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Sample records for related jmjc domain

  1. Emerging Roles of JmjC Domain-Containing Proteins.

    PubMed

    Accari, Sandra L; Fisher, Paul R

    2015-01-01

    Jumonji C (JmjC) domain-containing proteins are a diverse superfamily of proteins containing a characteristic, evolutionarily conserved β-barrel structure that normally contains binding sites for Fe(II) and α-ketoglutarate. In the best studied JmjC-domain proteins, the JmjC barrel has a histone demethylase catalytic activity. Histones are evolutionarily conserved proteins intimately involved in the packaging of DNA within the nucleus of eukaryotic organisms. The N-termini ("tails") of the histone proteins are subject to a diverse array of posttranslational modifications including methylation. Unlike many of the other histone modifications which are transient, methylation was thought to be permanent, until the relatively recent identification of the first demethylases. Jumonji C domain-containing proteins were first identified with a role in the modulation of histone methylation marks. This family of proteins is broken up into seven distinct subgroups based on domain architecture and their ability to antagonize specific histone methylation marks. Their biological functions derive from their ability to regulate gene expression and include roles in cell differentiation, growth, proliferation, and stress responses. However, one subgroup remains, the largest, in which the JmjC domain has no known biochemical function. These proteins belong to the JmjC-domain-only subgroup and as their name suggests, the only bioinformatically recognizable domain they contain is the highly conserved JmjC domain. PMID:26404469

  2. The JmjC domain of Gis1 is dispensable for transcriptional activation.

    PubMed

    Yu, Yao; Neiman, Aaron M; Sternglanz, Rolf

    2010-11-01

    Yeast Gis1 protein functions as a transcription factor after nutrient limitation and oxidative stress. In this report, we show that Gis1 also regulates the induction of several genes involved in spore wall synthesis during sporulation. Gis1 contains a JmjC domain near its N-terminus. In many proteins, JmjC domains provide histone demethylase activity. Whether the JmjC domain of Gis1 contributes to its transcriptional activation is still unknown. Here, we show that gis1 point mutations that abolish Fe (II) and α-ketoglutarate binding, known cofactors in other JmjC proteins, are still able to induce transcription normally during glucose starvation and sporulation. Even the deletion of the entire JmjC domain does not affect transcriptional activation by Gis1. Moreover, the JmjC domain is not required for the toxicity associated with Gis1 overexpression. The data demonstrate that the JmjC domain is dispensable for transcriptional activation by Gis1 during nutrient stress and sporulation.

  3. Structure of the JmjC domain-containing protein NO66 complexed with ribosomal protein Rpl8

    SciTech Connect

    Wang, Chengliang; Zhang, Qiongdi; Hang, Tianrong; Tao, Yue; Ma, Xukai; Wu, Minhao; Zhang, Xuan Zang, Jianye

    2015-08-28

    The structure of the complex of NO66 and Rpl8 was solved in the native state and NO66 recognizes the consensus motif NHXH . Tetramerization is required for efficient substrate binding and catalysis by NO66. The JmjC domain-containing proteins belong to a large family of oxygenases possessing distinct substrate specificities which are involved in the regulation of different biological processes, such as gene transcription, RNA processing and translation. Nucleolar protein 66 (NO66) is a JmjC domain-containing protein which has been reported to be a histone demethylase and a ribosome protein 8 (Rpl8) hydroxylase. The present biochemical study confirmed the hydroxylase activity of NO66 and showed that oligomerization is required for NO66 to efficiently catalyze the hydroxylation of Rpl8. The structures of NO66{sup 176–C} complexed with Rpl8{sup 204–224} in a tetrameric form and of the mutant protein M2 in a dimeric form were solved. Based on the results of structural and biochemical analyses, the consensus sequence motif NHXH recognized by NO66 was confirmed. Several potential substrates of NO66 were found by a BLAST search according to the consensus sequence motif. When binding to substrate, the relative positions of each subunit in the NO66 tetramer shift. Oligomerization may facilitate the motion of each subunit in the NO66 tetramer and affect the catalytic activity.

  4. Knockdown of a JmjC domain-containing gene JMJ524 confers altered gibberellin responses by transcriptional regulation of GRAS protein lacking the DELLA domain genes in tomato

    PubMed Central

    Li, Jinhua; Yu, Chuying; Wu, Hua; Luo, Zhidan; Ouyang, Bo; Cui, Long; Zhang, Junhong; Ye, Zhibiao

    2015-01-01

    Plants integrate responses to independent hormonal and environmental signals to survive adversity. In particular, the phytohormone gibberellin (GA) regulates a variety of developmental processes and stress responses. In this study, the Jumonji-C (JmjC) domain-containing gene JMJ524 was characterized in tomato. JMJ524 responded to circadian rhythms and was upregulated by GA treatment. Knockdown of JMJ524 by RNAi caused a GA-insensitive dwarf phenotype with shrunken leaves and shortened internodes. However, in these transgenic plants, higher levels of endogenous GAs were detected. A genome-wide gene expression analysis by RNA-seq indicated that the expression levels of two DELLA-like genes, SlGLD1 (‘GRAS protein Lacking the DELLA domain’) and SlGLD2, were increased in JMJ524-RNAi transgenic plants. Nevertheless, only the overexpression of SlGLD1 in tomato resulted in a GA-insensitive dwarf phenotype, suggesting that SlGLD1 acts as a repressor of GA signalling. This study proposes that JMJ524 is required for stem elongation by altering GA responses, at least partially by regulating SlGLD1. PMID:25680796

  5. JmjC Domain-containing Protein 6 (Jmjd6) Derepresses the Transcriptional Repressor Transcription Factor 7-like 1 (Tcf7l1) and Is Required for Body Axis Patterning during Xenopus Embryogenesis.

    PubMed

    Zhang, Xuena; Gao, Yan; Lu, Lei; Zhang, Zan; Gan, Shengchun; Xu, Liyang; Lei, Anhua; Cao, Ying

    2015-08-14

    Tcf7l1 (also known as Tcf3) is a bimodal transcription factor that plays essential roles in embryogenesis and embryonic and adult stem cells. On one hand, Tcf7l1 works as transcriptional repressor via the recruitment of Groucho-related transcriptional corepressors to repress the transcription of Wnt target genes, and, on the other hand, it activates Wnt target genes when Wnt-activated β-catenin interacts with it. However, how its activity is modulated is not well understood. Here we demonstrate that a JmjC-domain containing protein, Jmjd6, interacts with Tcf7l and derepresses Tcf7l. We show that Jmjd6 binds to a region of Tcf7l1 that is also responsible for Groucho interaction, therefore making it possible that Jmjd6 binding displaces the Groucho transcriptional corepressor from Tcf7l1. Moreover, we show that Jmjd6 antagonizes the repression effect of Tcf7l1 on target gene transcription and is able to enhance β-catenin-induced gene activation and that, vice versa, inhibition of Jmjd6 activity compromises gene activation in both cells and Xenopus early embryos. We also show that jmjd6 is both maternally and zygotically transcribed during Xenopus embryogenesis. Loss of Jmjd6 function causes defects in anterioposterior body axis formation and down-regulation of genes that are involved in anterioposterior axis patterning. The results elucidate a novel mechanism underlying the regulation of Tcf7l1 activity and the regulation of embryonic body axis formation.

  6. Arginine demethylation is catalysed by a subset of JmjC histone lysine demethylases

    PubMed Central

    Walport, Louise J.; Hopkinson, Richard J.; Chowdhury, Rasheduzzaman; Schiller, Rachel; Ge, Wei; Kawamura, Akane; Schofield, Christopher J.

    2016-01-01

    While the oxygen-dependent reversal of lysine Nɛ-methylation is well established, the existence of bona fide Nω-methylarginine demethylases (RDMs) is controversial. Lysine demethylation, as catalysed by two families of lysine demethylases (the flavin-dependent KDM1 enzymes and the 2-oxoglutarate- and oxygen-dependent JmjC KDMs, respectively), proceeds via oxidation of the N-methyl group, resulting in the release of formaldehyde. Here we report detailed biochemical studies clearly demonstrating that, in purified form, a subset of JmjC KDMs can also act as RDMs, both on histone and non-histone fragments, resulting in formaldehyde release. RDM catalysis is studied using peptides of wild-type sequences known to be arginine-methylated and sequences in which the KDM's methylated target lysine is substituted for a methylated arginine. Notably, the preferred sequence requirements for KDM and RDM activity vary even with the same JmjC enzymes. The demonstration of RDM activity by isolated JmjC enzymes will stimulate efforts to detect biologically relevant RDM activity. PMID:27337104

  7. On thick domain walls in general relativity

    NASA Technical Reports Server (NTRS)

    Goetz, Guenter; Noetzold, Dirk

    1989-01-01

    Planar scalar field configurations in general relativity differ considerably from those in flat space. It is shown that static domain walls of finite thickness in curved space-time do not possess a reflection symmetry. At infinity, the space-time tends to the Taub vacuum on one side of the wall and to the Minkowski vacuum (Rindler space-time) on the other. Massive test particles are always accelerated towards the Minkowski side, i.e., domain walls are attractive on the Taub side, but repulsive on the Minkowski side (Taub-vacuum cleaner). It is also proved that the pressure in all directions is always negative. Finally, a brief comment is made concerning the possibility of infinite, i.e., bigger than horizon size, domain walls in our universe. All of the results are independent of the form of the potential V(phi) greater than or equal to 0 of the scalar field phi.

  8. Relating Hippocampus to Relational Memory Processing across Domains and Delays

    PubMed Central

    Monti, Jim M.; Cooke, Gillian E.; Watson, Patrick D.; Voss, Michelle W.; Kramer, Arthur F.; Cohen, Neal J.

    2015-01-01

    The hippocampus has been implicated in a diverse set of cognitive domains and paradigms, including cognitive mapping, long-term memory, and relational memory, at long or short study–test intervals. Despite the diversity of these areas, their association with the hippocampus may rely on an underlying commonality of relational memory processing shared among them. Most studies assess hippocampal memory within just one of these domains, making it difficult to know whether these paradigms all assess a similar underlying cognitive construct tied to the hippocampus. Here we directly tested the commonality among disparate tasks linked to the hippocampus by using PCA on performance from a battery of 12 cognitive tasks that included two traditional, long-delay neuropsychological tests of memory and two laboratory tests of relational memory (one of spatial and one of visual object associations) that imposed only short delays between study and test. Also included were different tests of memory, executive function, and processing speed. Structural MRI scans from a subset of participants were used to quantify the volume of the hippocampus and other subcortical regions. Results revealed that the 12 tasks clustered into four components; critically, the two neuropsychological tasks of long-term verbal memory and the two laboratory tests of relational memory loaded onto one component. Moreover, bilateral hippocampal volume was strongly tied to performance on this component. Taken together, these data emphasize the important contribution the hippocampus makes to relational memory processing across a broad range of tasks that span multiple domains. PMID:25203273

  9. Cross-Domain Analogies as Relating Derived Relations among Two Separate Relational Networks

    ERIC Educational Resources Information Center

    Ruiz, Francisco J.; Luciano, Carmen

    2011-01-01

    Contemporary behavior analytic research is making headway in analyzing analogy as the establishment of a relation of coordination among common types of trained or derived relations. Previous studies have been focused on within-domain analogy. The current study expands previous research by analyzing cross-domain analogy as relating relations among…

  10. Between- and Within-Domain Relations of Students' Academic Emotions

    ERIC Educational Resources Information Center

    Goetz, Thomas; Frenzel, Anne C.; Pekrun, Reinhard; Hall, Nathan C.; Ludtke, Oliver

    2007-01-01

    The authors investigated between- and within-domain relations of academic emotions, including students' enjoyment, pride, anxiety, anger, and boredom experienced in mathematics, physics, German, and English classes (N = 542; Grades 8 and 11). Corroborating assumptions of domain specificity, the between-domains relations of these emotions were weak…

  11. Between-domain relations of students' academic emotions and their judgments of school domain similarity

    PubMed Central

    Goetz, Thomas; Haag, Ludwig; Lipnevich, Anastasiya A.; Keller, Melanie M.; Frenzel, Anne C.; Collier, Antonie P. M.

    2014-01-01

    With the aim to deepen our understanding of the between-domain relations of academic emotions, a series of three studies was conducted. We theorized that between-domain relations of trait (i.e., habitual) emotions reflected students' judgments of domain similarities, whereas between-domain relations of state (i.e., momentary) emotions did not. This supposition was based on the accessibility model of emotional self-report, according to which individuals' beliefs tend to strongly impact trait, but not state emotions. The aim of Study 1 (interviews; N = 40; 8th and 11th graders) was to gather salient characteristics of academic domains from students' perspective. In Study 2 (N = 1709; 8th and 11th graders) the 13 characteristics identified in Study 1 were assessed along with academic emotions in four different domains (mathematics, physics, German, and English) using a questionnaire-based trait assessment. With respect to the same domains, state emotions were assessed in Study 3 (N = 121; 8th and 11th graders) by employing an experience sampling approach. In line with our initial assumptions, between-domain relations of trait but not state academic emotions reflected between-domain relations of domain characteristics. Implications for research and practice are discussed. PMID:25374547

  12. The Definition, Dimensions, and Domain of Public Relations.

    ERIC Educational Resources Information Center

    Hutton, James G.

    1999-01-01

    Discusses how the field of public relations has left itself vulnerable to other fields that are making inroads into public relations' traditional domain, and to critics who are filling in their own definitions of public relations. Proposes a definition and a three-dimensional framework to compare competing philosophies of public relations and to…

  13. Domain fusion analysis by applying relational algebra to protein sequence and domain databases

    PubMed Central

    Truong, Kevin; Ikura, Mitsuhiko

    2003-01-01

    Background Domain fusion analysis is a useful method to predict functionally linked proteins that may be involved in direct protein-protein interactions or in the same metabolic or signaling pathway. As separate domain databases like BLOCKS, PROSITE, Pfam, SMART, PRINTS-S, ProDom, TIGRFAMs, and amalgamated domain databases like InterPro continue to grow in size and quality, a computational method to perform domain fusion analysis that leverages on these efforts will become increasingly powerful. Results This paper proposes a computational method employing relational algebra to find domain fusions in protein sequence databases. The feasibility of this method was illustrated on the SWISS-PROT+TrEMBL sequence database using domain predictions from the Pfam HMM (hidden Markov model) database. We identified 235 and 189 putative functionally linked protein partners in H. sapiens and S. cerevisiae, respectively. From scientific literature, we were able to confirm many of these functional linkages, while the remainder offer testable experimental hypothesis. Results can be viewed at . Conclusion As the analysis can be computed quickly on any relational database that supports standard SQL (structured query language), it can be dynamically updated along with the sequence and domain databases, thereby improving the quality of predictions over time. PMID:12734020

  14. Multiorder boundaries among discrete domains: relative fractal dimension and others.

    PubMed

    Xuan, Qi; Du, Fang; Wu, Tie-Jun

    2010-03-01

    In nature and society, most of competitions take place on the boundaries among a group of domains where different individuals or colonies share common resources; therefore, it is widely believed that domain boundaries play important roles in the evolution of many complex systems. Here, we first give a definition for multiorder boundaries among discrete domains and then propose a general method to calculate their relative fractal dimension, i.e., the ratio of the fractal dimension of the boundaries versus that of the domains themselves. Through analyzing three types of real-world discrete domains, several interesting results are revealed. For example, the limitation on the number of domains that an individual can join in may produce longer boundaries indicating more cruel competitions among the domains. Besides, the individuals with more social links are always considered more important in social networks, and it is found that these individuals as valuable resources of social domains are always centralized on the boundaries of higher order. PMID:20370288

  15. Cross-Domain Analogies as Relating Derived Relations among Two Separate Relational Networks

    PubMed Central

    Ruiz, Francisco J; Luciano, Carmen

    2011-01-01

    Contemporary behavior analytic research is making headway in analyzing analogy as the establishment of a relation of coordination among common types of trained or derived relations. Previous studies have been focused on within-domain analogy. The current study expands previous research by analyzing cross-domain analogy as relating relations among separate relational networks and by correlating participants' performance with a standard measure of analogical reasoning. In two experiments, adult participants first completed general intelligence and analogical reasoning tests. Subsequently, they were exposed to a computerized conditional discrimination training procedure designed to create two relational networks, each consisting of two 3-member equivalence classes. The critical test was a two-part analogical test in which participants had to relate combinatorial relations of coordination and distinction between the two relational networks. In Experiment 1, combinatorial relations for each network were individually tested prior to analogical testing, but in Experiment 2 they were not. Across both experiments, 65% of participants passed the analogical test on the first attempt. Moreover, results from the training procedure were strongly correlated with the standard measure of analogical reasoning. PMID:21547072

  16. Approximation method to compute domain related integrals in structural studies

    NASA Astrophysics Data System (ADS)

    Oanta, E.; Panait, C.; Raicu, A.; Barhalescu, M.; Axinte, T.

    2015-11-01

    Various engineering calculi use integral calculus in theoretical models, i.e. analytical and numerical models. For usual problems, integrals have mathematical exact solutions. If the domain of integration is complicated, there may be used several methods to calculate the integral. The first idea is to divide the domain in smaller sub-domains for which there are direct calculus relations, i.e. in strength of materials the bending moment may be computed in some discrete points using the graphical integration of the shear force diagram, which usually has a simple shape. Another example is in mathematics, where the surface of a subgraph may be approximated by a set of rectangles or trapezoids used to calculate the definite integral. The goal of the work is to introduce our studies about the calculus of the integrals in the transverse section domains, computer aided solutions and a generalizing method. The aim of our research is to create general computer based methods to execute the calculi in structural studies. Thus, we define a Boolean algebra which operates with ‘simple’ shape domains. This algebraic standpoint uses addition and subtraction, conditioned by the sign of every ‘simple’ shape (-1 for the shapes to be subtracted). By ‘simple’ shape or ‘basic’ shape we define either shapes for which there are direct calculus relations, or domains for which their frontiers are approximated by known functions and the according calculus is carried out using an algorithm. The ‘basic’ shapes are linked to the calculus of the most significant stresses in the section, refined aspect which needs special attention. Starting from this idea, in the libraries of ‘basic’ shapes, there were included rectangles, ellipses and domains whose frontiers are approximated by spline functions. The domain triangularization methods suggested that another ‘basic’ shape to be considered is the triangle. The subsequent phase was to deduce the exact relations for the

  17. Some proposed relations among the domains of behavior analysis

    PubMed Central

    Moore, J.; Cooper, John O.

    2003-01-01

    The present article examines the nature of and relations among the domains of behavior analysis. It first proposes a set of annotated, descriptive criteria to aid in distinguishing the experimental analysis of behavior, applied behavior analysis, and service delivery. It then argues that the experimental analysis of behavior lies at one end of a continuum of behavior-analytic activity, with applied behavior analysis in the middle, service delivery at the other end, and the theoretical-philosophical-conceptual position known as “radical behaviorism” informing the three domains on the continuum. Finally, it argues that clarifying the distinctions among the domains of behavior analysis will help the behavior-analytic community to focus its efforts in training programs and overall support of behavior analysis. PMID:22478395

  18. Mechanisms for integration of information models across related domains

    NASA Astrophysics Data System (ADS)

    Atkinson, Rob

    2010-05-01

    It is well recognised that there are opportunities and challenges in cross-disciplinary data integration. A significant barrier, however, is creating a conceptual model of the combined domains and the area of integration. For example, a groundwater domain application may require information from several related domains: geology, hydrology, water policy, etc. Each domain may have its own data holdings and conceptual models, but these will share various common concepts (eg. The concept of an aquifer). These areas of semantic overlap present significant challenges, firstly to choose a single representation (model) of a concept that appears in multiple disparate models,, then to harmonise these other models with the single representation. In addition, models may exist at different levels of abstraction depending on how closely aligned they are with a particular implementation. This makes it hard for modellers in one domain to introduce elements from another domain without either introducing a specific style of implementation, or conversely dealing with a set of abstract patterns that are hard to integrate with existing implementations. Models are easier to integrate if they are broken down into small units, with common concepts implemented using common models from well-known, and predictably managed shared libraries. This vision however requires development of a set of mechanisms (tools and procedures) for implementing and exploiting libraries of model components. These mechanisms need to handle publication, discovery, subscription, versioning and implementation of models in different forms. In this presentation a coherent suite of such mechanisms is proposed, using a scenario based on re-use of geosciences models. This approach forms the basis of a comprehensive strategy to empower domain modellers to create more interoperable systems. The strategy address a range of concerns and practice, and includes methodologies, an accessible toolkit, improvements to available

  19. Gender and the relative importance of mental health satisfaction domains.

    PubMed

    Robillos, Eliza; Lale, Rachel; Wooldridge, Jennalee; Heller, Richard; Sarkin, Andrew

    2014-04-01

    Consumer-reported satisfaction data is a tool used for measuring and targeting areas for quality improvement in mental healthcare. In this study, we investigated the relationship between gender and the relative importance of mental health service satisfaction domains to overall satisfaction, in addition to gender differences in satisfaction across domains. People receiving mental health services (1765 males and 1950 females) completed questionnaires regarding their overall service satisfaction and satisfaction along six domains: Access to Services, Quality and Appropriateness, Participation in Treatment Planning, Outcome of Services, Social Connectedness, and Functioning. While all were important to overall satisfaction across genders, women reported slightly higher overall satisfaction. Linear regression analyses were used to determine the relative importance of these subscales to overall satisfaction for each gender. While the correlations between each subscale and overall satisfaction were significant for both, gender was found to moderate the relationship between some subscales and overall satisfaction. Although predictive of overall service satisfaction across the sample, we found Functioning, Outcome of Services, Social Connectedness, and Access to Services were relatively more important to overall satisfaction for men than women. Consistent feedback of results and improved access to services may be particularly effective for engaging both men and women in treatment.

  20. Kernel-Based Learning for Domain-Specific Relation Extraction

    NASA Astrophysics Data System (ADS)

    Basili, Roberto; Giannone, Cristina; Del Vescovo, Chiara; Moschitti, Alessandro; Naggar, Paolo

    In a specific process of business intelligence, i.e. investigation on organized crime, empirical language processing technologies can play a crucial role. The analysis of transcriptions on investigative activities, such as police interrogatories, for the recognition and storage of complex relations among people and locations is a very difficult and time consuming task, ultimately based on pools of experts. We discuss here an inductive relation extraction platform that opens the way to much cheaper and consistent workflows. The presented empirical investigation shows that accurate results, comparable to the expert teams, can be achieved, and parametrization allows to fine tune the system behavior for fitting domain-specific requirements.

  1. Domain is a moving target for relational learning.

    PubMed

    Katz, Jeffrey S; Sturz, Bradley R; Wright, Anthony A

    2010-02-01

    The domain for relational learning was manipulated by varying the training set size for pigeons that had learned the same/different (S/D) concept. Six pigeons that had learned a S/D task with pairs of pictures with a set size of 1024 picture items had their training set size reduced to 8 items. Training on the reduced 8-item set was followed by transfer testing that was repeated four times. Transfer performance following reduction of the training set to 8 items was 9.2% less than it had been when the pigeons were trained with the 1024-item set, but 25.8% above chance. This partial abstract-concept learning remained constant over the four tests with novel stimuli. The results show that a broad domain established by a large expanding training set can once again become restricted by further training with a small training set. PMID:20006686

  2. A Time Domain Waveform for Testing General Relativity

    NASA Astrophysics Data System (ADS)

    Huwyler, Cédric; Porter, Edward K.; Jetzer, Philippe

    2015-05-01

    Gravitational-wave parameter estimation is only as good as the theory the waveform generation models are based upon. It is therefore crucial to test General Relativity (GR) once data becomes available. Many previous works, such as studies connected with the ppE framework by Yunes and Pretorius, rely on the stationary phase approximation (SPA) to model deviations from GR in the frequency domain. As Fast Fourier Transform algorithms have become considerably faster and in order to circumvent possible problems with the SPA, we test GR with corrected time domain waveforms instead of SPA waveforms. Since a considerable amount of work has been done already in the field using SPA waveforms, we establish a connection between leading-order-corrected waveforms in time and frequency domain, concentrating on phase-only corrected terms. In a Markov Chain Monte Carlo study, whose results are preliminary and will only be available later, we will assess the ability of the eLISA detector to measure deviations from GR for signals coming from supermassive black hole inspirals using these corrected waveforms.

  3. A relational metric, its application to domain analysis, and an example analysis and model of a remote sensing domain

    NASA Technical Reports Server (NTRS)

    Mcgreevy, Michael W.

    1995-01-01

    An objective and quantitative method has been developed for deriving models of complex and specialized spheres of activity (domains) from domain-generated verbal data. The method was developed for analysis of interview transcripts, incident reports, and other text documents whose original source is people who are knowledgeable about, and participate in, the domain in question. To test the method, it is applied here to a report describing a remote sensing project within the scope of the Earth Observing System (EOS). The method has the potential to improve the designs of domain-related computer systems and software by quickly providing developers with explicit and objective models of the domain in a form which is useful for design. Results of the analysis include a network model of the domain, and an object-oriented relational analysis report which describes the nodes and relationships in the network model. Other products include a database of relationships in the domain, and an interactive concordance. The analysis method utilizes a newly developed relational metric, a proximity-weighted frequency of co-occurrence. The metric is applied to relations between the most frequently occurring terms (words or multiword entities) in the domain text, and the terms found within the contexts of these terms. Contextual scope is selectable. Because of the discriminating power of the metric, data reduction from the association matrix to the network is simple. In addition to their value for design. the models produced by the method are also useful for understanding the domains themselves. They can, for example, be interpreted as models of presence in the domain.

  4. Protein domain analysis of genomic sequence data reveals regulation of LRR related domains in plant transpiration in Ficus.

    PubMed

    Lang, Tiange; Yin, Kangquan; Liu, Jinyu; Cao, Kunfang; Cannon, Charles H; Du, Fang K

    2014-01-01

    Predicting protein domains is essential for understanding a protein's function at the molecular level. However, up till now, there has been no direct and straightforward method for predicting protein domains in species without a reference genome sequence. In this study, we developed a functionality with a set of programs that can predict protein domains directly from genomic sequence data without a reference genome. Using whole genome sequence data, the programming functionality mainly comprised DNA assembly in combination with next-generation sequencing (NGS) assembly methods and traditional methods, peptide prediction and protein domain prediction. The proposed new functionality avoids problems associated with de novo assembly due to micro reads and small single repeats. Furthermore, we applied our functionality for the prediction of leucine rich repeat (LRR) domains in four species of Ficus with no reference genome, based on NGS genomic data. We found that the LRRNT_2 and LRR_8 domains are related to plant transpiration efficiency, as indicated by the stomata index, in the four species of Ficus. The programming functionality established in this study provides new insights for protein domain prediction, which is particularly timely in the current age of NGS data expansion.

  5. A Structure for the Affective Domain in Relation to Science Education.

    ERIC Educational Resources Information Center

    Klopfer, Leopold E.

    A classification scheme for the affective domain in relation to science education is presented in this article to clarify student's affective behaviors and their representative phenomena. Discussion is made in connection with the content-objectives grid in the cognitive domain. An analogous grid for the affective domain is delineated by a…

  6. Structure and evolution of ubiquitin and ubiquitin-related domains.

    PubMed

    Burroughs, A Maxwell; Iyer, Lakshminarayan M; Aravind, L

    2012-01-01

    Since its discovery over three decades ago, it has become abundantly clear that the ubiquitin (Ub) system is a quintessential feature of all aspects of eukaryotic biology. At the heart of the system lies the conjugation and deconjugation of Ub and Ub-like (Ubls) proteins to proteins or lipids drastically altering the biochemistry of the targeted molecules. In particular, it represents the primary mechanism by which protein stability is regulated in eukaryotes. Ub/Ubls are typified by the β-grasp fold (β-GF) that has additionally been recruited for a strikingly diverse range of biochemical functions. These include catalytic roles (e.g., NUDIX phosphohydrolases), scaffolding of iron-sulfur clusters, binding of RNA and other biomolecules such as co-factors, sulfur transfer in biosynthesis of diverse metabolites, and as mediators of key protein-protein interactions in practically every conceivable cellular context. In this chapter, we present a synthetic overview of the structure, evolution, and natural classification of Ub, Ubls, and other members of the β-GF. The β-GF appears to have differentiated into at least seven clades by the time of the last universal common ancestor of all extant organisms, encompassing much of the structural diversity observed in extant versions. The β-GF appears to have first emerged in the context of translation-related RNA-interactions and subsequently exploded to occupy various functional niches. Most biochemical diversification of the fold occurred in prokaryotes, with the eukaryotic phase of its evolution mainly marked by the expansion of the Ubl clade of the β-GF. Consequently, at least 70 distinct Ubl families are distributed across eukaryotes, of which nearly 20 families were already present in the eukaryotic common ancestor. These included multiple protein and one lipid conjugated forms and versions that functions as adapter domains in multimodule polypeptides. The early diversification of the Ubl families in eukaryotes

  7. Conserved Gene Regulatory Function of the Carboxy-Terminal Domain of Dictyostelid C-Module-Binding Factor

    PubMed Central

    Schmith, Anika; Groth, Marco; Ratka, Josephine; Gatz, Sara; Spaller, Thomas; Siol, Oliver; Glöckner, Gernot

    2013-01-01

    C-module-binding factor A (CbfA) is a jumonji-type transcription regulator that is important for maintaining the expression and mobility of the retrotransposable element TRE5-A in the social amoeba Dictyostelium discoideum. CbfA-deficient cells have lost TRE5-A retrotransposition, are impaired in the ability to feed on bacteria, and do not enter multicellular development because of a block in cell aggregation. In this study, we performed Illumina RNA-seq of growing CbfA mutant cells to obtain a list of CbfA-regulated genes. We demonstrate that the carboxy-terminal domain of CbfA alone is sufficient to mediate most CbfA-dependent gene expression. The carboxy-terminal domain of CbfA from the distantly related social amoeba Polysphondylium pallidum restored the expression of CbfA-dependent genes in the D. discoideum CbfA mutant, indicating a deep conservation in the gene regulatory function of this domain in the dictyostelid clade. The CbfA-like protein CbfB displays ∼25% sequence identity with CbfA in the amino-terminal region, which contains a JmjC domain and two zinc finger regions and is thought to mediate chromatin-remodeling activity. In contrast to CbfA proteins, where the carboxy-terminal domains are strictly conserved in all dictyostelids, CbfB proteins have completely unrelated carboxy-terminal domains. Outside the dictyostelid clade, CbfA-like proteins with the CbfA-archetypical JmjC/zinc finger arrangement and individual carboxy-terminal domains are prominent in filamentous fungi but are not found in yeasts, plants, and metazoans. Our data suggest that two functional regions of the CbfA-like proteins evolved at different rates to allow the occurrence of species-specific adaptation processes during genome evolution. PMID:23355006

  8. Ribosome origins: The relative age of 23S rRNA Domains

    NASA Astrophysics Data System (ADS)

    Hury, James; Nagaswamy, Uma; Larios-Sanz, Maia; Fox, George E.

    2006-08-01

    The modern ribosome and its component RNAs are quite large and it is likely that at an earlier time they were much smaller. Hence, not all regions of the modern ribosomal RNAs (rRNA) are likely to be equally old. In the work described here, it is hypothesized that the oldest regions of the RNAs will usually be highly integrated into the machinery. When this is the case, an examination of the interconnectivity between local RNA regions can provide insight to the relative age of the various regions. Herein, we describe an analysis of all known long-range RNA/RNA interactions within the 23S rRNA and between the 23S rRNA and the 16S rRNA in order to assess the interconnectivity between the usual Domains as defined by secondary structure. Domain V, which contains the peptidyl transferase center is centrally located, extensively connected, and therefore likely to be the oldest region. Domain IV and Domain II are extensively interconnected with both themselves and Domain V. A portion of Domain IV is also extensively connected with the 30S subunit and hence Domain IV may be older than Domain II. These results are consistent with other evidence relating to the relative age of RNA regions. Although the relative time of addition of the GTPase center can not be reliably deduced it is pointed out that the development of this may have dramatically affected the progenotes that preceded the last common ancestor.

  9. A Novel Approach to Predict Core Residues on Cancer-Related DNA-Binding Domains.

    PubMed

    Wong, Ka-Chun

    2016-01-01

    Protein-DNA interactions are involved in different cancer pathways. In particular, the DNA-binding domains of proteins can determine where and how gene regulatory regions are bound in different cell lines at different stages. Therefore, it is essential to develop a method to predict and locate the core residues on cancer-related DNA-binding domains. In this study, we propose a computational method to predict and locate core residues on DNA-binding domains. In particular, we have selected the cancer-related DNA-binding domains for in-depth studies, namely, winged Helix Turn Helix family, homeodomain family, and basic Helix-Loop-Helix family. The results demonstrate that the proposed method can predict the core residues involved in protein-DNA interactions, as verified by the existing structural data. Given its good performance, various aspects of the method are discussed and explored: for instance, different uses of prediction algorithm, different protein domains, and hotspot threshold setting.

  10. Histone Demethylase Jumonji AT-rich Interactive Domain 1B (JARID1B) Controls Mammary Gland Development by Regulating Key Developmental and Lineage Specification Genes*

    PubMed Central

    Zou, Mike Ran; Cao, Jian; Liu, Zongzhi; Huh, Sung Jin; Polyak, Kornelia; Yan, Qin

    2014-01-01

    The JmjC domain-containing H3K4 histone demethylase jumonji AT-rich interactive domain 1B (JARID1B) (also known as KDM5B and PLU1) is overexpressed in breast cancer and is a potential target for breast cancer treatment. To investigate the in vivo function of JARID1B, we developed Jarid1b−/− mice and characterized their phenotypes in detail. Unlike previously reported Jarid1b−/− strains, the majority of these Jarid1b−/− mice were viable beyond embryonic and neonatal stages. This allowed us to further examine phenotypes associated with the loss of JARID1B in pubertal development and pregnancy. These Jarid1b−/− mice exhibited decreased body weight, premature mortality, decreased female fertility, and delayed mammary gland development. Related to these phenotypes, JARID1B loss decreased serum estrogen level and reduced mammary epithelial cell proliferation in early puberty. In mammary epithelial cells, JARID1B loss diminished the expression of key regulators for mammary morphogenesis and luminal lineage specification, including FOXA1 and estrogen receptor α. Mechanistically, JARID1B was required for GATA3 recruitment to the Foxa1 promoter to activate Foxa1 expression. These results indicate that JARID1B positively regulates mammary ductal development through both extrinsic and cell-autonomous mechanisms. PMID:24802759

  11. The natural history of ubiquitin and ubiquitin-related domains.

    PubMed

    Burroughs, Alexander Maxwell; Iyer, Lakshminarayan M; Aravind, L

    2012-01-01

    The ubiquitin (Ub) system is centered on conjugation and deconjugation of Ub and Ub-like (Ubls) proteins by a system of ligases and peptidases, respectively. Ub/Ubls contain the beta-grasp fold, also found in numerous proteins with biochemically distinct roles unrelated to the conventional Ub-system. The beta-GF underwent an early radiation spawning at least seven clades prior to the divergence of extant organisms from their last universal common ancestor, first emerging in the context of translation-related RNA-interactions and subsequently exploding to occupy various functional niches. Most beta-GF diversification occurred in prokaryotes, with the Ubl clade showing dramatic expansion in the eukaryotes. Diversification of Ubl families in eukaryotes played a major role in emergence of characteristic eukaryotic cellular sub-structures and systems. Recent comparative genomics studies indicate precursors of the eukaryotic Ub-system emerged in prokaryotes. The simplest of these combine an Ubl and an E1-like enzyme in metabolic pathways. Sampylation in archaea and Urmylation in eukaryotes appear to represent recruitment of such systems as simple protein-tagging apparatuses. However, other prokaryotic systems incorporated further components and mirror the eukaryotic condition in possessing an E2, a RING-type E3 or both of these components. Additionally, prokaryotes have evolved conjugation systems independent of Ub ligases, such as the Pup system.

  12. The natural history of ubiquitin and ubiquitin-related domains.

    PubMed

    Burroughs, Alexander Maxwell; Iyer, Lakshminarayan M; Aravind, L

    2012-01-01

    The ubiquitin (Ub) system is centered on conjugation and deconjugation of Ub and Ub-like (Ubls) proteins by a system of ligases and peptidases, respectively. Ub/Ubls contain the beta-grasp fold, also found in numerous proteins with biochemically distinct roles unrelated to the conventional Ub-system. The beta-GF underwent an early radiation spawning at least seven clades prior to the divergence of extant organisms from their last universal common ancestor, first emerging in the context of translation-related RNA-interactions and subsequently exploding to occupy various functional niches. Most beta-GF diversification occurred in prokaryotes, with the Ubl clade showing dramatic expansion in the eukaryotes. Diversification of Ubl families in eukaryotes played a major role in emergence of characteristic eukaryotic cellular sub-structures and systems. Recent comparative genomics studies indicate precursors of the eukaryotic Ub-system emerged in prokaryotes. The simplest of these combine an Ubl and an E1-like enzyme in metabolic pathways. Sampylation in archaea and Urmylation in eukaryotes appear to represent recruitment of such systems as simple protein-tagging apparatuses. However, other prokaryotic systems incorporated further components and mirror the eukaryotic condition in possessing an E2, a RING-type E3 or both of these components. Additionally, prokaryotes have evolved conjugation systems independent of Ub ligases, such as the Pup system. PMID:22201813

  13. Exploring the Relation between Work Domains and Work-Related Learning: The Case of the Dutch Police Force

    ERIC Educational Resources Information Center

    Doornbos, Anja J.; Bolhuis, S.; Denessen, E.

    2004-01-01

    The principal aim of this study is to explore the relations between work domains and the work-related learning of workers. The article is intended to provide insight into the learning experiences of Dutch police officers during the course of their daily work. Interviews regarding actual learning events and subsequent changes in knowledge, skills…

  14. Structural genomics reveals EVE as a new ASCH/PUA-related domain.

    PubMed

    Bertonati, Claudia; Punta, Marco; Fischer, Markus; Yachdav, Guy; Forouhar, Farhad; Zhou, Weihong; Kuzin, Alexander P; Seetharaman, Jayaraman; Abashidze, Mariam; Ramelot, Theresa A; Kennedy, Michael A; Cort, John R; Belachew, Adam; Hunt, John F; Tong, Liang; Montelione, Gaetano T; Rost, Burkhard

    2009-05-15

    We report on several proteins recently solved by structural genomics consortia, in particular by the Northeast Structural Genomics consortium (NESG). The proteins considered in this study differ substantially in their sequences but they share a similar structural core, characterized by a pseudobarrel five-stranded beta sheet. This core corresponds to the PUA domain-like architecture in the SCOP database. By connecting sequence information with structural knowledge, we characterize a new subgroup of these proteins that we propose to be distinctly different from previously described PUA domain-like domains such as PUA proper or ASCH. We refer to these newly defined domains as EVE. Although EVE may have retained the ability of PUA domains to bind RNA, the available experimental and computational data suggests that both the details of its molecular function and its cellular function differ from those of other PUA domain-like domains. This study of EVE and its relatives illustrates how the combination of structure and genomics creates new insights by connecting a cornucopia of structures that map to the same evolutionary potential. Primary sequence information alone would have not been sufficient to reveal these evolutionary links.

  15. Phylogenetic and specificity studies of two-domain GNA-related lectins: generation of multispecificity through domain duplication and divergent evolution.

    PubMed

    Van Damme, Els J M; Nakamura-Tsuruta, Sachiko; Smith, David F; Ongenaert, Maté; Winter, Harry C; Rougé, Pierre; Goldstein, Irwin J; Mo, Hanqing; Kominami, Junko; Culerrier, Raphaël; Barre, Annick; Hirabayashi, Jun; Peumans, Willy J

    2007-05-15

    A re-investigation of the occurrence and taxonomic distribution of proteins built up of protomers consisting of two tandem arrayed domains equivalent to the GNA [Galanthus nivalis (snowdrop) agglutinin] revealed that these are widespread among monotyledonous plants. Phylogenetic analysis of the available sequences indicated that these proteins do not represent a monophylogenetic group but most probably result from multiple independent domain duplication/in tandem insertion events. To corroborate the relationship between inter-domain sequence divergence and the widening of specificity range, a detailed comparative analysis was made of the sequences and specificity of a set of two-domain GNA-related lectins. Glycan microarray analyses, frontal affinity chromatography and surface plasmon resonance measurements demonstrated that the two-domain GNA-related lectins acquired a marked diversity in carbohydrate-binding specificity that strikingly contrasts the canonical exclusive specificity of their single domain counterparts towards mannose. Moreover, it appears that most two-domain GNA-related lectins interact with both high mannose and complex N-glycans and that this dual specificity relies on the simultaneous presence of at least two different independently acting binding sites. The combined phylogenetic, specificity and structural data strongly suggest that plants used domain duplication followed by divergent evolution as a mechanism to generate multispecific lectins from a single mannose-binding domain. Taking into account that the shift in specificity of some binding sites from high mannose to complex type N-glycans implies that the two-domain GNA-related lectins are primarily directed against typical animal glycans, it is tempting to speculate that plants developed two-domain GNA-related lectins for defence purposes.

  16. A cross-cultural comparison of the coexistence and domain superiority of individuating and relating autonomy.

    PubMed

    Yeh, Kuang-Hui; Bedford, Olwen; Yang, Yung-Jui

    2009-06-01

    The consensus definition of autonomy in the psychological literature emphasizes self-governance through free volition, not separation or independence from others. Since the concept of self may differ cross-culturally, several researchers have tried to incorporate types of self into the notion of autonomy; however, only the dual model of autonomy has been able to do this while retaining an emphasis on volition. The dual model describes two distinct forms of autonomy-individuating and relating-each with superior function in a specific domain of individual functioning. Individuating autonomy represents a volitional capacity to act against social constraints and offers a route to achieve an independent self-identity by expressing individualistic attributes and distinctions. Relating autonomy represents a volitional capacity to act by emphasizing the harmony of self-in-relation-to-others, the quality of interpersonal relationships, and self-transcendence. These two forms of autonomy have been shown to coexist at the individual level in a Taiwanese sample. This study takes the next step, with a cross-cultural test of the coexistence and domain superiority hypotheses of individuating and relating autonomy. Participants included 306 college students from Taiwan and 183 college students from the United States. Structural equation modelling by multigroup analyses confirmed the cross-cultural equivalence of the two-factor individuating autonomy and relating autonomy measurement model. Across both samples the two forms of autonomy were shown to be mutually inclusive and not exclusive or independent. The domain-superior function of each form of autonomy was also confirmed cross-culturally; each form of autonomy has a dominant, but not necessarily exclusive, domain of functioning. Specifically, individuating autonomy was more associated with intrapersonal than interpersonal domain dependent variables, while relating autonomy was more associated with interpersonal than

  17. On a time-domain representation of the Kramers-Kronig dispersion relations

    PubMed

    Waters; Hughes; Brandenburger; Miller

    2000-11-01

    The development of Kramers-Kronig dispersion relations is typically carried out in the frequency domain. An alternative approach known as the time-causal theory develops dispersion relations for media with attenuation obeying a frequency power law through analysis in the time domain [T. L. Szabo, J. Acoust. Soc. Am. 96, 491-500 (1994)]. Although both approaches predict identical dispersion relations, it is perceived that these two approaches are distinct from each other. It is shown, however, that the time-causal theory is in essence a time-domain formulation of the Kramers-Kronig dispersion relations for the special case of media with attenuation obeying a frequency power law. Additionally, it is shown that time-domain representations of the Kramers-Kronig dispersion relations are available for a broader class of media than simply those with power law attenuation. The time-causal theory and the Kramers-Kronig dispersion relations can be viewed as two complementary, yet equivalent, approaches to the study of dispersion.

  18. The neurofibromin recruitment factor Spred1 binds to the GAP related domain without affecting Ras inactivation

    PubMed Central

    Dunzendorfer-Matt, Theresia; Mercado, Ellen L.; Maly, Karl; McCormick, Frank; Scheffzek, Klaus

    2016-01-01

    Neurofibromatosis type 1 (NF1) and Legius syndrome are related diseases with partially overlapping symptoms caused by alterations of the tumor suppressor genes NF1 (encoding the protein neurofibromin) and SPRED1 (encoding sprouty-related, EVH1 domain-containing protein 1, Spred1), respectively. Both proteins are negative regulators of Ras/MAPK signaling with neurofibromin functioning as a Ras-specific GTPase activating protein (GAP) and Spred1 acting on hitherto undefined components of the pathway. Importantly, neurofibromin has been identified as a key protein in the development of cancer, as it is genetically altered in a large number of sporadic human malignancies unrelated to NF1. Spred1 has previously been demonstrated to interact with neurofibromin via its N-terminal Ena/VASP Homology 1 (EVH1) domain and to mediate membrane translocation of its target dependent on its C-terminal Sprouty domain. However, the region of neurofibromin required for the interaction with Spred1 has remained unclear. Here we show that the EVH1 domain of Spred1 binds to the noncatalytic (GAPex) portion of the GAP-related domain (GRD) of neurofibromin. Binding is compatible with simultaneous binding of Ras and does not interfere with GAP activity. Our study points to a potential targeting function of the GAPex subdomain of neurofibromin that is present in all known canonical RasGAPs. PMID:27313208

  19. Bidirectional transfer between metaphorical related domains in implicit learning of form-meaning connections.

    PubMed

    Guo, Xiuyan; Li, Fengying; Yang, Zhiliang; Dienes, Zoltan

    2013-01-01

    People can implicitly learn a connection between linguistic forms and meanings, for example between specific determiners (e.g. this, that...) and the type of nouns to which they apply. Li et al (2013) recently found that transfer of form-meaning connections from a concrete domain (height) to an abstract domain (power) was achieved in a metaphor-consistent way without awareness, showing that unconscious knowledge can be abstract and flexibly deployed. The current study aims to determine whether people transfer knowledge of form-meaning connections not only from a concrete domain to an abstract one, but also vice versa, consistent with metaphor representation being bi-directional. With a similar paradigm as used by Li et al, participants learnt form- meaning connections of different domains (concrete vs. abstract) and then were tested on two kinds of generalizations (same and different domain generalization). As predicted, transfer of form-meaning connections occurred bidirectionally when structural knowledge was unconscious. Moreover, the present study also revealed that more transfer occurred between metaphorically related domains when judgment knowledge was conscious (intuition) rather than unconscious (guess). Conscious and unconscious judgment knowledge may have different functional properties.

  20. Bidirectional Transfer between Metaphorical Related Domains in Implicit Learning of Form-Meaning Connections

    PubMed Central

    Yang, Zhiliang; Dienes, Zoltan

    2013-01-01

    People can implicitly learn a connection between linguistic forms and meanings, for example between specific determiners (e.g. this, that…) and the type of nouns to which they apply. Li et al (2013) recently found that transfer of form-meaning connections from a concrete domain (height) to an abstract domain (power) was achieved in a metaphor-consistent way without awareness, showing that unconscious knowledge can be abstract and flexibly deployed. The current study aims to determine whether people transfer knowledge of form-meaning connections not only from a concrete domain to an abstract one, but also vice versa, consistent with metaphor representation being bi-directional. With a similar paradigm as used by Li et al, participants learnt form- meaning connections of different domains (concrete vs. abstract) and then were tested on two kinds of generalizations (same and different domain generalization). As predicted, transfer of form-meaning connections occurred bidirectionally when structural knowledge was unconscious. Moreover, the present study also revealed that more transfer occurred between metaphorically related domains when judgment knowledge was conscious (intuition) rather than unconscious (guess). Conscious and unconscious judgment knowledge may have different functional properties. PMID:23844159

  1. A Novel Approach to Predict Core Residues on Cancer-Related DNA-Binding Domains

    PubMed Central

    Wong, Ka-Chun

    2016-01-01

    Protein–DNA interactions are involved in different cancer pathways. In particular, the DNA-binding domains of proteins can determine where and how gene regulatory regions are bound in different cell lines at different stages. Therefore, it is essential to develop a method to predict and locate the core residues on cancer-related DNA-binding domains. In this study, we propose a computational method to predict and locate core residues on DNA-binding domains. In particular, we have selected the cancer-related DNA-binding domains for in-depth studies, namely, winged Helix Turn Helix family, homeodomain family, and basic Helix-Loop-Helix family. The results demonstrate that the proposed method can predict the core residues involved in protein–DNA interactions, as verified by the existing structural data. Given its good performance, various aspects of the method are discussed and explored: for instance, different uses of prediction algorithm, different protein domains, and hotspot threshold setting. PMID:27279732

  2. International Note: Between-Domain Relations of Chinese High School Students' Academic Achievements

    ERIC Educational Resources Information Center

    Yangyang, Liu

    2012-01-01

    The present study examined the between-domain relations of Chinese high school students' academic achievements. In a sample of 1870 Chinese 10th grade students, the results indicated that Chinese high school students' academic achievements were correlated across nine subjects. In line with the previous Western findings, the findings suggested that…

  3. Constructing Domain-Specific Knowledge in Kindergarten: Relations among Knowledge, Intelligence, and Strategic Performance

    ERIC Educational Resources Information Center

    Alexander, Joyce M.; Johnson, Kathy E.; Leibham, Mary E.; DeBauge, Christiane

    2005-01-01

    Thirty kindergarten children from two classrooms participated in a 3-week curricular unit on dinosaurs designed to teach taxonomic relations and distinguishing features aligned with 15 dinosaur species. Both domain-specific learning and strategic performance on a Twenty Questions game were assessed twice throughout the curriculum, as well as…

  4. Domain-based identification and analysis of glutamate receptor ion channels and their relatives in prokaryotes.

    PubMed

    Ger, Mao-Feng; Rendon, Gloria; Tilson, Jeffrey L; Jakobsson, Eric

    2010-10-06

    Voltage-gated and ligand-gated ion channels are used in eukaryotic organisms for the purpose of electrochemical signaling. There are prokaryotic homologues to major eukaryotic channels of these sorts, including voltage-gated sodium, potassium, and calcium channels, Ach-receptor and glutamate-receptor channels. The prokaryotic homologues have been less well characterized functionally than their eukaryotic counterparts. In this study we identify likely prokaryotic functional counterparts of eukaryotic glutamate receptor channels by comprehensive analysis of the prokaryotic sequences in the context of known functional domains present in the eukaryotic members of this family. In particular, we searched the nonredundant protein database for all proteins containing the following motif: the two sections of the extracellular glutamate binding domain flanking two transmembrane helices. We discovered 100 prokaryotic sequences containing this motif, with a wide variety of functional annotations. Two groups within this family have the same topology as eukaryotic glutamate receptor channels. Group 1 has a potassium-like selectivity filter. Group 2 is most closely related to eukaryotic glutamate receptor channels. We present analysis of the functional domain architecture for the group of 100, a putative phylogenetic tree, comparison of the protein phylogeny with the corresponding species phylogeny, consideration of the distribution of these proteins among classes of prokaryotes, and orthologous relationships between prokaryotic and human glutamate receptor channels. We introduce a construct called the Evolutionary Domain Network, which represents a putative pathway of domain rearrangements underlying the domain composition of present channels. We believe that scientists interested in ion channels in general, and ligand-gated ion channels in particular, will be interested in this work. The work should also be of interest to bioinformatics researchers who are interested in the use

  5. Domain-specific physical activity and health-related quality of life in university students.

    PubMed

    Pedišić, Zeljko; Rakovac, Marija; Titze, Sylvia; Jurakić, Danijel; Oja, Pekka

    2014-01-01

    Information on the relationship between domain-specific physical activity (PA) and health-related quality of life (HRQoL) in the general population and specific groups is still scarce. The aim of this study was to determine the relationship between PA in work, transport, domestic and leisure-time domains and HRQoL among university students. PA and HRQoL were assessed in a random stratified sample of 1750 university students using the International Physical Activity Questionnaire - long form and 12-item Short Form Health Survey, respectively. The Spearman's rank correlations, adjusted for age, community size, personal monthly budget, body mass index, smoking habits and alcohol intake ranged from -0.11 to 0.18 in female students and -0.29 to 0.19 in male students. Leisure-time, domestic, transport-related PA and total PA were positively related to HRQoL. Inverse correlations with HRQoL were only found for work-related PA in male students. Multiple linear regression analysis showed that only leisure-time PA was related to the Physical Summary Component score (β = 0.08 for females and β = 0.10 for males, P < 0.05). Domain-specific PA levels were not significantly related to the Mental Component Summary score. To get a more comprehensive insight in the relationship between PA and HRQoL, future studies should not only analyse total PA levels but also domain-specific PA levels. The evidence on the positive relationship of leisure-time, transport and domestic PA with HRQoL can potentially be used to support evidence-based promotion of PA in a university setting, and as a hypothesis for future longitudinal studies on such potential causal relationships.

  6. EN FACE SPECTRAL-DOMAIN OPTICAL COHERENCE TOMOGRAPHY OUTER RETINAL ANALYSIS AND RELATION TO VISUAL ACUITY

    PubMed Central

    Kiernan, Daniel F.; Zelkha, Ruth; Hariprasad, Seenu M.; Lim, Jennifer I.; Blair, Michael P.; Mieler, William F.

    2013-01-01

    Purpose To describe a method of en face visualization and quantification of the photoreceptor inner segment/outer segment junction area, using spectral-domain optical coherence tomography, and association with visual acuity. Methods Case series of 74 eyes in 53 patients. Central 1-mm and 400-mm en face areas were analyzed with a computer algorithm. Results The presence or absence of inner segment/outer segment junction was visible on both spectral-domain optical coherence tomography en face and retinal cross sections. Thirty eyes (40.6%) had no retinal pathology and an average logMAR visual acuity of 0.116. Twenty-five eyes (33.8%) had intraretinal edema, with visual acuity of 0.494. Nineteen eyes had nonneovascular age-related macular degeneration (dry age-related macular degeneration, 25.6%), with visual acuity of 0.392. In all eyes, central 1-mm and 400-µm en face areas were 58.3 ± 25.0% and 56.4 ± 26.0%, which showed significant correlation with visual acuity (Pearson correlation, r = −0.66 and −0.56, both P < 0.001). This correlation was greater than correlation of visual acuity with central subfield thickness (r = 0.39, P < 0.001), macular volume (r = 0.36, P = 0.002), and average macular thickness (r = 0.37, P = 0.001). However, no variables were significantly correlated with dry age-related macular degeneration eyes. Conclusion Central en face inner segment/outer segment junction areas are significantly correlated with visual acuity in most eyes. This may correlate better with visual acuity than other spectral-domain optical coherence tomography values, as a reflection of photoreceptor integrity. Dry age-related macular degeneration may disrupt the plane used to formulate the en face display. Advancements in spectral-domain optical coherence tomography may provide routine en face visualization analysis. PMID:22466459

  7. Ring-like oligomers of Synaptotagmins and related C2 domain proteins

    PubMed Central

    Zanetti, Maria N; Bello, Oscar D; Wang, Jing; Coleman, Jeff; Cai, Yiying; Sindelar, Charles V; Rothman, James E; Krishnakumar, Shyam S

    2016-01-01

    We recently reported that the C2AB portion of Synaptotagmin 1 (Syt1) could self-assemble into Ca2+-sensitive ring-like oligomers on membranes, which could potentially regulate neurotransmitter release. Here we report that analogous ring-like oligomers assemble from the C2AB domains of other Syt isoforms (Syt2, Syt7, Syt9) as well as related C2 domain containing protein, Doc2B and extended Synaptotagmins (E-Syts). Evidently, circular oligomerization is a general and conserved structural aspect of many C2 domain proteins, including Synaptotagmins. Further, using electron microscopy combined with targeted mutations, we show that under physiologically relevant conditions, both the Syt1 ring assembly and its rapid disruption by Ca2+ involve the well-established functional surfaces on the C2B domain that are important for synaptic transmission. Our data suggests that ring formation may be triggered at an early step in synaptic vesicle docking and positions Syt1 to synchronize neurotransmitter release to Ca2+ influx. DOI: http://dx.doi.org/10.7554/eLife.17262.001 PMID:27434670

  8. Recognizing Mantle Domains Related to an Extensional Cycle: the Record from Western Europe

    NASA Astrophysics Data System (ADS)

    Picazo, S.; Muntener, O.; Manatschal, G.

    2015-12-01

    Most of the studies on rifted margins have shown that the classical predictions of models assuming a "homogeneous" mantle lithosphere without some inheritance are unable to capture the observed large variety of magmatic budgets as a function of extension. More recently, new ideas and concepts have been developed to understand the evolution of the mantle lithosphere in hyper-extended magma-poor rifted margins that are mainly based on observations from the present-day Iberia-Newfoundland and ancient Alpine Tethys rifted margins and the Pyrenean systems. In contrast to the classical assumption assuming a simple, isotropic mantle lithosphere, these new models integrate observations from exposed and drilled mantle rocks and propose that the mantle lithosphere evolved and was modified during an extensional cycle from post-orogenic collapse through several periods of rifting to embryonic oceanic (ultra-) slow seafloor spreading. But it is, at present, unclear how far these ideas can be generalized and if they can explain the nature of mantle rocks observed across Western Europe and, in a more general way, at Atlantic type rifted margins. We review the available mantle data from Western Europe, i.e. ophiolite massifs, xenoliths and dredged samples, revisit the available terminology concerning mantle massifs and xenoliths and compile the available data to identify different mantle domains. We define chemical and petrological characteristics of mantle domains based on clinopyroxene and spinel compositions and compile them on present-day and paleo-geographic maps of Western Europe. Finally we link the observed distribution of mantle domains to the post-Variscan extensional cycle and link domains to processes related to the late post-Variscan extension, the rift evolution and refertilization associated to hyper-extension and the development of embryonic oceanic domains.

  9. Statistical significance of task related deep brain EEG dynamic changes in the time-frequency domain.

    PubMed

    Chládek, J; Brázdil, M; Halámek, J; Plešinger, F; Jurák, P

    2013-01-01

    We present an off-line analysis procedure for exploring brain activity recorded from intra-cerebral electroencephalographic data (SEEG). The objective is to determine the statistical differences between different types of stimulations in the time-frequency domain. The procedure is based on computing relative signal power change and subsequent statistical analysis. An example of characteristic statistically significant event-related de/synchronization (ERD/ERS) detected across different frequency bands following different oddball stimuli is presented. The method is used for off-line functional classification of different brain areas. PMID:24109865

  10. Suppression of relative flow by multiple domains in two-component Bose-Einstein condensates

    NASA Astrophysics Data System (ADS)

    Eto, Yujiro; Kunimi, Masaya; Tokita, Hidekatsu; Saito, Hiroki; Hirano, Takuya

    2015-07-01

    We investigate flow properties of immiscible Bose-Einstein condensates composed of two different Zeeman spin states of 87Rb. Two spatially overlapping condensates in the optical trap are prepared by application of a resonant radio-frequency pulse, and then the magnetic field gradient is applied in order to produce the atomic flow. We find that the spontaneous multiple-domain formation arising from the immiscible nature drastically changes the fluidity. The homogeneously overlapping condensates readily separate under the magnetic field gradient, and they form a stable configuration composed of the two layers. In contrast, the relative flow between two condensates is largely suppressed in the case where the magnetic field gradient is applied after spontaneous domain formation.

