PubMed

    Walker, Sophie; Ullman, Orly; Stultz, Collin M

    2012-03-16

    Because tau aggregation likely plays a role in a number of neurodegenerative diseases, understanding the processes that affect tau aggregation is of considerable importance. One factor that has been shown to influence the aggregation propensity is the oxidation state of the protein itself. Tau protein, which contains two naturally occurring cysteine residues, can form both intermolecular disulfide bonds and intramolecular disulfide bonds. Several studies suggest that intermolecular disulfide bonds can promote tau aggregation in vitro. By contrast, although there are data to suggest that intramolecular disulfide bond formation retards tau aggregation in vitro, the precise mechanism underlying this observation remains unclear. While it has been hypothesized that a single intramolecular disulfide bond in tau leads to compact conformations that cannot form extended structure consistent with tau fibrils, there are few data to support this conjecture. In the present study we generate oxidized forms of the truncation mutant, K18, which contains all four microtubule binding repeats, and isolate the monomeric fraction, which corresponds to K18 monomers that have a single intramolecular disulfide bond. We study the aggregation propensity of the oxidized monomeric fraction and relate these data to an atomistic model of the K18 unfolded ensemble. Our results argue that the main effect of intramolecular disulfide bond formation is to preferentially stabilize conformers within the unfolded ensemble that place the aggregation-prone tau subsequences, PHF6* and PHF6, in conformations that are inconsistent with the formation of cross-β-structure. These data further our understanding of the precise structural features that retard tau aggregation.

  6. Conserved Features in the Structure, Mechanism, and Biogenesis of the Inverse Autotransporter Protein Family

    PubMed Central

    Heinz, Eva; Stubenrauch, Christopher J.; Grinter, Rhys; Croft, Nathan P.; Purcell, Anthony W.; Strugnell, Richard A.; Dougan, Gordon; Lithgow, Trevor

    2016-01-01

    The bacterial cell surface proteins intimin and invasin are virulence factors that share a common domain structure and bind selectively to host cell receptors in the course of bacterial pathogenesis. The β-barrel domains of intimin and invasin show significant sequence and structural similarities. Conversely, a variety of proteins with sometimes limited sequence similarity have also been annotated as “intimin-like” and “invasin” in genome datasets, while other recent work on apparently unrelated virulence-associated proteins ultimately revealed similarities to intimin and invasin. Here we characterize the sequence and structural relationships across this complex protein family. Surprisingly, intimins and invasins represent a very small minority of the sequence diversity in what has been previously the “intimin/invasin protein family”. Analysis of the assembly pathway for expression of the classic intimin, EaeA, and a characteristic example of the most prevalent members of the group, FdeC, revealed a dependence on the translocation and assembly module as a common feature for both these proteins. While the majority of the sequences in the grouping are most similar to FdeC, a further and widespread group is two-partner secretion systems that use the β-barrel domain as the delivery device for secretion of a variety of virulence factors. This comprehensive analysis supports the adoption of the “inverse autotransporter protein family” as the most accurate nomenclature for the family and, in turn, has important consequences for our overall understanding of the Type V secretion systems of bacterial pathogens. PMID:27190006

  7. Structural features in the HIV-1 repeat region facilitate strand transfer during reverse transcription.

    PubMed Central

    Berkhout, B; Vastenhouw, N L; Klasens, B I; Huthoff, H

    2001-01-01

    Two obligatory DNA strand transfers take place during reverse transcription of a retroviral RNA genome. The first strand transfer is facilitated by terminal repeat (R) elements in the viral genome. This strand-transfer reaction depends on base pairing between the cDNA of the 5'R and the 3'R. There is accumulating evidence that retroviral R regions contain features other than sequence complementarity that stimulate this critical nucleic acid hybridization step. The R region of the human immunodeficiency virus type 1 (HIV-1) is relatively extended (97 nt) and encodes two well-conserved stem-loop structures, the TAR and poly(A) hairpins. The role of these motifs was studied in an in vitro strand-transfer assay with two separate templates, the 5'R donor and the 3'R acceptor, and mutants thereof. The results indicate that the upper part of the TAR hairpin structure in the 5'R donor is critical for efficient strand transfer. This seems to pose a paradox, as the 5'R template is degraded by RNase H before strand transfer occurs. We propose that it is not the RNA hairpin motif in the 5'R donor, but rather the antisense motif in the ssDNA copy, which can also fold a hairpin structure, that is critical for strand transfer. Mutation of the loop sequence in the TAR hairpin of the donor RNA, which is copied in the loop of the cDNA hairpin, reduces the transfer efficiency more than fivefold. It is proposed that the natural strand-transfer reaction is enhanced by interaction of the anti-TAR ssDNA hairpin with the TAR hairpin in the 3'R acceptor. Base pairing can occur between the complementary loops ("loop-loop kissing"), and strand transfer is completed by the subsequent formation of an extended RNA-cDNA duplex. PMID:11497429

  8. The Cenozoic volcanic province of Tibesti (Sahara of Chad): major units, chronology, and structural features

    NASA Astrophysics Data System (ADS)

    Deniel, C.; Vincent, P. M.; Beauvilain, A.; Gourgaud, A.

    2015-09-01

    Using both field relationships and some absolute ages, the sequence of volcanic units in the Cenozoic Tibesti Volcanic Province (TVP) (Chad) is established as follows: (1) plateau volcanism, between at least 17 and 8 Ma, consisting of flood basalts and silicic lava plugs, with intercalated ignimbritic sheets in the upper basalt succession increasing in amount upwards. Ages decrease from NE to SW, following the migration of the small NW-SE flexures concentrating the feeding dike swarms; (2) Late Miocene large central composite volcanoes exhibiting diverse and original structures. Some of them (Tarso Toon, Ehi Oyé, and Tarso Yéga) are located along a major NNE fault, representing the main tectonic direction in Tibesti since Precambrian times; (3) construction of three large ignimbritic volcanoes, associated with significant updoming of the basement, ending with the collapse of large calderas: Voon (about 5-7 Ma), Emi Koussi (2.4-1.33 Ma), and Yirrigué (0.43 Ma); (4) basaltic activity, starting at about 5-7 Ma, and essentially consisting of cinder cones and associated lava flows (Tarso Tôh, Tarso Ahon, and Tarso Emi Chi); and (5) final volcanic activity represented by post-Yirrigué caldera activity in the Tarso Toussidé Volcanic Complex, and especially Ehi Toussidé (the only active volcano in Tibesti), plus Ehi Timi and Ehi Mousgou volcanoes, similar to Ehi Toussidé. The two tectonic directions controlling some volcanic features of the province correspond to the major old lithospheric structures delimiting the volcanic province, namely, the great NW-SE Tassilian flexure to the SW and a major NE-NNE fault zone to the E. Unusual conditions of uplift and erosion in the TVP enable exceptional exposure of the internal structure of its volcanoes.

  9. Structural features of soluble cereal arabinoxylan fibers associated with a slow rate of in vitro fermentation by human fecal microbiota.

    PubMed

    Rumpagaporn, Pinthip; Reuhs, Brad L; Kaur, Amandeep; Patterson, John A; Keshavarzian, Ali; Hamaker, Bruce R

    2015-10-01

    Most soluble dietary fibers ferment rapidly in the proximal colon, potentially causing discomfort and poor tolerability. Alkali-extracted arabinoxylan isolates from corn, wheat, rice and sorghum brans were prepared, through hydrolysis (except sorghum) and ethanol fractionation, to have a broad range of initial fermentation rates, and their linkage patterns were determined to understand structural aspects related to slow fermentation rate. They were all highly branched polymers with degree of substitution greater than 64%. There was no relationship of molecular mass, arabinose:xylose ratio, or degree of substitution to fermentation rate patterns. Slow fermenting wheat and corn arabinoxylans had much higher amount of terminal xylose in branches than fast fermenting rice and sorghum arabinoxylans. The slowest fermenting wheat arabinoxylan additionally contained a complex trisaccharide side chain with two arabinoses linked at the O-2 and O-3 positions of an arabinose that is O-2 linked to the xylan backbone. Structural features were proposed for tolerable slowly fermentable arabinoxylan with possible beneficial fermentation function into the distal colon.

  10. Structural features of soluble cereal arabinoxylan fibers associated with a slow rate of in vitro fermentation by human fecal microbiota.

    PubMed

    Rumpagaporn, Pinthip; Reuhs, Brad L; Kaur, Amandeep; Patterson, John A; Keshavarzian, Ali; Hamaker, Bruce R

    2015-10-01

    Most soluble dietary fibers ferment rapidly in the proximal colon, potentially causing discomfort and poor tolerability. Alkali-extracted arabinoxylan isolates from corn, wheat, rice and sorghum brans were prepared, through hydrolysis (except sorghum) and ethanol fractionation, to have a broad range of initial fermentation rates, and their linkage patterns were determined to understand structural aspects related to slow fermentation rate. They were all highly branched polymers with degree of substitution greater than 64%. There was no relationship of molecular mass, arabinose:xylose ratio, or degree of substitution to fermentation rate patterns. Slow fermenting wheat and corn arabinoxylans had much higher amount of terminal xylose in branches than fast fermenting rice and sorghum arabinoxylans. The slowest fermenting wheat arabinoxylan additionally contained a complex trisaccharide side chain with two arabinoses linked at the O-2 and O-3 positions of an arabinose that is O-2 linked to the xylan backbone. Structural features were proposed for tolerable slowly fermentable arabinoxylan with possible beneficial fermentation function into the distal colon. PMID:26076616

  11. Optimal design of high damping force engine mount featuring MR valve structure with both annular and radial flow paths

    NASA Astrophysics Data System (ADS)

    Nguyen, Q. H.; Choi, S. B.; Lee, Y. S.; Han, M. S.

    2013-11-01

    This paper focuses on the optimal design of a compact and high damping force engine mount featuring magnetorheological fluid (MRF). In the mount, a MR valve structure with both annular and radial flows is employed to generate a high damping force. First, the configuration and working principle of the proposed MR mount is introduced. The MRF flows in the mount are then analyzed and the governing equations of the MR mount are derived based on the Bingham plastic behavior of the MRF. An optimal design of the MR mount is then performed to find the optimal structure of the MR valve to generate a maximum damping force with certain design constraints. In addition, the gap size of MRF ducts is empirically chosen considering the ‘lockup’ problem of the mount at high frequency. Performance of the optimized MR mount is then evaluated based on finite element analysis and discussions on performance results of the optimized MR mount are given. The effectiveness of the proposed MR engine mount is demonstrated via computer simulation by presenting damping force and power consumption.

  12. Cloning, structural features, and expression analysis of the gene encoding thioredoxin reductase 1 from Apis cerana cerana.

    PubMed

    Yang, Haifang; Kang, Mingjiang; Guo, Xingqi; Xu, Baohua

    2010-07-01

    Previous studies have demonstrated that mammalian thioredoxin reductases 1 (TrxRs; EC 1.6.4.5) play roles in protection against oxidant injury, cell growth and transformation, and the recycling of ascorbate from its oxidized form. However, little is known about the function of TrxRs in insects, especially in Apis cerana cerana. To gain a better understanding of its role in insects, we cloned TrxR1 from A.cerana cerana (AccTrxR1) and investigated its structural features and expression. The full-length cDNA is 1998 bp long and contains an open reading frame (ORF) of 1485 bp. The deduced AccTrxR1 protein has 494 aa, a calculated molecular mass (MW) of 54.24 kDa, and an isoelectric point of pH 7.35. The full-length genomic DNA of AccTrxR1 is 3500 bp and contains eight exons and seven introns. In addition, the sequence and putative transcription factor-binding sites of the 5'-flanking region were examined. We also looked for conserved domains/motifs, generated homologous alignments, conducted phylogenetic analysis, and made secondary and tertiary structure predictions using web software. RT-PCR revealed that the expression of AccTrxR1 could be induced by UV and heat (37 degrees C). These results indicate that AccTrxR1 may play a key role in protection against oxidant stress.

  13. Three-Dimensional Elastomeric Scaffolds Designed with Cardiac-Mimetic Structural and Mechanical Features

    PubMed Central

    Neal, Rebekah A.; Jean, Aurélie; Park, Hyoungshin; Wu, Patrick B.; Hsiao, James; Engelmayr, George C.; Langer, Robert

    2013-01-01

    Tissue-engineered constructs, at the interface of material science, biology, engineering, and medicine, have the capacity to improve outcomes for cardiac patients by providing living cells and degradable biomaterials that can regenerate the native myocardium. With an ultimate goal of both delivering cells and providing mechanical support to the healing heart, we designed three-dimensional (3D) elastomeric scaffolds with (1) stiffnesses and anisotropy mimicking explanted myocardial specimens as predicted by finite-element (FE) modeling, (2) systematically varied combinations of rectangular pore pattern, pore aspect ratio, and strut width, and (3) structural features approaching tissue scale. Based on predicted mechanical properties, three scaffold designs were selected from eight candidates for fabrication from poly(glycerol sebacate) by micromolding from silicon wafers. Large 20×20 mm scaffolds with high aspect ratio features (5:1 strut height:strut width) were reproducibly cast, cured, and demolded at a relatively high throughput. Empirically measured mechanical properties demonstrated that scaffolds were cardiac mimetic and validated FE model predictions. Two-layered scaffolds providing fully interconnected pore networks were fabricated by layer-by-layer assembly. C2C12 myoblasts cultured on one-layered scaffolds exhibited specific patterns of cell elongation and interconnectivity that appeared to be guided by the scaffold pore pattern. Neonatal rat heart cells cultured on two-layered scaffolds for 1 week were contractile, both spontaneously and in response to electrical stimulation, and expressed sarcomeric α-actinin, a cardiac biomarker. This work not only demonstrated several scaffold designs that promoted functional assembly of rat heart cells, but also provided the foundation for further computational and empirical investigations of 3D elastomeric scaffolds for cardiac tissue engineering. PMID:23190320

  14. Avidin related protein 2 shows unique structural and functional features among the avidin protein family

    PubMed Central

    Hytönen, Vesa P; Määttä, Juha AE; Kidron, Heidi; Halling, Katrin K; Hörhä, Jarno; Kulomaa, Tuomas; Nyholm, Thomas KM; Johnson, Mark S; Salminen, Tiina A; Kulomaa, Markku S; Airenne, Tomi T

    2005-01-01

    Background The chicken avidin gene family consists of avidin and several avidin related genes (AVRs). Of these gene products, avidin is the best characterized and is known for its extremely high affinity for D-biotin, a property that is utilized in numerous modern life science applications. Recently, the AVR genes have been expressed as recombinant proteins, which have shown different biotin-binding properties as compared to avidin. Results In the present study, we have employed multiple biochemical methods to better understand the structure-function relationship of AVR proteins focusing on AVR2. Firstly, we have solved the high-resolution crystal structure of AVR2 in complex with a bound ligand, D-biotin. The AVR2 structure reveals an overall fold similar to the previously determined structures of avidin and AVR4. Major differences are seen, especially at the 1–3 subunit interface, which is stabilized mainly by polar interactions in the case of AVR2 but by hydrophobic interactions in the case of AVR4 and avidin, and in the vicinity of the biotin binding pocket. Secondly, mutagenesis, competitive dissociation analysis and differential scanning calorimetry were used to compare and study the biotin-binding properties as well as the thermal stability of AVRs and avidin. These analyses pinpointed the importance of residue 109 for biotin binding and stability of AVRs. The I109K mutation increased the biotin-binding affinity of AVR2, whereas the K109I mutation decreased the biotin-binding affinity of AVR4. Furthermore, the thermal stability of AVR2(I109K) increased in comparison to the wild-type protein and the K109I mutation led to a decrease in the thermal stability of AVR4. Conclusion Altogether, this study broadens our understanding of the structural features determining the ligand-binding affinities and stability as well as the molecular evolution within the protein family. This novel information can be applied to further develop and improve the tools already

  15. Categorical Structure among Shared Features in Networks of Early-Learned Nouns

    ERIC Educational Resources Information Center

    Hills, Thomas T.; Maouene, Mounir; Maouene, Josita; Sheya, Adam; Smith, Linda

    2009-01-01

    The shared features that characterize the noun categories that young children learn first are a formative basis of the human category system. To investigate the potential categorical information contained in the features of early-learned nouns, we examine the graph-theoretic properties of noun-feature networks. The networks are built from the…

  16. Bio-inspired device: a novel smart MR spring featuring tendril structure

    NASA Astrophysics Data System (ADS)

    Kaluvan, Suresh; Park, Chun-Yong; Choi, Seung-Bok

    2016-01-01

    Smart materials such as piezoelectric patches, shape memory alloy, electro and magneto rheological fluid, magnetostrictive materials, etc are involved by far to design intelligent and high performance smart devices like injectors, dental braces, dampers, actuators and sensors. In this paper, an interesting smart device is proposed by inspiring on the structure of the bio climber plant. The key enabling concept of this proposed work is to design the smart spring damper as a helical shaped tendril structure using magneto-rheological (MR) fluid. The proposed smart spring consists of a hollow helical structure filled with MR fluid. The viscosity of the MR fluid decides the damping force of helical shaped smart spring, while the fluid intensity in the vine decides the strength of the tendril in the climber plant. Thus, the proposed smart spring can provide a new concept design of the damper which can be applicable to various damping system industries with tuneable damping force. The proposed smart spring damper has several advantageous such as cost effective, easy implementation compared with the conventional damper. In addition, the proposed spring damper can be easily designed to adapt different damping force levels without any alteration.

  17. Structural Features Essential to the Antimicrobial Functions of Human SPLUNC1.

    PubMed

    Walton, William G; Ahmad, Saira; Little, Michael S; Kim, Christine S K; Tyrrell, Jean; Lin, Qiao; Di, Y Peter; Tarran, Robert; Redinbo, Matthew R

    2016-05-31

    SPLUNC1 is an abundantly secreted innate immune protein in the mammalian respiratory tract that exerts bacteriostatic and antibiofilm effects, binds to lipopolysaccharide (LPS), and acts as a fluid-spreading surfactant. Here, we unravel the structural elements essential for the surfactant and antimicrobial functions of human SPLUNC1 (short palate lung nasal epithelial clone 1). A unique α-helix (α4) that extends from the body of SPLUNC1 is required for the bacteriostatic, surfactant, and LPS binding activities of this protein. Indeed, we find that mutation of just four leucine residues within this helical motif to alanine is sufficient to significantly inhibit the fluid spreading abilities of SPLUNC1, as well as its bacteriostatic actions against Gram-negative pathogens Burkholderia cenocepacia and Pseudomonas aeruginosa. Conformational flexibility in the body of SPLUNC1 is also involved in the bacteriostatic, surfactant, and LPS binding functions of the protein as revealed by disulfide mutants introduced into SPLUNC1. In addition, SPLUNC1 exerts antibiofilm effects against Gram-negative bacteria, although α4 is not involved in this activity. Interestingly, though, the introduction of surface electrostatic mutations away from α4 based on the unique dolphin SPLUNC1 sequence, and confirmed by crystal structure, is shown to impart antibiofilm activity against Staphylococcus aureus, the first SPLUNC1-dependent effect against a Gram-positive bacterium reported to date. Together, these data pinpoint SPLUNC1 structural motifs required for the antimicrobial and surfactant actions of this protective human protein. PMID:27145151

  18. Fundamental structural aspects and features in the bioengineering of the gas exchangers: comparative perspectives.

    PubMed

    Maina, J N

    2002-01-01

    the ubiquitous method of transfer of O2 across biological tissues. Gills, evaginated gas exchangers, were the primordial respiratory organs that evolved for water breathing, whereas lungs (invaginated gas exchangers) developed for terrestrial (air) breathing. Transitional (= bimodal = amphibious) breathing has evolved in animals with specialized organs that extract O2 from both water and air. Lungs are tidally (= bidirectionally) ventilated, while gills are unidirectionally ventilated, a feature that allows the highly efficient counter-current disposition between blood and water. Since animals occupy inconstant environmental milieus and their metabolic states vary, gas exchangers are designed to operate optimally across a spectrum of conditions that range from resting to exercise and even under hypoxia. Inbuilt structural and functional flexibility provides the requisite safety factors that allow adjustments to modest pressures. The fundamental structural features that determine the respiratory function of a gas exchanger are respiratory surface area, thickness of the blood-water/gas (tissue) barrier and volume of the pulmonary capillary blood. The diffusing capacity of a gas exchanger correlates directly with the surface area and inversely with the thickness of the blood-water/gas (tissue) barrier. An extensive surface area is generated in gills by extensive stratification of the gas exchanger and in lungs by profuse internal subdivision. Compartmentalization yields small terminal gas exchange compartments that compel greater commitment of energy to ventilate. The surfactant, a phospholipid lining, reduces the forces of surface tension at the air-water interface. This attenuates the propensity of physical collapse of the minute gas exchange units and minimizes the cost of ventilation. The surfactant characterizes all the gas exchangers derived from the piscine air bladder. In the lower air-breathing vertebrates, such as the lungfishes (Dipnoi), amphibians and certain

  19. Identifying Key Structural Features and Spatial Relationships in Archean Microbialites Using 2D and 3D Visualization Methods

    NASA Astrophysics Data System (ADS)

    Stevens, E. W.; Sumner, D. Y.

    2009-12-01

    Microbialites in the 2521 ± 3 Ma Gamohaan Formation, South Africa, have several different end-member morphologies which show distinct growth structures and spatial relationships. We characterized several growth structures and spatial relationships in two samples (DK20 and 2_06) using a combination of 2D and 3D analytical techniques. There are two main goals in studying complicated microbialites with a combination of 2D and 3D methods. First, one can better understand microbialite growth by identifying important structures and structural relationships. Once structures are identified, the order in which the structures formed and how they are related can be inferred from observations of crosscutting relationships. Second, it is important to use both 2D and 3D methods to correlate 3D observations with those in 2D that are more common in the field. Combining analysis provides significantly more insight into the 3D morphology of microbial structures. In our studies, 2D analysis consisted of describing polished slabs and serial sections created by grinding down the rock 100 microns at a time. 3D analysis was performed on serial sections visualized in 3D using Vrui and 3DVisualizer software developed at KeckCAVES, UCD (http://keckcaves.org). Data were visualized on a laptop and in an immersive cave system. Both samples contain microbial laminae and more vertically orients microbial "walls" called supports. The relationships between these features created voids now filled with herringbone and blocky calcite crystals. DK20, a classic plumose structure, contains two types of support structures. Both are 1st order structures (1st order structures with organic inclusions and 1st without organic inclusions) interpreted as planar features based on 2D analysis. In the 2D analysis the 1st order structures show v branching relationships as well as single cuspate relationships (two 1st order structures with inclusions merging upward), and single tented relationships (three supports

  20. A Pilot Study to Examine the Effect of Additional Structured Outdoor Playtime on Preschoolers' Physical Activity Levels

    ERIC Educational Resources Information Center

    Alhassan, Sofiya; Nwaokelemeh, Ogechi; Lyden, Kate; Goldsby, TaShauna; Mendoza, Albert

    2013-01-01

    The impact of additional structured outdoor playtime on preschoolers'; physical activity (PA) level is unclear. The purpose of this pilot study was to explore the effects of increasing structured outdoor playtime on preschoolers'; PA levels. Eight full-day classrooms (n = 134 children) from two preschool programmes were randomised into a treatment…

  1. Crystal structure and nanotopographical features on the surface of heat-treated and anodized porous titanium biomaterials produced using selective laser melting

    NASA Astrophysics Data System (ADS)

    Amin Yavari, S.; Wauthle, R.; Böttger, A. J.; Schrooten, J.; Weinans, H.; Zadpoor, A. A.