  11. Source-domain spectral EEG analysis of sports-related concussion via Measure Projection Analysis.

    PubMed

    Balkan, Ozgur; Virji-Babul, Naznin; Miyakoshi, Makoto; Makeig, Scott; Garudadri, Harinath

    2015-01-01

    Here, we investigated EEG-based source-level spectral differences between adolescents with sports-related concussions and healthy age matched controls. We transformed resting state EEG collected in both groups to the source domain using Independent Component Analysis (ICA) and computed the component process power spectra. For group-level analysis in the source domain, we used a probabilistic framework, Measure Projection Analysis (MPA), that has advantages over parametric k-means clustering of brain sources. MPA revealed that some frontal brain sources in the concussed group had significantly more power in the beta band (p<;0.005) and significantly less delta (p<;0.01) and theta band power (p<;0.05) than the healthy control group. These results suggest that a shift in spectral profile toward higher frequencies in some frontal brain regions might distinguish individuals with concussion from healthy controls. PMID:26737184

  12. On the relation between traditional iterative methods and modern multilevel/domain decomposition methods

    SciTech Connect

    Griebel, M.

    1994-12-31

    In recent years, it has turned out that many modern iterative algorithms (multigrid schemes, multilevel preconditioners, domain decomposition methods etc.) for solving problems resulting from the discretization of PDEs can be interpreted as additive (Jacobi-like) or multiplicative (Gauss-Seidel-like) subspace correction methods. The key to their analysis is the study of certain metric properties of the underlying splitting of the discretization space V into a sum of subspaces V{sub j}, j = 1{hor_ellipsis}, J resp. of the variational problem on V into auxiliary problems on these subspaces. Here, the author proposes a modified approach to the abstract convergence theory of these additive and multiplicative Schwarz iterative methods, that makes the relation to traditional iteration methods more explicit. To this end he introduces the enlarged Hilbert space V = V{sub 0} x {hor_ellipsis} x V{sub j} which is nothing else but the usual construction of the Cartesian product of the Hilbert spaces V{sub j} and use it now in the discretization process. This results in an enlarged, semidefinite linear system to be solved instead of the usual definite system. Then, modern multilevel methods as well as domain decomposition methods simplify to just traditional (block-) iteration methods. Now, the convergence analysis can be carried out directly for these traditional iterations on the enlarged system, making convergence proofs of multilevel and domain decomposition methods more clear, or, at least, more classical. The terms that enter the convergence proofs are exactly the ones of the classical iterative methods. It remains to estimate them properly. The convergence proof itself follow basically line by line the old proofs of the respective traditional iterative methods. Additionally, new multilevel/domain decomposition methods are constructed straightforwardly by now applying just other old and well known traditional iterative methods to the enlarged system.

  13. Examining Complexity across Domains: Relating Subjective and Objective Measures of Affective Environmental Scenes, Paintings and Music

    PubMed Central

    Marin, Manuela M.; Leder, Helmut

    2013-01-01

    Subjective complexity has been found to be related to hedonic measures of preference, pleasantness and beauty, but there is no consensus about the nature of this relationship in the visual and musical domains. Moreover, the affective content of stimuli has been largely neglected so far in the study of complexity but is crucial in many everyday contexts and in aesthetic experiences. We thus propose a cross-domain approach that acknowledges the multidimensional nature of complexity and that uses a wide range of objective complexity measures combined with subjective ratings. In four experiments, we employed pictures of affective environmental scenes, representational paintings, and Romantic solo and chamber music excerpts. Stimuli were pre-selected to vary in emotional content (pleasantness and arousal) and complexity (low versus high number of elements). For each set of stimuli, in a between-subjects design, ratings of familiarity, complexity, pleasantness and arousal were obtained for a presentation time of 25 s from 152 participants. In line with Berlyne’s collative-motivation model, statistical analyses controlling for familiarity revealed a positive relationship between subjective complexity and arousal, and the highest correlations were observed for musical stimuli. Evidence for a mediating role of arousal in the complexity-pleasantness relationship was demonstrated in all experiments, but was only significant for females with regard to music. The direction and strength of the linear relationship between complexity and pleasantness depended on the stimulus type and gender. For environmental scenes, the root mean square contrast measures and measures of compressed file size correlated best with subjective complexity, whereas only edge detection based on phase congruency yielded equivalent results for representational paintings. Measures of compressed file size and event density also showed positive correlations with complexity and arousal in music, which is

  14. Examining complexity across domains: relating subjective and objective measures of affective environmental scenes, paintings and music.

    PubMed

    Marin, Manuela M; Leder, Helmut

    2013-01-01

    Subjective complexity has been found to be related to hedonic measures of preference, pleasantness and beauty, but there is no consensus about the nature of this relationship in the visual and musical domains. Moreover, the affective content of stimuli has been largely neglected so far in the study of complexity but is crucial in many everyday contexts and in aesthetic experiences. We thus propose a cross-domain approach that acknowledges the multidimensional nature of complexity and that uses a wide range of objective complexity measures combined with subjective ratings. In four experiments, we employed pictures of affective environmental scenes, representational paintings, and Romantic solo and chamber music excerpts. Stimuli were pre-selected to vary in emotional content (pleasantness and arousal) and complexity (low versus high number of elements). For each set of stimuli, in a between-subjects design, ratings of familiarity, complexity, pleasantness and arousal were obtained for a presentation time of 25 s from 152 participants. In line with Berlyne's collative-motivation model, statistical analyses controlling for familiarity revealed a positive relationship between subjective complexity and arousal, and the highest correlations were observed for musical stimuli. Evidence for a mediating role of arousal in the complexity-pleasantness relationship was demonstrated in all experiments, but was only significant for females with regard to music. The direction and strength of the linear relationship between complexity and pleasantness depended on the stimulus type and gender. For environmental scenes, the root mean square contrast measures and measures of compressed file size correlated best with subjective complexity, whereas only edge detection based on phase congruency yielded equivalent results for representational paintings. Measures of compressed file size and event density also showed positive correlations with complexity and arousal in music, which is

  15. Examining complexity across domains: relating subjective and objective measures of affective environmental scenes, paintings and music.

    PubMed

    Marin, Manuela M; Leder, Helmut

    2013-01-01

    Subjective complexity has been found to be related to hedonic measures of preference, pleasantness and beauty, but there is no consensus about the nature of this relationship in the visual and musical domains. Moreover, the affective content of stimuli has been largely neglected so far in the study of complexity but is crucial in many everyday contexts and in aesthetic experiences. We thus propose a cross-domain approach that acknowledges the multidimensional nature of complexity and that uses a wide range of objective complexity measures combined with subjective ratings. In four experiments, we employed pictures of affective environmental scenes, representational paintings, and Romantic solo and chamber music excerpts. Stimuli were pre-selected to vary in emotional content (pleasantness and arousal) and complexity (low versus high number of elements). For each set of stimuli, in a between-subjects design, ratings of familiarity, complexity, pleasantness and arousal were obtained for a presentation time of 25 s from 152 participants. In line with Berlyne's collative-motivation model, statistical analyses controlling for familiarity revealed a positive relationship between subjective complexity and arousal, and the highest correlations were observed for musical stimuli. Evidence for a mediating role of arousal in the complexity-pleasantness relationship was demonstrated in all experiments, but was only significant for females with regard to music. The direction and strength of the linear relationship between complexity and pleasantness depended on the stimulus type and gender. For environmental scenes, the root mean square contrast measures and measures of compressed file size correlated best with subjective complexity, whereas only edge detection based on phase congruency yielded equivalent results for representational paintings. Measures of compressed file size and event density also showed positive correlations with complexity and arousal in music, which is

  16. Determine the Dispersion Relation of an A6 Magnetron Using Conformal Finite Difference Time Domain Method

    NASA Astrophysics Data System (ADS)

    Lin, M. C.; Nieter, C.; Stoltz, P. H.; Smithe, D. N.

    2009-05-01

    This work introduces a conformal finite difference time domain (CFDTD) method to accurately determine the dispersion relation of an A6 relativistic magnetron. The accuracy is measured by comparing with accurate SUPERFISH calculations based on finite element method. The results show that an accuracy of 99.4% can be achieved by using only 10,000 mesh points with Dey-Mittra algorithm. By comparison, a mesh number of 360,000 is needed to preserve 99% accuracy using conventional FDTD method. This suggests one can efficiently and accurately study the hot tests of microwave tubes using CFDTD particle-in-cell method instead of conventional FDTD one.

  17. The NIMH Research Domain Criteria initiative and error-related brain activity.

    PubMed

    Hanna, Gregory L; Gehring, William J

    2016-03-01

    Research on the neural response to errors has an important role in the Research Domain Criteria (RDoC) project, since it is likely to link psychopathology to the dysfunction of neural systems underlying basic behavioral functions, with the error-related negativity (ERN) appearing as a unit of measurement in three RDoC domains. A recent report builds on previous research by examining the ERN as a measure of the sustained threat construct and providing evidence that the ERN may reflect sensitivity more specifically to endogenous threat. Data from 515 adolescent females indicate that the ERN was enlarged primarily in older adolescents with self-reported checking behaviors, although it was blunted in adolescents with depressive symptoms regardless of age. Potential future studies for replicating and extending the research on the ERN and obsessive-compulsive (OC) behaviors are discussed, including studies that more fully characterize OC symptom dimensions, studies that integrate other measures of error-related brain activity and use computational modeling, studies that combine longitudinal, family, and molecular genetic measures, and interventional studies that specifically modulate error-related brain activity in individuals with OC behaviors. PMID:26877130

  18. A topologically related singularity suggests a maximum preferred size for protein domains.

    PubMed

    Zbilut, Joseph P; Chua, Gek Huey; Krishnan, Arun; Bossa, Cecilia; Rother, Kristian; Webber, Charles L; Giuliani, Alessandro

    2007-02-15

    A variety of protein physicochemical as well as topological properties, demonstrate a scaling behavior relative to chain length. Many of the scalings can be modeled as a power law which is qualitatively similar across the examples. In this article, we suggest a rational explanation to these observations on the basis of both protein connectivity and hydrophobic constraints of residues compactness relative to surface volume. Unexpectedly, in an examination of these relationships, a singularity was shown to exist near 255-270 residues length, and may be associated with an upper limit for domain size. Evaluation of related G-factor data points to a wide range of conformational plasticity near this point. In addition to its theoretical importance, we show by an application of CASP experimental and predicted structures, that the scaling is a practical filter for protein structure prediction. PMID:17154417

  19. The ATM-related domain of TRRAP is required for histone acetyltransferase recruitment and Myc-dependent oncogenesis

    PubMed Central

    Park, Jeonghyeon; Kunjibettu, Sudeesha; McMahon, Steven B.; Cole, Michael D.

    2001-01-01

    The ATM-related TRRAP protein is a component of several different histone acetyltransferase (HAT) complexes but lacks the kinase activity characteristic of other ATM family members. We identified a novel function for this evolutionarily conserved domain in its requirement for the assembly of a functional HAT complex. Ectopic expression of TRRAP protein with a mutation in the ATM-related domain inhibits Myc-mediated oncogenic transformation. The Myc-binding region of TRRAP maps to a separable domain, and ectopic expression of this domain inhibits cell growth. These findings demonstrate that the ATM-related domain of TRRAP forms a structural core for the assembly and recruitment of HAT complexes by transcriptional activators. PMID:11445536

  20. Cysteine-rich domains related to Frizzled receptors and Hedgehog-interacting proteins

    PubMed Central

    Pei, Jimin; Grishin, Nick V

    2012-01-01

    Frizzled and Smoothened are homologous seven-transmembrane proteins functioning in the Wnt and Hedgehog signaling pathways, respectively. They harbor an extracellular cysteine-rich domain (FZ-CRD), a mobile evolutionary unit that has been found in a number of other metazoan proteins and Frizzled-like proteins in Dictyostelium. Domains distantly related to FZ-CRDs, in Hedgehog-interacting proteins (HHIPs), folate receptors and riboflavin-binding proteins (FRBPs), and Niemann-Pick Type C1 proteins (NPC1s), referred to as HFN-CRDs, exhibit similar structures and disulfide connectivity patterns compared with FZ-CRDs. We used computational analyses to expand the homologous set of FZ-CRDs and HFN-CRDs, providing a better understanding of their evolution and classification. First, FZ-CRD-containing proteins with various domain compositions were identified in several major eukaryotic lineages including plants and Chromalveolata, revealing a wider phylogenetic distribution of FZ-CRDs than previously recognized. Second, two new and distinct groups of highly divergent FZ-CRDs were found by sensitive similarity searches. One of them is present in the calcium channel component Mid1 in fungi and the uncharacterized FAM155 proteins in metazoans. Members of the other new FZ-CRD group occur in the metazoan-specific RECK (reversion-inducing-cysteine-rich protein with Kazal motifs) proteins that are putative tumor suppressors acting as inhibitors of matrix metalloproteases. Finally, sequence and three-dimensional structural comparisons helped us uncover a divergent HFN-CRD in glypicans, which are important morphogen-binding heparan sulfate proteoglycans. Such a finding reinforces the evolutionary ties between the Wnt and Hedgehog signaling pathways and underscores the importance of gene duplications in creating essential signaling components in metazoan evolution. PMID:22693159

  1. Polarized Defense Against Fungal Pathogens Is Mediated by the Jacalin-Related Lectin Domain of Modular Poaceae-Specific Proteins.

    PubMed

    Weidenbach, Denise; Esch, Lara; Möller, Claudia; Hensel, Goetz; Kumlehn, Jochen; Höfle, Caroline; Hückelhoven, Ralph; Schaffrath, Ulrich

    2016-04-01

    Modular proteins are an evolutionary answer to optimize performance of proteins that physically interact with each other for functionality. Using a combination of genetic and biochemical experiments, we characterized the rice protein OsJAC1, which consists of a jacalin-related lectin (JRL) domain predicted to bind mannose-containing oligosaccharides, and a dirigent domain which might function in stereoselective coupling of monolignols. Transgenic overexpression of OsJAC1 in rice resulted in quantitative broad-spectrum resistance against different pathogens including bacteria, oomycetes, and fungi. Overexpression of this gene or its wheat ortholog TAJA1 in barley enhanced resistance against the powdery mildew fungus. Both protein domains of OsJAC1 are required to establish resistance as indicated by single or combined transient expression of individual domains. Expression of artificially separated and fluorescence-tagged protein domains showed that the JRL domain is sufficient for targeting the powdery mildew penetration site. Nevertheless, co-localization of the lectin and the dirigent domain occurred. Phylogenetic analyses revealed orthologs of OsJAC1 exclusively within the Poaceae plant family. Dicots, by contrast, only contain proteins with either JRL or dirigent domain(s). Altogether, our results identify OsJAC1 as a representative of a novel type of resistance protein derived from a plant lineage-specific gene fusion event for better function in local pathogen defense. PMID:26708413

  2. Application of wearable computing in the manufacture and other related domain

    NASA Astrophysics Data System (ADS)

    XiaHou, Shi-Ji; Chen, Dong-Yi

    2005-12-01

    A survey of application of Wearable Computing in the Manufacture and other correlative domain is presented. At first, a short introduction to the Wearable Computing, such as the characters and its applications in some large manufacturing enterprises, is given, and then, an elaborate analysis of its typical applications scenario in the manufacture and other correlative domains is provided. Thirdly, a few typical wearable application research works on equipment installment, maintenance, operation watch, and fault diagnose, repair and corresponding operation training, is summed up. Fourthly, these scenarios character in special working environment and complex task process is analyzed. Fifthly, the related research works and depict the typical work flow of the wearable computer operators in these application scenarios is summarized, and the demand of the wearable computer's support soft system is depicted. Some key technologies for implementing this support soft system is presented according to these demands include Adaptive Human-Computer Interface, Augment Reality, Workflow Design and Sensor Network, etc. At last, an infrastructure for the system design, include software and hardware architecture, is introduced.

  3. Between-Domain Relations of Academic Emotions: Does Having the Same Instructor Make a Difference?

    ERIC Educational Resources Information Center

    Goetz, Thomas; Frenzel, Anne C.; Ludtke, Oliver; Hall, Nathan C.

    2011-01-01

    Previous research indicates that academic emotions are largely organized along domain-specific lines. In the present study (N = 1,687; Grades 8/11), the authors explored the domain specificity of academic emotions in terms of the moderating influence of having the same versus a different course instructor across domains. The authors evaluated…

  4. Dual-band Fourier domain optical coherence tomography with depth-related compensations

    PubMed Central

    Zhang, Miao; Ma, Lixin; Yu, Ping

    2013-01-01

    Dual-band Fourier domain optical coherence tomography (FD-OCT) provides depth-resolved spectroscopic imaging that enhances tissue contrast and reduces image speckle. However, previous dual-band FD-OCT systems could not correctly give the tissue spectroscopic contrast due to depth-related discrepancy in the imaging method and attenuation in biological tissue samples. We designed a new dual-band full-range FD-OCT imaging system and developed an algorithm to compensate depth-related fall-off and light attenuation. In our imaging system, the images from two wavelength bands were intrinsically overlapped and their intensities were balanced. The processing time of dual-band OCT image reconstruction and depth-related compensations were minimized by using multiple threads that execute in parallel. Using the newly developed system, we studied tissue phantoms and human cancer xenografts and muscle tissues dissected from severely compromised immune deficient mice. Improved spectroscopic contrast and sensitivity were achieved, benefiting from the depth-related compensations. PMID:24466485

  5. Domain General Mediators of the Relation between Kindergarten Number Sense and First-Grade Mathematics Achievement

    PubMed Central

    Hassinger-Das, Brenna; Jordan, Nancy C.; Glutting, Joseph; Irwin, Casey; Dyson, Nancy

    2013-01-01

    Domain general skills that mediate the relation between kindergarten number sense and first-grade mathematics skills were investigated. Participants were 107 children who displayed low number sense in the fall of kindergarten. Controlling for background variables, multiple regression analyses showed that attention problems and executive functioning both were unique predictors of mathematics outcomes. Attention problems were more important for predicting first-grade calculation performance while executive functioning was more important for predicting first-grade performance on applied problems. Moreover, both executive functioning and attention problems were unique partial mediators of the relationship between kindergarten and first-grade mathematics skills. The results provide empirical support for developing interventions that target executive functioning and attention problems in addition to instruction in number skills for kindergartners with initial low number sense. PMID:24237789

  6. Domain repeats related to innate immunity in the South African abalone, Haliotis midae.

    PubMed

    Picone, Barbara; Rhode, Clint; Roodt-Wilding, Rouvay

    2015-10-01

    Molluscs predominately use the cellular defence system as the primary mechanism of defence against pathogenic infection, in which haemocytes play a pivotal role. Haliotis midae is a commercially important South African species that it is susceptible to bacterial pathogens, fungal and yeast infections in the farming environment. The current study aims to enrich the current knowledge regarding H. midae innate immunity by investigating the presence and evolution of domain repeats. The bioinformatics approach used in this study, detected five repeat families in the H. midae transcriptome. These repeats families include mixed alpha and beta (leucine-rich and ankyrin), spectrin repeats, beta-propellers (WD40) and alfa-structure repeat (TPR-like). The expansion of key gene families related to host defence may be important to abalone adaptation to life in a pathogen-rich environment. PMID:25936498

  7. Calcium domains associated with individual channels can account for anomalous voltage relations of CA-dependent responses.

    PubMed Central

    Chad, J E; Eckert, R

    1984-01-01

    Computer-assisted modeling of calcium influx through voltage-activated membrane channels predicted that buffer-limited elevation of cytoplasmic free calcium ion concentration occurs within microscopic hemispherical "domains" centered upon the active Ca channels. With increasing depolarization, the number of activated channels, and hence the number of Ca domains, should increase; the single-channel current should, however, decrease, thereby decreasing Ca2+ accumulation in each domain relative to the macroscopic current. Such voltage dependence of the microscopic distribution of Ca2+ may influence relations between total Ca2+ entry and Ca-dependent processes. Ca-mediated inactivation of Ca channels in Aplysia neurons exhibits behavior consistent with the calcium domain hypothesis. PMID:6329349

  8. The Jumonji gene family in Crassostrea gigas suggests evolutionary conservation of Jmj-C histone demethylases orthologues in the oyster gametogenesis and development.

    PubMed

    Fellous, Alexandre; Favrel, Pascal; Guo, Ximing; Riviere, Guillaume

    2014-03-15

    Jumonji (Jmj) proteins are histone demethylases, which control the identity of stem cells. Jmj genes were characterized from plants to mammals where they have been implicated in the epigenetic regulation of development. Despite the Pacific oyster Crassostrea gigas representing one of the most important aquaculture resources worldwide, the molecular mechanisms governing the embryogenesis and reproduction of this lophotrochozoan species remain poorly understood. However, annotations in the C. gigas EST library suggested the presence of putative Jumonji genes, raising the question of the conservation of this family of histone demethylases in the oyster. Using Primer walking, 5'-RACE PCR and in silico analyses, we characterized nine Jumonji orthologues in the oyster, called Cg-Jmj, bearing conserved domains critical for putative histone demethylase activity. Phylogenic analyses revealed that oyster Jumonji cluster into two distinct groups: 'single-domain Jmj' and 'multi-domain Jmj', and define 8 subgroups corresponding to each cognate orthologues in metazoans. RT-qPCR investigations showed specific regulations of Cg-Jmj mRNAs during the early development and along the reproduction cycle. Furthermore, in situ and in toto hybridizations indicate that oyster Jumonji genes are transcribed mostly within the gonad in adult oysters whereas they display a ubiquitous expression during embryonic and larval development. Our study demonstrates the presence of nine Jumonji orthologues in the oyster C. gigas. Their domain conservation and their expression profile suggest an implication during reproduction and development, questioning about the epigenetic regulation by histone methylation in lophotrochozoans.

  9. A method for finding candidate conformations for molecular replacement using relative rotation between domains of a known structure.

    PubMed

    Jeong, Jay I; Lattman, Eaton E; Chirikjian, Gregory S

    2006-04-01

    This paper presents a methodology to obtain candidate conformations of multidomain proteins for use in molecular replacement. For each separate domain, the orientational relationship between the template and the target structure is obtained using standard molecular replacement. The orientational relationships of the domains are then used to calculate the relative rotation between the domains in the target conformation by using pose-estimation techniques from the field of robotics and computer vision. With the angle of relative rotation between the domains as a cost function, iterative normal-mode analysis is used to drive the template structure to a candidate conformation that matches the X-ray crystallographic data obtained for the target conformation. The selection of the correct intra-protein domain orientations from among the many spurious maxima in the rotation function (including orientations obtained from domains in symmetry mates rather than within the same copy of the protein) presents a challenge. This problem is resolved by checking R factors of each domain, measuring the absolute value of relative rotation between domains, and evaluating the cost value after each candidate conformation is driven to convergence with iterative NMA. As a validation, the proposed method is applied to three test proteins: ribose-binding protein, lactoferrin and calcium ATPase. In each test case, the orientation and translation of the final candidate conformation in the unit cell are generated correctly from the suggested procedure. The results show that the proposed method can yield viable candidate conformations for use in molecular replacement and can reveal the structural details and pose of the target conformation in the crystallographic unit cell. PMID:16552141

  10. Relations between the Development of Future Time Perspective in Three Life Domains, Investment in Learning, and Academic Achievement

    ERIC Educational Resources Information Center

    Peetsma, Thea; van der Veen, Ineke

    2011-01-01

    Relations between the development of future time perspectives in three life domains (i.e., school and professional career, social relations, and leisure time) and changes in students' investment in learning and academic achievement were examined in this study. Participants were 584 students in the first and 584 in the second year of the lower…

  11. Medical Resident Ability to Self-Assess in Relation to Their Competence within the Assessed Domain

    ERIC Educational Resources Information Center

    Whicker, Shari Ann

    2012-01-01

    The purpose of the study was to examine the relationship between resident communication skills competence and their ability to self-assess within that domain. Six research questions guided the study. The first research question sought to explore the varied levels with which residents demonstrated competence within the domain of communication…

  12. Issues Related to the Construction of a Purpose-Built Domain-Specific Word Corpus

    ERIC Educational Resources Information Center

    Thomas, Lisa; Pfister, H. Peter; Peterson, Peter

    2004-01-01

    There is growing interest in the use of semantic collections in order to identify and analyse domain knowledge. This paper describes some technical issues to consider when contemplating research which incorporates small-to-medium domain-specific word sets. The purpose of the corpus construction described was to provide an external word collection…

  13. Characterization of the SAM domain of the PKD-related protein ANKS6 and its interaction with ANKS3

    PubMed Central

    2014-01-01

    Background Autosomal dominant polycystic kidney disease (ADPKD) is the most common genetic disorder leading to end-stage renal failure in humans. In the PKD/Mhm(cy/+) rat model of ADPKD, the point mutation R823W in the sterile alpha motif (SAM) domain of the protein ANKS6 is responsible for disease. SAM domains are known protein-protein interaction domains, capable of binding each other to form polymers and heterodimers. Despite its physiological importance, little is known about the function of ANKS6 and how the R823W point mutation leads to PKD. Recent work has revealed that ANKS6 interacts with a related protein called ANKS3. Both ANKS6 and ANKS3 have a similar domain structure, with ankyrin repeats at the N-terminus and a SAM domain at the C-terminus. Results The SAM domain of ANKS3 is identified as a direct binding partner of the ANKS6 SAM domain. We find that ANKS3-SAM polymerizes and ANKS6-SAM can bind to one end of the polymer. We present crystal structures of both the ANKS3-SAM polymer and the ANKS3-SAM/ANKS6-SAM complex, revealing the molecular details of their association. We also learn how the R823W mutation disrupts ANKS6 function by dramatically destabilizing the SAM domain such that the interaction with ANKS3-SAM is lost. Conclusions ANKS3 is a direct interacting partner of ANKS6. By structurally and biochemically characterizing the interaction between the ANKS3 and ANKS6 SAM domains, our work provides a basis for future investigation of how the interaction between these proteins mediates kidney function. PMID:24998259

  14. Reconstitution of the NF1 GAP-related domain in NF1-deficient human Schwann cells

    SciTech Connect

    Thomas, Stacey L.; Deadwyler, Gail D.; Tang, Jun; Stubbs, Evan B.; Muir, David; Hiatt, Kelly K. . E-mail: George.Devries@med.va.gov

    2006-09-29

    Schwann cells derived from peripheral nerve sheath tumors from individuals with Neurofibromatosis Type 1 (NF1) are deficient for the protein neurofibromin, which contains a GAP-related domain (NF1-GRD). Neurofibromin-deficient Schwann cells have increased Ras activation, increased proliferation in response to certain growth stimuli, increased angiogenic potential, and altered cell morphology. This study examined whether expression of functional NF1-GRD can reverse the transformed phenotype of neurofibromin-deficient Schwann cells from both benign and malignant peripheral nerve sheath tumors. We reconstituted the NF1-GRD using retroviral transduction and examined the effects on cell morphology, growth potential, and angiogenic potential. NF1-GRD reconstitution resulted in morphologic changes, a 16-33% reduction in Ras activation, and a 53% decrease in proliferation in neurofibromin-deficient Schwann cells. However, NF1-GRD reconstitution was not sufficient to decrease the in vitro angiogenic potential of the cells. This study demonstrates that reconstitution of the NF1-GRD can at least partially reverse the transformation of human NF1 tumor-derived Schwann cells.

  15. Plasmodium alveolins possess distinct but structurally and functionally related multi-repeat domains.

    PubMed

    Al-Khattaf, Fatimah S; Tremp, Annie Z; Dessens, Johannes T

    2015-02-01

    The invasive and motile life stages of malaria parasites (merozoite, ookinete and sporozoite) possess a distinctive cortical structure termed the pellicle. The pellicle is characterised by a double-layered 'inner membrane complex' (IMC) located underneath the plasma membrane, which is supported by a cytoskeletal structure termed the subpellicular network (SPN). The SPN consists of intermediate filaments, whose major constituents include a family of proteins called alveolins. Here, we re-appraise the alveolins in the genus Plasmodium with respect to their repertoire, structure and interrelatedness. Amongst 13 family members identified, we distinguish two domain types that, albeit distinct at the primary structure level, are structurally related and contain tandem repeats with a consensus 12-amino acid periodicity. Analysis in Plasmodium berghei of the most divergent alveolin, PbIMC1d, reveals a zoite-specific expression in ookinetes and a subcellular localisation in the pellicle, consistent with its predicted role as a SPN component. Knockout of PbIMC1d gives rise to a wild-type phenotype with respect to ookinete morphogenesis, tensile strength, gliding motility and infectivity, presenting the first example of apparent functional redundancy amongst alveolin family members.

  16. A Computer Program to Relate Factors Across Separately Factor Analyzed Variable Domains

    ERIC Educational Resources Information Center

    Morris, John D.; Guertin, Wilson H.

    1976-01-01

    A Fortran IV program is presented which will cross-correlate least squares estimated factor scores across separately factor analyzed variable domains without the tedious necessity of actually calculating the factor scores. (RC)

  17. Relative Orientation of POTRA Domains from Cyanobacterial Omp85 Studied by Pulsed EPR Spectroscopy.

    PubMed

    Dastvan, Reza; Brouwer, Eva-Maria; Schuetz, Denise; Mirus, Oliver; Schleiff, Enrico; Prisner, Thomas F

    2016-05-24

    Many proteins of the outer membrane of Gram-negative bacteria and of the outer envelope of the endosymbiotically derived organelles mitochondria and plastids have a β-barrel fold. Their insertion is assisted by membrane proteins of the Omp85-TpsB superfamily. These proteins are composed of a C-terminal β-barrel and a different number of N-terminal POTRA domains, three in the case of cyanobacterial Omp85. Based on structural studies of Omp85 proteins, including the five POTRA-domain-containing BamA protein of Escherichia coli, it is predicted that anaP2 and anaP3 bear a fixed orientation, whereas anaP1 and anaP2 are connected via a flexible hinge. We challenged this proposal by investigating the conformational space of the N-terminal POTRA domains of Omp85 from the cyanobacterium Anabaena sp. PCC 7120 using pulsed electron-electron double resonance (PELDOR, or DEER) spectroscopy. The pronounced dipolar oscillations observed for most of the double spin-labeled positions indicate a rather rigid orientation of the POTRA domains in frozen liquid solution. Based on the PELDOR distance data, structure refinement of the POTRA domains was performed taking two different approaches: 1) treating the individual POTRA domains as rigid bodies; and 2) using an all-atom refinement of the structure. Both refinement approaches yielded ensembles of model structures that are more restricted compared to the conformational ensemble obtained by molecular dynamics simulations, with only a slightly different orientation of N-terminal POTRA domains anaP1 and anaP2 compared with the x-ray structure. The results are discussed in the context of the native environment of the POTRA domains in the periplasm. PMID:27224485

  18. Crystal structures of the reverse transcriptase-associated ribonuclease H domain of xenotropic murine leukemia-virus related virus

    SciTech Connect

    Zhou, Dongwen; Chung, Suhman; Miller, Maria; Le Grice, Stuart F.J.; Wlodawer, Alexander

    2012-06-19

    The ribonuclease H (RNase H) domain of retroviral reverse transcriptase (RT) plays a critical role in the life cycle by degrading the RNA strands of DNA/RNA hybrids. In addition, RNase H activity is required to precisely remove the RNA primers from nascent (-) and (+) strand DNA. We report here three crystal structures of the RNase H domain of xenotropic murine leukemia virus-related virus (XMRV) RT, namely (i) the previously identified construct from which helix C was deleted, (ii) the intact domain, and (iii) the intact domain complexed with an active site {alpha}-hydroxytropolone inhibitor. Enzymatic assays showed that the intact RNase H domain retained catalytic activity, whereas the variant lacking helix C was only marginally active, corroborating the importance of this helix for enzymatic activity. Modeling of the enzyme-substrate complex elucidated the essential role of helix C in binding a DNA/RNA hybrid and its likely mode of recognition. The crystal structure of the RNase H domain complexed with {beta}-thujaplicinol clearly showed that coordination by two divalent cations mediates recognition of the inhibitor.

  19. Molecular evolution and domain structure of plasminogen-related growth factors (HGF/SF and HGF1/MSP).

    PubMed Central

    Donate, L. E.; Gherardi, E.; Srinivasan, N.; Sowdhamini, R.; Aparicio, S.; Blundell, T. L.

    1994-01-01

    Plasminogen-related growth factors, a new family of polypeptide growth factors with the basic domain organization and mechanism of activation of the blood proteinase plasminogen, include hepatocyte growth factor/scatter factor (HGF/SF), a potent effector of the growth, movement, and differentiation of epithelia and endothelia, and hepatocyte growth factor-like/macrophage stimulating protein (HGF1/MSP), an effector of macrophage chemotaxis and phagocytosis. Phylogeny of the serine proteinase domains and analysis of intron-exon boundaries and kringle sequences indicate that HGF/SF, HGF1/MSP, plasminogen, and apolipoprotein (a) have evolved from a common ancestral gene that consisted of an N-terminal domain corresponding to plasminogen activation peptide (PAP), 3 copies of the kringle domain, and a serine proteinase domain. Models of the N domains of HGF/SF, HGF1/MSP, and plasminogen, characterized by the presence of 4 conserved Cys residues forming a loop in a loop, have been modeled based on disulfide-bond constraints. There is a distinct pattern of charged and hydrophobic residues in the helix-strand-helix motif proposed for the PAP domain of HGF/SF; these may be important for receptor interaction. Three-dimensional structures of the 4 kringle and the serine proteinase domains of HGF/SF were constructed by comparative modeling using the suite of programs COMPOSER and were energy minimized. Docking of a lysine analogue indicates a putative lysine-binding pocket within kringle 2 (and possibly another in kringle 4). The models suggest a mechanism for the formation of a noncovalent HGF/SF homodimer that may be responsible for the activation of the Met receptor. These data provide evidence for the divergent evolution and structural similarity of plasminogen, HGF/SF, and HGF1/MSP, and highlight a new strategy for growth factor evolution, namely the adaptation of a proteolytic enzyme to a role in receptor activation. PMID:7756992

  20. Mutational analysis of the NF1 GAP-related domain in neuroectodermal tumors

    SciTech Connect

    Vinanzi, C.; Basso, G.; Perilongo, G.

    1994-09-01

    To try to contribute to the more precise characterization of the function of the NF1 gene in tumorigenesis we have analyzed the most conserved region of its coding sequence, the GAP-related domain (NF1 GRD), which is attributed with tumor suppressor function. The rationale for the study was based on the likelihood of finding structural alterations resulting in loss of function of this region, in situations such as tumors of neuroepithelial tissues. In these situations, the activity of the NF1 gene product, neurofibromis, a GTPase activating protein, seems to be crucial in regulating the mechanisms of signal transduction mediated by p21 ras. We have studied the NF1 GRD region by PCR amplification of each exon (exons 21-27a) followed by subsequent PAGE and SSCP analysis of the amplification products in 60 primary sporadic neuroectodermal tumors. Our sample included: 14 neuroblastoma, 11 glioblastoma, 8 medulloblastoma, 7 ependimoma, 6 peripheral PNET, 1 ganglioneuroma, 1 glioma, 1 Ewing sarcoma, 1 meningioma and 1 schwannoma. We have not identified structural alterations of the NF1 GRD region in the tumors analysed, with one possible exception now in the process of being characterized. We can conclude that the loss of the NF1 gene tumor suppressor function that might lead or contribute to the development of malignancies in tissues of neuroectodermal origin is not due to structural abnormalities of the region of the gene interacting with p21 ras, either as a negative regulator or as a downstream effector of it. These data, together with the observation that the oncogene ras 21 is not typically mutated in neuroectodermal tumors, and that GTP-ras has been found normally regulated in neurofibromis-deficient melanoma and neuroblastoma cell lines, seem to support the hypothesis that the antioncogene activity of the NF1 gene could be totally independent from its interaction with ras.

  1. Comparative Analysis of Barophily-Related Amino Acid Content in Protein Domains of Pyrococcus abyssi and Pyrococcus furiosus

    PubMed Central

    Yafremava, Liudmila S.; Di Giulio, Massimo; Caetano-Anollés, Gustavo

    2013-01-01

    Amino acid substitution patterns between the nonbarophilic Pyrococcus furiosus and its barophilic relative P. abyssi confirm that hydrostatic pressure asymmetry indices reflect the extent to which amino acids are preferred by barophilic archaeal organisms. Substitution patterns in entire protein sequences, shared protein domains defined at fold superfamily level, domains in homologous sequence pairs, and domains of very ancient and very recent origin now provide further clues about the environment that led to the genetic code and diversified life. The pyrococcal proteomes are very similar and share a very early ancestor. Relative amino acid abundance analyses showed that biases in the use of amino acids are due to their shared fold superfamilies. Within these repertoires, only two of the five amino acids that are preferentially barophilic, aspartic acid and arginine, displayed this preference significantly and consistently across structure and in domains appearing in the ancestor. The more primordial asparagine, lysine and threonine displayed a consistent preference for nonbarophily across structure and in the ancestor. Since barophilic preferences are already evident in ancient domains that are at least ~3 billion year old, we conclude that barophily is a very ancient trait that unfolded concurrently with genetic idiosyncrasies in convergence towards a universal code. PMID:24187517

  2. Relations between Young Students' Strategic Behaviours, Domain-Specific Self-Concept, and Performance in a Problem-Solving Situation

    ERIC Educational Resources Information Center

    Dermitzaki, Irini; Leondari, Angeliki; Goudas, Marios

    2009-01-01

    This study aimed at investigating the relations between students' strategic behaviour during problem solving, task performance and domain-specific self-concept. A total of 167 first- and second-graders were individually examined in tasks involving cubes assembly and in academic self-concept in mathematics. Students' cognitive, metacognitive, and…

  3. Relative roles of the different Pax6 domains for pancreatic alpha cell development

    PubMed Central

    2010-01-01

    Background The transcription factor Pax6 functions in the specification and maintenance of the differentiated cell lineages in the endocrine pancreas. It has two DNA binding domains, the paired domain and the homeodomain, in addition to a C-terminal transactivation domain. The phenotype of Pax6-/- knockout mice suggests non-redundant functions of the transcription factor in the development of glucagon-expressing α-cells as this cell type is absent in the mutants. We ask the question of how the differentiation of pancreatic endocrine cells, in particular that of α-cells, is affected by selective inactivation of either one of the three major domains of Pax6. Results The Pax6Aey18 mutant mouse line, in which the paired domain is inactivated, showed a phenotype similar to that of Pax6-/- knockout mice with a near complete absence of glucagon-positive α-cells (0-4 cells/section; ≤1% of wt), reduced β-cell area (74% of wt) and disorganized islets. The proportion of ghrelin-positive ε-cells was expanded. In Pax6Sey-Neu mutants, which lack the transactivation domain, α-and β-cells where reduced to 25 and 40% of wt, respectively. We also studied two mouse lines with mutations in the homeodomain, Pax64Neu and Pax6132-14Neu. Neighboring amino acids are affected in the two lines and both point mutations abolish DNA binding of the classical P3 homeodomain target sequence. The pancreatic phenotype of the two mutants however was divergent. While Pax64Neu homozygotes showed a reduction of α- and β-cells to 59 and 61%, respectively, pancreatic endocrine development was unaltered in the Pax6132-14Neu mutant strain. Conclusions We show that inactivation of the Pax6 paired domain leads to a more severe phenotype with regards to the differentiation of pancreatic α-cells than the loss of the transactivation domain. The analysis of two different homeodomain mutants suggests that the binding of Pax6 to P3 homeodomain consensus sequences is not required for α-cell development

  4. Redistribution of demethylated RNA helicase A during foot-and-mouth disease virus infection: Role of Jumonji C-domain containing protein 6 in RHA demethylation

    SciTech Connect

    Lawrence, Paul; Conderino, Joseph S.; Rieder, Elizabeth

    2014-03-15

    Previously, RNA helicase A (RHA) re-localization from the nucleus to the cytoplasm in foot-and-mouth disease virus (FMDV) infected cells was shown to coincide with loss of RHA methylated arginine residues at its C-terminus. The potential interaction between RHA and Jumonji C-domain (JmjC) protein 6 (JMJD6) arginine demethylase in infected cells was investigated. Treatment with N-oxalylglycine (NOG) inhibitor of JmjC demethylases prevented FMDV-induced RHA demethylation and re-localization, and also decreased viral protein synthesis and virus titers. Physical interaction between JMJD6 and RHA was demonstrated via reciprocal co-immunoprecipitation, where RHA preferentially bound JMJD6 monomers. Nuclear efflux of demethylated RHA (DM-RHA) coincided with nuclear influx of JMJD6, which was not observed using another picornavirus. A modified biochemical assay demonstrated JMJD6 induced dose-dependent demethylation of RHA and two RHA-derived isoforms, which could be inhibited by NOG. We propose a role for JMJD6 in RHA demethylation stimulated by FMDV, that appears to facilitate virus replication. - Highlights: • We examined the role of JMJD6 in FMDV-induced RHA demethylation process. • Using an arginine demethylation assay showed that JMJD6 is involved in RHA demethylation. • A demethylases inhibitor reduced cytoplasmic accumulation of RHA and FMDV titers.

  5. Structural and Biochemical Basis for Ubiquitin Ligase Recruitment by Arrestin-related Domain-containing Protein-3 (ARRDC3)*

    PubMed Central

    Qi, Shiqian; O'Hayre, Morgan; Gutkind, J. Silvio; Hurley, James H.

    2014-01-01

    After protracted stimulation, the β2-adrenergic receptor and many other G-protein-coupled receptors are ubiquitinated and down-regulated. Arrestin-related domain-containing protein-3 (ARRDC3) has been proposed to recruit the ubiquitin ligase Nedd4 to the β2-adrenergic receptor. ARRDC3 contains two PPXY motifs that could potentially interact with any of the four WW domains of Nedd4. Here we dissect the interaction determinants. ARRDC3 PPXY-Nedd4 WW dissociation constants vary from unmeasurable to Kd = 3 μm for the third WW domain of Nedd4 binding to the first PPXY motif of ARRDC3. Structures of the uncomplexed and PPXY1-bound WW3 domain were determined at 1.1 and 1.7 Å resolution. The structures revealed conformational changes upon binding and the hydrogen bonding network in exquisite detail. Tight packing of ARRDC3 Val-352′, part of a 310 helix at the C terminus of PPXY1, is important for high affinity binding to WW3. Although no single WW domain is strictly essential for the binding of Nedd4 and ARRDC3 expressed in HEK293 cells, high affinity binding of full-length ARRDC3 and Nedd4 is driven by the avid interaction of both PPXY motifs with either the WW2-WW3 or WW3-WW4 combinations, with Kd values as low as 300 nm. PMID:24379409

  6. Modulation of neurotransmitter receptors and synaptic differentiation by proteins containing complement-related domains.

    PubMed

    Nakayama, Minoru; Hama, Chihiro

    2011-02-01

    Neurotransmitter receptors play central roles in basic neurotransmission and synaptic plasticity. Recent studies have revealed that some transmembrane and extracellular proteins bind to neurotransmitter receptors, forming protein complexes that are required for proper synaptic localization or gating of core receptor molecules. Consequently, the components of these complexes contribute to long-term potentiation, a process that is critical for learning and memory. Here, we review factors that regulate neurotransmitter receptors, with a focus on proteins containing CUB (complement C1r/C1s, Uegf, Bmp1) or CCP (complement control protein) domains, which are frequently found in complement system proteins. Proteins that contain these domains are structurally distinct from TARPs (transmembrane AMPA receptor regulatory proteins), and may constitute new protein families that modulate either the localization or function of neurotransmitter receptors. In addition, other CCP domain-containing proteins participate in dendritic patterning and/or synaptic differentiation, although current evidence has not identified any direct activities on neurotransmitter receptors. Some of these proteins are involved in pathologic conditions such as epileptic seizure and mental retardation. Together, these lines of information have shown that CUB and CCP domain-containing proteins contribute to a wide variety of neuronal events that ultimately establish neural circuits.

  7. Domain-Specific Self-Concept in Relation to Traditional and Cyber Peer Aggression

    ERIC Educational Resources Information Center

    Toledano, Shanee; Werch, Brittany L.; Wiens, Brenda A.

    2015-01-01

    Individuals who aggress against others have been described both as having overall low self-concept and as having high, inflated self-concept. The conceptualization of self-concept as domain specific provides an alternate means to resolving this controversy. In this study, 223 middle school students completed self-report measures assessing…

  8. The Relative Influence of Different Domains of Social Connectedness on Self-Directed Violence in Adolescence

    ERIC Educational Resources Information Center

    Kaminski, Jennifer W.; Puddy, Richard W.; Hall, Diane M.; Cashman, Sandra Y.; Crosby, Alexander E.; Ortega, LaVonne A. G.

    2010-01-01

    Previous research has linked greater social connectedness with a lowered risk of self-directed violence among adolescents. However, few studies have analyzed the comparative strength of different domains of connectedness (e.g., family, peers and school) to determine where limited resources might best be focused. Data to address that gap were taken…

  9. Axionic domain wall number related to U(1)anom global symmetry

    NASA Astrophysics Data System (ADS)

    Kim, Jihn E.

    2016-08-01

    The QCD axion with fa at an intermediate scale, 109 GeV ∼1012 GeV, seems in conflict with the gravity spoil of global symmetries and may face the axionic domain wall problem. We point out that the string compactifications with an anomalous U(1) gauge symmetry, allowing desirable chiral matter spectra, circumvent these two problems simultaneously.

  10. Boundary shape identification problems in two-dimensional domains related to thermal testing of materials

    NASA Technical Reports Server (NTRS)

    Banks, H. T.; Kojima, Fumio

    1988-01-01

    The identification of the geometrical structure of the system boundary for a two-dimensional diffusion system is reported. The domain identification problem treated here is converted into an optimization problem based on a fit-to-data criterion and theoretical convergence results for approximate identification techniques are discussed. Results of numerical experiments to demonstrate the efficacy of the theoretical ideas are reported.

  11. The Separate, Relative, and Joint Effects of Employee Job Performance Domains on Supervisors' Willingness to Mentor

    ERIC Educational Resources Information Center

    Lapierre, Laurent M.; Bonaccio, Silvia; Allen, Tammy D.

    2009-01-01

    The purpose of our study was to further elucidate how employees should behave at work to increase their chances of being mentored by their immediate supervisor. To that end, we experimentally tested how three domains of employee performance [task performance (TP), organizational citizenship behavior (OCB) targeting the supervisor, and…

  12. Structural priming across cognitive domains: from simple arithmetic to relative-clause attachment.

    PubMed

    Scheepers, Christoph; Sturt, Patrick; Martin, Catherine J; Myachykov, Andriy; Teevan, Kay; Viskupova, Izabela

    2011-10-01

    In the two experiments reported here, we uncovered evidence for shared structural representations between arithmetic and language. Specifically, we primed subjects using mathematical equations either with or without parenthetical groupings, such as 80 - (9 + 1) × 5 or 80 - 9 + 1 × 5, and then presented a target sentence fragment, such as "The tourist guide mentioned the bells of the church that . . .," which subjects had to complete. When the mathematical equations were solved correctly, their structure influenced the noun phrase--for example, either "the bells of the church" or "the church," respectively--that subjects chose to attach their sentence completion to. These experiments provide the first demonstration of cross-domain structural priming from mathematics to language. They highlight the importance of global structural representations at a very high level of abstraction and have potentially far-reaching implications regarding the domain generality of structural representations. PMID:21873569

  13. 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.

  14. Persistent Complex Bereavement Disorder Symptom Domains Relate Differentially to PTSD and Depression: A Study of War-Exposed Bosnian Adolescents.

    PubMed

    Claycomb, Meredith A; Charak, Ruby; Kaplow, Julie; Layne, Christopher M; Pynoos, Robert; Elhai, Jon D

    2016-10-01

    Persistent Complex Bereavement Disorder (PCBD) is a newly proposed diagnosis placed in the Appendix of the 5th edition of the Diagnostic and Statistical Manual of Mental Disorders (DSM-5) as an invitation for further research. To date, no studies have examined the dimensionality of PCBD or explored whether different PCBD criteria domains relate in similar, versus differential, ways to other psychological conditions common to war-exposed bereaved youth, including symptoms of Posttraumatic Stress Disorder (PTSD) and depression. We evaluated the dimensionality of proposed PCBD B and C symptom domains, and their respective relations with measures of PTSD and depression, in 1142 bereaved Bosnian adolescents exposed to the 1992-1995 Bosnian civil war. Instruments included the UCLA PTSD Reaction Index, the Depression Self-Rating Scale, and the UCLA Grief Screening Scale (a prototype measure of PCBD symptoms). We investigated potential differences in grief, PTSD, and depression scores as a function of cause of death. We then examined hypothesized differential relations between PCBD B and C symptom domain subscales and selected external correlates, specifically measures of depression and the four-factor emotional numbing model of PTSD. Results of both analyses provide preliminary evidence of a multidimensional structure for PCBD in this population, in that the PCBD Criterion C subscale score covaried more strongly with each of the four PTSD factors and with depression than did PCBD Criterion B. We conclude by discussing theoretical, methodological, clinical, and policy-related implications linked to the ongoing study of essential features of PCBD. PMID:26695010

  15. A novel Krueppel related factor consisting of only a KRAB domain is expressed in the murine trigeminal ganglion

    SciTech Connect

    Nikulina, Karina; Bodeker, MacDara; Warren, John; Matthews, Philip; Margolis, Todd P. . E-mail: todd.margolis@ucsf.edu

    2006-09-29

    The largest family of zinc-finger (ZnF) transcription factors is that containing the Krueppel-associated box, or KRAB domain. The amino-terminal KRAB domain of these proteins functions as a transcriptional repressor with the downstream ZnF motifs providing DNA-binding specificity. Here we report the identification and characterization of a novel murine Krueppel-related factor (KLF), MIF1, which contains a KRAB domain but lacks a ZnF motif. Western blot analysis identified MIF1-like proteins in the murine trigeminal ganglion (TG) and immunostaining localized these proteins primarily to the cytoplasm of TG neuronal cell bodies. In situ hybridization for Mif1 transcripts confirms the selective expression of Mif1 in TG neurons. Consistent with the non-nuclear localization of MIF1 we could detect no transcriptional repressor activity of the MIF1 protein. However MIF1 appears to be capable of interacting with the co-repressor TIF1{beta} and exhibits transcription repressor activity when fused to yeast GAL4 binding domain protein. Genomic analysis of Mif1 sequence suggests that the Mif1 transcript may result from splicing of a longer KRAB-ZnF containing transcript.

  16. An exact solution for a thick domain wall in general relativity

    NASA Technical Reports Server (NTRS)

    Goetz, Guenter; Noetzold, Dirk

    1989-01-01

    An exact solution of the Einstein equations for a static, planar domain wall with finite thickness is presented. At infinity, density and pressure vanish and the space-time tends to the Minkowski vacuum on one side of the wall and to the Taub vacuum on the other side. A surprising feature of this solution is that the density and pressure distribution are symmetric about the central plane of the wall whereas the space-time metric and therefore also the gravitational field experienced by a test particle is asymmetric.

  17. Heat conductivity in graphene and related materials: A time-domain modal analysis

    NASA Astrophysics Data System (ADS)

    Gill-Comeau, Maxime; Lewis, Laurent J.

    2015-11-01

    We use molecular dynamics (MD) simulations to study heat conductivity in single-layer graphene and graphite. We analyze the MD trajectories through a time-domain modal analysis and show that this is essential for obtaining a reliable representation of the heat flow in graphene and graphite as it permits the proper treatment of collective vibrational excitations, in contrast to a frequency-domain formulation. Our temperature-dependent results are in very good agreement with experiment and, for temperatures in the range 300-1200 K, we find that the ZA branch allows more heat flow than all other branches combined while the contributions of the TA, LA, and ZO branches are comparable at all temperatures. Conductivity mappings reveal strong collective excitations associated with low-frequency ZA modes. We demonstrate that these collective effects are a consequence of the quadratic nature of the ZA branch as they also show up in graphite but are reduced in strained graphene, where the dispersion becomes linear, and are absent in diamond, where acoustic branches are linear. In general, neglecting collective excitations yields errors similar to those from the single-mode relaxation-time approximation.

  18. The New Health-Related Top-Level Domains Are Coming: Will Cureforcancer.health Go to the Highest Bidder?

    PubMed Central

    2014-01-01

    In 2012, the Internet Corporation for Assigned Names and Numbers (ICANN) opened a new round of applications for generic top-level domain (gTLD) names, receiving 1930 applications, of which at least 18 were related to health (eg, “.doctor”, “.health”, “.med”). The entry of new, commercial players applying to create health-related names reopens the debate on the role of international organizations, governments, non-governmental organizations, and other stakeholders regarding the safeguards and policies needed to protect consumers. PMID:24598704

  19. Nano-domains and related phenomena in congruent lithium tantalate single crystals studied by scanning nonlinear dielectric microscopy.

    PubMed

    Cho, Yasuo

    2014-08-01

    Nanodomains and their related phenomena in congruent lithium tantalate (CLT) single crystals are studied using scanning nonlinear dielectric microscopy (SNDM). We carried out two specific investigations: super higher order nonlinear dielectric spectroscopy studies on thick multi-domain congruent CLT single crystals and electrical conduction in nanodomains in thin CLT single crystals. First, without using a special sharp tip, we achieve improved lateral resolution in SNDM through the measurement of super higher order nonlinearity up to the fourth order. We also found a marked enhancement of nonlinear dielectric constants when the applied tip-sample voltage exceeded a particular threshold value. This is due to domain nucleation activated by a huge electric field under the tip. Low frequencies (less than a few hundred hertz) do not enhance nonlinearity. An effectively lower electric field caused by ion conduction in the sample under the tip is a possible reason for the frequency-dependent characteristics of the enhanced nonlinearity for the applied voltage. Finally, electrical current flow behavior was investigated for nanodomains formed in a thin CLT single-crystal plate. When the nanodomains are relatively large, with diameters of about 100 nm, current flow is detected along the domain wall. However, when the nanodomains were about 40 nm or smaller in size, current flowed through the entire nanodomain. Schottky-like rectifying behavior was observed. A clear temperature dependence of the current is found, indicating that the conduction mechanism for nanodomains in CLT may involve thermally activated carrier hopping.

  20. Trait physical disgust is related to moral judgments outside of the purity domain.

    PubMed

    Chapman, Hanah A; Anderson, Adam K

    2014-04-01

    Although there is an emerging consensus that disgust plays a role in human morality, it remains unclear whether this role is limited to transgressions that contain elements of physical disgust (e.g., gory murders, sexual crimes), or whether disgust is also involved in "pure" forms of morality. To address this issue, we examined the relationship between individual differences in the tendency to experience disgust toward physical stimuli (i.e., trait physical disgust) and reactions to pure moral transgressions. Across two studies, individuals higher in trait physical disgust judged moral transgressions to be more wrong than did their low-disgust counterparts, and were also more likely to moralize violations of social convention. Controlling for gender, trait anxiety, trait anger, and social conservatism did not eliminate trait disgust effects. These results suggest that disgust's role in morality is not limited to issues of purity or bodily norms, and that disgust may play a role in setting the boundaries of the moral domain.

  1. Time-domain simulation of constitutive relations for nonlinear acoustics including relaxation for frequency power law attenuation media modeling

    NASA Astrophysics Data System (ADS)

    Jiménez, Noé; Camarena, Francisco; Redondo, Javier; Sánchez-Morcillo, Víctor; Konofagou, Elisa E.

    2015-10-01

    We report a numerical method for solving the constitutive relations of nonlinear acoustics, where multiple relaxation processes are included in a generalized formulation that allows the time-domain numerical solution by an explicit finite differences scheme. Thus, the proposed physical model overcomes the limitations of the one-way Khokhlov-Zabolotskaya-Kuznetsov (KZK) type models and, due to the Lagrangian density is implicitly included in the calculation, the proposed method also overcomes the limitations of Westervelt equation in complex configurations for medical ultrasound. In order to model frequency power law attenuation and dispersion, such as observed in biological media, the relaxation parameters are fitted to both exact frequency power law attenuation/dispersion media and also empirically measured attenuation of a variety of tissues that does not fit an exact power law. Finally, a computational technique based on artificial relaxation is included to correct the non-negligible numerical dispersion of the finite difference scheme, and, on the other hand, improve stability trough artificial attenuation when shock waves are present. This technique avoids the use of high-order finite-differences schemes leading to fast calculations. The present algorithm is especially suited for practical configuration where spatial discontinuities are present in the domain (e.g. axisymmetric domains or zero normal velocity boundary conditions in general). The accuracy of the method is discussed by comparing the proposed simulation solutions to one dimensional analytical and k-space numerical solutions.

  2. Expression and purification of human MHC class I-related chain molecule B-α1 domain.

    PubMed

    Wang, Shufen; Xiang, Zemin; Wang, Ya; Xu, Huanhuan; Zhang, Dengyang; Wang, Xuanjun; Sheng, Jun

    2016-07-01

    Major histocompatibility complex (MHC) class I-related chain A/B (MICA/B) is a type of stress-induced molecule that plays an important role in tumor surveillance. MICA/B shares a similar structure with MHC class I molecules, but MICA/B contains a closed cleft, not an open one, in its N-terminal alpha1 domain. The alpha 1 domain was believed to have no roles in antigen presentation, because the closed cleft provides limited space for binding with known molecules, and the cleft of MICA/B have been reported no known functions. To study the possible function of the cleft located in human MICA/B's alpha 1 domain, we attempted to express the human MICB-α1 (hMICB-α1) domain allele protein, which is approximately 20.5 kDa, by utilizing an Escherichia coli (E. coli) secretory pathway. Protein expression was accomplished through the phosphate-limited inducible promoter. After purification using ammonium sulfate precipitation, phenyl hydrophobic Sepharose, SP Sepharose and HisTrap affinity Sepharose, recombinant human MICB-α1 (rhMICB-α1) was obtained with 94.3% purity. The binding capacity of rhMICB-α1 with natural killer group 2, member D (NKG2D) was evaluated in vitro. The results demonstrated that rhMICB-α1 can be prepared through the E. coli secretory pathway. Purified rhMICB-α1 protein was able to functionally bind with NKG2D. This method can be further used to obtain functionally active rhMICB-α1 protein, which can served as the basis for further studies of the possible function of the MICB cleft. PMID:27036081

  3. College Students' Storytelling of Ethnicity-Related Events in the Academic Domain

    ERIC Educational Resources Information Center

    Syed, Moin

    2012-01-01

    The purpose of the present study was to examine storytelling of ethnicity-related events among college-going, emerging adults. A total of 280 ethnically diverse participants recounted a memory about a time in which they told a previously reported, ethnicity-related story to others. Analysis centered on the function of the telling and on to whom…

  4. Domain-Specific Expertise of Chemistry Teachers on Context-Based Education about Macro-Micro Thinking in Structure-Property Relations

    ERIC Educational Resources Information Center

    Dolfing, Ria; Bulte, Astrid M. W.; Pilot, Albert; Vermunt, Jan D.

    2012-01-01

    This study aims to determine and describe the new domain-specific expertise of experienced chemistry teachers in teaching an innovative context-based unit about macro-micro thinking in structure-property relations. The construct of "teachers' domain-specific expertise" was used to analyse the new repertoire chemistry teachers need to acquire to…

  5. Using Conjoined Rigid Body/Torsion Angle Simulated Annealing to Determine the Relative Orientation of Covalently Linked Protein Domains from Dipolar Couplings

    NASA Astrophysics Data System (ADS)

    Clore, G. Marius; Bewley, Carole A.

    2002-02-01

    A simple and robust method for determining the relative orientations of covalently linked protein domains using conjoined rigid body/torsion angle dynamics simulated annealing on the basis of residual dipolar couplings is presented. In this approach each domain is treated as a rigid body and the relevant degrees of conformational freedom are restricted to the backbone torsion angles (φ, ψ) of the linker between the domains. By this means translational information afforded by the presence of an intact linker is preserved. We illustrate this approach using the domain-swapped dimer of the HIV-inactivating protein cyanovirin-N as an example.

  6. Evolution of paired domains: isolation and sequencing of jellyfish and hydra Pax genes related to Pax-5 and Pax-6.

    PubMed

    Sun, H; Rodin, A; Zhou, Y; Dickinson, D P; Harper, D E; Hewett-Emmett, D; Li, W H

    1997-05-13

    Pax proteins are a family of transcription factors with a highly conserved paired domain; many members also contain a paired-type homeodomain and/or an octapeptide. Nine mammalian Pax genes are known and classified into four subgroups: Pax-1/9, Pax-2/5/8, Pax-3/7, and Pax-4/6. Most of these genes are involved in nervous system development. In particular, Pax-6 is a key regulator that controls eye development in vertebrates and Drosophila. Although the Pax-4/6 subgroup seems to be more closely related to Pax-2/5/8 than to Pax-3/7 or Pax-1/9, its evolutionary origin is unknown. We therefore searched for a Pax-6 homolog and related genes in Cnidaria, which is the lowest phylum of animals that possess a nervous system and eyes. A sea nettle (a jellyfish) genomic library was constructed and two pax genes (Pax-A and -B) were isolated and partially sequenced. Surprisingly, unlike most known Pax genes, the paired box in these two genes contains no intron. In addition, the complete cDNA sequences of hydra Pax-A and -B were obtained. Hydra Pax-B contains both the homeodomain and the octapeptide, whereas hydra Pax-A contains neither. DNA binding assays showed that sea nettle Pax-A and -B and hydra Pax-A paired domains bound to a Pax-5/6 site and a Pax-5 site, although hydra Pax-B paired domain bound neither. An alignment of all available paired domain sequences revealed two highly conserved regions, which cover the DNA binding contact positions. Phylogenetic analysis showed that Pax-A and especially Pax-B were more closely related to Pax-2/5/8 and Pax-4/6 than to Pax-1/9 or Pax-3/7 and that the Pax genes can be classified into two supergroups: Pax-A/Pax-B/Pax-2/5/8/4/6 and Pax-1/9/3/7. From this analysis and the gene structure, we propose that modern Pax-4/6 and Pax-2/5/8 genes evolved from an ancestral gene similar to cnidarian Pax-B, having both the homeodomain and the octapeptide.

  7. Working memory and language: skill-specific or domain-general relations to mathematics?

    PubMed

    Purpura, David J; Ganley, Colleen M

    2014-06-01

    Children's early mathematics skills develop in a cumulative fashion; foundational skills form a basis for the acquisition of later skills. However, non-mathematical factors such as working memory and language skills have also been linked to mathematical development at a broad level. Unfortunately, little research has been conducted to evaluate the specific relations of these two non-mathematical factors to individual aspects of early mathematics. Thus, the focus of this study was to determine whether working memory and language were related to only individual aspects of early mathematics or related to many components of early mathematics skills. A total of 199 4- to 6-year-old preschool and kindergarten children were assessed on a battery of early mathematics tasks as well as measures of working memory and language. Results indicated that working memory has a specific relation to only a few-but critically important-early mathematics skills and language has a broad relation to nearly all early mathematics skills. PMID:24549230

  8. Working memory and language: skill-specific or domain-general relations to mathematics?

    PubMed

    Purpura, David J; Ganley, Colleen M

    2014-06-01

    Children's early mathematics skills develop in a cumulative fashion; foundational skills form a basis for the acquisition of later skills. However, non-mathematical factors such as working memory and language skills have also been linked to mathematical development at a broad level. Unfortunately, little research has been conducted to evaluate the specific relations of these two non-mathematical factors to individual aspects of early mathematics. Thus, the focus of this study was to determine whether working memory and language were related to only individual aspects of early mathematics or related to many components of early mathematics skills. A total of 199 4- to 6-year-old preschool and kindergarten children were assessed on a battery of early mathematics tasks as well as measures of working memory and language. Results indicated that working memory has a specific relation to only a few-but critically important-early mathematics skills and language has a broad relation to nearly all early mathematics skills.

  9. Academic Self-Concept and Emotion Relations: Domain Specificity and Age Effects

    ERIC Educational Resources Information Center

    Goetz, Thomas; Cronjaeger, Hanna; Frenzel, Anne C.; Ludtke, Oliver; Hall, Nathan C.

    2010-01-01

    The present study investigated the relations between academic self-concepts and the emotions of enjoyment, pride, anxiety, anger, and boredom as experienced in mathematics, physics, German, and English classes (N=1710; grades 8 and 11). In line with our hypotheses derived from appraisal-based emotion theories and self-efficacy research,…

  10. Quality of Parental Homework Involvement: Predictors and Reciprocal Relations with Academic Functioning in the Reading Domain

    ERIC Educational Resources Information Center

    Dumont, Hanna; Trautwein, Ulrich; Nagy, Gabriel; Nagengast, Benjamin

    2014-01-01

    This study examined predictors of the quality of parental homework involvement and reciprocal relations between the quality of parental homework involvement and students' reading achievement and academic functioning in a reading-intensive subject (German). Data from 2,830 students in nonacademic tracks and their parents who were surveyed in both…

  11. What Is Learned when Concept Learning Fails?--A Theory of Restricted-Domain Relational Learning

    ERIC Educational Resources Information Center

    Wright, Anthony A.; Lickteig, Mark T.

    2010-01-01

    Two matching-to-sample (MTS) and four same/different (S/D) experiments employed tests to distinguish between item-specific learning and relational learning. One MTS experiment showed item-specific learning when concept learning failed (i.e., no novel-stimulus transfer). Another MTS experiment showed item-specific learning when pigeons'…

  12. Structural and functional characterization of the CAP domain of pathogen-related yeast 1 (Pry1) protein

    NASA Astrophysics Data System (ADS)

    Darwiche, Rabih; Kelleher, Alan; Hudspeth, Elissa M.; Schneiter, Roger; Asojo, Oluwatoyin A.

    2016-06-01

    The production, crystal structure, and functional characterization of the C-terminal cysteine-rich secretory protein/antigen 5/pathogenesis related-1 (CAP) domain of pathogen-related yeast protein-1 (Pry1) from Saccharomyces cerevisiae is presented. The CAP domain of Pry1 (Pry1CAP) is functional in vivo as its expression restores cholesterol export to yeast mutants lacking endogenous Pry1 and Pry2. Recombinant Pry1CAP forms dimers in solution, is sufficient for in vitro cholesterol binding, and has comparable binding properties as full-length Pry1. Two crystal structures of Pry1CAP are reported, one with Mg2+ coordinated to the conserved CAP tetrad (His208, Glu215, Glu233 and His250) in spacegroup I41 and the other without divalent cations in spacegroup P6122. The latter structure contains four 1,4-dioxane molecules from the crystallization solution, one of which sits in the cholesterol binding site. Both structures reveal that the divalent cation and cholesterol binding sites are connected upon dimerization, providing a structural basis for the observed Mg2+-dependent sterol binding by Pry1.

  13. Structural and functional characterization of the CAP domain of pathogen-related yeast 1 (Pry1) protein

    PubMed Central

    Darwiche, Rabih; Kelleher, Alan; Hudspeth, Elissa M.; Schneiter, Roger; Asojo, Oluwatoyin A.

    2016-01-01

    The production, crystal structure, and functional characterization of the C-terminal cysteine-rich secretory protein/antigen 5/pathogenesis related-1 (CAP) domain of pathogen-related yeast protein-1 (Pry1) from Saccharomyces cerevisiae is presented. The CAP domain of Pry1 (Pry1CAP) is functional in vivo as its expression restores cholesterol export to yeast mutants lacking endogenous Pry1 and Pry2. Recombinant Pry1CAP forms dimers in solution, is sufficient for in vitro cholesterol binding, and has comparable binding properties as full-length Pry1. Two crystal structures of Pry1CAP are reported, one with Mg2+ coordinated to the conserved CAP tetrad (His208, Glu215, Glu233 and His250) in spacegroup I41 and the other without divalent cations in spacegroup P6122. The latter structure contains four 1,4-dioxane molecules from the crystallization solution, one of which sits in the cholesterol binding site. Both structures reveal that the divalent cation and cholesterol binding sites are connected upon dimerization, providing a structural basis for the observed Mg2+-dependent sterol binding by Pry1. PMID:27344972

  14. Student Agency: an Analysis of Students' Networked Relations Across the Informal and Formal Learning Domains

    NASA Astrophysics Data System (ADS)

    Rappa, Natasha Anne; Tang, Kok-Sing

    2016-05-01

    Agency is a construct facilitating our examination of when and how young people extend their own learning across contexts. However, little is known about the role played by adolescent learners' sense of agency. This paper reports two cases of students' agentively employing and developing science literacy practices—one in Singapore and the other in the USA. The paper illustrates how these two adolescent learners in different ways creatively accessed, navigated and integrated in-school and out-of-school discourses to support and nurture their learning of physics. Data were gleaned from students' work and interviews with students participating in a physics curricular programme in which they made linkages between their chosen out-of-school texts and several physics concepts learnt in school. The students' agentive moves were identified by means of situational mapping, which involved a relational analysis of the students' chosen artefacts and discourses across time and space. This relational analysis enabled us to address questions of student agency—how it can be effected, realised, construed and examined. It highlights possible ways to intervene in these networked relations to facilitate adolescents' agentive moves in their learning endeavours.

  15. Structure of the catalytic domain of the human mitochondrial Lon protease: proposed relation of oligomer formation and activity.

    PubMed

    García-Nafría, Javier; Ondrovicová, Gabriela; Blagova, Elena; Levdikov, Vladimir M; Bauer, Jacob A; Suzuki, Carolyn K; Kutejová, Eva; Wilkinson, Anthony J; Wilson, Keith S

    2010-05-01

    ATP-dependent proteases are crucial for cellular homeostasis. By degrading short-lived regulatory proteins, they play an important role in the control of many cellular pathways and, through the degradation of abnormally misfolded proteins, protect the cell from a buildup of aggregates. Disruption or disregulation of mammalian mitochondrial Lon protease leads to severe changes in the cell, linked with carcinogenesis, apoptosis, and necrosis. Here we present the structure of the proteolytic domain of human mitochondrial Lon at 2 A resolution. The fold resembles those of the three previously determined Lon proteolytic domains from Escherichia coli, Methanococcus jannaschii, and Archaeoglobus fulgidus. There are six protomers in the asymmetric unit, four arranged as two dimers. The intersubunit interactions within the two dimers are similar to those between adjacent subunits of the hexameric ring of E. coli Lon, suggesting that the human Lon proteolytic domain also forms hexamers. The active site contains a 3(10) helix attached to the N-terminal end of alpha-helix 2, which leads to the insertion of Asp852 into the active site, as seen in M. jannaschii. Structural considerations make it likely that this conformation is proteolytically inactive. When comparing the intersubunit interactions of human with those of E. coli Lon taken with biochemical data leads us to propose a mechanism relating the formation of Lon oligomers with a conformational shift in the active site region coupled to a movement of a loop in the oligomer interface, converting the proteolytically inactive form seen here to the active one in the E. coli hexamer.

  16. Structure of the catalytic domain of the human mitochondrial Lon protease: Proposed relation of oligomer formation and activity

    PubMed Central

    García-Nafría, Javier; Ondrovičová, Gabriela; Blagova, Elena; Levdikov, Vladimir M; Bauer, Jacob A; Suzuki, Carolyn K; Kutejová, Eva; Wilkinson, Anthony J; Wilson, Keith S

    2010-01-01

    ATP-dependent proteases are crucial for cellular homeostasis. By degrading short-lived regulatory proteins, they play an important role in the control of many cellular pathways and, through the degradation of abnormally misfolded proteins, protect the cell from a buildup of aggregates. Disruption or disregulation of mammalian mitochondrial Lon protease leads to severe changes in the cell, linked with carcinogenesis, apoptosis, and necrosis. Here we present the structure of the proteolytic domain of human mitochondrial Lon at 2 Å resolution. The fold resembles those of the three previously determined Lon proteolytic domains from Escherichia coli, Methanococcus jannaschii, and Archaeoglobus fulgidus. There are six protomers in the asymmetric unit, four arranged as two dimers. The intersubunit interactions within the two dimers are similar to those between adjacent subunits of the hexameric ring of E. coli Lon, suggesting that the human Lon proteolytic domain also forms hexamers. The active site contains a 310 helix attached to the N-terminal end of α-helix 2, which leads to the insertion of Asp852 into the active site, as seen in M. jannaschii. Structural considerations make it likely that this conformation is proteolytically inactive. When comparing the intersubunit interactions of human with those of E. coli Lon taken with biochemical data leads us to propose a mechanism relating the formation of Lon oligomers with a conformational shift in the active site region coupled to a movement of a loop in the oligomer interface, converting the proteolytically inactive form seen here to the active one in the E. coli hexamer. PMID:20222013

  17. Assessing the co-occurrence of intimate partner violence domains across the life-course: relating typologies to mental health

    PubMed Central

    Armour, Cherie; Sleath, Emma

    2014-01-01

    Background The inter-generational transmission of violence (ITV) hypothesis and polyvictimisation have been studied extensively. The extant evidence suggests that individuals from violent families are at increased risk of subsequent intimate partner violence (IPV) and that a proportion of individuals experience victimisation across multiple rather than single IPV domains. Both ITV and polyvictimisation are shown to increase the risk of psychiatric morbidity, alcohol use, and anger expression. Objective The current study aimed to 1) ascertain if underlying typologies of victimisation across the life-course and over multiple victimisation domains were present and 2) ascertain if groupings differed on mean scores of posttraumatic stress disorder (PTSD), depression, alcohol use, and anger expression. Method University students (N=318) were queried in relation to victimisation experiences and psychological well-being. Responses across multiple domains of IPV spanning the life-course were used in a latent profile analysis. ANOVA was subsequently used to determine if profiles differed in their mean scores on PTSD, depression, alcohol use, and anger expression. Results Three distinct profiles were identified; one of which comprised individuals who experienced “life-course polyvictimisation,” another showing individuals who experienced “witnessing parental victimisation,” and one which experienced “psychological victimisation only.” Life-course polyvictims scored the highest across most assessed measures. Conclusion Witnessing severe physical aggression and injury in parental relationships as a child has an interesting impact on the ITV into adolescence and adulthood. Life-course polyvictims are shown to experience increased levels of psychiatric morbidity and issues with alcohol misuse and anger expression. PMID:25279106

  18. GNBP domain of Anopheles darlingi: are polymorphic inversions and gene variation related to adaptive evolution?

    PubMed

    Bridi, L C; Rafael, M S

    2016-02-01

    Anopheles darlingi is the main malaria vector in humans in South America. In the Amazon basin, it lives along the banks of rivers and lakes, which responds to the annual hydrological cycle (dry season and rainy season). In these breeding sites, the larvae of this mosquito feed on decomposing organic and microorganisms, which can be pathogenic and trigger the activation of innate immune system pathways, such as proteins Gram-negative binding protein (GNBP). Such environmental changes affect the occurrence of polymorphic inversions especially at the heterozygote frequency, which confer adaptative advantage compared to homozygous inversions. We mapped the GNBP probe to the An. darlingi 2Rd inversion by fluorescent in situ hybridization (FISH), which was a good indicator of the GNBP immune response related to the chromosomal polymorphic inversions and adaptative evolution. To better understand the evolutionary relations and time of divergence of the GNBP of An. darlingi, we compared it with nine other mosquito GNBPs. The results of the phylogenetic analysis of the GNBP sequence between the species of mosquitoes demonstrated three clades. Clade I and II included the GNBPB5 sequence, and clade III the sequence of GNBPB1. Most of these sequences of GNBP analyzed were homologous with that of subfamily B, including that of An. gambiae (87 %), therefore suggesting that GNBP of An. darling belongs to subfamily B. This work helps us understand the role of inversion polymorphism in evolution of An. darlingi.

  19. Typhoon Strength, Related Precipitation, and Sea Surface Temperatures in the Southeastern Part of the NEESPI domain

    NASA Astrophysics Data System (ADS)

    Groisman, P. Y.; Knight, R. W.; Reynolds, R. W.; Bulygina, O. N.; Zhai, P.; Karl, T. R.

    2006-12-01

    Model simulations using CO2-induced sea surface temperature increases indicate that TC wind speeds and related daily precipitation may increase. We investigated changes in the TC-related rainfall distributions as a function of TC strength at landfall and impact of SST ahead of TCs on the TC strength for several preferred tropical cyclone regions. Our findings were that a warmer climate and (projected with it) SST increases over the tropical North Atlantic and Pacific Oceans will likely be accompanied by more frequent strong landfalling hurricanes over the U.S. and China coasts. The fraction of strong hurricanes that make landfall on these coasts is positively correlated with daily SSTs in the path of the TCs. But, there were no landfalling strong hurricanes at, or above Category 3 in the Saffir-Simpson Hurricane Scale (strong to catastrophic hurricanes) when the SST was below the threshold of 28°C, which is likely a primary reason of their absence at the Russian Far East coast during the past fifty years. However, during the past 20 years there have already been strong landfalling typhoons north of Shanghai (with SST = 28.9°C) and several tropical storms that hit China north of 40°N and/or Russia with SST ahead of the storm tracks well above 28.5°C. With the ongoing warming (including the SST increases in the western part of the Northern Pacific by 0.8°C 100yr-1 during the typhoon season) these situations may become more frequent. Therefore, we focus on the southeastern edge of the NEESPI region (Russian Far East, northern China, Korea, and northern Japan) to assess the relationships that control the TC activity changes with the SST increase and to trace the above mentioned threshold shift northward during the typhoon season.

  20. Domain-related differentiation of working memory in the Japanese macaque (Macaca fuscata) frontal cortex: a positron emission tomography study.

    PubMed

    Kojima, T; Onoe, H; Hikosaka, K; Tsutsui, K; Tsukada, H; Watanabe, M

    2007-04-01

    The lateral prefrontal cortex (LPFC) is important for working memory (WM) task performance. Neuropsychological and neurophysiological studies in monkeys suggest that the lateral prefrontal cortex is functionally segregated based on the working memory domain (spatial vs. non-spatial). However, this is not supported by most human neuroimaging studies, and the discrepancy might be due to differences in methods and/or species (monkey neuropsychology/physiology vs. human neuroimaging). We used positron emission topography to examine the functional segregation of the lateral prefrontal cortex of Japanese macaques (Macaca fuscata) that showed near 100% accuracy on spatial and non-spatial working memory tasks. Compared with activity during the non-working memory control tasks, the dorsolateral prefrontal cortex (DLPFC) was more active during the non-spatial, but not during the spatial, working memory task, although a muscimol microinjection into the dorsolateral prefrontal cortex significantly impaired the performance of both working memory tasks. A direct comparison of the brain activity between the two working memory tasks revealed no differences within the lateral prefrontal cortex, whereas the premotor area was more active during the spatial working memory task. Comparing the delay-specific activity, which did not include task-associated stimulus/response-related activity, revealed more spatial working memory-related activity in the posterior parietal and premotor areas, and more non-spatial working memory-related activity in the dorsolateral prefrontal cortex and hippocampus. These results suggest that working memory in the monkey brain is segregated based on domain, not within the lateral prefrontal cortex but rather between the posterior parietal-premotor areas and the dorsolateral prefrontal-hippocampus areas.

  1. Development of the serotonergic cells in murine raphe nuclei and their relations with rhombomeric domains.

    PubMed

    Alonso, Antonia; Merchán, Paloma; Sandoval, Juan E; Sánchez-Arrones, Luisa; Garcia-Cazorla, Angels; Artuch, Rafael; Ferrán, José L; Martínez-de-la-Torre, Margaret; Puelles, Luis

    2013-09-01

    The raphe nuclei represent the origin of central serotonergic projections. The literature distinguishes seven nuclei grouped into rostral and caudal clusters relative to the pons. The boundaries of these nuclei have not been defined precisely enough, particularly with regard to developmental units, notably hindbrain rhombomeres. We hold that a developmental point of view considering rhombomeres may explain observed differences in connectivity and function. There are twelve rhombomeres characterized by particular genetic profiles, and each develops between one and four distinct serotonergic populations. We have studied the distribution of the conventional seven raphe nuclei among these twelve units. To this aim, we correlated 5-HT-immunoreacted neurons with rhombomeric boundary landmarks in sagittal mouse brain sections at different developmental stages. Furthermore, we performed a partial genoarchitectonic analysis of the developing raphe nuclei, mapping all known serotonergic differentiation markers, and compared these results, jointly with others found in the literature, with our map of serotonin-containing populations, in order to examine regional variations in correspondence. Examples of regionally selective gene patterns were identified. As a result, we produced a rhombomeric classification of some 45 serotonergic populations, and suggested a corresponding modified terminology. Only a minor rostral part of the dorsal raphe nucleus lies in the midbrain. Some serotonergic neurons were found in rhombomere 4, contrary to the conventional assumption that it lacks such neurons. We expect that our reclassification of raphe nuclei may be useful for causal analysis of their differential molecular specification, as well as for studies of differential connectivity and function.

  2. Domain-general mediators of the relation between kindergarten number sense and first-grade mathematics achievement.

    PubMed

    Hassinger-Das, Brenna; Jordan, Nancy C; Glutting, Joseph; Irwin, Casey; Dyson, Nancy

    2014-02-01

    Domain-general skills that mediate the relation between kindergarten number sense and first-grade mathematics skills were investigated. Participants were 107 children who displayed low number sense in the fall of kindergarten. Controlling for background variables, multiple regression analyses showed that both attention problems and executive functioning were unique predictors of mathematics outcomes. Attention problems were more important for predicting first-grade calculation performance, whereas executive functioning was more important for predicting first-grade performance on applied problems. Moreover, both executive functioning and attention problems were unique partial mediators of the relationship between kindergarten and first-grade mathematics skills. The results provide empirical support for developing interventions that target executive functioning and attention problems in addition to instruction in number skills for kindergartners with initial low number sense. PMID:24237789

  3. Domain-general mediators of the relation between kindergarten number sense and first-grade mathematics achievement.

    PubMed

    Hassinger-Das, Brenna; Jordan, Nancy C; Glutting, Joseph; Irwin, Casey; Dyson, Nancy

    2014-02-01

    Domain-general skills that mediate the relation between kindergarten number sense and first-grade mathematics skills were investigated. Participants were 107 children who displayed low number sense in the fall of kindergarten. Controlling for background variables, multiple regression analyses showed that both attention problems and executive functioning were unique predictors of mathematics outcomes. Attention problems were more important for predicting first-grade calculation performance, whereas executive functioning was more important for predicting first-grade performance on applied problems. Moreover, both executive functioning and attention problems were unique partial mediators of the relationship between kindergarten and first-grade mathematics skills. The results provide empirical support for developing interventions that target executive functioning and attention problems in addition to instruction in number skills for kindergartners with initial low number sense.

  4. A highly conserved family of domains related to the DNA-glycosylase fold helps predict multiple novel pathways for RNA modifications

    PubMed Central

    Burroughs, A Maxwell; Aravind, L

    2014-01-01

    A protein family including mammalian NEMF, Drosophila caliban, yeast Tae2, and bacterial FpbA-like proteins was first defined over a decade ago and found to be universally distributed across the three domains/superkingdoms of life. Since its initial characterization, this family of proteins has been tantalizingly linked to a wide range of biochemical functions. Tapping the enormous wealth of genome information that has accumulated since the initial characterization of these proteins, we perform a detailed computational analysis of the family, identifying multiple conserved domains. Domains identified include an enzymatic domain related to the formamidopyrimidine (Fpg), MutM, and Nei/EndoVIII family of DNA glycosylases, a novel, predicted RNA-binding domain, and a domain potentially mediating protein–protein interactions. Through this characterization, we predict that the DNA glycosylase-like domain catalytically operates on double-stranded RNA, as part of a hitherto unknown base modification mechanism that probably targets rRNAs. At least in archaea, and possibly eukaryotes, this pathway might additionally include the AMMECR1 family of proteins. The predicted RNA-binding domain associated with this family is also observed in distinct architectural contexts in other proteins across phylogenetically diverse prokaryotes. Here it is predicted to play a key role in a new pathway for tRNA 4-thiouridylation along with TusA-like sulfur transfer proteins. PMID:24646681

  5. Synthesis and Characterization of Liquid Chromatographic Columns Containing the Immobilized Ligand Binding Domain of the Estrogen Related Receptor α and Estrogen Related Receptor γ

    PubMed Central

    Sanghvi, M.; Moaddel, R.; Frazier, C.; Wainer, I.W.

    2010-01-01

    The ligand binding domains of the estrogen related receptors, ERRα and ERRγ were covalently immobilized onto the surface of an aminopropyl silica liquid chromatography stationary phase to create the ERRα-silica and ERRγ-silica columns and onto the surface of open tubular capillaries to create the ERRα-OT and ERRγ-OT columns. The ERR-silica and ERR-OT columns were characterized using frontal chromatographic techniques with diethylstibesterol and the binding affinities, Kd values, to the immobilized receptors were consistent with the values obtained by a radioligand binding assay. The ERRγ-silica column was also characterized using non-linear chromatographic techniques using a series of tamoxifen derivatives. The relative Kd values obtained for the derivatives were consistent with the relative ability of the compounds to inhibit the cellular proliferation of the human-derived T98G glioma cell line, expressed as IC50 values. The results indicate that the columns containing immobilized ERRα and ERRγ can be created and used to characterize the binding of compounds to the immobilized receptors and that the relative retention of compounds on these columns reflects the magnitude of their inhibitory activity. PMID:20542653

  6. (In)Consistent estimates of changes in relative precipitation in an European domain over the last 350 years

    NASA Astrophysics Data System (ADS)

    Bothe, Oliver; Wagner, Sebastian; Zorita, Eduardo

    2015-04-01

    estimates are generally not consistent among the different data sets. Only few common signals are evident. Even the relatively strong exogenous forcing history of the late 18th and early 19th century appears to have only small effects on the precipitation distributions. The reconstructions differ systematically from the long instrumental data in displaying much stronger variability compared to the observations over their common period. Distributional properties for both data sets show to some extent opposite evolutions. The reconstructions do not reliably represent the distributions in specific periods but rather reflect low-frequency changes in the mean plus a certain amount of noise. Moreover, also multi-model simulations do not agree on the changes over this period. The lack of consistent simulated relations under purely naturally forced and internal variability on multi-decadal time-scales therefore questions our ability to conclude on dynamical inferences about regional climate variability in the PMIP3 ensemble and, in turn, in climate simulations in general. The potentially opposite evolution of reconstructions and instrumental data for the chosen domain further hampers reconciling available information about past regional precipitation variability in England and Wales. However, we find some possibly surprising but encouraging agreement between the observed data and the regional simulation.

  7. Maize beta-glucosidase-aggregating factor is a polyspecific jacalin-related chimeric lectin, and its lectin domain is responsible for beta-glucosidase aggregation.

    PubMed

    Kittur, Farooqahmed S; Lalgondar, Mallikarjun; Yu, Hyun Young; Bevan, David R; Esen, Asim

    2007-03-01

    In certain maize genotypes, called "null," beta-glucosidase does not enter gels and therefore cannot be detected on zymograms after electrophoresis. Such genotypes were originally thought to be homozygous for a null allele at the glu1 gene and thus devoid of enzyme. We have shown that a beta-glucosidase-aggregating factor (BGAF) is responsible for the "null" phenotype. BGAF is a chimeric protein consisting of two distinct domains: the disease response or "dirigent" domain and the jacalin-related lectin (JRL) domain. First, it was not known whether the lectin domain in BGAF is functional. Second, it was not known which of the two BGAF domains is involved in beta-glucosidase binding and aggregation. To this end, we purified BGAF to homogeneity from a maize null inbred line called H95. The purified protein gave a single band on SDS-PAGE, and the native protein was a homodimer of 32-kDa monomers. Native and recombinant BGAF (produced in Escherichia coli) agglutinated rabbit erythrocytes, and various carbohydrates and glycoproteins inhibited their hemagglutination activity. Sugars did not have any effect on the binding of BGAF to the beta-glucosidase isozyme 1 (Glu1), and the BGAF-Glu1 complex could still bind lactosyl-agarose, indicating that the sugar-binding site of BGAF is distinct from the beta-glucosidase-binding site. Neither the dirigent nor the JRL domains alone (produced separately in E. coli) produced aggregates of Glu1 based on results from pull-down assays. However, gel shift and competitive binding assays indicated that the JRL domain binds beta-glucosidase without causing it to aggregate. These results with those from deletion mutagenesis and replacement of the JRL domain of a BGAF homolog from sorghum, which does not bind Glu1, with that from maize allowed us to conclude that the JRL domain of BGAF is responsible for its lectin and beta-glucosidase binding and aggregating activities. PMID:17210577

  8. Grading of Age-Related Macular Degeneration: Comparison between Color Fundus Photography, Fluorescein Angiography, and Spectral Domain Optical Coherence Tomography

    PubMed Central

    Mokwa, Nils F.; Keane, Pearse A.; Kirchhof, Bernd; Sadda, Srinivas R.

    2013-01-01

    Purpose. To compare color fundus photography (FP), fluorescein angiography (FA), and spectral domain optical coherence tomography (SDOCT) for the detection of age-related macular degeneration (AMD), choroidal neovascularisation (CNV), and CNV activity. Methods. FPs, FAs, and SDOCT volume scans from 120 eyes of 66 AMD and control patients were randomly collected. Control eyes were required to show no AMD, but other retinal pathology was allowed. The presence of drusen, pigmentary changes, CNV, and signs for CNV activity was independently analyzed for all imaging modalities. Results. AMD was diagnosed based on FP in 75 eyes. SDOCT and FA showed sensitivity (specificity) of 89% (76%) and 92% (82%), respectively. CNV was present on FA in 68 eyes. Sensitivity (specificity) was 78% (100%) for FP and 94% (98%) for SDOCT. CNV activity was detected by SDOCT or FA in 60 eyes with an agreement in 46 eyes. Sensitivity was 88% for SDOCT and 88% for FA. FP showed sensitivity of 38% and specificity of 98%. Conclusions. CNV lesions and activity may be missed by FP alone, but FP may help identifying drusen and pigmentary changes. SDOCT is highly sensitive for the detection of AMD, CNV, and CNV activity; however, it cannot fully replace FA. PMID:23762528

  9. Verticillium infection triggers VASCULAR-RELATED NAC DOMAIN7-dependent de novo xylem formation and enhances drought tolerance in Arabidopsis.

    PubMed

    Reusche, Michael; Thole, Karin; Janz, Dennis; Truskina, Jekaterina; Rindfleisch, Sören; Drübert, Christine; Polle, Andrea; Lipka, Volker; Teichmann, Thomas

    2012-09-01

    The soilborne fungal plant pathogen Verticillium longisporum invades the roots of its Brassicaceae hosts and proliferates in the plant vascular system. Typical aboveground symptoms of Verticillium infection on Brassica napus and Arabidopsis thaliana are stunted growth, vein clearing, and leaf chloroses. Here, we provide evidence that vein clearing is caused by pathogen-induced transdifferentiation of chloroplast-containing bundle sheath cells to functional xylem elements. In addition, our findings suggest that reinitiation of cambial activity and transdifferentiation of xylem parenchyma cells results in xylem hyperplasia within the vasculature of Arabidopsis leaves, hypocotyls, and roots. The observed de novo xylem formation correlates with Verticillium-induced expression of the VASCULAR-RELATED NAC DOMAIN (VND) transcription factor gene VND7. Transgenic Arabidopsis plants expressing the chimeric repressor VND7-SRDX under control of a Verticillium infection-responsive promoter exhibit reduced de novo xylem formation. Interestingly, infected Arabidopsis wild-type plants show higher drought stress tolerance compared with noninfected plants, whereas this effect is attenuated by suppression of VND7 activity. Together, our results suggest that V. longisporum triggers a tissue-specific developmental plant program that compensates for compromised water transport and enhances the water storage capacity of infected Brassicaceae host plants. In conclusion, we provide evidence that this natural plant-fungus pathosystem has conditionally mutualistic features.

  10. Enrichment and analysis of rice seedling ubiquitin-related proteins using four UBA domains (GST-qUBAs).

    PubMed

    Meng, Qingshi; Rao, Liqun; Pan, Yinghong

    2014-12-01

    Protein ubiquitination is a common posttranslational modification that often occurs on lysine residues. It controls the half-life, interaction and trafficking of intracellular proteins and is involved in different plant development stages and responses to environment stresses. Four Ubiquitin-Associated (UBA) domains were sequentially fused with Glutathione S-transferase (GST) tag (GST-qUBA) as bait protein in this study. A two-step affinity protocol was successfully developed and the identification of ubiquitinated proteins and their interaction proteins increased almost threefold compared to methods that directly identify ubiquitinated proteins from crude samples. A total of 170 ubiquitin-related proteins were identified in GST-qUBAs enriched samples taken from rice seedlings. There were 134 ubiquitinated proteins, 5 ubiquitin-activating enzymes (E1s), 5 ubiquitin-conjugating enzymes (E2s), 19 ubiquitin ligases (E3s) and 7 deubiquitinating enzymes (DUBs), which all contained various key factors that regulated a wide range of biological processes. Moreover, a series of novel ubiquitinated proteins and E3s were identified that had not been previously reported. This study investigated a high-efficiency method for identifying novel ubiquitinated proteins involved in biological processes and a primary mapping of the ubiquitylome during rice seedling development, which could extend our understanding of how ubiquitin modification regulates plant proteins, pathways and cellular processes.

  11. Structure-function relations in the NTPase domain of the antiviral tRNA ribotoxin Escherichia coli PrrC

    SciTech Connect

    Meineke, Birthe; Shuman, Stewart

    2012-06-05

    Breakage of tRNA by Escherichia coli anticodon nuclease PrrC (EcoPrrC) underlies a host antiviral response to phage T4 infection. Expression of EcoPrrC is cytocidal in yeast, signifying that PrrC ribotoxicity crosses phylogenetic domain boundaries. EcoPrrC consists of an N-terminal NTPase module that resembles ABC transporters and a C-terminal nuclease module that is sui generis. PrrC homologs are prevalent in many other bacteria. Here we report that Haemophilus influenzae PrrC is toxic in E. coli and yeast. To illuminate structure-activity relations, we conducted a new round of mutational analysis of EcoPrrC guided by primary structure conservation among toxic PrrC homologs. We indentify 17 candidate active site residues in the NTPase module that are essential for toxicity in yeast when EcoPrrC is expressed at high gene dosage. Their functions could be educed by integrating mutational data with the atomic structure of the transition-state complex of a homologous ABC protein.

  12. Synergy between loss of NF1 and overexpression of MYCN in neuroblastoma is mediated by the GAP-related domain

    PubMed Central

    He, Shuning; Mansour, Marc R; Zimmerman, Mark W; Ki, Dong Hyuk; Layden, Hillary M; Akahane, Koshi; Gjini, Evisa; de Groh, Eric D; Perez-Atayde, Antonio R; Zhu, Shizhen; Epstein, Jonathan A; Look, A Thomas

    2016-01-01

    Earlier reports showed that hyperplasia of sympathoadrenal cell precursors during embryogenesis in Nf1-deficient mice is independent of Nf1’s role in down-modulating RAS-MAPK signaling. We demonstrate in zebrafish that nf1 loss leads to aberrant activation of RAS signaling in MYCN-induced neuroblastomas that arise in these precursors, and that the GTPase-activating protein (GAP)-related domain (GRD) is sufficient to suppress the acceleration of neuroblastoma in nf1-deficient fish, but not the hypertrophy of sympathoadrenal cells in nf1 mutant embryos. Thus, even though neuroblastoma is a classical “developmental tumor”, NF1 relies on a very different mechanism to suppress malignant transformation than it does to modulate normal neural crest cell growth. We also show marked synergy in tumor cell killing between MEK inhibitors (trametinib) and retinoids (isotretinoin) in primary nf1a-/- zebrafish neuroblastomas. Thus, our model system has considerable translational potential for investigating new strategies to improve the treatment of very high-risk neuroblastomas with aberrant RAS-MAPK activation. DOI: http://dx.doi.org/10.7554/eLife.14713.001 PMID:27130733

  13. Verticillium infection triggers VASCULAR-RELATED NAC DOMAIN7-dependent de novo xylem formation and enhances drought tolerance in Arabidopsis.

    PubMed

    Reusche, Michael; Thole, Karin; Janz, Dennis; Truskina, Jekaterina; Rindfleisch, Sören; Drübert, Christine; Polle, Andrea; Lipka, Volker; Teichmann, Thomas

    2012-09-01

    The soilborne fungal plant pathogen Verticillium longisporum invades the roots of its Brassicaceae hosts and proliferates in the plant vascular system. Typical aboveground symptoms of Verticillium infection on Brassica napus and Arabidopsis thaliana are stunted growth, vein clearing, and leaf chloroses. Here, we provide evidence that vein clearing is caused by pathogen-induced transdifferentiation of chloroplast-containing bundle sheath cells to functional xylem elements. In addition, our findings suggest that reinitiation of cambial activity and transdifferentiation of xylem parenchyma cells results in xylem hyperplasia within the vasculature of Arabidopsis leaves, hypocotyls, and roots. The observed de novo xylem formation correlates with Verticillium-induced expression of the VASCULAR-RELATED NAC DOMAIN (VND) transcription factor gene VND7. Transgenic Arabidopsis plants expressing the chimeric repressor VND7-SRDX under control of a Verticillium infection-responsive promoter exhibit reduced de novo xylem formation. Interestingly, infected Arabidopsis wild-type plants show higher drought stress tolerance compared with noninfected plants, whereas this effect is attenuated by suppression of VND7 activity. Together, our results suggest that V. longisporum triggers a tissue-specific developmental plant program that compensates for compromised water transport and enhances the water storage capacity of infected Brassicaceae host plants. In conclusion, we provide evidence that this natural plant-fungus pathosystem has conditionally mutualistic features. PMID:23023171

  14. Incorporating significant amino acid pairs and protein domains to predict RNA splicing-related proteins with functional roles.

    PubMed

    Hsu, Justin Bo-Kai; Huang, Kai-Yao; Weng, Tzu-Ya; Huang, Chien-Hsun; Lee, Tzong-Yi

    2014-01-01

    Machinery of pre-mRNA splicing is carried out through the interaction of RNA sequence elements and a variety of RNA splicing-related proteins (SRPs) (e.g. spliceosome and splicing factors). Alternative splicing, which is an important post-transcriptional regulation in eukaryotes, gives rise to multiple mature mRNA isoforms, which encodes proteins with functional diversities. However, the regulation of RNA splicing is not yet fully elucidated, partly because SRPs have not yet been exhaustively identified and the experimental identification is labor-intensive. Therefore, we are motivated to design a new method for identifying SRPs with their functional roles in the regulation of RNA splicing. The experimentally verified SRPs were manually curated from research articles. According to the functional annotation of Splicing Related Gene Database, the collected SRPs were further categorized into four functional groups including small nuclear Ribonucleoprotein, Splicing Factor, Splicing Regulation Factor and Novel Spliceosome Protein. The composition of amino acid pairs indicates that there are remarkable differences among four functional groups of SRPs. Then, support vector machines (SVMs) were utilized to learn the predictive models for identifying SRPs as well as their functional roles. The cross-validation evaluation presents that the SVM models trained with significant amino acid pairs and functional domains could provide a better predictive performance. In addition, the independent testing demonstrates that the proposed method could accurately identify SRPs in mammals/plants as well as effectively distinguish between SRPs and RNA-binding proteins. This investigation provides a practical means to identifying potential SRPs and a perspective for exploring the regulation of RNA splicing.

  15. Models of the Joint Structure of Domain-Related and Global Distress: Implications for the Reconciliation of Quality of Life and Mental Health Perspectives

    ERIC Educational Resources Information Center

    Magee, William; St-Arnaud, Sebastien

    2012-01-01

    Research on subjective wellbeing includes studies of both domain-related and global distress. The mental health literature, though, focuses almost exclusively on global distress. This seems to be partly due to a common belief that psychological distress, and the moods that comprise distress, necessarily lack referential content. However, if that…

  16. Structure of the Novel C-terminal Domain of Vacuolar Protein Sorting 30/Autophagy-related Protein 6 and Its Specific Role in Autophagy*

    PubMed Central

    Noda, Nobuo N.; Kobayashi, Takafumi; Adachi, Wakana; Fujioka, Yuko; Ohsumi, Yoshinori; Inagaki, Fuyuhiko

    2012-01-01

    Vacuolar protein sorting 30 (Vps30)/autophagy-related protein 6 (Atg6) is a common component of two distinct phosphatidylinositol 3-kinase complexes. In complex I, Atg14 links Vps30 to Vps34 lipid kinase and exerts its specific role in autophagy, whereas in complex II, Vps38 links Vps30 to Vps34 and plays a crucial role in vacuolar protein sorting. However, the molecular role of Vps30 in each pathway remains unclear. Here, we report the crystal structure of the carboxyl-terminal domain of Vps30. The structure is a novel globular fold comprised of three β-sheet-α-helix repeats. Truncation analyses showed that the domain is dispensable for the construction of both complexes, but is specifically required for autophagy through the targeting of complex I to the pre-autophagosomal structure. Thus, the domain is named the β-α repeated, autophagy-specific (BARA) domain. On the other hand, the N-terminal region of Vps30 was shown to be specifically required for vacuolar protein sorting. These structural and functional investigations of Vps30 domains, which are also conserved in the mammalian ortholog, Beclin 1, will form the basis for studying the molecular functions of this protein family in various biological processes. PMID:22437838

  17. The Relation between Preschool Children's False-Belief Understanding and Domain-General Experimentation Skills

    ERIC Educational Resources Information Center

    Piekny, Jeanette; Grube, Dietmar; Maehler, Claudia

    2013-01-01

    The focus of the present study is on the developmental antecedents of domain-general experimentation skills. We hypothesized that false-belief understanding would predict the ability to distinguish a conclusive from an inconclusive experiment. We conducted a longitudinal study with two assessment points (t1 and t2) to investigate this hypothesis.…

  18. Sensing the Coherence of Biology in Contrast to Psychology: Young Children's Use of Causal Relations to Distinguish Two Foundational Domains

    ERIC Educational Resources Information Center

    Erickson, Jane E.; Keil, Frank C.; Lockhart, Kristi L.

    2010-01-01

    To what extent do children understand that biological processes fall into 1 coherent domain unified by distinct causal principles? In Experiments 1 and 2 (N = 125) kindergartners are given triads of biological and psychological processes and asked to identify which 2 members of the triad belong together. Results show that 5-year-olds correctly…

  19. The relative contribution of domains of quality of life to overall quality of life for different chronic diseases.

    PubMed

    Arnold, R; Ranchor, A V; Sanderman, R; Kempen, G I J M; Ormel, J; Suurmeijer, T P B M

    2004-06-01

    This study examined the contribution of the quality of life (QoL) domains physical, social and psychological functioning to the explanation of overall QoL. Various disorders may differentially affect QoL domains due to disease-specific factors and, consequently, the relationship between QoL domains and overall QoL may vary between diseases. We therefore studied this relationship for several diseases as well as the differential impact of these diseases on QoL. The present study had a cross-sectional design. We selected patients (aged 57 years and older) with one of the following eight chronic medical conditions: lung disorder, heart condition, hypertension, diabetes mellitus, back problems, rheumatoid arthritis, migraine, or dermatological disorders. The total group of respondents included 1457 patients and 1851 healthy subjects. Regression analyses showed that the domain of psychological functioning contributed to overall QoL for all disorders, whereas physical and social functioning contributed to overall QoL for some disorders. Differences were found between most patient groups and healthy subjects with respect to physical functioning; with respect to social and psychological functioning some groups differed from the healthy group. Explanations for the findings and implications for clinical practice are discussed. PMID:15233502

  20. The Relative Contribution of Health Status and Quality of Life Domains in Subjective Health in Old Age

    ERIC Educational Resources Information Center

    Prieto-Flores, Maria-Eugenia; Moreno-Jimenez, Antonio; Fernandez-Mayoralas, Gloria; Rojo-Perez, Fermina; Forjaz, Maria Joao

    2012-01-01

    To analyze the influence of different health status dimensions and quality of life (QoL) domains on older adults' subjective health, and to assess the role that residential satisfaction plays in these relationships. A QoL survey was conducted on a representative sample of the community-dwelling older adult population in Madrid province (Spain).…

  1. Functional diversification between two related Plasmodium falciparum merozoite invasion ligands is determined by changes in the cytoplasmic domain

    PubMed Central

    Dvorin, Jeffrey D.; Bei, Amy K.; Coleman, Bradley I.; Duraisingh, Manoj T.

    2013-01-01

    Summary The pathogenesis of Plasmodium falciparum depends on efficient invasion into host erythrocytes. Parasite ligands encoded by multi-gene families interact with erythrocyte receptors. P. falciparum reticulocyte binding protein homologues (PfRhs) are expressed at the apical surface of invasive merozoites and have divergent ectodomains that are postulated to bind different erythrocyte receptors. Variant expression of these paralogues results in the use of alternative invasion pathways. Two PfRh proteins, PfRh2a and PfRh2b, are identical for 2700 N-terminal amino acids and differ only in a C-terminal 500 amino acid region, which includes a unique ectodomain, transmembrane domain and cytoplasmic domain. Despite their similarity, PfRh2b is required for a well-defined invasion pathway while PfRh2a is not required or sufficient for this pathway. Mapping the genomic region encoding these proteins revealed a recombinogenic locus with PfRh2a and PfRh2b in a head-to-head orientation. We have generated viable PfRh2a/2b chimeric parasites to identify the regions required for alternative invasion pathway utilization. We find that the differential ability to use these pathways is conferred by the cytoplasmic domains of PfRh2a and PfRh2b, not the ectodomain or transmembrane regions. Our results highlight the importance of the cytoplasmic domain for functional diversification of a major adhesive ligand family in malaria parasites. PMID:20487292

  2. Effects of gender-related domain violations and sexual orientation on perceptions of male and female targets: an analogue study.

    PubMed

    Blashill, Aaron J; Powlishta, Kimberly K

    2012-10-01

    The current study examined factors that influenced heterosexual male and female raters' evaluations of male and female targets who were gay or heterosexual, and who displayed varying gender roles (i.e., typical vs. atypical) in multiple domains (i.e., activities, traits, and appearance). Participants were 305 undergraduate students from a private, midwestern Jesuit institution who read vignettes describing one of 24 target types and then rated the target on possession of positive and negative characteristics, psychological adjustment, and on measures reflecting the participants' anticipated behavior toward or comfort with the target. Results showed that gender atypical appearance and activity attributes (but not traits) were viewed more negatively than their gender typical counterparts. It was also found that male participants in particular viewed gay male targets as less desirable than lesbian and heterosexual male targets. These findings suggest a nuanced approach for understanding sexual prejudice, which incorporates a complex relationship among sex, gender, sexual orientation, and domain of gendered attributes. PMID:22722956

  3. Effects of gender-related domain violations and sexual orientation on perceptions of male and female targets: an analogue study.

    PubMed

    Blashill, Aaron J; Powlishta, Kimberly K

    2012-10-01

    The current study examined factors that influenced heterosexual male and female raters' evaluations of male and female targets who were gay or heterosexual, and who displayed varying gender roles (i.e., typical vs. atypical) in multiple domains (i.e., activities, traits, and appearance). Participants were 305 undergraduate students from a private, midwestern Jesuit institution who read vignettes describing one of 24 target types and then rated the target on possession of positive and negative characteristics, psychological adjustment, and on measures reflecting the participants' anticipated behavior toward or comfort with the target. Results showed that gender atypical appearance and activity attributes (but not traits) were viewed more negatively than their gender typical counterparts. It was also found that male participants in particular viewed gay male targets as less desirable than lesbian and heterosexual male targets. These findings suggest a nuanced approach for understanding sexual prejudice, which incorporates a complex relationship among sex, gender, sexual orientation, and domain of gendered attributes.

  4. Crystallization and preliminary X-ray analysis of Na-ASP-1, a multi-domain pathogenesis-related-1 protein from the human hookworm parasite Necator americanus

    SciTech Connect

    Asojo, Oluwatoyin A.; Loukas, Alex; Inan, Mehmet; Barent, Rick; Huang, Jicai; Plantz, Brad; Swanson, Amber; Gouthro, Mark; Meagher, Michael M.; Hotez, Peter J.

    2005-04-01

    In order to clarify the structural basis of the pathogenesis-related-1 domain, Na-ASP-1, the first multi-domain ASP from the human hookworm parasite N. americanus, has been crystallized. 2.2 Å resolution data have been collected from a crystal belonging to the monoclinic space group P2{sub 1}. Human hookworm infection is a major cause of anemia and malnutrition in the developing world. In an effort to control hookworm infection, the Human Hookworm Vaccine Initiative has identified candidate vaccine antigens from the infective larval stage (L3) of the parasite, including a family of pathogenesis-related-1 (PR-1) proteins known as the ancylostoma-secreted proteins (ASPs). The functions of the ASPs are unknown. In addition, it is unclear why some ASPs have one while others have multiple PR-1 domains. There are no known structures of a multi-domain ASP and in an effort to remedy this situation, recombinant Na-ASP-1 has been expressed, purified and crystallized. Na-ASP-1 is a 406-amino-acid multi-domain ASP from the prevalent human hookworm parasite Necator americanus. Useful X-ray data to 2.2 Å have been collected from a crystal that belongs to the monoclinic space group P2{sub 1} with unit-cell parameters a = 67.7, b = 74.27, c = 84.60 Å, β = 112.12°. An initial molecular-replacement solution has been obtained with one monomer in the asymmetric unit.

  5. Social anxiety disorder and quality of life: How fears of negative and positive evaluation relate to specific domains of life satisfaction.

    PubMed

    Dryman, M Taylor; Gardner, Shani; Weeks, Justin W; Heimberg, Richard G

    2016-03-01

    Individuals with social anxiety disorder (SAD) experience functional impairment in social, educational, and occupational arenas, contributing to poor quality of life. Previous research using the Quality of Life Inventory (QOLI) has identified four distinct domains of quality of life among individuals with SAD: Achievement, Personal Growth, Social Functioning, and Surroundings. The present study was designed to investigate how fear of negative evaluation (FNE) and fear of positive evaluation (FPE) relate to the four QOLI domains among individuals with SAD. We also examined the relationships of FNE and FPE to Satisfaction and Importance ratings on the QOLI. Individuals with SAD (N=129) completed a battery of questionnaires prior to initiating treatment. FNE and FPE showed distinct relationships with the four QOLI domains, even after controlling for demographic characteristics and comorbid depression. Both FNE and FPE were associated with ratings of Satisfaction with the QOLI domains, but neither was associated with ratings of Importance. Our findings highlight the differential impacts of FNE and FPE on SAD. Treatment implications are discussed.

  6. The relative role of the T-domain and flanking sequences for developmental control and transcriptional regulation in protein chimeras of Drosophila OMB and ORG-1.

    PubMed

    Porsch, Matthias; Sauer, Markus; Schulze, Sabine; Bahlo, Angela; Roth, Martin; Pflugfelder, Gert O

    2005-01-01

    optomotor-blind (omb) and optomotor-blind related-1 (org-1) encode T-domain DNA binding proteins in Drosophila. Members of this family of transcription factors play widely varying roles during early development and organogenesis in both vertebrates and invertebrates. Functional specificity differs in spite of similar DNA binding preferences of all family members. Using a series of domain swap chimeras, in which different parts of OMB and ORG-1 were mutually exchanged, we investigated the relevance of individual domains in vitro and in vivo. In cell culture transfection assays, ORG-1 was a strong transcriptional activator, whereas OMB appeared neutral. The main transcriptional activation function was identified in the C-terminal part of ORG-1. Also in vivo, OMB and ORG-1 showed qualitative differences when the proteins were ectopically expressed during development. Gain-of-function expression of OMB is known to counteract eye formation and resulted in the loss of the arista, whereas ORG-1 had little effect on eye development but caused antenna-to-leg transformations and shortened legs in the corresponding gain-of-function situations. The functional properties of OMB/ORG-1 chimeras in several developmental contexts was dominated by the origin of the C-terminal region, suggesting that the transcriptional activation potential can be one major determinant of developmental specificity. In late eye development, we observed, however, a strong influence of the T-domain on ommatidial differentiation. The specificity of chimeric omb/org-1transgenes, thus, depended on the cellular context in which they were expressed. This suggests that both transcriptional activation/repression properties as well as intrinsic DNA binding specificity can contribute to the functional characteristics of T-domain factors.

  7. Novel interactions of ankyrins-G at the costameres: The muscle-specific Obscurin/Titin-Binding-related Domain (OTBD) binds plectin and filamin C

    SciTech Connect

    Maiweilidan, Yimingjiang; Klauza, Izabela; Kordeli, Ekaterini

    2011-04-01

    Ankyrins, the adapters of the spectrin skeleton, are involved in local accumulation and stabilization of integral proteins to the appropriate membrane domains. In striated muscle, tissue-dependent alternative splicing generates unique Ank3 gene products (ankyrins-G); they share the Obscurin/Titin-Binding-related Domain (OTBD), a muscle-specific insert of the C-terminal domain which is highly conserved among ankyrin genes, and binds obscurin and titin to Ank1 gene products. We previously proposed that OTBD sequences constitute a novel domain of protein-protein interactions which confers ankyrins with specific cellular functions in muscle. Here we searched for muscle proteins binding to ankyrin-G OTBD by yeast two hybrid assay, and we found plectin and filamin C, two organizing elements of the cytoskeleton with essential roles in myogenesis, muscle cell cytoarchitecture, and muscle disease. The three proteins coimmunoprecipitate from skeletal muscle extracts and colocalize at costameres in adult muscle fibers. During in vitro myogenesis, muscle ankyrins-G are first expressed in postmitotic myocytes undergoing fusion to myotubes. In western blots of subcellular fractions from C2C12 cells, the majority of muscle ankyrins-G appear associated with membrane compartments. Occasional but not extensive co-localization at nascent costameres suggested that ankyrin-G interactions with plectin and filamin C are not involved in costamere assembly; they would rather reinforce stability and/or modulate molecular interactions in sarcolemma microdomains by establishing novel links between muscle-specific ankyrins-G and the two costameric dystrophin-associated glycoprotein and integrin-based protein complexes. These results report the first protein-protein interactions involving the ankyrin-G OTBD domain and support the hypothesis that OTBD sequences confer ankyrins with a gain of function in vertebrates, bringing further consolidation and resilience of the linkage between sarcomeres

  8. Using Common Spatial Distributions of Atoms to Relate Functionally Divergent Influenza Virus N10 and N11 Protein Structures to Functionally Characterized Neuraminidase Structures, Toxin Cell Entry Domains, and Non-Influenza Virus Cell Entry Domains

    PubMed Central

    Weininger, Arthur; Weininger, Susan

    2015-01-01

    The ability to identify the functional correlates of structural and sequence variation in proteins is a critical capability. We related structures of influenza A N10 and N11 proteins that have no established function to structures of proteins with known function by identifying spatially conserved atoms. We identified atoms with common distributed spatial occupancy in PDB structures of N10 protein, N11 protein, an influenza A neuraminidase, an influenza B neuraminidase, and a bacterial neuraminidase. By superposing these spatially conserved atoms, we aligned the structures and associated molecules. We report spatially and sequence invariant residues in the aligned structures. Spatially invariant residues in the N6 and influenza B neuraminidase active sites were found in previously unidentified spatially equivalent sites in the N10 and N11 proteins. We found the corresponding secondary and tertiary structures of the aligned proteins to be largely identical despite significant sequence divergence. We found structural precedent in known non-neuraminidase structures for residues exhibiting structural and sequence divergence in the aligned structures. In N10 protein, we identified staphylococcal enterotoxin I-like domains. In N11 protein, we identified hepatitis E E2S-like domains, SARS spike protein-like domains, and toxin components shared by alpha-bungarotoxin, staphylococcal enterotoxin I, anthrax lethal factor, clostridium botulinum neurotoxin, and clostridium tetanus toxin. The presence of active site components common to the N6, influenza B, and S. pneumoniae neuraminidases in the N10 and N11 proteins, combined with the absence of apparent neuraminidase function, suggests that the role of neuraminidases in H17N10 and H18N11 emerging influenza A viruses may have changed. The presentation of E2S-like, SARS spike protein-like, or toxin-like domains by the N10 and N11 proteins in these emerging viruses may indicate that H17N10 and H18N11 sialidase-facilitated cell

  9. Using common spatial distributions of atoms to relate functionally divergent influenza virus N10 and N11 protein structures to functionally characterized neuraminidase structures, toxin cell entry domains, and non-influenza virus cell entry domains.