    2014-01-01

    Porous titanium biomaterials manufactured using additive manufacturing techniques such as selective laser melting are considered promising materials for orthopedic applications where the biomaterial needs to mimic the properties of bone. Despite their appropriate mechanical properties and the ample pore space they provide for bone ingrowth and osseointegration, porous titanium structures have an intrinsically bioinert surface and need to be subjected to surface bio-functionalizing procedures to enhance their in vivo performance. In this study, we used a specific anodizing process to build a hierarchical oxide layer on the surface of porous titanium structures made by selective laser melting of Ti6Al4V ELI powder. The hierarchical structure included both nanotopographical features (nanotubes) and micro-features (micropits). After anodizing, the biomaterial was heat treated in Argon at different temperatures ranging between 400 and 600 °C for either 1 or 2 h to improve its bioactivity. The effects of applied heat treatment on the crystal structure of TiO2 nanotubes and the nanotopographical features of the surface were studied using scanning electron microscopy and X-ray diffraction. It was shown that the transition from the initial crystal structure, i.e. anatase, to rutile occurs between 500 and 600 °C and that after 2 h of heat treatment at 600 °C the crystal structure is predominantly rutile. The nanotopographical features of the surface were found to be largely unchanged for heat treatments carried out at 500 °C or below, whereas they were partially or largely disrupted after heat treatment at 600 °C. The possible implications of these findings for the bioactivity of porous titanium structures are discussed.

  2. Structural Features of a Bacteroidetes-Affiliated Cellulase Linked with a Polysaccharide Utilization Locus

    PubMed Central

    Naas, A.E.; MacKenzie, A.K.; Dalhus, B.; Eijsink, V.G.H.; Pope, P.B.

    2015-01-01

    Previous gene-centric analysis of a cow rumen metagenome revealed the first potentially cellulolytic polysaccharide utilization locus, of which the main catalytic enzyme (AC2aCel5A) was identified as a glycoside hydrolase (GH) family 5 endo-cellulase. Here we present the 1.8 Å three-dimensional structure of AC2aCel5A, and characterization of its enzymatic activities. The enzyme possesses the archetypical (β/α)8-barrel found throughout the GH5 family, and contains the two strictly conserved catalytic glutamates located at the C-terminal ends of β-strands 4 and 7. The enzyme is active on insoluble cellulose and acts exclusively on linear β-(1,4)-linked glucans. Co-crystallization of a catalytically inactive mutant with substrate yielded a 2.4 Å structure showing cellotriose bound in the −3 to −1 subsites. Additional electron density was observed between Trp178 and Trp254, two residues that form a hydrophobic “clamp”, potentially interacting with sugars at the +1 and +2 subsites. The enzyme’s active-site cleft was narrower compared to the closest structural relatives, which in contrast to AC2aCel5A, are also active on xylans, mannans and/or xyloglucans. Interestingly, the structure and function of this enzyme seem adapted to less-substituted substrates such as cellulose, presumably due to the insufficient space to accommodate the side-chains of branched glucans in the active-site cleft. PMID:26133573

  3. Structural and Functional Features of a Developmentally Regulated Lipopolysaccharide-Binding Protein

    PubMed Central

    Krasity, Benjamin C.; Troll, Joshua V.; Lehnert, Erik M.; Hackett, Kathleen T.; Dillard, Joseph P.; Apicella, Michael A.; Goldman, William E.

    2015-01-01

    ABSTRACT Mammalian lipopolysaccharide (LPS) binding proteins (LBPs) occur mainly in extracellular fluids and promote LPS delivery to specific host cell receptors. The function of LBPs has been studied principally in the context of host defense; the possible role of LBPs in nonpathogenic host-microbe interactions has not been well characterized. Using the Euprymna scolopes-Vibrio fischeri model, we analyzed the structure and function of an LBP family protein, E. scolopes LBP1 (EsLBP1), and provide evidence for its role in triggering a symbiont-induced host developmental program. Previous studies showed that, during initial host colonization, the LPS of V. fischeri synergizes with peptidoglycan (PGN) monomer to induce morphogenesis of epithelial tissues of the host animal. Computationally modeled EsLBP1 shares some but not all structural features of mammalian LBPs that are thought important for LPS binding. Similar to human LBP, recombinant EsLBP1 expressed in insect cells bound V. fischeri LPS and Neisseria meningitidis lipooligosaccharide (LOS) with nanomolar or greater affinity but bound Francisella tularensis LPS only weakly and did not bind PGN monomer. Unlike human LBP, EsLBP1 did not bind N. meningitidis LOS:CD14 complexes. The eslbp1 transcript was upregulated ~22-fold by V. fischeri at 24 h postinoculation. Surprisingly, this upregulation was not induced by exposure to LPS but, rather, to the PGN monomer alone. Hybridization chain reaction-fluorescent in situ hybridization (HCR-FISH) and immunocytochemistry (ICC) localized eslbp1 transcript and protein in crypt epithelia, where V. fischeri induces morphogenesis. The data presented here provide a window into the evolution of LBPs and the scope of their roles in animal symbioses. PMID:26463160

  4. Fine structural features of radio-frequency radiation of the solar flare of February 12, 2010

    NASA Astrophysics Data System (ADS)

    Chernov, G. P.; Fomichev, V. V.; Gorgutsa, R. V.; Markeev, A. K.; Sobolev, D. E.; Hillaris, A.; Alissandrakis, K.

    2014-07-01

    Solar radio emission records received at the IZMIRAN spectrograph (25-270 MHz) during the solar flare event of February 12, 2010 are analyzed. Different fine structures were observed in three large groups of type III bursts against a low continuum. According to data from the Nancay radioheliograph, sources of all three groups of bursts were located in one active region, 11046, and their emissions were accompanied by soft X-ray bursts (GOES satellite): C7.9 at 0721 UT, B9.6 at 0940 UT, and M8.3 at 1125 UT. After the first group of bursts, classical fiber bursts were observed in combination with reverse-drift fiber bursts with unusual arc drift. After the third (the most powerful) group, stable second-length pulsations and slow-drift fiber bursts were observed, the instantaneous frequency bands of which were an order of magnitude larger than the frequency band of classical fiber bursts, and the frequency drift was several times lower. More complex fiber bursts were observed in the weakest group in the time range 0940:39-0942:00 UT. They were narrow-band (˜0.5 MHz) fiber bursts, periodically recurring in a narrow frequency band (5-6 MHz) during several seconds. The presence of many chaotically drifting ensembles of fibers, crossing and superimposing on one another, is a feature of this event. It is assumed that occurrence of these structures can be connected with the existence of many small shock fronts behind the leading edge of a coronal mass ejection.

  5. PEG-induced osmotic stress in Mentha x piperita L.: Structural features and metabolic responses.

    PubMed

    Búfalo, Jennifer; Rodrigues, Tatiane Maria; de Almeida, Luiz Fernando Rolim; Tozin, Luiz Ricardo Dos Santos; Marques, Marcia Ortiz Mayo; Boaro, Carmen Silvia Fernandes

    2016-08-01

    The present study investigated whether osmotic stress induced by the exposure of peppermint (Mentha x piperita L.) to moderate and severe stress for short periods of time changes the plant's physiological parameters, leaf anatomy and ultrastructure and essential oil. Plants were exposed to two levels of polyethyleneglycol (50 g L(-1) and 100 g L(-1) of PEG) in a hydroponic experiment. The plants exposed to 50 g L(-1) maintained metabolic functions similar to those of the control group (0 g L(-1)) without changes in gas exchange or structural characteristics. The increase in antioxidant enzyme activity reduced the presence of free radicals and protected membranes, including chloroplasts and mitochondria. In contrast, the osmotic stress caused by 100 g L(-1) of PEG inhibited leaf gas exchange, reduced the essential oil content and changed the oil composition, including a decrease in menthone and an increase in menthofuran. These plants also showed an increase in peroxidase activity, but this increase was not sufficient to decrease the lipid peroxidation level responsible for damaging the membranes of organelles. Morphological changes were correlated with the evaluated physiological features: plants exposed to 100 g L(-1) of PEG showed areas with collapsed cells, increases in mesophyll thickness and the area of the intercellular space, cuticle shrinkage, morphological changes in plastids, and lysis of mitochondria. In summary, our results revealed that PEG-induced osmotic stress in M. x piperita depends on the intensity level of the osmotic stress applied; severe osmotic stress changed the structural characteristics, caused damage at the cellular level, and reduced the essential oil content and quality. PMID:27107175

  6. Structural Features of the αβTCR Mechanotransduction Apparatus That Promote pMHC Discrimination

    PubMed Central

    Brazin, Kristine N.; Mallis, Robert J.; Das, Dibyendu Kumar; Feng, Yinnian; Hwang, Wonmuk; Wang, Jia-huai; Wagner, Gerhard; Lang, Matthew J.; Reinherz, Ellis L.

    2015-01-01

    The αβTCR was recently revealed to function as a mechanoreceptor. That is, it leverages mechanical energy generated during immune surveillance and at the immunological synapse to drive biochemical signaling following ligation by a specific foreign peptide–MHC complex (pMHC). Here, we review the structural features that optimize this transmembrane (TM) receptor for mechanotransduction. Specialized adaptations include (1) the CβFG loop region positioned between Vβ and Cβ domains that allosterically gates both dynamic T cell receptor (TCR)–pMHC bond formation and lifetime; (2) the rigid super β-sheet amalgams of heterodimeric CD3εγ and CD3εδ ectodomain components of the αβTCR complex; (3) the αβTCR subunit connecting peptides linking the extracellular and TM segments, particularly the oxidized CxxC motif in each CD3 heterodimeric subunit that facilitates force transfer through the TM segments and surrounding lipid, impacting cytoplasmic tail conformation; and (4) quaternary changes in the αβTCR complex that accompany pMHC ligation under load. How bioforces foster specific αβTCR-based pMHC discrimination and why dynamic bond formation is a primary basis for kinetic proofreading are discussed. We suggest that the details of the molecular rearrangements of individual αβTCR subunit components can be analyzed utilizing a combination of structural biology, single-molecule FRET, optical tweezers, and nanobiology, guided by insightful atomistic molecular dynamic studies. Finally, we review very recent data showing that the pre-TCR complex employs a similar mechanobiology to that of the αβTCR to interact with self-pMHC ligands, impacting early thymic repertoire selection prior to the CD4+CD8+ double positive thymocyte stage of development. PMID:26388869

  7. PEG-induced osmotic stress in Mentha x piperita L.: Structural features and metabolic responses.

    PubMed

    Búfalo, Jennifer; Rodrigues, Tatiane Maria; de Almeida, Luiz Fernando Rolim; Tozin, Luiz Ricardo Dos Santos; Marques, Marcia Ortiz Mayo; Boaro, Carmen Silvia Fernandes

    2016-08-01

    The present study investigated whether osmotic stress induced by the exposure of peppermint (Mentha x piperita L.) to moderate and severe stress for short periods of time changes the plant's physiological parameters, leaf anatomy and ultrastructure and essential oil. Plants were exposed to two levels of polyethyleneglycol (50 g L(-1) and 100 g L(-1) of PEG) in a hydroponic experiment. The plants exposed to 50 g L(-1) maintained metabolic functions similar to those of the control group (0 g L(-1)) without changes in gas exchange or structural characteristics. The increase in antioxidant enzyme activity reduced the presence of free radicals and protected membranes, including chloroplasts and mitochondria. In contrast, the osmotic stress caused by 100 g L(-1) of PEG inhibited leaf gas exchange, reduced the essential oil content and changed the oil composition, including a decrease in menthone and an increase in menthofuran. These plants also showed an increase in peroxidase activity, but this increase was not sufficient to decrease the lipid peroxidation level responsible for damaging the membranes of organelles. Morphological changes were correlated with the evaluated physiological features: plants exposed to 100 g L(-1) of PEG showed areas with collapsed cells, increases in mesophyll thickness and the area of the intercellular space, cuticle shrinkage, morphological changes in plastids, and lysis of mitochondria. In summary, our results revealed that PEG-induced osmotic stress in M. x piperita depends on the intensity level of the osmotic stress applied; severe osmotic stress changed the structural characteristics, caused damage at the cellular level, and reduced the essential oil content and quality.

  8. Crystal structures and inhibitor binding properties of plant class V chitinases: the cycad enzyme exhibits unique structural and functional features.

    PubMed

    Umemoto, Naoyuki; Kanda, Yuka; Ohnuma, Takayuki; Osawa, Takuo; Numata, Tomoyuki; Sakuda, Shohei; Taira, Toki; Fukamizo, Tamo

    2015-04-01

    A class V (glycoside hydrolase family 18) chitinase from the cycad Cycas revoluta (CrChiA) is a plant chitinase that has been reported to possess efficient transglycosylation (TG) activity. We solved the crystal structure of CrChiA, and compared it with those of class V chitinases from Nicotiana tabacum (NtChiV) and Arabidopsis thaliana (AtChiC), which do not efficiently catalyze the TG reaction. All three chitinases had a similar (α/β)8 barrel fold with an (α + β) insertion domain. In the acceptor binding site (+1, +2 and +3) of CrChiA, the Trp168 side chain was found to stack face-to-face with the +3 sugar. However, this interaction was not found in the identical regions of NtChiV and AtChiC. In the DxDxE motif, which is essential for catalysis, the carboxyl group of the middle Asp (Asp117) was always oriented toward the catalytic acid Glu119 in CrChiA, whereas the corresponding Asp in NtChiV and AtChiC was oriented toward the first Asp. These structural features of CrChiA appear to be responsible for the efficient TG activity. When binding of the inhibitor allosamidin was evaluated using isothermal titration calorimetry, the changes in binding free energy of the three chitinases were found to be similar to each other, i.e. between -9.5 and -9.8 kcal mol(-1) . However, solvation and conformational entropy changes in CrChiA were markedly different from those in NtChiV and AtChiC, but similar to those of chitinase A from Serratia marcescens (SmChiA), which also exhibits significant TG activity. These results provide insight into the molecular mechanism underlying the TG reaction and the molecular evolution from bacterial chitinases to plant class V chitinases.

  9. Structural features of cartilage matrix protein deduced from cDNA.

    PubMed Central

    Argraves, W S; Deák, F; Sparks, K J; Kiss, I; Goetinck, P F

    1987-01-01

    cDNAs encoding the Mr 54,000 chicken cartilage matrix protein (CMP) were selected from a cartilage cDNA expression library by immunological means. Antibodies elicited against insert-encoded protein purified from one of the clones reacted specifically with chicken CMP in immunoblots of total cartilage extract, providing positive identification of the cDNA clones isolated. The cDNAs detect a 3.4-kilobase transcript that was present in sternal cartilage and in cartilaginous but not in precartilaginous embryonic limb tissues. The cDNAs code for 416 amino acids of the chicken CMP, including its COOH terminus. There are two striking features in the deduced CMP amino acid sequence: first, it contains a region with significant homologies to repeat sequences in the precursor for epidermal growth factor; and second, it is made up of two large homologous repeat sequences. These results provide the first detailed structural information on the CMP and establish it as a developmentally regulated marker of cartilage differentiation. Images PMID:3025875

  10. Structural features of Fab fragments of rheumatoid factor IgM-RF in solution

    SciTech Connect

    Volkov, V. V.; Lapuk, V. A.; Shtykova, E. V.; Stepina, N. D.; Dembo, K. A.; Sokolova, A. V.; Amarantov, S. V.; Timofeev, V. P.; Ziganshin, R. Kh.; Varlamova, E. Yu.

    2008-05-15

    The structural features of the Fab fragments of monoclonal (Waldenstroem's disease) immunoglobulin M (IgM) and rheumatoid immunoglobulin M (IgM-RF) were studied by a complex of methods, including small-angle X-ray scattering (SAXS), electron spin resonance (ESR), and mass spectrometry (MS). The Fab-RF fragment was demonstrated to be much more flexible in the region of interdomain contacts, the molecular weights and the shapes of the Fab and Fab-RF macromolecules in solution being only slightly different. According to the ESR data, the rotational correlation time for a spin label introduced into the peptide sequence for Fab is twice as large as that for Fab-RF (21{+-}2 and 11{+-}1 ns, respectively), whereas the molecular weights of these fragments differ by only 0.5% (mass-spectrometric data), which correlates with the results of molecular-shape modeling by small-angle X-ray scattering. The conclusion about the higher flexibility of the Fab-RF fragment contributes to an understanding of the specificity of interactions between the rheumatoid factor and the antigens of the own organism.

  11. Structural features of Fab fragments of rheumatoid factor IgM-RF in solution

    NASA Astrophysics Data System (ADS)

    Volkov, V. V.; Lapuk, V. A.; Shtykova, E. V.; Stepina, N. D.; Dembo, K. A.; Sokolova, A. V.; Amarantov, S. V.; Timofeev, V. P.; Ziganshin, R. Kh.; Varlamova, E. Yu.

    2008-05-01

    The structural features of the Fab fragments of monoclonal (Waldenström’s disease) immunoglobulin M (IgM) and rheumatoid immunoglobulin M (IgM-RF) were studied by a complex of methods, including small-angle X-ray scattering (SAXS), electron spin resonance (ESR), and mass spectrometry (MS). The Fab-RF fragment was demonstrated to be much more flexible in the region of interdomain contacts, the molecular weights and the shapes of the Fab and Fab-RF macromolecules in solution being only slightly different. According to the ESR data, the rotational correlation time for a spin label introduced into the peptide sequence for Fab is twice as large as that for Fab-RF (21±2 and 11±1 ns, respectively), whereas the molecular weights of these fragments differ by only 0.5% (mass-spectrometric data), which correlates with the results of molecular-shape modeling by small-angle X-ray scattering. The conclusion about the higher flexibility of the Fab-RF fragment contributes to an understanding of the specificity of interactions between the rheumatoid factor and the antigens of the own organism.

  12. Shear horizontal feature guided ultrasonic waves in plate structures with 90° transverse bends.

    PubMed

    Yu, Xudong; Manogharan, Prabhakaran; Fan, Zheng; Rajagopal, Prabhu

    2016-02-01

    Antisymmetric and symmetric Lamb-type feature guided waves (FGW) have recently been shown to exist in small angle plate bends. This paper reports Semi-Analytical Finite Element (SAFE) method simulations revealing the existence of a new family of Shear Horizontal (SHB) type of FGW mode in 90° bends in plate structures. Mode shapes and velocity dispersion curves are extracted, demonstrating the SH-like nature of a bend-confined mode identified in studies of power flow across the bend. The SHB mode is shown to have reduced attenuation in the higher frequency range, making it an ideal choice for high-resolution inspection of such bends. Further modal studies examine the physical basis for mode confinement, and argue that this is strongly related to FGW phenomena reported earlier, and also linked to the curvature at the bend region. Wedge acoustic waves discussed widely in literature are shown as arising from surface-limiting of the SHB mode at higher frequencies. The results are validated by experiments and supported by 3D Finite Element (FE) simulations. PMID:26409768

  13. Structural and Dynamic Features of F-recruitment Site Driven Substrate Phosphorylation by ERK2

    PubMed Central

    Piserchio, Andrea; Ramakrishan, Venkatesh; Wang, Hsin; Kaoud, Tamer S.; Arshava, Boris; Dutta, Kaushik; Dalby, Kevin N.; Ghose, Ranajeet

    2015-01-01

    The F-recruitment site (FRS) of active ERK2 binds F-site (Phe-x-Phe-Pro) sequences found downstream of the Ser/Thr phospho-acceptor on cellular substrates. Here we apply NMR methods to analyze the interaction between active ERK2 (ppERK2), and a 13-residue F-site-bearing peptide substrate derived from its cellular target, the transcription factor Elk-1. Our results provide detailed insight into previously elusive structural and dynamic features of FRS/F-site interactions and FRS-driven substrate phosphorylation. We show that substrate F-site engagement significantly quenches slow dynamics involving the ppERK2 activation-loop and the FRS. We also demonstrate that the F-site phenylalanines make critical contacts with ppERK2, in contrast to the proline whose cis-trans isomerization has no significant effect on F-site recognition by the kinase FRS. Our results support a mechanism where phosphorylation of the disordered N-terminal phospho-acceptor is facilitated by its increased productive encounters with the ppERK2 active site due to docking of the proximal F-site at the kinase FRS. PMID:26054059

  14. Computation identifies structural features that govern neuronal firing properties in slowly adapting touch receptors

    PubMed Central

    Lesniak, Daine R; Marshall, Kara L; Wellnitz, Scott A; Jenkins, Blair A; Baba, Yoshichika; Rasband, Matthew N; Gerling, Gregory J; Lumpkin, Ellen A

    2014-01-01

    Touch is encoded by cutaneous sensory neurons with diverse morphologies and physiological outputs. How neuronal architecture influences response properties is unknown. To elucidate the origin of firing patterns in branched mechanoreceptors, we combined neuroanatomy, electrophysiology and computation to analyze mouse slowly adapting type I (SAI) afferents. These vertebrate touch receptors, which innervate Merkel cells, encode shape and texture. SAI afferents displayed a high degree of variability in touch-evoked firing and peripheral anatomy. The functional consequence of differences in anatomical architecture was tested by constructing network models representing sequential steps of mechanosensory encoding: skin displacement at touch receptors, mechanotransduction and action-potential initiation. A systematic survey of arbor configurations predicted that the arrangement of mechanotransduction sites at heminodes is a key structural feature that accounts in part for an afferent’s firing properties. These findings identify an anatomical correlate and plausible mechanism to explain the driver effect first described by Adrian and Zotterman. DOI: http://dx.doi.org/10.7554/eLife.01488.001 PMID:24448409

  15. Melting and cataclastic features in shatter cones in basalt from the Vista Alegre impact structure, Brazil

    NASA Astrophysics Data System (ADS)

    Pittarello, Lidia; Nestola, Fabrizio; Viti, Cecilia; Crósta, Alvaro Penteado; Koeberl, Christian

    2015-07-01

    Shatter cones are one of the most widely recognized pieces of evidence for meteorite impact events on Earth, but the process responsible for their formation is still debated. Evidence of melting on shatter cone surfaces has been rarely reported in the literature from terrestrial impact craters but has been recently observed in impact experiments. Although several models for shatter cones formation have been proposed, so far, no one can explain all the observed features. Shatter cones' from the Vista Alegre impact structure, Brazil, formed in fine-grained basalt of the Jurassic-Cretaceous Serra Geral Formation (Paraná large igneous province). A continuous quenched melt film, consisting of a crystalline phase, mica, and amorphous material, decorates the striated surface. Ultracataclasites, containing subrounded pyroxene clasts in an ultrafine-grained matrix, occur subparallel to the striated surface. Several techniques were applied to characterize the crystalline phase in the melt, including Raman spectroscopy and transmission electron microscopy. Results are not consistent with any known mineral, but they do suggest a possible rare or new type of clinopyroxene. This peculiar evidence of melting and cataclasis in relation with shatter cone surfaces is interpreted as the result of tensile fracturing at the tip of a fast propagating shock-induced rupture, which led to the formation of shatter cones at the tail of the shock front, likely during the early stage of the impact events.

  16. The effects of major structural features in Western China on explosion seismograms

    SciTech Connect

    Jones, E.M.; App, F.N.; Bos, R.J.

    1997-11-01

    Synthetic explosion seismograms have been calculated on paths from Lop Nor to the NIL station in northern Pakistan, from NIL to Lop Nor, and from Lop Nor to the TLY station in the Baikal Rift. Computational studies were done of the influence on the character of the seismograms of major structural features such as sedimentary basins, topography associated with the Himalayas and the Tibetan Plateau, roughness of the Moho, and the presence of a deep Moho depression under the Tibetan Plateau, roughness of the Moho, and the presence of a deep Moho done with a 1-Hz Kelly waves source and 500-m resolution. Uniform elastic constants and frequency-independent quality factors, Q{sub p} and Q{sub s}, were used in each of three materials: basin sediments, crust, and mantle. The deep basins which due to the generation of large-amplitude Rayleigh waves at source-ward basin edges. In simulations done with the effects of anelastic attenuation included, the amplitude of passage across the 800-km-wide Tarim Basin on the Lop Nor -> NIL path but not on the 200-km path across the basin that straddles the Lop Nor -> TLY path.

  17. Segmentation of anatomical branching structures based on texture features and conditional random field

    NASA Astrophysics Data System (ADS)

    Nuzhnaya, Tatyana; Bakic, Predrag; Kontos, Despina; Megalooikonomou, Vasileios; Ling, Haibin

    2012-02-01

    This work is a part of our ongoing study aimed at understanding a relation between the topology of anatomical branching structures with the underlying image texture. Morphological variability of the breast ductal network is associated with subsequent development of abnormalities in patients with nipple discharge such as papilloma, breast cancer and atypia. In this work, we investigate complex dependence among ductal components to perform segmentation, the first step for analyzing topology of ductal lobes. Our automated framework is based on incorporating a conditional random field with texture descriptors of skewness, coarseness, contrast, energy and fractal dimension. These features are selected to capture the architectural variability of the enhanced ducts by encoding spatial variations between pixel patches in galactographic image. The segmentation algorithm was applied to a dataset of 20 x-ray galactograms obtained at the Hospital of the University of Pennsylvania. We compared the performance of the proposed approach with fully and semi automated segmentation algorithms based on neural network classification, fuzzy-connectedness, vesselness filter and graph cuts. Global consistency error and confusion matrix analysis were used as accuracy measurements. For the proposed approach, the true positive rate was higher and the false negative rate was significantly lower compared to other fully automated methods. This indicates that segmentation based on CRF incorporated with texture descriptors has potential to efficiently support the analysis of complex topology of the ducts and aid in development of realistic breast anatomy phantoms.

  18. Structural and immunological feature of rhamnogalacturonan I-rich polysaccharide from Korean persimmon vinegar.

    PubMed

    Kim, Hoon; Hong, Hee-Do; Suh, Hyung-Joo; Shin, Kwang-Soon

    2016-08-01

    The crude polysaccharide (KPV-0) isolated from Korean persimmon vinegar was fractionated using gel filtration chromatography to enhance the immunostimulatory activity and to identify the structural features of active fraction. Among three fractions, KPV-I obtained in a void volume, demonstrated the potent production of macrophage-stimulating mediators, including tumor necrosis factor-α, interleukin (IL)-6, IL-12, and nitric oxide. KPV-I showed a combined single peak with high molecular weight of 55,000Da by high performance size exclusion chromatography. Component sugar analysis revealed that KPV-I contained mainly of arabinose, mannose, galactose, rhamnose and galacturonic acid. Single radial gel diffusion assay using β-glucosyl Yariv reagent showed that KPV-I contained arabinogalactan protein with 13.7%. Methylation analysis indicated that KPV-I contained 21 kinds of neutral glycosidic linkages, which seemed to be composed three kinds of polysaccharide; that is a rhamnogalacturonan-I (65-70%) derived from persimmon as a raw material, a mannan (20-25%) derived from fermentation-associated microorganisms, and a linear glucans (less than 10%). In conclusion, polysaccharide isolated from persimmon vinegar could augment the macrophage stimulation, and a large amounts of RG-I polysaccharide derived from persimmon is likely a crucial role in expression of the activity in persimmon vinegar. PMID:27131731

  19. A new magnetorheological mount featured by changeable damping gaps using a moved-plate valve structure

    NASA Astrophysics Data System (ADS)

    Phu, Do Xuan; Shah, Kruti; Choi, Seung-Bok

    2014-12-01

    In this work, a new type of a magnetorheological (MR) fluid mount is proposed and its performances are experimentally investigated. The design of this MR mount is based on two operating modes of MR fluid: flow mode and shear mode. These modes are applied to the mechanism design consisting of two components: a fixed plate for applying the flow mode, and a moved plate for applying the shear mode of MR fluid motion. These plates belong to the valve-type structure of MR mount. The primary objective using the moved plate is to overcome the block-up phenomenon which frequently occurs in the conventional-type MR mount, in which there is no flow of MR fluid through the damping gap. In this research, a laboratorial fluid (MRF140) is used in the design and optimization of MR mount. This fluid features plate-like particles unlike the sphere particles. The yield stress of the fluid is measured as a function of the magnetic field and the theoretical analysis for the mount design is undertaken using the properties of the MR fluid, followed by design optimization. The objective function is concentrated on maximal damping force of the MR mount subjected to parameter constraints. Based on the results of optimization, the proposed MR mount is manufactured and tested for the performance evaluation. Vibration control capability and block-up phenomenon are investigated and compared between the proposed and conventional MR mounts.

  20. Mental Imagery Scale: a new measurement tool to assess structural features of mental representations

    NASA Astrophysics Data System (ADS)

    D'Ercole, Martina; Castelli, Paolo; Giannini, Anna Maria; Sbrilli, Antonella

    2010-05-01

    Mental imagery is a quasi-perceptual experience which resembles perceptual experience, but occurring without (appropriate) external stimuli. It is a form of mental representation and is often considered centrally involved in visuo-spatial reasoning and inventive and creative thought. Although imagery ability is assumed to be functionally independent of verbal systems, it is still considered to interact with verbal representations, enabling objects to be named and names to evoke images. In literature, most measurement tools for evaluating imagery capacity are self-report instruments focusing on differences in individuals. In the present work, we applied a Mental Imagery Scale (MIS) to mental images derived from verbal descriptions in order to assess the structural features of such mental representations. This is a key theme for those disciplines which need to turn objects and representations into words and vice versa, such as art or architectural didactics. To this aim, an MIS questionnaire was administered to 262 participants. The questionnaire, originally consisting of a 33-item 5-step Likert scale, was reduced to 28 items covering six areas: (1) Image Formation Speed, (2) Permanence/Stability, (3) Dimensions, (4) Level of Detail/Grain, (5) Distance and (6) Depth of Field or Perspective. Factor analysis confirmed our six-factor hypothesis underlying the 28 items.

  1. Rhamnoarabinosyl and rhamnoarabinoarabinosyl side chains as structural features of coffee arabinogalactans.

    PubMed

    Nunes, Fernando M; Reis, Ana; Silva, Artur M S; Domingues, M Rosário M; Coimbra, Manuel A

    2008-05-01

    The hot water soluble green coffee arabinogalactans, representing nearly 7% of total coffee bean arabinogalactans, were characterized by (1)H and (13)C NMR and, after partial acid hydrolysis, by ESI-MS/MS. Data obtained showed that these are highly branched type II arabinogalactans covalently linked to proteins (AGP), with a protein moiety containing 10% of 4-hydroxyproline residues. They possess a beta-(1-->3)-Galp/beta-(1-->3,6)-Galp ratio of 0.80, with a sugars composition of Rha:Ara:Gal of 0.25:1.0:1.5, and containing 2mol% of glucuronic acid residues. Beyond the occurrence of single alpha-L-Araf residues and [alpha-L-Araf-(1-->5)-alpha-L-Araf-(1-->] disaccharide residues as side chains, these AGPs contain unusual side chains at O-3 position of the beta-(1-->6)-linked galactopyranosyl residues composed by [alpha-L-Rhap-(1-->5)-alpha-L-Araf-(1-->] and [alpha-L-Rhap-(1-->5)-alpha-L-Araf-(1-->5)-alpha-L-Araf-(1-->] oligosaccharides. Rhamnoarabinosyl and rhamnoarabinoarabinosyl side chains are reported for the first time as structural features of plant arabinogalactan-proteins.

  2. Structural and immunological feature of rhamnogalacturonan I-rich polysaccharide from Korean persimmon vinegar.

    PubMed

    Kim, Hoon; Hong, Hee-Do; Suh, Hyung-Joo; Shin, Kwang-Soon

    2016-08-01

    The crude polysaccharide (KPV-0) isolated from Korean persimmon vinegar was fractionated using gel filtration chromatography to enhance the immunostimulatory activity and to identify the structural features of active fraction. Among three fractions, KPV-I obtained in a void volume, demonstrated the potent production of macrophage-stimulating mediators, including tumor necrosis factor-α, interleukin (IL)-6, IL-12, and nitric oxide. KPV-I showed a combined single peak with high molecular weight of 55,000Da by high performance size exclusion chromatography. Component sugar analysis revealed that KPV-I contained mainly of arabinose, mannose, galactose, rhamnose and galacturonic acid. Single radial gel diffusion assay using β-glucosyl Yariv reagent showed that KPV-I contained arabinogalactan protein with 13.7%. Methylation analysis indicated that KPV-I contained 21 kinds of neutral glycosidic linkages, which seemed to be composed three kinds of polysaccharide; that is a rhamnogalacturonan-I (65-70%) derived from persimmon as a raw material, a mannan (20-25%) derived from fermentation-associated microorganisms, and a linear glucans (less than 10%). In conclusion, polysaccharide isolated from persimmon vinegar could augment the macrophage stimulation, and a large amounts of RG-I polysaccharide derived from persimmon is likely a crucial role in expression of the activity in persimmon vinegar.

  3. Features of Bayou Choctaw SPR caverns and internal structure of the salt dome.

    SciTech Connect

    Munson, Darrell E.

    2007-07-01

    The intent of this study is to examine the internal structure of the Bayou Choctaw salt dome utilizing the information obtained from graphical representations of sonar survey data of the internal cavern surfaces. Many of the Bayou Choctaw caverns have been abandoned. Some existing caverns were purchased by the Strategic Petroleum Reserve (SPR) program and have rather convoluted histories and complex cavern geometries. In fact, these caverns are typically poorly documented and are not particularly constructive to this study. Only two Bayou Choctaw caverns, 101 and 102, which were constructed using well-controlled solutioning methods, are well documented. One of these was constructed by the SPR for their use while the other was constructed and traded for another existing cavern. Consequently, compared to the SPR caverns of the West Hackberry and Big Hill domes, it is more difficult to obtain a general impression of the stratigraphy of the dome. Indeed, caverns of Bayou Choctaw show features significantly different than those encountered in the other two SPR facilities. In the number of abandoned caverns, and some of those existing caverns purchased by the SPR, extremely irregular solutioning has occurred. The two SPR constructed caverns suggest that some sections of the caverns may have undergone very regular solutioning to form uniform cylindrical shapes. Although it is not usually productive to speculate, some suggestions that point to the behavior of the Bayou Choctaw dome are examined. Also the primary differences in the Bayou Choctaw dome and the other SPR domes are noted.

  4. Shear horizontal feature guided ultrasonic waves in plate structures with 90° transverse bends.

    PubMed

    Yu, Xudong; Manogharan, Prabhakaran; Fan, Zheng; Rajagopal, Prabhu

    2016-02-01

    Antisymmetric and symmetric Lamb-type feature guided waves (FGW) have recently been shown to exist in small angle plate bends. This paper reports Semi-Analytical Finite Element (SAFE) method simulations revealing the existence of a new family of Shear Horizontal (SHB) type of FGW mode in 90° bends in plate structures. Mode shapes and velocity dispersion curves are extracted, demonstrating the SH-like nature of a bend-confined mode identified in studies of power flow across the bend. The SHB mode is shown to have reduced attenuation in the higher frequency range, making it an ideal choice for high-resolution inspection of such bends. Further modal studies examine the physical basis for mode confinement, and argue that this is strongly related to FGW phenomena reported earlier, and also linked to the curvature at the bend region. Wedge acoustic waves discussed widely in literature are shown as arising from surface-limiting of the SHB mode at higher frequencies. The results are validated by experiments and supported by 3D Finite Element (FE) simulations.

  5. The modern face of prejudice and structural features that moderate the effect of cooperation on affect.

    PubMed

    Vanman, E J; Paul, B Y; Ito, T A; Miller, N

    1997-11-01

    Facial muscle activity and self-reports were examined for racial bias in 3 studies. In the first 2 experiments, While participants imagined cooperating with a Black or White partner. Experiment 1 manipulated reward structure in the context of cooperating with a deficient partner. Experiment 2 manipulated partner deficiency and willingness to expend compensatory effort. On both facial EMG and self-report measures, joint rewards produced more negative affect than independent rewards. However, all partners were liked more when they were willing to try to compensate for their deficits. In addition, more liking was reported for Black partners, but EMG activity indicated bias against Blacks. Experiment 3 investigated individual differences in prejudice. Again, a greater preference for Blacks than Whites occurred on self-report measures, but in their facial muscle activity, high-prejudiced participants exhibited bias against Blacks. PMID:9364754

  6. Impact of zeolite-based nanomodified additive on the structure and strength of the cement stone

    NASA Astrophysics Data System (ADS)

    Egorova, A. D.; Filippova, K. E.

    2015-01-01

    Portland cement is the main binder in the building materials industry; its properties strongly influence properties of mortars and concretes. Some regions experience difficulties with delivery and storage of Portland cement, raising the need to develop an effective additive from the available raw materials. Such materials for the Republic of Sakha (Yakutia) are zeolite-containing rocks. Studies have shown that introducing of dibutylphthalate to the composition of modified additive during mechanochemical activation leads to achievement of up to 11% of total amount particles with the size of 3-30 nm. After introducing 0.5% of the obtained additives, the compressive strength of cement-sand slurry samples increases up to 28%. Positive effect of additives introduction is also observed at high flow rate of water (W / C = 0.7). Gaining strength reaches 23%, allowing the efficient use of additive for movable mixtures with enhanced strength properties. In general, the proposed supplement allows reducing the water flow in the solution without decreasing its mobility, and increasing strength properties, which makes it possible to obtain a whole class of solutions of modified cement binder. The market value of the developed additives is 18 rubles per 1 kg, making sound competition in the market of modifying additives.

  7. Mutagenicity in a Molecule: Identification of Core Structural Features of Mutagenicity Using a Scaffold Analysis

    PubMed Central

    Hsu, Kuo-Hsiang; Su, Bo-Han; Tu, Yi-Shu; Lin, Olivia A.; Tseng, Yufeng J.

    2016-01-01

    With advances in the development and application of Ames mutagenicity in silico prediction tools, the International Conference on Harmonisation (ICH) has amended its M7 guideline to reflect the use of such prediction models for the detection of mutagenic activity in early drug safety evaluation processes. Since current Ames mutagenicity prediction tools only focus on functional group alerts or side chain modifications of an analog series, these tools are unable to identify mutagenicity derived from core structures or specific scaffolds of a compound. In this study, a large collection of 6512 compounds are used to perform scaffold tree analysis. By relating different scaffolds on constructed scaffold trees with Ames mutagenicity, four major and one minor novel mutagenic groups of scaffold are identified. The recognized mutagenic groups of scaffold can serve as a guide for medicinal chemists to prevent the development of potentially mutagenic therapeutic agents in early drug design or development phases, by modifying the core structures of mutagenic compounds to form non-mutagenic compounds. In addition, five series of substructures are provided as recommendations, for direct modification of potentially mutagenic scaffolds to decrease associated mutagenic activities. PMID:26863515

  8. The "dark side" of β-lactoglobulin: unedited structural features suggest unexpected functions.

    PubMed

    Ferranti, Pasquale; Mamone, Gianfranco; Picariello, Gianluca; Addeo, Francesco

    2011-06-01

    The in-depth characterization of water buffalo (WB) whey proteins based on chromatographic and mass spectrometric techniques revealed unexpected structural co- and post-translational modifications for β-lactoglobulin (β-Lg). The residues Lys⁴⁷ and Lys⁶⁹ of β-Lg were found to be lactosylated early, at the time of milking. Thiol groups of β-Lg underwent a dynamic sulfhydryl/disulfide exchange that is probably essential in accomplishing specific physiological requirements in which proteins may alternatively act either as a trigger or as a target. In this sense, the free sulfhydryl group of β-Lg established a glutathionylation/deglutathionylation equilibrium, which could be functional in conveying and delivering glutathione. Furthermore, the N-lauroylated β-Lg occurring exclusively in WB milk has been characterized for the first time. N-acylation could be an evolutionary remnant of ancestral lipocalins. Combined with the known aptitude of β-Lg to interact with phospholipid bilayers, this suggests that the protein could also be involved in the membrane translocation of small molecules, in addition to targeting, trafficking or the maintenance of membrane integrity. This structural characterization of β-Lg adds to the currently existing data and expands our understanding of the possible biological roles of this enigmatic protein.

  9. Performing effective feature selection by investigating the deep structure of the data

    SciTech Connect

    Richeldi, M.; Lanzi, P.L.

    1996-12-31

    This paper introduces ADHOC (Automatic Discoverer of Fligher-Order Correlation), an algorithm that combines the advantages of both filter and feedback models to enhance the understanding of the given data and to increase the efficiency of the feature selection process. ADHOC partitions the observed features into a number of groups, called factors, that reflect the major dimensions of the phenomenon under consideration. The set of learned factors define the starting point of the search of the best performing feature subset. A genetic algorithm is used to explore the feature space originated by the factors and to determine the set of most informative feature configurations. The feature subset evaluation function is the performance of the induction algorithm. This approach offers three main advantages: (i) the likelihood of selecting good performing features grows; (ii) the complexity of search diminishes consistently; (iii) the possibility of selecting a bad feature subset due to overfitting problems decreases. Extensive experiments on real-world data have been conducted to demonstrate the effectiveness of ADHOC as data reduction technique as well as feature selection method.

  10. Effects of meat addition on pasta structure, nutrition and in vitro digestibility.

    PubMed

    Liu, Tingting; Hamid, Nazimah; Kantono, Kevin; Pereira, Loveena; Farouk, Mustafa M; Knowles, Scott O

    2016-12-15

    In our study, semolina flour was substituted with beef emulsion (EM) at three different levels of 15, 30 and 45% (w/w) to develop a pasta with enhanced nutritional profile. The protein, fat, and water content significantly increased with addition of meat. The addition of meat enhanced the pasta gluten network. The redness and yellowness of cooked pasta increased with meat addition. Tensile strength increased from 0.018N/mm(2) in the control sample to 0.046N/mm(2) in 45% beef emulsion (45EM) sample. All meat-containing samples had significantly higher elasticity than control (0.039N/mm(2)). GI significantly decreased and IVPD value increased in 45EM sample. Five essential amino acids (leucine, lysine, methionine, threonine, tryptophan) in pasta digesta increased significantly with increasing meat addition.

  11. Effects of meat addition on pasta structure, nutrition and in vitro digestibility.

    PubMed

    Liu, Tingting; Hamid, Nazimah; Kantono, Kevin; Pereira, Loveena; Farouk, Mustafa M; Knowles, Scott O

    2016-12-15

    In our study, semolina flour was substituted with beef emulsion (EM) at three different levels of 15, 30 and 45% (w/w) to develop a pasta with enhanced nutritional profile. The protein, fat, and water content significantly increased with addition of meat. The addition of meat enhanced the pasta gluten network. The redness and yellowness of cooked pasta increased with meat addition. Tensile strength increased from 0.018N/mm(2) in the control sample to 0.046N/mm(2) in 45% beef emulsion (45EM) sample. All meat-containing samples had significantly higher elasticity than control (0.039N/mm(2)). GI significantly decreased and IVPD value increased in 45EM sample. Five essential amino acids (leucine, lysine, methionine, threonine, tryptophan) in pasta digesta increased significantly with increasing meat addition. PMID:27451161

  12. Effect of additives on the structure, nanomorphology and efficiency of PCPDTBT: PC71BM solar cells

    NASA Astrophysics Data System (ADS)

    Imamura, Shogo; Palanisamy, Kumar; Kannappan, Santhakumar; Ochiai, Shizuyasu

    2012-08-01

    We investigated the effect of additives on the morphology of a poly[2,6-(4,4-bis-(2-ethylhexyl)-4H-cyclopenta[2,1-b;3,4-b']dithiophene)-alt-4,7-(2,1,3-benzothiadiazole)] (PCPDTBT):(6,6)-phenyl C71-butyric acid methyl ester (PC71BM) blended onto a surface of poly (3, 4-ethylendioxythiophene): poly(styrensulfonate)(PEDOT:PSS) to form photoactive films. Films of PCPDTBT: PC71-BM bulk heterojunctions were prepared by spin-coating from a solution in chlorobenzene (CB) and were processed with and without the addition of 2%, 4%, and 6 vol% 1-chloro naphthalene (CN) or 1, 8-octanedithiol (ODT) as additives. For all samples, the PCPDTBT:PC71BM molar ratio was 1:2 (wt%), and the additives in 1 ml were prepared with a concentration of 30 mg of PCPDTBT:PC71BM. Optical absorption spectroscopy measurements of the films indicated shifts in the absorption peaks in the range from 500-800 nm which was attributed to PCPDTBT. XRay diffraction (XRD) was used to investigate the nature of the molecular stacking in the polymer thin films. Topographic images which were obtained by using an atomic force microscope, of the PCPDTBT:PC71BM layers with 2 vol% ODT additive, were found to have the highest surface roughness. The best performing device shows a power conversion efficiency of 2.15% for a 2-vol% ODT additive.

  13. Stable feature selection for clinical prediction: exploiting ICD tree structure using Tree-Lasso.

    PubMed

    Kamkar, Iman; Gupta, Sunil Kumar; Phung, Dinh; Venkatesh, Svetha

    2015-02-01

    Modern healthcare is getting reshaped by growing Electronic Medical Records (EMR). Recently, these records have been shown of great value towards building clinical prediction models. In EMR data, patients' diseases and hospital interventions are captured through a set of diagnoses and procedures codes. These codes are usually represented in a tree form (e.g. ICD-10 tree) and the codes within a tree branch may be highly correlated. These codes can be used as features to build a prediction model and an appropriate feature selection can inform a clinician about important risk factors for a disease. Traditional feature selection methods (e.g. Information Gain, T-test, etc.) consider each variable independently and usually end up having a long feature list. Recently, Lasso and related l1-penalty based feature selection methods have become popular due to their joint feature selection property. However, Lasso is known to have problems of selecting one feature of many correlated features randomly. This hinders the clinicians to arrive at a stable feature set, which is crucial for clinical decision making process. In this paper, we solve this problem by using a recently proposed Tree-Lasso model. Since, the stability behavior of Tree-Lasso is not well understood, we study the stability behavior of Tree-Lasso and compare it with other feature selection methods. Using a synthetic and two real-world datasets (Cancer and Acute Myocardial Infarction), we show that Tree-Lasso based feature selection is significantly more stable than Lasso and comparable to other methods e.g. Information Gain, ReliefF and T-test. We further show that, using different types of classifiers such as logistic regression, naive Bayes, support vector machines, decision trees and Random Forest, the classification performance of Tree-Lasso is comparable to Lasso and better than other methods. Our result has implications in identifying stable risk factors for many healthcare problems and therefore can

  14. Assessment of the micro-structure and depletion potentials in two-dimensional binary mixtures of additive hard-disks.