    PubMed

    Weininger, Arthur; Weininger, Susan

    2015-01-01

    The ability to identify the functional correlates of structural and sequence variation in proteins is a critical capability. We related structures of influenza A N10 and N11 proteins that have no established function to structures of proteins with known function by identifying spatially conserved atoms. We identified atoms with common distributed spatial occupancy in PDB structures of N10 protein, N11 protein, an influenza A neuraminidase, an influenza B neuraminidase, and a bacterial neuraminidase. By superposing these spatially conserved atoms, we aligned the structures and associated molecules. We report spatially and sequence invariant residues in the aligned structures. Spatially invariant residues in the N6 and influenza B neuraminidase active sites were found in previously unidentified spatially equivalent sites in the N10 and N11 proteins. We found the corresponding secondary and tertiary structures of the aligned proteins to be largely identical despite significant sequence divergence. We found structural precedent in known non-neuraminidase structures for residues exhibiting structural and sequence divergence in the aligned structures. In N10 protein, we identified staphylococcal enterotoxin I-like domains. In N11 protein, we identified hepatitis E E2S-like domains, SARS spike protein-like domains, and toxin components shared by alpha-bungarotoxin, staphylococcal enterotoxin I, anthrax lethal factor, clostridium botulinum neurotoxin, and clostridium tetanus toxin. The presence of active site components common to the N6, influenza B, and S. pneumoniae neuraminidases in the N10 and N11 proteins, combined with the absence of apparent neuraminidase function, suggests that the role of neuraminidases in H17N10 and H18N11 emerging influenza A viruses may have changed. The presentation of E2S-like, SARS spike protein-like, or toxin-like domains by the N10 and N11 proteins in these emerging viruses may indicate that H17N10 and H18N11 sialidase-facilitated cell

  10. Domain Engineering

    NASA Astrophysics Data System (ADS)

    Bjørner, Dines

    Before software can be designed we must know its requirements. Before requirements can be expressed we must understand the domain. So it follows, from our dogma, that we must first establish precise descriptions of domains; then, from such descriptions, “derive” at least domain and interface requirements; and from those and machine requirements design the software, or, more generally, the computing systems.

  11. The pepper GNA-related lectin and PAN domain protein gene, CaGLP1, is required for plant cell death and defense signaling during bacterial infection.

    PubMed

    Kim, Nak Hyun; Lee, Dong Hyuk; Choi, Du Seok; Hwang, Byung Kook

    2015-12-01

    Carbohydrate-binding proteins, commonly referred to as lectins or agglutinins, function in defense responses to microbial pathogens. Pepper (Capsicum annuum) GNA-related lectin and PAN-domain protein gene CaGLP1 was isolated and functionally characterized from pepper leaves infected with Xanthomonas campestris pv. vesicatoria (Xcv). CaGLP1 contained an amine-terminus prokaryotic membrane lipoprotein lipid attachment site, a Galanthus nivalis agglutinin (GNA)-related lectin domain responsible for the recognition of high-mannose N-glycans, and a carboxyl-terminus PAN/apple domain. RNA gel blot and immunoblot analyses determined that CaGLP1 was strongly induced in pepper by compatible and incompatible Xcv infection. CaGLP1 protein localized primarily to the plasma membrane and exhibited mannose-binding specificity. CaGLP1-silenced pepper plants were more susceptible to compatible or incompatible Xcv infection compared with that of non-silenced control plants. CaGLP1 silencing in pepper leaves did not accumulate H2O2 and induce cell death during incompatible Xcv infection. Defense-related CaDEF1 (defensin) gene expression was significantly reduced in CaGLP1-silenced pepper plants. CaGLP1-overexpression in Arabidopsis thaliana enhanced resistance to Pseudomonas syringae pv. tomato. Defense-related AtPDF1.2 expression was elevated in CaGLP1-overexpression lines. Together, these results suggest that CaGLP1 is required for plant cell death and defense responses through the reactive oxygen species burst and downstream defense-related gene expression in response to bacterial pathogen challenge.

  12. Emotional Modulation of Conflict Processing in the Affective Domain: Evidence from Event-related Potentials and Event-related Spectral Perturbation Analysis.

    PubMed

    Ma, Jianling; Liu, Chang; Chen, Xu

    2016-01-01

    Previous studies have revealed the impact of emotion on conflict processing. The present study was conducted to investigate whether cognitive control in the affective domain is also affected by emotion. Emotional face-word and body-word Stroop tasks were explored and contrasted, and both behavioural and electrophysiological measures were recorded. Behavioural results showed that both tasks replicated previous robust interference effects. At the physiological level, the two tasks showed dissociable neural activity in the early attention and perception stages. It was also found that the face-word task evoked more pronounced N1 and P2 amplitudes than the body-word task. However, the two tasks evoked comparable N450 amplitudes. At later processing stages, positive slow potentials were modulated by target emotion and congruency. In addition, time-frequency analyses also revealed that the face-word task induced enhanced theta activity compared to the body-word task at both early and later stages of processing. The present findings provide support for the dual competition framework and suggest the dynamic modulation of emotion on cognitive control in the affective domain. PMID:27511609

  13. Emotional Modulation of Conflict Processing in the Affective Domain: Evidence from Event-related Potentials and Event-related Spectral Perturbation Analysis

    PubMed Central

    Ma, Jianling; Liu, Chang; Chen, Xu

    2016-01-01

    Previous studies have revealed the impact of emotion on conflict processing. The present study was conducted to investigate whether cognitive control in the affective domain is also affected by emotion. Emotional face-word and body-word Stroop tasks were explored and contrasted, and both behavioural and electrophysiological measures were recorded. Behavioural results showed that both tasks replicated previous robust interference effects. At the physiological level, the two tasks showed dissociable neural activity in the early attention and perception stages. It was also found that the face-word task evoked more pronounced N1 and P2 amplitudes than the body-word task. However, the two tasks evoked comparable N450 amplitudes. At later processing stages, positive slow potentials were modulated by target emotion and congruency. In addition, time-frequency analyses also revealed that the face-word task induced enhanced theta activity compared to the body-word task at both early and later stages of processing. The present findings provide support for the dual competition framework and suggest the dynamic modulation of emotion on cognitive control in the affective domain. PMID:27511609

  14. PASS2 database for the structure-based sequence alignment of distantly related SCOP domain superfamilies: update to version 5 and added features

    PubMed Central

    Gandhimathi, Arumugam; Ghosh, Pritha; Hariharaputran, Sridhar; Mathew, Oommen K.; Sowdhamini, R.

    2016-01-01

    Structure-based sequence alignment is an essential step in assessing and analysing the relationship of distantly related proteins. PASS2 is a database that records such alignments for protein domain superfamilies and has been constantly updated periodically. This update of the PASS2 version, named as PASS2.5, directly corresponds to the SCOPe 2.04 release. All SCOPe structural domains that share less than 40% sequence identity, as defined by the ASTRAL compendium of protein structures, are included. The current version includes 1977 superfamilies and has been assembled utilizing the structure-based sequence alignment protocol. Such an alignment is obtained initially through MATT, followed by a refinement through the COMPARER program. The JOY program has been used for structural annotations of such alignments. In this update, we have automated the protocol and focused on inclusion of new features such as mapping of GO terms, absolutely conserved residues among the domains in a superfamily and inclusion of PDBs, that are absent in SCOPe 2.04, using the HMM profiles from the alignments of the superfamily members and are provided as a separate list. We have also implemented a more user-friendly manner of data presentation and options for downloading more features. PASS2.5 version is available at http://caps.ncbs.res.in/pass2/. PMID:26553811

  15. Crystallization and preliminary X-ray analysis of Na-ASP-1, a multi-domain pathogenesis-related-1 protein from the human hookworm parasite Necator americanus

    PubMed Central

    Asojo, Oluwatoyin A.; Loukas, Alex; Inan, Mehmet; Barent, Rick; Huang, Jicai; Plantz, Brad; Swanson, Amber; Gouthro, Mark; Meagher, Michael M.; Hotez, Peter J.

    2005-01-01

    Human hookworm infection is a major cause of anemia and malnutrition in the developing world. In an effort to control hookworm infection, the Human Hookworm Vaccine Initiative has identified candidate vaccine antigens from the infective larval stage (L3) of the parasite, including a family of pathogenesis-related-1 (PR-1) proteins known as the ancylostoma-secreted proteins (ASPs). The functions of the ASPs are unknown. In addition, it is unclear why some ASPs have one while others have multiple PR-1 domains. There are no known structures of a multi-domain ASP and in an effort to remedy this situation, recombinant Na-ASP-1 has been expressed, purified and crystallized. Na-ASP-1 is a 406-amino-acid multi-domain ASP from the prevalent human hookworm parasite Necator americanus. Useful X-ray data to 2.2 Å have been collected from a crystal that belongs to the monoclinic space group P21 with unit-cell parameters a = 67.7, b = 74.27, c = 84.60 Å, β = 112.12°. An initial molecular-replacement solution has been obtained with one monomer in the asymmetric unit. PMID:16511050

  16. PASS2 database for the structure-based sequence alignment of distantly related SCOP domain superfamilies: update to version 5 and added features.

    PubMed

    Gandhimathi, Arumugam; Ghosh, Pritha; Hariharaputran, Sridhar; Mathew, Oommen K; Sowdhamini, R

    2016-01-01

    Structure-based sequence alignment is an essential step in assessing and analysing the relationship of distantly related proteins. PASS2 is a database that records such alignments for protein domain superfamilies and has been constantly updated periodically. This update of the PASS2 version, named as PASS2.5, directly corresponds to the SCOPe 2.04 release. All SCOPe structural domains that share less than 40% sequence identity, as defined by the ASTRAL compendium of protein structures, are included. The current version includes 1977 superfamilies and has been assembled utilizing the structure-based sequence alignment protocol. Such an alignment is obtained initially through MATT, followed by a refinement through the COMPARER program. The JOY program has been used for structural annotations of such alignments. In this update, we have automated the protocol and focused on inclusion of new features such as mapping of GO terms, absolutely conserved residues among the domains in a superfamily and inclusion of PDBs, that are absent in SCOPe 2.04, using the HMM profiles from the alignments of the superfamily members and are provided as a separate list. We have also implemented a more user-friendly manner of data presentation and options for downloading more features. PASS2.5 version is available at http://caps.ncbs.res.in/pass2/. PMID:26553811

  17. Relationship of work-family conflict with burnout and marital satisfaction: cross-domain or source attribution relations?

    PubMed Central

    Bagherzadeh, Razieh; Taghizadeh, Ziba; Mohammadi, Eesa; Kazemnejad, Anoshirvan; Pourreza, Abolghasem; Ebadi, Abbas

    2016-01-01

    Background: The present study was conducted to examine the relationship between two dimensions of work-family conflict (WFC) with marital satisfaction and burnout in a society in which few studies have been done about the consequences of WFC. Methods: A cross-sectional study was conducted in 2015. Surveys were distributed to 420 employed married women with various jobs living in Bushehr province, Iran. Data were collected using a questionnaire for demographic characteristic, the Netmeyer’s WFC questionnaire, Maslach Burnout Inventory: General Survey (MBI-GS), and Enrich maritalsatisfaction questionnaire. The data were analyzed using descriptive and inferential statistics. Results: There was a negatively significant association between work interference with family(WIF) and overall burnout as well as emotional exhaustion (P < .01). Family interference with work (FIW) was significantly associated with depersonalization (P < .01). The overall marital satisfaction and its subscales were significantly associated with WIF (P < .01) and FIW (P < .01 for overall marital satisfaction and P < .05 for its subscales). Conclusion: In terms of practical implication, to avoid creating disadvantages of WIF and FIW,facilitation in two domains of improving work and family conditions can be a useful means to prevent WFC and its consequences. PMID:27123434

  18. Rational and efficient site-directed mutagenesis of adenylation domain alters relative yields of luminmide derivatives in vivo.

    PubMed

    Bian, Xiaoying; Plaza, Alberto; Yan, Fu; Zhang, Youming; Müller, Rolf

    2015-07-01

    Cloning and engineering of natural product biosynthetic pathways followed by heterologous expression in a tractable host is a widely used approach for expression and genetic modification of microbial secondary metabolites. Herein, we employed ccdB counterselection combined with oligonucleotide-mediated recombineering to efficiently create point mutations in a complex nonribosomal peptide synthetase (NRPS) from Photorabdus luminescens directing the biosynthesis of luminmides. After in depth analysis of the luminmide production profile from the native NRPS, single and double point mutations were rationally constructed within the adenylation (A) domain from NRPS module 3 which turned out to have a broad substrate tolerance. Expression of mutated versions of the 15.6 kb NRPS gene plu3263 in E. coli led to alterations in luminmide production profiles and allowed to direct the biosynthesis towards certain derivatives. These results demonstrate the suitability of counterselection recombineering for site-directed mutagenesis of complex expression constructs, e.g., genes encoding NRPS biosynthetic pathways in multi-copy plasmids. PMID:25683597

  19. Xerostomia After Treatment for Oral and Oropharyngeal Cancer Using the University of Washington Saliva Domain and a Xerostomia-Related Quality-of-Life Scale

    SciTech Connect

    Rogers, Simon N.; Johnson, Ian A.; Lowe, Derek

    2010-05-01

    Purpose: The first aim of this study was to identify which clinical factors are associated with xerostomia in patients after treatment for oral and oropharyngeal squamous cell carcinoma, using the Xerostomia-Related Quality-of-Life Scale (XeQoLS) and the University of Washington Quality-of-Life Questionnaire Version 4 dry mouth item (UW-QOL v4). The second aim was to compare these two questionnaires and postulate a cutoff in the UW-QOL below which patients are doing sufficient badly to warrant further evaluation and support. Methods and Materials: In all, 371 patients alive and disease free treated between 1992 and 2005 were sent the survey, of whom 250 (67%) responded. Various clinical factors correlated with xerostomia, particularly adjuvant radiotherapy and Pstage. Results: In logistic regression analyses to predict three or more problems on the XeQoLS, only adjuvant radiotherapy (p < 0.001) was significant at the 5% level. There were significant (p < 0.001) correlations between the XeQoLS scores (total average and domain) with all the UW-QOL domain scores, the strongest with swallowing (-0.69), taste (-0.64), chewing (-0.64), mood (-0.60), and saliva (-0.59) domains. Patients scoring <70 (i.e., 0 or 30) on the UW-QOL could be used as a screening cutoff because it formed 1 in 5 of all patients (49/242) but accounted for half (299/566) of the significant problems generated by the XeQoLS. This also identified 13/21 patients with 10 or more problems. Conclusion: The UW-QOL saliva domain seems to be a suitable means of screening for dry mouth in head-and-neck clinics and could be used to trigger interventions.

  20. Catalytic domain of plasmid pAD1 relaxase TraX defines a group of relaxases related to restriction endonucleases

    PubMed Central

    Francia, María Victoria; Clewell, Don B.; de la Cruz, Fernando; Moncalián, Gabriel

    2013-01-01

    Plasmid pAD1 is a 60-kb conjugative element commonly found in clinical isolates of Enterococcus faecalis. The relaxase TraX and the primary origin of transfer oriT2 are located close to each other and have been shown to be essential for conjugation. The oriT2 site contains a large inverted repeat (where the nic site is located) adjacent to a series of short direct repeats. TraX does not show any of the typical relaxase sequence motifs but is the prototype of a unique family of relaxases (MOBC). The present study focuses on the genetic, biochemical, and structural analysis of TraX, whose 3D structure could be predicted by protein threading. The structure consists of two domains: (i) an N-terminal domain sharing the topology of the DNA binding domain of the MarR family of transcriptional regulators and (ii) a C-terminal catalytic domain related to the PD-(D/E)XK family of restriction endonucleases. Alignment of MOBC relaxase amino acid sequences pointed to several conserved polar amino acid residues (E28, D152, E170, E172, K176, R180, Y181, and Y203) that were mutated to alanine. Functional analysis of these mutants (in vivo DNA transfer and cleavage assays) revealed the importance of these residues for relaxase activity and suggests Y181 as a potential catalytic residue similarly to His-hydrophobe-His relaxases. We also show that TraX binds specifically to dsDNA containing the oriT2 direct repeat sequences, confirming their role in transfer specificity. The results provide insights into the catalytic mechanism of MOBC relaxases, which differs radically from that of His-hydrophobe-His relaxases. PMID:23904483

  1. Learning and Domain Adaptation

    NASA Astrophysics Data System (ADS)

    Mansour, Yishay

    Domain adaptation is a fundamental learning problem where one wishes to use labeled data from one or several source domains to learn a hypothesis performing well on a different, yet related, domain for which no labeled data is available. This generalization across domains is a very significant challenge for many machine learning applications and arises in a variety of natural settings, including NLP tasks (document classification, sentiment analysis, etc.), speech recognition (speakers and noise or environment adaptation) and face recognition (different lighting conditions, different population composition).

  2. Just how versatile are domains?

    PubMed Central

    2008-01-01

    Background Creating new protein domain arrangements is a frequent mechanism of evolutionary innovation. While some domains always form the same combinations, others form many different arrangements. This ability, which is often referred to as versatility or promiscuity of domains, its a random evolutionary model in which a domain's promiscuity is based on its relative frequency of domains. Results We show that there is a clear relationship across genomes between the promiscuity of a given domain and its frequency. However, the strength of this relationship differs for different domains. We thus redefine domain promiscuity by defining a new index, DV I ("domain versatility index"), which eliminates the effect of domain frequency. We explore links between a domain's versatility, when unlinked from abundance, and its biological properties. Conclusion Our results indicate that domains occurring as single domain proteins and domains appearing frequently at protein termini have a higher DV I. This is consistent with previous observations that the evolution of domain re-arrangements is primarily driven by fusion of pre-existing arrangements and single domains as well as loss of domains at protein termini. Furthermore, we studied the link between domain age, defined as the first appearance of a domain in the species tree, and the DV I. Contrary to previous studies based on domain promiscuity, it seems as if the DV I is age independent. Finally, we find that contrary to previously reported findings, versatility is lower in Eukaryotes. In summary, our measure of domain versatility indicates that a random attachment process is sufficient to explain the observed distribution of domain arrangements and that several views on domain promiscuity need to be revised. PMID:18854028

  3. The cytoplasmic domain of the cell adhesion molecule uvomorulin associates with three independent proteins structurally related in different species.

    PubMed Central

    Ozawa, M; Baribault, H; Kemler, R

    1989-01-01

    Uvomorulin belongs to the group of Ca2+-dependent cell adhesion molecules, which are integral membrane proteins with several structural features in common. In particular, the cytoplasmic part of these proteins is highly conserved in different species, suggesting a common biological function. To test this assumption we transfected a uvomorulin full-length cDNA into uvomorulin-negative mouse NIH 3T3 and L cells. Immunoprecipitations with anti-uvomorulin antibodies detected, in addition to uvomorulin, three independent proteins of 102, 88 and 80 kd which are of host origin and which form complexes with uvomorulin. Using cDNA constructs coding for uvomorulin with cytoplasmic or extracellular deletions it is shown that the 102, 88 and 80 kd proteins complex with the cytoplasmic domain of uvomorulin. Peptide pattern analysis revealed that these three proteins are identical in different mouse cells. When uvomorulin cDNA was introduced into cell lines from other species, such as human HeLa and avian fibroblasts, the expressed uvomorulin was also associated with endogenous 102, 88 and 80 kd proteins and, moreover, each of these proteins showed structural similarities to the respective mouse molecule. A panel of antibodies specific for known cytoplasmic proteins of mol. wts similar to those of the three proteins did not react with any of the described components. This suggests that the 102, 88 and 80 kd proteins constitute a new group of proteins for which we propose the nomenclature of catenin alpha, beta and gamma respectively. The characterization of these proteins provides a first molecular basis for a possible cytoplasmic anchorage of uvomorulin to the cytoskeleton. Images PMID:2788574

  4. Measuring postural-related changes of spontaneous baroreflex sensitivity after repeated long-duration diving: frequency domain approaches.

    PubMed

    Faes, Luca; Masè, Michela; Nollo, Giandomenico; Chon, Ki H; Florian, John P

    2013-11-01

    Sustained water immersion is thought to modulate orthostatic tolerance to an extent dependent on the duration and repetition over consecutive days of the diving sessions. We tested this hypothesis investigating in ten healthy subjects the potential changes in the cardiovascular response to head-up tilt induced by single and multiple resting air dives. Parametric cross-spectral analysis of spontaneous RR interval and systolic arterial pressure variability was performed in three experimental sessions: before diving (BD), after single 6-hour dive (ASD), and after multiple 6-hour dives (AMD, 5 consecutive days with 18-hour surface interval). From this analysis, baroreflex sensitivity (BRS) was computed as spectral power ratio (αBRS), non-causal transfer function gain (tfBRS) and causal transfer function gain (γBRS) evaluated at low frequency (0.04-0.14Hz) in the supine position (su) as well as in the standing upright position in the early tilt (et) and late tilt (lt) epochs. We found that, while αBRS decreased significantly in et and lt compared to su during all sessions, tfBRS and γBRS decreased during ASD and AMD but not during BD; moreover γBRS evidenced a progressive decrease from BD to ASD and to AMD in both et and lt epochs. These results indicate the necessity of following a causal approach for the estimation of BRS in the frequency domain, and suggest a progressive impairment of the baroreflex response to postural stress after single and multiple dives, which may reflect symptoms of increasing orthostatic intolerance.

  5. Candida albicans ALS1: domains related to a Saccharomyces cerevisiae sexual agglutinin separated by a repeating motif.

    PubMed

    Hoyer, L L; Scherer, S; Shatzman, A R; Livi, G P

    1995-01-01

    Transfer of budding Candida albicans yeast cells from the rich, complex medium YEPD to the defined tissue culture medium RPMI 1640 (RPMI) at 37 degrees C and 5% CO2 causes rapid onset of hyphal induction. Among the genes induced under these conditions are hyphal-specific genes as well as genes expressed in response to changes in temperature, CO2 and specific media components. A cDNA library constructed from cells incubated for 20 min in RPMI was differentially screened with yeast (YEPD)- and hyphal (RPMI)-specific probes resulting in identification of a gene expressed in response to culture conditions but not regulated by the yeast-hyphal transition. The deduced gene product displays significant identity to Saccharomyces cerevisiae alpha-agglutinin, encoded by AG alpha 1, an adhesion glycoprotein that mediates mating of haploid cells. The presence of this gene in C. albicans is curious since the organism has not been observed to undergo meiosis. We designate the C. albicans gene ALS1 (for agglutinin-like sequence). While the N- and C-termini of the predicted 1260-amino-acid ALS1 protein resemble those of the 650-amino-acid AG alpha 1, ALS1 contains a central domain of tandem repeats consisting of a highly conserved 36-amino-acid sequence not present in AG alpha 1. These repeats are also present on the nucleotide level as a highly conserved 108 bp motif. Southern and Northern blot analyses indicate a family of C. albicans genes that contain the tandem repeat motif; at least one gene in addition to ALS1 is expressed under conditions similar to those for ALS1 expression. Genomic Southern blots from several C. albicans isolates indicate that the number of copies of the tandem repeat element in ALS1 differs across strains and, in some cases, between ALS1 alleles in the same strain, suggesting a strain-dependent variability in ALS1 protein size. Potential roles for the ALS1 protein are discussed.

  6. Chinese Students' Implicit Theories of Intelligence and Other Personal Attributes: Cross-Domain Generality and Age-Related Differences.

    ERIC Educational Resources Information Center

    Cheng, Zi-Juan; Hau, Kit-Tai; Wen, Jian-Bing; Kong, Chit-Kwong

    Using structural equation modeling (SEM), researchers examined whether there was a general dominating factor that governed students' implicit theories of intelligence, morality, personality, creativity, and social intelligence. The possible age-related changes of students' implicit theories were also studied. In all, 1,650 elementary and junior…

  7. Inhibition deficit in the spatial tendency of the response in multiple-domain amnestic mild cognitive impairment. An event-related potential study

    PubMed Central

    Cespón, Jesús; Galdo-Álvarez, Santiago; Díaz, Fernando

    2015-01-01

    Longitudinal studies have shown that a high percentage of people with amnestic mild cognitive impairment (MCI) develop Alzheimer’s disease (AD). Prodromal AD is known to involve deficits in executive control processes. In the present study, we examined such deficits by recording EEG in 13 single-domain amnestic MCI (sdaMCI), 12 multiple-domain amnestic MCI (mdaMCI) and 18 healthy elderly (control group, CG) participants while they performed a Simon task. The Simon task demands deployment of executive processes because participants have to respond to non-spatial features of a lateralized stimulus and inhibit the more automatic spatial tendency of the response. We specifically focused on the negativity central contralateral (N2cc), an event-related potential (ERP) component related to brain activity that prevents the cross-talk between direction of spatial attention and manual response preparation. The reaction time (RT) was not significantly different among the three groups of participants. The percentage of errors (PE) was higher in mdaMCI than in CG and sdaMCI participants. In addition, N2cc latency was delayed in mdaMCI (i.e., delayed implementation of mechanisms for controlling the spatial tendency of the response). The N2cc latency clearly distinguished among mdaMCI and CG/sdaMCI participants (area under curve: 0.91). Longer N2cc was therefore associated with executive control deficits, which suggests that N2cc latency is a correlate of mdaMCI. PMID:25999853

  8. Health-Related Quality of Life of Adolescent and Young Adult Survivors of Central Nervous System Tumors: Identifying Domains From a Survivor Perspective.

    PubMed

    Kuhlthau, Karen; Luff, Donna; Delahaye, Jennifer; Wong, Alicia; Yock, Torunn; Huang, Mary; Park, Elyse R

    2015-01-01

    This article uses qualitative methods to describe the domains of health-related quality of life (HRQoL) that adolescent and young adult (AYA) survivors of central nervous system (CNS) tumors identify as important. Survivors clearly attributed aspects of their current HRQoL to their disease or its treatment. We identified 7 key domains of AYA CNS tumor survivorship: physical health, social well-being, mental health, cognitive functioning, health behaviors, sexual and reproductive health, and support systems. Although most aspects of HRQoL that survivors discussed represented new challenges, there were several areas where survivors pointed out positive outcomes. There is a need for a HRQoL tool designed for this population of survivors, given their unique treatment and survivorship experience. Aspects of HRQoL related to cognition, sexual and reproductive health, health behaviors, and support systems are not typically included in generic HRQoL tools but should be assessed for this population. Developing HRQoL measurement instruments that capture the most significant aspects of HRQoL will improve the ability to track HRQoL in AYA CNS tumor survivors and in the long-term management of common sequelae from CNS tumors and their treatments.

  9. A Preliminary Prospective Study of an Escalation in 'Maximum Daily Drinks', Fronto-Parietal Circuitry and Impulsivity-Related Domains in Young Adult Drinkers.

    PubMed

    Worhunsky, Patrick D; Dager, Alecia D; Meda, Shashwath A; Khadka, Sabin; Stevens, Michael C; Austad, Carol S; Raskin, Sarah A; Tennen, Howard; Wood, Rebecca M; Fallahi, Carolyn R; Potenza, Marc N; Pearlson, Godfrey D

    2016-05-01

    Excessive alcohol use in young adults is associated with greater impulsivity and neurobiological alterations in executive control systems. The maximum number of drinks consumed during drinking occasions ('MaxDrinks') represents a phenotype linked to vulnerability of alcohol use disorders, and an increase, or 'escalation', in MaxDrinks may be indicative of greater risk for problematic drinking. Thirty-six young adult drinkers performed a Go/No-Go task during fMRI, completed impulsivity-related assessments, and provided monthly reports of alcohol use during a 12-month follow-up period. Participants were characterized by MaxDrinks at baseline and after follow-up, identifying 18 escalating drinkers and 18 constant drinkers. Independent component analysis was used to investigate functional brain networks associated with response inhibition, and relationships with principal component analysis derived impulsivity-related domains were examined. Greater baseline MaxDrinks was associated with an average reduction in the engagement of a right-lateralized fronto-parietal functional network, while an escalation in MaxDrinks was associated with a greater difference in fronto-parietal engagement between successful inhibitions and error trials. Escalating drinkers displayed greater impulsivity/compulsivity-related domain scores that were positively associated with fronto-parietal network engagement and change in MaxDrinks during follow-up. In young adults, an escalating MaxDrinks trajectory was prospectively associated with altered fronto-parietal control mechanisms and greater impulsivity/compulsivity scores. Continued longitudinal studies of MaxDrinks trajectories, functional network activity, and impulsivity/compulsivity-related features may lend further insight into an intermediate phenotype vulnerable for alcohol use and addictive disorders. PMID:26514582

  10. GEm-Related 5 (GER5), an ABA and stress-responsive GRAM domain protein regulating seed development and inflorescence architecture.

    PubMed

    Baron, Kevin N; Schroeder, Dana F; Stasolla, Claudio

    2014-06-01

    We have identified an abscisic acid (ABA) and stress-responsive GRAM (Glucosyltransferases, Rab-like GTPase activators and Myotubularins) domain protein GER5 (GEm-Related 5) closely related to GEM (GLABRA2 Expression Modulator), a novel regulator of cell division and cell fate determination in epidermal cells. A loss-of-function T-DNA line (ger5-2) and transgenic lines silencing (GER5(RNAi)) or overexpressing (GER5(OE)) GER5 displayed several defects in reproductive development affecting seed and embryo development. RNA in situ studies revealed GER5 and related GRAM genes (GEM and GEm-Related 1 (GER1)) have both overlapping and unique expression domains in male and female reproductive organs. Hormone immunolocalization experiments further indicate GER5 transcripts preferentially localize to reproductive tissues which accumulate ABA. Expression analysis revealed members of the GRAM family (GER5, GER1, GEM) display tissue-specific expression patterns and are responsive to phytohormones and abiotic stress, in addition to genetic lesions (aba1, aba2, ctr1) affecting ABA biosynthesis or ethylene signalling. Mature seeds of ger5-2 mutants also exhibit reduced sensitivity to ABA during seed germination assays. Microarray analysis of aborting and developing seeds isolated from ger5-2 mutants revealed underlying transcriptional changes in carbohydrate metabolism, hormone signalling and catabolic processes (e.g. protein degradation, autophagy). Taken together, our results indicate ABA-responsive GRAM genes play a novel role in regulating the reproductive development of plants, and raise intriguing questions regarding the functional relationship between members of the GRAM gene family.

  11. A unique GCN5-related glucosamine N-acetyltransferase region exist in the fungal multi-domain glycoside hydrolase family 3 β-N-acetylglucosaminidase

    PubMed Central

    Qin, Zhen; Xiao, Yibei; Yang, Xinbin; Mesters, Jeroen R.; Yang, Shaoqing; Jiang, Zhengqiang

    2015-01-01

    Glycoside hydrolase (GH) family 3 β-N-acetylglucosaminidases widely exist in the filamentous fungi, which may play a key role in chitin metabolism of fungi. A multi-domain GH family 3 β-N-acetylglucosaminidase from Rhizomucor miehei (RmNag), exhibiting a potential N-acetyltransferase region, has been recently reported to show great potential in industrial applications. In this study, the crystal structure of RmNag was determined at 2.80 Å resolution. The three-dimensional structure of RmNag showed four distinctive domains, which belong to two distinguishable functional regions — a GH family 3 β-N-acetylglucosaminidase region (N-terminal) and a N-acetyltransferase region (C-terminal). From structural and functional analysis, the C-terminal region of RmNag was identified as a unique tandem array linking general control non-derepressible 5 (GCN5)-related N-acetyltransferase (GNAT), which displayed glucosamine N-acetyltransferase activity. Structural analysis of this glucosamine N-acetyltransferase region revealed that a unique glucosamine binding pocket is located in the pantetheine arm binding terminal region of the conserved CoA binding pocket, which is different from all known GNAT members. This is the first structural report of a glucosamine N-acetyltransferase, which provides novel structural information about substrate specificity of GNATs. The structural and functional features of this multi-domain β-N-acetylglucosaminidase could be useful in studying the catalytic mechanism of GH family 3 proteins. PMID:26669854

  12. The La-related protein 1-specific domain repurposes HEAT-like repeats to directly bind a 5'TOP sequence

    SciTech Connect

    Lahr, Roni M.; Mack, Seshat M.; Heroux, Annie; Blagden, Sarah P.; Bousquet-Antonelli, Cecile; Deragon, Jean -Marc; Berman, Andrea J.

    2015-07-22

    La-related protein 1 (LARP1) regulates the stability of many mRNAs. These include 5'TOPs, mTOR-kinase responsive mRNAs with pyrimidine-rich 5' UTRs, which encode ribosomal proteins and translation factors. We determined that the highly conserved LARP1-specific C-terminal DM15 region of human LARP1 directly binds a 5'TOP sequence. The crystal structure of this DM15 region refined to 1.86 Å resolution has three structurally related and evolutionarily conserved helix-turn-helix modules within each monomer. These motifs resemble HEAT repeats, ubiquitous helical protein-binding structures, but their sequences are inconsistent with consensus sequences of known HEAT modules, suggesting this structure has been repurposed for RNA interactions. A putative mTORC1-recognition sequence sits within a flexible loop C-terminal to these repeats. We also present modelling of pyrimidine-rich single-stranded RNA onto the highly conserved surface of the DM15 region. Ultimately, these studies lay the foundation necessary for proceeding toward a structural mechanism by which LARP1 links mTOR signalling to ribosome biogenesis.

  13. The La-related protein 1-specific domain repurposes HEAT-like repeats to directly bind a 5'TOP sequence

    DOE PAGES

    Lahr, Roni M.; Mack, Seshat M.; Heroux, Annie; Blagden, Sarah P.; Bousquet-Antonelli, Cecile; Deragon, Jean -Marc; Berman, Andrea J.

    2015-07-22

    La-related protein 1 (LARP1) regulates the stability of many mRNAs. These include 5'TOPs, mTOR-kinase responsive mRNAs with pyrimidine-rich 5' UTRs, which encode ribosomal proteins and translation factors. We determined that the highly conserved LARP1-specific C-terminal DM15 region of human LARP1 directly binds a 5'TOP sequence. The crystal structure of this DM15 region refined to 1.86 Å resolution has three structurally related and evolutionarily conserved helix-turn-helix modules within each monomer. These motifs resemble HEAT repeats, ubiquitous helical protein-binding structures, but their sequences are inconsistent with consensus sequences of known HEAT modules, suggesting this structure has been repurposed for RNA interactions. Amore » putative mTORC1-recognition sequence sits within a flexible loop C-terminal to these repeats. We also present modelling of pyrimidine-rich single-stranded RNA onto the highly conserved surface of the DM15 region. Ultimately, these studies lay the foundation necessary for proceeding toward a structural mechanism by which LARP1 links mTOR signalling to ribosome biogenesis.« less

  14. Minor Lesion Mutational Spectrum of the Entire NF1 Gene Does Not Explain Its High Mutability but Points to a Functional Domain Upstream of the GAP-Related Domain

    PubMed Central

    Fahsold, Raimund; Hoffmeyer, Sven; Mischung, Claudia; Gille, Christoph; Ehlers, Christian; Kücükceylan, Nazan; Abdel-Nour, Maher; Gewies, Andreas; Peters, Hartmut; Kaufmann, Dieter; Buske, Annegret; Tinschert, Sigrid; Nürnberg, Peter

    2000-01-01

    More than 500 unrelated patients with neurofibromatosis type 1 (NF1) were screened for mutations in the NF1 gene. For each patient, the whole coding sequence and all splice sites were studied for aberrations, either by the protein truncation test (PTT), temperature-gradient gel electrophoresis (TGGE) of genomic PCR products, or, most often, by direct genomic sequencing (DGS) of all individual exons. A total of 301 sequence variants, including 278 bona fide pathogenic mutations, were identified. As many as 216 or 183 of the genuine mutations, comprising 179 or 161 different ones, can be considered novel when compared to the recent findings of Upadhyaya and Cooper, or to the NNFF mutation database. Mutation-detection efficiencies of the various screening methods were similar: 47.1% for PTT, 53.7% for TGGE, and 54.9% for DGS. Some 224 mutations (80.2%) yielded directly or indirectly premature termination codons. These mutations showed even distribution over the whole gene from exon 1 to exon 47. Of all sequence variants determined in our study, <20% represent C→T or G→A transitions within a CpG dinucleotide, and only six different mutations also occur in NF1 pseudogenes, with five being typical C→T transitions in a CpG. Thus, neither frequent deamination of 5-methylcytosines nor interchromosomal gene conversion may account for the high mutation rate of the NF1 gene. As opposed to the truncating mutations, the 28 (10.1%) missense or single-amino-acid-deletion mutations identified clustered in two distinct regions, the GAP-related domain (GRD) and an upstream gene segment comprising exons 11–17. The latter forms a so-called cysteine/serine-rich domain with three cysteine pairs suggestive of ATP binding, as well as three potential cAMP-dependent protein kinase (PKA) recognition sites obviously phosphorylated by PKA. Coincidence of mutated amino acids and those conserved between human and Drosophila strongly suggest significant functional relevance of this region

  15. Convergent Signaling Pathways Controlled by LRP1 (Receptor-related Protein 1) Cytoplasmic and Extracellular Domains Limit Cellular Cholesterol Accumulation.

    PubMed

    El Asmar, Zeina; Terrand, Jérome; Jenty, Marion; Host, Lionel; Mlih, Mohamed; Zerr, Aurélie; Justiniano, Hélène; Matz, Rachel L; Boudier, Christian; Scholler, Estelle; Garnier, Jean-Marie; Bertaccini, Diego; Thiersé, Danièle; Schaeffer, Christine; Van Dorsselaer, Alain; Herz, Joachim; Bruban, Véronique; Boucher, Philippe

    2016-03-01

    The low density lipoprotein receptor-related protein 1 (LRP1) is a ubiquitously expressed cell surface receptor that protects from intracellular cholesterol accumulation. However, the underlying mechanisms are unknown. Here we show that the extracellular (α) chain of LRP1 mediates TGFβ-induced enhancement of Wnt5a, which limits intracellular cholesterol accumulation by inhibiting cholesterol biosynthesis and by promoting cholesterol export. Moreover, we demonstrate that the cytoplasmic (β) chain of LRP1 suffices to limit cholesterol accumulation in LRP1(-/-) cells. Through binding of Erk2 to the second of its carboxyl-terminal NPXY motifs, LRP1 β-chain positively regulates the expression of ATP binding cassette transporter A1 (ABCA1) and of neutral cholesterol ester hydrolase (NCEH1). These results highlight the unexpected functions of LRP1 and the canonical Wnt5a pathway and new therapeutic potential in cholesterol-associated disorders including cardiovascular diseases.

  16. A truncated fragment of Ov-ASP-1 consisting of the core pathogenesis-related-1 (PR-1) domain maintains adjuvanticity as the full-length protein.

    PubMed

    Guo, Jingjing; Yang, Yi; Xiao, Wenjun; Sun, Weilai; Yu, Hong; Du, Lanying; Lustigman, Sara; Jiang, Shibo; Kou, Zhihua; Zhou, Yusen

    2015-04-15

    The Onchocerca volvulus activation-associated secreted protein-1 (Ov-ASP-1) has good adjuvanticity for a variety of antigens and vaccines, probably due to its ability activate antigen-processing cells (APCs). However, the functional domain of Ov-ASP-1 as an adjuvant is not clearly defined. Based on the structural prediction of this protein family, we constructed a 16-kDa recombinant protein of Ov-ASP-1 that contains only the core pathogenesis-related-1 (PR-1) domain (residues 10-153), designated ASPPR. We found that ASPPR exhibits adjuvanticity similar to that of the full-length Ov-ASP-1 (residues 10-220) for various antigens, including ovalbumin (OVA), HBsAg protein antigen, and the HIV peptide 5 (Pep5) antigen, but it is more suitable for vaccine design in ASPPR-antigen fusion proteins, and more stable in PBS than Ov-ASP-1 stored at -70 °C. These results suggest that ASPPR might be the functional region of Ov-ASP-1 as an adjuvant, and therefore could be developed as an adjuvant for human use. PMID:25736195

  17. Multiple classes of transcription factors regulate the expression of VASCULAR-RELATED NAC-DOMAIN7, a master switch of xylem vessel differentiation.

    PubMed

    Endo, Hitoshi; Yamaguchi, Masatoshi; Tamura, Taizo; Nakano, Yoshimi; Nishikubo, Nobuyuki; Yoneda, Arata; Kato, Ko; Kubo, Minoru; Kajita, Shinya; Katayama, Yoshihiro; Ohtani, Misato; Demura, Taku

    2015-02-01

    The secondary cell walls of xylem cells, including vessel elements, provide mechanical strength and contribute to the conduction of water and minerals. VASCULAR-RELATED NAC-DOMAIN7 (VND7) is a NAC-domain transcription factor that regulates the expression of genes required for xylem vessel element formation. Transient expression assays using 68 transcription factors that are expressed during xylem vessel differentiation showed that 14 transcription factors, including VND1-VND7, are putative positive regulators of VND7 expression. Electrophoretic mobility shift assays revealed that all seven VND proteins bound to the VND7 promoter region at its SMBE/TERE motif, indicating that VND7 is a direct target of all of the VND transcription factors. Overexpression of VND1-VND5, GATA12 and ANAC075, newly identified transcription factors that function upstream of VND7, resulted in ectopic xylem vessel element formation. These data suggest that VND7 transcription is a regulatory target of multiple classes of transcription factors.

  18. A truncated fragment of Ov-ASP-1 consisting of the core pathogenesis-related-1 (PR-1) domain maintains adjuvanticity as the full-length protein.

    PubMed

    Guo, Jingjing; Yang, Yi; Xiao, Wenjun; Sun, Weilai; Yu, Hong; Du, Lanying; Lustigman, Sara; Jiang, Shibo; Kou, Zhihua; Zhou, Yusen

    2015-04-15

    The Onchocerca volvulus activation-associated secreted protein-1 (Ov-ASP-1) has good adjuvanticity for a variety of antigens and vaccines, probably due to its ability activate antigen-processing cells (APCs). However, the functional domain of Ov-ASP-1 as an adjuvant is not clearly defined. Based on the structural prediction of this protein family, we constructed a 16-kDa recombinant protein of Ov-ASP-1 that contains only the core pathogenesis-related-1 (PR-1) domain (residues 10-153), designated ASPPR. We found that ASPPR exhibits adjuvanticity similar to that of the full-length Ov-ASP-1 (residues 10-220) for various antigens, including ovalbumin (OVA), HBsAg protein antigen, and the HIV peptide 5 (Pep5) antigen, but it is more suitable for vaccine design in ASPPR-antigen fusion proteins, and more stable in PBS than Ov-ASP-1 stored at -70 °C. These results suggest that ASPPR might be the functional region of Ov-ASP-1 as an adjuvant, and therefore could be developed as an adjuvant for human use.

  19. Connective tissue disease related interstitial lung diseases and idiopathic pulmonary fibrosis: provisional core sets of domains and instruments for use in clinical trials

    PubMed Central

    Saketkoo, Lesley Ann; Mittoo, Shikha; Huscher, Dörte; Khanna, Dinesh; Dellaripa, Paul F; Distler, Oliver; Flaherty, Kevin R; Frankel, Sid; Oddis, Chester V; Denton, Christopher P; Fischer, Aryeh; Kowal-Bielecka, Otylia M; LeSage, Daphne; Merkel, Peter A; Phillips, Kristine; Pittrow, David; Swigris, Jeffrey; Antoniou, Katerina; Baughman, Robert P; Castelino, Flavia V; Christmann, Romy B; Christopher-Stine, Lisa; Collard, Harold R; Cottin, Vincent; Danoff, Sonye; Highland, Kristin B; Hummers, Laura; Shah, Ami A; Kim, Dong Soon; Lynch, David A; Miller, Frederick W; Proudman, Susanna M; Richeldi, Luca; Ryu, Jay H; Sandorfi, Nora; Sarver, Catherine; Wells, Athol U; Strand, Vibeke; Matteson, Eric L; Brown, Kevin K; Seibold, James R

    2014-01-01

    Rationale Clinical trial design in interstitial lung diseases (ILDs) has been hampered by lack of consensus on appropriate outcome measures for reliably assessing treatment response. In the setting of connective tissue diseases (CTDs), some measures of ILD disease activity and severity may be confounded by non-pulmonary comorbidities. Methods The Connective Tissue Disease associated Interstitial Lung Disease (CTD-ILD) working group of Outcome Measures in Rheumatology—a non-profit international organisation dedicated to consensus methodology in identification of outcome measures—conducted a series of investigations which included a Delphi process including >248 ILD medical experts as well as patient focus groups culminating in a nominal group panel of ILD experts and patients. The goal was to define and develop a consensus on the status of outcome measure candidates for use in randomised controlled trials in CTD-ILD and idiopathic pulmonary fibrosis (IPF). Results A core set comprising specific measures in the domains of lung physiology, lung imaging, survival, dyspnoea, cough and health-related quality of life is proposed as appropriate for consideration for use in a hypothetical 1-year multicentre clinical trial for either CTD-ILD or IPF. As many widely used instruments were found to lack full validation, an agenda for future research is proposed. Conclusion Identification of consensus preliminary domains and instruments to measure them was attained and is a major advance anticipated to facilitate multicentre RCTs in the field. PMID:24368713

  20. A KS-type dehydrin and its related domains reduce Cu-promoted radical generation and the histidine residues contribute to the radical-reducing activities

    PubMed Central

    Hara, Masakazu

    2013-01-01

    Dehydrin is a plant disordered protein whose functions are not yet totally understood. Here it is reported that a KS-type dehydrin can reduce the formation of reactive oxygen species (ROS) from Cu. AtHIRD11, which is the Arabidopsis KS-type dehydrin, inhibited generation of hydrogen peroxide and hydroxyl radicals in the Cu–ascorbate system. The radical-reducing activity of AtHIRD11 was stronger than those of radical-silencing peptides such as glutathione and serum albumin. The addition of Cu2+ reduced the disordered state, decreased the trypsin susceptibility, and promoted the self-association of AtHIRD11. Domain analyses indicated that the five domains containing histidine showed ROS-reducing activities. Histidine/alanine substitutions indicated that histidine is a crucial residue for reducing ROS generation. Using the 27 peptides which are related to the KnS-type dehydrins of 14 plant species, it was found that the strengths of ROS-reducing activities can be determined by two factors, namely the histidine contents and the length of the peptides. The degree of ROS-reducing activities of a dehydrin can be predicted using these indices. PMID:23382551

  1. PL3 Amidase, a Tailor-made Lysin Constructed by Domain Shuffling with Potent Killing Activity against Pneumococci and Related Species

    PubMed Central

    Blázquez, Blas; Fresco-Taboada, Alba; Iglesias-Bexiga, Manuel; Menéndez, Margarita; García, Pedro

    2016-01-01

    The emergence and spread of antibiotic-resistant bacteria is pushing the need of alternative treatments. In this context, phage therapy is already a reality to successfully fight certain multiresistant bacteria. Among different phage gene products, murein hydrolases responsible of phage progeny liberation (also called lysins or endolysins) are weapons that target specific peptidoglycan bonds, leading to lysis and death of susceptible bacteria when added from the outside. In the pneumococcal system, all but one phage murein hydrolases reported to date share a choline-binding domain that recognizes cell walls containing choline residues in the (lipo)teichoic acids. Some purified pneumococcal or phage murein hydrolases, as well as several chimeric proteins combining natural catalytic and cell wall-binding domains (CBDs) have been used as effective antimicrobials. In this work we have constructed a novel chimeric N-acetylmuramoyl-L-alanine amidase (PL3) by fusing the catalytic domain of the Pal amidase (a phage-coded endolysin) to the CBD of the LytA amidase, the major pneumococcal autolysin. The physicochemical properties of PL3 and the bacteriolytic effect against several pneumococci (including 48 multiresistant representative strain) and related species, like Streptococcus pseudopneumoniae, Streptococcus mitis, and Streptococcus oralis, have been studied. Results have shown that low doses of PL3, in the range of 0.5–5 μg/ml, are enough to practically sterilize all choline-containing strains tested. Moreover, a single 20-μg dose of PL3 fully protected zebrafish embryos from infection by S. pneumoniae D39 strain. Importantly, PL3 keeps 95% enzymatic activity after 4 weeks at 37°C and can be lyophilized without losing activity, demonstrating a remarkable robustness. Such stability, together with a prominent efficacy against a narrow spectrum of human pathogens, confers to PL3 the characteristic to be an effective therapeutic. In addition, our results demonstrate

  2. PL3 Amidase, a Tailor-made Lysin Constructed by Domain Shuffling with Potent Killing Activity against Pneumococci and Related Species.

    PubMed

    Blázquez, Blas; Fresco-Taboada, Alba; Iglesias-Bexiga, Manuel; Menéndez, Margarita; García, Pedro

    2016-01-01

    The emergence and spread of antibiotic-resistant bacteria is pushing the need of alternative treatments. In this context, phage therapy is already a reality to successfully fight certain multiresistant bacteria. Among different phage gene products, murein hydrolases responsible of phage progeny liberation (also called lysins or endolysins) are weapons that target specific peptidoglycan bonds, leading to lysis and death of susceptible bacteria when added from the outside. In the pneumococcal system, all but one phage murein hydrolases reported to date share a choline-binding domain that recognizes cell walls containing choline residues in the (lipo)teichoic acids. Some purified pneumococcal or phage murein hydrolases, as well as several chimeric proteins combining natural catalytic and cell wall-binding domains (CBDs) have been used as effective antimicrobials. In this work we have constructed a novel chimeric N-acetylmuramoyl-L-alanine amidase (PL3) by fusing the catalytic domain of the Pal amidase (a phage-coded endolysin) to the CBD of the LytA amidase, the major pneumococcal autolysin. The physicochemical properties of PL3 and the bacteriolytic effect against several pneumococci (including 48 multiresistant representative strain) and related species, like Streptococcus pseudopneumoniae, Streptococcus mitis, and Streptococcus oralis, have been studied. Results have shown that low doses of PL3, in the range of 0.5-5 μg/ml, are enough to practically sterilize all choline-containing strains tested. Moreover, a single 20-μg dose of PL3 fully protected zebrafish embryos from infection by S. pneumoniae D39 strain. Importantly, PL3 keeps 95% enzymatic activity after 4 weeks at 37°C and can be lyophilized without losing activity, demonstrating a remarkable robustness. Such stability, together with a prominent efficacy against a narrow spectrum of human pathogens, confers to PL3 the characteristic to be an effective therapeutic. In addition, our results demonstrate

  3. Diabetic status and the relation of the three domains of glycemic control to mortality in critically ill patients: an international multicenter cohort study

    PubMed Central

    2013-01-01

    Introduction Hyperglycemia, hypoglycemia, and increased glycemic variability have each been independently associated with increased risk of mortality in critically ill patients. The role of diabetic status on modulating the relation of these three domains of glycemic control with mortality remains uncertain. The purpose of this investigation was to determine how diabetic status affects the relation of hyperglycemia, hypoglycemia, and increased glycemic variability with the risk of mortality in critically ill patients. Methods This is a retrospective analysis of prospectively collected data involving 44,964 patients admitted to 23 intensive care units (ICUs) from nine countries, between February 2001 and May 2012. We analyzed mean blood glucose concentration (BG), coefficient of variation (CV), and minimal BG and created multivariable models to analyze their independent association with mortality. Patients were stratified according to the diagnosis of diabetes. Results Among patients without diabetes, mean BG bands between 80 and 140 mg/dl were independently associated with decreased risk of mortality, and mean BG bands >140 mg/dl, with increased risk of mortality. Among patients with diabetes, mean BG from 80 to 110 mg/dl was associated with increased risk of mortality and mean BG from 110 to 180 mg/dl with decreased risk of mortality. An effect of center was noted on the relation between mean BG and mortality. Hypoglycemia, defined as minimum BG <70 mg/dl, was independently associated with increased risk of mortality among patients with and without diabetes and increased glycemic variability, defined as CV >20%, was independently associated with increased risk of mortality only among patients without diabetes. Derangements of more than one domain of glycemic control had a cumulative association with mortality, especially for patients without diabetes. Conclusions Although hyperglycemia, hypoglycemia, and increased glycemic variability is each independently

  4. Laboratory permittivity measurements of icy planetary analogs in the millimeter and submillimeter domains, in relation with JUICE mission.

    NASA Astrophysics Data System (ADS)

    Brouet, Y.; Jacob, K.; Murk, A.; Poch, O.; Pommerol, A.; Thomas, N.; Levasseur-Regourd, A. C.

    2015-12-01

    The European Space Agency's JUpiter ICy moons Explorer (JUICE) spacecraft is planned for launch in 2022 and arrival at Jupiter in 2030. It will observe the planet Jupiter and three of its largest moons, Ganymede, Callisto and Europa. One instrument on the JUICE spacecraft is the Sub-millimeter Wave Instrument (SWI), which will measure brightness temperatures from Jupiter's stratosphere and troposphere, and from subsurfaces of Jupiter's icy moons. In the baseline configuration SWI consists of two tunable sub-millimeter wave receivers operating from 530 to 625 GHz. As an alternative one of the receivers could cover the range of 1080 and 1275 GHz. Inversion models are strongly dependent on the knowledge of the complex relative permittivity (hereafter permittivity) of the target material to retrieve the physical properties of the subsurface (e.g. [1][2]). We set up a laboratory experiment allowing us to perform reproducible measurements of the complex scattering parameters S11 and S21 in the ranges of 70 to 110 GHz, of 100 to 160 GHz, of 140 to 220 GHz, of 140 to 220 GHz and of 510 to 715 GHz. These scattering parameters can be used to retrieve the permittivity of icy analogs of the surfaces and subsurfaces of Jupiter's icy moons in order to prepare the data interpretation of SWI [3]. The measurements are performed under laboratory conditions with a quasi-optical bench (Institute of Applied Physics, University of Bern). The icy analogs that we prepare in the Laboratory for Outflow Studies of Sublimating Materials (LOSSy, Physics Institute, University of Bern), include two different porous water ice samples composed of fine-grained ice particles with a size range of 4 to 6 microns and ice particles with a size range of 50 to 100 microns [4][5]; and possibly CO2 ice. We will present the general experimental set-up and the first results in the context to prepare the data interpretation of SWI. [1] Ulaby, F. T., Long, D. G., 2014. Microwave radar and radiometric remote

  5. Fixation-related FMRI analysis in the domain of reading research: using self-paced eye movements as markers for hemodynamic brain responses during visual letter string processing.

    PubMed

    Richlan, Fabio; Gagl, Benjamin; Hawelka, Stefan; Braun, Mario; Schurz, Matthias; Kronbichler, Martin; Hutzler, Florian

    2014-10-01

    The present study investigated the feasibility of using self-paced eye movements during reading (measured by an eye tracker) as markers for calculating hemodynamic brain responses measured by functional magnetic resonance imaging (fMRI). Specifically, we were interested in whether the fixation-related fMRI analysis approach was sensitive enough to detect activation differences between reading material (words and pseudowords) and nonreading material (line and unfamiliar Hebrew strings). Reliable reading-related activation was identified in left hemisphere superior temporal, middle temporal, and occipito-temporal regions including the visual word form area (VWFA). The results of the present study are encouraging insofar as fixation-related analysis could be used in future fMRI studies to clarify some of the inconsistent findings in the literature regarding the VWFA. Our study is the first step in investigating specific visual word recognition processes during self-paced natural sentence reading via simultaneous eye tracking and fMRI, thus aiming at an ecologically valid measurement of reading processes. We provided the proof of concept and methodological framework for the analysis of fixation-related fMRI activation in the domain of reading research.

  6. Fibrinogen-Related Proteins in Tissue Repair: How a Unique Domain with a Common Structure Controls Diverse Aspects of Wound Healing

    PubMed Central

    Zuliani-Alvarez, Lorena; Midwood, Kim S.

    2015-01-01

    Significance: Fibrinogen-related proteins (FRePs) comprise an intriguing collection of extracellular molecules, each containing a conserved fibrinogen-like globe (FBG). This group includes the eponymous fibrinogen as well as the tenascin, angiopoietin, and ficolin families. Many of these proteins are upregulated during tissue repair and exhibit diverse roles during wound healing. Recent Advances: An increasing body of evidence highlights the specific expression of a number of FRePs following tissue injury and infection. Upon induction, each FReP uses its FBG domain to mediate quite distinct effects that contribute to different stages of tissue repair, such as driving coagulation, pathogen detection, inflammation, angiogenesis, and tissue remodeling. Critical Issues: Despite a high degree of homology among FRePs, each contains unique sequences that enable their diversification of function. Comparative analysis of the structure and function of FRePs and precise mapping of regions that interact with a variety of ligands has started to reveal the underlying molecular mechanisms by which these proteins play very different roles using their common domain. Future Directions: Fibrinogen has long been used in the clinic as a synthetic matrix serving as a scaffold or a delivery system to aid tissue repair. Novel therapeutic strategies are now emerging that harness the use of other FRePs to improve wound healing outcomes. As we learn more about the underlying mechanisms by which each FReP contributes to the repair response, specific blockade, or indeed potentiation, of their function offers real potential to enable regulation of distinct processes during pathological wound healing. PMID:26005593

  7. Self-Esteem is Relatively Stable Late in Life: The Role of Resources in the Health, Self-Regulation, and Social Domains

    PubMed Central

    Wagner, Jenny; Hoppmann, Christiane; Ram, Nilam; Gerstorf, Denis

    2015-01-01

    A large body of research has documented changes in self-esteem across adulthood and individual-difference correlates thereof. However, little is known about whether people maintain their self-esteem until the end of life and what role key risk factors in the health, cognitive, self-regulatory, and social domains play. To examine these questions, we apply growth modeling to 13-year longitudinal data obtained from by now deceased participants of the Berlin Aging Study (BASE, N = 462; age 70 – 103, M = 86.3 yrs., SD = 8.3; 51% male). Results revealed that self-esteem, on average, does decline in very old age and close to death, but the amount of typical decline is minor. Health-related constraints and disabilities as well as lower control beliefs and higher loneliness were each associated with lower self-esteem late in life. We obtained initial evidence that some of these associations were stronger among the oldest-old participants. Our results corroborate and extend initial reports that self-esteem is, on average, fairly stable into the last years of life. We discuss possible pathways by which common and often severe late-life challenges may undermine an otherwise relatively robust self-esteem system. PMID:25546600

  8. Development of a high capacity bubble domain memory element and related epitaxial garnet materials for application in spacecraft data recorders. Item 2: The optimization of material-device parameters for application in bubble domain memory elements for spacecraft data recorders

    NASA Technical Reports Server (NTRS)

    Besser, P. J.