    PubMed

    Perera-Burgos, Jorge Adrián; Méndez-Alcaraz, José Miguel; Pérez-Ángel, Gabriel; Castañeda-Priego, Ramón

    2016-09-14

    Depletion forces are a particular class of effective interactions that have been mainly investigated in binary mixtures of hard-spheres in bulk. Although there are a few contributions that point toward the effects of confinement on the depletion potential, little is known about such entropic potentials in two-dimensional colloidal systems. From theoretical point of view, the problem resides in the fact that there is no general formulation of depletion forces in arbitrary dimensions and, typically, any approach that works well in three dimensions has to be reformulated for lower dimensionality. However, we have proposed a theoretical framework, based on the formalism of contraction of the description within the integral equations theory of simple liquids, to account for effective interactions in colloidal liquids, whose main feature is that it does not need to be readapted to the problem under consideration. We have also shown that such an approach allows one to determine the depletion pair potential in three-dimensional colloidal mixtures even near to the demixing transition, provided the bridge functions are sufficiently accurate to correctly describe the spatial correlation between colloids [E. López-Sánchez et al., J. Chem. Phys. 139, 104908 (2013)]. We here report an extensive analysis of the structure and the entropic potentials in binary mixtures of additive hard-disks. In particular, we show that the same functional form of the modified-Verlet closure relation used in three dimensions can be straightforwardly employed to obtain an accurate solution for two-dimensional colloidal mixtures in a wide range of packing fractions, molar fractions, and size asymmetries. Our theoretical results are explicitly compared with the ones obtained by means of event-driven molecular dynamics simulations and recent experimental results. Furthermore, to assess the accuracy of our predictions, the depletion potentials are used in an effective one-component model to reproduce

  15. Landscape structure, organization and processes revealed through micro-topographic features

    NASA Astrophysics Data System (ADS)

    Kumar, Praveen; Le, Phong; Dutta, Debsunder; Goodwell, Allison

    2014-05-01

    High-resolution Lidar topography and Airborne Visible/Infrared Imaging Spectrometer (AVIRIS) remote sensing data are becoming increasingly available over large regions of the Earth's surface. These data sets can be linked to reveal processes and landscape features that cannot be detected at lower resolutions. In May 2011, the Bird's Point New Madrid Floodway in southeastern Missouri was intentionally breached during extreme Mississippi and Ohio River flooding. Pre- and post-flood Lidar and post-flood AVIRIS data enable study of flood geomorphic impacts and the biogeochemical state of the floodplain. Differential Lidar quantifies erosion and deposition, while empirical, statistical and data mining techniques are employed to investigate soil properties from AVIRIS. Vegetation, soil properties, and flood exposure are linked to observed geomorphic impacts that indicate landscape vulnerability to flood events. We find that the distribution of micro-topographic depressions in the landscape, such as surface area, volume storage, and the distance to the nearest neighbor follows a power scaling law. Additionally, we develop an approach to characterize and quantify the spatial correlations of different surface textural properties and chemical constituents with the distribution of depressions using the same high resolution Lidar and AVIRIS data sets. Topographical floodplain legacies such as former meander scar ridges correlate to soil characteristics and vegetation within the floodplain, and also dictate much of the geomorphic impacts of the levee breach and subsequent inundation. This study highlights approaches in which high-resolution data sets can be linked to reveal important landscape properties and analyze impacts of extreme events and long-term legacy effects.

  16. Telomere Capping Proteins are Structurally Related to RPA with an additional Telomere-Specific Domain

    SciTech Connect

    Gelinas, A.; Paschini, M; Reyes, F; Heroux, A; Batey, R; Lundblad, V; Wuttke, D

    2009-01-01

    Telomeres must be capped to preserve chromosomal stability. The conserved Stn1 and Ten1 proteins are required for proper capping of the telomere, although the mechanistic details of how they contribute to telomere maintenance are unclear. Here, we report the crystal structures of the C-terminal domain of the Saccharomyces cerevisiae Stn1 and the Schizosaccharomyces pombe Ten1 proteins. These structures reveal striking similarities to corresponding subunits in the replication protein A complex, further supporting an evolutionary link between telomere maintenance proteins and DNA repair complexes. Our structural and in vivo data of Stn1 identify a new domain that has evolved to support a telomere-specific role in chromosome maintenance. These findings endorse a model of an evolutionarily conserved mechanism of DNA maintenance that has developed as a result of increased chromosomal structural complexity.

  17. Prediction of Conversion from Mild Cognitive Impairment to Alzheimer's Disease Using MRI and Structural Network Features.

    PubMed

    Wei, Rizhen; Li, Chuhan; Fogelson, Noa; Li, Ling

    2016-01-01

    Optimized magnetic resonance imaging (MRI) features and abnormalities of brain network architectures may allow earlier detection and accurate prediction of the progression from mild cognitive impairment (MCI) to Alzheimer's disease (AD). In this study, we proposed a classification framework to distinguish MCI converters (MCIc) from MCI non-converters (MCInc) by using a combination of FreeSurfer-derived MRI features and nodal features derived from the thickness network. At the feature selection step, we first employed sparse linear regression with stability selection, for the selection of discriminative features in the iterative combinations of MRI and network measures. Subsequently the top K features of available combinations were selected as optimal features for classification. To obtain unbiased results, support vector machine (SVM) classifiers with nested cross validation were used for classification. The combination of 10 features including those from MRI and network measures attained accuracies of 66.04, 76.39, 74.66, and 73.91% for mixed conversion time, 6, 12, and 18 months before diagnosis of probable AD, respectively. Analysis of the diagnostic power of different time periods before diagnosis of probable AD showed that short-term prediction (6 and 12 months) achieved more stable and higher AUC scores compared with long-term prediction (18 months), with K-values from 1 to 30. The present results suggest that meaningful predictors composed of MRI and network measures may offer the possibility for early detection of progression from MCI to AD. PMID:27148045

  18. Prediction of Conversion from Mild Cognitive Impairment to Alzheimer's Disease Using MRI and Structural Network Features

    PubMed Central

    Wei, Rizhen; Li, Chuhan; Fogelson, Noa; Li, Ling

    2016-01-01

    Optimized magnetic resonance imaging (MRI) features and abnormalities of brain network architectures may allow earlier detection and accurate prediction of the progression from mild cognitive impairment (MCI) to Alzheimer's disease (AD). In this study, we proposed a classification framework to distinguish MCI converters (MCIc) from MCI non-converters (MCInc) by using a combination of FreeSurfer-derived MRI features and nodal features derived from the thickness network. At the feature selection step, we first employed sparse linear regression with stability selection, for the selection of discriminative features in the iterative combinations of MRI and network measures. Subsequently the top K features of available combinations were selected as optimal features for classification. To obtain unbiased results, support vector machine (SVM) classifiers with nested cross validation were used for classification. The combination of 10 features including those from MRI and network measures attained accuracies of 66.04, 76.39, 74.66, and 73.91% for mixed conversion time, 6, 12, and 18 months before diagnosis of probable AD, respectively. Analysis of the diagnostic power of different time periods before diagnosis of probable AD showed that short-term prediction (6 and 12 months) achieved more stable and higher AUC scores compared with long-term prediction (18 months), with K-values from 1 to 30. The present results suggest that meaningful predictors composed of MRI and network measures may offer the possibility for early detection of progression from MCI to AD. PMID:27148045

  19. Structural and functional analysis of amphioxus HIFα reveals ancient features of the HIFα family.

    PubMed

    Gao, Shan; Lu, Ling; Bai, Yan; Zhang, Peng; Song, Weibo; Duan, Cunming

    2014-04-01

    Hypoxia-inducible factors (HIFs) are master regulators of the transcriptional response to hypoxia. To gain insight into the structural and functional evolution of the HIF family, we characterized the HIFα gene from amphioxus, an invertebrate chordate, and identified several alternatively spliced HIFα isoforms. Whereas HIFα Ia, the full-length isoform, contained a complete oxygen-dependent degradation (ODD) domain, the isoforms Ib, Ic, and Id had 1 or 2 deletions in the ODD domain. When tagged with GFP and tested in mammalian cells, the amphioxus HIFα Ia protein level increased in response to hypoxia or CoCl2 treatment, whereas HIFα Ib, Ic, and Id showed reduced or no hypoxia regulation. Deletion of the ODD sequence in HIFα Ia up-regulated the HIFα Ia levels under normoxia. Gene expression analysis revealed HIFα Ic to be the predominant isoform in embryos and larvae, whereas isoform Ia was the most abundant form in the adult stage. The expression levels of Ib and Id were very low. Hypoxia treatment of adults had no effect on the mRNA levels of these HIFα isoforms. Functional analyses in mammalian cells showed all 4 HIFα isoforms capable of entering the nucleus and activating hypoxia response element-dependent reporter gene expression. The functional nuclear location signal (NLS) mapped to 3 clusters of basic residues. (775)KKARL functioned as the primary NLS, but (737)KRK and (754)KK also contributed to the nuclear localization. All amphioxus HIFα isoforms had 2 functional transactivation domains (TADs). Its C-terminal transactivation (C-TAD) shared high sequence identity with the human HIF-1α and HIF-2α C-TAD. This domain contained a conserved asparagine, and its mutation resulted in an increase in transcriptional activity. These findings reveal many ancient features of the HIFα family and provide novel insights into the evolution of the HIFα family.

  20. Structural features of sugars that trigger or support conidial germination in the filamentous fungus Aspergillus niger.

    PubMed

    Hayer, Kimran; Stratford, Malcolm; Archer, David B

    2013-11-01

    The asexual spores (conidia) of Aspergillus niger germinate to produce hyphae under appropriate conditions. Germination is initiated by conidial swelling and mobilization of internal carbon and energy stores, followed by polarization and emergence of a hyphal germ tube. The effects of different pyranose sugars, all analogues of d-glucose, on the germination of A. niger conidia were explored, and we define germination as the transition from a dormant conidium into a germling. Within germination, we distinguish two distinct stages, the initial swelling of the conidium and subsequent polarized growth. The stage of conidial swelling requires a germination trigger, which we define as a compound that is sensed by the conidium and which leads to catabolism of d-trehalose and isotropic growth. Sugars that triggered germination and outgrowth included d-glucose, d-mannose, and d-xylose. Sugars that triggered germination but did not support subsequent outgrowth included d-tagatose, d-lyxose, and 2-deoxy-d-glucose. Nontriggering sugars included d-galactose, l-glucose, and d-arabinose. Certain nontriggering sugars, including d-galactose, supported outgrowth if added in the presence of a complementary triggering sugar. This division of functions indicates that sugars are involved in two separate events in germination, triggering and subsequent outgrowth, and the structural features of sugars that support each, both, or none of these events are discussed. We also present data on the uptake of sugars during the germination process and discuss possible mechanisms of triggering in the absence of apparent sugar uptake during the initial swelling of conidia.

  1. Structural and functional analysis of amphioxus HIFα reveals ancient features of the HIFα family.

    PubMed

    Gao, Shan; Lu, Ling; Bai, Yan; Zhang, Peng; Song, Weibo; Duan, Cunming

    2014-04-01

    Hypoxia-inducible factors (HIFs) are master regulators of the transcriptional response to hypoxia. To gain insight into the structural and functional evolution of the HIF family, we characterized the HIFα gene from amphioxus, an invertebrate chordate, and identified several alternatively spliced HIFα isoforms. Whereas HIFα Ia, the full-length isoform, contained a complete oxygen-dependent degradation (ODD) domain, the isoforms Ib, Ic, and Id had 1 or 2 deletions in the ODD domain. When tagged with GFP and tested in mammalian cells, the amphioxus HIFα Ia protein level increased in response to hypoxia or CoCl2 treatment, whereas HIFα Ib, Ic, and Id showed reduced or no hypoxia regulation. Deletion of the ODD sequence in HIFα Ia up-regulated the HIFα Ia levels under normoxia. Gene expression analysis revealed HIFα Ic to be the predominant isoform in embryos and larvae, whereas isoform Ia was the most abundant form in the adult stage. The expression levels of Ib and Id were very low. Hypoxia treatment of adults had no effect on the mRNA levels of these HIFα isoforms. Functional analyses in mammalian cells showed all 4 HIFα isoforms capable of entering the nucleus and activating hypoxia response element-dependent reporter gene expression. The functional nuclear location signal (NLS) mapped to 3 clusters of basic residues. (775)KKARL functioned as the primary NLS, but (737)KRK and (754)KK also contributed to the nuclear localization. All amphioxus HIFα isoforms had 2 functional transactivation domains (TADs). Its C-terminal transactivation (C-TAD) shared high sequence identity with the human HIF-1α and HIF-2α C-TAD. This domain contained a conserved asparagine, and its mutation resulted in an increase in transcriptional activity. These findings reveal many ancient features of the HIFα family and provide novel insights into the evolution of the HIFα family. PMID:24174425

  2. Thermal structure and dynamics of the Jovian atmosphere. 2: Visible cloud features

    NASA Technical Reports Server (NTRS)

    Conrath, B. J.; Flasar, F. M.; Pirraglia, J. A.; Gierasch, P. J.; Hunt, G. E.

    1980-01-01

    Voyager IRIS data reveal strong similarities among a broad range of features which differ considerably in visual appearance. The atmosphere above anticyclonic features, including the major white ovals, the Great Red Spot, and a zone, are cold relative to the immediate surroundings in the upper troposphere and tropopause region. These results are consistent with upwelling and divergence in this part of the atmosphere. A hot spot and a barge, which are localized cyclonic features, are found to be warm relative to their surroundings, implying subsidence with accompanying convergence. In all cases, the thermal wind shear associated with the features indicates a decay of the vorticity with height in the upper troposphere and lower stratosphere. Vertical velocities inferred from the observed temperature perturbations imply an upper limit of vertical mixing times near the tropopause of approximately 20 years. Temperatures in the upper stratosphere above the anticyclonic features show considerable variation, but in most cases are found to be relatively warm.

  3. An Analysis of the Structure and Dynamics of Inner Core Precipitation Features in a Tropical Cyclone

    NASA Astrophysics Data System (ADS)

    Didlake, Anthony C., Jr.

    circulation of the secondary eyewall. This outflow was associated with a low-level tangential wind maximum which was strongly supergradient, mimicking the low-level circulation of the primary eyewall. Axisymmetric and asymmetric processes contributed comparably to strengthening the secondary eyewall tangential wind maximum. The evolution of these inner-core features likely played an important role in modifying the structure and intensity of the total vortex.

  4. Structural and molecular features of intestinal strictures in rats with Crohn's-like disease

    PubMed Central

    Talapka, Petra; Berkó, Anikó; Nagy, Lajos István; Chandrakumar, Lalitha; Bagyánszki, Mária; Puskás, László Géza; Fekete, Éva; Bódi, Nikolett

    2016-01-01

    AIM: To develop a new rat model we wanted to gain a better understanding of stricture formation in Crohn’s disease (CD). METHODS: Chronic colitis was induced locally by the administration of 2,4,6-trinitrobenzenesulfonic acid (TNBS). The relapsing inflammation characteristic to CD was mimicked by repeated TNBS treatments. Animals were randomly divided into control, once, twice and three times TNBS-treated groups. Control animals received an enema of saline. Tissue samples were taken from the strictured colonic segments and also adjacent proximally and distally to its 60, 90 or 120 d after the last TNBS or saline administrations. The frequency and macroscopic extent of the strictures were measured on digital photographs. The structural features of strictured gut wall were studied by light- and electron microscopy. Inflammation related alterations in TGF-beta 2 and 3, matrix metalloproteinases 9 (MMP9) and TIMP1 mRNA and protein expression were determined by quantitative real-time PCR and western blot analysis. The quantitative distribution of caspase 9 was determined by post-embedding immunohistochemistry. RESULTS: Intestinal strictures first appeared 60 d after TNBS treatments and the frequency of them increased up to day 120. From day 90 an intact lamina epithelialis, reversible thickening of lamina muscularis mucosae and irreversible thickening of the muscularis externa were demonstrated in the strictured colonic segments. Nevertheless the morphological signs of apoptosis were frequently seen and excess extracellular matrix deposition was recorded between smooth muscle cells (SMCs). Enhanced caspase 9 expression on day 90 in the SMCs and on day 120 also in myenteric neurons indicated the induction of apoptosis. The mRNA expression profile of TGF-betas after repeated TNBS doses was characteristic to CD, TGF-beta 2, but not TGF-beta 3 was up-regulated. Overexpression of MMP9 and down-regulation of TIMP1 were demonstrated. The progressive increase in the amount of

  5. Priming word order by thematic roles: no evidence for an additional involvement of phrase structure.

    PubMed

    Pappert, Sandra; Pechmann, Thomas

    2014-01-01

    Three experiments are reported that studied the priming of word order in German. Experiment 1 demonstrated priming of the order of case-marked verb arguments. However, order of noun phrases and order of thematic roles were confounded. In Experiment 2, we therefore aimed at disentangling the impact of these two possible factors. By using primes that differed from targets in phrase structure but were parallel with regard to the order of thematic roles, we nevertheless found priming demonstrating the critical impact of thematic roles. Experiment 3 replicated the priming effects from Experiments 1 and 2 within participants and revealed no evidence for a modulation of priming by phrase structure. Consequently, our findings suggest that word order priming crucially depends on the structural outline of thematic roles rather than on the linearization of phrases.

  6. Studies on the Food Additive Propyl Gallate: Synthesis, Structural Characterization, and Evaluation of the Antioxidant Activity

    ERIC Educational Resources Information Center

    Garrido, Jorge; Garrido, E. Manuela; Borges, Fernanda

    2012-01-01

    Antioxidants are additives largely used in industry for delaying, retarding, or preventing the development of oxidative deterioration. Propyl gallate (E310) is a phenolic antioxidant extensively used in the food, cosmetics, and pharmaceutical industries. A series of lab experiments have been developed to teach students about the importance and…

  7. Influence of Additive and Multiplicative Structure and Direction of Comparison on the Reversal Error

    ERIC Educational Resources Information Center

    González-Calero, José Antonio; Arnau, David; Laserna-Belenguer, Belén

    2015-01-01

    An empirical study has been carried out to evaluate the potential of word order matching and static comparison as explanatory models of reversal error. Data was collected from 214 undergraduate students who translated a set of additive and multiplicative comparisons expressed in Spanish into algebraic language. In these multiplicative comparisons…

  8. Visual odometry based on structural matching of local invariant features using stereo camera sensor.

    PubMed

    Núñez, Pedro; Vázquez-Martín, Ricardo; Bandera, Antonio

    2011-01-01

    This paper describes a novel sensor system to estimate the motion of a stereo camera. Local invariant image features are matched between pairs of frames and linked into image trajectories at video rate, providing the so-called visual odometry, i.e., motion estimates from visual input alone. Our proposal conducts two matching sessions: the first one between sets of features associated to the images of the stereo pairs and the second one between sets of features associated to consecutive frames. With respect to previously proposed approaches, the main novelty of this proposal is that both matching algorithms are conducted by means of a fast matching algorithm which combines absolute and relative feature constraints. Finding the largest-valued set of mutually consistent matches is equivalent to finding the maximum-weighted clique on a graph. The stereo matching allows to represent the scene view as a graph which emerge from the features of the accepted clique. On the other hand, the frame-to-frame matching defines a graph whose vertices are features in 3D space. The efficiency of the approach is increased by minimizing the geometric and algebraic errors to estimate the final displacement of the stereo camera between consecutive acquired frames. The proposed approach has been tested for mobile robotics navigation purposes in real environments and using different features. Experimental results demonstrate the performance of the proposal, which could be applied in both industrial and service robot fields.

  9. Visual Odometry Based on Structural Matching of Local Invariant Features Using Stereo Camera Sensor

    PubMed Central

    Núñez, Pedro; Vázquez-Martín, Ricardo; Bandera, Antonio

    2011-01-01

    This paper describes a novel sensor system to estimate the motion of a stereo camera. Local invariant image features are matched between pairs of frames and linked into image trajectories at video rate, providing the so-called visual odometry, i.e., motion estimates from visual input alone. Our proposal conducts two matching sessions: the first one between sets of features associated to the images of the stereo pairs and the second one between sets of features associated to consecutive frames. With respect to previously proposed approaches, the main novelty of this proposal is that both matching algorithms are conducted by means of a fast matching algorithm which combines absolute and relative feature constraints. Finding the largest-valued set of mutually consistent matches is equivalent to finding the maximum-weighted clique on a graph. The stereo matching allows to represent the scene view as a graph which emerge from the features of the accepted clique. On the other hand, the frame-to-frame matching defines a graph whose vertices are features in 3D space. The efficiency of the approach is increased by minimizing the geometric and algebraic errors to estimate the final displacement of the stereo camera between consecutive acquired frames. The proposed approach has been tested for mobile robotics navigation purposes in real environments and using different features. Experimental results demonstrate the performance of the proposal, which could be applied in both industrial and service robot fields. PMID:22164016

  10. Visual odometry based on structural matching of local invariant features using stereo camera sensor.

    PubMed

    Núñez, Pedro; Vázquez-Martín, Ricardo; Bandera, Antonio

    2011-01-01

    This paper describes a novel sensor system to estimate the motion of a stereo camera. Local invariant image features are matched between pairs of frames and linked into image trajectories at video rate, providing the so-called visual odometry, i.e., motion estimates from visual input alone. Our proposal conducts two matching sessions: the first one between sets of features associated to the images of the stereo pairs and the second one between sets of features associated to consecutive frames. With respect to previously proposed approaches, the main novelty of this proposal is that both matching algorithms are conducted by means of a fast matching algorithm which combines absolute and relative feature constraints. Finding the largest-valued set of mutually consistent matches is equivalent to finding the maximum-weighted clique on a graph. The stereo matching allows to represent the scene view as a graph which emerge from the features of the accepted clique. On the other hand, the frame-to-frame matching defines a graph whose vertices are features in 3D space. The efficiency of the approach is increased by minimizing the geometric and algebraic errors to estimate the final displacement of the stereo camera between consecutive acquired frames. The proposed approach has been tested for mobile robotics navigation purposes in real environments and using different features. Experimental results demonstrate the performance of the proposal, which could be applied in both industrial and service robot fields. PMID:22164016

  11. Multiclass Classification for the Differential Diagnosis on the ADHD Subtypes Using Recursive Feature Elimination and Hierarchical Extreme Learning Machine: Structural MRI Study

    PubMed Central

    Qureshi, Muhammad Naveed Iqbal; Min, Beomjun; Jo, Hang Joon; Lee, Boreom

    2016-01-01

    The classification of neuroimaging data for the diagnosis of certain brain diseases is one of the main research goals of the neuroscience and clinical communities. In this study, we performed multiclass classification using a hierarchical extreme learning machine (H-ELM) classifier. We compared the performance of this classifier with that of a support vector machine (SVM) and basic extreme learning machine (ELM) for cortical MRI data from attention deficit/hyperactivity disorder (ADHD) patients. We used 159 structural MRI images of children from the publicly available ADHD-200 MRI dataset. The data consisted of three types, namely, typically developing (TDC), ADHD-inattentive (ADHD-I), and ADHD-combined (ADHD-C). We carried out feature selection by using standard SVM-based recursive feature elimination (RFE-SVM) that enabled us to achieve good classification accuracy (60.78%). In this study, we found the RFE-SVM feature selection approach in combination with H-ELM to effectively enable the acquisition of high multiclass classification accuracy rates for structural neuroimaging data. In addition, we found that the most important features for classification were the surface area of the superior frontal lobe, and the cortical thickness, volume, and mean surface area of the whole cortex. PMID:27500640

  12. Multiclass Classification for the Differential Diagnosis on the ADHD Subtypes Using Recursive Feature Elimination and Hierarchical Extreme Learning Machine: Structural MRI Study.

    PubMed

    Qureshi, Muhammad Naveed Iqbal; Min, Beomjun; Jo, Hang Joon; Lee, Boreom

    2016-01-01

    The classification of neuroimaging data for the diagnosis of certain brain diseases is one of the main research goals of the neuroscience and clinical communities. In this study, we performed multiclass classification using a hierarchical extreme learning machine (H-ELM) classifier. We compared the performance of this classifier with that of a support vector machine (SVM) and basic extreme learning machine (ELM) for cortical MRI data from attention deficit/hyperactivity disorder (ADHD) patients. We used 159 structural MRI images of children from the publicly available ADHD-200 MRI dataset. The data consisted of three types, namely, typically developing (TDC), ADHD-inattentive (ADHD-I), and ADHD-combined (ADHD-C). We carried out feature selection by using standard SVM-based recursive feature elimination (RFE-SVM) that enabled us to achieve good classification accuracy (60.78%). In this study, we found the RFE-SVM feature selection approach in combination with H-ELM to effectively enable the acquisition of high multiclass classification accuracy rates for structural neuroimaging data. In addition, we found that the most important features for classification were the surface area of the superior frontal lobe, and the cortical thickness, volume, and mean surface area of the whole cortex. PMID:27500640

  13. The structure of Haemophilus influenzae prephenate dehydrogenase suggests unique features of bifunctional TyrA enzymes

    PubMed Central

    Chiu, Hsiu-Ju; Abdubek, Polat; Astakhova, Tamara; Axelrod, Herbert L.; Carlton, Dennis; Clayton, Thomas; Das, Debanu; Deller, Marc C.; Duan, Lian; Feuerhelm, Julie; Grant, Joanna C.; Grzechnik, Anna; Han, Gye Won; Jaroszewski, Lukasz; Jin, Kevin K.; Klock, Heath E.; Knuth, Mark W.; Kozbial, Piotr; Krishna, S. Sri; Kumar, Abhinav; Marciano, David; McMullan, Daniel; Miller, Mitchell D.; Morse, Andrew T.; Nigoghossian, Edward; Okach, Linda; Reyes, Ron; Tien, Henry J.; Trame, Christine B.; van den Bedem, Henry; Weekes, Dana; Xu, Qingping; Hodgson, Keith O.; Wooley, John; Elsliger, Marc-André; Deacon, Ashley M.; Godzik, Adam; Lesley, Scott A.; Wilson, Ian A.

    2010-01-01

    Chorismate mutase/prephenate dehydrogenase from Haemophilus influenzae Rd KW20 is a bifunctional enzyme that catalyzes the rearrangement of chorismate to prephenate and the NAD(P)+-dependent oxidative decarboxyl­ation of prephenate to 4-hydroxyphenylpyruvate in tyrosine biosynthesis. The crystal structure of the prephenate dehydrogenase component (HinfPDH) of the TyrA protein from H. influenzae Rd KW20 in complex with the inhibitor tyrosine and cofactor NAD+ has been determined to 2.0 Å resolution. HinfPDH is a dimeric enzyme, with each monomer consisting of an N-terminal α/β dinucleotide-binding domain and a C-terminal α-helical dimerization domain. The structure reveals key active-site residues at the domain interface, including His200, Arg297 and Ser179 that are involved in catalysis and/or ligand binding and are highly conserved in TyrA proteins from all three kingdoms of life. Tyrosine is bound directly at the catalytic site, suggesting that it is a competitive inhibitor of HinfPDH. Comparisons with its structural homologues reveal important differences around the active site, including the absence of an α–β motif in HinfPDH that is present in other TyrA proteins, such as Synechocystis sp. arogenate dehydrogenase. Residues from this motif are involved in discrimination between NADP+ and NAD+. The loop between β5 and β6 in the N-terminal domain is much shorter in HinfPDH and an extra helix is present at the C-terminus. Furthermore, HinfPDH adopts a more closed conformation compared with TyrA proteins that do not have tyrosine bound. This conformational change brings the substrate, cofactor and active-site residues into close proximity for catalysis. An ionic network consisting of Arg297 (a key residue for tyrosine binding), a water molecule, Asp206 (from the loop between β5 and β6) and Arg365′ (from the additional C-terminal helix of the adjacent monomer) is observed that might be involved in gating the active site. PMID:20944228

  14. Linguistic Features and Schematic Textual Structure in Look-Good Advertisements in the Indian Print Media in English

    ERIC Educational Resources Information Center

    Singh, Sukhdev; Bedi, Navkiran Kaur

    2013-01-01

    Every text has a communicative purpose that it performs by dividing itself into generic stages. These stages are assigned specific goals and have differing linguistic structures. This paper makes an attempt to investigate whether there is a definable co-relation between linguistic features and stages in the genre of look-good advertisements. It…

  15. Supporting Ease-of-Use and User Control: Desired Features and Structure of Web-Based Online IR Systems.

    ERIC Educational Resources Information Center

    Xie, Hong

    2003-01-01

    Describes a study that investigated users' perceptions of ease of use versus user control in Web-based online information retrieval (IR) systems. Discusses desired features and functionalities as well as desired interface structures that support both ease of use and user control. (Author/LRW)

  16. Does My Face FIT?: A Face Image Task Reveals Structure and Distortions of Facial Feature Representation

    PubMed Central

    Fuentes, Christina T.; Runa, Catarina; Blanco, Xenxo Alvarez; Orvalho, Verónica; Haggard, Patrick

    2013-01-01

    Despite extensive research on face perception, few studies have investigated individuals’ knowledge about the physical features of their own face. In this study, 50 participants indicated the location of key features of their own face, relative to an anchor point corresponding to the tip of the nose, and the results were compared to the true location of the same individual’s features from a standardised photograph. Horizontal and vertical errors were analysed separately. An overall bias to underestimate vertical distances revealed a distorted face representation, with reduced face height. Factor analyses were used to identify separable subconfigurations of facial features with correlated localisation errors. Independent representations of upper and lower facial features emerged from the data pattern. The major source of variation across individuals was in representation of face shape, with a spectrum from tall/thin to short/wide representation. Visual identification of one’s own face is excellent, and facial features are routinely used for establishing personal identity. However, our results show that spatial knowledge of one’s own face is remarkably poor, suggesting that face representation may not contribute strongly to self-awareness. PMID:24130790

  17. Effect of biodiesel addition on microbial community structure in a simulated fuel storage system.

    PubMed

    Restrepo-Flórez, Juan-Manuel; Bassi, Amarjeet; Rehmann, Lars; Thompson, Michael R

    2013-11-01

    Understanding changes in microbial structure due to biodiesel storage is important both for protecting integrity of storage systems and fuel quality management. In this work a simulated storage system was used to study the effect of biodiesel (0%, 25%, 50%, 75% and 100%) on a microbial population, which was followed by community level physiological profiling (CLPP), 16s rDNA analysis and plating in selective media. Results proved that structure and functionality were affected by biodiesel. CLPP showed at least three populations: one corresponding to diesel, one to biodiesel and one to blends of diesel and biodiesel. Analysis of 16s rDNA revealed that microbial composition was different for populations growing in diesel and biodiesel. Genera identified are known for degradation of hydrocarbons and emulsifier production. Maximum growth was obtained in biodiesel; however, microbial counts in standard media were lower for this samples. Acidification of culture media was observed at high biodiesel concentration.

  18. Structure alterations in Al-Y-based metallic glasses with La and Ni addition

    NASA Astrophysics Data System (ADS)

    Shi, X. M.; Wang, X. D.; Yu, Q.; Cao, Q. P.; Zhang, D. X.; Zhang, J.; Hu, T. D.; Lai, L. H.; Xie, H. L.; Xiao, T. Q.; Jiang, J. Z.

    2016-03-01

    The atomic structures of Al89Y11, Al90Y6.5La3.5, and Al82.8Y6.07Ni8La3.13 metallic glasses have been studied by using high energy X-ray diffraction, X-ray absorption fine structure combined with the ab initio molecular dynamics and reverse Monte Carlo simulations. It is demonstrated that the partial replacement of Y atoms by La has limited improvement of the glass forming ability (GFA), although La atoms reduce the ordering around Y atoms and also the fractions of icosahedron-like polyhedra centered by Al atoms. In contrast, Ni atoms can significantly improve the GFA, which are inclined to locate in the shell of polyhedra centered by Al, Y, and La atoms, mainly forming Ni-centered icosahedron-like polyhedra to enhance the spatial connectivity between clusters and suppress the crystallization.

  19. Structure-property effects of tantalum additions to nickel-base superalloys

    NASA Technical Reports Server (NTRS)

    Heckel, R. W.; Pletka, B. J.; Koss, D. A.; Jackson, M. R.

    1982-01-01

    The characterization of the effect of Ta on the structure of Ni base superalloys, the determination of the effects of Ta (structure) variations on the mechanical, thermal, and oxidation behavior, and the identification of alloying elements which have potential as substitutes for Ta are investigated. Mar M247 type alloys are emphasized; nominal and analyzed compositions of ten alloys under study are given. X-ray and composition analysis are being used to determine the partitioning of alloying elements between gamma, gamma primes, and MC (cubic) as a function of Ta content. The diffusional interactions of the Mar M247-type alloys with as cast beta + gamma alloys are studied to determine the effects of Ta on alloy/coating degradation.

  20. Photocatalytic activation of pyridine for addition reactions: an unconventional reaction feature between a photo-induced hole and electron on TiO2.

    PubMed

    Ma, Dongge; Yan, Yan; Ji, Hongwei; Chen, Chuncheng; Zhao, Jincai

    2015-12-21

    TiO2 photocatalysis can be performed for the addition of pyridines to vinylarenes in an anti-Markovnikov manner. Seven examples with considerable yields (56-91%) and selectivity were demonstrated. A comparative survey of the involved process through ESR revealed a novel concerted two electron transfer pathway for these photocatalytic bimolecular addition reactions.

  1. Experiments to Populate and Validate a Processing Model for Polyurethane Foam: Additional Data for Structural Foams.

    SciTech Connect

    Rao, Rekha R.; Celina, Mathias C.; Giron, Nicholas Henry; Long, Kevin Nicholas; Russick, Edward M.

    2015-01-01

    We are developing computational models to help understand manufacturing processes, final properties and aging of structural foam, polyurethane PMDI. Th e resulting model predictions of density and cure gradients from the manufacturing process will be used as input to foam heat transfer and mechanical models. BKC 44306 PMDI-10 and BKC 44307 PMDI-18 are the most prevalent foams used in structural parts. Experiments needed to parameterize models of the reaction kinetics and the equations of motion during the foam blowing stages were described for BKC 44306 PMDI-10 in the first of this report series (Mondy et al. 2014). BKC 44307 PMDI-18 is a new foam that will be used to make relatively dense structural supports via over packing. It uses a different catalyst than those in the BKC 44306 family of foams; hence, we expect that the reaction kineti cs models must be modified. Here we detail the experiments needed to characteriz e the reaction kinetics of BKC 44307 PMDI-18 and suggest parameters for the model based on these experiments. In additi on, the second part of this report describes data taken to provide input to the preliminary nonlinear visco elastic structural response model developed for BKC 44306 PMDI-10 foam. We show that the standard cu re schedule used by KCP does not fully cure the material, and, upon temperature elevation above 150 o C, oxidation or decomposition reactions occur that alter the composition of the foam. These findings suggest that achieving a fully cured foam part with this formulation may be not be possible through therma l curing. As such, visco elastic characterization procedures developed for curing thermosets can provide only approximate material properties, since the state of the material continuously evolves during tests.

  2. [Error structure and additivity of individual tree biomass model for four natural conifer species in Northeast China].

    PubMed

    Dogn, Li-hu; Li, Feng-ri; Song, Yu-wen

    2015-03-01

    Based on the biomass data of 276 sampling trees of Pinus koraiensis, Abies nephrolepis, Picea koraiensis and Larix gmelinii, the mono-element and dual-element additive system of biomass equations for the four conifer species was developed. The model error structure (additive vs. multiplicative) of the allometric equation was evaluated using the likelihood analysis, while nonlinear seemly unrelated regression was used to estimate the parameters in the additive system of biomass equations. The results indicated that the assumption of multiplicative error structure was strongly supported for the biomass equations of total and tree components for the four conifer species. Thus, the additive system of log-transformed biomass equations was developed. The adjusted coefficient of determination (Ra 2) of the additive system of biomass equations for the four conifer species was 0.85-0.99, the mean relative error was between -7.7% and 5.5%, and the mean absolute relative error was less than 30.5%. Adding total tree height in the additive systems of biomass equations could significantly improve model fitting performance and predicting precision, and the biomass equations of total, aboveground and stem were better than biomass equations of root, branch, foliage and crown. The precision of each biomass equation in the additive system varied from 77.0% to 99.7% with a mean value of 92.3% that would be suitable for predicting the biomass of the four natural conifer species.

  3. [Effects of nitrogen and water addition on soil bacterial diversity and community structure in temperate grasslands in northern China].

    PubMed

    Yang, Shan; Li, Xiao-bing; Wang, Ru-zhen; Cai, Jiang-ping; Xu, Zhu-wen; Zhang, Yu-ge; Li, Hui; Jiang, Yong

    2015-03-01

    In this study, we measured the responses of soil bacterial diversity and community structure to nitrogen (N) and water addition in the typical temperate grassland in northern China. Results showed that N addition significantly reduced microbial biomass carbon (MBC) and microbial biomass nitrogen (MBN) under regular precipitation treatment. Similar declined trends of MBC and MBN caused by N addition were also found under increased precipitation condition. Nevertheless, water addition alleviated the inhibition by N addition. N addition exerted no significant effects. on bacterial α-diversity indices, including richness, Shannon diversity and evenness index under regular precipitation condition. Precipitation increment tended to increase bacterial α-diversity, and the diversity indices of each N gradient under regular precipitation were much lower than that of the corresponding N addition rate under increased precipitation. Correlation analysis showed that soil moisture, nitrate (NO3(-)-N) and ammonium (NH4+-N) were significantly negatively correlated with bacterial evenness index, and MBC and MBN had a significant positive correlation with bacterial richness and evenness. Non-metric multidimensional scaling (NMDS) ordination illustrated that the bacterial communities were significantly separated by N addition rates, under both water ambient and water addition treatments. Redundancy analysis (RDA) revealed that soil MBC, MBN, pH and NH4+-N were the key environmental factors for shaping bacterial communities.

  4. Synthesis and characterization of high-surface-area millimeter-sized silica beads with hierarchical multi-modal pore structure by the addition of agar

    SciTech Connect

    Han, Yosep; Choi, Junhyun; Tong, Meiping; Kim, Hyunjung

    2014-04-01

    Millimeter-sized spherical silica foams (SSFs) with hierarchical multi-modal pore structure featuring high specific surface area and ordered mesoporous frameworks were successfully prepared using aqueous agar addition, foaming and drop-in-oil processes. The pore-related properties of the prepared spherical silica (SSs) and SSFs were systematically characterized by field emission-scanning electron microscopy (FE-SEM), transmission electron microscopy (TEM), small-angle X-ray diffraction (SAXRD), Hg intrusion porosimetry, and N{sub 2} adsorption–desorption isotherm measurements. Improvements in the BET surface area and total pore volume were observed at 504 m{sup 2} g{sup −1} and 5.45 cm{sup 3} g{sup −1}, respectively, after an agar addition and foaming process. Despite the increase in the BET surface area, the mesopore wall thickness and the pore size of the mesopores generated from the block copolymer with agar addition were unchanged based on the SAXRD, TEM, and BJH methods. The SSFs prepared in the present study were confirmed to have improved BET surface area and micropore volume through the agar loading, and to exhibit interconnected 3-dimensional network macropore structure leading to the enhancement of total porosity and BET surface area via the foaming process. - Highlights: • Millimeter-sized spherical silica foams (SSFs) are successfully prepared. • SSFs exhibit high BET surface area and ordered hierarchical pore structure. • Agar addition improves BET surface area and micropore volume of SSFs. • Foaming process generates interconnected 3-D network macropore structure of SSFs.

  5. Effect of reduction of strategic Columbium addition in 718 Alloy on the structure and properties

    NASA Technical Reports Server (NTRS)

    Ziegler, K. R.; Wallace, J. F.

    1985-01-01

    A series of alloys was developed having a base composition similar to Inconel 718, with reduced Cb levels of 3.00 and 1.10 wt% Cb. Substitutions of 3.0% W, 3.0W + 0.9V or Mo increased from 3.0% to 5.8% were made for the Cb in these alloys. Two additional alloys, one containing 3.49% Cb and 1.10% Ti and another containing 3.89% Cb and 1.29% Ti were also studied. Tensile properties at rooom and elevated temperatures, stress-rupture tests, and an analysis of extracted phases were carried out for each of the alloys. Additions of solid solution elements to a reduced Cb alloy had no significant effect on the properties of the alloys under either process condition. The solution and age alloys with substitutions of 1.27% i at 3.89% Cb had tensile properties similar top hose of the original alloy and stress-rupture properties superior to the original alloy. The improved stress-rupture properties were the result of significant precipitation of Ni3Ti-gamma prime in the alloy, which is more stable than gamma' at the elevated temperatures. At lower temperatures, the new alloy benefits from gamma' strengthening. With more precise control and proper processing, the reduced Cb direct-age alloy could substitute for Alloy 718 in high strength applications.

  6. Modifying structure-sensitive reactions by addition of Zn to Pd

    SciTech Connect

    Childers, David J.; Schweitzer, Neil M.; Kamali Shahari, Seyed Mehdi; Rioux, Robert M.; Miller, Jeffrey T.; Meyer, Randall J.

    2014-10-01

    Silica-supported Pd and PdZn nanoparticles of a similar size were evaluated for neopentane hydrogenolysis/isomerization and propane hydrogenolysis/dehydrogenation. Monometallic Pd showed high neopentane hydrogenolysis selectivity. Addition of small amounts of Zn to Pd lead Pd–Zn scatters in the EXAFS spectrum and an increase in the linear bonded CO by IR. In addition, the neopentane turnover rate decreased by nearly 10 times with little change in the selectivity. Increasing amounts of Zn lead to greater Pd–Zn interactions, higher linear-to-bridging CO ratios by IR and complete loss of neopentane conversion. Pd NPs also had high selectivity for propane hydrogenolysis and thus were poorly selective for propylene. The PdZn bimetallic catalysts, however, were able to preferentially catalyze dehydrogenation, were not active for propane hydrogenolysis, and thus were highly selective for propylene formation. The decrease in hydrogenolysis selectivity was attributed to the isolation of active Pd atoms by inactive metallic Zn,demonstrating that hydrogenolysis requires a particular reactive ensemble whereas propane dehydrogenation does not.

  7. Influence of additives on the structure of surfactant-free microemulsions.

    PubMed

    Marcus, J; Touraud, D; Prévost, S; Diat, O; Zemb, T; Kunz, W

    2015-12-28

    We study the addition of electrolytes to surfactant-free microemulsions in the domain where polydisperse pre-Ouzo aggregates are present. As in previous studies, the microemulsion is the ternary system water/ethanol/1-octanol, where ethanol acts as co-solvent. Addition of electrolytes modifies the static X-ray and neutron scattering, and dynamic light scattering patterns, as well as the position of the miscibility gap, where spontaneous emulsification occurs upon dilution with water. All observations can be rationalized considering that electrolytes are either "salting out" the ethanol, which is the main component of the interface stabilizing the aggregates, or producing charge separation via the antagonistic ion effect discovered by Onuki et al. Amphiphilic electrolytes, such as sodium dodecylsulfate or sodium dietheylhexylphosphate, induce a gradual transition towards monodisperse ionic micelles with their characteristic broad scattering "peak". In these micelles the ethanol plays then the role of a cosurfactant. Dynamic light scattering can only be understood by combination of fluctuations of aggregate concentration due to the vicinity of a critical point and in-out fluctuations of ethanol. PMID:26593697

  8. Characterization of embedded fiber optic strain sensors into metallic structures via ultrasonic additive manufacturing

    NASA Astrophysics Data System (ADS)

    Schomer, John J.; Hehr, Adam J.; Dapino, Marcelo J.

    2016-04-01

    Fiber Bragg Grating (FBG) sensors measure deviation in a reflected wavelength of light to detect in-situ strain. These sensors are immune to electromagnetic interference, and the inclusion of multiple FBGs on the same fiber allows for a seamlessly integrated sensing network. FBGs are attractive for embedded sensing in aerospace applications due to their small noninvasive size and prospect of constant, real-time nondestructive evaluation. In this study, FBG sensors are embedded in aluminum 6061 via ultrasonic additive manufacturing (UAM), a rapid prototyping process that uses high power ultrasonic vibrations to weld similar and dissimilar metal foils together. UAM was chosen due to the desire to embed FBG sensors at low temperatures, a requirement that excludes other additive processes such as selective laser sintering or fusion deposition modeling. In this paper, the embedded FBGs are characterized in terms of birefringence losses, post embedding strain shifts, consolidation quality, and strain sensing performance. Sensors embedded into an ASTM test piece are compared against an exterior surface mounted foil strain gage at both room and elevated temperatures using cyclic tensile tests.

  9. Modeling the Structure of Complex Aluminosilicate Glasses: The Effect of Zinc Addition.

    PubMed

    Bernasconi, Andrea; Dapiaggi, Monica; Pavese, Alessandro; Agostini, Giovanni; Bernasconi, Maurizio; Bowron, Daniel T

    2016-03-10

    An empirical potential structure refinement of neutron and X-ray diffraction data combined with extended absorption fine structure evidence has been applied to the investigation of two distinct sets of complex aluminosilicate glasses containing different quantities of zinc. Data come from (i) neutron and X-ray total scattering experiments, which have been performed at the ISIS neutron spallation source (SANDALS beamline) and at the European Synchrotron Radiation Facility (ID11 beamline), and (ii) EXAFS experiments which have been performed at the European Synchrotron Radiation Facility (BM23 beamline). By careful examination of the modeled ensemble of atoms, a wide range of structural information has been extracted: coordination numbers, bond distances, cluster sizes, type of oxygen sharing, and the preference of large cations to adopt a charge-compensating role. The first series of glasses, which is characterized by a fixed network modifier element content (i.e., Na), shows how the introduction of Zn at the expense of Si and Al network forming elements does not significantly alter the polymerization degree, as a result of its dominant 4-fold coordination. In the case of the second series, which is characterized by fixed network forming element content (i.e., Si and Al), it is shown how the replacement of a network modifier element (i.e., Ca) with the introduction of Zn does not change the propensity of Zn to be mainly 4-fold coordinated by promoting the network. Where appropriate the experimental results have been compared with classical theoretical approaches such as stoichiometric models based on Zachariasen's rules and computational routines. PMID:26848740

  10. Direct Experimental Evidence of the Relationship between Intermediate-Range Order in Topologically Disordered Matter and Discernible Features in the Static Structure Factor

    NASA Astrophysics Data System (ADS)

    Fayos, R.; Bermejo, F. J.; Dawidowski, J.; Fischer, H. E.; González, M. A.

    1996-10-01

    The relationship between order at intermediate length scales and discernible features in the diffraction pattern of glassy and liquid materials is demonstrated experimentally by means of a direct comparison of the static structure factors of a material in its liquid, stable crystal, rotator-phase crystal, orientational glass, and amorphous phases. In addition, the relevance of orientationally disordered crystalline phases (i.e., either the dynamic disorder of a rotator-phase crystal or the quenched disorder of an orientational glass), as intermediate stages between the stable crystal and the topologically disordered (i.e., amorphous) solid, is evidenced. The material studied is ethyl alcohol.

  11. Structural Coherence and Temporal Stability of Psychopathic Personality Features During Emerging Adulthood

    PubMed Central

    Hawes, Samuel W.; Mulvey, Edward P.; Schubert, Carol A.; Pardini, Dustin A.

    2015-01-01

    Psychopathy is a complex personality disorder characterized by affective, interpersonal, and behavioral dimensions. Although features of psychopathy have been extended downwardly to earlier developmental periods, there is a discerning lack of studies that have focused on critically important issues such as longitudinal invariance and stability/change in these features across time. The current study examines these issues using a large sample of male adolescent offenders (N = 1,170) assessed across 7 annual time points during the transition into emerging adulthood (ages ~ 17 to 24 years). Findings demonstrated that features of psychopathy remained longitudinally invariant across this developmental period, and showed temporally consistent and theoretically coherent associations with other measures of personality, psychopathology, and criminal behaviors. Results also demonstrated that mean levels of psychopathic personality features tended to decrease into emerging adulthood and showed relatively modest rank-order stability across assessments with 7-year lags. These findings suggest that reductions in maladaptive personality features seem to parallel the well-documented decreases in offending that occur during the early 20s. PMID:24978692

  12. The evaluation of multi-structure, multi-atlas pelvic anatomy features in a prostate MR lymphography CAD system

    NASA Astrophysics Data System (ADS)

    Meijs, M.; Debats, O.; Huisman, H.