    1976-01-01

    Bubble domain materials and devices are discussed. One of the materials development goals was a materials system suitable for operation of 16 micrometer period bubble domain devices at 150 kHz over the temperature range -10 C to +60 C. Several material compositions and hard bubble suppression techniques were characterized and the most promising candidates were evaluated in device structures. The technique of pulsed laser stroboscopic microscopy was used to characterize bubble dynamic properties and device performance at 150 kHz. Techniques for large area LPE film growth were developed as a separate task. Device studies included detector optimization, passive replicator design and test and on-chip bridge evaluation. As a technology demonstration an 8 chip memory cell was designed, tested and delivered. The memory elements used in the cell were 10 kilobit serial registers.

  9. Verticillium Infection Triggers VASCULAR-RELATED NAC DOMAIN7–Dependent de Novo Xylem Formation and Enhances Drought Tolerance in Arabidopsis[W

    PubMed Central

    Reusche, Michael; Thole, Karin; Janz, Dennis; Truskina, Jekaterina; Rindfleisch, Sören; Drübert, Christine; Polle, Andrea; Lipka, Volker; Teichmann, Thomas

    2012-01-01

    The soilborne fungal plant pathogen Verticillium longisporum invades the roots of its Brassicaceae hosts and proliferates in the plant vascular system. Typical aboveground symptoms of Verticillium infection on Brassica napus and Arabidopsis thaliana are stunted growth, vein clearing, and leaf chloroses. Here, we provide evidence that vein clearing is caused by pathogen-induced transdifferentiation of chloroplast-containing bundle sheath cells to functional xylem elements. In addition, our findings suggest that reinitiation of cambial activity and transdifferentiation of xylem parenchyma cells results in xylem hyperplasia within the vasculature of Arabidopsis leaves, hypocotyls, and roots. The observed de novo xylem formation correlates with Verticillium-induced expression of the VASCULAR-RELATED NAC DOMAIN (VND) transcription factor gene VND7. Transgenic Arabidopsis plants expressing the chimeric repressor VND7-SRDX under control of a Verticillium infection-responsive promoter exhibit reduced de novo xylem formation. Interestingly, infected Arabidopsis wild-type plants show higher drought stress tolerance compared with noninfected plants, whereas this effect is attenuated by suppression of VND7 activity. Together, our results suggest that V. longisporum triggers a tissue-specific developmental plant program that compensates for compromised water transport and enhances the water storage capacity of infected Brassicaceae host plants. In conclusion, we provide evidence that this natural plant–fungus pathosystem has conditionally mutualistic features. PMID:23023171

  10. The pipsqueak-domain proteins Distal antenna and Distal antenna-related restrict Hunchback neuroblast expression and early-born neuronal identity.

    PubMed

    Kohwi, Minoree; Hiebert, Laurel S; Doe, Chris Q

    2011-05-01

    A fundamental question in brain development is how precursor cells generate a diverse group of neural progeny in an ordered manner. Drosophila neuroblasts sequentially express the transcription factors Hunchback (Hb), Krüppel (Kr), Pdm1/Pdm2 (Pdm) and Castor (Cas). Hb is necessary and sufficient to specify early-born temporal identity and, thus, Hb downregulation is essential for specification of later-born progeny. Here, we show that distal antenna (dan) and distal antenna-related (danr), encoding pipsqueak motif DNA-binding domain protein family members, are detected in all neuroblasts during the Hb-to-Cas expression window. Dan and Danr are required for timely downregulation of Hb in neuroblasts and for limiting the number of early-born neurons. Dan and Danr function independently of Seven-up (Svp), an orphan nuclear receptor known to repress Hb expression in neuroblasts, because Dan, Danr and Svp do not regulate each other and dan danr svp triple mutants have increased early-born neurons compared with either dan danr or svp mutants. Interestingly, misexpression of Hb can induce Dan and Svp expression in neuroblasts, suggesting that Hb might activate a negative feedback loop to limit its own expression. We conclude that Dan/Danr and Svp act in parallel pathways to limit Hb expression and allow neuroblasts to transition from making early-born neurons to late-born neurons at the proper time.

  11. Rearrangements in the Relative Orientation of Cytoplasmic Domains Induced by a Membrane-anchored Protein Mediate Modulations in Kv Channel Gating*

    PubMed Central

    Lvov, Anatoli; Greitzer, Dafna; Berlin, Shai; Chikvashvili, Dodo; Tsuk, Sharon; Lotan, Ilana; Michaelevski, Izhak

    2009-01-01

    Interdomain interactions between intracellular N and C termini have been described for various K+ channels, including the voltage-gated Kv2.1, and suggested to affect channel gating. However, no channel regulatory protein directly affecting N/C interactions has been demonstrated. Most Kv2.1 channel interactions with regulatory factors occur at its C terminus. The vesicular SNARE that is also present at a high concentration in the neuronal plasma membrane, VAMP2, is the only protein documented to affect Kv2.1 gating by binding to its N terminus. As its binding target has been mapped near a site implicated in Kv2.1 N/C interactions, we hypothesized that VAMP2 binding to the N terminus requires concomitant conformational changes in the C terminus, which wraps around the N terminus from the outside, to give VAMP2 access. Here, we first determined that the Kv2.1 N terminus, although crucial, is not sufficient to convey functional interaction with VAMP2, and that, concomitant to its binding to the “docking loop” at the Kv2.1 N terminus, VAMP2 binds to the proximal part of the Kv2.1 C terminus, C1a. Next, using computational biology approaches (ab initio modeling, docking, and molecular dynamics simulations) supported by molecular biology, biochemical, electrophysiological, and fluorescence resonance energy transfer analyses, we mapped the interaction sites on both VAMP2 and Kv2.1 and found that this interaction is accompanied by rearrangements in the relative orientation of Kv2.1 cytoplasmic domains. We propose that VAMP2 modulates Kv2.1 inactivation by interfering with the interaction between the docking loop and C1a, a mechanism for gating regulation that may pertain also to other Kv channels. PMID:19690160

  12. Cloning, expression analysis, and RNA interference study of a HORMA domain containing autophagy-related gene 13 (ATG13) from the coleopteran beetle, Tenebrio molitor

    PubMed Central

    Lee, Jung Hee; Jo, Yong Hun; Patnaik, Bharat Bhusan; Park, Ki Beom; Tindwa, Hamisi; Seo, Gi Won; Chandrasekar, Raman; Lee, Yong Seok; Han, Yeon Soo

    2015-01-01

    Autophagy is a process that is necessary during starvation, as it replenishes metabolic precursors by eliminating damaged organelles. Autophagy is mediated by more than 35 autophagy-related (Atg) proteins that participate in the nucleation, elongation, and curving of the autophagosome membrane. In a pursuit to address the role of autophagy during development and immune resistance of the mealworm beetle, Tenebrio molitor, we screened ATG gene sequences from the whole-larva transcriptome database. We identified a homolog of ATG13 gene in T. molitor (designated as TmATG13) that comprises a cDNA of 1176 bp open reading frame (ORF) encoding a protein of 391 amino acids. Analyses of the structure-specific features of TmAtg13 showed an intrinsically disordered middle and C-terminal region that was rich in regulatory phosphorylation sites. The N-terminal Atg13 domain had a HORMA (Hop1, Rev7, and Mad2) fold containing amino acid residues conserved across the Atg13 insect orthologs. A quantitative reverse-transcription-polymerase chain reaction analysis revealed that TmATG13 was expressed ubiquitously during all developmental stages of the insect. TmATG13 mRNA expression was high in the fat body and gut of the larval and adult stages of the insect. The TmATG13 transcripts were expressed at a high level until 6 days of ovarian development, followed by a significant decline. Silencing of ATG13 transcripts in T. molitor larvae showed a reduced survivability of 39 and 38% in response to Escherichia coli and Staphylococcus aureus infection. Furthermore, the role of TmAtg13 in initiating autophagy as a part of the host cell autophagic complex of the host cells against the intracellular pathogen Listeria monocytogenes is currently under study and will be critical to unfold the structure-function relationships. PMID:26136688

  13. Differences in activation of aryl hydrocarbon receptors of white sturgeon relative to lake sturgeon are predicted by identities of key amino acids in the ligand binding domain.

    PubMed

    Doering, Jon A; Farmahin, Reza; Wiseman, Steve; Beitel, Shawn C; Kennedy, Sean W; Giesy, John P; Hecker, Markus

    2015-04-01

    Dioxin-like compounds (DLCs) are pollutants of global environmental concern. DLCs elicit their adverse outcomes through activation of the aryl hydrocarbon receptor (AhR). However, there is limited understanding of the mechanisms that result in differences in sensitivity to DLCs among different species of fishes. Understanding these mechanisms is critical for protection of the diversity of fishes exposed to DLCs, including endangered species. This study investigated specific mechanisms that drive responses of two endangered fishes, white sturgeon (Acipenser transmontanus) and lake sturgeon (Acipenser fulvescens) to DLCs. It determined whether differences in sensitivity to activation of AhRs (AhR1 and AhR2) can be predicted based on identities of key amino acids in the ligand binding domain (LBD). White sturgeon were 3- to 30-fold more sensitive than lake sturgeon to exposure to 5 different DLCs based on activation of AhR2. There were no differences in sensitivity between white sturgeon and lake sturgeon based on activation of AhR1. Adverse outcomes as a result of exposure to DLCs have been shown to be mediated through activation of AhR2, but not AhR1, in all fishes studied to date. This indicates that white sturgeon are likely to have greater sensitivity in vivo relative to lake sturgeon. Homology modeling and in silico mutagenesis suggests that differences in sensitivity to activation of AhR2 result from differences in key amino acids at position 388 in the LBD of AhR2 of white sturgeon (Ala-388) and lake sturgeon (Thr-388). This indicates that identities of key amino acids in the LBD of AhR2 could be predictive of both in vitro activation by DLCs and in vivo sensitivity to DLCs in these, and potentially other, fishes.

  14. Cloning, expression analysis, and RNA interference study of a HORMA domain containing autophagy-related gene 13 (ATG13) from the coleopteran beetle, Tenebrio molitor.

    PubMed

    Lee, Jung Hee; Jo, Yong Hun; Patnaik, Bharat Bhusan; Park, Ki Beom; Tindwa, Hamisi; Seo, Gi Won; Chandrasekar, Raman; Lee, Yong Seok; Han, Yeon Soo

    2015-01-01

    Autophagy is a process that is necessary during starvation, as it replenishes metabolic precursors by eliminating damaged organelles. Autophagy is mediated by more than 35 autophagy-related (Atg) proteins that participate in the nucleation, elongation, and curving of the autophagosome membrane. In a pursuit to address the role of autophagy during development and immune resistance of the mealworm beetle, Tenebrio molitor, we screened ATG gene sequences from the whole-larva transcriptome database. We identified a homolog of ATG13 gene in T. molitor (designated as TmATG13) that comprises a cDNA of 1176 bp open reading frame (ORF) encoding a protein of 391 amino acids. Analyses of the structure-specific features of TmAtg13 showed an intrinsically disordered middle and C-terminal region that was rich in regulatory phosphorylation sites. The N-terminal Atg13 domain had a HORMA (Hop1, Rev7, and Mad2) fold containing amino acid residues conserved across the Atg13 insect orthologs. A quantitative reverse-transcription-polymerase chain reaction analysis revealed that TmATG13 was expressed ubiquitously during all developmental stages of the insect. TmATG13 mRNA expression was high in the fat body and gut of the larval and adult stages of the insect. The TmATG13 transcripts were expressed at a high level until 6 days of ovarian development, followed by a significant decline. Silencing of ATG13 transcripts in T. molitor larvae showed a reduced survivability of 39 and 38% in response to Escherichia coli and Staphylococcus aureus infection. Furthermore, the role of TmAtg13 in initiating autophagy as a part of the host cell autophagic complex of the host cells against the intracellular pathogen Listeria monocytogenes is currently under study and will be critical to unfold the structure-function relationships. PMID:26136688

  15. NON-CONFORMING FINITE ELEMENTS; MESH GENERATION, ADAPTIVITY AND RELATED ALGEBRAIC MULTIGRID AND DOMAIN DECOMPOSITION METHODS IN MASSIVELY PARALLEL COMPUTING ENVIRONMENT

    SciTech Connect

    Lazarov, R; Pasciak, J; Jones, J

    2002-02-01

    Construction, analysis and numerical testing of efficient solution techniques for solving elliptic PDEs that allow for parallel implementation have been the focus of the research. A number of discretization and solution methods for solving second order elliptic problems that include mortar and penalty approximations and domain decomposition methods for finite elements and finite volumes have been investigated and analyzed. Techniques for parallel domain decomposition algorithms in the framework of PETC and HYPRE have been studied and tested. Hierarchical parallel grid refinement and adaptive solution methods have been implemented and tested on various model problems. A parallel code implementing the mortar method with algebraically constructed multiplier spaces was developed.

  16. Cetacean distribution and abundance in relation to oceanographic domains on the eastern Bering Sea shelf, June and July of 2002, 2008, and 2010

    NASA Astrophysics Data System (ADS)

    Friday, Nancy A.; Zerbini, Alexandre N.; Waite, Janice M.; Moore, Sue E.; Clapham, Phillip J.

    2013-10-01

    As part of the Bering Sea Project, cetacean surveys were conducted to describe distribution and estimate abundance on the eastern Bering Sea shelf. Three marine mammal observers conducted visual surveys along transect lines sampled during the Alaska Fisheries Science Center walleye pollock assessment survey in June and July of 2008 and 2010. Distribution and abundance in 2008 and 2010 (cold years) are compared with results from a similar survey conducted in 2002 (a warm year), as the only three years that the entire survey area was sampled; patterns largely match those previously observed. Abundance estimates for comparable areas in 2002, 2008 and 2010 were as follows: humpback whales (Megaptera novaeangliae): 231 (CV=0.63), 436 (CV=0.45), and 675 (CV=0.80); fin whales (Balaenoptera physalus): 419 (CV=0.33), 1368 (CV=0.34), and 1061 (CV=0.38); minke whales (Balaenoptera acutorostrata): 389 (CV=0.52), 517 (CV=0.69), and 2020 (CV=0.73); Dall's porpoise (Phocoenoides dalli): 35,303 (CV=0.53), 14,543 (CV=0.32), and 11,143 (CV=0.32); and harbor porpoise (Phocoena phocoena): 1971 (CV=0.46), 4056 (CV=0.40), and 833 (CV=0.66). It should be noted that these abundance estimates are not corrected for biases due to perception, availability, or responsive movement. Estimates for humpback, fin and minke whales increased from 2002 to 2010, while those for harbor and Dall's porpoise decreased; trends were significant for fin whales. It is likely that changes in estimated abundance are due at least in part to shifts in distribution and not just changes in overall population size. Annual abundance estimates were examined by oceanographic domain. Humpback whales were consistently concentrated in coastal waters north of Unimak Pass. Fin whales were broadly distributed in the outer domain and slope in 2008 and 2010, but sightings were sparse in 2002. Minke whales were distributed throughout the study area in 2002 and 2008, but in 2010 they were concentrated in the outer domain and

  17. What are archaebacteria: life's third domain or monoderm prokaryotes related to gram-positive bacteria? A new proposal for the classification of prokaryotic organisms.

    PubMed

    Gupta, R S

    1998-08-01

    The evolutionary relationship within prokaryotes is examined based on signature sequences (defined as conserved inserts or deletions shared by specific taxa) and phylogenies derived from different proteins. Archaebacteria are indicated as being monophyletic by a number of proteins related to the information transfer processes. In contrast, for several other highly conserved proteins, common signature sequences are present in archaebacteria and Gram-positive bacteria, whereas Gram-negative bacteria are indicated as being distinct. For these proteins, archaebacteria do not form a phylogenetically distinct clade but show polyphyletic branching within Gram-positive bacteria. A closer relationship of archaebacteria to Gram-positive bacteria in comparison with Gram-negative bacteria is generally seen for the majority of the available gene/ protein sequences. To account for these results and the fact that both archaebacteria and Gram-positive bacteria are prokaryotes surrounded by a single cell membrane, I propose that the primary division within prokaryotes is between monoderm prokaryotes (surrounded by a single membrane) and diderm prokaryotes (i.e. all true Gram-negative bacteria containing both an inner cytoplasmic membrane and an outer membrane). This proposal is consistent with both cell morphology and signature sequences in different proteins. The monophyletic nature of archaebacteria for some genes, and their polyphyletic branching within Gram-positive bacteria as suggested by others, is critically examined, and several explanations, including derivation of archaebacteria from Gram-positive bacteria in response to antibiotic selection pressure, are proposed. Signature sequences in proteins also indicate that the low-G+C Gram-positive bacteria are phylogenetically distinct from the high-G+C Gram-positive group and that the diderm prokaryotes (i.e. Gram-negative bacteria) appear to have evolved from the latter group. Protein phylogenies and signature sequences also

  18. Multifunctionalities driven by ferroic domains

    SciTech Connect

    Yang, J. C.; Huang, Y. L.; Chu, Y. H.; He, Q.

    2014-08-14

    Considerable attention has been paid to ferroic systems in pursuit of advanced applications in past decades. Most recently, the emergence and development of multiferroics, which exhibit the coexistence of different ferroic natures, has offered a new route to create functionalities in the system. In this manuscript, we step from domain engineering to explore a roadmap for discovering intriguing phenomena and multifunctionalities driven by periodic domain patters. As-grown periodic domains, offering exotic order parameters, periodic local perturbations and the capability of tailoring local spin, charge, orbital and lattice degrees of freedom, are introduced as modeling templates for fundamental studies and novel applications. We discuss related significant findings on ferroic domain, nanoscopic domain walls, and conjunct heterostructures based on the well-organized domain patterns, and end with future prospects and challenges in the field.

  19. Integration of New Domain-Related States and Events from Texts and Illustrations by Subjects with High and Low Prior Knowledge

    ERIC Educational Resources Information Center

    Molinari, Gaelle; Tapiero, Isabelle

    2007-01-01

    The aim of this article is to investigate with high and low knowledge subjects in the scientific domain of the neuron, the way information should be presented and illustrated to promote the integration of new information. This fundamental process for learning was examined in two experiments using a primed recognition task. In the first study, the…

  20. Convergence in the Domains of Static Spatial Relations and Events of Putting and Taking: Evidence from Bilingual Speakers of Romansh and German

    ERIC Educational Resources Information Center

    Berthele, Raphael

    2015-01-01

    In this article the way bilinguals handle differing semantic categories in their two languages will be investigated. Drawing on bilingual data from multilingual speakers of Romansh as well as from speakers of (Swiss) German, the tensions that emerge from "conflicting habits" in the two languages are analyzed in the semantic domain of…

  1. Self-Esteem Is Relatively Stable Late in Life: The Role of Resources in the Health, Self-Regulation, and Social Domains

    ERIC Educational Resources Information Center

    Wagner, Jenny; Hoppmann, Christiane; Ram, Nilam; Gerstorf, Denis

    2015-01-01

    A large body of research has documented changes in self-esteem across adulthood and individual-difference correlates thereof. However, little is known about whether people maintain their self-esteem until the end of life and what role key risk factors in the health, cognitive, self-regulatory, and social domains play. To examine these questions,…

  2. Do Nice Guys Really Finish Last? Exploring the Relations between Ethical Conduct, Motivation and Satisfaction among Undergraduates in the Domains of Academics and Athletics

    ERIC Educational Resources Information Center

    Yukhymenko, Mariya A.

    2012-01-01

    This study explored patterns of the ethical conduct of collegiate students in academic and athletic domains employing social cognitive theory (Bandura, 1986, 1997) using non-experimental, comparative and correlational designs. The study explored response patterns on anonymous surveys between varsity (N = 1151) and non-varsity (N = 227)…

  3. Identification of a novel cell death-inducing domain reveals that fungal amyloid-controlled programmed cell death is related to necroptosis

    PubMed Central

    Daskalov, Asen; Habenstein, Birgit; Sabaté, Raimon; Berbon, Mélanie; Martinez, Denis; Chaignepain, Stéphane; Coulary-Salin, Bénédicte; Hofmann, Kay; Loquet, Antoine; Saupe, Sven J.

    2016-01-01

    Recent findings have revealed the role of prion-like mechanisms in the control of host defense and programmed cell death cascades. In fungi, HET-S, a cell death-inducing protein containing a HeLo pore-forming domain, is activated through amyloid templating by a Nod-like receptor (NLR). Here we characterize the HELLP protein behaving analogously to HET-S and bearing a new type of N-terminal cell death-inducing domain termed HeLo-like (HELL) and a C-terminal regulatory amyloid motif known as PP. The gene encoding HELLP is part of a three-gene cluster also encoding a lipase (SBP) and a Nod-like receptor, both of which display the PP motif. The PP motif is similar to the RHIM amyloid motif directing formation of the RIP1/RIP3 necrosome in humans. The C-terminal region of HELLP, HELLP(215-278), encompassing the motif, allows prion propagation and assembles into amyloid fibrils, as demonstrated by X-ray diffraction and FTIR analyses. Solid-state NMR studies reveal a well-ordered local structure of the amyloid core residues and a primary sequence that is almost entirely arranged in a rigid conformation, and confirm a β-sheet structure in an assigned stretch of three amino acids. HELLP is activated by amyloid templating and displays membrane-targeting and cell death-inducing activity. HELLP targets the SBP lipase to the membrane, suggesting a synergy between HELLP and SBP in membrane dismantling. Remarkably, the HeLo-like domain of HELLP is homologous to the pore-forming domain of MLKL, the cell death-execution protein in necroptosis, revealing a transkingdom evolutionary relationship between amyloid-controlled fungal programmed cell death and mammalian necroptosis. PMID:26903619

  4. Identification of a novel cell death-inducing domain reveals that fungal amyloid-controlled programmed cell death is related to necroptosis.

    PubMed

    Daskalov, Asen; Habenstein, Birgit; Sabaté, Raimon; Berbon, Mélanie; Martinez, Denis; Chaignepain, Stéphane; Coulary-Salin, Bénédicte; Hofmann, Kay; Loquet, Antoine; Saupe, Sven J

    2016-03-01

    Recent findings have revealed the role of prion-like mechanisms in the control of host defense and programmed cell death cascades. In fungi, HET-S, a cell death-inducing protein containing a HeLo pore-forming domain, is activated through amyloid templating by a Nod-like receptor (NLR). Here we characterize the HELLP protein behaving analogously to HET-S and bearing a new type of N-terminal cell death-inducing domain termed HeLo-like (HELL) and a C-terminal regulatory amyloid motif known as PP. The gene encoding HELLP is part of a three-gene cluster also encoding a lipase (SBP) and a Nod-like receptor, both of which display the PP motif. The PP motif is similar to the RHIM amyloid motif directing formation of the RIP1/RIP3 necrosome in humans. The C-terminal region of HELLP, HELLP(215-278), encompassing the motif, allows prion propagation and assembles into amyloid fibrils, as demonstrated by X-ray diffraction and FTIR analyses. Solid-state NMR studies reveal a well-ordered local structure of the amyloid core residues and a primary sequence that is almost entirely arranged in a rigid conformation, and confirm a β-sheet structure in an assigned stretch of three amino acids. HELLP is activated by amyloid templating and displays membrane-targeting and cell death-inducing activity. HELLP targets the SBP lipase to the membrane, suggesting a synergy between HELLP and SBP in membrane dismantling. Remarkably, the HeLo-like domain of HELLP is homologous to the pore-forming domain of MLKL, the cell death-execution protein in necroptosis, revealing a transkingdom evolutionary relationship between amyloid-controlled fungal programmed cell death and mammalian necroptosis. PMID:26903619

  5. The C1q domain containing proteins of the Mediterranean mussel Mytilus galloprovincialis: a widespread and diverse family of immune-related molecules.

    PubMed

    Gerdol, Marco; Manfrin, Chiara; De Moro, Gianluca; Figueras, Antonio; Novoa, Beatriz; Venier, Paola; Pallavicini, Alberto

    2011-06-01

    The key component of the classical complement pathway C1q is regarded as a major connecting link between innate and acquired immunity due to the highly adaptive binding properties of its trimeric globular domain gC1q. The gC1q domain also characterizes many non-complement proteins involved in a broad range of biological processes including apoptosis, inflammation, cell adhesion and cell differentiation. In molluscs and many other invertebrates lacking of adaptive immunity, C1q domain containing (C1qDC) proteins are abundant, they most probably emerged as lectins and subsequently evolved in a specialized class of pattern recognition molecules through the expanding interaction properties of gC1q. Here we report the identification of 168 C1qDC transcript sequences of Mytilus galloprovincialis. The remarkable abundance of C1qDC transcripts in the Mediterranean mussel suggests an evolutionary strategy of gene duplication, functional diversification and selection of many specific C1qDC variants. A comprehensive transcript sequence survey in Protostomia also revealed that the C1qDC family expansion observed in mussel could have occurred in some specific taxa independently from the events leading to the establishment of a large complement of C1qDC genes in the Chordates lineage. PMID:21295069

  6. Functional representation of living and nonliving domains across the cerebral hemispheres: a combined event-related potential/transcranial magnetic stimulation study.

    PubMed

    Fuggetta, Giorgio; Rizzo, Silvia; Pobric, Gorana; Lavidor, Michal; Walsh, Vincent

    2009-02-01

    Transcranial magnetic stimulation (TMS) over the left hemisphere has been shown to disrupt semantic processing but, to date, there has been no direct demonstration of the electrophysiological correlates of this interference. To gain insight into the neural basis of semantic systems, and in particular, study the temporal and functional organization of object categorization processing, we combined repetitive TMS (rTMS) and ERPs. Healthy volunteers performed a picture-word matching task in which Snodgrass drawings of natural (e.g., animal) and artifactual (e.g., tool) categories were associated with a word. When short trains of high-frequency rTMS were applied over Wernicke's area (in the region of the CP5 electrode) immediately before the stimulus onset, we observed delayed response times to artifactual items, and thus, an increased dissociation between natural and artifactual domains. This behavioral effect had a direct ERP correlate. In the response period, the stimuli from the natural domain elicited a significant larger late positivity complex than those from the artifactual domain. These differences were significant over the centro-parietal region of the right hemisphere. These findings demonstrate that rTMS interferes with post-perceptual categorization processing of natural and artifactual stimuli that involve separate subsystems in distinct cortical areas. PMID:18510439

  7. Domain wall orientation and domain shape in KTiOPO4 crystals

    NASA Astrophysics Data System (ADS)

    Shur, V. Ya.; Vaskina, E. M.; Pelegova, E. V.; Chuvakova, M. A.; Akhmatkhanov, A. R.; Kizko, O. V.; Ivanov, M.; Kholkin, A. L.

    2016-09-01

    Domain shape evolution and domain wall motion have been studied in KTiOPO4 (KTP) ferroelectric single crystals using complementary experimental methods. The in situ visualization of domain kinetics has allowed revealing: (1) qualitative change of the domain shape, (2) dependence of the domain wall velocity on its orientation, (3) jump-like domain wall motion caused by domain merging, (4) effect of domain shape stability. The model of domain wall motion driven by generation of elementary steps (kink-pair nucleation) and subsequent kink motion is presented. The decrease in the relative velocity of the approaching parallel domain walls is attributed to electrostatic interaction. The effect of polarization reversal induced by chemical etching is observed. The obtained results are important for the development of domain engineering in the crystals of KTP family.

  8. Diversity in protein domain superfamilies

    PubMed Central

    Das, Sayoni; Dawson, Natalie L; Orengo, Christine A

    2015-01-01

    Whilst ∼93% of domain superfamilies appear to be relatively structurally and functionally conserved based on the available data from the CATH-Gene3D domain classification resource, the remainder are much more diverse. In this review, we consider how domains in some of the most ubiquitous and promiscuous superfamilies have evolved, in particular the plasticity in their functional sites and surfaces which expands the repertoire of molecules they interact with and actions performed on them. To what extent can we identify a core function for these superfamilies which would allow us to develop a ‘domain grammar of function’ whereby a protein's biological role can be proposed from its constituent domains? Clearly the first step is to understand the extent to which these components vary and how changes in their molecular make-up modifies function. PMID:26451979

  9. Hydrophobic Compounds Reshape Membrane Domains

    PubMed Central

    Barnoud, Jonathan; Rossi, Giulia; Marrink, Siewert J.; Monticelli, Luca

    2014-01-01

    Cell membranes have a complex lateral organization featuring domains with distinct composition, also known as rafts, which play an essential role in cellular processes such as signal transduction and protein trafficking. In vivo, perturbations of membrane domains (e.g., by drugs or lipophilic compounds) have major effects on the activity of raft-associated proteins and on signaling pathways, but they are difficult to characterize because of the small size of the domains, typically below optical resolution. Model membranes, instead, can show macroscopic phase separation between liquid-ordered and liquid-disordered domains, and they are often used to investigate the driving forces of membrane lateral organization. Studies in model membranes have shown that some lipophilic compounds perturb membrane domains, but it is not clear which chemical and physical properties determine domain perturbation. The mechanisms of domain stabilization and destabilization are also unknown. Here we describe the effect of six simple hydrophobic compounds on the lateral organization of phase-separated model membranes consisting of saturated and unsaturated phospholipids and cholesterol. Using molecular simulations, we identify two groups of molecules with distinct behavior: aliphatic compounds promote lipid mixing by distributing at the interface between liquid-ordered and liquid-disordered domains; aromatic compounds, instead, stabilize phase separation by partitioning into liquid-disordered domains and excluding cholesterol from the disordered domains. We predict that relatively small concentrations of hydrophobic species can have a broad impact on domain stability in model systems, which suggests possible mechanisms of action for hydrophobic compounds in vivo. PMID:25299598

  10. Supporting multiple domains in a single reuse repository

    NASA Technical Reports Server (NTRS)

    Eichmann, David A.

    1992-01-01

    Domain analysis typically results in the construction of a domain-specific repository. Such a repository imposes artificial boundaries on the sharing of similar assets between related domains. A lattice-based approach to repository modeling can preserve a reuser's domain specific view of the repository, while avoiding replication of commonly used assets and supporting a more general perspective on domain interrelationships.

  11. Generic domain models in software engineering

    NASA Technical Reports Server (NTRS)

    Maiden, Neil

    1992-01-01

    This paper outlines three research directions related to domain-specific software development: (1) reuse of generic models for domain-specific software development; (2) empirical evidence to determine these generic models, namely elicitation of mental knowledge schema possessed by expert software developers; and (3) exploitation of generic domain models to assist modelling of specific applications. It focuses on knowledge acquisition for domain-specific software development, with emphasis on tool support for the most important phases of software development.

  12. Mid-infrared pump-related electric-field domains in GaAs/(Al,Ga)As quantum-cascade structures for terahertz lasing without population inversion

    SciTech Connect

    Giehler, M.; Wienold, M.; Schrottke, L.; Hey, R.; Grahn, H. T.; Pavlov, S. G.; Huebers, H.-W.; Winnerl, S.; Schneider, H.

    2011-11-15

    We investigate the effect of mid-infrared (MIR) pumping on the transport properties of GaAs/(Al,Ga)As terahertz (THz) quantum lasers (TQLs), which rely on quantum coherence effects of intersubband transitions. Aiming at THz lasing at elevated temperatures, we extend the concept of THz gain with and without population inversion of a single, MIR-pumped, electrically driven THz stage proposed by Waldmueller et al.[Phys. Rev. Lett. 99, 117401 (2007)] to an entire TQL. However, experiments using a CO{sub 2} as well as a free-electron laser and numerical simulations show that this resonant MIR pumping causes a negative differential conductivity (NDC) in addition to the NDC caused by sequential tunneling. Lasing of these TQLs is prevented by the formation of electric-field domains below the resonance field strength for gain of each single THz stage.

  13. Sensing the Coherence of Biology in Contrast to Psychology: Young Children’s Use of Causal Relations to Distinguish Two Foundational Domains

    PubMed Central

    Erickson, Jane E.; Keil, Frank C.; Lockhart, Kristi L.

    2011-01-01

    To what extent do children understand that biological processes fall into 1 coherent domain unified by distinct causal principles? In Experiments 1 and 2 (N = 125) kindergartners are given triads of biological and psychological processes and asked to identify which 2 members of the triad belong together. Results show that 5-year-olds correctly cluster biological processes and separate them from psychological ones. Experiments 3 and 4 (N = 64) examine whether or not children make this distinction because they understand that biological and psychological processes operate according to fundamentally different causal mechanisms. The results suggest that 5-year-olds do possess this understanding, and furthermore, they have intuitions about the nature of these different mechanisms. PMID:20331675

  14. Distinct phenotypes of new transmembrane-domain neuregulin 1 mutant mice and the rescue effects of valproate on the observed schizophrenia-related cognitive deficits

    PubMed Central

    Pei, Ju-Chun; Liu, Chih-Min; Lai, Wen-Sung

    2014-01-01

    Accumulating evidence suggests that neuregulin 1 (NRG1) might be involved in the neurodevelopment, neural plasticity, GABAergic neurotransmission, and pathogenesis of schizophrenia. NRG1 is abundantly expressed in the hippocampus, and emerging studies have begun to reveal the link between NRG1 signaling and cognitive deficits in schizophrenic patients. Because the transmembrane domain of NRG1 is vital for both forward and reverse signaling cascades, new Nrg1-deficient mice that carry a truncation of the transmembrane domain of the Nrg1 gene were characterized and used in this study to test a NRG1 loss-of-function hypothesis for schizophrenia. Both male and female Nrg1 heterozygous mutant mice and their wild-type littermates were used in a series of 4 experiments to characterize the impact of Nrg1 on behavioral phenotypes and to determine the importance of Nrg1 in the regulation of hippocampal neuromorphology and local GABAergic interneurons. First, a comprehensive battery of behavioral tasks indicated that male Nrg1-deficient mice exhibited significant impairments in cognitive functions. Second, pharmacological challenges were conducted and revealed that Nrg1 haploinsufficiency altered GABAergic activity in males. Third, although no genotype-specific neuromorphological alterations were found in the hippocampal CA1 pyramidal neurons, significant reductions in the hippocampal expressions of GAD67 and parvalbumin were revealed in the Nrg1-deficient males. Fourth, chronic treatment with valproate rescued the observed behavioral deficits and hippocampal GAD67 reduction in Nrg1-deficient males. Collectively, these results indicate the potential therapeutic effect of valproate and the importance of Nrg1 in the regulation of cognitive functions and hippocampal GABAergic interneurons, especially in males. PMID:24782733

  15. Blocking metabotropic glutamate receptor subtype 7 (mGlu7) via the Venus flytrap domain (VFTD) inhibits amygdala plasticity, stress, and anxiety-related behavior.

    PubMed

    Gee, Christine E; Peterlik, Daniel; Neuhäuser, Christoph; Bouhelal, Rochdi; Kaupmann, Klemens; Laue, Grit; Uschold-Schmidt, Nicole; Feuerbach, Dominik; Zimmermann, Kaspar; Ofner, Silvio; Cryan, John F; van der Putten, Herman; Fendt, Markus; Vranesic, Ivo; Glatthar, Ralf; Flor, Peter J

    2014-04-18

    The metabotropic glutamate receptor subtype 7 (mGlu7) is an important presynaptic regulator of neurotransmission in the mammalian CNS. mGlu7 function has been linked to autism, drug abuse, anxiety, and depression. Despite this, it has been difficult to develop specific blockers of native mGlu7 signaling in relevant brain areas such as amygdala and limbic cortex. Here, we present the mGlu7-selective antagonist 7-hydroxy-3-(4-iodophenoxy)-4H-chromen-4-one (XAP044), which inhibits lateral amygdala long term potentiation (LTP) in brain slices from wild type mice with a half-maximal blockade at 88 nm. There was no effect of XAP044 on LTP of mGlu7-deficient mice, indicating that this pharmacological effect is mGlu7-dependent. Unexpectedly and in contrast to all previous mGlu7-selective drugs, XAP044 does not act via the seven-transmembrane region but rather via a binding pocket localized in mGlu7's extracellular Venus flytrap domain, a region generally known for orthosteric agonist binding. This was shown by chimeric receptor studies in recombinant cell line assays. XAP044 demonstrates good brain exposure and wide spectrum anti-stress and antidepressant- and anxiolytic-like efficacy in rodent behavioral paradigms. XAP044 reduces freezing during acquisition of Pavlovian fear and reduces innate anxiety, which is consistent with the phenotypes of mGlu7-deficient mice, the results of mGlu7 siRNA knockdown studies, and the inhibition of amygdala LTP by XAP044. Thus, we present an mGlu7 antagonist with a novel molecular mode of pharmacological action, providing significant application potential in psychiatry. Modeling the selective interaction between XAP044 and mGlu7's Venus flytrap domain, whose three-dimensional structure is already known, will facilitate future drug development supported by computer-assisted drug design.

  16. Protein domain architectures.

    PubMed

    Mulder, Nicola J

    2010-01-01

    Proteins are composed of functional units, or domains, that can be found alone or in combination with other domains. Analysis of protein domain architectures and the movement of protein domains within and across different genomes provide clues about the evolution of protein function. The classification of proteins into families and domains is provided through publicly available tools and databases that use known protein domains to predict other members in new proteins sequences. Currently at least 80% of the main protein sequence databases can be classified using these tools, thus providing a large data set to work from for analyzing protein domain architectures. Each of the protein domain databases provide intuitive web interfaces for viewing and analyzing their domain classifications and provide their data freely for downloading. Some of the main protein family and domain databases are described here, along with their Web-based tools for analyzing domain architectures.

  17. Structure of a conserved hypothetical protein, TTHA0849 from Thermus thermophilus HB8, at 2.4 Å resolution: a putative member of the StAR-related lipid-transfer (START) domain superfamily

    SciTech Connect

    Nakabayashi, Makoto; Shibata, Naoki; Komori, Hirofumi; Ueda, Yasufumi; Iino, Hitoshi; Ebihara, Akio; Kuramitsu, Seiki; Higuchi, Yoshiki

    2005-12-01

    The crystal structure of a conserved hypothetical protein, TTHA0849 from T. thermophilus HB8, has been determined at 2.4 Å resolution. The compact α+β structure shows the typical folding of the steroidogenic acute regulatory-related lipid-transfer (START) domain. The crystal structure of a conserved hypothetical protein, TTHA0849 from Thermus thermophilus HB8, has been determined at 2.4 Å resolution as a part of a structural and functional genomics project on T. thermophilus HB8. The main-chain folding shows a compact α+β motif, forming a hydrophobic cavity in the molecule. A structural similarity search reveals that it resembles those steroidogenic acute regulatory proteins that contain the lipid-transfer (START) domain, even though TTHA0849 shows comparatively weak sequence identity to polyketide cyclases. However, the size of the ligand-binding cavity is distinctly smaller than other START domain-containing proteins, suggesting that it catalyses the transfer of smaller ligand molecules.

  18. On Probability Domains III

    NASA Astrophysics Data System (ADS)

    Frič, Roman; Papčo, Martin

    2015-12-01

    Domains of generalized probability have been introduced in order to provide a general construction of random events, observables and states. It is based on the notion of a cogenerator and the properties of product. We continue our previous study and show how some other quantum structures fit our categorical approach. We discuss how various epireflections implicitly used in the classical probability theory are related to the transition to fuzzy probability theory and describe the latter probability theory as a genuine categorical extension of the former. We show that the IF-probability can be studied via the fuzzy probability theory. We outline a "tensor modification" of the fuzzy probability theory.

  19. Functional differentiation in the leucine-rich repeat domains of closely related plant virus-resistance proteins that recognize common avr proteins.

    PubMed

    Sekine, Ken-Taro; Tomita, Reiko; Takeuchi, Shigeharu; Atsumi, Go; Saitoh, Hiromasa; Mizumoto, Hiroyuki; Kiba, Akinori; Yamaoka, Naoto; Nishiguchi, Masamichi; Hikichi, Yasufumi; Kobayashi, Kappei

    2012-09-01

    The N' gene of Nicotiana sylvestris and L genes of Capsicum plants confer the resistance response accompanying the hypersensitive response (HR) elicited by tobamovirus coat proteins (CP) but with different viral specificities. Here, we report the identification of the N' gene. We amplified and cloned an N' candidate using polymerase chain reaction primers designed from L gene sequences. The N' candidate gene was a single 4143 base pairs fragment encoding a coiled-coil nucleotide-binding leucine-rich repeat (LRR)-type resistance protein of 1,380 amino acids. The candidate gene induced the HR in response to the coexpression of tobamovirus CP with the identical specificity as reported for N'. Analysis of N'-containing and tobamovirus-susceptible N. tabacum accessions supported the hypothesis that the candidate is the N' gene itself. Chimera analysis between N' and L(3) revealed that their LRR domains determine the spectrum of their tobamovirus CP recognition. Deletion and mutation analyses of N' and L(3) revealed that the conserved sequences in their C-terminal regions have important roles but contribute differentially to the recognition of common avirulence proteins. The results collectively suggest that Nicotiana N' and Capsicum L genes, which most likely evolved from a common ancestor, differentiated in their recognition specificity through changes in the structural requirements for LRR function.

  20. Origin and evolution of the archaeo-eukaryotic primase superfamily and related palm-domain proteins: structural insights and new members

    PubMed Central

    Iyer, Lakshminarayan M.; Koonin, Eugene V.; Leipe, Detlef D.; Aravind, L.

    2005-01-01

    We report an in-depth computational study of the protein sequences and structures of the superfamily of archaeo-eukaryotic primases (AEPs). This analysis greatly expands the range of diversity of the AEPs and reveals the unique active site shared by all members of this superfamily. In particular, it is shown that eukaryotic nucleo-cytoplasmic large DNA viruses, including poxviruses, asfarviruses, iridoviruses, phycodnaviruses and the mimivirus, encode AEPs of a distinct family, which also includes the herpesvirus primases whose relationship to AEPs has not been recognized previously. Many eukaryotic genomes, including chordates and plants, encode previously uncharacterized homologs of these predicted viral primases, which might be involved in novel DNA repair pathways. At a deeper level of evolutionary connections, structural comparisons indicate that AEPs, the nucleases involved in the initiation of rolling circle replication in plasmids and viruses, and origin-binding domains of papilloma and polyoma viruses evolved from a common ancestral protein that might have been involved in a protein-priming mechanism of initiation of DNA replication. Contextual analysis of multidomain protein architectures and gene neighborhoods in prokaryotes and viruses reveals remarkable parallels between AEPs and the unrelated DnaG-type primases, in particular, tight associations with the same repertoire of helicases. These observations point to a functional equivalence of the two classes of primases, which seem to have repeatedly displaced each other in various extrachromosomal replicons. PMID:16027112

  1. Understanding the Public Domain.

    ERIC Educational Resources Information Center

    Russell, Carrie

    2003-01-01

    This overview of the public domain covers: defining the public domain; figuring out if a work is protected by copyright; being sure a work is in the public domain; asserting the copyright protection and term; the Creative Commons initiative; building the Information Commons; when permission is needed for using a public domain work; and special…

  2. Mutation in domain II of IAA1 confers diverse auxin-related phenotypes and represses auxin-activated expression of Aux/IAA genes in steroid regulator-inducible system.

    PubMed

    Park, Jin-Young; Kim, Hye-Joung; Kim, Jungmook

    2002-12-01

    Most of Aux/IAA genes are rapidly induced by auxin. The Aux/IAA proteins are short-lived nuclear proteins sharing the four conserved domains. Domain II is critical for rapid degradation of Aux/IAA proteins. Among these gene family members, IAA1 is one of the earliest auxin-inducible genes. We used a steroid hormone-inducible system to reveal putative roles and downstream signaling of IAA1 in auxin response. Arabidopsis transgenic plants were generated expressing fusion protein of IAA1 (IAA1-GR) or IAA1 with a mutation in domain II (iaa1-GR) and the glucocorticoid hormone-binding domain (GR). IAA1-GR transgenic plants did not exhibit any discernable phenotypic differences by DEX treatment that allows nuclear translocation of the fusion protein. In contrast, diverse auxin-related physiological processes including gravitropism and phototropism were impaired by DEX treatment in roots, hypocotyls, stems, and leaves in iaa1-GR transgenic plants. Auxin induction of seven Aux/IAA mRNAs including IAA1 itself was repressed by DEX treatment, suggesting that IAA1 functions in the nucleus by mediating auxin response and might act as a negative feedback regulator for the expression of Aux/IAA genes including IAA1 itself. Auxin induction of Aux/IAA genes in the presence of cycloheximide can be repressed by DEX treatment, showing that the repression of transcription of the Aux/IAAs by the iaa1 mutant protein is primary. Wild-type IAA1-GR could not suppress auxin induction of IAA1 and IAA2. These results indicate that inhibition of auxin-activated transcription of Aux/IAA genes by the iaa1 mutant protein might be responsible for alteration of various auxin responses.

  3. High Affinity Binding of the Receptor-associated Protein D1D2 Domains with the Low Density Lipoprotein Receptor-related Protein (LRP1) Involves Bivalent Complex Formation: CRITICAL ROLES OF LYSINES 60 AND 191.

    PubMed

    Prasad, Joni M; Young, Patricia A; Strickland, Dudley K

    2016-08-26

    The LDL receptor-related protein 1 (LRP1) is a large endocytic receptor that binds and mediates the endocytosis of numerous structurally diverse ligands. Currently, the basis for ligand recognition by LRP1 is not well understood. LRP1 requires a molecular chaperone, termed the receptor-associated protein (RAP), to escort the newly synthesized receptor from the endoplasmic reticulum to the Golgi. RAP is a three-domain protein that contains the following two high affinity binding sites for LRP1: one is located within domains 1 and 2, and one is located in its third domain. Studies on the interaction of the RAP third domain with LRP1 reveal critical contributions by lysine 256 and lysine 270 for this interaction. From these studies, a model for ligand recognition by this class of receptors has been proposed. Here, we employed surface plasmon resonance to investigate the binding of RAP D1D2 to LRP1. Our results reveal that the high affinity of D1D2 for LRP1 results from avidity effects mediated by the simultaneous interactions of lysine 60 in D1 and lysine 191 in D2 with sites on LRP1 to form a bivalent D1D2-LRP1 complex. When lysine 60 and 191 are both mutated to alanine, the binding of D1D2 to LRP1 is ablated. Our data also reveal that D1D2 is able to bind to a second distinct site on LRP1 to form a monovalent complex. The studies confirm the canonical model for ligand recognition by this class of receptors, which is initiated by pairs of lysine residues that dock into acidic pockets on the receptor. PMID:27402839

  4. Students' tripartite efficacy beliefs in high school physical education: within- and cross-domain relations with motivational processes and leisure-time physical activity.

    PubMed

    Jackson, Ben; Whipp, Peter R; Chua, K L Peter; Dimmock, James A; Hagger, Martin S

    2013-02-01

    Within instructional settings, individuals form relational efficacy appraisals that complement their self-efficacy beliefs. In high school physical education (PE), for instance, students develop a level of confidence in their teacher's capabilities, as well as estimating how confident they think their teacher is in their (i.e., the students') ability. Grounded in existing transcontextual work, we examined the motivational pathways through which students' relational efficacy and self-efficacy beliefs in PE were predictive of their leisure-time physical activity. Singaporean students (N = 990; age M = 13.95, SD = 1.02) completed instruments assessing efficacy beliefs, perceptions of teacher relatedness support, and autonomous motivation toward PE, and 2 weeks later they reported their motivation toward, and engagement in, leisure-time physical activity. Structural equation modeling revealed that students reported stronger other-efficacy and RISE beliefs when they felt that their teacher created a highly relatedness-supportive environment. In turn, their relational efficacy beliefs (a) supported their confidence in their own ability, (b) directly and indirectly predicted more autonomous motives for participation in PE, and (c) displayed prospective transcontextual effects in relation to leisure-time variables. By emphasizing the adaptive motivational effects associated with the tripartite constructs, these findings highlight novel pathways linking students' efficacy perceptions with leisure-time outcomes.

  5. Structural and Semiotic Diversity in the Didactic Transition from the Natural-Number Domain to the Integers: A Study of Understanding in the Field of Additive Relativity

    ERIC Educational Resources Information Center

    Gonzalez-Mari, Jose Luis; Rico, Luis; Gallardo, Jesus

    2009-01-01

    Introduction: In the present-day didactic process of transition from natural numbers to integers, a certain kind of measure is involved which is neither easy nor appropriate to integrate into the familiar numerical systems. We refer to measures and comparisons for which we need a third numerical system--what we will call "relative natural"…

  6. Students' tripartite efficacy beliefs in high school physical education: within- and cross-domain relations with motivational processes and leisure-time physical activity.

    PubMed

    Jackson, Ben; Whipp, Peter R; Chua, K L Peter; Dimmock, James A; Hagger, Martin S

    2013-02-01

    Within instructional settings, individuals form relational efficacy appraisals that complement their self-efficacy beliefs. In high school physical education (PE), for instance, students develop a level of confidence in their teacher's capabilities, as well as estimating how confident they think their teacher is in their (i.e., the students') ability. Grounded in existing transcontextual work, we examined the motivational pathways through which students' relational efficacy and self-efficacy beliefs in PE were predictive of their leisure-time physical activity. Singaporean students (N = 990; age M = 13.95, SD = 1.02) completed instruments assessing efficacy beliefs, perceptions of teacher relatedness support, and autonomous motivation toward PE, and 2 weeks later they reported their motivation toward, and engagement in, leisure-time physical activity. Structural equation modeling revealed that students reported stronger other-efficacy and RISE beliefs when they felt that their teacher created a highly relatedness-supportive environment. In turn, their relational efficacy beliefs (a) supported their confidence in their own ability, (b) directly and indirectly predicted more autonomous motives for participation in PE, and (c) displayed prospective transcontextual effects in relation to leisure-time variables. By emphasizing the adaptive motivational effects associated with the tripartite constructs, these findings highlight novel pathways linking students' efficacy perceptions with leisure-time outcomes. PMID:23404881

  7. The Temporal Context Model in Spatial Navigation and Relational Learning: Toward a Common Explanation of Medial Temporal Lobe Function Across Domains

    ERIC Educational Resources Information Center

    Howard, Marc W.; Fotedar, Mrigankka S.; Datey, Aditya V.; Hasselmo, Michael E.

    2005-01-01

    The medial temporal lobe (MTL) has been studied extensively at all levels of analysis, yet its function remains unclear. Theory regarding the cognitive function of the MTL has centered along 3 themes. Different authors have emphasized the role of the MTL in episodic recall, spatial navigation, or relational memory. Starting with the temporal…

  8. The Temporal Context Model in spatial navigation and relational learning: Toward a common explanation of medial temporal lobe function across domains

    PubMed Central

    Howard, Marc W.; Fotedar, Mrigankka S.; Datey, Aditya V.; Hasselmo, Michael E.

    2005-01-01

    The medial temporal lobe (MTL) has been studied extensively at all levels of analysis, yet its function remains unclear. Theory regarding the cognitive function of the MTL has centered along 3 themes. Different authors have emphasized the role of the MTL in episodic recall, spatial navigation, or relational memory. Starting with the temporal context model (M. W. Howard and M. J. Kahana, 2002), a distributed memory model that has been applied to benchmark data from episodic recall tasks, the authors propose that the entorhinal cortex supports a gradually changing representation of temporal context and the hippocampus proper enables retrieval of these contextual states. Simulation studies show this hypothesis explains the firing of place cells in the entorhinal cortex and the behavioral effects of hippocampal lesion in relational memory tasks. These results constitute a first step towards a unified computational theory of MTL function that integrates neurophysiological, neuropsychological and cognitive findings. PMID:15631589

  9. Patterns of depressive symptoms and social relating behaviors differ over time from other behavioral domains for young people with Down syndrome.

    PubMed

    Foley, Kitty-Rose; Bourke, Jenny; Einfeld, Stewart L; Tonge, Bruce J; Jacoby, Peter; Leonard, Helen

    2015-05-01

    People with intellectual disabilities are at a higher risk for experiencing behavioral, emotional, and psychiatric problems in comparison with the general population. People with Down syndrome have been reported as experiencing fewer behavioral problems than others with intellectual disability, although still at a greater level than the non-intellectually disabled population, except for depression and Alzheimer disease. The aim of this study was to describe the trajectories of subscales of behavior, including depressive symptoms, communication disturbance, anxiety, disruptiveness, and social relating abilities, for young adults with Down syndrome.Families of young adults with Down syndrome living in Perth, Western Australia, participated in a questionnaire study over 8 years, 2004 (n = 255), 2009 (n = 191), and 2011 (n = 188). Questionnaires collected information about young person characteristics and family functioning. The parent-completed Developmental Behavior Checklist-Adult (DBC-A) and Developmental Behavior Checklist-Primary Carer Version (DBC-P) were used to measure emotional and behavioral problems. These measures include the following subscales: disruptive, communication and anxiety disturbances, self-absorbed, antisocial, depressive, and social relating.DBC score declined from 2004 to 2011 reflecting an improvement in behavior in the self-absorbed (coeff -0.011, 95% confidence interval (CI) -0.031, -0.008), anxiety (coef -0.009 95%CI -0.129, -0.006), communication disturbances (coeff -0.008, 95% CI -0.012, -0.005) and disruptive/antisocial behavior (coeff -0.013, 95% CI -0.016, -0.009) subscales. Subscales for depressive symptoms and social relating problems decreased less (coeff -0.003, 95% CI -0.007, -0.0001) (coeff -0.003 95% CI -0.007, 0.001). Young people who were lower functioning were reported as exhibiting significantly more behavioral problems across every subscale when compared with those who were higher functioning.Behavior of

  10. The La-related protein 1-specific domain repurposes HEAT-like repeats to directly bind a 5′TOP sequence

    PubMed Central

    Lahr, Roni M.; Mack, Seshat M.; Héroux, Annie; Blagden, Sarah P.; Bousquet-Antonelli, Cécile; Deragon, Jean-Marc; Berman, Andrea J.

    2015-01-01

    La-related protein 1 (LARP1) regulates the stability of many mRNAs. These include 5′TOPs, mTOR-kinase responsive mRNAs with pyrimidine-rich 5′ UTRs, which encode ribosomal proteins and translation factors. We determined that the highly conserved LARP1-specific C-terminal DM15 region of human LARP1 directly binds a 5′TOP sequence. The crystal structure of this DM15 region refined to 1.86 Å resolution has three structurally related and evolutionarily conserved helix-turn-helix modules within each monomer. These motifs resemble HEAT repeats, ubiquitous helical protein-binding structures, but their sequences are inconsistent with consensus sequences of known HEAT modules, suggesting this structure has been repurposed for RNA interactions. A putative mTORC1-recognition sequence sits within a flexible loop C-terminal to these repeats. We also present modelling of pyrimidine-rich single-stranded RNA onto the highly conserved surface of the DM15 region. These studies lay the foundation necessary for proceeding toward a structural mechanism by which LARP1 links mTOR signalling to ribosome biogenesis. PMID:26206669

  11. Predicting students' physical activity and health-related well-being: a prospective cross-domain investigation of motivation across school physical education and exercise settings.

    PubMed

    Standage, Martyn; Gillison, Fiona B; Ntoumanis, Nikos; Treasure, Darren C

    2012-02-01

    A three-wave prospective design was used to assess a model of motivation guided by self-determination theory (Ryan & Deci, 2008) spanning the contexts of school physical education (PE) and exercise. The outcome variables examined were health-related quality of life (HRQoL), physical self-concept (PSC), and 4 days of objectively assessed estimates of activity. Secondary school students (n = 494) completed questionnaires at three separate time points and were familiarized with how to use a sealed pedometer. Results of structural equation modeling supported a model in which perceptions of autonomy support from a PE teacher positively predicted PE-related need satisfaction (autonomy, competence, and relatedness). Competence predicted PSC, whereas relatedness predicted HRQoL. Autonomy and competence positively predicted autonomous motivation toward PE, which in turn positively predicted autonomous motivation toward exercise (i.e., 4-day pedometer step count). Autonomous motivation toward exercise positively predicted step count, HRQoL, and PSC. Results of multisample structural equation modeling supported gender invariance. Suggestions for future work are discussed.

  12. Crystallization of the receptor-binding domain of parathyroid hormone-related protein in complex with a neutralizing monoclonal antibody Fab fragment

    SciTech Connect

    McKinstry, William J.; Polekhina, Galina; Diefenbach-Jagger, Hannelore; Sato, Koh; Onuma, Etsuro; Gillespie, Matthew T.; Martin, Thomas J.; Parker, Michael W.

    2009-04-01

    Parathyroid hormone-related protein (PTHrP) plays an important role in regulating embryonic skeletal development and is abnormally regulated in the pathogenesis of skeletal complications observed with many cancers and osteoporosis. It exerts its action through binding to a G-protein-coupled seven-transmembrane cell-surface receptor (GPCR). Structurally, GPCRs are very difficult to study by X-ray crystallography. In this study, a monoclonal antibody Fab fragment which recognizes the same region of PTHrP as its receptor, PTH1R, was used to aid in the crystallization of PTHrP. The resultant protein complex was crystallized using the hanging-drop vapour-diffusion method with polyethylene glycol as a precipitant. The crystals belonged to the orthorhombic space group P2{sub 1}2{sub 1}2, with unit-cell parameters a = 72.6, b = 96.3, c = 88.5 {angstrom}, and diffracted to 2.0 {angstrom} resolution using synchrotron radiation. The crystal structure will shed light on the nature of the key residues of PTHrP that interact with the antibody and will provide insights into how the antibody is able to discriminate between PTHrP and the related molecule parathyroid homone.

  13. Reporting Valid and Reliable Overall Scores and Domain Scores

    ERIC Educational Resources Information Center

    Yao, Lihua

    2010-01-01

    In educational assessment, overall scores obtained by simply averaging a number of domain scores are sometimes reported. However, simply averaging the domain scores ignores the fact that different domains have different score points, that scores from those domains are related, and that at different score points the relationship between overall…

  14. The Inventory of Personality Organization: psychometric properties, factorial composition, and criterion relations with affect, aggressive dyscontrol, psychosis proneness, and self-domains in a nonclinical sample.

    PubMed

    Lenzenweger, M F; Clarkin, J F; Kernberg, O F; Foelsch, P A

    2001-12-01

    This report describes 2 studies of the psychometric characteristics of the primary clinical scales of the Inventory of Personality Organization (IPO; O. F. Kernberg & J. F. Clarkin, 1995), which assess reality testing, primitive psychological defenses, and identity diffusion, in a nonclinical sample. The 3 IPO scales display adequate internal consistency and good test-retest reliability. Item-level confirmatory factor analysis supported a two-factor structure of the IPO consistent with O. F. Kernberg's (1984, 1996) model of borderline personality organization. Each of the 3 IPO scales was associated with increased negative affect, aggressive dyscontrol, and dysphoria as well as lower levels of positive affect consistent with Kernberg's model of borderline personality organization. The IPO Reality Testing scale is closely related to various measures of psychotic-like phenomena. PMID:11793901

  15. Large-Scale Brain Networks in Board Game Experts: Insights from a Domain-Related Task and Task-Free Resting State

    PubMed Central

    Duan, Xujun; Liao, Wei; Liang, Dongmei; Qiu, Lihua; Gao, Qing; Liu, Chengyi; Gong, Qiyong; Chen, Huafu

    2012-01-01

    Cognitive performance relies on the coordination of large-scale networks of brain regions that are not only temporally correlated during different tasks, but also networks that show highly correlated spontaneous activity during a task-free state. Both task-related and task-free network activity has been associated with individual differences in cognitive performance. Therefore, we aimed to examine the influence of cognitive expertise on four networks associated with cognitive task performance: the default mode network (DMN) and three other cognitive networks (central-executive network, dorsal attention network, and salience network). During fMRI scanning, fifteen grandmaster and master level Chinese chess players (GM/M) and fifteen novice players carried out a Chinese chess task and a task-free resting state. Modulations of network activity during task were assessed, as well as resting-state functional connectivity of those networks. Relative to novices, GM/Ms showed a broader task-induced deactivation of DMN in the chess problem-solving task, and intrinsic functional connectivity of DMN was increased with a connectivity pattern associated with the caudate nucleus in GM/Ms. The three other cognitive networks did not exhibit any difference in task-evoked activation or intrinsic functional connectivity between the two groups. These findings demonstrate the effect of long-term learning and practice in cognitive expertise on large-scale brain networks, suggesting the important role of DMN deactivation in expert performance and enhanced functional integration of spontaneous activity within widely distributed DMN-caudate circuitry, which might better support high-level cognitive control of behavior. PMID:22427852

  16. C2-domain abscisic acid-related proteins mediate the interaction of PYR/PYL/RCAR abscisic acid receptors with the plasma membrane and regulate abscisic acid sensitivity in Arabidopsis.

    PubMed

    Rodriguez, Lesia; Gonzalez-Guzman, Miguel; Diaz, Maira; Rodrigues, Americo; Izquierdo-Garcia, Ana C; Peirats-Llobet, Marta; Fernandez, Maria A; Antoni, Regina; Fernandez, Daniel; Marquez, Jose A; Mulet, Jose M; Albert, Armando; Rodriguez, Pedro L

    2014-12-01

    Membrane-delimited abscisic acid (ABA) signal transduction plays a critical role in early ABA signaling, but the molecular mechanisms linking core signaling components to the plasma membrane are unclear. We show that transient calcium-dependent interactions of PYR/PYL ABA receptors with membranes are mediated through a 10-member family of C2-domain ABA-related (CAR) proteins in Arabidopsis thaliana. Specifically, we found that PYL4 interacted in an ABA-independent manner with CAR1 in both the plasma membrane and nucleus of plant cells. CAR1 belongs to a plant-specific gene family encoding CAR1 to CAR10 proteins, and bimolecular fluorescence complementation and coimmunoprecipitation assays showed that PYL4-CAR1 as well as other PYR/PYL-CAR pairs interacted in plant cells. The crystal structure of CAR4 was solved, which revealed that, in addition to a classical calcium-dependent lipid binding C2 domain, a specific CAR signature is likely responsible for the interaction with PYR/PYL receptors and their recruitment to phospholipid vesicles. This interaction is relevant for PYR/PYL function and ABA signaling, since different car triple mutants affected in CAR1, CAR4, CAR5, and CAR9 genes showed reduced sensitivity to ABA in seedling establishment and root growth assays. In summary, we identified PYR/PYL-interacting partners that mediate a transient Ca(2+)-dependent interaction with phospholipid vesicles, which affects PYR/PYL subcellular localization and positively regulates ABA signaling. PMID:25465408

  17. C2-domain abscisic acid-related proteins mediate the interaction of PYR/PYL/RCAR abscisic acid receptors with the plasma membrane and regulate abscisic acid sensitivity in Arabidopsis.

    PubMed

    Rodriguez, Lesia; Gonzalez-Guzman, Miguel; Diaz, Maira; Rodrigues, Americo; Izquierdo-Garcia, Ana C; Peirats-Llobet, Marta; Fernandez, Maria A; Antoni, Regina; Fernandez, Daniel; Marquez, Jose A; Mulet, Jose M; Albert, Armando; Rodriguez, Pedro L

    2014-12-01

    Membrane-delimited abscisic acid (ABA) signal transduction plays a critical role in early ABA signaling, but the molecular mechanisms linking core signaling components to the plasma membrane are unclear. We show that transient calcium-dependent interactions of PYR/PYL ABA receptors with membranes are mediated through a 10-member family of C2-domain ABA-related (CAR) proteins in Arabidopsis thaliana. Specifically, we found that PYL4 interacted in an ABA-independent manner with CAR1 in both the plasma membrane and nucleus of plant cells. CAR1 belongs to a plant-specific gene family encoding CAR1 to CAR10 proteins, and bimolecular fluorescence complementation and coimmunoprecipitation assays showed that PYL4-CAR1 as well as other PYR/PYL-CAR pairs interacted in plant cells. The crystal structure of CAR4 was solved, which revealed that, in addition to a classical calcium-dependent lipid binding C2 domain, a specific CAR signature is likely responsible for the interaction with PYR/PYL receptors and their recruitment to phospholipid vesicles. This interaction is relevant for PYR/PYL function and ABA signaling, since different car triple mutants affected in CAR1, CAR4, CAR5, and CAR9 genes showed reduced sensitivity to ABA in seedling establishment and root growth assays. In summary, we identified PYR/PYL-interacting partners that mediate a transient Ca(2+)-dependent interaction with phospholipid vesicles, which affects PYR/PYL subcellular localization and positively regulates ABA signaling.

  18. C2-Domain Abscisic Acid-Related Proteins Mediate the Interaction of PYR/PYL/RCAR Abscisic Acid Receptors with the Plasma Membrane and Regulate Abscisic Acid Sensitivity in Arabidopsis[C][W

    PubMed Central

    Rodriguez, Lesia; Diaz, Maira; Rodrigues, Americo; Izquierdo-Garcia, Ana C.; Peirats-Llobet, Marta; Fernandez, Maria A.; Antoni, Regina; Fernandez, Daniel; Marquez, Jose A.; Mulet, Jose M.; Albert, Armando; Rodriguez, Pedro L.

    2014-01-01

    Membrane-delimited abscisic acid (ABA) signal transduction plays a critical role in early ABA signaling, but the molecular mechanisms linking core signaling components to the plasma membrane are unclear. We show that transient calcium-dependent interactions of PYR/PYL ABA receptors with membranes are mediated through a 10-member family of C2-domain ABA-related (CAR) proteins in Arabidopsis thaliana. Specifically, we found that PYL4 interacted in an ABA-independent manner with CAR1 in both the plasma membrane and nucleus of plant cells. CAR1 belongs to a plant-specific gene family encoding CAR1 to CAR10 proteins, and bimolecular fluorescence complementation and coimmunoprecipitation assays showed that PYL4-CAR1 as well as other PYR/PYL-CAR pairs interacted in plant cells. The crystal structure of CAR4 was solved, which revealed that, in addition to a classical calcium-dependent lipid binding C2 domain, a specific CAR signature is likely responsible for the interaction with PYR/PYL receptors and their recruitment to phospholipid vesicles. This interaction is relevant for PYR/PYL function and ABA signaling, since different car triple mutants affected in CAR1, CAR4, CAR5, and CAR9 genes showed reduced sensitivity to ABA in seedling establishment and root growth assays. In summary, we identified PYR/PYL-interacting partners that mediate a transient Ca2+-dependent interaction with phospholipid vesicles, which affects PYR/PYL subcellular localization and positively regulates ABA signaling. PMID:25465408

  19. Oral health related quality of life in pregnant and post partum women in two social network domains; predominantly home-based and work-based networks

    PubMed Central

    2012-01-01

    Background Individuals connected to supportive social networks have better general and oral health quality of life. The objective of this study was to assess whether there were differences in oral health related quality of life (OHRQoL) between women connected to either predominantly home-based and work-based social networks. Methods A follow-up prevalence study was conducted on 1403 pregnant and post-partum women (mean age of 25.2 ± 6.3 years) living in two cities in the State of Rio de Janeiro, Brazil. Women were participants in an established cohort followed from pregnancy (baseline) to post-partum period (follow-up). All participants were allocated to two groups; 1. work-based social network group - employed women with paid work, and, 2. home-based social network group - women with no paid work, housewives or unemployed women. Measures of social support and social network were used as well as questions on sociodemographic characteristics and OHRQoL and health related behaviors. Multinomial logistic regression was performed to obtain OR of relationships between occupational contexts, affectionate support and positive social interaction on the one hand, and oral health quality of life, using the Oral Health Impacts Profile (OHIP) measure, adjusted for age, ethnicity, family income, schooling, marital status and social class. Results There was a modifying effect of positive social interaction on the odds of occupational context on OHRQoL. The odds of having a poorer OHIP score, ≥4, was significantly higher for women with home-based social networks and moderate levels of positive social interactions [OR 1.64 (95% CI: 1.08-2.48)], and for women with home-based social networks and low levels of positive social interactions [OR 2.15 (95% CI: 1.40-3.30)] compared with women with work-based social networks and high levels of positive social interactions. Black ethnicity was associated with OHIP scores ≥4 [OR 1.73 (95% CI: 1.23-2.42)]. Conclusions Pregnant and post

  20. Fixation-Related fMRI Analysis in the Domain of Reading Research: Using Self-Paced Eye Movements as Markers for Hemodynamic Brain Responses During Visual Letter String Processing

    PubMed Central

    Richlan, Fabio; Gagl, Benjamin; Hawelka, Stefan; Braun, Mario; Schurz, Matthias; Kronbichler, Martin; Hutzler, Florian

    2014-01-01

    The present study investigated the feasibility of using self-paced eye movements during reading (measured by an eye tracker) as markers for calculating hemodynamic brain responses measured by functional magnetic resonance imaging (fMRI). Specifically, we were interested in whether the fixation-related fMRI analysis approach was sensitive enough to detect activation differences between reading material (words and pseudowords) and nonreading material (line and unfamiliar Hebrew strings). Reliable reading-related activation was identified in left hemisphere superior temporal, middle temporal, and occipito-temporal regions including the visual word form area (VWFA). The results of the present study are encouraging insofar as fixation-related analysis could be used in future fMRI studies to clarify some of the inconsistent findings in the literature regarding the VWFA. Our study is the first step in investigating specific visual word recognition processes during self-paced natural sentence reading via simultaneous eye tracking and fMRI, thus aiming at an ecologically valid measurement of reading processes. We provided the proof of concept and methodological framework for the analysis of fixation-related fMRI activation in the domain of reading research. PMID:23645718

  1. Association of Piebaldism, multiple café-au-lait macules, and intertriginous freckling: clinical evidence of a common pathway between KIT and sprouty-related, ena/vasodilator-stimulated phosphoprotein homology-1 domain containing protein 1 (SPRED1).

    PubMed

    Chiu, Yvonne E; Dugan, Stefanie; Basel, Donald; Siegel, Dawn H

    2013-01-01

    Piebaldism is a rare genodermatosis caused by KIT mutations. We report the case of a 5-year-old boy who had the white forelock and leukoderma of piebaldism, but the presence of many café-au-lait macules and axillary and inguinal freckling complicated the diagnosis. Patients with similar cutaneous findings have been previously reported, and their disorder has been attributed to an overlap of piebaldism and neurofibromatosis type 1. Legius syndrome is a recently described syndrome caused by Sprouty-related, Ena/vasodilator-stimulated phosphoprotein homology-1 domain containing protein 1 (SPRED1) mutations that also has multiple café-au-lait macules and intertriginous freckling. Based on our current understanding of KIT and SPRED1 protein interactions, we propose that café-au-lait macules and freckling may be seen in some patients with piebaldism and does not necessarily represent coexistence of neurofibromatosis type 1.

  2. Generation of a Potent Low Density Lipoprotein Receptor-related Protein 1 (LRP1) Antagonist by Engineering a Stable Form of the Receptor-associated Protein (RAP) D3 Domain.

    PubMed

    Prasad, Joni M; Migliorini, Mary; Galisteo, Rebeca; Strickland, Dudley K

    2015-07-10

    The low density lipoprotein receptor-related protein 1 (LRP1) is a member of the low density lipoprotein receptor family and plays important roles in a number of physiological and pathological processes. Expression of LRP1 requires the receptor-associated protein (RAP), a molecular chaperone that binds LRP1 and other low density lipoprotein receptor family members in the endoplasmic reticulum and traffics with them to the Golgi where the acidic environment causes its dissociation. Exogenously added RAP is a potent LRP1 antagonist and binds to LRP1 on the cell surface, preventing ligands from binding. Following endocytosis, RAP dissociates in the acidic endosome, allowing LRP1 to recycle back to the cell surface. The acid-induced dissociation of RAP is mediated by its D3 domain, a relatively unstable three-helical bundle that denatures at pH <6.2 due to protonation of key histidine residues on helices 2 and 3. To develop an LRP1 inhibitor that does not dissociate at low pH, we introduced a disulfide bond between the second and third helices in the RAP D3 domain. By combining this disulfide bond with elimination of key histidine residues, we generated a stable RAP molecule that is resistant to both pH- and heat-induced denaturation. This molecule bound to LRP1 with high affinity at both neutral and acidic pH and proved to be a potent inhibitor of LRP1 function both in vitro and in vivo, suggesting that our stable RAP molecule may be useful in multiple pathological settings where LRP1 blockade has been shown to be effective.

  3. Functional domain walls in multiferroics

    NASA Astrophysics Data System (ADS)

    Meier, Dennis

    2015-11-01

    During the last decade a wide variety of novel and fascinating correlation phenomena has been discovered at domain walls in multiferroic bulk systems, ranging from unusual electronic conductance to inseparably entangled spin and charge degrees of freedom. The domain walls represent quasi-2D functional objects that can be induced, positioned, and erased on demand, bearing considerable technological potential for future nanoelectronics. Most of the challenges that remain to be solved before turning related device paradigms into reality, however, still fall in the field of fundamental condensed matter physics and materials science. In this topical review seminal experimental findings gained on electric and magnetic domain walls in multiferroic bulk materials are addressed. A special focus is put on the physical properties that emerge at so-called charged domain walls and the added functionality that arises from coexisting magnetic order. The research presented in this review highlights that we are just entering a whole new world of intriguing nanoscale physics that is yet to be explored in all its details. The goal is to draw attention to the persistent challenges and identify future key directions for the research on functional domain walls in multiferroics.

  4. Frequency domain FIR and IIR adaptive filters

    NASA Technical Reports Server (NTRS)

    Lynn, D. W.

    1990-01-01

    A discussion of the LMS adaptive filter relating to its convergence characteristics and the problems associated with disparate eigenvalues is presented. This is used to introduce the concept of proportional convergence. An approach is used to analyze the convergence characteristics of block frequency-domain adaptive filters. This leads to a development showing how the frequency-domain FIR adaptive filter is easily modified to provide proportional convergence. These ideas are extended to a block frequency-domain IIR adaptive filter and the idea of proportional convergence is applied. Experimental results illustrating proportional convergence in both FIR and IIR frequency-domain block adaptive filters is presented.

  5. Distinction of magnetic non-ferroelastic domains.

    PubMed

    Litvin, D B; Janovec, V

    2006-03-01

    It is shown that there always exists a coordinate system in which components of property tensors that distinguish between the domains of a magnetic non-ferroelastic domain pair differ solely in the two domains by a change in sign. The 309 classes of twin laws of magnetic non-ferroelastic domain pairs are listed and the twin laws, which are given in a coordinate system where the tensor distinction is provided by a change in sign of tensor components, are specified. If the twin law is not given in such a coordinate system, then a new coordinate system, related by a rotation, is specified. PMID:16489246

  6. Phenotypic variation caused by variation in the relative copy number of pDU1-based plasmids expressing the GAF domain of Pkn41 or Pkn42 in Anabaena sp. PCC 7120.

    PubMed

    Yang, Yang; Huang, Xiao-Zhen; Wang, Li; Risoul, Veronique; Zhang, Cheng-Cai; Chen, Wen-Li

    2013-01-01

    The cyanobacterium Anabaena (Nostoc) sp. PCC 7120 is a model for cyanobacterial cell differentiation studies. pDU1, an endogenous plasmid in Nostoc sp. PCC 7524, is used as the only cyanobacterial replicon for Anabaena (Nostoc) studies. However, the relative copy numbers of pDU1-based plasmids in Anabaena (Nostoc) sp. PCC 7120 are not well studied. We found that the relative plasmid copy number of one such vector, pRL25T, varied widely, especially when the vector carried a recombinant insert, under different conditions, ranging from 0.53 to 1812 per chromosome in different recombinant strains tested, either in independent clones of the same strain or in the same clone under different growth conditions. The phenotypes caused by pRL25T-driven expression of green fluorescent protein or the GAF domain of Pkn41 or Pkn42 varied depending on the independent clones analyzed. This phenotypic variation correlated with the relative plasmid copy number present in cells.

  7. Domains and Naive Theories

    PubMed Central

    Gelman, Susan A.; Noles, Nicholaus S.

    2013-01-01

    Human cognition entails domain-specific cognitive processes that influence memory, attention, categorization, problem-solving, reasoning, and knowledge organization. This review examines domain-specific causal theories, which are of particular interest for permitting an examination of how knowledge structures change over time. We first describe the properties of commonsense theories, and how commonsense theories differ from scientific theories, illustrating with children’s classification of biological and non-biological kinds. We next consider the implications of domain-specificity for broader issues regarding cognitive development and conceptual change. We then examine the extent to which domain-specific theories interact, and how people reconcile competing causal frameworks. Future directions for research include examining how different content domains interact, the nature of theory change, the role of context (including culture, language, and social interaction) in inducing different frameworks, and the neural bases for domain-specific reasoning. PMID:24187603

  8. Is the myonuclear domain size fixed?

    PubMed

    Van der Meer, S F T; Jaspers, R T; Degens, H

    2011-12-01

    It has been suggested that the number of myonuclei in a muscle fibre changes in proportion to the change in fibre size, resulting in a constant myonuclear domain size, defined as the cytoplasmic volume per myonucleus. The myonuclear domain size varies, however, between fibre types and is inversely related with the oxidative capacity of a fibre. Overall, the observations of an increase in myonuclear domain size during both maturational growth and overload-induced hypertrophy, and the decrease in myonuclear domain size during disuse- and ageing-associated muscle atrophy suggest that the concept of a constant myonuclear domain size needs to be treated cautiously. It also suggests that only when the myonuclear domain size exceeds a certain threshold during growth or overload-induced hypertrophy acquisition of new myonuclei is required for further fibre hypertrophy. PMID:22130137

  9. K Domain CR9 of Low Density Lipoprotein (LDL) Receptor-related Protein 1 (LRP1) Is Critical for Aggregated LDL-induced Foam Cell Formation from Human Vascular Smooth Muscle Cells*

    PubMed Central

    Costales, Paula; Fuentes-Prior, Pablo; Castellano, Jose; Revuelta-Lopez, Elena; Corral-Rodríguez, Maria Ángeles; Nasarre, Laura; Badimon, Lina; Llorente-Cortes, Vicenta

    2015-01-01

    Low density lipoprotein receptor-related protein (LRP1) mediates the internalization of aggregated LDL (AgLDL), which in turn increases the expression of LRP1 in human vascular smooth muscle cells (hVSMCs). This positive feedback mechanism is thus highly efficient to promote the formation of hVSMC foam cells, a crucial vascular component determining the susceptibility of atherosclerotic plaque to rupture. Here we have determined the LRP1 domains involved in AgLDL recognition with the aim of specifically blocking AgLDL internalization in hVSMCs. The capacity of fluorescently labeled AgLDL to bind to functional LRP1 clusters was tested in a receptor-ligand fluorometric assay made by immobilizing soluble LRP1 “minireceptors” (sLRP1-II, sLRP1-III, and sLRP1-IV) recombinantly expressed in CHO cells. This assay showed that AgLDL binds to cluster II. We predicted three well exposed and potentially immunogenic peptides in the CR7–CR9 domains of this cluster (termed P1 (Cys1051–Glu1066), P2 (Asp1090–Cys1104), and P3 (Gly1127–Cys1140)). AgLDL, but not native LDL, bound specifically and tightly to P3-coated wells. Rabbit polyclonal antibodies raised against P3 prevented AgLDL uptake by hVSMCs and were almost twice as effective as anti-P1 and anti-P2 Abs in reducing intracellular cholesteryl ester accumulation. Moreover, anti-P3 Abs efficiently prevented AgLDL-induced LRP1 up-regulation and counteracted the down-regulatory effect of AgLDL on hVSMC migration. In conclusion, domain CR9 appears to be critical for LRP1-mediated AgLDL binding and internalization in hVSMCs. Our results open new avenues for an innovative anti-VSMC foam cell-based strategy for the treatment of vascular lipid deposition in atherosclerosis. PMID:25918169

  10. The Dynamic Interdependence of Developmental Domains across Emerging Adulthood

    ERIC Educational Resources Information Center

    Sneed, Joel R.; Hamagami, Fumiaki; McArdle, John J.; Cohen, Patricia; Chen, Henian

    2007-01-01

    Emerging adulthood is a period in which profound role changes take place across a number of life domains including finance, romance, and residence. On the basis of dynamic systems theory, change in one domain should be related to change in another domain, because the concept of development according to this approach is a relational one. To…

  11. Visualizing domain wall and reverse domain superconductivity.

    PubMed

    Iavarone, M; Moore, S A; Fedor, J; Ciocys, S T; Karapetrov, G; Pearson, J; Novosad, V; Bader, S D

    2014-08-28

    In magnetically coupled, planar ferromagnet-superconductor (F/S) hybrid structures, magnetic domain walls can be used to spatially confine the superconductivity. In contrast to a superconductor in a uniform applied magnetic field, the nucleation of the superconducting order parameter in F/S structures is governed by the inhomogeneous magnetic field distribution. The interplay between the superconductivity localized at the domain walls and far from the walls leads to effects such as re-entrant superconductivity and reverse domain superconductivity with the critical temperature depending upon the location. Here we use scanning tunnelling spectroscopy to directly image the nucleation of superconductivity at the domain wall in F/S structures realized with Co-Pd multilayers and Pb thin films. Our results demonstrate that such F/S structures are attractive model systems that offer the possibility to control the strength and the location of the superconducting nucleus by applying an external magnetic field, potentially useful to guide vortices for computing application.

  12. Visualizing domain wall and reverse domain superconductivity

    PubMed Central

    Iavarone, M.; Moore, S. A.; Fedor, J.; Ciocys, S. T.; Karapetrov, G.; Pearson, J.; Novosad, V.; Bader, S. D.

    2014-01-01

    In magnetically coupled, planar ferromagnet-superconductor (F/S) hybrid structures, magnetic domain walls can be used to spatially confine the superconductivity. In contrast to a superconductor in a uniform applied magnetic field, the nucleation of the superconducting order parameter in F/S structures is governed by the inhomogeneous magnetic field distribution. The interplay between the superconductivity localized at the domain walls and far from the walls leads to effects such as re-entrant superconductivity and reverse domain superconductivity with the critical temperature depending upon the location. Here we use scanning tunnelling spectroscopy to directly image the nucleation of superconductivity at the domain wall in F/S structures realized with Co-Pd multilayers and Pb thin films. Our results demonstrate that such F/S structures are attractive model systems that offer the possibility to control the strength and the location of the superconducting nucleus by applying an external magnetic field, potentially useful to guide vortices for computing application. PMID:25164004

  13. Causal Learning Across Domains

    ERIC Educational Resources Information Center

    Schulz, Laura E.; Gopnik, Alison

    2004-01-01

    Five studies investigated (a) children's ability to use the dependent and independent probabilities of events to make causal inferences and (b) the interaction between such inferences and domain-specific knowledge. In Experiment 1, preschoolers used patterns of dependence and independence to make accurate causal inferences in the domains of…

  14. Domain wall filters

    SciTech Connect

    Baer, Oliver; Narayanan, Rajamani; Neuberger, Herbert; Witzel, Oliver

    2007-03-15

    We propose using the extra dimension separating the domain walls carrying lattice quarks of opposite handedness to gradually filter out the ultraviolet fluctuations of the gauge fields that are felt by the fermionic excitations living in the bulk. This generalization of the homogeneous domain wall construction has some theoretical features that seem nontrivial.

  15. Modeling Protein Domain Function

    ERIC Educational Resources Information Center

    Baker, William P.; Jones, Carleton "Buck"; Hull, Elizabeth

    2007-01-01

    This simple but effective laboratory exercise helps students understand the concept of protein domain function. They use foam beads, Styrofoam craft balls, and pipe cleaners to explore how domains within protein active sites interact to form a functional protein. The activity allows students to gain content mastery and an understanding of the…

  16. Domain Transfer Learning for MCI Conversion Prediction.

    PubMed

    Cheng, Bo; Liu, Mingxia; Zhang, Daoqiang; Munsell, Brent C; Shen, Dinggang

    2015-07-01

    Machine learning methods have successfully been used to predict the conversion of mild cognitive impairment (MCI) to Alzheimer's disease (AD), by classifying MCI converters (MCI-C) from MCI nonconverters (MCI-NC). However, most existing methods construct classifiers using data from one particular target domain (e.g., MCI), and ignore data in other related domains (e.g., AD and normal control (NC)) that may provide valuable information to improve MCI conversion prediction performance. To address is limitation, we develop a novel domain transfer learning method for MCI conversion prediction, which can use data from both the target domain (i.e., MCI) and auxiliary domains (i.e., AD and NC). Specifically, the proposed method consists of three key components: 1) a domain transfer feature selection component that selects the most informative feature-subset from both target domain and auxiliary domains from different imaging modalities; 2) a domain transfer sample selection component that selects the most informative sample-subset from the same target and auxiliary domains from different data modalities; and 3) a domain transfer support vector machine classification component that fuses the selected features and samples to separate MCI-C and MCI-NC patients. We evaluate our method on 202 subjects from the Alzheimer's Disease Neuroimaging Initiative (ADNI) that have MRI, FDG-PET, and CSF data. The experimental results show the proposed method can classify MCI-C patients from MCI-NC patients with an accuracy of 79.4%, with the aid of additional domain knowledge learned from AD and NC.

  17. XML Based Markup Languages for Specific Domains

    NASA Astrophysics Data System (ADS)

    Varde, Aparna; Rundensteiner, Elke; Fahrenholz, Sally

    A challenging area in web based support systems is the study of human activities in connection with the web, especially with reference to certain domains. This includes capturing human reasoning in information retrieval, facilitating the exchange of domain-specific knowledge through a common platform and developing tools for the analysis of data on the web from a domain expert's angle. Among the techniques and standards related to such work, we have XML, the eXtensible Markup Language. This serves as a medium of communication for storing and publishing textual, numeric and other forms of data seamlessly. XML tag sets are such that they preserve semantics and simplify the understanding of stored information by users. Often domain-specific markup languages are designed using XML, with a user-centric perspective. Standardization bodies and research communities may extend these to include additional semantics of areas within and related to the domain. This chapter outlines the issues to be considered in developing domain-specific markup languages: the motivation for development, the semantic considerations, the syntactic constraints and other relevant aspects, especially taking into account human factors. Illustrating examples are provided from domains such as Medicine, Finance and Materials Science. Particular emphasis in these examples is on the Materials Markup Language MatML and the semantics of one of its areas, namely, the Heat Treating of Materials. The focus of this chapter, however, is not the design of one particular language but rather the generic issues concerning the development of domain-specific markup languages.

  18. SOT1, a pentatricopeptide repeat protein with a small MutS-related domain, is required for correct processing of plastid 23S-4.5S rRNA precursors in Arabidopsis thaliana.

    PubMed

    Wu, Wenjuan; Liu, Sheng; Ruwe, Hannes; Zhang, Delin; Melonek, Joanna; Zhu, Yajuan; Hu, Xupeng; Gusewski, Sandra; Yin, Ping; Small, Ian D; Howell, Katharine A; Huang, Jirong

    2016-03-01

    Ribosomal RNA processing is essential for plastid ribosome biogenesis, but is still poorly understood in higher plants. Here, we show that SUPPRESSOR OF THYLAKOID FORMATION1 (SOT1), a plastid-localized pentatricopeptide repeat (PPR) protein with a small MutS-related domain, is required for maturation of the 23S-4.5S rRNA dicistron. Loss of SOT1 function leads to slower chloroplast development, suppression of leaf variegation, and abnormal 23S and 4.5S processing. Predictions based on the PPR motif sequences identified the 5' end of the 23S-4.5S rRNA dicistronic precursor as a putative SOT1 binding site. This was confirmed by electrophoretic mobility shift assay, and by loss of the abundant small RNA 'footprint' associated with this site in sot1 mutants. We found that more than half of the 23S-4.5S rRNA dicistrons in sot1 mutants contain eroded and/or unprocessed 5' and 3' ends, and that the endonucleolytic cleavage product normally released from the 5' end of the precursor is absent in a sot1 null mutant. We postulate that SOT1 binding protects the 5' extremity of the 23S-4.5S rRNA dicistron from exonucleolytic attack, and favours formation of the RNA structure that allows endonucleolytic processing of its 5' and 3' ends.

  19. Phylogenetic Analysis of Brassica rapa MATH-Domain Proteins.

    PubMed

    Zhao, Liming; Huang, Yong; Hu, Yan; He, Xiaoli; Shen, Wenhui; Liu, Chunlin; Ruan, Ying

    2013-05-01

    The MATH (meprin and TRAF-C homology) domain is a fold of seven anti-parallel β-helices involved in protein-protein interaction. Here, we report the identification and characterization of 90 MATH-domain proteins from the Brassica rapa genome. By sequence analysis together with MATH-domain proteins from other species, the B. rapa MATH-domain proteins can be grouped into 6 classes. Class-I protein has one or several MATH domains without any other recognizable domain; Class-II protein contains a MATH domain together with a conserved BTB (Broad Complex, Tramtrack, and Bric-a-Brac ) domain; Class-III protein belongs to the MATH/Filament domain family; Class-IV protein contains a MATH domain frequently combined with some other domains; Class-V protein has a relative long sequence but contains only one MATH domain; Class-VI protein is characterized by the presence of Peptidase and UBQ (Ubiquitinylation) domains together with one MATH domain. As part of our study regarding seed development of B. rapa, six genes are screened by SSH (Suppression Subtractive Hybridization) and their expression levels are analyzed in combination with seed developmental stages, and expression patterns suggested that Bra001786, Bra03578 and Bra036572 may be seed development specific genes, while Bra001787, Bra020541 and Bra040904 may be involved in seed and flower organ development. This study provides the first characterization of the MATH domain proteins in B. rapa.

  20. Requirements analysis, domain knowledge, and design

    NASA Technical Reports Server (NTRS)

    Potts, Colin

    1988-01-01

    Two improvements to current requirements analysis practices are suggested: domain modeling, and the systematic application of analysis heuristics. Domain modeling is the representation of relevant application knowledge prior to requirements specification. Artificial intelligence techniques may eventually be applicable for domain modeling. In the short term, however, restricted domain modeling techniques, such as that in JSD, will still be of practical benefit. Analysis heuristics are standard patterns of reasoning about the requirements. They usually generate questions of clarification or issues relating to completeness. Analysis heuristics can be represented and therefore systematically applied in an issue-based framework. This is illustrated by an issue-based analysis of JSD's domain modeling and functional specification heuristics. They are discussed in the context of the preliminary design of simple embedded systems.

  1. Visualizing Knowledge Domains.

    ERIC Educational Resources Information Center

    Borner, Katy; Chen, Chaomei; Boyack, Kevin W.

    2003-01-01

    Reviews visualization techniques for scientific disciplines and information retrieval and classification. Highlights include historical background of scientometrics, bibliometrics, and citation analysis; map generation; process flow of visualizing knowledge domains; measures and similarity calculations; vector space model; factor analysis;…

  2. A single lysine of the two-lysine recognition motif of the D3 domain of receptor-associated protein is sufficient to mediate endocytosis by low-density lipoprotein receptor-related protein.

    PubMed

    van den Biggelaar, Maartje; Sellink, Erica; Klein Gebbinck, Jacqueline W T M; Mertens, Koen; Meijer, Alexander B

    2011-03-01

    Ligand binding of the low-density lipoprotein (LDL) receptor family is mediated by complement-type repeats (CR) each comprising a binding pocket for a single basic amino acid residue. It has been proposed that at least two CRs are required for high-affinity interaction by utilising two spatially distinct lysine residues on the ligand surface. LDL receptor-related protein (LRP) mediates the cellular uptake of a multitude of ligands, some of which bind LRP with a relatively low affinity suggesting a suboptimal positioning of the two critical lysines. We now addressed the role of the two critical lysines not only in LRP binding but also in LRP-dependent endocytosis. Variants of the third domain (D3) of receptor-associated protein (RAP) were created carrying lysine to alanine or arginine replacements at the putative contact residues K253, K256 and K270. Surface plasmon resonance revealed that replacement of K253 did not affect high-affinity LRP binding at all, whereas replacement of either K256 or K270 markedly reduced the affinity by approximately 10-fold. Binding was abolished when both lysines were replaced. Substitution by either alanine or arginine exerted an almost identical effect on LRP binding. This suggests that despite their positive charge, arginine residues do not support receptor binding at all. Confocal microscopy and flow cytometry studies surprisingly revealed that the single mutants were still taken up and still competed for the uptake of full length RAP despite their receptor binding defect. We therefore propose that the presence of only one of the two critical lysines is sufficient to drive endocytosis. PMID:21144910

  3. Certifying Domain-Specific Policies

    NASA Technical Reports Server (NTRS)

    Lowry, Michael; Pressburger, Thomas; Rosu, Grigore; Koga, Dennis (Technical Monitor)

    2001-01-01

    Proof-checking code for compliance to safety policies potentially enables a product-oriented approach to certain aspects of software certification. To date, previous research has focused on generic, low-level programming-language properties such as memory type safety. In this paper we consider proof-checking higher-level domain -specific properties for compliance to safety policies. The paper first describes a framework related to abstract interpretation in which compliance to a class of certification policies can be efficiently calculated Membership equational logic is shown to provide a rich logic for carrying out such calculations, including partiality, for certification. The architecture for a domain-specific certifier is described, followed by an implemented case study. The case study considers consistency of abstract variable attributes in code that performs geometric calculations in Aerospace systems.

  4. Domain transfer learning for MCI conversion prediction.

    PubMed

    Cheng, Bo; Zhang, Daoqiang; Shen, Dinggang

    2012-01-01

    In recent studies of Alzheimer's disease (AD), it has increasing attentions in identifying mild cognitive impairment (MCI) converters (MCI-C) from MCI non-converters (MCI-NC). Note that MCI is a prodromal stage of AD, with possibility to convert to AD. Most traditional methods for MCI conversion prediction learn information only from MCI subjects (including MCI-C and MCI-NC), not from other related subjects, e.g., AD and normal controls (NC), which can actually aid the classification between MCI-C and MCI-NC. In this paper, we propose a novel domain-transfer learning method for MCI conversion prediction. Different from most existing methods, we classify MCI-C and MCI-NC with aid from the domain knowledge learned with AD and NC subjects as auxiliary domain to further improve the classification performance. Our method contains two key components: (1) the cross-domain kernel learning for transferring auxiliary domain knowledge, and (2) the adapted support vector machine (SVM) decision function construction for cross-domain and auxiliary domain knowledge fusion. Experimental results on the Alzheimer's Disease neuroimaging initiative (ADNI) database show that the proposed method can significantly improve the classification performance between MCI-C and MCI-NC, with aid of domain knowledge learned from AD and NC subjects.

  5. Changing Your Domain Name in 25 Nail-Biting Steps

    ERIC Educational Resources Information Center

    Hassler, Carol

    2012-01-01

    When staff at the Wisconsin State Law Library began compiling a wish list for a new website, the topic of a new domain name came up almost immediately. Their old website was located at http://wsll.state.wi.us. Spelling that relatively complex domain over the phone day after day provided the impetus to explore other options. Whatever domain name…

  6. Inhalational anesthetics disrupt postsynaptic density protein-95, Drosophila disc large tumor suppressor, and zonula occludens-1 domain protein interactions critical to action of several excitatory receptor channels related to anesthesia

    PubMed Central

    Tao, Feng; Chen, Qiang; Sato, Yuko; Skinner, John; Tang, Pei; Johns, Roger A.

    2015-01-01

    Background We have shown previously that inhaled anesthetics disrupt the interaction between the second postsynaptic density protein-95, Drosophila disc large tumor suppressor, and zonula occludens-1 (PDZ) domain of postsynaptic density protein-95 (PSD-95) and the C-terminus of N-methyl-D-aspartate receptor subunits NR2A and NR2B. Our data indicate that PDZ domains may serve as a molecular target for inhaled anesthetics. However, the underlying molecular mechanisms remain to be illustrated. Methods Glutathione S-transferase pull-down assay, co-immunoprecipitation and yeast two-hybrid analysis were used to assess PDZ domain-mediated protein-protein interactions in different conditions. Nuclear magnetic resonance spectroscopy was used to investigate isoflurane-induced chemical shift changes in the PDZ1–3 domains of PSD-95. A surface plasmon resonance-based BIAcore assay was used to examine the ability of isoflurane to inhibit the PDZ domain-mediated protein-protein interactions in real time. Results Halothane and isoflurane dose dependently inhibited PDZ domain-mediated interactions between PSD-95 and Shaker-type potassium channel Kv1.4 and between α-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid receptor subunit GluA2 and its interacting proteins— glutamate receptor interacting protein or protein interacting with c kinase 1. However, halothane and isoflurane had no effect on PDZ domain-mediated interactions between γ-aminobutyric acid, type B receptor and its interacting proteins. The inhaled anesthetic isoflurane mostly affected the residues close to or in the peptide binding groove of PSD-95 PDZ1 and PDZ2 (especially PDZ2), while barely affecting the peptide binding groove of PSD-95 PDZ3. Conclusion These results suggest that inhaled anesthetics interfere with PDZ domain-mediated protein-protein interactions at several receptors important to neuronal excitation, anesthesia and pain processing. PMID:25654436

  7. Domains in Ferroelectric Nanostructures

    NASA Astrophysics Data System (ADS)

    Gregg, Marty

    2010-03-01

    Ferroelectric materials have great potential in influencing the future of small scale electronics. At a basic level, this is because ferroelectric surfaces are charged, and so interact strongly with charge-carrying metals and semiconductors - the building blocks for all electronic systems. Since the electrical polarity of the ferroelectric can be reversed, surfaces can both attract and repel charges in nearby materials, and can thereby exert complete control over both charge distribution and movement. It should be no surprise, therefore, that microelectronics industries have already looked very seriously at harnessing ferroelectric materials in a variety of applications, from solid state memory chips (FeRAMs) to field effect transistors (FeFETs). In all such applications, switching the direction of the polarity of the ferroelectric is a key aspect of functional behavior. The mechanism for switching involves the field-induced nucleation and growth of domains. Domain coarsening, through domain wall propagation, eventually causes the entire ferroelectric to switch its polar direction. It is thus the existence and behavior of domains that determine the switching response, and ultimately the performance of the ferroelectric device. A major issue, associated with the integration of ferroelectrics into microelectronic devices, has been that the fundamental properties associated with ferroelectrics, when in bulk form, appear to change quite dramatically and unpredictably when at the nanoscale: new modes of behaviour, and different functional characteristics from those seen in bulk appear. For domains, in particular, the proximity of surfaces and boundaries have a dramatic effect: surface tension and depolarizing fields both serve to increase the equilibrium density of domains, such that minor changes in scale or morphology can have major ramifications for domain redistribution. Given the importance of domains in dictating the overall switching characteristics of a device

  8. The bldC Developmental Locus of Streptomyces coelicolor Encodes a Member of a Family of Small DNA-Binding Proteins Related to the DNA-Binding Domains of the MerR Family

    PubMed Central

    Hunt, Alison C.; Servín-González, Luis; Kelemen, Gabriella H.; Buttner, Mark J.

    2005-01-01

    The bldC locus, required for formation of aerial hyphae in Streptomyces coelicolor, was localized by map-based cloning to the overlap between cosmids D17 and D25 of a minimal ordered library. Subcloning and sequencing showed that bldC encodes a member of a previously unrecognized family of small (58- to 78-residue) DNA-binding proteins, related to the DNA-binding domains of the MerR family of transcriptional activators. BldC family members are found in a wide range of gram-positive and gram-negative bacteria. Constructed ΔbldC mutants were defective in differentiation and antibiotic production. They failed to form an aerial mycelium on minimal medium and showed severe delays in aerial mycelium formation on rich medium. In addition, they failed to produce the polyketide antibiotic actinorhodin, and bldC was shown to be required for normal and sustained transcription of the pathway-specific activator gene actII-orf4. Although ΔbldC mutants produced the tripyrrole antibiotic undecylprodigiosin, transcripts of the pathway-specific activator gene (redD) were reduced to almost undetectable levels after 48 h in the bldC mutant, in contrast to the bldC+ parent strain in which redD transcription continued during aerial mycelium formation and sporulation. This suggests that bldC may be required for maintenance of redD transcription during differentiation. bldC is expressed from a single promoter. S1 nuclease protection assays and immunoblotting showed that bldC is constitutively expressed and that transcription of bldC does not depend on any of the other known bld genes. The bldC18 mutation that originally defined the locus causes a Y49C substitution that results in instability of the protein. PMID:15629942

  9. Axion domain wall baryogenesis

    SciTech Connect

    Daido, Ryuji; Kitajima, Naoya; Takahashi, Fuminobu

    2015-07-28

    We propose a new scenario of baryogenesis, in which annihilation of axion domain walls generates a sizable baryon asymmetry. Successful baryogenesis is possible for a wide range of the axion mass and decay constant, m≃10{sup 8}–10{sup 13} GeV and f≃10{sup 13}–10{sup 16} GeV. Baryonic isocurvature perturbations are significantly suppressed in our model, in contrast to various spontaneous baryogenesis scenarios in the slow-roll regime. In particular, the axion domain wall baryogenesis is consistent with high-scale inflation which generates a large tensor-to-scalar ratio within the reach of future CMB B-mode experiments. We also discuss the gravitational waves produced by the domain wall annihilation and its implications for the future gravitational wave experiments.

  10. The effects of domain knowledge on metacomprehension accuracy.

    PubMed

    Griffin, Thomas D; Jee, Benjamin D; Wiley, Jennifer

    2009-10-01

    In the present research, we examined the relationship between readers' domain knowledge and their ability to judge their comprehension of novel domain-related material. Participants with varying degrees of baseball knowledge read five texts on baseball-related topics and five texts on non-baseball-related topics, predicted their performance, and completed tests for each text. Baseball knowledge was positively related to absolute accuracy within the baseball domain but was unrelated to relative accuracy within the baseball domain. Also, the readers showed a general underconfidence bias, but the bias was less extreme for higher knowledge readers. The results challenge common assumptions that experts' metacognitive judgments are less accurate than novices'. Results involving topic familiarity ratings and a no-reading control group suggest that higher knowledge readers are not more likely to ignore text-specific cues in favor of a domain familiarity heuristic, but they do appear to make more effective use of domain familiarity in predicting absolute performance levels.

  11. Construction of Galerkin's matrix for elementary potentials and an ellipsoidal solution domain based on series developments and general relations between Legendre's functions of the first and the second kind: Application in Earth's gravity field studies

    NASA Astrophysics Data System (ADS)

    Holota, Petr; Nesvadba, Otakar

    2016-04-01

    The role of boundary value problems in physical geodesy and in Earth's gravity field studies in particular is well-known. The paper focuses on Neumann's problem formulated for the exterior of an oblate ellipsoid of revolution as this is considered a basis for an iteration solution of the linear gravimetric boundary value problem in the determination of the disturbing potential. The approach follows the concept of variational methods and the notion of the weak solution. Hence Galerkin's approximations are applied, which means that the solution of the problem is approximated by linear combinations of basis functions with scalar coefficients. Our aim is to discuss the construction of Galerkin's matrix for basis functions generated by elementary potentials. Possibly, the computation of the entries of Galerkin's matrix is expected to be very simple for the elementary functions like these. Nevertheless, the opposite is true. Ellipsoidal harmonics are applied as a natural tool and elementary potentials are expressed by means of series of ellipsoidal harmonics. The problem, however, is the summation of the series that represent the entries of Galerkin's matrix. It is difficult to reduce the number of summation indices since in the ellipsoidal case there is no analogue to the addition theorem known for spherical harmonics. This makes the computation of Galerkin's matrix rather demanding. Therefore, the straightforward application of series of ellipsoidal harmonics is complemented by deeper relations contained in the theory of ordinary differential equations of second order and Legendre's functions. Subsequently, hypergeometric functions and series are used. Moreover, within some approximations the entries are split into parts. Some of the resulting series may be summed relatively easily, apart from technical tricks. For the remaining series the summation needs more complex tools. It was converted to elliptic integrals. The approach made it possible to deduce a closed

  12. The BH4 domain of anti-apoptotic Bcl-XL, but not that of the related Bcl-2, limits the voltage-dependent anion channel 1 (VDAC1)-mediated transfer of pro-apoptotic Ca2+ signals to mitochondria.

    PubMed

    Monaco, Giovanni; Decrock, Elke; Arbel, Nir; van Vliet, Alexander R; La Rovere, Rita M; De Smedt, Humbert; Parys, Jan B; Agostinis, Patrizia; Leybaert, Luc; Shoshan-Barmatz, Varda; Bultynck, Geert

    2015-04-01

    Excessive Ca(2+) fluxes from the endoplasmic reticulum to the mitochondria result in apoptotic cell death. Bcl-2 and Bcl-XL proteins exert part of their anti-apoptotic function by directly targeting Ca(2+)-transport systems, like the endoplasmic reticulum-localized inositol 1,4,5-trisphosphate receptors (IP3Rs) and the voltage-dependent anion channel 1 (VDAC1) at the outer mitochondrial membranes. We previously demonstrated that the Bcl-2 homology 4 (BH4) domain of Bcl-2 protects against Ca(2+)-dependent apoptosis by binding and inhibiting IP3Rs, although the BH4 domain of Bcl-XL was protective independently of binding IP3Rs. Here, we report that in contrast to the BH4 domain of Bcl-2, the BH4 domain of Bcl-XL binds and inhibits VDAC1. In intact cells, delivery of the BH4-Bcl-XL peptide via electroporation limits agonist-induced mitochondrial Ca(2+) uptake and protects against staurosporine-induced apoptosis, in line with the results obtained with VDAC1(-/-) cells. Moreover, the delivery of the N-terminal domain of VDAC1 as a synthetic peptide (VDAC1-NP) abolishes the ability of BH4-Bcl-XL to suppress mitochondrial Ca(2+) uptake and to protect against apoptosis. Importantly, VDAC1-NP did not affect the ability of BH4-Bcl-2 to suppress agonist-induced Ca(2+) release in the cytosol or to prevent apoptosis, as done instead by an IP3R-derived peptide. In conclusion, our data indicate that the BH4 domain of Bcl-XL, but not that of Bcl-2, selectively targets VDAC1 and inhibits apoptosis by decreasing VDAC1-mediated Ca(2+) uptake into the mitochondria.

  13. Cellulose binding domain proteins

    DOEpatents

    Shoseyov, O.; Shpiegl, I.; Goldstein, M.; Doi, R.

    1998-11-17

    A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques. 16 figs.

  14. Cellulose binding domain proteins

    DOEpatents

    Shoseyov, Oded; Shpiegl, Itai; Goldstein, Marc; Doi, Roy

    1998-01-01

    A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production thereof. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques.

  15. Putative Domain-Domain Interactions in the Vesicular Stomatitis Virus L Polymerase Protein Appendage Region

    PubMed Central

    Ruedas, John B.

    2014-01-01

    concert to enable virus genome transcription and replication. But how the unique L protein carries out the multiplicity of individual steps in these two distinct processes is poorly understood. Using two different approaches, i.e., exchanging individual domains in the C-terminal appendage region of the protein between two closely related VSV serotypes and inserting unrelated protein domains, we shed light on requirements for domain-domain interactions and domain contiguity in polymerase function. These findings further our understanding of the conformational dynamics of NNS L polymerase proteins, which play an essential role in the pathogenic properties of these viruses and represent attractive targets for the development of antiviral measures. PMID:25297996

  16. Rating knowledge sharing in cross-domain collaborative filtering.

    PubMed

    Li, Bin; Zhu, Xingquan; Li, Ruijiang; Zhang, Chengqi

    2015-05-01

    Cross-domain collaborative filtering (CF) aims to share common rating knowledge across multiple related CF domains to boost the CF performance. In this paper, we view CF domains as a 2-D site-time coordinate system, on which multiple related domains, such as similar recommender sites or successive time-slices, can share group-level rating patterns. We propose a unified framework for cross-domain CF over the site-time coordinate system by sharing group-level rating patterns and imposing user/item dependence across domains. A generative model, say ratings over site-time (ROST), which can generate and predict ratings for multiple related CF domains, is developed as the basic model for the framework. We further introduce cross-domain user/item dependence into ROST and extend it to two real-world cross-domain CF scenarios: 1) ROST (sites) for alleviating rating sparsity in the target domain, where multiple similar sites are viewed as related CF domains and some items in the target domain depend on their correspondences in the related ones; and 2) ROST (time) for modeling user-interest drift over time, where a series of time-slices are viewed as related CF domains and a user at current time-slice depends on herself in the previous time-slice. All these ROST models are instances of the proposed unified framework. The experimental results show that ROST (sites) can effectively alleviate the sparsity problem to improve rating prediction performance and ROST (time) can clearly track and visualize user-interest drift over time.

  17. Protein-Protein Interactions Inferred from Domain-Domain Interactions in Genogroup II Genotype 4 Norovirus Sequences

    PubMed Central

    Huang, Chuan-Ching

    2013-01-01

    Severe gastroenteritis and foodborne illness caused by Noroviruses (NoVs) during the winter are a worldwide phenomenon. Vulnerable populations including young children and elderly and immunocompromised people often require hospitalization and may die. However, no efficient vaccine for NoVs exists because of their variable genome sequences. This study investigates the infection processes in protein-protein interactions between hosts and NoVs. Protein-protein interactions were collected from related Pfam NoV domains. The related Pfam domains were accumulated incrementally from the protein domain interaction database. To examine the influence of domain intimacy, the 7 NoV domains were grouped by depth. The number of domain-domain interactions increased exponentially as the depth increased. Many protein-protein interactions were relevant; therefore, cloud techniques were used to analyze data because of their computational capacity. The infection relationship between hosts and NoVs should be used in clinical applications and drug design. PMID:23738320

  18. Crystal structure of domain-swapped STE20 OSR1 kinase domain

    SciTech Connect

    Lee, Seung-Jae; Cobb, Melanie H.; Goldsmith, Elizabeth J.

    2009-09-15

    OSR1 (oxidative stress-responsive-1) and SPAK (Ste20/Sps1-related proline/alanine-rich kinase) belong to the GCK-VI subfamily of Ste20 group kinases. OSR1 and SPAK are key regulators of NKCCs (Na{sup +}/K{sup +}/2Cl{sup -} cotransporters) and activated by WNK family members (with-no-lysine kinase), mutations of which are known to cause Gordon syndrome, an autosomal dominant form of inherited hypertension. The crystal structure of OSR1 kinase domain has been solved at 2.25 {angstrom}. OSR1 forms a domain-swapped dimer in an inactive conformation, in which P+1 loop and {alpha}EF helix are swapped between dimer-related monomers. Structural alignment with nonswapped Ste20 TAO2 kinase indicates that the integrity of chemical interactions in the kinase domain is well preserved in the domain-swapped interfaces. The OSR1 kinase domain has now been added to a growing list of domain-swapped protein kinases recently reported, suggesting that the domain-swapping event provides an additional layer of complexity in regulating protein kinase activity.

  19. Incubational domain characterization in lightly doped ceria

    SciTech Connect

    Li Zhipeng; Mori, Toshiyuki; John Auchterlonie, Graeme; Zou Jin; Drennan, John

    2012-08-15

    Microstructures of both Gd- and Y-doped ceria with different doping level (i.e., 10 at% and 25 at%) have been comprehensively characterized by means of high resolution transmission electron microscopy and selected area electron diffraction. Coherent nano-sized domains can be widely observed in heavily doped ceria. Nevertheless, it was found that a large amount of dislocations actually exist in lightly doped ceria instead of heavily doped ones. Furthermore, incubational domains can be detected in lightly doped ceria, with dislocations located at the interfaces. The interactions between such linear dislocations and dopant defects have been simulated accordingly. As a consequence, the formation mechanism of incubational domains is rationalized in terms of the interaction between intrinsic dislocations of doped ceria and dopant defects. This study offers the insights into the initial state and related mechanism of the formation of nano-sized domains, which have been widely observed in heavily rare-earth-doped ceria in recent years. - Graphical abstract: Interactions between dislocations and dopants lead to incubational domain formation in lightly doped ceria. Highlights: Black-Right-Pointing-Pointer Microstructures were characterized in both heavily and light Gd-/Y-doped ceria. Black-Right-Pointing-Pointer Dislocations are existed in lightly doped ceria rather than heavily doped one. Black-Right-Pointing-Pointer Interactions between dislocations and dopant defects were simulated. Black-Right-Pointing-Pointer Formation of dislocation associated incubational domain is rationalized.

  20. Comparison of the domain and frequency domain state feedbacks

    SciTech Connect

    Zhang, S.Y.

    1986-01-01

    In this paper, we present explicitly the equivalence of the time domain and frequency domain state feedbacks, as well as the dynamic state feedback and a modified frequency domain state feedback, from the closed-loop transfer function point of view. The difference of the two approaches is also shown.

  1. Domain Specific vs Domain General: Implications for Dynamic Assessment

    ERIC Educational Resources Information Center

    Kaniel, Shlomo

    2010-01-01

    The article responds to the need for evidence-based dynamic assessment. The article is divided into two sections: In Part 1 we examine the scientific answer to the question of how far human mental activities and capabilities are domain general (DG) / domain specific (DS). A highly complex answer emerges from the literature review of domains such…

  2. Frequency domain nonlinear optics

    NASA Astrophysics Data System (ADS)

    Legare, Francois

    2016-05-01

    The universal dilemma of gain narrowing occurring in fs amplifiers prevents ultra-high power lasers from delivering few-cycle pulses. This problem is overcome by a new amplification concept: Frequency domain Optical Parametric Amplification - FOPA. It enables simultaneous up-scaling of peak power and amplified spectral bandwidth and can be performed at any wavelength range of conventional amplification schemes, however, with the capability to amplify single cycles of light. The key idea for amplification of octave-spanning spectra without loss of spectral bandwidth is to amplify the broad spectrum ``slice by slice'' in the frequency domain, i.e. in the Fourier plane of a 4f-setup. The striking advantages of this scheme, are its capability to amplify (more than) one octave of bandwidth without shorting the corresponding pulse duration. This is because ultrabroadband phase matching is not defined by the properties of the nonlinear crystal employed but the number of crystals employed. In the same manner, to increase the output energy one simply has to increase the spectral extension in the Fourier plane and to add one more crystal. Thus, increasing pulse energy and shortening its duration accompany each other. A proof of principle experiment was carried out at ALLS on the sub-two cycle IR beam line and yielded record breaking performance in the field of few-cycle IR lasers. 100 μJ two-cycle pulses from a hollow core fibre compression setup were amplified to 1.43mJ without distorting spatial or temporal properties. Pulse duration at the input of FOPA and after FOPA remains the same. Recently, we have started upgrading this system to be pumped by 250 mJ to reach 40 mJ two-cycle IR few-cycle pulses and latest results will be presented at the conference. Furthermore, the extension of the concept of FOPA to other nonlinear optical processes will be discussed. Frequency domain nonlinear optics.

  3. Transfer of high domain knowledge to a similar domain.

    PubMed

    Jessup, Ryan K

    2009-01-01

    Researchers have widely examined domain knowledge yet rarely investigate the transfer of knowledge from one domain to another. This study sought to fill in the literature gap concerning the impact of domain knowledge on memory in a similar situation. Specifically, this study examined whether high knowledge of baseball could enhance memory for the similar yet unknown domain of cricket, using a 2 (knowledge) x 2 (prime) design. An interaction occurred, indicating that when primed, baseball knowledge improves memory for cricket events in participants with high baseball knowledge but reduces memory in their low-knowledge counterparts. These results suggest that extensive knowledge in one domain allows it to serve as an organizational framework for incoming information in a similar domain; conversely, priming poorly understood domain knowledge results in negative transfer.

  4. Transfer of high domain knowledge to a similar domain.

    PubMed

    Jessup, Ryan K

    2009-01-01

    Researchers have widely examined domain knowledge yet rarely investigate the transfer of knowledge from one domain to another. This study sought to fill in the literature gap concerning the impact of domain knowledge on memory in a similar situation. Specifically, this study examined whether high knowledge of baseball could enhance memory for the similar yet unknown domain of cricket, using a 2 (knowledge) x 2 (prime) design. An interaction occurred, indicating that when primed, baseball knowledge improves memory for cricket events in participants with high baseball knowledge but reduces memory in their low-knowledge counterparts. These results suggest that extensive knowledge in one domain allows it to serve as an organizational framework for incoming information in a similar domain; conversely, priming poorly understood domain knowledge results in negative transfer. PMID:19353932

  5. Simplicity and Specificity in Language: Domain-General Biases Have Domain-Specific Effects

    PubMed Central

    Culbertson, Jennifer; Kirby, Simon

    2016-01-01

    The extent to which the linguistic system—its architecture, the representations it operates on, the constraints it is subject to—is specific to language has broad implications for cognitive science and its relation to evolutionary biology. Importantly, a given property of the linguistic system can be “specific” to the domain of language in several ways. For example, if the property evolved by natural selection under the pressure of the linguistic function it serves then the property is domain-specific in the sense that its design is tailored for language. Equally though, if that property evolved to serve a different function or if that property is domain-general, it may nevertheless interact with the linguistic system in a way that is unique. This gives a second sense in which a property can be thought of as specific to language. An evolutionary approach to the language faculty might at first blush appear to favor domain-specificity in the first sense, with individual properties of the language faculty being specifically linguistic adaptations. However, we argue that interactions between learning, culture, and biological evolution mean any domain-specific adaptations that evolve will take the form of weak biases rather than hard constraints. Turning to the latter sense of domain-specificity, we highlight a very general bias, simplicity, which operates widely in cognition and yet interacts with linguistic representations in domain-specific ways. PMID:26793132

  6. Simplicity and Specificity in Language: Domain-General Biases Have Domain-Specific Effects.

    PubMed

    Culbertson, Jennifer; Kirby, Simon

    2015-01-01

    The extent to which the linguistic system-its architecture, the representations it operates on, the constraints it is subject to-is specific to language has broad implications for cognitive science and its relation to evolutionary biology. Importantly, a given property of the linguistic system can be "specific" to the domain of language in several ways. For example, if the property evolved by natural selection under the pressure of the linguistic function it serves then the property is domain-specific in the sense that its design is tailored for language. Equally though, if that property evolved to serve a different function or if that property is domain-general, it may nevertheless interact with the linguistic system in a way that is unique. This gives a second sense in which a property can be thought of as specific to language. An evolutionary approach to the language faculty might at first blush appear to favor domain-specificity in the first sense, with individual properties of the language faculty being specifically linguistic adaptations. However, we argue that interactions between learning, culture, and biological evolution mean any domain-specific adaptations that evolve will take the form of weak biases rather than hard constraints. Turning to the latter sense of domain-specificity, we highlight a very general bias, simplicity, which operates widely in cognition and yet interacts with linguistic representations in domain-specific ways. PMID:26793132

  7. In vivo mouse imaging using frequency domain optoacoustic tomography

    NASA Astrophysics Data System (ADS)

    Kellnberger, Stephan; Deliolanis, Nikolaos C.; Queirós, Daniel; Sergiadis, George; Ntziachristos, Vasilis

    2013-06-01

    Frequency domain optoacoustics relates to stimulation of optoacoustic signals using intensity modulated continuous wave light instead of pulsed laser light employed in time domain optoacoustic imaging. We present a method to generate frequency domain tomographic images of optical absorbers and cross sectional in-vivo mouse images, showing the changes of optical absorption before and after injection of indocyanine green (ICG). OCIS codes: 170.6960, 170.3880, 170.5220

  8. STAS Domain Structure and Function

    PubMed Central

    Sharma, Alok K.; Rigby, Alan C.; Alper, Seth L.