    2015-03-01

    In prostate cancer, the detection of metastatic lymph nodes indicates progression from localized disease to metastasized cancer. The detection of positive lymph nodes is, however, a complex and time consuming task for experienced radiologists. Assistance of a two-stage Computer-Aided Detection (CAD) system in MR Lymphography (MRL) is not yet feasible due to the large number of false positives in the first stage of the system. By introducing a multi-structure, multi-atlas segmentation, using an affine transformation followed by a B-spline transformation for registration, the organ location is given by a mean density probability map. The atlas segmentation is semi-automatically drawn with ITK-SNAP, using Active Contour Segmentation. Each anatomic structure is identified by a label number. Registration is performed using Elastix, using Mutual Information and an Adaptive Stochastic Gradient optimization. The dataset consists of the MRL scans of ten patients, with lymph nodes manually annotated in consensus by two expert readers. The feature map of the CAD system consists of the Multi-Atlas and various other features (e.g. Normalized Intensity and multi-scale Blobness). The voxel-based Gentleboost classifier is evaluated using ROC analysis with cross validation. We show in a set of 10 studies that adding multi-structure, multi-atlas anatomical structure likelihood features improves the quality of the lymph node voxel likelihood map. Multiple structure anatomy maps may thus make MRL CAD more feasible.

  13. Structural and phylogenetic analysis of Rhodobacter capsulatus NifF: uncovering general features of nitrogen-fixation (nif)-flavodoxins.

    PubMed

    Pérez-Dorado, Inmaculada; Bortolotti, Ana; Cortez, Néstor; Hermoso, Juan A

    2013-01-09

    Analysis of the crystal structure of NifF from Rhodobacter capsulatus and its homologues reported so far reflects the existence of unique structural features in nif flavodoxins: a leucine at the re face of the isoalloxazine, an eight-residue insertion at the C-terminus of the 50's loop and a remarkable difference in the electrostatic potential surface with respect to non-nif flavodoxins. A phylogenetic study on 64 sequences from 52 bacterial species revealed four clusters, including different functional prototypes, correlating the previously defined as "short-chain" with the firmicutes flavodoxins and the "long-chain" with gram-negative species. The comparison of Rhodobacter NifF structure with other bacterial flavodoxin prototypes discloses the concurrence of specific features of these functional electron donors to nitrogenase.

  14. Control-group feature normalization for multivariate pattern analysis of structural MRI data using the support vector machine.

    PubMed

    Linn, Kristin A; Gaonkar, Bilwaj; Satterthwaite, Theodore D; Doshi, Jimit; Davatzikos, Christos; Shinohara, Russell T

    2016-05-15

    Normalization of feature vector values is a common practice in machine learning. Generally, each feature value is standardized to the unit hypercube or by normalizing to zero mean and unit variance. Classification decisions based on support vector machines (SVMs) or by other methods are sensitive to the specific normalization used on the features. In the context of multivariate pattern analysis using neuroimaging data, standardization effectively up- and down-weights features based on their individual variability. Since the standard approach uses the entire data set to guide the normalization, it utilizes the total variability of these features. This total variation is inevitably dependent on the amount of marginal separation between groups. Thus, such a normalization may attenuate the separability of the data in high dimensional space. In this work we propose an alternate approach that uses an estimate of the control-group standard deviation to normalize features before training. We study our proposed approach in the context of group classification using structural MRI data. We show that control-based normalization leads to better reproducibility of estimated multivariate disease patterns and improves the classifier performance in many cases.

  15. A highly accurate protein structural class prediction approach using auto cross covariance transformation and recursive feature elimination.

    PubMed

    Li, Xiaowei; Liu, Taigang; Tao, Peiying; Wang, Chunhua; Chen, Lanming

    2015-12-01

    Structural class characterizes the overall folding type of a protein or its domain. Many methods have been proposed to improve the prediction accuracy of protein structural class in recent years, but it is still a challenge for the low-similarity sequences. In this study, we introduce a feature extraction technique based on auto cross covariance (ACC) transformation of position-specific score matrix (PSSM) to represent a protein sequence. Then support vector machine-recursive feature elimination (SVM-RFE) is adopted to select top K features according to their importance and these features are input to a support vector machine (SVM) to conduct the prediction. Performance evaluation of the proposed method is performed using the jackknife test on three low-similarity datasets, i.e., D640, 1189 and 25PDB. By means of this method, the overall accuracies of 97.2%, 96.2%, and 93.3% are achieved on these three datasets, which are higher than those of most existing methods. This suggests that the proposed method could serve as a very cost-effective tool for predicting protein structural class especially for low-similarity datasets.

  16. Additive gene-environment effects on hippocampal structure in healthy humans.

    PubMed

    Rabl, Ulrich; Meyer, Bernhard M; Diers, Kersten; Bartova, Lucie; Berger, Andreas; Mandorfer, Dominik; Popovic, Ana; Scharinger, Christian; Huemer, Julia; Kalcher, Klaudius; Pail, Gerald; Haslacher, Helmuth; Perkmann, Thomas; Windischberger, Christian; Brocke, Burkhard; Sitte, Harald H; Pollak, Daniela D; Dreher, Jean-Claude; Kasper, Siegfried; Praschak-Rieder, Nicole; Moser, Ewald; Esterbauer, Harald; Pezawas, Lukas

    2014-07-23

    Hippocampal volume loss has been related to chronic stress as well as genetic factors. Although genetic and environmental variables affecting hippocampal volume have extensively been studied and related to mental illness, limited evidence is available with respect to G × E interactions on hippocampal volume. The present MRI study investigated interaction effects on hippocampal volume between three well-studied functional genetic variants (COMT Val158Met, BDNF Val66Met, 5-HTTLPR) associated with hippocampal volume and a measure of environmental adversity (life events questionnaire) in a large sample of healthy humans (n = 153). All three variants showed significant interactions with environmental adversity with respect to hippocampal volume. Observed effects were additive by nature and driven by both recent as well as early life events. A consecutive analysis of hippocampal subfields revealed a spatially distinct profile for each genetic variant suggesting a specific role of 5-HTTLPR for the subiculum, BDNF Val66Met for CA4/dentate gyrus, and COMT Val158Met for CA2/3 volume changes. The present study underscores the importance of G × E interactions as determinants of hippocampal volume, which is crucial for the neurobiological understanding of stress-related conditions, such as mood disorders or post-traumatic stress disorder (PTSD). PMID:25057194

  17. Additive Gene–Environment Effects on Hippocampal Structure in Healthy Humans

    PubMed Central

    Rabl, Ulrich; Meyer, Bernhard M.; Diers, Kersten; Bartova, Lucie; Berger, Andreas; Mandorfer, Dominik; Popovic, Ana; Scharinger, Christian; Huemer, Julia; Kalcher, Klaudius; Pail, Gerald; Haslacher, Helmuth; Perkmann, Thomas; Windischberger, Christian; Brocke, Burkhard; Sitte, Harald H.; Pollak, Daniela D.; Dreher, Jean-Claude; Kasper, Siegfried; Praschak-Rieder, Nicole; Moser, Ewald; Esterbauer, Harald

    2014-01-01

    Hippocampal volume loss has been related to chronic stress as well as genetic factors. Although genetic and environmental variables affecting hippocampal volume have extensively been studied and related to mental illness, limited evidence is available with respect to G × E interactions on hippocampal volume. The present MRI study investigated interaction effects on hippocampal volume between three well-studied functional genetic variants (COMT Val158Met, BDNF Val66Met, 5-HTTLPR) associated with hippocampal volume and a measure of environmental adversity (life events questionnaire) in a large sample of healthy humans (n = 153). All three variants showed significant interactions with environmental adversity with respect to hippocampal volume. Observed effects were additive by nature and driven by both recent as well as early life events. A consecutive analysis of hippocampal subfields revealed a spatially distinct profile for each genetic variant suggesting a specific role of 5-HTTLPR for the subiculum, BDNF Val66Met for CA4/dentate gyrus, and COMT Val158Met for CA2/3 volume changes. The present study underscores the importance of G × E interactions as determinants of hippocampal volume, which is crucial for the neurobiological understanding of stress-related conditions, such as mood disorders or post-traumatic stress disorder (PTSD). PMID:25057194

  18. Additive gene-environment effects on hippocampal structure in healthy humans.

    PubMed

    Rabl, Ulrich; Meyer, Bernhard M; Diers, Kersten; Bartova, Lucie; Berger, Andreas; Mandorfer, Dominik; Popovic, Ana; Scharinger, Christian; Huemer, Julia; Kalcher, Klaudius; Pail, Gerald; Haslacher, Helmuth; Perkmann, Thomas; Windischberger, Christian; Brocke, Burkhard; Sitte, Harald H; Pollak, Daniela D; Dreher, Jean-Claude; Kasper, Siegfried; Praschak-Rieder, Nicole; Moser, Ewald; Esterbauer, Harald; Pezawas, Lukas

    2014-07-23

    Hippocampal volume loss has been related to chronic stress as well as genetic factors. Although genetic and environmental variables affecting hippocampal volume have extensively been studied and related to mental illness, limited evidence is available with respect to G × E interactions on hippocampal volume. The present MRI study investigated interaction effects on hippocampal volume between three well-studied functional genetic variants (COMT Val158Met, BDNF Val66Met, 5-HTTLPR) associated with hippocampal volume and a measure of environmental adversity (life events questionnaire) in a large sample of healthy humans (n = 153). All three variants showed significant interactions with environmental adversity with respect to hippocampal volume. Observed effects were additive by nature and driven by both recent as well as early life events. A consecutive analysis of hippocampal subfields revealed a spatially distinct profile for each genetic variant suggesting a specific role of 5-HTTLPR for the subiculum, BDNF Val66Met for CA4/dentate gyrus, and COMT Val158Met for CA2/3 volume changes. The present study underscores the importance of G × E interactions as determinants of hippocampal volume, which is crucial for the neurobiological understanding of stress-related conditions, such as mood disorders or post-traumatic stress disorder (PTSD).

  19. A study of alternative metal particle structures and mixtures for dental amalgams based on mercury additions.

    PubMed

    Marquez, J A; Murr, L E; Agüero, V

    2000-08-01

    The perception that mercury in dental amalgam is toxic to the human organism has prompted worldwide efforts by the scientific community to develop alternative amalgam-like materials that utilize little or no mercury. In this investigation, an attempt is made to develop a new dental alloy system by adding liquid mercury to silver-coated Ag4Sn intermetallic particles in lesser amounts than are used in conventional amalgam alloys. An effort to precipitate the important eta-prime (Cu6Sn5) phase was made by adding pure Cu and Sn powders to the alloy formulation during trituration. Tytin a popular Ag-Sn-Cu single-composition, spray-atomized conventional dental alloy was used as the control to obtain baseline data for comparisons of microstructures and mechanical properties. Amalgamation of the coated particles with mercury, with or without the addition of Cu and Sn powders, mostly produced specimens with chemically non-coherent microstructures that were relatively weak in compression. These results were due, in part, to mercury's inability to chemically wet the Ag-coated particles and Cu and Sn powders because of naturally occurring surface oxide films. The strongest specimens tested had silver dendritic coatings, resulting in compression strength values up to 40% of the control's. Their higher strength is attributed to mechanical interlocking at the particle/matrix interfaces.

  20. Flexible Structural Features of Pentafulvene Titanium Derivatives: Isolation and Characterization of NHC Complexes.

    PubMed

    Manßen, Manfred; Adler, Christian; Beckhaus, Rüdiger

    2016-03-18

    The reaction of η(5),η(1)-pentafulvene titanium complexes with the strong N-heterocyclic carbene (NHC) donor 1,3,4,5-tetramethylimidazole-2-ylidene, leads to the formation of isolable NHC titanium adducts, featuring a haptotropic shift of the pentafulvene ligand, proved by single crystal X-ray diffraction as well as NMR spectroscopy studies. PMID:26852891

  1. LASER Additive Manufacturing of Titanium-Tantalum Alloy Structured Interfaces for Modular Orthopedic Devices

    NASA Astrophysics Data System (ADS)

    Fuerst, Jacob; Medlin, Dana; Carter, Michael; Sears, James; Vander Voort, George

    2015-04-01

    Tantalum is recognized to have better biocompatibility and osseointegrative properties than other more commonly used orthopedic grade alloys. There are several novel methods that tantalum or tantalum-titanium could be used to augment orthopedic implants. A tantalum or tantalum-titanium alloy at the bone/implant or modular component interfaces would substantially increase the longevity and performance of modular devices. Bonding a functional tantalum coating to a titanium orthopedic device is inherently difficult because of the small difference between the melting temperature of tantalum, 3017°C, and the boiling point of titanium, 3287°C. LASER powder deposition (LPD) is a fusion operation using an Nd:YAG to melt a small volume of substrate into which metal powder is sprayed achieving high temperature with a high solidification rate. LPD of Ti-Ta onto a Ti-6Al-4V substrate produced both a solid surface and structured coating with a pore size in the optimal 350-500 μm range.

  2. Numerical simulation of the fatigue behavior of additive manufactured titanium porous lattice structures.

    PubMed

    Zargarian, A; Esfahanian, M; Kadkhodapour, J; Ziaei-Rad, S

    2016-03-01

    In this paper, the effects of cell geometry and relative density on the high-cycle fatigue behavior of Titanium scaffolds produced by selective laser melting and electron beam melting techniques were numerically investigated by finite element analysis. The regular titanium lattice samples with three different unit cell geometries, namely, diamond, rhombic dodecahedron and truncated cuboctahedron, and the relative density range of 0.1-0.3 were analyzed under uniaxial cyclic compressive loading. A failure event based algorithm was employed to simulate fatigue failure in the cellular material. Stress-life approach was used to model fatigue failure of both bulk (struts) and cellular material. The predicted fatigue life and the damage pattern of all three structures were found to be in good agreement with the experimental fatigue investigations published in the literature. The results also showed that the relationship between fatigue strength and cycles to failure obeyed the power law. The coefficient of power function was shown to depend on relative density, geometry and fatigue properties of the bulk material while the exponent was only dependent on the fatigue behavior of the bulk material. The results also indicated the failure surface at an angle of 45° to the loading direction. PMID:26706539

  3. Numerical simulation of the fatigue behavior of additive manufactured titanium porous lattice structures.

    PubMed

    Zargarian, A; Esfahanian, M; Kadkhodapour, J; Ziaei-Rad, S

    2016-03-01

    In this paper, the effects of cell geometry and relative density on the high-cycle fatigue behavior of Titanium scaffolds produced by selective laser melting and electron beam melting techniques were numerically investigated by finite element analysis. The regular titanium lattice samples with three different unit cell geometries, namely, diamond, rhombic dodecahedron and truncated cuboctahedron, and the relative density range of 0.1-0.3 were analyzed under uniaxial cyclic compressive loading. A failure event based algorithm was employed to simulate fatigue failure in the cellular material. Stress-life approach was used to model fatigue failure of both bulk (struts) and cellular material. The predicted fatigue life and the damage pattern of all three structures were found to be in good agreement with the experimental fatigue investigations published in the literature. The results also showed that the relationship between fatigue strength and cycles to failure obeyed the power law. The coefficient of power function was shown to depend on relative density, geometry and fatigue properties of the bulk material while the exponent was only dependent on the fatigue behavior of the bulk material. The results also indicated the failure surface at an angle of 45° to the loading direction.

  4. Feasibility Study on 3-D Printing of Metallic Structural Materials with Robotized Laser-Based Metal Additive Manufacturing

    NASA Astrophysics Data System (ADS)

    Ding, Yaoyu; Kovacevic, Radovan

    2016-07-01

    Metallic structural materials continue to open new avenues in achieving exotic mechanical properties that are naturally unavailable. They hold great potential in developing novel products in diverse industries such as the automotive, aerospace, biomedical, oil and gas, and defense. Currently, the use of metallic structural materials in industry is still limited because of difficulties in their manufacturing. This article studied the feasibility of printing metallic structural materials with robotized laser-based metal additive manufacturing (RLMAM). In this study, two metallic structural materials characterized by an enlarged positive Poisson's ratio and a negative Poisson's ratio were designed and simulated, respectively. An RLMAM system developed at the Research Center for Advanced Manufacturing of Southern Methodist University was used to print them. The results of the tensile tests indicated that the printed samples successfully achieved the corresponding mechanical properties.

  5. Modeling of geomagnetic activity due to passage of different structures and features of high speed streams

    NASA Astrophysics Data System (ADS)

    Mustajab, Fainana

    2016-07-01

    The modeling of terrestrial environment and relative geoeffectiveness due to high speed streams of different type and also compare their geoeffectiveness due to fine structures associated with streams, for example i) streams with different speed, ii) streams with different durations, iii) streams from different solar source and iv) associated fine structures. We also observed high speed streams during 1996 to 2011, and divided them into convenient groups based on their i) speed, ii) durations, iii) solar sources and iv) Dst groups. Performed them method of superposed-epoch analysis and other some statistical-analysis and correlation analysis between geomagnetic index Dst and plasma/field parameters during for both main phase and recovery phase. Streams having the passage duration ranging from 4.5 days to 10.5 days is 59% while other groups, having passage duration <4.5 days and > 10.5 days, contribute only near about 13%. When we observe group according to speed of streams, 30% of high speed streams are having the speed >650km/s and other groups are near about equally distributed in the range 400km/s to 650km/s. Out of 575 high speed streams, 45% streams are caused by single coronal hole, 20% due to multiple coronal hole, 24% by compound i.e: due to coronal hole and coronal mass ejections and only 10% from coronal mass ejections. The streams which are responsible for quiet, weak, moderate storms are nearly equal and only 12% streams cause severe storms. Dst gives best correlation with V(km/s) and BVres to the power 2 (x10res to the power 6) for over all storm time. B(nT) and BV(x10res to the power 3) represent good correlation with Dst during recovery phase duration for the speed groups. I observed the percentage of quiet storms decreases with increasing speed of streams. Near about equal percentage of weak storm are observed in each set of speed of stream. 17% moderate storms are found to contribute for the speed range 400-550km/s and ≈33% contribution is

  6. A comparison of supervised machine learning algorithms and feature vectors for MS lesion segmentation using multimodal structural MRI.

    PubMed

    Sweeney, Elizabeth M; Vogelstein, Joshua T; Cuzzocreo, Jennifer L; Calabresi, Peter A; Reich, Daniel S; Crainiceanu, Ciprian M; Shinohara, Russell T

    2014-01-01

    Machine learning is a popular method for mining and analyzing large collections of medical data. We focus on a particular problem from medical research, supervised multiple sclerosis (MS) lesion segmentation in structural magnetic resonance imaging (MRI). We examine the extent to which the choice of machine learning or classification algorithm and feature extraction function impacts the performance of lesion segmentation methods. As quantitative measures derived from structural MRI are important clinical tools for research into the pathophysiology and natural history of MS, the development of automated lesion segmentation methods is an active research field. Yet, little is known about what drives performance of these methods. We evaluate the performance of automated MS lesion segmentation methods, which consist of a supervised classification algorithm composed with a feature extraction function. These feature extraction functions act on the observed T1-weighted (T1-w), T2-weighted (T2-w) and fluid-attenuated inversion recovery (FLAIR) MRI voxel intensities. Each MRI study has a manual lesion segmentation that we use to train and validate the supervised classification algorithms. Our main finding is that the differences in predictive performance are due more to differences in the feature vectors, rather than the machine learning or classification algorithms. Features that incorporate information from neighboring voxels in the brain were found to increase performance substantially. For lesion segmentation, we conclude that it is better to use simple, interpretable, and fast algorithms, such as logistic regression, linear discriminant analysis, and quadratic discriminant analysis, and to develop the features to improve performance. PMID:24781953

  7. The Vertical Structure of Major Meteorological Features on Jupiter: The Great Red Spot and White Ovals BC and DE

    NASA Technical Reports Server (NTRS)

    Baines, Kevin H.; Carlson, Robert W.

    1999-01-01

    Multi-spectral imagery of Jupiter's Great Red Spot (GRS) and two White ovals acquired by the Galileo/NIMS are used to constrain the spatial variability of the vertical aerosol structure and the distribution of ammonia in and around these most-prominent anti-cyclonic features. All three features exhibit a high-altitude core spanning about 3/4 of their visual size when viewed with moderate absorption wavelengths, indicating a bulk elliptical, "wedding cake" shape in their overall three-dimensional cloud structure. A distinctive spiral pattern within the GRS core is seen in moderate methane and hydrogen absorption bandpasses. This pattern - which has been modelled to show a 2 km variation in cloudtop pressure within the GRS - is inconsistent with a different spiral-shaped pattern observed in ammonia-sensitive wavelengths, thus indicating spatial variability not only in the column abundance of ammonia within the GRS, but in its mixing ratio as well. White Ovals BC and DE were observed in February 1997, just a year before their unusual merger into a single feature. At the time of these observations, the centers of the two anti-cyclones were about 16 degrees apart, separated by a complex cyclonic feature which exhibited unusual spatial variability in its appearance in images acquired at ammonia-sensitive wavelengths. In particular, the northern half of this feature has the largest ammonia column abundance seen within the environs around the white ovals, indicating unusual variability in either cloud structure/altitude and/or ammonia humidity within the cyclone.

  8. Electromagnetic turbulent structures: A ubiquitous feature of the edge region of toroidal plasma configurations

    SciTech Connect

    Spolaore, M. Vianello, N.; Agostini, M.; Cavazzana, R.; De Masi, G.; Martines, E.; Momo, B.; Scaggion, A.; Scarin, P.; Spagnolo, S.; Spizzo, G.; Zuin, M.; Furno, I.; Avino, F.; Fasoli, A.; Theiler, C.; Carralero, D.; Alonso, J. A.; Hidalgo, C.

    2015-01-15

    Electromagnetic features of turbulent filaments, emerging from a turbulent plasma background, have been studied in four different magnetic configurations: the stellarator TJ-II, the Reversed Field Pinch RFX-mod, a device that can be operated also as a ohmic tokamak, and the Simple Magnetized Torus, TORPEX. By applying an analogous diagnostic concept in all cases, direct measurements of both field-aligned current density and vorticity were performed inside the filament. The inter-machine comparison reveals a clear dependence of the filament vorticity upon the local time-averaged E × B flow shear. Furthermore, a wide range of local beta was explored allowing concluding that this parameter plays a fundamental role in the appearance of filament electromagnetic features.

  9. Design Features and Initial RF Performance of a Gradient Hardened 17 GHz TW Linac Structure

    SciTech Connect

    Haimson, J.; Mecklenburg, B.

    2009-01-22

    To avoid surface erosion damage and to assist in studying RF breakdown thresholds in 17 GHz TW linac structures, a gradient hardened structure has been fabricated with high temperature brazed and machined stainless steel surfaces located in the peak E-field region of the beam apertures and the peak H-field regions of the input coupler cavity. The microwave design parameters and physical dimensions of this 22 cavity, 120 degree phase advance structure were chosen to allow the high gradient performance to be compared against a similar design all-copper structure that has been tested in a dual ring, power recirculating amplifier system. The final design parameters of the gradient hardened structure are discussed; the influence of stainless steel RF losses on the power buildup of the resonant ring and on the structure gradient distribution are described; waveforms are shown of the unique ability of the power amplifier to rapidly quench RF breakdown discharges in the linac structure by automatically sensing and redirecting the RF source power to a matched load; and preliminary test results during high power RF processing of the gradient hardened linac structure are presented.

  10. One-step synthesis of mesoporous pentasil zeolite with single-unit-cell lamellar structural features

    SciTech Connect

    Tsapstsis, Michael; Zhang, Xueyi

    2015-11-17

    A method for making a pentasil zeolite material includes forming an aqueous solution that includes a structure directing agent and a silica precursor; and heating the solution at a sufficient temperature and for sufficient time to form a pentasil zeolite material from the silica precursor, wherein the structure directing agent includes a quaternary phosphonium ion.

  11. Routing Corners of Building Structures - by the Method of Vector Addition - Measured with RTN GNSS Surveying Technology

    NASA Astrophysics Data System (ADS)

    Krzyżek, Robert

    2015-12-01

    The paper deals with the problem of surveying buildings in the RTN GNSS mode using modernized indirect methods of measurement. As a result of the classical realtime measurements using indirect methods (intersection of straight lines or a point on a straight line), we obtain a building structure (a building) which is largely deformed. This distortion is due to the inconsistency of the actual dimensions of the building (tie distances) relative to the obtained measurement results. In order to eliminate these discrepancies, and thus to ensure full consistency of the building geometric structure, an innovative solution was applied - the method of vector addition - to modify the linear values (tie distances) of the external face of the building walls. A separate research problem tackled in the article, although not yet fully solved, is the issue of coordinates of corners of a building obtained after the application of the method of vector addition.