    2011-01-01

    Pendrin shares with nearly all SLC26/SulP anion transporters a carboxy-terminal cytoplasmic segment organized around a Sulfate Transporter and Anti-Sigma factor antagonist (STAS) domain. STAS domains of divergent amino acid sequence exhibit a conserved fold of 4 β strands interspersed among 5 α helices. The first STAS domain proteins studied were single-domain anti-sigma factor antagonists (anti-anti-σ). These anti-anti-σ indirectly stimulate bacterial RNA polymerase by inactivating inhibitory anti-σ kinases, liberating σ factors to direct specific transcription of target genes or operons. Some STAS domains are nucleotide-binding phosphoproteins or nucleotidases. Others are interaction/transduction modules within multidomain sensors of light, oxygen and other gasotransmitters, cyclic nucleotides, inositol phosphates, and G proteins. Additional multidomain STAS protein sequences suggest functions in sensing, metabolism, or transport of nutrients such as sugars, amino acids, lipids, anions, vitamins, or hydrocarbons. Still other multidomain STAS polypeptides include histidine and serine/threonine kinase domains and ligand-activated transcription factor domains. SulP/SLC26 STAS domains and adjacent sequences interact with other transporters, cytoskeletal scaffolds, and with enzymes metabolizing transported anion substrates, forming putative metabolons. STAS domains are central to membrane targeting of many SulP/SLC26 anion transporters, and STAS domain mutations are associated with at least three human recessive diseases. This review summarizes STAS domain structure and function. PMID:22116355

  9. Small domain-size multiblock copolymer electrolytes

    DOEpatents

    Pistorino, Jonathan; Eitouni, Hany Basam

    2016-09-20

    New block polymer electrolytes have been developed which have higher conductivities than previously reported for other block copolymer electrolytes. The new materials are constructed of multiple blocks (>5) of relatively low domain size. The small domain size provides greater protection against formation of dendrites during cycling against lithium in an electrochemical cell, while the large total molecular weight insures poor long range alignment, which leads to higher conductivity. In addition to higher conductivity, these materials can be more easily synthesized because of reduced requirements on the purity level of the reagents.

  10. Nano and micro reoriented domains and their relation with the crystal structure in the New Fe1.5Zn1.5B7O13Cl boracite.

    PubMed

    Ulloa-Godínez, S; Barrera, A; Rosales, I; Bucio, L; Castillon, F F; Farias, M H; Siqueiros, J M; Campa-Molina, J

    2011-06-01

    New iron-zinc chlorine single crystals of Fe1.5Zn1.5B7O13Cl boracite were grown by chemical transport reactions in closed quartz ampoules, at a temperature of 1173 K. The crystal structure was characterized by X-ray powder diffraction (XRD) using the Rietveld refinement method and belongs to the trigonal/rombohedral system with space group R3c (No. 161). The cell parameters were a = 8.5726(1) angstroms, c = 21.0116(4) angstroms, V = 1337.26(3) angstroms3 and Z = 6. The refinement successfully proceeded and ended with sound merit figure values chi2 = 2.25, R(B) = 6.12%. Chemical analysis was performed with X-ray energy dispersive spectroscopy (EDS) and X-ray fluorescence (XRF). Ferroelectric nano and micro reoriented domains were found in this material using polarizing optical microscopy (PLM), scanning electron microscopy (SEM) and transmission electron microscopy (TEM). The examination by TEM showed that in the trigonal/rombohedral system of Fe1.5Zn1.5B7O13Cl nanodomain structures exist. Thin (50-100 nm) mostly planar domains parallel to (100) were frequently observed in Fe1.5Zn1.5B7O13Cl boracite.

  11. Nano and micro reoriented domains and their relation with the crystal structure in the New Fe1.5Zn1.5B7O13Cl boracite.

    PubMed

    Ulloa-Godínez, S; Barrera, A; Rosales, I; Bucio, L; Castillon, F F; Farias, M H; Siqueiros, J M; Campa-Molina, J

    2011-06-01

    New iron-zinc chlorine single crystals of Fe1.5Zn1.5B7O13Cl boracite were grown by chemical transport reactions in closed quartz ampoules, at a temperature of 1173 K. The crystal structure was characterized by X-ray powder diffraction (XRD) using the Rietveld refinement method and belongs to the trigonal/rombohedral system with space group R3c (No. 161). The cell parameters were a = 8.5726(1) angstroms, c = 21.0116(4) angstroms, V = 1337.26(3) angstroms3 and Z = 6. The refinement successfully proceeded and ended with sound merit figure values chi2 = 2.25, R(B) = 6.12%. Chemical analysis was performed with X-ray energy dispersive spectroscopy (EDS) and X-ray fluorescence (XRF). Ferroelectric nano and micro reoriented domains were found in this material using polarizing optical microscopy (PLM), scanning electron microscopy (SEM) and transmission electron microscopy (TEM). The examination by TEM showed that in the trigonal/rombohedral system of Fe1.5Zn1.5B7O13Cl nanodomain structures exist. Thin (50-100 nm) mostly planar domains parallel to (100) were frequently observed in Fe1.5Zn1.5B7O13Cl boracite. PMID:21770219

  12. NMR studies of the R2 repeat and related peptide fragments of the DNA binding domain of c-Myb. New light on the structure and folding of R2.

    NASA Astrophysics Data System (ADS)

    Ségalas, I.; Desjardins, S.; Oulyadi, H.; Prigent, Y.; Tribouillard, S.; Bernardi, E.; Schoofs, A. R.; Davoust1, D.; Toma, F.

    1999-10-01

    The solution structure of the R2 repeat of the DNA binding domain of the protooncogene c-Myb contains a N-terminal structural motif comprising two antiparallel helices. The motif is stabilized by interactions involving conserved residues. The recognition region in C-terminal position is flexible. This structure differs from that of R2 of another c-Myb protein. La structure en solution de la répétition R2 du domaine de liaison à l'ADN du protooncogène c-Myb possède un motif à deux hélices antiparallèles dans la moitié N-terminale, stabilisé par des interactions entre résidus conservés. La région de reconnaissance à l'ADN en position C-terminale est flexible. Cette structure diffère de celle montrée pour la répétition R2 d'une autre protéine c-Myb.

  13. Networked Ontologies from the Fisheries Domain

    NASA Astrophysics Data System (ADS)

    Caracciolo, Caterina; Heguiabehere, Juan; Sini, Margherita; Keizer, Johannes

    In this paper we report on ongoing work concerning the creation of a network of ontologies based on metadata for time series relative to the domain of fisheries, and hint at the possibility of exploiting the network for web service applications. The results obtained so far show that the reengineering of classification systems stored as relational databases is possible, although some technical problems is still to be addressed.

  14. Clarifying domains of internalizing psychopathology using neurophysiology.

    PubMed

    Vaidyanathan, U; Nelson, L D; Patrick, C J

    2012-03-01

    Current initiatives such as the National Institute of Mental Health's Research Domain Criteria project aim to reorganize classification of mental disorders along neurobiological lines. Here, we describe how consideration of findings from psychiatric research employing two physiological measures with distinct neural substrates--the startle blink reflex and the error-related negativity (ERN)--can help to clarify relations among disorders entailing salient anxiety or depressive symptomatology. Specifically, findings across various studies and reviews reveal distinct patterns of association for both the startle blink reflex and the ERN with three key domains of psychopathology: (1) Fear (or phobic) disorders (distinguished by increased startle to unpleasant stimuli, but normal-range ERN). (2) Non-phobic anxiety disorders and negative affect (associated with increased ERN, increased startle across all types of emotional stimuli and increased baseline startle) and, more tentatively (3) Major depression (for which patterns of response for both startle and ERN appear to vary, as a function of severity and distinct symptomatology). Findings from this review point to distinct neurobiological indicators of key psychopathology domains that have been previously demarcated using personality and diagnostic data. Notably, these indicators exhibit more specificity in their relations with these three domains than has been seen in quantitative-dimensional models. Implications of these findings are discussed. PMID:21854683

  15. Domain walls as probes of gravity

    SciTech Connect

    Dvali, Gia; Gabadadze, Gregory; Pujolas, Oriol; Rahman, Rakibur

    2007-06-15

    We show that domain walls are probes that enable one to distinguish large-distance modified gravity from general relativity (GR) at short distances. For example, low-tension domain walls are stealth in modified gravity, while they do produce global gravitational effects in GR. We demonstrate this by finding exact solutions for various domain walls in the DGP model. A wall with tension lower than the fundamental Planck scale does not inflate and has no gravitational effects on a 4D observer, since its 4D tension is completely screened by gravity itself. We argue that this feature remains valid in a generic class of models of infrared modified gravity. As a byproduct, we obtain exact solutions for supermassive codimension-2 branes.

  16. Formal Problem Domain Modeling within MDA

    NASA Astrophysics Data System (ADS)

    Osis, Janis; Asnina, Erika; Grave, Andrejs

    The proposed approach called Topological Functioning Modeling for Model Driven Architecture (TFM4MDA) uses formal mathematical foundations of Topological Functioning Model (TFM). It introduces the main feature of MDA - Separation of Concerns by formal analysis of a business system, enables mapping to functional requirements and verifying whether those requirements are in conformity with the TFM of the problem domain. By using a goal-based method, a holistic behavior of the planned application can be decomposed in accordance with the goals. Graph transformation from the TFM to a conceptual model (or a domain object model) enables establishing the definition of domain concepts and their relations. The paper also suggests a concept of a tool for TFM4MDA, which is realized as an Eclipse plug-in.

  17. Targeting SH2 domains in breast cancer

    PubMed Central

    Morlacchi, Pietro; Robertson, Fredika M; Klostergaard, Jim; McMurray, John S

    2014-01-01

    Breast cancer is among the most commonly diagnosed cancer types in women worldwide and is the second leading cause of cancer-related disease in the USA. SH2 domains recruit signaling proteins to phosphotyrosine residues on aberrantly activated growth factor and cytokine receptors and contribute to cancer cell cycling, metastasis, angiogenesis and so on. Herein we review phosphopeptide mimetic and small-molecule approaches targeting the SH2 domains of Grb2, Grb7 and STAT3 that inhibit their targets and reduce proliferation in in vitro breast cancer models. Only STAT3 inhibitors have been evaluated in in vivo models and have led to tumor reduction. Taken together, these studies suggest that targeting SH2 domains is an important approach to the treatment of breast cancer. PMID:25495984

  18. Method for identification of rigid domains and hinge residues in proteins based on exhaustive enumeration.

    PubMed

    Sim, Jaehyun; Sim, Jun; Park, Eunsung; Lee, Julian

    2015-06-01

    Many proteins undergo large-scale motions where relatively rigid domains move against each other. The identification of rigid domains, as well as the hinge residues important for their relative movements, is important for various applications including flexible docking simulations. In this work, we develop a method for protein rigid domain identification based on an exhaustive enumeration of maximal rigid domains, the rigid domains not fully contained within other domains. The computation is performed by mapping the problem to that of finding maximal cliques in a graph. A minimal set of rigid domains are then selected, which cover most of the protein with minimal overlap. In contrast to the results of existing methods that partition a protein into non-overlapping domains using approximate algorithms, the rigid domains obtained from exact enumeration naturally contain overlapping regions, which correspond to the hinges of the inter-domain bending motion. The performance of the algorithm is demonstrated on several proteins.

  19. Spectral Domain Phase Microscopy

    NASA Astrophysics Data System (ADS)

    Hendargo, Hansford C.; Ellerbee, Audrey K.; Izatt, Joseph A.

    Spectral domain phase microscopy (SDPM) is a functional extension of optical coherence tomography (OCT) using common-path interferometry to produce phase-referenced images of dynamic samples. Like OCT, axial resolution in SDPM is determined by the source coherence length, while lateral resolution is limited by diffraction in the microscope optics. However, the quantitative phase information SDPM generates is sensitive to nanometer-scale displacements of scattering structures. The use of a common-path optical geometry yields an imaging system with high phase stability. Due to coherence gating, SDPM can achieve full depth discrimination, allowing for independent motion resolution of subcellular structures throughout the sample volume. Here we review the basic theory of OCT and SDPM along with applications of SDPM in cellular imaging to measure topology, Doppler flow in single-celled organisms, time-resolved motions, rheological information of the cytoskeleton, and optical signaling of neural activation. Phase imaging limitations, artifacts, and sensitivity considerations are discussed.

  20. Beyond the Number Domain

    PubMed Central

    Cantlon, Jessica F.; Platt, Michael L.; Brannon, Elizabeth M.

    2009-01-01

    In a world without numbers, we would be unable to build a skyscraper, hold a national election, plan a wedding, or pay for a chicken at the market. The numerical symbols used in all these behaviors build on the approximate number system (ANS) which represents the number of discrete objects or events as a continuous mental magnitude. In this review, we first discuss evidence that the ANS bears a set of behavioral and brain signatures that are universally displayed across animal species, human cultures, and development. We then turn to the question of whether the ANS constitutes a specialized cognitive and neural domain--a question central to understanding how this system works, the nature of its evolutionary and developmental trajectory, and its physical instantiation in the brain. PMID:19131268

  1. Fifth Graders Metacognitive Knowledge: General or Domain-Specific?

    ERIC Educational Resources Information Center

    Neuenhaus, Nora; Artelt, Cordula; Lingel, Klaus; Schneider, Wolfgang

    2011-01-01

    The purpose of the present study was to investigate the structure of metacognitive knowledge in fifth grade pupils and its relation to school achievement. Since the structure of metacognitive knowledge is controversially discussed with little empirical evidence for either its domain specificity or its domain transferability, the debate remains…

  2. Domain specificity in social interactions, social thought, and social development.

    PubMed

    Turiel, Elliot

    2010-01-01

    J. E. Grusec and M. Davidov (this issue) have taken good steps in formulating a domain-specific view of parent-child interactions. This commentary supports the introduction of domain specificity to analyses of parenting. Their formulation is an advance over formulations that characterized parental practices globally. This commentary calls for inclusion of definitions of the classification system of domain-specific interactions and criteria for each domain. It is also maintained that Grusec and Davidov's domains of social interaction imply that processes of development are involved, along with socialization; that bidirectionality in parent-child relations needs to be extended to include mutual influences and the construction of domains of social thought; and that conflicts and opposition within families coexist with compliance and social harmony.

  3. Dynamical domain wall and localization

    NASA Astrophysics Data System (ADS)

    Toyozato, Yuta; Higuchi, Masafumi; Nojiri, Shin'ichi

    2016-03-01

    Based on the previous works (Toyozato et al., 2013 [24]; Higuchi and Nojiri, 2014 [25]), we investigate the localization of the fields on the dynamical domain wall, where the four-dimensional FRW universe is realized on the domain wall in the five-dimensional space-time. Especially we show that the chiral spinor can localize on the domain wall, which has not been succeeded in the past works as the seminal work in George et al. (2009) [23].

  4. Mapping the Moral Domain

    PubMed Central

    Graham, Jesse; Nosek, Brian A.; Haidt, Jonathan; Iyer, Ravi; Koleva, Spassena; Ditto, Peter H.

    2010-01-01

    The moral domain is broader than the empathy and justice concerns assessed by existing measures of moral competence, and it is not just a subset of the values assessed by value inventories. To fill the need for reliable and theoretically-grounded measurement of the full range of moral concerns, we developed the Moral Foundations Questionnaire (MFQ) based on a theoretical model of five universally available (but variably developed) sets of moral intuitions: Harm/care, Fairness/reciprocity, Ingroup/loyalty, Authority/respect, and Purity/sanctity. We present evidence for the internal and external validity of the scale and the model, and in doing so present new findings about morality: 1. Comparative model fitting of confirmatory factor analyses provides empirical justification for a five-factor structure of moral concerns. 2. Convergent/discriminant validity evidence suggests that moral concerns predict personality features and social group attitudes not previously considered morally relevant. 3. We establish pragmatic validity of the measure in providing new knowledge and research opportunities concerning demographic and cultural differences in moral intuitions. These analyses provide evidence for the usefulness of Moral Foundations Theory in simultaneously increasing the scope and sharpening the resolution of psychological views of morality. PMID:21244182

  5. Skyrmion domain wall collision and domain wall-gated skyrmion logic

    NASA Astrophysics Data System (ADS)

    Xing, Xiangjun; Pong, Philip W. T.; Zhou, Yan

    2016-08-01

    Skyrmions and domain walls are significant spin textures of great technological relevance to magnetic memory and logic applications, where they can be used as carriers of information. The unique topology of skyrmions makes them display emergent dynamical properties as compared with domain walls. Some studies have demonstrated that the two topologically inequivalent magnetic objects could be interconverted by using cleverly designed geometric structures. Here, we numerically address the skyrmion domain wall collision in a magnetic racetrack by introducing relative motion between the two objects based on a specially designed junction. An electric current serves as the driving force that moves a skyrmion toward a trapped domain wall pair. We see different types of collision dynamics depending on the driving parameters. Most importantly, the modulation of skyrmion transport using domain walls is realized in this system, allowing a set of domain wall-gated logical NOT, NAND, and NOR gates to be constructed. This work provides a skyrmion-based spin-logic architecture that is fully compatible with racetrack memories.

  6. Domain view: a web tool for protein domain visualization and analysis.

    PubMed

    Pan, Xiaokang; Bingman, Craig A; Wesenberg, Gary E; Sun, Zhaohui; Phillips, George N

    2010-12-01

    The identification of sequence-based protein domains and their boundaries is often a prelude to structure determination. An accurate prediction of disordered regions, secondary structures and low complexity segments of target protein sequences can improve the efficiency of selection in structural genomics and also aid in design of constructs for directed structural biology studies. At the Center for Eukaryotic Structural Genomics (CESG) we have developed DomainView, a web tool to visualize and analyze predicted protein domains, disordered regions, secondary structures and low complexity segments of target protein sequences for selection of experimental protein structure attempts. DomainView consists of a relational database and a web graphical-user interface. The database was developed based on MySQL, which stores data from target protein sequences and their domains, disordered regions, secondary structures and low complexity segments. The program of the web user interface is a Perl CGI script. When a user searches for a target protein sequence, the script displays the combinational information about the domains and other features of that target sequence graphically on a web page by querying the database. The graphical representation for each feature is linked to a web page showing more detailed annotation information or to a new window directly running the corresponding prediction program to show further information about that feature.

  7. Repeated evolution of identical domain architecture in metazoan netrin domain-containing proteins.

    PubMed

    Leclère, Lucas; Rentzsch, Fabian

    2012-01-01

    The majority of proteins in eukaryotes are composed of multiple domains, and the number and order of these domains is an important determinant of protein function. Although multidomain proteins with a particular domain architecture were initially considered to have a common evolutionary origin, recent comparative studies of protein families or whole genomes have reported that a minority of multidomain proteins could have appeared multiple times independently. Here, we test this scenario in detail for the signaling molecules netrin and secreted frizzled-related proteins (sFRPs), two groups of netrin domain-containing proteins with essential roles in animal development. Our primary phylogenetic analyses suggest that the particular domain architectures of each of these proteins were present in the eumetazoan ancestor and evolved a second time independently within the metazoan lineage from laminin and frizzled proteins, respectively. Using an array of phylogenetic methods, statistical tests, and character sorting analyses, we show that the polyphyly of netrin and sFRP is well supported and cannot be explained by classical phylogenetic reconstruction artifacts. Despite their independent origins, the two groups of netrins and of sFRPs have the same protein interaction partners (Deleted in Colorectal Cancer/neogenin and Unc5 for netrins and Wnts for sFRPs) and similar developmental functions. Thus, these cases of convergent evolution emphasize the importance of domain architecture for protein function by uncoupling shared domain architecture from shared evolutionary history. Therefore, we propose the terms merology to describe the repeated evolution of proteins with similar domain architecture and discuss the potential of merologous proteins to help understanding protein evolution. PMID:22813778

  8. On Probability Domains

    NASA Astrophysics Data System (ADS)

    Frič, Roman; Papčo, Martin

    2010-12-01

    Motivated by IF-probability theory (intuitionistic fuzzy), we study n-component probability domains in which each event represents a body of competing components and the range of a state represents a simplex S n of n-tuples of possible rewards-the sum of the rewards is a number from [0,1]. For n=1 we get fuzzy events, for example a bold algebra, and the corresponding fuzzy probability theory can be developed within the category ID of D-posets (equivalently effect algebras) of fuzzy sets and sequentially continuous D-homomorphisms. For n=2 we get IF-events, i.e., pairs ( μ, ν) of fuzzy sets μ, ν∈[0,1] X such that μ( x)+ ν( x)≤1 for all x∈ X, but we order our pairs (events) coordinatewise. Hence the structure of IF-events (where ( μ 1, ν 1)≤( μ 2, ν 2) whenever μ 1≤ μ 2 and ν 2≤ ν 1) is different and, consequently, the resulting IF-probability theory models a different principle. The category ID is cogenerated by I=[0,1] (objects of ID are subobjects of powers I X ), has nice properties and basic probabilistic notions and constructions are categorical. For example, states are morphisms. We introduce the category S n D cogenerated by Sn=\\{(x1,x2,ldots ,xn)in In;sum_{i=1}nxi≤ 1\\} carrying the coordinatewise partial order, difference, and sequential convergence and we show how basic probability notions can be defined within S n D.

  9. Fractional diffusion on bounded domains

    SciTech Connect

    Defterli, Ozlem; D'Elia, Marta; Du, Qiang; Gunzburger, Max Donald; Lehoucq, Richard B.; Meerschaert, Mark M.

    2015-03-13

    We found that the mathematically correct specification of a fractional differential equation on a bounded domain requires specification of appropriate boundary conditions, or their fractional analogue. In this paper we discuss the application of nonlocal diffusion theory to specify well-posed fractional diffusion equations on bounded domains.

  10. Examining the Domain-Specificity of Metacognition Using Academic Domains and Task-Specific Individual Differences

    ERIC Educational Resources Information Center

    Scott, Brianna M.; Berman, Ashleigh F.

    2013-01-01

    Metacognition refers to students' knowledge and regulation of cognition, as well as their accuracy in predicting their academic performance. This study addressed two major questions: 1) how do metacognitive knowledge, regulation and accuracy differ across domains?, and 2) how do students' individual differences relate to their reported…

  11. Separated matter and antimatter domains with vanishing domain walls

    SciTech Connect

    Dolgov, A.D.; Godunov, S.I.; Rudenko, A.S.; Tkachev, I.I. E-mail: sgodunov@itep.ru E-mail: tkachev@ms2.inr.ac.ru

    2015-10-01

    We present a model of spontaneous (or dynamical) C and CP violation where it is possible to generate domains of matter and antimatter separated by cosmologically large distances. Such C(CP) violation existed only in the early universe and later it disappeared with the only trace of generated baryonic and/or antibaryonic domains. So the problem of domain walls in this model does not exist. These features are achieved through a postulated form of interaction between inflaton and a new scalar field, realizing short time C(CP) violation.

  12. VOLUME CALCULATION OF RATS' ORGANS AND ITS APPLICATION IN THE VALIDATION OF THE VOLUME RELATION BETWEEN THE ABDOMINAL CAVITY AND THE HERNIAL SAC IN INCISIONAL HERNIAS WITH "LOSS OF ABDOMINAL DOMAIN"

    PubMed Central

    de ARAÚJO, Luz Marina Gonçalves; SERIGIOLLE, Leonardo Carvalho; GOMES, Helbert Minuncio Pereira; RODRIGUES, Daren Athiê Boy; LOPES, Carolina Marques; LEME, Pedro Luiz Squilacci

    2014-01-01

    Background The calculation of the volume ratio between the hernia sac and the abdominal cavity of incisional hernias is based on tomographic sections as well as the mathematical formula of the volume of the ellipsoid, which allows determining whether this is a giant hernia or there is a "loss of domain". As the images used are not exact geometric figures, the study of the volume of two solid organs of Wistar rats was performed to validate these calculations. Aim To correlate two methods for determining the volume of the kidney and spleen of rats, comparing a direct method of observation of the volume with the mathematical calculation of this value. Methods The volume of left kidney, geometrically more regular, and spleen, with its peculiar shape, of ten animals was established in cubic centimeters after complete immersion in water with the aid of a beaker graduated in millimeters. These values ​​were compared with those obtained by calculating the same volume with a specific mathematical formula: V = 4/3 × π × (r1 x r2 x r3). Data were compared and statistically analyzed by Student's t test. RESULTS: Although the average volume obtained was higher through the direct method (1.13 cm3 for the left kidney and 0.71 cm3 for the spleen) than the values ​​calculated with the mathematical formula (0.81 cm3 and 0.54 cm3), there were no statistically significant differences between the values ​​found for the two organs (p>0.05). Conclusion There was adequate correlation between the direct calculation of the volume of the kidney and spleen with the result of mathematical calculation of these values ​​in the animals' studies. PMID:25184766

  13. Development of sulfonamide AKT PH domain inhibitors

    PubMed Central

    Ahad, Ali Md.; Zuohe, Song; Du-Cuny, Lei; Moses, Sylvestor A.; Zhou, Li Li; Zhang, Shuxing; Powis, Garth; Meuillet, Emmanuelle J.; Mash, Eugene A.

    2011-01-01

    Disruption of the phosphatidylinositol 3-kinase/AKT signaling pathway can lead to apoptosis in cancer cells. Previously we identified a lead sulfonamide that selectively bound to the pleckstrin homology (PH) domain of AKT and induced apoptosis when present at low micromolar concentrations. To examine the effects of structural modification, a set of sulfonamides related to the lead compound was designed, synthesized, and tested for binding to the expressed PH domain of AKT using a surface plasmon resonance-based competitive binding assay. Cellular activity was determined by means of an assay for pAKT production and a cell killing assay using BxPC3 cells. The most active compounds in the set are lipophilic and possess an aliphatic chain of the proper length. Results were interpreted with the aid of computational modeling. This paper represents the first structure-activity relationship (SAR) study of a large family of AKT PH domain inhibitors. Information obtained will be used in the design of the next generation of inhibitors of AKT PH domain function. PMID:21353784

  14. Critical role of domain crystallinity, domain purity and domain interface sharpness for reduced bimolecular recombination in polymer solar cells

    DOE PAGES

    Venkatesan, Swaminathan; Chen, Jihua; Ngo, Evan C.; Dubey, Ashish; Khatiwada, Devendra; Zhang, Cheng; Qiao, Qiquan

    2014-12-31

    In this study, inverted bulk heterojunction solar cells were fabricated using poly(3-hexylthiophene) (P3HT) blended with two different fullerene derivatives namely phenyl-C61-butyric acid methyl ester (PC60BM) and indene-C60 bis-adduct (IC60BA). The effects of annealing temperatures on the morphology, optical and structural properties were studied and correlated to differences in photovoltaic device performance. It was observed that annealing temperature significantly improved the performance of P3HT:IC60BA solar cells while P3HT:PC60BM cells showed relatively less improvement. The performance improvement is attributed to the extent of fullerene mixing with polymer domains. Energy filtered transmission electron microscopy (EFTEM) and x-ray diffraction (XRD) results showed that ICBAmore » mixes with disordered P3HT much more readily than PC60BM which leads to lower short circuit current density and fill factor for P3HT:IC60BA cells annealed below 120°C. Annealing above 120°C improves the crystallinity of P3HT in case of P3HT:IC60BA whereas in P3HT:PC60BM films, annealing above 80°C leads to negligible change in crystallinity. Crystallization of P3HT also leads to higher domain purity as seen EFTEM. Further it is seen that cells processed with additive nitrobenzene (NB) showed enhanced short circuit current density and power conversion efficiency regardless of the fullerene derivative used. Addition of NB led to nanoscale phase separation between purer polymer and fullerene domains. Kelvin probe force microscopy (KPFM) images showed that enhanced domain purity in additive casted films led to a sharper interface between polymer and fullerene. Lastly, enhanced domain purity and interfacial sharpness led to lower bimolecular recombination and higher mobility and charge carrier lifetime in NB modified devices.« less

  15. Modeling software systems by domains

    NASA Technical Reports Server (NTRS)

    Dippolito, Richard; Lee, Kenneth

    1992-01-01

    The Software Architectures Engineering (SAE) Project at the Software Engineering Institute (SEI) has developed engineering modeling techniques that both reduce the complexity of software for domain-specific computer systems and result in systems that are easier to build and maintain. These techniques allow maximum freedom for system developers to apply their domain expertise to software. We have applied these techniques to several types of applications, including training simulators operating in real time, engineering simulators operating in non-real time, and real-time embedded computer systems. Our modeling techniques result in software that mirrors both the complexity of the application and the domain knowledge requirements. We submit that the proper measure of software complexity reflects neither the number of software component units nor the code count, but the locus of and amount of domain knowledge. As a result of using these techniques, domain knowledge is isolated by fields of engineering expertise and removed from the concern of the software engineer. In this paper, we will describe kinds of domain expertise, describe engineering by domains, and provide relevant examples of software developed for simulator applications using the techniques.

  16. Expansion and Functional Divergence of Jumonji C-Containing Histone Demethylases: Significance of Duplications in Ancestral Angiosperms and Vertebrates.

    PubMed

    Qian, Shengzhan; Wang, Yingxiang; Ma, Hong; Zhang, Liangsheng

    2015-08-01

    Histone modifications, such as methylation and demethylation, are crucial mechanisms altering chromatin structure and gene expression. Recent biochemical and molecular studies have uncovered a group of histone demethylases called Jumonji C (JmjC) domain proteins. However, their evolutionary history and patterns have not been examined systematically. Here, we report extensive analyses of eukaryotic JmjC genes and define 14 subfamilies, including the Lysine-Specific Demethylase3 (KDM3), KDM5, JMJD6, Putative-Lysine-Specific Demethylase11 (PKDM11), and PKDM13 subfamilies, shared by plants, animals, and fungi. Other subfamilies are detected in plants and animals but not in fungi (PKDM12) or in animals and fungi but not in plants (KDM2 and KDM4). PKDM7, PKDM8, and PKDM9 are plant-specific groups, whereas Jumonji, AT-Rich Interactive Domain2, KDM6, and PKDM10 are animal specific. In addition to known domains, most subfamilies have characteristic conserved amino acid motifs. Whole-genome duplication (WGD) was likely an important mechanism for JmjC duplications, with four pairs from an angiosperm-wide WGD and others from subsequent WGDs. Vertebrates also experienced JmjC duplications associated with the vertebrate ancestral WGDs, with additional mammalian paralogs from tandem duplication and possible transposition. The sequences of paralogs have diverged in both known functional domains and other regions, showing evidence of selection pressure. The increases of JmjC copy number and the divergences in sequence and expression might have contributed to the divergent functions of JmjC genes, allowing the angiosperms and vertebrates to adapt to a great number of ecological niches and contributing to their evolutionary successes.

  17. ECOD: An Evolutionary Classification of Protein Domains

    PubMed Central

    Kinch, Lisa N.; Pei, Jimin; Shi, Shuoyong; Kim, Bong-Hyun; Grishin, Nick V.

    2014-01-01

    Understanding the evolution of a protein, including both close and distant relationships, often reveals insight into its structure and function. Fast and easy access to such up-to-date information facilitates research. We have developed a hierarchical evolutionary classification of all proteins with experimentally determined spatial structures, and presented it as an interactive and updatable online database. ECOD (Evolutionary Classification of protein Domains) is distinct from other structural classifications in that it groups domains primarily by evolutionary relationships (homology), rather than topology (or “fold”). This distinction highlights cases of homology between domains of differing topology to aid in understanding of protein structure evolution. ECOD uniquely emphasizes distantly related homologs that are difficult to detect, and thus catalogs the largest number of evolutionary links among structural domain classifications. Placing distant homologs together underscores the ancestral similarities of these proteins and draws attention to the most important regions of sequence and structure, as well as conserved functional sites. ECOD also recognizes closer sequence-based relationships between protein domains. Currently, approximately 100,000 protein structures are classified in ECOD into 9,000 sequence families clustered into close to 2,000 evolutionary groups. The classification is assisted by an automated pipeline that quickly and consistently classifies weekly releases of PDB structures and allows for continual updates. This synchronization with PDB uniquely distinguishes ECOD among all protein classifications. Finally, we present several case studies of homologous proteins not recorded in other classifications, illustrating the potential of how ECOD can be used to further biological and evolutionary studies. PMID:25474468

  18. The evolutionary analysis reveals domain fusion of proteins with Frizzled-like CRD domain.

    PubMed

    Yan, Jun; Jia, Haibo; Ma, Zhaowu; Ye, Huashan; Zhou, Mi; Su, Li; Liu, Jianfeng; Guo, An-Yuan

    2014-01-01

    Frizzleds (FZDs) are transmembrane receptors in the Wnt signaling pathway and they play pivotal roles in developments. The Frizzled-like extracellular Cysteine-rich domain (Fz-CRD) has been identified in FZDs and other proteins. The origin and evolution of these proteins with Fz-CRD is the main interest of this study. We found that the Fz-CRD exists in FZD, SFRP, RTK, MFRP, CPZ, CORIN, COL18A1 and other proteins. Our systematic analysis revealed that the Fz-CRD domain might have originated in protists and then fused with the Frizzled-like seven-transmembrane domain (7TM) to form the FZD receptors, which duplicated and diversified into about 11 members in Vertebrates. The SFRPs and RTKs with the Fz-CRD were found in sponge and expanded in Vertebrates. Other proteins with Fz-CRD may have emerged during Vertebrate evolution through domain fusion. Moreover, we found a glycosylation site and several conserved motifs in FZDs, which may be related to Wnt interaction. Based on these results, we proposed a model showing that the domain fusion and expansion of Fz-CRD genes occurred in Metazoa and Vertebrates. Our study may help to pave the way for further research on the conservation and diversification of Wnt signaling functions during evolution.

  19. Phase Transitions and Domain Structures in Nanoferroelectrics.

    NASA Astrophysics Data System (ADS)

    Levanyuk, Arkadi

    2006-03-01

    A review of the Landau-type theory of size effects in ferroelectric phase transitions will be presented. An aspect of this theory, a question about the ``critical thickness'' of ferroelectric thin films will be the main emphasis. This question can be reduced to that of the size dependence of temperature of ferroelectric phase transition by taking into account two possibilities for such a transition: formation of (i) single- or (ii) multi-domain ferroelectric state. In a defect-free sample, two factors would define which of these possibilities is realized: the depolarizing field and the specific features of the sample surface reflected in the boundary conditions for the Landau-type equations in addition to the conventional electrodynamics boundary conditions. The possibility of the transition into the single domain state strongly depends on a character of electrodes and the additional boundary conditions, while it is much less important for the multi-domain case. In realistic conditions, the transition would proceed into the multi-domain state, especially in near cubic ferroelectrics, e.g. films of cubic perovskites with an elastic mismatch between the film and a substrate. Importantly, the shift of a transition temperature with respect to a bulk is relatively small in this case. The message is that, while studying the question about the ``critical thickness'', multi-domain states rather than single domain ones should be considered first of all, contrary to the approach in some recent papers where only monodomain state was studied.. In particular, there is no definite indication of ultimate ``critical thickness'' for a multi domain ferroelectric state in nearly cubic samples. Along with ultra thin films the ferroelectric nanopowders are also intensively studied now. Here the size effects are more complicated because of long-range interaction between the particles. The problems which the theory faces here are briefly commented upon. It is worth mentioning that

  20. Concept Convergence in Empirical Domains

    NASA Astrophysics Data System (ADS)

    Ontañón, Santiago; Plaza, Enric

    How to achieve shared meaning is a significant issue when more than one intelligent agent is involved in the same domain. We define the task of concept convergence, by which intelligent agents can achieve a shared, agreed-upon meaning of a concept (restricted to empirical domains). For this purpose we present a framework that, integrating computational argumentation and inductive concept learning, allows a pair of agents to (1) learn a concept in an empirical domain, (2) argue about the concept's meaning, and (3) reach a shared agreed-upon concept definition. We apply this framework to marine sponges, a biological domain where the actual definitions of concepts such as orders, families and species are currently open to discussion. An experimental evaluation on marine sponges shows that concept convergence is achieved, within a reasonable number of interchanged arguments, and reaching short and accurate definitions (with respect to precision and recall).

  1. Altered Specificity of DNA-Binding Proteins with Transition Metal Dimerization Domains

    NASA Astrophysics Data System (ADS)

    Cuenoud, Bernard; Schepartz, Alanna

    1993-01-01

    The bZIP motif is characterized by a leucine zipper domain that mediates dimerization and a basic domain that contacts DNA. A series of transition metal dimerization domains were used to alter systematically the relative orientation of basic domain peptides. Both the affinity and the specificity of the peptide-DNA interaction depend on domain orientation. These results indicate that the precise configuration linking the domains is important; dimerization is not always sufficient for DNA binding. This approach to studying the effect of orientation on protein function complements mutagenesis and could be used in many systems.

  2. Alterations of the Wnt/beta-catenin pathway and its target genes for the N- and C-terminal domains of parathyroid hormone-related protein in bone from diabetic mice.

    PubMed

    Portal-Núñez, S; Lozano, D; de Castro, L Fernández; de Gortázar, A R; Nogués, X; Esbrit, P

    2010-07-16

    Type 1 diabetes mellitus (T1D) is associated with bone loss. Given that the Wnt/beta-catenin pathway is a major regulator of bone accrual, we assessed this pathway in mice with streptozotozin-induced T1D. In diabetic mouse long bones, we found alterations favouring the suppression of this pathway by using PCR arrays and beta-catenin immunostaining. Downregulation of sclerostin, an inhibitor of this pathway, also occurred, and related to increased osteocyte apoptosis. Our data show that both N- and C-terminal parathyroid hormone-related peptide fragments might exert osteogenic effects in this setting by targeting several genes of this pathway and increasing beta-catenin in osteoblastic cells.

  3. PREFACE: Domain wall dynamics in nanostructures Domain wall dynamics in nanostructures

    NASA Astrophysics Data System (ADS)

    Marrows, C. H.; Meier, G.

    2012-01-01

    forms of ordered phases such as antiferromagnetism and ferroelectricity. We would like to thank the scientists from all over the world who happily agreed to contribute their latest results to this special issue, and the Journal of Physics: Condensed Matter staff for their help, patience and professionalism. In such a fast-moving field it is not possible to give a definitive account, and this special issue can be no more than a snapshot of the current state of knowledge regarding this topic. Nevertheless, we hope that this collection of papers is a useful resource for experienced workers in the field, forms a useful introduction to researchers early in their careers and inspires others in related areas of nanotechnology to enter into the study of domain dynamics in nanostructures. Domain wall dynamics in nanostructures contents Temperature estimation in a ferromagnetic Fe-Ni nanowire involving a current-driven domain wall motionA Yamaguchi, A Hirohata, T Ono and H Miyajima Magnetization reversal in magnetic nanostripes via Bloch wall formation M Zeisberger and R Mattheis Magnetic soft x-ray microscopy of the domain wall depinning process in permalloy magnetic nanowiresMi-Young Im, Lars Bocklage, Guido Meier and Peter Fischer Domain wall propagation in meso- and nanoscale ferroelectrics R G P McQuaid, M McMillen, L-W Chang, A Gruverman and J M Gregg Transverse and vortex domain wall structure in magnetic nanowires with uniaxial in-plane anisotropyM T Bryan, S Bance, J Dean, T Schrefl and D A Allwood The stochastic nature of the domain wall motion along high perpendicular anisotropy strips with surface roughness Eduardo Martinez Temperature-dependent dynamics of stochastic domain-wall depinning in nanowiresClemens Wuth, Peter Lendecke and Guido Meier Controlled pinning and depinning of domain walls in nanowires with perpendicular magnetic anisotropyTheo Gerhardt, André Drews and Guido Meier The interaction of transverse domain wallsBenjamin Krüger The increase of the

  4. Entropy gives rise to topologically associating domains

    PubMed Central

    Vasquez, Paula A.; Hult, Caitlin; Adalsteinsson, David; Lawrimore, Josh; Forest, Mark G.; Bloom, Kerry

    2016-01-01

    We investigate chromosome organization within the nucleus using polymer models whose formulation is closely guided by experiments in live yeast cells. We employ bead-spring chromosome models together with loop formation within the chains and the presence of nuclear bodies to quantify the extent to which these mechanisms shape the topological landscape in the interphase nucleus. By investigating the genome as a dynamical system, we show that domains of high chromosomal interactions can arise solely from the polymeric nature of the chromosome arms due to entropic interactions and nuclear confinement. In this view, the role of bio-chemical related processes is to modulate and extend the duration of the interacting domains. PMID:27257057

  5. Entropy gives rise to topologically associating domains.

    PubMed

    Vasquez, Paula A; Hult, Caitlin; Adalsteinsson, David; Lawrimore, Josh; Forest, Mark G; Bloom, Kerry

    2016-07-01

    We investigate chromosome organization within the nucleus using polymer models whose formulation is closely guided by experiments in live yeast cells. We employ bead-spring chromosome models together with loop formation within the chains and the presence of nuclear bodies to quantify the extent to which these mechanisms shape the topological landscape in the interphase nucleus. By investigating the genome as a dynamical system, we show that domains of high chromosomal interactions can arise solely from the polymeric nature of the chromosome arms due to entropic interactions and nuclear confinement. In this view, the role of bio-chemical related processes is to modulate and extend the duration of the interacting domains. PMID:27257057

  6. LHC RF System Time-Domain Simulation

    SciTech Connect

    Mastorides, T.; Rivetta, C.; /SLAC

    2010-09-14

    Non-linear time-domain simulations have been developed for the Positron-Electron Project (PEP-II) and the Large Hadron Collider (LHC). These simulations capture the dynamic behavior of the RF station-beam interaction and are structured to reproduce the technical characteristics of the system (noise contributions, non-linear elements, and more). As such, they provide useful results and insight for the development and design of future LLRF feedback systems. They are also a valuable tool for the study of diverse longitudinal beam dynamics effects such as coupled-bunch impedance driven instabilities and single bunch longitudinal emittance growth. Results from these studies and related measurements from PEP-II and LHC have been presented in multiple places. This report presents an example of the time-domain simulation implementation for the LHC.

  7. Multiple domains in endoglucanase B (CenB) from Cellulomonas fimi: functions and relatedness to domains in other polypeptides.

    PubMed Central

    Meinke, A; Gilkes, N R; Kilburn, D G; Miller, R C; Warren, R A

    1991-01-01

    Endoglucanase B (CenB) from the bacterium Cellulomonas fimi is divided into five discrete domains by linker sequences rich in proline and hydroxyamino acids (A. Meinke, C. Braun, N. R. Gilkes, D. G. Kilburn, R. C. Miller, Jr., and R. A. J. Warren, J. Bacteriol. 173:308-314, 1991). The catalytic domain of 608 amino acids is at the N terminus. The sequence of the first 477 amino acids in the catalytic domain is related to the sequences of cellulases in family E, which includes procaryotic and eucaryotic enzymes. The sequence of the last 131 amino acids of the catalytic domain is related to sequences present in a number of cellulases from different families. The catalytic domain alone can bind to cellulose, and this binding is mediated at least in part by the C-terminal 131 amino acids. Deletion of these 131 amino acids reduces but does not eliminate activity. The catalytic domain is followed by three domains which are repeats of a 98-amino-acid sequence. The repeats are approximately 50% identical to two repeats of 95 amino acids in a chitinase from Bacillus circulans which are related to fibronectin type III repeats (T. Watanabe, K. Suzuki, K. Oyanagi, K. Ohnishi, and H. Tanaka, J. Biol. Chem. 265:15659-15665, 1990). The C-terminal domain of 101 amino acids is related to sequences, present in a number of bacterial cellulases and xylanases from different families, which form cellulose-binding domains (CBDs). It functions as a CBD when fused to a heterologous polypeptide. Cells of Escherichia coli expressing the wild-type cenB gene accumulate both native CenB and a stable proteolytic fragment of 41 kDa comprising the three repeats and the C-terminal CBD. The 41-kDa polypeptide binds to cellulose but lacks enzymatic activity. Images FIG. 7 FIG. 8 PMID:1938913

  8. Highly Efficient Domain Walls Injection in Perpendicular Magnetic Anisotropy Nanowire

    NASA Astrophysics Data System (ADS)

    Zhang, S. F.; Gan, W. L.; Kwon, J.; Luo, F. L.; Lim, G. J.; Wang, J. B.; Lew, W. S.

    2016-04-01

    Electrical injection of magnetic domain walls in perpendicular magnetic anisotropy nanowire is crucial for data bit writing in domain wall-based magnetic memory and logic devices. Conventionally, the current pulse required to nucleate a domain wall is approximately ~1012 A/m2. Here, we demonstrate an energy efficient structure to inject domain walls. Under an applied electric potential, our proposed Π-shaped stripline generates a highly concentrated current distribution. This creates a highly localized magnetic field that quickly initiates the nucleation of a magnetic domain. The formation and motion of the resulting domain walls can then be electrically detected by means of Ta Hall bars across the nanowire. Our measurements show that the Π-shaped stripline can deterministically write a magnetic data bit in 15 ns even with a relatively low current density of 5.34 × 1011 A/m2. Micromagnetic simulations reveal the evolution of the domain nucleation – first, by the formation of a pair of magnetic bubbles, then followed by their rapid expansion into a single domain. Finally, we also demonstrate experimentally that our injection geometry can perform bit writing using only about 30% of the electrical energy as compared to a conventional injection line.

  9. Highly Efficient Domain Walls Injection in Perpendicular Magnetic Anisotropy Nanowire.

    PubMed

    Zhang, S F; Gan, W L; Kwon, J; Luo, F L; Lim, G J; Wang, J B; Lew, W S

    2016-01-01

    Electrical injection of magnetic domain walls in perpendicular magnetic anisotropy nanowire is crucial for data bit writing in domain wall-based magnetic memory and logic devices. Conventionally, the current pulse required to nucleate a domain wall is approximately ~10(12) A/m(2). Here, we demonstrate an energy efficient structure to inject domain walls. Under an applied electric potential, our proposed Π-shaped stripline generates a highly concentrated current distribution. This creates a highly localized magnetic field that quickly initiates the nucleation of a magnetic domain. The formation and motion of the resulting domain walls can then be electrically detected by means of Ta Hall bars across the nanowire. Our measurements show that the Π-shaped stripline can deterministically write a magnetic data bit in 15 ns even with a relatively low current density of 5.34 × 10(11) A/m(2). Micromagnetic simulations reveal the evolution of the domain nucleation - first, by the formation of a pair of magnetic bubbles, then followed by their rapid expansion into a single domain. Finally, we also demonstrate experimentally that our injection geometry can perform bit writing using only about 30% of the electrical energy as compared to a conventional injection line. PMID:27098108

  10. Further insight into BRUTUS domain composition and functionality

    PubMed Central

    Matthiadis, Anna; Long, Terri A.

    2016-01-01

    ABSTRACT BRUTUS (BTS) is a hemerythrin (HHE) domain containing E3 ligase that facilitates the degradation of POPEYE-like (PYEL) proteins in a proteasomal-dependent manner. Deletion of BTS HHE domains enhances BTS stability in the presence of iron and also complements loss of BTS function, suggesting that the HHE domains are critical for protein stability but not for enzymatic function. The RING E3 domain plays an essential role in BTS' capacity to both interact with PYEL proteins and to act as an E3 ligase. Here we show that removal of the RING domain does not complement loss of BTS function. We conclude that enzymatic activity of BTS via the RING domain is essential for response to iron deficiency in plants. Further, we analyze possible BTS domain structure evolution and predict that the combination of domains found in BTS is specific to photosynthetic organisms, potentially indicative of a role for BTS and its orthologs in mitigating the iron-related challenges presented by photosynthesis. PMID:27359166

  11. Further insight into BRUTUS domain composition and functionality.

    PubMed

    Matthiadis, Anna; Long, Terri A

    2016-08-01

    BRUTUS (BTS) is a hemerythrin (HHE) domain containing E3 ligase that facilitates the degradation of POPEYE-like (PYEL) proteins in a proteasomal-dependent manner. Deletion of BTS HHE domains enhances BTS stability in the presence of iron and also complements loss of BTS function, suggesting that the HHE domains are critical for protein stability but not for enzymatic function. The RING E3 domain plays an essential role in BTS' capacity to both interact with PYEL proteins and to act as an E3 ligase. Here we show that removal of the RING domain does not complement loss of BTS function. We conclude that enzymatic activity of BTS via the RING domain is essential for response to iron deficiency in plants. Further, we analyze possible BTS domain structure evolution and predict that the combination of domains found in BTS is specific to photosynthetic organisms, potentially indicative of a role for BTS and its orthologs in mitigating the iron-related challenges presented by photosynthesis. PMID:27359166

  12. Highly Efficient Domain Walls Injection in Perpendicular Magnetic Anisotropy Nanowire

    PubMed Central

    Zhang, S. F.; Gan, W. L.; Kwon, J.; Luo, F. L.; Lim, G. J.; Wang, J. B.; Lew, W. S.

    2016-01-01

    Electrical injection of magnetic domain walls in perpendicular magnetic anisotropy nanowire is crucial for data bit writing in domain wall-based magnetic memory and logic devices. Conventionally, the current pulse required to nucleate a domain wall is approximately ~1012 A/m2. Here, we demonstrate an energy efficient structure to inject domain walls. Under an applied electric potential, our proposed Π-shaped stripline generates a highly concentrated current distribution. This creates a highly localized magnetic field that quickly initiates the nucleation of a magnetic domain. The formation and motion of the resulting domain walls can then be electrically detected by means of Ta Hall bars across the nanowire. Our measurements show that the Π-shaped stripline can deterministically write a magnetic data bit in 15 ns even with a relatively low current density of 5.34 × 1011 A/m2. Micromagnetic simulations reveal the evolution of the domain nucleation – first, by the formation of a pair of magnetic bubbles, then followed by their rapid expansion into a single domain. Finally, we also demonstrate experimentally that our injection geometry can perform bit writing using only about 30% of the electrical energy as compared to a conventional injection line. PMID:27098108

  13. Protein domain definition should allow for conditional disorder

    PubMed Central

    Yegambaram, Kavestri; Bulloch, Esther MM; Kingston, Richard L

    2013-01-01

    Abstract: Proteins are often classified in a binary fashion as either structured or disordered. However this approach has several deficits. Firstly, protein folding is always conditional on the physiochemical environment. A protein which is structured in some circumstances will be disordered in others. Secondly, it hides a fundamental asymmetry in behavior. While all structured proteins can be unfolded through a change in environment, not all disordered proteins have the capacity for folding. Failure to accommodate these complexities confuses the definition of both protein structural domains and intrinsically disordered regions. We illustrate these points with an experimental study of a family of small binding domains, drawn from the RNA polymerase of mumps virus and its closest relatives. Assessed at face value the domains fall on a structural continuum, with folded, partially folded, and near unstructured members. Yet the disorder present in the family is conditional, and these closely related polypeptides can access the same folded state under appropriate conditions. Any heuristic definition of the protein domain emphasizing conformational stability divides this domain family in two, in a way that makes no biological sense. Structural domains would be better defined by their ability to adopt a specific tertiary structure: a structure that may or may not be realized, dependent on the circumstances. This explicitly allows for the conditional nature of protein folding, and more clearly demarcates structural domains from intrinsically disordered regions that may function without folding. PMID:23963781

  14. Domain and Specification Models for Software Engineering

    NASA Technical Reports Server (NTRS)

    Iscoe, Neil; Liu, Zheng-Yang; Feng, Guohui

    1992-01-01

    This paper discusses our approach to representing application domain knowledge for specific software engineering tasks. Application domain knowledge is embodied in a domain model. Domain models are used to assist in the creation of specification models. Although many different specification models can be created from any particular domain model, each specification model is consistent and correct with respect to the domain model. One aspect of the system-hierarchical organization is described in detail.

  15. Localization of resistive domains in inhomogeneous superconductors

    SciTech Connect

    Gurevich, A.V.; Mints, R.G.

    1981-01-01

    The properties of resistive domains due to the Joule heating in inhomogeneous superconductors with transport currents are studied. The equilibrium of a domain at an inhomogeneity of arbitrary type and with dimensions much smaller than the dimensions of the domain is investigated. It is shown that resistive domains can become localized at inhomogeneities. The temperature distribution in a domain and the current--voltage characteristic of the domain are determined. The stability of localized domains is discussed. It is shown that such domains give rise to a hysteresis in the destruction (recovery) of the superconductivity by the transport current.

  16. Predicting cognitive change within domains

    PubMed Central

    Duff, Kevin; Beglinger, Leigh J.; Moser, David J.; Paulsen, Jane S.

    2010-01-01

    Standardized regression based (SRB) formulas, a method for predicting cognitive change across time, traditionally use baseline performance on a neuropsychological measure to predict future performance on that same measure. However, there are instances in which the same tests may not be given at follow-up assessments (e.g., lack of continuity of provider, avoiding practice effects). The current study sought to expand this methodology by developing SRBs to predict performance on different tests within the same cognitive domain. Using a sample of 127 non-demented community-dwelling older adults assessed at baseline and after one year, two sets of SRBs were developed: 1. those predicting performance on the same test, and 2. those predicting performance on a different test within the same cognitive domain. The domains examined were learning and memory, processing speed, and language. Across both sets of SRBs, one year scores were significantly predicted by baseline scores, especially for the learning and memory and processing speed measures. Although SRBs developed for the same test were comparable to those developed for different tests within the same domain, less variance was accounted for as tests became less similar. The current results lend preliminary support for additional development of SRBs, both for same- and different-tests, as well as beginning to examine domain-based SRBs. PMID:20358479

  17. Time domain referencing in intensity modulation fiber optic sensing systems

    NASA Technical Reports Server (NTRS)

    Adamovsky, G.

    1986-01-01

    Intensity modulation sensors are classified depending on the way in which the reference and signal channels are separated: in space, wavelength (frequency), or time domains. To implement the time domain referencing different types of fiber optic (FO) loops have been used. A pulse of short duration sent into the loop results in a series of pulses of different amplitudes. The information about the measured parameter is retrieved from the relative amplitudes of pulses in the same train.

  18. Unconstrained invoice processing in the health insurance domain

    NASA Astrophysics Data System (ADS)

    Hurst, Matthew; Barney, Dave

    2003-01-01

    We present an overview of an information extraction application in the health insurance invoice processing domain. The system is novel in that it is not constrained by the document type - it has no explicit document model or document type classification phase. The system relies on constraints derived from a domain model, constraints derived from world state, and simple models of layout, including the use of labeled fields and the proximity of related information.

  19. Linking in domain-swapped protein dimers

    PubMed Central

    Baiesi, Marco; Orlandini, Enzo; Trovato, Antonio; Seno, Flavio

    2016-01-01

    The presence of knots has been observed in a small fraction of single-domain proteins and related to their thermodynamic and kinetic properties. The exchanging of identical structural elements, typical of domain-swapped proteins, makes such dimers suitable candidates to validate the possibility that mutual entanglement between chains may play a similar role for protein complexes. We suggest that such entanglement is captured by the linking number. This represents, for two closed curves, the number of times that each curve winds around the other. We show that closing the curves is not necessary, as a novel parameter G′, termed Gaussian entanglement, is strongly correlated with the linking number. Based on 110 non redundant domain-swapped dimers, our analysis evidences a high fraction of chains with a significant intertwining, that is with |G′| > 1. We report that Nature promotes configurations with negative mutual entanglement and surprisingly, it seems to suppress intertwining in long protein dimers. Supported by numerical simulations of dimer dissociation, our results provide a novel topology-based classification of protein-swapped dimers together with some preliminary evidence of its impact on their physical and biological properties. PMID:27659606

  20. Birdsong dialect patterns explained using magnetic domains.

    PubMed

    Burridge, James; Kenney, Steven

    2016-06-01

    The songs and calls of many bird species, like human speech, form distinct regional dialects. We suggest that the process of dialect formation is analogous to the physical process of magnetic domain formation. We take the coastal breeding grounds of the Puget Sound white crowned sparrow as an example. Previous field studies suggest that birds of this species learn multiple songs early in life, and when establishing a territory for the first time, retain one of these dialects in order to match the majority of their neighbors. We introduce a simple lattice model of the process, showing that this matching behavior can produce single dialect domains provided the death rate of adult birds is sufficiently low. We relate death rate to thermodynamic temperature in magnetic materials, and calculate the critical death rate by analogy with the Ising model. Using parameters consistent with the known behavior of these birds we show that coastal dialect domain shapes may be explained by viewing them as low-temperature "stripe states."