  12. Effect of Nano-Particle Addition on Grain Structure Evolution of Friction Stir-Processed Al 6061 During Postweld Annealing

    NASA Astrophysics Data System (ADS)

    Guo, Junfeng; Lee, Bing Yang; Du, Zhenglin; Bi, Guijun; Tan, Ming Jen; Wei, Jun

    2016-08-01

    The fabrication of nano-composites is challenging because uniform dispersion of nano-sized reinforcements in metallic substrate is difficult to achieve using powder metallurgy or liquid processing methods. In the present study, Al-based nano-composites reinforced with Al2O3 particles have been successfully fabricated using friction stir processing. The effects of nano-Al2O3 particle addition on grain structure evolution of friction stir-processed Al matrix during post-weld annealing were investigated. It was revealed that the pinning effect of Al2O3 particles retarded grain growth and completely prevented abnormal grain growth during postweld annealing at 470°C. However, abnormal grain growth can still occur when the composite material was annealed at 530°C. The mechanism involved in the grain structure evolution and the effect of nano-sized particle addition on the mechanical properties were discussed therein.

  13. Effect of Nano-Particle Addition on Grain Structure Evolution of Friction Stir-Processed Al 6061 During Postweld Annealing

    NASA Astrophysics Data System (ADS)

    Guo, Junfeng; Lee, Bing Yang; Du, Zhenglin; Bi, Guijun; Tan, Ming Jen; Wei, Jun

    2016-06-01

    The fabrication of nano-composites is challenging because uniform dispersion of nano-sized reinforcements in metallic substrate is difficult to achieve using powder metallurgy or liquid processing methods. In the present study, Al-based nano-composites reinforced with Al2O3 particles have been successfully fabricated using friction stir processing. The effects of nano-Al2O3 particle addition on grain structure evolution of friction stir-processed Al matrix during post-weld annealing were investigated. It was revealed that the pinning effect of Al2O3 particles retarded grain growth and completely prevented abnormal grain growth during postweld annealing at 470°C. However, abnormal grain growth can still occur when the composite material was annealed at 530°C. The mechanism involved in the grain structure evolution and the effect of nano-sized particle addition on the mechanical properties were discussed therein.

  14. Structural insights into species-specific features of the ribosome from the pathogen Staphylococcus aureus.

    PubMed

    Eyal, Zohar; Matzov, Donna; Krupkin, Miri; Wekselman, Itai; Paukner, Susanne; Zimmerman, Ella; Rozenberg, Haim; Bashan, Anat; Yonath, Ada

    2015-10-27

    The emergence of bacterial multidrug resistance to antibiotics threatens to cause regression to the preantibiotic era. Here we present the crystal structure of the large ribosomal subunit from Staphylococcus aureus, a versatile Gram-positive aggressive pathogen, and its complexes with the known antibiotics linezolid and telithromycin, as well as with a new, highly potent pleuromutilin derivative, BC-3205. These crystal structures shed light on specific structural motifs of the S. aureus ribosome and the binding modes of the aforementioned antibiotics. Moreover, by analyzing the ribosome structure and comparing it with those of nonpathogenic bacterial models, we identified some unique internal and peripheral structural motifs that may be potential candidates for improving known antibiotics and for use in the design of selective antibiotic drugs against S. aureus. PMID:26464510

  15. Structural insights into species-specific features of the ribosome from the pathogen Staphylococcus aureus

    PubMed Central

    Eyal, Zohar; Matzov, Donna; Krupkin, Miri; Wekselman, Itai; Paukner, Susanne; Zimmerman, Ella; Rozenberg, Haim; Bashan, Anat; Yonath, Ada

    2015-01-01

    The emergence of bacterial multidrug resistance to antibiotics threatens to cause regression to the preantibiotic era. Here we present the crystal structure of the large ribosomal subunit from Staphylococcus aureus, a versatile Gram-positive aggressive pathogen, and its complexes with the known antibiotics linezolid and telithromycin, as well as with a new, highly potent pleuromutilin derivative, BC-3205. These crystal structures shed light on specific structural motifs of the S. aureus ribosome and the binding modes of the aforementioned antibiotics. Moreover, by analyzing the ribosome structure and comparing it with those of nonpathogenic bacterial models, we identified some unique internal and peripheral structural motifs that may be potential candidates for improving known antibiotics and for use in the design of selective antibiotic drugs against S. aureus. PMID:26464510

  16. Benzenediol lactones: a class of fungal metabolites with diverse structural features and biological activities.

    PubMed

    Shen, Weiyun; Mao, Hongqiang; Huang, Qian; Dong, Jinyan

    2015-06-01

    Benzenediol lactones are a structurally variable family of fungal polyketide metabolites possessing a macrolide core structure fused into a resorcinol aromatic ring. These compounds are widespread in fungi mainly in the genera such as Aigialus, Cochliobolus, Curvularia, Fusarium, Humicola, Lasiodiplodia, Penicillium and Pochonia etc. Most of these fungal metabolites were reported to possess several interesting biological activities, such as cytotoxicities, nematicidal properties, inhibition of various kinases, receptor agonists, anti-inflammatory activities, heat shock response and immune system modulatory activities etc. This review summarizes the research on the isolation, structure elucidation, and biological activities of the benzenediol lactones, along with some available structure-activity relationships, biosynthetic studies, first syntheses, and syntheses that lead to the revision of structure or stereochemistry, published up to the year of 2014. More than 190 benzenediol lactones are described, and over 300 references cited. PMID:25559850

  17. Insights into the Electronic Structure of Ozone and Sulfur Dioxide from Generalized Valence Bond Theory: Addition of Hydrogen Atoms.

    PubMed

    Lindquist, Beth A; Takeshita, Tyler Y; Dunning, Thom H

    2016-05-01

    Ozone (O3) and sulfur dioxide (SO2) are valence isoelectronic species, yet their properties and reactivities differ dramatically. In particular, O3 is highly reactive, whereas SO2 is chemically relatively stable. In this paper, we investigate serial addition of hydrogen atoms to both the terminal atoms of O3 and SO2 and to the central atom of these species. It is well-known that the terminal atoms of O3 are much more amenable to bond formation than those of SO2. We show that the differences in the electronic structure of the π systems in the parent triatomic species account for the differences in the addition of hydrogen atoms to the terminal atoms of O3 and SO2. Further, we find that the π system in SO2, which is a recoupled pair bond dyad, facilitates the addition of hydrogen atoms to the sulfur atom, resulting in stable HSO2 and H2SO2 species.

  18. NMR and X-ray analysis of structural additivity in metal binding site-swapped hybrids of rubredoxin

    PubMed Central

    LeMaster, David M; Anderson, Janet S; Wang, Limin; Guo, Yi; Li, Hongmin; Hernández, Griselda

    2007-01-01

    Background Chimeric hybrids derived from the rubredoxins of Pyrococcus furiosus (Pf) and Clostridium pasteurianum (Cp) provide a robust system for the characterization of protein conformational stability and dynamics in a differential mode. Interchange of the seven nonconserved residues of the metal binding site between the Pf and Cp rubredoxins yields a complementary pair of hybrids, for which the sum of the thermodynamic stabilities is equal to the sum for the parental proteins. Furthermore, the increase in amide hydrogen exchange rates for the hyperthermophile-derived metal binding site hybrid is faithfully mirrored by a corresponding decrease for the complementary hybrid that is derived from the less thermostable rubredoxin, indicating a degree of additivity in the conformational fluctuations that underlie these exchange reactions. Results Initial NMR studies indicated that the structures of the two complementary hybrids closely resemble "cut-and-paste" models derived from the parental Pf and Cp rubredoxins. This protein system offers a robust opportunity to characterize differences in solution structure, permitting the quantitative NMR chemical shift and NOE peak intensity data to be analyzed without recourse to the conventional conversion of experimental NOE peak intensities into distance restraints. The intensities for 1573 of the 1652 well-resolved NOE crosspeaks from the hybrid rubredoxins were statistically indistinguishable from the intensities of the corresponding parental crosspeaks, to within the baseplane noise level of these high sensitivity data sets. The differences in intensity for the remaining 79 NOE crosspeaks were directly ascribable to localized dynamical processes. Subsequent X-ray analysis of the metal binding site-swapped hybrids, to resolution limits of 0.79 Å and 1.04 Å, demonstrated that the backbone and sidechain heavy atoms in the NMR-derived structures lie within the range of structural variability exhibited among the individual

  19. On the gauge features of gravity on a Lie algebroid structure

    SciTech Connect

    Fabi, S. Harms, B. Hou, S.

    2014-03-15

    We present the geometric formulation of gravity based on the mathematical structure of a Lie Algebroid. We show that this framework provides the geometrical setting to describe the gauge propriety of gravity.

  20. Preflame zone structure and main features of fuel conversion in atmospheric pressure premixed laminar hydrocarbon flames

    SciTech Connect

    Ksandopulo, G.I.

    1995-08-25

    This report describes the structure study of the premixed hydrocarbon-oxidizer Bunsen flames burning at the atmospheric pressure and also the ones with some inhibitors added. Studies were performed on hexane, propane, methane, acetylene, and hexene flames.

  1. Features of electromagnetic radiation time-and-frequency fluctuation intensity distributions from human brain structures.

    PubMed

    Kublanov, V S; Gasilov, V L; Kazakov, Y E

    2000-01-01

    Time-and-frequency fluctuation intensity distributions' analysis is made of the electromagnetic radiation obtained from deep human brain structures. The role of monitoring the distribution changes due to various cerebral circulation disorders is explained.

  2. Basic features of the structure of the Bulgarian offshore and some aspects of its hydrocarbon potential

    SciTech Connect

    Bokov, P.; Guendovich, K.; Radev, M.; Chakarov, P. )

    1993-09-01

    Most recent publications dealing with the structural configuration of the Bulgarian offshore area and its hydrocarbon potential focus on the offshore continuation of key structural elements recognized on land. However, newly acquired geological and geophysical information throws some light on this problem. New tectonic elements are recognized that do not find equivalents onshore; these are characterized by their own oil and gas potential (e.g. Rezovska zone and Michurin saddle). In general terms the Bulgarian Black Sea shelf can be subdivided into three structural units, which differ in their geohistorical development. (1) The northern platform part includes the Varna and east Moesian monoclines, which are separated by the Kaliakra fault zone. The area is characterized by block-faulted structures and a clearly expressed disconformity between Triassic and Upper Jurassic-Valanginian levels. (2) The southern borderland area, which comprises the eastern continuations of the Sredogorie, Balkan, and Strandza zones, is strongly differentiated and less well studied. The Balkan is characterized by flower structures and the Rezovska zone by diapir-like structures. (3) The continental slope is less well studied. Observed slope types vary between sedimentary constructional and tectonic erosional. The hydrocarbon potential of the shelf is related to Devonian and Carboniferous as well as Upper Jurassic-Early Cretaceous carbonates. Organogenic buildups, particularly in the latter, are primary prospects. Tertiary prospects are related to Eocene sands and potential early Eocene and Oligocene source rocks.

  3. Structural Feature Ions for Distinguishing N- and O-Linked Glycan Isomers by LC-ESI-IT MS/MS

    NASA Astrophysics Data System (ADS)

    Everest-Dass, Arun V.; Abrahams, Jodie L.; Kolarich, Daniel; Packer, Nicolle H.; Campbell, Matthew P.

    2013-06-01

    Glycomics is the comprehensive study of glycan expression in an organism, cell, or tissue that relies on effective analytical technologies to understand glycan structure-function relationships. Owing to the macro- and micro-heterogeneity of oligosaccharides, detailed structure characterization has required an orthogonal approach, such as a combination of specific exoglycosidase digestions, LC-MS/MS, and the development of bioinformatic resources to comprehensively profile a complex biological sample. Liquid chromatography-electrospray ionization-mass spectrometry (LC-ESI-MS/MS) has emerged as a key tool in the structural analysis of oligosaccharides because of its high sensitivity, resolution, and robustness. Here, we present a strategy that uses LC-ESI-MS/MS to characterize over 200 N- and O-glycans from human saliva glycoproteins, complemented by sequential exoglycosidase treatment, to further verify the annotated glycan structures. Fragment-specific substructure diagnostic ions were collated from an extensive screen of the literature available on the detailed structural characterization of oligosaccharides and, together with other specific glycan structure feature ions derived from cross-ring and glycosidic-linkage fragmentation, were used to characterize the glycans and differentiate isomers. The availability of such annotated mass spectrometric fragmentation spectral libraries of glycan structures, together with such substructure diagnostic ions, will be key inputs for the future development of the automated elucidation of oligosaccharide structures from MS/MS data.

  4. Porous calcium polyphosphate bone substitutes: additive manufacturing versus conventional gravity sinter processing-effect on structure and mechanical properties.

    PubMed

    Hu, Youxin; Shanjani, Yaser; Toyserkani, Ehsan; Grynpas, Marc; Wang, Rizhi; Pilliar, Robert

    2014-02-01

    Porous calcium polyphosphate (CPP) structures proposed as bone-substitute implants and made by sintering CPP powders to form bending test samples of approximately 35 vol % porosity were machined from preformed blocks made either by additive manufacturing (AM) or conventional gravity sintering (CS) methods and the structure and mechanical characteristics of samples so made were compared. AM-made samples displayed higher bending strengths (≈1.2-1.4 times greater than CS-made samples), whereas elastic constant (i.e., effective elastic modulus of the porous structures) that is determined by material elastic modulus and structural geometry of the samples was ≈1.9-2.3 times greater for AM-made samples. X-ray diffraction analysis showed that samples made by either method displayed the same crystal structure forming β-CPP after sinter annealing. The material elastic modulus, E, determined using nanoindentation tests also showed the same value for both sample types (i.e., E ≈ 64 GPa). Examination of the porous structures indicated that significantly larger sinter necks resulted in the AM-made samples which presumably resulted in the higher mechanical properties. The development of mechanical properties was attributed to the different sinter anneal procedures required to make 35 vol % porous samples by the two methods. A primary objective of the present study, in addition to reporting on bending strength and sample stiffness (elastic constant) characteristics, was to determine why the two processes resulted in the observed mechanical property differences for samples of equivalent volume percentage of porosity. An understanding of the fundamental reason(s) for the observed effect is considered important for developing improved processes for preparation of porous CPP implants as bone substitutes for use in high load-bearing skeletal sites.

  5. Inferring population structure and relationship using minimal independent evolutionary markers in Y-chromosome: a hybrid approach of recursive feature selection for hierarchical clustering

    PubMed Central

    Srivastava, Amit Kumar; Chopra, Rupali; Ali, Shafat; Aggarwal, Shweta; Vig, Lovekesh; Koul Bamezai, Rameshwar Nath

    2014-01-01

    Inundation of evolutionary markers expedited in Human Genome Project and 1000 Genome Consortium has necessitated pruning of redundant and dependent variables. Various computational tools based on machine-learning and data-mining methods like feature selection/extraction have been proposed to escape the curse of dimensionality in large datasets. Incidentally, evolutionary studies, primarily based on sequentially evolved variations have remained un-facilitated by such advances till date. Here, we present a novel approach of recursive feature selection for hierarchical clustering of Y-chromosomal SNPs/haplogroups to select a minimal set of independent markers, sufficient to infer population structure as precisely as deduced by a larger number of evolutionary markers. To validate the applicability of our approach, we optimally designed MALDI-TOF mass spectrometry-based multiplex to accommodate independent Y-chromosomal markers in a single multiplex and genotyped two geographically distinct Indian populations. An analysis of 105 world-wide populations reflected that 15 independent variations/markers were optimal in defining population structure parameters, such as FST, molecular variance and correlation-based relationship. A subsequent addition of randomly selected markers had a negligible effect (close to zero, i.e. 1 × 10−3) on these parameters. The study proves efficient in tracing complex population structures and deriving relationships among world-wide populations in a cost-effective and expedient manner. PMID:25030906

  6. Molecular features related to HIV integrase inhibition obtained from structure- and ligand-based approaches.

    PubMed

    de Carvalho, Luciana L; Maltarollo, Vinícius G; de Lima, Emmanuela Ferreira; Weber, Karen C; Honorio, Kathia M; da Silva, Albérico B F

    2014-01-01

    Among several biological targets to treat AIDS, HIV integrase is a promising enzyme that can be employed to develop new anti-HIV agents. The aim of this work is to propose a mechanistic interpretation of HIV-1 integrase inhibition and to rationalize the molecular features related to the binding affinity of studied ligands. A set of 79 HIV-1 integrase inhibitors and its relationship with biological activity are investigated employing 2D and 3D QSAR models, docking analysis and DFT studies. Analyses of docking poses and frontier molecular orbitals revealed important features on the main ligand-receptor interactions. 2D and 3D models presenting good internal consistency, predictive power and stability were obtained in all cases. Significant correlation coefficients (r(2) = 0.908 and q(2)= 0.643 for 2D model; r(2)= 0.904 and q(2)= 0.719 for 3D model) were obtained, indicating the potential of these models for untested compounds. The generated holograms and contribution maps revealed important molecular requirements to HIV-1 IN inhibition and several evidences for molecular modifications. The final models along with information resulting from molecular orbitals, 2D contribution and 3D contour maps should be useful in the design of new inhibitors with increased potency and selectivity within the chemical diversity of the data. PMID:24416129

  7. Structure and spectral features of H+(H2O)7: Eigen versus Zundel forms

    NASA Astrophysics Data System (ADS)

    Shin, Ilgyou; Park, Mina; Min, Seung Kyu; Lee, Eun Cheol; Suh, Seung Bum; Kim, Kwang S.

    2006-12-01

    The two dimensional (2D) to three dimensional (3D) transition for the protonated water cluster has been controversial, in particular, for H+(H2O)7. For H+(H2O)7 the 3D structure is predicted to be lower in energy than the 2D structure at most levels of theory without zero-point energy (ZPE) correction. On the other hand, with ZPE correction it is predicted to be either 2D or 3D depending on the calculational levels. Although the ZPE correction favors the 3D structure at the level of coupled cluster theory with singles, doubles, and perturbative triples excitations [CCSD(T)] using the aug-cc-pVDZ basis set, the result based on the anharmonic zero-point vibrational energy correction favors the 2D structure. Therefore, the authors investigated the energies based on the complete basis set limit scheme (which we devised in an unbiased way) at the resolution of the identity approximation Møller-Plesset second order perturbation theory and CCSD(T) levels, and found that the 2D structure has the lowest energy for H+(H2O)7 [though nearly isoenergetic to the 3D structure for D+(D2O)7]. This structure has the Zundel-type configuration, but it shows the quantum probabilistic distribution including some of the Eigen-type configuration. The vibrational spectra of MP2/aug-cc-pVDZ calculations and Car-Parrinello molecular dynamics simulations, taking into account the thermal and dynamic effects, show that the 2D Zundel-type form is in good agreement with experiments.

  8. Fractal Model of a Compact Intracloud Discharge. I. Features of the Structure and Evolution

    NASA Astrophysics Data System (ADS)

    Iudin, D. I.; Davydenko, S. S.

    2015-12-01

    We propose a new model of a compact intracloud discharge considered as the result of interaction between two (or more) bipolar streamer structures formed in a strong large-scale electric field of a thundercloud. The model assumes two stages of the compact discharge development. At the preliminary stage, two or more bipolar streamer structures appear successively in the thundercloud in the region of a strong electric field (at the boundaries between the regions of the main positive and the main negative electric charges or between the main positive charge region and the top negative screening layer). The time of development of such structures is determined by the characteristics of the conducting channels that form them and can reach tens of milliseconds. Spatiotemporal synchronization of the bipolar streamer structures is provided by the altitude modulation of the electric field, which, in particular, can originate from a large-scale turbulence of the cloud medium or the stream instability. It is shown that a single bipolar streamer structure accumulates significant electric charges of different signs at its ends as it develops. The start of the main stage of a compact intracloud discharge corresponds to the occurrence of the conducting channel (breakdown of the gap) between the mature streamer structures. The electric charge accumulated at the adjacent ends of the structures at this stage is neutralized over a time much shorter than the duration of the preliminary stage. The parameters of the current pulse are in good agreement with the estimates of the current of a compact intracloud discharge which were obtained in the transmission-line approximation.

  9. Self-assembly, hydration, and structures in N-decanoyl-N-methylglucamide aqueous solutions: effect of salt addition and temperature.

    PubMed

    Molina-Bolívar, J A; Hierrezuelo, J M; Carnero Ruiz, C

    2007-09-15

    The influence of NaCl addition and temperature on the self-assembly, hydration, and structures of N-decanoyl-N-methylglucamide (MEGA-10) in dilute solution has been investigated by using several experimental techniques, including tensiometry, steady-state fluorescence, density, viscosity, and static and dynamic light scattering. Tensiometry and fluorescence probe studies, by using pyrene as a probe, were used to obtain the critical micelle concentration (cmc) upon the electrolyte addition. The mean micellar aggregation numbers (N(agg)) as a function of the salt addition were obtained by both static light scattering and static quenching methods. The N(agg) values estimated by both methods were found to be in good agreement. It was found that the increase in the micelle size, produced by the addition of NaCl, is due to the increase in the aggregation number and in the amount of water non-specifically associated to the micelle. On the other hand, we have observed that the aggregation number remains invariant in the temperature range studied, whereas the hydrodynamic radius slightly decreases. The effect of electrolyte addition and temperature on the properties of MEGA-10 micelles is much less pronounced than those observed in the traditionally used POE-based surfactants.

  10. Flynn Creek Impact Structure: New Insights from Breccias, Melt Features, Shatter Cones, and Remote Sensing

    NASA Technical Reports Server (NTRS)

    Evenick, J. C.; Lee, P.; Deane, B.

    2004-01-01

    The Flynn Creek impact structure is located in Tennessee, USA (36 deg.17 min.N, 85 deg.40 min.W). The structure was first mapped as a crypto-volcanic by Wilson and Born in 1936 [1]. Although they did not properly identify the stratigraphy within the crater or the causal mechanism, they did correctly define the horizontal extent of the crater. More detailed surface and subsurface research by Roddy (1979) accurately described the crater as being an impact structure with a diameter of 3.8 km. It formed around 360 Ma, which corresponds to the interval between the deposition of the Nashville Group and the Chattanooga Shale. Although there is limited rock outcrop in the area, there are exposed surface faults, folds, and large outcrops of impact breccia within the crater.

  11. Basaltic Ring Structures as an Analog for Ring Features in Athabasca Valles, Mars

    NASA Technical Reports Server (NTRS)

    Jaeger, W. L.; Keszthelyi, L. P.; Burr, D. M.; Emery, J. P.; Baker, V. R.; McEwen, A. S.; Miyamoto, H.

    2005-01-01

    Basaltic ring structures (BRSs) are enigmatic, quasi-circular landforms in eastern Washington State that were first recognized in 1965. They remained a subject of geologic scrutiny through the 1970 s and subsequently faded from the spotlight, but recent Mars Orbiter Camera (MOC) images showing morphologically similar structures in Athabasca Valles, Mars, have sparked renewed interest in BRSs. The only known BRSs occur in the Channeled Scabland, a region where catastrophic Pleistocene floods from glacial Lake Missoula eroded into the Miocene flood basalts of the Columbia Plateau. The geologic setting of the martian ring structures (MRSs) is similar; Athabasca Valles is a young channel system that formed when catastrophic aqueous floods carved into a volcanic substrate. This study investigates the formation of terrestrial BRSs and examines the extent to which they are appropriate analogs for the MRSs in Athabasca Valles.

  12. [Structural features of the pulp ground substance and its significance for acute and chronic pulpitis].

    PubMed

    Davarashvili, Capital Ka Cyrillich; Dgebuadze, M; Melikadze, E; Zhvitiashvili, T; Jandieri, K

    2012-12-01

    The goal of the research study is an analysis of amorphous material, fibers and cellular elements of the dental pulp and evaluation of their interactions with a variety of fibrouse structures in the norm and inflammation. To solve this problem used dental pulp tissue bioptats (10 cases) of patients with acute and chronic pulpitis and 10 control specimens (orthodontic operations). The material was studied by histological and electron microscopic methods of research. It was determined that in acute pulpitis develope changes promoting dissociation of fibrouse and cellular structures of pulp components, and thus, loss the cementing binding role of the ground substance. Acute pulpitis characterized by the recruitment of mast cells. ; The reorganization and remodeling of ground substance associated with neoangiogenesis, especially capillaries, and the replacement of collagen fibers by the fibrouse structures are major points in chronic pulpitis. PMID:23293226

  13. Contrasting effects of landscape features on genetic structure in different geographic regions in the ornate dragon lizard, Ctenophorus ornatus.

    PubMed

    Levy, Esther; Tomkins, Joseph L; Lebas, Natasha R; Kennington, W Jason

    2013-08-01

    Habitat fragmentation can have profound effects on the distribution of genetic variation within and between populations. Previously, we showed that in the ornate dragon lizard, Ctenophorus ornatus, lizards residing on outcrops that are separated by cleared agricultural land are significantly more isolated and hold less genetic variation than lizards residing on neighbouring outcrops connected by undisturbed native vegetation. Here, we extend the fine-scale study to examine the pattern of genetic variation and population structure across the species' range. Using a landscape genetics approach, we test whether land clearing for agricultural purposes has affected the population structure of the ornate dragon lizard. We found significant genetic differentiation between outcrop populations (FST  = 0.12), as well as isolation by distance within each geographic region. In support of our previous study, land clearing was associated with higher genetic divergences between outcrops and lower genetic variation within outcrops, but only in the region that had been exposed to intense agriculture for the longest period of time. No other landscape features influenced population structure in any geographic region. These results show that the effects of landscape features can vary across species' ranges and suggest there may be a temporal lag in response to contemporary changes in land use. These findings therefore highlight the need for caution when assessing the impact of contemporary land use practices on genetic variation and population structure.

  14. The influence of contemporary and historic landscape features on the genetic structure of the sand dune endemic, Cirsium pitcheri (Asteraceae)

    PubMed Central

    Fant, J B; Havens, K; Keller, J M; Radosavljevic, A; Yates, E D

    2014-01-01

    Narrow endemics are at risk from climate change because of their restricted habitat preferences, lower colonization ability and dispersal distances. Landscape genetics combines new tools and analyses that allow us to test how both past and present landscape features have facilitated or hindered previous range expansion and local migration patterns, and thereby identifying potential limitations to future range shifts. We have compared current and historic habitat corridors in Cirsium pitcheri, an endemic of the linear dune ecosystem of the Great Lakes, to determine the relative contributions of contemporary migration and post-glacial range expansion on genetic structure. We used seven microsatellite loci to characterize the genetic structure for 24 populations of Cirsium pitcheri, spanning the center to periphery of the range. We tested genetic distance against different measures of geographic distance and landscape permeability, based on contemporary and historic landscape features. We found moderate genetic structure (Fst=0.14), and a north–south pattern to the distribution of genetic diversity and inbreeding, with northern populations having the highest diversity and lowest levels of inbreeding. High allelic diversity, small average pairwise distances and mixed genetic clusters identified in Structure suggest that populations in the center of the range represent the point of entry to the Lake Michigan and a refugium of diversity for this species. A strong association between genetic distances and lake-level changes suggests that historic lake fluctuations best explain the broad geographic patterns, and sandy habitat best explains local patterns of movement. PMID:24398882

  15. Changes in the structure and function of microbial communities in drinking water treatment bioreactors upon addition of phosphorus.

    PubMed

    Li, Xu; Upadhyaya, Giridhar; Yuen, Wangki; Brown, Jess; Morgenroth, Eberhard; Raskin, Lutgarde

    2010-11-01

    Phosphorus was added as a nutrient to bench-scale and pilot-scale biologically active carbon (BAC) reactors operated for perchlorate and nitrate removal from contaminated groundwater. The two bioreactors responded similarly to phosphorus addition in terms of microbial community function (i.e., reactor performance), while drastically different responses in microbial community structure were detected. Improvement in reactor performance with respect to perchlorate and nitrate removal started within a few days after phosphorus addition for both reactors. Microbial community structures were evaluated using molecular techniques targeting 16S rRNA genes. Clone library results showed that the relative abundance of perchlorate-reducing bacteria (PRB) Dechloromonas and Azospira in the bench-scale reactor increased from 15.2% and 0.6% to 54.2% and 11.7% after phosphorus addition, respectively. Real-time quantitative PCR (qPCR) experiments revealed that these increases started within a few days after phosphorus addition. In contrast, after phosphorus addition, the relative abundance of Dechloromonas in the pilot-scale reactor decreased from 7.1 to 0.6%, while Zoogloea increased from 17.9 to 52.0%. The results of this study demonstrated that similar operating conditions for bench-scale and pilot-scale reactors resulted in similar contaminant removal performances, despite dramatically different responses from microbial communities. These findings suggest that it is important to evaluate the microbial community compositions inside bioreactors used for drinking water treatment, as they determine the microbial composition in the effluent and impact downstream treatment requirements for drinking water production. This information could be particularly relevant to drinking water safety, if pathogens or disinfectant-resistant bacteria are detected in the bioreactors.

  16. NOBAI: a web server for character coding of geometrical and statistical features in RNA structure.

    PubMed

    Knudsen, Vegeir; Caetano-Anollés, Gustavo

    2008-07-01

    The Numeration of Objects in Biology: Alignment Inferences (NOBAI) web server provides a web interface to the applications in the NOBAI software package. This software codes topological and thermodynamic information related to the secondary structure of RNA molecules as multi-state phylogenetic characters, builds character matrices directly in NEXUS format and provides sequence randomization options. The web server is an effective tool that facilitates the search for evolutionary history embedded in the structure of functional RNA molecules. The NOBAI web server is accessible at 'http://www.manet.uiuc.edu/nobai/nobai.php'. This web site is free and open to all users and there is no login requirement.

  17. Special Features of the Structure of Copper-containing Products of Plasma Dynamic Synthesis

    NASA Astrophysics Data System (ADS)

    Ivashutenko, A. S.; Nazarenko, O. B.; Sivkov, A. A.; Saigash, A. S.; Stepanov, K. I.

    2015-03-01

    Results of investigation of the dispersed, phase, and chemical compositions of products of plasma dynamic synthesis in a high-speed pulsed jet of copper-containing electroerosive plasma flowing into a closed volume with the air atmosphere are presented. Products of synthesis are investigated by the methods of x-ray phase and thermal analyses, electron microscopy, and IR spectroscopy. The structure of the synthesized powder includes metal copper, Cu2O and CuO copper oxides, and hydrated copper hydroxide Cu(OH)2·N2O. Results of investigations of structural changes of the synthesized products during heating in vacuum and air are presented.

  18. Aerosol based direct-write micro-additive fabrication method for sub-mm 3D metal-dielectric structures

    NASA Astrophysics Data System (ADS)

    Rahman, Taibur; Renaud, Luke; Heo, Deuk; Renn, Michael; Panat, Rahul

    2015-10-01

    The fabrication of 3D metal-dielectric structures at sub-mm length scale is highly important in order to realize low-loss passives and GHz wavelength antennas with applications in wearable and Internet-of-Things (IoT) devices. The inherent 2D nature of lithographic processes severely limits the available manufacturing routes to fabricate 3D structures. Further, the lithographic processes are subtractive and require the use of environmentally harmful chemicals. In this letter, we demonstrate an additive manufacturing method to fabricate 3D metal-dielectric structures at sub-mm length scale. A UV curable dielectric is dispensed from an Aerosol Jet system at 10-100 µm length scale and instantaneously cured to build complex 3D shapes at a length scale  <1 mm. A metal nanoparticle ink is then dispensed over the 3D dielectric using a combination of jetting action and tilted dispense head, also using the Aerosol Jet technique and at a length scale 10-100 µm, followed by the nanoparticle sintering. Simulation studies are carried out to demonstrate the feasibility of using such structures as mm-wave antennas. The manufacturing method described in this letter opens up the possibility of fabricating an entirely new class of custom-shaped 3D structures at a sub-mm length scale with potential applications in 3D antennas and passives.

  19. Crystal Structure of the First Eubacterial Mre11 Nuclease Reveals Novel Features that may Discriminate Substrates During DNA Repair

    PubMed Central

    Das, Debanu; Moiani, Davide; Axelrod, Herbert L.; Miller, Mitchell D.; McMullan, Daniel; Jin, Kevin K.; Abdubek, Polat; Astakhova, Tamara; Burra, Prasad; Carlton, Dennis; Chiu, Hsiu-Ju; Clayton, Thomas; Deller, Marc C.; Duan, Lian; Ernst, Dustin; Feuerhelm, Julie; Grant, Joanna C.; Grzechnik, Anna; Grzechnik, Slawomir K.; Han, Gye Won; Jaroszewski, Lukasz; Klock, Heath E.; Knuth, Mark W.; Kozbial, Piotr; Krishna, S. Sri; Kumar, Abhinav; Marciano, David; Morse, Andrew T.; Nigoghossian, Edward; Okach, Linda; Paulsen, Jessica; Reyes, Ron; Rife, Christopher L.; Sefcovic, Natasha; Tien, Henry J.; Trame, Christine B.; van den Bedem, Henry; Weekes, Dana; Xu, Qingping; Hodgson, Keith O.; Wooley, John; Elsliger, Marc-André; Deacon, Ashley M.; Godzik, Adam; Lesley, Scott A.; Tainer, John A.; Wilson, Ian A.

    2010-01-01

    Mre11 nuclease plays a central role in the repair of cytotoxic and mutagenic DNA double-strand breaks (DSBs). As x-ray structural information has only been available for the Pyrococcus furiosus enzyme (PfMre11), the conserved and variable features of this nuclease across the domains of life have not been experimentally defined. Our crystal structure and biochemical studies demonstrate that TM1635 from Thermotoga maritima, originally annotated as a putative nuclease, is the Mre11 endo/exonuclease from T. maritima (TmMre11) and the first such structure from eubacteria. TmMre11 and PfMre11 display similar overall structures, despite sequence identity in the twilight zone of only ∼20%. However, they differ substantially in their DNA specificity domains and in their dimeric organization. Residues in the nuclease domain are highly conserved, but those in the DNA specificity domain are not. The structural differences likely affect how Mre11s from different organisms recognize and interact with single-stranded DNA, double-stranded DNA and DNA hairpin structures during DNA repair. The TmMre11 nuclease active site has no bound metal ions, but is conserved in sequence and structure with exception of a histidine that is important in PfMre11 nuclease activity. Nevertheless, biochemical characterization confirms that TmMre11 possesses both endonuclease and exonuclease activities on ssDNA and dsDNA substrates, respectively. PMID:20122942

  20. A Raman Spectroscopic Study of the Structural Modifications Associated with the Addition of Calcium Oxide and Boron Oxide to Silica

    NASA Astrophysics Data System (ADS)

    Kline, Jeff; Tangstad, Merete; Tranell, Gabriella

    2015-02-01

    Raman spectroscopy as an instrumental technique for the determination of silicate structure is widely accepted. This method was utilized for analysis of structural modifications associated with the addition of network modifying species. Silicate melts are described by the extent of oxygen bridging. Therefore, understanding the effect different oxides have on modifying the silicate structure will provide valuable information regarding the removal of boron from silicon in slag refining processes. Samples in the range CaO/SiO2 = 0.56 to 1.2 were evaluated with and without varying concentrations of B2O3. As expected, increasing the CaO content resulted in an increase in the Q 0 and Q 1 species and a decrease in the Q 3 species indicating a depolymerization of the silicate network. The addition of B2O3 to the 36 wt pct CaO-64 wt pct SiO2 system resulted in a decrease in ring-typed structures associated with the vibrational mode near 600 cm-1, an increase in the Q 3 species and a decrease in the Q 2 species. Adding B2O3 to the 54.5 wt pct CaO-45.5 wt pct SiO2 system resulted in decrease in the Q 0 and Q 2 species and an increase in the Q 3 species. Thus, both systems indicate the introduction of B2O3 to the more polymerized structural units in the silicate network. The increase in the peak near 630 cm-1 signifies some formation of ring-type metaborate groups or ring-type danburite groups. A correlation between the experimentally determined Q n distribution and optical basicity is proposed. Viscosity and optical basicity are correlated for the CaO-SiO2 system as well as viscosity and.

  1. A Raman Spectroscopic Study of the Structural Modifications Associated with the Addition of Calcium Oxide and Boron Oxide to Silica

    NASA Astrophysics Data System (ADS)

    Kline, Jeff; Tangstad, Merete; Tranell, Gabriella

    2014-09-01

    Raman spectroscopy as an instrumental technique for the determination of silicate structure is widely accepted. This method was utilized for analysis of structural modifications associated with the addition of network modifying species. Silicate melts are described by the extent of oxygen bridging. Therefore, understanding the effect different oxides have on modifying the silicate structure will provide valuable information regarding the removal of boron from silicon in slag refining processes. Samples in the range CaO/SiO2 = 0.56 to 1.2 were evaluated with and without varying concentrations of B2O3. As expected, increasing the CaO content resulted in an increase in the Q 0 and Q 1 species and a decrease in the Q 3 species indicating a depolymerization of the silicate network. The addition of B2O3 to the 36 wt pct CaO-64 wt pct SiO2 system resulted in a decrease in ring-typed structures associated with the vibrational mode near 600 cm-1, an increase in the Q 3 species and a decrease in the Q 2 species. Adding B2O3 to the 54.5 wt pct CaO-45.5 wt pct SiO2 system resulted in decrease in the Q 0 and Q 2 species and an increase in the Q 3 species. Thus, both systems indicate the introduction of B2O3 to the more polymerized structural units in the silicate network. The increase in the peak near 630 cm-1 signifies some formation of ring-type metaborate groups or ring-type danburite groups. A correlation between the experimentally determined Q n distribution and optical basicity is proposed. Viscosity and optical basicity are correlated for the CaO-SiO2 system as well as viscosity and Q_{{exp}}^n.

  2. Spectral and structural features of Lu1 - x RE x BO3 compounds

    NASA Astrophysics Data System (ADS)

    Shmurak, S. Z.; Kedrov, V. V.; Kiselev, A. P.; Fursova, T. N.; Shmyt'ko, I. M.

    2015-08-01

    The luminescence spectra, luminescence excitation spectra, IR absorption spectra, and crystal structure of orthoborates Lu1 - x RE x BO3 ( RE = Eu, Gd, Tb, Y, Dy) have been investigated. It has been found that the solid solution consisting of a LuBO3 orthoborate, which has two stable structural modifications (calcite and vaterite), and an REBO3 orthoborate, which has one structural modification (vaterite), crystallizes only in the vaterite structure when the concentration of a rare-earth ion substituting for lutetium exceeds 15-20 at %. The investigation of the photoluminescence spectra has demonstrated that, for rare-earth ions Lu3+, Eu3+, Y3+, and Gd3+ in the vaterite modification of Lu1 - x RE x BO3 orthoborates, there are at least two positions that are not equivalent in the symmetry of the local environment. It has been established that the maximum intensity of the luminescence of the vaterite modification of Lu1 - x Tb x BO3 compounds synthesized at 970°C, which is observed at a terbium concentration of 15 at %, is several times higher than the maximum intensity of the luminescence of the calcite modification.

  3. Structural and hydrogeological features of a Lias carbonate aquifer in the Triffa Plain, NE Morocco

    NASA Astrophysics Data System (ADS)

    Sardinha, J.; Carneiro, J. F.; Zarhloule, Y.; Barkaoui, A.; Correia, A.; Boughriba, M.; Rimi, A.; El Houadi, B.

    2012-09-01

    The rising demand for water and the contamination of shallow water table aquifers has led authorities in NE Morocco to look for deeper groundwater resources in the Triffa Plain, namely in Lower Jurassic (Lias) dolomitic limestones. The liassic aquifer is of strategic importance for the development of the region, however, its hydrodynamic behaviour is poorly understood due to lack of hydrogeological data and block structure. This article presents a first effort towards understanding the structure and hydraulic behaviour of the aquifer. Exploration borehole data and results from geophysical campaigns were integrated into a GIS environment to build a preliminary model of the aquifer structure. The aquifer behaves as an unconfined aquifer in the northern part of the Béni Snassen Mountains (the recharge area), but as it dips to the north, it becomes confined by marls and shales of the Middle/Upper Jurassic. Even though piezometric level data are scarce, a tentative piezometric map was produced. Three blocks separated by NW-SE trending faults in a horst and graben structure, with distinct flow behaviours were identified: Berkane, Fezouane and Sidi Rahmoun blocks. Those blocks also show differences in hydraulic conductivity distribution. As a result of the reaction with the dolomitic limestones, the groundwater is of calcium-magnesium bicarbonate type. Groundwater temperature as measured in springs ranges from 29 °C to 37 °C in springs and constitutes a potential low enthalpy geothermal resource.

  4. Structural and biochemical features of acidic α-amylase of Bacillus acidicola.

    PubMed

    Sharma, Archana; Satyanarayana, T

    2013-10-01

    The investigation is aimed at understanding structure-function aspect of α-amylase of an acidophilic bacterium Bacillus acidicola (BAamy), which is Ca(2+)-independent and active at acidic pH of native starch, and thus, suits better in starch saccharification process. The CD spectroscopic data analysis revealed that the enzyme has 30% α-helices, 14.2% β-sheets, and 55.8% random coils at 60 °C and pH 4.0. Using Bacillus stearothermophilus α-amylase (BStA) as the template, 3-D structure of rBAamy has been proposed. A complete loss in α-amylase activity was recorded when the amino acid residues (D231, E261 and D328) were substituted that confirmed their role in catalysis. The CD studies indicated a decrease in the α-helices content below and beyond the optimum pH and temperature that suggests a critical role of α-helix in maintaining the structural conformation of the enzyme. Fluorescence-quenching by N-bromosuccinimide (NBS) suggested the role of tryptophan in maintaining structural integrity of α-amylase and that by acrylamide indicated interaction by simple collision process.

  5. Structural basis for the requirement of additional factors for MLL1 SET domain activity and recognition of epigenetic marks.

    PubMed

    Southall, Stacey M; Wong, Poon-Sheng; Odho, Zain; Roe, S Mark; Wilson, Jon R

    2009-01-30

    The mixed-lineage leukemia protein MLL1 is a transcriptional regulator with an essential role in early development and hematopoiesis. The biological function of MLL1 is mediated by the histone H3K4 methyltransferase activity of the carboxyl-terminal SET domain. We have determined the crystal structure of the MLL1 SET domain in complex with cofactor product AdoHcy and a histone H3 peptide. This structure indicates that, in order to form a well-ordered active site, a highly variable but essential component of the SET domain must be repositioned. To test this idea, we compared the effect of the addition of MLL complex members on methyltransferase activity and show that both RbBP5 and Ash2L but not Wdr5 stimulate activity. Additionally, we have determined the effect of posttranslational modifications on histone H3 residues downstream and upstream from the target lysine and provide a structural explanation for why H3T3 phosphorylation and H3K9 acetylation regulate activity. PMID:19187761

  6. Sensitivity of near field GIA response with respect to rheological features of the Earth structure

    NASA Astrophysics Data System (ADS)

    Hagedoorn, Jan M.; Klemann, Volker; Sasgen, Ingo; Thomas, Maik

    2016-04-01

    One task of the German National Climate Modeling Initiative PalMod will be to couple earth system models representing the atmospere, ocean and ice dynamics during the last glacial cycle with the dynamic loading response of a viscoelastic earth model. In preparation, we discuss in this study the influence of viscosity stratification and of lateral heterogeneities in the Earth structure on the solid-earth response to glacial loading. As discussed in literature, there is a controversy about the impact of lateral heterogeneity on the prediction of present and past GIA signals. The influence of the Earth structure on the far-field response is governed by the flexural behaviour of the regional lithosphere and upper-mantle structure in response to the varying ocean load. The influence at and around the glacial ice sheets is substantial with respect to the amplitudes and also with respect to the temporal evolution of the earth's response. Depending on the region of interest, lithospheric variations are present over the extent of the glacial ice sheets varying between 40 and 200 km, and lateral variations in viscosity can vary by one or two orders of magnitude. The focus will be to what extent the behaviour of a laterally heterogeneous viscosity structure can be parameterised by an adjusted spherical earth model representation. Accordingly, we apply predefined ice-sheet histories (like ICE5G and ICE6G) and analyse ensemble runs representing the variability of relative sea-level and palaeo-topography predictions. Spatial pattern of deformation fields will be discussed as the behaviour at specific sea-level curves. Furthermore, we compare the sensitivity on earth structure during the evolution of sea level and palaeo topography during the termination phase of the last glaciation to present-day rates of relative sea-level height and radial displacement.

  7. Unravelling the impact of hydrocarbon structure on the fumarate addition mechanism--a gas-phase ab initio study.

    PubMed

    Bharadwaj, Vivek S; Vyas, Shubham; Villano, Stephanie M; Maupin, C Mark; Dean, Anthony M

    2015-02-14

    The fumarate addition reaction mechanism is central to the anaerobic biodegradation pathway of various hydrocarbons, both aromatic (e.g., toluene, ethyl benzene) and aliphatic (e.g., n-hexane, dodecane). Succinate synthase enzymes, which belong to the glycyl radical enzyme family, are the main facilitators of these biochemical reactions. The overall catalytic mechanism that converts hydrocarbons to a succinate molecule involves three steps: (1) initial H-abstraction from the hydrocarbon by the radical enzyme, (2) addition of the resulting hydrocarbon radical to fumarate, and (3) hydrogen abstraction by the addition product to regenerate the radical enzyme. Since the biodegradation of hydrocarbon fuels via the fumarate addition mechanism is linked to bio-corrosion, an improved understanding of this reaction is imperative to our efforts of predicting the susceptibility of proposed alternative fuels to biodegradation. An improved understanding of the fuel biodegradation process also has the potential to benefit bioremediation. In this study, we consider model aromatic (toluene) and aliphatic (butane) compounds to evaluate the impact of hydrocarbon structure on the energetics and kinetics of the fumarate addition mechanism by means of high level ab initio gas-phase calculations. We predict that the rate of toluene degradation is ∼100 times faster than butane at 298 K, and that the first abstraction step is kinetically significant for both hydrocarbons, which is consistent with deuterium isotope effect studies on toluene degradation. The detailed computations also show that the predicted stereo-chemical preference of the succinate products for both toluene and butane are due to the differences in the radical addition rate constants for the various isomers. The computational and kinetic modeling work presented here demonstrates the importance of considering pre-reaction and product complexes in order to accurately treat gas phase systems that involve intra and inter

  8. Features of structures formation on the basis of chitosan derivatives by a prototype of 263 nm laser stereolithograph

    NASA Astrophysics Data System (ADS)

    Dudova, D. S.; Bardakova, K. N.; Akopova, T. A.; Timashev, P. S.; Minaev, N. V.

    2016-08-01

    We have developed technology of polysaccharides based matrices formation by laser stereolithography (SLA) method using UV range laser radiation. Experimental data on a laser parameters selection of single-layer structures polymerization for compositions based on unsaturated chitosan derivatives with different degree of substitution and with the addition of polyethylene glycol diacrylate is shown.

  9. Incidental and Context-Responsive Activation of Structure- and Function-Based Action Features during Object Identification

    ERIC Educational Resources Information Center

    Lee, Chia-lin; Middleton, Erica; Mirman, Daniel; Kalenine, Solene; Buxbaum, Laurel J.

    2013-