  1. Birdsong dialect patterns explained using magnetic domains

    NASA Astrophysics Data System (ADS)

    Burridge, James; Kenney, Steven

    2016-06-01

    The songs and calls of many bird species, like human speech, form distinct regional dialects. We suggest that the process of dialect formation is analogous to the physical process of magnetic domain formation. We take the coastal breeding grounds of the Puget Sound white crowned sparrow as an example. Previous field studies suggest that birds of this species learn multiple songs early in life, and when establishing a territory for the first time, retain one of these dialects in order to match the majority of their neighbors. We introduce a simple lattice model of the process, showing that this matching behavior can produce single dialect domains provided the death rate of adult birds is sufficiently low. We relate death rate to thermodynamic temperature in magnetic materials, and calculate the critical death rate by analogy with the Ising model. Using parameters consistent with the known behavior of these birds we show that coastal dialect domain shapes may be explained by viewing them as low-temperature "stripe states."

  2. Domain theoretic structures in quantum information theory

    NASA Astrophysics Data System (ADS)

    Feng, Johnny

    2011-12-01

    In this thesis, we continue the study of domain theoretic structures in quantum information theory initiated by Keye Martin and Bob Coecke in 2002. The first part of the thesis is focused on exploring the domain theoretic properties of qubit channels. We discover that the Scott continuous qubit channels are exactly those that are unital or constant. We then prove that the unital qubit channels form a continuous dcpo, and identify various measurements on them. We show that Holevo capacity is a measurement on unital qubit channels, and discover the natural measurement in this setting. We find that qubit channels also form a continuous dcpo, but capacity fails to be a measurement. In the second part we focus on the study of exact dcpos, a domain theoretic structure, closely related to continuous dcpos, possessed by quantum states. Exact dcpos admit a topology, called the exact topology, and we show that the exact topology has an order theoretic characterization similar to the characterization of the Scott topology on continuous dcpos. We then explore the connection between exact and continuous dcpos; first, by identifying an important set of points, called the split points, that distinguishes between exact and continuous structures; second, by exploring a continuous completion of exact dcpos, and showing that we can recover the exact topology from the Scott topology of the completion.

  3. Birdsong dialect patterns explained using magnetic domains.

    PubMed

    Burridge, James; Kenney, Steven

    2016-06-01

    The songs and calls of many bird species, like human speech, form distinct regional dialects. We suggest that the process of dialect formation is analogous to the physical process of magnetic domain formation. We take the coastal breeding grounds of the Puget Sound white crowned sparrow as an example. Previous field studies suggest that birds of this species learn multiple songs early in life, and when establishing a territory for the first time, retain one of these dialects in order to match the majority of their neighbors. We introduce a simple lattice model of the process, showing that this matching behavior can produce single dialect domains provided the death rate of adult birds is sufficiently low. We relate death rate to thermodynamic temperature in magnetic materials, and calculate the critical death rate by analogy with the Ising model. Using parameters consistent with the known behavior of these birds we show that coastal dialect domain shapes may be explained by viewing them as low-temperature "stripe states." PMID:27415293

  4. Bayesian Models for Multiple Outcomes in Domains with Application to the Seychelles Child Development Study.

    PubMed

    Xiao, Luo; Thurston, Sally W; Ruppert, David; Love, Tanzy M T; Davidson, Philip W

    2014-01-01

    The Seychelles Child Development Study (SCDS) examines the effects of prenatal exposure to methylmercury on the functioning of the central nervous system. The SCDS data include 20 outcomes measured on 9-year old children that can be classified broadly in four outcome classes or "domains": cognition, memory, motor, and social behavior. Previous analyses and scientific theory suggest that these outcomes may belong to more than one of these domains, rather than only a single domain as is frequently assumed for modeling. We present a framework for examining the effects of exposure and other covariates when the outcomes may each belong to more than one domain and where we also want to learn about the assignment of outcomes to domains. Each domain is defined by a sentinel outcome which is preassigned to that domain only. All other outcomes can belong to multiple domains and are not preassigned. Our model allows exposure and covariate effects to differ across domains and across outcomes within domains, and includes random subject-specific effects which model correlations between outcomes within and across domains. We take a Bayesian MCMC approach. Results from the Seychelles study and from extensive simulations show that our model can effectively determine sparse domain assignment, and at the same time give increased power to detect overall, domain-specific and outcome-specific exposure and covariate effects relative to separate models for each endpoint. When fit to the Seychelles data, several outcomes were classified as partly belonging to domains other than their originally assigned domains. In retrospect, the new partial domain assignments are reasonable and, as we discuss, suggest important scientific insights about the nature of the outcomes. Checks of model misspecification were improved relative to a model that assumes each outcome is in a single domain. PMID:24729645

  5. Gradient Domain Guided Image Filtering.

    PubMed

    Kou, Fei; Chen, Weihai; Wen, Changyun; Li, Zhengguo

    2015-11-01

    Guided image filter (GIF) is a well-known local filter for its edge-preserving property and low computational complexity. Unfortunately, the GIF may suffer from halo artifacts, because the local linear model used in the GIF cannot represent the image well near some edges. In this paper, a gradient domain GIF is proposed by incorporating an explicit first-order edge-aware constraint. The edge-aware constraint makes edges be preserved better. To illustrate the efficiency of the proposed filter, the proposed gradient domain GIF is applied for single-image detail enhancement, tone mapping of high dynamic range images and image saliency detection. Both theoretical analysis and experimental results prove that the proposed gradient domain GIF can produce better resultant images, especially near the edges, where halos appear in the original GIF. PMID:26285153

  6. Faraday instability in deformable domains

    NASA Astrophysics Data System (ADS)

    Pucci, Giuseppe; Ben Amar, Martine; Couder, Yves

    2014-11-01

    We investigate the Faraday instability in floating liquid lenses, as an example of hydrodynamic instability that develops in a domain with flexible boundaries. We show that a mutual adaptation of the instability pattern and the domain shape occurs, as a result of the competition between the wave radiation pressure and the capillary response of the lens border. Two archetypes of behaviour are observed. In the first, stable shapes are obtained experimentally and predicted theoretically as the exact solutions of a Riccati equation, and they result from the equilibrium between wave radiation pressure and capillarity. In the second, the radiation pressure exceeds the capillary response of the lens border and leads to non-equilibrium behaviours, with breaking into smaller domains that have a complex dynamics including spontaneous propagation. The authors are grateful to Université Franco-Italienne (UFI) for financial support.

  7. Metrology for terahertz time-domain spectrometers

    NASA Astrophysics Data System (ADS)

    Molloy, John F.; Naftaly, Mira

    2015-12-01

    In recent years the terahertz time-domain spectrometer (THz TDS) [1] has emerged as a key measurement device for spectroscopic investigations in the frequency range of 0.1-5 THz. To date, almost every type of material has been studied using THz TDS, including semiconductors, ceramics, polymers, metal films, liquid crystals, glasses, pharmaceuticals, DNA molecules, proteins, gases, composites, foams, oils, and many others. Measurements with a TDS are made in the time domain; conversion from the time domain data to a frequency spectrum is achieved by applying the Fourier Transform, calculated numerically using the Fast Fourier Transform (FFT) algorithm. As in many other types of spectrometer, THz TDS requires that the sample data be referenced to similarly acquired data with no sample present. Unlike frequency-domain spectrometers which detect light intensity and measure absorption spectra, a TDS records both amplitude and phase information, and therefore yields both the absorption coefficient and the refractive index of the sample material. The analysis of the data from THz TDS relies on the assumptions that: a) the frequency scale is accurate; b) the measurement of THz field amplitude is linear; and c) that the presence of the sample does not affect the performance characteristics of the instrument. The frequency scale of a THz TDS is derived from the displacement of the delay line; via FFT, positioning errors may give rise to frequency errors that are difficult to quantify. The measurement of the field amplitude in a THz TDS is required to be linear with a dynamic range of the order of 10 000. And attention must be given to the sample positioning and handling in order to avoid sample-related errors.

  8. Parental behavioral control in academic and non-academic domains: a three-year longitudinal study in the Chinese culture.

    PubMed

    Shek, Daniel T L; Lee, Tak Yan

    2007-01-01

    For over three consecutive years, 2559 Chinese adolescents (mean age = 12.65 years at Wave 1) responded to instruments assessing their perceived parental behavioral control based on measures of parental knowledge, expectation, monitoring, and discipline. The results show that compared with parental control in the academic domain, parental control in the non-academic domain (peer relations domain) was relatively weaker, using parental knowledge, parental expectation, parental monitoring, and parental discipline as indicators, and a decline in parental behavioral control occurred over time. Although domain (academic domain versus non-academic domain) X time (Time 1, Time 2 versus Time 3) interaction effects were found, the findings mirrored the main effects of domain and time. Parental education and economic sufficiency were linearly related to differences in parental behavioral control in the academic domain and non-academic domain. The present findings suggest that traditional Chinese cultural emphasis on academic excellence still prevails in the contemporary Chinese culture.

  9. FIND: Fluorescence Imaging in the Nuclear Domain

    SciTech Connect

    Barty, C J

    2005-02-14

    This document examines the potential use of Thomson-Radiated Extreme X-ray (T-REX) sources for Fluorescence Imaging in the Nuclear Domain (FIND) of special nuclear materials. A back-of-the-envelope, relative comparison of T-REX sources vs. Bremsstrahlung sources for this application is presented. It is estimated that use of T-REX for FIND could be as much as 5 x 10{sup 12} more effective than the use of anode based sources. Furthermore it is estimated that illumination of samples of dimension 1 cm on a side could produce up to {approx}10{sup 9} detectable photons per second.

  10. A frequency domain method for the generation of partially coherent normal stationary time domain signals

    SciTech Connect

    Smallwood, D.O.; Paez, T.L.

    1991-01-01

    A procedure for generating vectors of time domain signals which are partially coherent in a prescribed manner is described. The procedure starts with the spectral density matrix, (G{sub xx}(f)), that relates pairs of elements of the vector random process (x(t), {minus}{infinity} < t < {infinity}). The spectral density matrix is decomposed into the form (G{sub xx}(f)) = (U(f)) (S(f)) (U(f)){prime} where (U(f)) is a matrix of complex frequency response functions, and (S(f)) is a diagonal matrix of real functions which can vary with frequency. The factors of the spectral density matrix, (U(f)) and (S(f)), are then used to generate a frame of random data in the frequency domain. The data is transformed into the time domain using an inverse FFT to generate a frame of data in the time domain. Successive frames of data are then windowed, overlapped, and added to form a vector of normal stationary sampled time histories, (x(t)), of arbitrary length. 11 refs., 4 figs., 1 tab.

  11. A position-dependent transcription-activating domain in TFIIIA.

    PubMed Central

    Mao, X; Darby, M K

    1993-01-01

    Transcription of the Xenopus 5S RNA gene by RNA polymerase III requires the gene-specific factor TFIIIA. To identify domains within TFIIIA that are essential for transcriptional activation, we have expressed C-terminal deletion, substitution, and insertion mutants of TFIIIA in bacteria as fusions with maltose-binding protein (MBP). The MBP-TFIIIA fusion protein specifically binds to the 5S RNA gene internal control region and complements transcription in a TFIIIA-depleted oocyte nuclear extract. Random, cassette-mediated mutagenesis of the carboxyl region of TFIIIA, which is not required for promoter binding, has defined a 14-amino-acid region that is critical for transcriptional activation. In contrast to activators of RNA polymerase II, the activity of the TFIIIA activation domain is strikingly sensitive to its position relative to the DNA-binding domain. When the eight amino acids that separate the transcription-activating domain from the last zinc finger are deleted, transcriptional activity is lost. Surprisingly, diverse amino acids can replace these eight amino acids with restoration of full transcriptional activity, suggesting that the length and not the sequence of this region is important. Insertion of amino acids between the zinc finger region and the transcription-activating domain causes a reduction in transcription proportional to the number of amino acids introduced. We propose that to function, the transcription-activating domain of TFIIIA must be correctly positioned at a minimum distance from the DNA-binding domain. Images PMID:8246967

  12. X-ray study of aligned magnetic stripe domains in perpendicular multilayers

    SciTech Connect

    Hellwig, O.; Denbeaux, G.P.; Kortright, J.B.; Fullerton, Eric E.

    2003-03-03

    We have investigated the stripe domain structure and the magnetic reversal of perpendicular Co/Pt based multilayers at room temperature using magnetometry, magnetic imaging and magnetic x-ray scattering. In-plane field cycling aligns the stripe domains along the field direction. In magnetic x-ray scattering the parallel stripe domains act as a magnetic grating resulting in observed Bragg reflections up to 5th order. We model the scattering profile to extract and quantify the domain as well as domain wall widths. Applying fields up to {approx}1.2 kOe perpendicular to the film reversibly changes the relative width of up versus down domains while maintaining the overall stripe periodicity. Fields above 1.2 kOe introduce irreversible changes into the domain structure by contracting and finally annihilating individual stripe domains. We compare the current results with modeling and previous measurements of films with perpendicular anisotropy.

  13. A Method to Examine Content Domain Structures

    ERIC Educational Resources Information Center

    D'Agostino, Jerome; Karpinski, Aryn; Welsh, Megan

    2011-01-01

    After a test is developed, most content validation analyses shift from ascertaining domain definition to studying domain representation and relevance because the domain is assumed to be set once a test exists. We present an approach that allows for the examination of alternative domain structures based on extant test items. In our example based on…

  14. Domain Specificity and Variability in Cognitive Development.

    ERIC Educational Resources Information Center

    Gelman, Rochel

    2000-01-01

    Maintains that there are core-specific and non-core-specific domains of knowledge, but that only the core-specific domains benefit from innate skeletal structures. Asserts that core skeletal domains are universally shared, even though their particular foci may vary. Emphasizes that individuals vary in terms of the noncore domains they acquire.…

  15. Critical role of domain crystallinity, domain purity and domain interface sharpness for reduced bimolecular recombination in polymer solar cells

    SciTech Connect

    Venkatesan, Swaminathan; Chen, Jihua; Ngo, Evan C.; Dubey, Ashish; Khatiwada, Devendra; Zhang, Cheng; Qiao, Qiquan

    2014-12-31

    In this study, inverted bulk heterojunction solar cells were fabricated using poly(3-hexylthiophene) (P3HT) blended with two different fullerene derivatives namely phenyl-C61-butyric acid methyl ester (PC60BM) and indene-C60 bis-adduct (IC60BA). The effects of annealing temperatures on the morphology, optical and structural properties were studied and correlated to differences in photovoltaic device performance. It was observed that annealing temperature significantly improved the performance of P3HT:IC60BA solar cells while P3HT:PC60BM cells showed relatively less improvement. The performance improvement is attributed to the extent of fullerene mixing with polymer domains. Energy filtered transmission electron microscopy (EFTEM) and x-ray diffraction (XRD) results showed that ICBA mixes with disordered P3HT much more readily than PC60BM which leads to lower short circuit current density and fill factor for P3HT:IC60BA cells annealed below 120°C. Annealing above 120°C improves the crystallinity of P3HT in case of P3HT:IC60BA whereas in P3HT:PC60BM films, annealing above 80°C leads to negligible change in crystallinity. Crystallization of P3HT also leads to higher domain purity as seen EFTEM. Further it is seen that cells processed with additive nitrobenzene (NB) showed enhanced short circuit current density and power conversion efficiency regardless of the fullerene derivative used. Addition of NB led to nanoscale phase separation between purer polymer and fullerene domains. Kelvin probe force microscopy (KPFM) images showed that enhanced domain purity in additive casted films led to a sharper interface between polymer and fullerene. Lastly, enhanced domain purity and interfacial sharpness led to lower bimolecular recombination and higher mobility and charge carrier lifetime in NB modified devices.

  16. Propagating and reflecting of spin wave in permalloy nanostrip with 360° domain wall

    SciTech Connect

    Zhang, Senfu; Mu, Congpu; Zhu, Qiyuan; Zheng, Qi; Liu, Xianyin; Wang, Jianbo; Liu, Qingfang

    2014-01-07

    By micromagnetic simulation, we investigated the interaction between propagating spin wave (or magnonic) and a 360° domain wall in a nanostrip. It is found that propagating spin wave can drive a 360° domain wall motion, and the velocity and direction are closely related to the transmission coefficient of the spin wave of the domain wall. When the spin wave passes through the domain wall completely, the 360° domain wall moves toward the spin wave source. When the spin wave is reflected by the domain wall, the 360° domain wall moves along the spin wave propagation direction. Moreover, when the frequency of the spin wave is coincident with that of the 360° domain wall normal mode, the 360° domain wall velocity will be resonantly enhanced no matter which direction the 360 DW moves along. On the other hand, when the spin wave is reflected from the moving 360° domain wall, we observed the Doppler effect clearly. After passing through a 360° domain wall, the phase of the spin wave is changed, and the phase shift is related to the frequency. Nevertheless, phase shift could be manipulated by the number of 360° domain walls that spin wave passing through.

  17. Cellulose binding domain fusion proteins

    DOEpatents

    Shoseyov, O.; Yosef, K.; Shpiegl, I.; Goldstein, M.A.; Doi, R.H.

    1998-02-17

    A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques. 16 figs.

  18. Development in the Food Domain.

    ERIC Educational Resources Information Center

    Rozin, Paul

    1990-01-01

    Discusses problems of general interest in developmental psychology that can be successfully studied in the domain of food; these include (1) development of food likes and dislikes; (2) establishment of the edible/inedible distinction; (3) disgust and contagion; (4) transgenerational communication of preferences; and (5) transition to food…

  19. Cellulose binding domain fusion proteins

    DOEpatents

    Shoseyov, Oded; Shpiegl, Itai; Goldstein, Marc A.; Doi, Roy H.

    1998-01-01

    A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production thereof. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques.

  20. Evolution of ferroelectric domain structures embedded inside polychrystalline BaTiO3 during heating

    SciTech Connect

    Varlioglu, Mesut; Ustundag, Ersan; Tamura, Nobumichi; Jones, Jacob L.

    2010-01-01

    The evolution of ferroelectric domains inside a single grain of a polycrystalline BaTiO{sub 3} ceramic was investigated under quasistatic heating by using polychromatic scanning x-ray microdiffraction. Four domain orientations were observed, three of which exhibited a classic of {approx}90{sup o} ferroelastic relationship. The fourth domain orientation was found to be crystallographically related with one of the other orientations by a rotation of either 180.47{sup o} or 0.47{sup o}. While heating the polycrystalline BaTiO{sub 3} from room temperature to above the Curie temperature (125 C), all four ferroelectric domain orientations rotated toward a paraelectric cubic orientation which was found to be at an intermediate orientation relative to the four domain orientations. The crystallographic relationships of the domains with respect to paraelectric phase were explained using a domain structure model by Nepochatenko.

  1. DOUTfinder--identification of distant domain outliers using subsignificant sequence similarity.

    PubMed

    Novatchkova, Maria; Schneider, Georg; Fritz, Richard; Eisenhaber, Frank; Schleiffer, Alexander

    2006-07-01

    DOUTfinder is a web-based tool facilitating protein domain detection among related protein sequences in the twilight zone of sequence similarity. The sequence set required for this analysis can be provided by the user or will be collected using PSI-BLAST if a single sequence is given as an input. The obtained sequence family is analyzed for known Pfam and SMART domains, and the thereby identified subsignificant domain similarities are evaluated further. Domains with several subthreshold hits in the query set are ranked based on a sum-score function and likely homologous domains are suggested according to established cut-offs. By providing a post-filtering procedure for subsignificant domain hits DOUTfinder allows the detection of non-trivial domain relationships and can thereby lead to new insights into the function and evolution of distantly related sequence families. DOUTfinder is available at http://mendel.imp.ac.at/dout/.

  2. Creativity as action: findings from five creative domains

    PubMed Central

    Glaveanu, Vlad; Lubart, Todd; Bonnardel, Nathalie; Botella, Marion; de Biaisi, Pierre-Marc; Desainte-Catherine, Myriam; Georgsdottir, Asta; Guillou, Katell; Kurtag, Gyorgy; Mouchiroud, Christophe; Storme, Martin; Wojtczuk, Alicja; Zenasni, Franck

    2013-01-01

    The present paper outlines an action theory of creativity and substantiates this approach by investigating creative expression in five different domains. We propose an action framework for the analysis of creative acts built on the assumption that creativity is a relational, inter-subjective phenomenon. This framework, drawing extensively from the work of Dewey (1934) on art as experience, is used to derive a coding frame for the analysis of interview material. The article reports findings from the analysis of 60 interviews with recognized French creators in five creative domains: art, design, science, scriptwriting, and music. Results point to complex models of action and inter-action specific for each domain and also to interesting patterns of similarity and differences between domains. These findings highlight the fact that creative action takes place not “inside” individual creators but “in between” actors and their environment. Implications for the field of educational psychology are discussed. PMID:23596431

  3. Domain adaptation for semantic role labeling of clinical text

    PubMed Central

    Zhang, Yaoyun; Tang, Buzhou; Jiang, Min; Wang, Jingqi

    2015-01-01

    Objective Semantic role labeling (SRL), which extracts a shallow semantic relation representation from different surface textual forms of free text sentences, is important for understanding natural language. Few studies in SRL have been conducted in the medical domain, primarily due to lack of annotated clinical SRL corpora, which are time-consuming and costly to build. The goal of this study is to investigate domain adaptation techniques for clinical SRL leveraging resources built from newswire and biomedical literature to improve performance and save annotation costs. Materials and Methods Multisource Integrated Platform for Answering Clinical Questions (MiPACQ), a manually annotated SRL clinical corpus, was used as the target domain dataset. PropBank and NomBank from newswire and BioProp from biomedical literature were used as source domain datasets. Three state-of-the-art domain adaptation algorithms were employed: instance pruning, transfer self-training, and feature augmentation. The SRL performance using different domain adaptation algorithms was evaluated by using 10-fold cross-validation on the MiPACQ corpus. Learning curves for the different methods were generated to assess the effect of sample size. Results and Conclusion When all three source domain corpora were used, the feature augmentation algorithm achieved statistically significant higher F-measure (83.18%), compared to the baseline with MiPACQ dataset alone (F-measure, 81.53%), indicating that domain adaptation algorithms may improve SRL performance on clinical text. To achieve a comparable performance to the baseline method that used 90% of MiPACQ training samples, the feature augmentation algorithm required <50% of training samples in MiPACQ, demonstrating that annotation costs of clinical SRL can be reduced significantly by leveraging existing SRL resources from other domains. PMID:26063745

  4. Using domain knowledge and domain-inspired discourse model for coreference resolution for clinical narratives

    PubMed Central

    Roth, Dan

    2013-01-01

    Objective This paper presents a coreference resolution system for clinical narratives. Coreference resolution aims at clustering all mentions in a single document to coherent entities. Materials and methods A knowledge-intensive approach for coreference resolution is employed. The domain knowledge used includes several domain-specific lists, a knowledge intensive mention parsing, and task informed discourse model. Mention parsing allows us to abstract over the surface form of the mention and represent each mention using a higher-level representation, which we call the mention's semantic representation (SR). SR reduces the mention to a standard form and hence provides better support for comparing and matching. Existing coreference resolution systems tend to ignore discourse aspects and rely heavily on lexical and structural cues in the text. The authors break from this tradition and present a discourse model for “person” type mentions in clinical narratives, which greatly simplifies the coreference resolution. Results This system was evaluated on four different datasets which were made available in the 2011 i2b2/VA coreference challenge. The unweighted average of F1 scores (over B-cubed, MUC and CEAF) varied from 84.2% to 88.1%. These experiments show that domain knowledge is effective for different mention types for all the datasets. Discussion Error analysis shows that most of the recall errors made by the system can be handled by further addition of domain knowledge. The precision errors, on the other hand, are more subtle and indicate the need to understand the relations in which mentions participate for building a robust coreference system. Conclusion This paper presents an approach that makes an extensive use of domain knowledge to significantly improve coreference resolution. The authors state that their system and the knowledge sources developed will be made publicly available. PMID:22781192

  5. In the Multi-domain Protein Adenylate Kinase, Domain Insertion Facilitates Cooperative Folding while Accommodating Function at Domain Interfaces

    PubMed Central

    Giri Rao, V. V. Hemanth; Gosavi, Shachi

    2014-01-01

    Having multiple domains in proteins can lead to partial folding and increased aggregation. Folding cooperativity, the all or nothing folding of a protein, can reduce this aggregation propensity. In agreement with bulk experiments, a coarse-grained structure-based model of the three-domain protein, E. coli Adenylate kinase (AKE), folds cooperatively. Domain interfaces have previously been implicated in the cooperative folding of multi-domain proteins. To understand their role in AKE folding, we computationally create mutants with deleted inter-domain interfaces and simulate their folding. We find that inter-domain interfaces play a minor role in the folding cooperativity of AKE. On further analysis, we find that unlike other multi-domain proteins whose folding has been studied, the domains of AKE are not singly-linked. Two of its domains have two linkers to the third one, i.e., they are inserted into the third one. We use circular permutation to modify AKE chain-connectivity and convert inserted-domains into singly-linked domains. We find that domain insertion in AKE achieves the following: (1) It facilitates folding cooperativity even when domains have different stabilities. Insertion constrains the N- and C-termini of inserted domains and stabilizes their folded states. Therefore, domains that perform conformational transitions can be smaller with fewer stabilizing interactions. (2) Inter-domain interactions are not needed to promote folding cooperativity and can be tuned for function. In AKE, these interactions help promote conformational dynamics limited catalysis. Finally, using structural bioinformatics, we suggest that domain insertion may also facilitate the cooperative folding of other multi-domain proteins. PMID:25393408

  6. Cross-domain human action recognition.

    PubMed

    Bian, Wei; Tao, Dacheng; Rui, Yong

    2012-04-01

    Conventional human action recognition algorithms cannot work well when the amount of training videos is insufficient. We solve this problem by proposing a transfer topic model (TTM), which utilizes information extracted from videos in the auxiliary domain to assist recognition tasks in the target domain. The TTM is well characterized by two aspects: 1) it uses the bag-of-words model trained from the auxiliary domain to represent videos in the target domain; and 2) it assumes each human action is a mixture of a set of topics and uses the topics learned from the auxiliary domain to regularize the topic estimation in the target domain, wherein the regularization is the summation of Kullback-Leibler divergences between topic pairs of the two domains. The utilization of the auxiliary domain knowledge improves the generalization ability of the learned topic model. Experiments on Weizmann and KTH human action databases suggest the effectiveness of the proposed TTM for cross-domain human action recognition.

  7. Spline interpolation on unbounded domains

    NASA Astrophysics Data System (ADS)

    Skeel, Robert D.

    2016-06-01

    Spline interpolation is a splendid tool for multiscale approximation on unbounded domains. In particular, it is well suited for use by the multilevel summation method (MSM) for calculating a sum of pairwise interactions for a large set of particles in linear time. Outlined here is an algorithm for spline interpolation on unbounded domains that is efficient and elegant though not so simple. Further gains in efficiency are possible via quasi-interpolation, which compromises collocation but with minimal loss of accuracy. The MSM, which may also be of value for continuum models, embodies most of the best features of both hierarchical clustering methods (tree methods, fast multipole methods, hierarchical matrix methods) and FFT-based 2-level methods (particle-particle particle-mesh methods, particle-mesh Ewald methods).

  8. Gabor domain optical coherence microscopy

    NASA Astrophysics Data System (ADS)

    Murali, Supraja

    Time domain Optical Coherence Tomography (TD-OCT), first reported in 1991, makes use of the low temporal coherence properties of a NIR broadband laser to create depth sectioning of up to 2mm under the surface using optical interferometry and point to point scanning. Prior and ongoing work in OCT in the research community has concentrated on improving axial resolution through the development of broadband sources and speed of image acquisition through new techniques such as Spectral domain OCT (SD-OCT). In SD-OCT, an entire depth scan is acquired at once with a low numerical aperture (NA) objective lens focused at a fixed point within the sample. In this imaging geometry, a longer depth of focus is achieved at the expense of lateral resolution, which is typically limited to 10 to 20 mum. Optical Coherence Microscopy (OCM), introduced in 1994, combined the advantages of high axial resolution obtained in OCT with high lateral resolution obtained by increasing the NA of the microscope placed in the sample arm. However, OCM presented trade-offs caused by the inverse quadratic relationship between the NA and the DOF of the optics used. For applications requiring high lateral resolution, such as cancer diagnostics, several solutions have been proposed including the periodic manual re-focusing of the objective lens in the time domain as well as the spectral domain C-mode configuration in order to overcome the loss in lateral resolution outside the DOF. In this research, we report for the first time, high speed, sub-cellular imaging (lateral resolution of 2 mum) in OCM using a Gabor domain image processing algorithm with a custom designed and fabricated dynamic focus microscope interfaced to a Ti:Sa femtosecond laser centered at 800 nm within an SD-OCM configuration. It is envisioned that this technology will provide a non-invasive replacement for the current practice of multiple biopsies for skin cancer diagnosis. The research reported here presents three important advances

  9. Frequency domain optical parametric amplification

    NASA Astrophysics Data System (ADS)

    Schmidt, Bruno E.; Thiré, Nicolas; Boivin, Maxime; Laramée, Antoine; Poitras, François; Lebrun, Guy; Ozaki, Tsuneyuki; Ibrahim, Heide; Légaré, François

    2014-05-01

    Today’s ultrafast lasers operate at the physical limits of optical materials to reach extreme performances. Amplification of single-cycle laser pulses with their corresponding octave-spanning spectra still remains a formidable challenge since the universal dilemma of gain narrowing sets limits for both real level pumped amplifiers as well as parametric amplifiers. We demonstrate that employing parametric amplification in the frequency domain rather than in time domain opens up new design opportunities for ultrafast laser science, with the potential to generate single-cycle multi-terawatt pulses. Fundamental restrictions arising from phase mismatch and damage threshold of nonlinear laser crystals are not only circumvented but also exploited to produce a synergy between increased seed spectrum and increased pump energy. This concept was successfully demonstrated by generating carrier envelope phase stable, 1.43 mJ two-cycle pulses at 1.8 μm wavelength.

  10. Frequency domain optical parametric amplification

    PubMed Central

    Schmidt, Bruno E.; Thiré, Nicolas; Boivin, Maxime; Laramée, Antoine; Poitras, François; Lebrun, Guy; Ozaki, Tsuneyuki; Ibrahim, Heide; Légaré, François

    2014-01-01

    Today’s ultrafast lasers operate at the physical limits of optical materials to reach extreme performances. Amplification of single-cycle laser pulses with their corresponding octave-spanning spectra still remains a formidable challenge since the universal dilemma of gain narrowing sets limits for both real level pumped amplifiers as well as parametric amplifiers. We demonstrate that employing parametric amplification in the frequency domain rather than in time domain opens up new design opportunities for ultrafast laser science, with the potential to generate single-cycle multi-terawatt pulses. Fundamental restrictions arising from phase mismatch and damage threshold of nonlinear laser crystals are not only circumvented but also exploited to produce a synergy between increased seed spectrum and increased pump energy. This concept was successfully demonstrated by generating carrier envelope phase stable, 1.43 mJ two-cycle pulses at 1.8 μm wavelength. PMID:24805968

  11. Domain decomposition methods in aerodynamics

    NASA Technical Reports Server (NTRS)

    Venkatakrishnan, V.; Saltz, Joel

    1990-01-01

    Compressible Euler equations are solved for two-dimensional problems by a preconditioned conjugate gradient-like technique. An approximate Riemann solver is used to compute the numerical fluxes to second order accuracy in space. Two ways to achieve parallelism are tested, one which makes use of parallelism inherent in triangular solves and the other which employs domain decomposition techniques. The vectorization/parallelism in triangular solves is realized by the use of a recording technique called wavefront ordering. This process involves the interpretation of the triangular matrix as a directed graph and the analysis of the data dependencies. It is noted that the factorization can also be done in parallel with the wave front ordering. The performances of two ways of partitioning the domain, strips and slabs, are compared. Results on Cray YMP are reported for an inviscid transonic test case. The performances of linear algebra kernels are also reported.

  12. Flexible time domain averaging technique

    NASA Astrophysics Data System (ADS)

    Zhao, Ming; Lin, Jing; Lei, Yaguo; Wang, Xiufeng

    2013-09-01

    Time domain averaging(TDA) is essentially a comb filter, it cannot extract the specified harmonics which may be caused by some faults, such as gear eccentric. Meanwhile, TDA always suffers from period cutting error(PCE) to different extent. Several improved TDA methods have been proposed, however they cannot completely eliminate the waveform reconstruction error caused by PCE. In order to overcome the shortcomings of conventional methods, a flexible time domain averaging(FTDA) technique is established, which adapts to the analyzed signal through adjusting each harmonic of the comb filter. In this technique, the explicit form of FTDA is first constructed by frequency domain sampling. Subsequently, chirp Z-transform(CZT) is employed in the algorithm of FTDA, which can improve the calculating efficiency significantly. Since the signal is reconstructed in the continuous time domain, there is no PCE in the FTDA. To validate the effectiveness of FTDA in the signal de-noising, interpolation and harmonic reconstruction, a simulated multi-components periodic signal that corrupted by noise is processed by FTDA. The simulation results show that the FTDA is capable of recovering the periodic components from the background noise effectively. Moreover, it can improve the signal-to-noise ratio by 7.9 dB compared with conventional ones. Experiments are also carried out on gearbox test rigs with chipped tooth and eccentricity gear, respectively. It is shown that the FTDA can identify the direction and severity of the eccentricity gear, and further enhances the amplitudes of impulses by 35%. The proposed technique not only solves the problem of PCE, but also provides a useful tool for the fault symptom extraction of rotating machinery.

  13. Field-Domain Ion Spectrometry

    NASA Technical Reports Server (NTRS)

    Bowers, W. D.; Chuan, R. L.

    1992-01-01

    Field-domain ion spectrometry (FDIS) is variant of established technique known as ion-mobility spectrometry. Operates at atmospheric pressure and only requires small pump to draw air sample into instrument. Strength of retarding electric field varied to distinguish among ions of different mobilities. New concept offers potential for development of small, (hand-held), low-power, portable devices detecting airborne chemical substances in real-time at concentrations at parts-per-billion level.

  14. Pyramidal inversion domain boundaries revisited

    SciTech Connect

    Remmele, T.; Albrecht, M.; Irmscher, K.; Fornari, R.; Strassburg, M.

    2011-10-03

    The structure of pyramidal inversion domain boundaries in GaN:Mg was investigated by aberration corrected transmission electron microscopy. The analysis shows the upper (0001) boundary to consist of a single Mg layer inserted between polarity inverted GaN layers in an abcab stacking. The Mg bound in these defects is at least one order of magnitude lower than the chemical Mg concentration. Temperature dependent Hall effect measurements show that up to 27% of the Mg acceptors is electrically compensated.

  15. Dynamics of domain wall networks

    SciTech Connect

    Eto, Minoru; Fujimori, Toshiaki; Nagashima, Takayuki; Sakai, Norisuke; Nitta, Muneto; Ohashi, Keisuke

    2007-12-15

    Networks or webs of domain walls are admitted in Abelian or non-Abelian gauge theory coupled to fundamental Higgs fields with complex masses. We examine the dynamics of the domain wall loops by using the moduli approximation and find a phase rotation induces a repulsive force which can be understood as a Noether charge of Q-solitons. Non-Abelian gauge theory allows different types of loops which can be deformed to each other by changing a modulus. This admits the moduli geometry like a sandglass made by gluing the tips of the two cigar-(cone-)like metrics of a single triangle loop. We conclude that the sizes of all loops tend to grow for a late time in general models with complex Higgs masses, while the sizes are stabilized at some values once triplet masses are introduced for the Higgs fields. We also show that the stationary motion on the moduli space of the domain wall webs represents 1/4 Bogomol'nyi-Prasad-Sommerfield Q-webs of walls.

  16. Aversive control: A separate domain?

    PubMed Central

    Hineline, Philip N.

    1984-01-01

    Traditionally, aversive control has been viewed as a separate domain within behavior theory. Sometimes this separateness has been based upon a distinction between reinforcement and punishment, and sometimes upon a distinction between positive and negative reinforcement. The latter is regarded here as the more compelling basis, due to some inherent procedural asymmetries. An approach to the interpretation of negative reinforcement is presented, with indication of types of experiments that support it and that also point to promising directions for further work. However, most of the interpretive issues that arise here are relevant to positively reinforced behavior as well. These include: possible reformulation of the operant/respondent distinction; the place of emotional concepts in behavior analysis; the need for simultaneous, complementary analysis on differing time scales; the understanding of behavioral situations with rewarding or aversive properties that depend as much upon the contingencies that the situations involve as upon the primary rewarding or aversive stimuli that they include. Thus, an adequate understanding of this domain, which has been traditionally viewed as distinct, has implications for all domains of behavior-analytic theory. PMID:16812404

  17. Aversive control: A separate domain?

    PubMed

    Hineline, P N

    1984-11-01

    Traditionally, aversive control has been viewed as a separate domain within behavior theory. Sometimes this separateness has been based upon a distinction between reinforcement and punishment, and sometimes upon a distinction between positive and negative reinforcement. The latter is regarded here as the more compelling basis, due to some inherent procedural asymmetries. An approach to the interpretation of negative reinforcement is presented, with indication of types of experiments that support it and that also point to promising directions for further work. However, most of the interpretive issues that arise here are relevant to positively reinforced behavior as well. These include: possible reformulation of the operant/respondent distinction; the place of emotional concepts in behavior analysis; the need for simultaneous, complementary analysis on differing time scales; the understanding of behavioral situations with rewarding or aversive properties that depend as much upon the contingencies that the situations involve as upon the primary rewarding or aversive stimuli that they include. Thus, an adequate understanding of this domain, which has been traditionally viewed as distinct, has implications for all domains of behavior-analytic theory.

  18. Aversive control: A separate domain?

    PubMed

    Hineline, P N

    1984-11-01

    Traditionally, aversive control has been viewed as a separate domain within behavior theory. Sometimes this separateness has been based upon a distinction between reinforcement and punishment, and sometimes upon a distinction between positive and negative reinforcement. The latter is regarded here as the more compelling basis, due to some inherent procedural asymmetries. An approach to the interpretation of negative reinforcement is presented, with indication of types of experiments that support it and that also point to promising directions for further work. However, most of the interpretive issues that arise here are relevant to positively reinforced behavior as well. These include: possible reformulation of the operant/respondent distinction; the place of emotional concepts in behavior analysis; the need for simultaneous, complementary analysis on differing time scales; the understanding of behavioral situations with rewarding or aversive properties that depend as much upon the contingencies that the situations involve as upon the primary rewarding or aversive stimuli that they include. Thus, an adequate understanding of this domain, which has been traditionally viewed as distinct, has implications for all domains of behavior-analytic theory. PMID:16812404

  19. The Influence of Domain Knowledge on the Functional Capacity of Working Memory

    ERIC Educational Resources Information Center

    Ricks, Travis Rex; Wiley, Jennifer

    2009-01-01

    Theories of expertise have proposed that superior cognitive performance is in part due to increases in the functional capacity of working memory during domain-related tasks. Consistent with this approach Fincher-Kiefer et al. (1988), found that domain knowledge increased scores on baseball-related reading span tasks. The present studies extended…

  20. Preparation for Old Age in Different Life Domains: Dimensions and Age Differences

    ERIC Educational Resources Information Center

    Kornadt, Anna E.; Rothermund, Klaus

    2014-01-01

    We investigated preparation for age-related changes from a multidimensional, life span perspective and administered a newly developed questionnaire to a large sample aged 30-80 years. Preparing for age-related changes was organized by life domains, with domain-specific types of preparation addressing obstacles and opportunities in the respective…

  1. Structural studies of FF domains of the transcription factor CA150 provide insights into the organization of FF domain tandem arrays.

    PubMed

    Murphy, James M; Hansen, D Flemming; Wiesner, Silke; Muhandiram, D Ranjith; Borg, Mikael; Smith, Matthew J; Sicheri, Frank; Kay, Lewis E; Forman-Kay, Julie D; Pawson, Tony

    2009-10-23

    FF domains are poorly understood protein interaction modules that are present within eukaryotic transcription factors, such as CA150 (TCERG-1). The CA150 FF domains have been shown to mediate interactions with the phosphorylated C-terminal domain of RNA polymerase II (phosphoCTD) and a multitude of transcription factors and RNA processing proteins, and may therefore have a central role in organizing transcription. FF domains occur in tandem arrays of up to six domains, although it is not known whether they adopt higher-order structures. We have used the CA150 FF1+FF2 domains as a model system to examine whether tandem FF domains form higher-order structures in solution using NMR spectroscopy. In the solution structure of FF1 fused to the linker that joins FF1 to FF2, we observed that the highly conserved linker peptide is ordered and forms a helical extension of helix alpha3, suggesting that the interdomain linker might have a role in orientating FF1 relative to FF2. However, examination of the FF1+FF2 domains using relaxation NMR experiments revealed that although these domains are not rigidly orientated relative to one another, they do not tumble independently. Thus, the FF1+FF2 structure conforms to a dumbbell-shape in solution, where the helical interdomain linker maintains distance between the two dynamic FF domains without cementing their relative orientations. This model for FF domain organization within tandem arrays suggests a general mechanism by which individual FF domains can manoeuvre to achieve optimal recognition of flexible binding partners, such as the intrinsically-disordered phosphoCTD.

  2. Prevalence of the F-type lectin domain.

    PubMed

    Bishnoi, Ritika; Khatri, Indu; Subramanian, Srikrishna; Ramya, T N C

    2015-08-01

    F-type lectins are fucolectins with characteristic fucose and calcium-binding sequence motifs and a unique lectin fold (the "F-type" fold). F-type lectins are phylogenetically widespread with selective distribution. Several eukaryotic F-type lectins have been biochemically and structurally characterized, and the F-type lectin domain (FLD) has also been studied in the bacterial proteins, Streptococcus mitis lectinolysin and Streptococcus pneumoniae SP2159. However, there is little knowledge about the extent of occurrence of FLDs and their domain organization, especially, in bacteria. We have now mined the extensive genomic sequence information available in the public databases with sensitive sequence search techniques in order to exhaustively survey prokaryotic and eukaryotic FLDs. We report 437 FLD sequence clusters (clustered at 80% sequence identity) from eukaryotic, eubacterial and viral proteins. Domain architectures are diverse but mostly conserved in closely related organisms, and domain organizations of bacterial FLD-containing proteins are very different from their eukaryotic counterparts, suggesting unique specialization of FLDs to suit different requirements. Several atypical phylogenetic associations hint at lateral transfer. Among eukaryotes, we observe an expansion of FLDs in terms of occurrence and domain organization diversity in the taxa Mollusca, Hemichordata and Branchiostomi, perhaps coinciding with greater emphasis on innate immune strategies in these organisms. The naturally occurring FLDs with diverse domain organizations that we have identified here will be useful for future studies aimed at creating designer molecular platforms for directing desired biological activities to fucosylated glycoconjugates in target niches. PMID:25943580

  3. Screening retinal transplants with Fourier-domain OCT

    NASA Astrophysics Data System (ADS)

    Rao, Bin

    2009-02-01

    Transplant technologies have been studied for the recovery of vision loss from retinitis pigmentosa (RP) and age-related macular degeneration (AMD). In several rodent retinal degeneration models and in patients, retinal progenitor cells transplanted as layers to the subretinal space have been shown to restore or preserve vision. The methods for evaluation of transplants are expensive considering the large amount of animals. Alternatively, time-domain Stratus OCT was previously shown to be able to image the morphological structure of transplants to some extent, but could not clearly identify laminated transplants. The efficacy of screening retinal transplants with Fourier-domain OCT was studied on 37 S334ter line 3 rats with retinal degeneration 6-67 days after transplant surgery. The transplants were morphologically categorized as no transplant, detachment, rosettes, small laminated area and larger laminated area with both Fourier-domain OCT and histology. The efficacy of Fourier-domain OCT in screening retinal transplants was evaluated by comparing the categorization results with OCT and histology. Additionally, 4 rats were randomly selected for multiple OCT examinations (1, 5, 9, 14 and 21days post surgery) in order to determine the earliest image time of OCT examination since the transplanted tissue may need some time to show its tendency of growing. Finally, we demonstrated the efficacy of Fourier-domain OCT in screening retinal transplants in early stages and determined the earliest imaging time for OCT. Fourier-domain OCT makes itself valuable in saving resource spent on animals with unsuccessful transplants.

  4. Prevalence of the F-type lectin domain.

    PubMed

    Bishnoi, Ritika; Khatri, Indu; Subramanian, Srikrishna; Ramya, T N C

    2015-08-01

    F-type lectins are fucolectins with characteristic fucose and calcium-binding sequence motifs and a unique lectin fold (the "F-type" fold). F-type lectins are phylogenetically widespread with selective distribution. Several eukaryotic F-type lectins have been biochemically and structurally characterized, and the F-type lectin domain (FLD) has also been studied in the bacterial proteins, Streptococcus mitis lectinolysin and Streptococcus pneumoniae SP2159. However, there is little knowledge about the extent of occurrence of FLDs and their domain organization, especially, in bacteria. We have now mined the extensive genomic sequence information available in the public databases with sensitive sequence search techniques in order to exhaustively survey prokaryotic and eukaryotic FLDs. We report 437 FLD sequence clusters (clustered at 80% sequence identity) from eukaryotic, eubacterial and viral proteins. Domain architectures are diverse but mostly conserved in closely related organisms, and domain organizations of bacterial FLD-containing proteins are very different from their eukaryotic counterparts, suggesting unique specialization of FLDs to suit different requirements. Several atypical phylogenetic associations hint at lateral transfer. Among eukaryotes, we observe an expansion of FLDs in terms of occurrence and domain organization diversity in the taxa Mollusca, Hemichordata and Branchiostomi, perhaps coinciding with greater emphasis on innate immune strategies in these organisms. The naturally occurring FLDs with diverse domain organizations that we have identified here will be useful for future studies aimed at creating designer molecular platforms for directing desired biological activities to fucosylated glycoconjugates in target niches.

  5. PDE and cognitive processing: beyond the memory domain.

    PubMed

    Heckman, P R A; Blokland, A; Ramaekers, J; Prickaerts, J

    2015-03-01

    Phosphodiesterase inhibitors (PDE-Is) enhance cAMP and/or cGMP signaling via reducing the degradation of these cyclic nucleotides. Both cAMP and cGMP signaling are essential for a variety of cellular functions and exert their effects both pre- and post-synaptically. Either of these second messengers relays and amplifies incoming signals at receptors on the cell surface making them important elements in signal transduction cascades and essential in cellular signaling in a variety of cell functions including neurotransmitter release and neuroprotection. Consequently, these processes can be influenced by PDE-Is as they increase cAMP and/or cGMP concentrations. PDE-Is have been considered as possible therapeutic agents to treat impaired memory function linked to several brain disorders, including depression, schizophrenia and Alzheimer's disease (AD). This review will, however, focus on the possible role of phosphodiesterases (PDEs) in cognitive decline beyond the memory domain. Here we will discuss the involvement of PDEs on three related domains: attention, information filtering (sensory- and sensorimotor gating) and response inhibition (drug-induced hyperlocomotion). Currently, these are emerging cognitive domains in the field of PDE research. Here we discuss experimental studies and the potential beneficial effects of PDE-I drugs on these cognitive domains, as effects of PDE-Is on these domains could potentially influence effects on memory performance. Overall, PDE4 seems to be the most promising target for all domains discussed in this review.

  6. Ferroelectricity of domain walls in rare earth iron garnet films.

    PubMed

    Popov, A I; Zvezdin, K A; Gareeva, Z V; Mazhitova, F A; Vakhitov, R M; Yumaguzin, A R; Zvezdin, A K

    2016-11-16

    In this paper, we report on electric polarization arising in a vicinity of Bloch-like domain walls in rare-earth iron garnet films. The domain walls generate an intrinsic magnetic field that breaks an antiferroelectric structure formed in the garnets due to an exchange interaction between rare earth and iron sublattices. We explore 180° domain walls whose formation is energetically preferable in the films with perpendicular magnetic anisotropy. Magnetic and electric structures of the 180° quasi-Bloch domain walls have been simulated at various relations between system parameters. Singlet, doublet ground states of rare earth ions and strongly anisotropic rare earth Ising ions have been considered. Our results show that electric polarization appears in rare earth garnet films at Bloch domain walls, and the maximum of magnetic inhomogeneity is not always linked to the maximum of electric polarization. A number of factors including the temperature, the state of the rare earth ion and the type of a wall influence magnetically induced electric polarization. We show that the value of polarization can be enhanced by the shrinking of the Bloch domain wall width, decreasing the temperature, and increasing the deviations of magnetization from the Bloch rotation that are regulated by impacts given by magnetic anisotropies of the films. PMID:27620369

  7. Ferroelectricity of domain walls in rare earth iron garnet films

    NASA Astrophysics Data System (ADS)

    Popov, A. I.; Zvezdin, K. A.; Gareeva, Z. V.; Mazhitova, F. A.; Vakhitov, R. M.; Yumaguzin, A. R.; Zvezdin, A. K.

    2016-11-01

    In this paper, we report on electric polarization arising in a vicinity of Bloch-like domain walls in rare-earth iron garnet films. The domain walls generate an intrinsic magnetic field that breaks an antiferroelectric structure formed in the garnets due to an exchange interaction between rare earth and iron sublattices. We explore 180° domain walls whose formation is energetically preferable in the films with perpendicular magnetic anisotropy. Magnetic and electric structures of the 180° quasi-Bloch domain walls have been simulated at various relations between system parameters. Singlet, doublet ground states of rare earth ions and strongly anisotropic rare earth Ising ions have been considered. Our results show that electric polarization appears in rare earth garnet films at Bloch domain walls, and the maximum of magnetic inhomogeneity is not always linked to the maximum of electric polarization. A number of factors including the temperature, the state of the rare earth ion and the type of a wall influence magnetically induced electric polarization. We show that the value of polarization can be enhanced by the shrinking of the Bloch domain wall width, decreasing the temperature, and increasing the deviations of magnetization from the Bloch rotation that are regulated by impacts given by magnetic anisotropies of the films.

  8. Micro- and nano-domain engineering in lithium niobate

    NASA Astrophysics Data System (ADS)

    Shur, V. Ya.; Akhmatkhanov, A. R.; Baturin, I. S.

    2015-12-01

    The physical basis of the domain engineering in ferroelectrics and its application to lithium niobate crystals were reviewed. The unified kinetic approach to the domain structure evolution in electric field was formulated and its validity for understanding the variety of observed domain evolution scenarios was demonstrated. The kinetics and statics of the domain structure in the crystals of lithium niobate family including congruent, stoichiometric, and MgO doped ones have been discussed. The main stages of the periodical poling process and related problems have been pointed out. The basic poling techniques applied for creation of the periodical domain structures in bulk crystals and waveguides were compared. The recent applications of the periodically poled lithium niobate for light frequency conversion using second harmonic generation and optical parametric oscillation, excitation of the surface acoustic waves, and generation of terahertz radiation have been discussed. The special attention has been paid for achievements in fabrication of high-power optical parametric oscillation and integrated optical devices with periodically poled lithium niobate. The future trends in periodical poling and development of the nanodomain engineering which will allow to create the nanoscale domain patterns necessary for utilization of the new nonlinear interactions were reviewed.

  9. Ferroelectricity of domain walls in rare earth iron garnet films.

    PubMed

    Popov, A I; Zvezdin, K A; Gareeva, Z V; Mazhitova, F A; Vakhitov, R M; Yumaguzin, A R; Zvezdin, A K

    2016-11-16

    In this paper, we report on electric polarization arising in a vicinity of Bloch-like domain walls in rare-earth iron garnet films. The domain walls generate an intrinsic magnetic field that breaks an antiferroelectric structure formed in the garnets due to an exchange interaction between rare earth and iron sublattices. We explore 180° domain walls whose formation is energetically preferable in the films with perpendicular magnetic anisotropy. Magnetic and electric structures of the 180° quasi-Bloch domain walls have been simulated at various relations between system parameters. Singlet, doublet ground states of rare earth ions and strongly anisotropic rare earth Ising ions have been considered. Our results show that electric polarization appears in rare earth garnet films at Bloch domain walls, and the maximum of magnetic inhomogeneity is not always linked to the maximum of electric polarization. A number of factors including the temperature, the state of the rare earth ion and the type of a wall influence magnetically induced electric polarization. We show that the value of polarization can be enhanced by the shrinking of the Bloch domain wall width, decreasing the temperature, and increasing the deviations of magnetization from the Bloch rotation that are regulated by impacts given by magnetic anisotropies of the films.

  10. Micro- and nano-domain engineering in lithium niobate

    SciTech Connect

    Shur, V. Ya.; Akhmatkhanov, A. R.; Baturin, I. S.

    2015-12-15

    The physical basis of the domain engineering in ferroelectrics and its application to lithium niobate crystals were reviewed. The unified kinetic approach to the domain structure evolution in electric field was formulated and its validity for understanding the variety of observed domain evolution scenarios was demonstrated. The kinetics and statics of the domain structure in the crystals of lithium niobate family including congruent, stoichiometric, and MgO doped ones have been discussed. The main stages of the periodical poling process and related problems have been pointed out. The basic poling techniques applied for creation of the periodical domain structures in bulk crystals and waveguides were compared. The recent applications of the periodically poled lithium niobate for light frequency conversion using second harmonic generation and optical parametric oscillation, excitation of the surface acoustic waves, and generation of terahertz radiation have been discussed. The special attention has been paid for achievements in fabrication of high-power optical parametric oscillation and integrated optical devices with periodically poled lithium niobate. The future trends in periodical poling and development of the nanodomain engineering which will allow to create the nanoscale domain patterns necessary for utilization of the new nonlinear interactions were reviewed.

  11. Recurrent adenylation domain replacement in the microcystin synthetase gene cluster

    PubMed Central

    Fewer, David P; Rouhiainen, Leo; Jokela, Jouni; Wahlsten, Matti; Laakso, Kati; Wang, Hao; Sivonen, Kaarina

    2007-01-01

    Background Microcystins are small cyclic heptapeptide toxins produced by a range of distantly related cyanobacteria. Microcystins are synthesized on large NRPS-PKS enzyme complexes. Many structural variants of microcystins are produced simulatenously. A recombination event between the first module of mcyB (mcyB1) and mcyC in the microcystin synthetase gene cluster is linked to the simultaneous production of microcystin variants in strains of the genus Microcystis. Results Here we undertook a phylogenetic study to investigate the order and timing of recombination between the mcyB1 and mcyC genes in a diverse selection of microcystin producing cyanobacteria. Our results provide support for complex evolutionary processes taking place at the mcyB1 and mcyC adenylation domains which recognize and activate the amino acids found at X and Z positions. We find evidence for recent recombination between mcyB1 and mcyC in strains of the genera Anabaena, Microcystis, and Hapalosiphon. We also find clear evidence for independent adenylation domain conversion of mcyB1 by unrelated peptide synthetase modules in strains of the genera Nostoc and Microcystis. The recombination events replace only the adenylation domain in each case and the condensation domains of mcyB1 and mcyC are not transferred together with the adenylation domain. Our findings demonstrate that the mcyB1 and mcyC adenylation domains are recombination hotspots in the microcystin synthetase gene cluster. Conclusion Recombination is thought to be one of the main mechanisms driving the diversification of NRPSs. However, there is very little information on how recombination takes place in nature. This study demonstrates that functional peptide synthetases are created in nature through transfer of adenylation domains without the concomitant transfer of condensation domains. PMID:17908306

  12. Tandem-repeat protein domains across the tree of life

    PubMed Central

    Jernigan, Kristin K.

    2015-01-01

    Tandem-repeat protein domains, composed of repeated units of conserved stretches of 20–40 amino acids, are required for a wide array of biological functions. Despite their diverse and fundamental functions, there has been no comprehensive assessment of their taxonomic distribution, incidence, and associations with organismal lifestyle and phylogeny. In this study, we assess for the first time the abundance of armadillo (ARM) and tetratricopeptide (TPR) repeat domains across all three domains in the tree of life and compare the results to our previous analysis on ankyrin (ANK) repeat domains in this journal. All eukaryotes and a majority of the bacterial and archaeal genomes analyzed have a minimum of one TPR and ARM repeat. In eukaryotes, the fraction of ARM-containing proteins is approximately double that of TPR and ANK-containing proteins, whereas bacteria and archaea are enriched in TPR-containing proteins relative to ARM- and ANK-containing proteins. We show in bacteria that phylogenetic history, rather than lifestyle or pathogenicity, is a predictor of TPR repeat domain abundance, while neither phylogenetic history nor lifestyle predicts ARM repeat domain abundance. Surprisingly, pathogenic bacteria were not enriched in TPR-containing proteins, which have been associated within virulence factors in certain species. Taken together, this comparative analysis provides a newly appreciated view of the prevalence and diversity of multiple types of tandem-repeat protein domains across the tree of life. A central finding of this analysis is that tandem repeat domain-containing proteins are prevalent not just in eukaryotes, but also in bacterial and archaeal species. PMID:25653910

  13. Domains of discussion in psychotherapy: what do patients really want?

    PubMed

    Miovic, Michael; McCarthy, Mary; Badaracco, Mary Anne; Greenberg, William; Fitzmaurice, Garrett M; Peteet, John R

    2006-01-01

    Little quantitative data exist on what the content of non-manualized psychotherapy in contemporary clinical settings actually is, and what patients and clinicians think it ought to be. This descriptive pilot study identified potential content areas to address in psychotherapy, quantified the relative importance of these domains of discussion to patients vs. clinicians, and attempted to measure the frequency with which these domains are actually addressed in current clinical practice at two academic, urban hospitals. The conteni areas assessed included health habits, avocations, work, family, friendships, community involvement, spirituality/religion, finance, sexuality, political activities, educational and cultural pursuits, and ethnicity/race. Overall, clinicians and patients agreed about the relative personal importance and importance to treatment of these content areas, and they rated work, family, friends, and sexuality as the most important domains of discussion for psychotherapy. Also, this sample of patients did not feel that clinicians undervalue the importance of religion and spirituality.

  14. Ferroelectric domain inversion and its stability in lithium niobate thin film on insulator with different thicknesses

    NASA Astrophysics Data System (ADS)

    Shao, Guang-hao; Bai, Yu-hang; Cui, Guo-xin; Li, Chen; Qiu, Xiang-biao; Geng, De-qiang; Wu, Di; Lu, Yan-qing

    2016-07-01

    Ferroelectric domain inversion and its effect on the stability of lithium niobate thin films on insulator (LNOI) are experimentally characterized. Two sets of specimens with different thicknesses varying from submicron to microns are selected. For micron thick samples (˜28 μm), domain structures are achieved by pulsed electric field poling with electrodes patterned via photolithography. No domain structure deterioration has been observed for a month as inspected using polarizing optical microscopy and etching. As for submicron (540 nm) films, large-area domain inversion is realized by scanning a biased conductive tip in a piezoelectric force microscope. A graphic processing method is taken to evaluate the domain retention. A domain life time of 25.0 h is obtained and possible mechanisms are discussed. Our study gives a direct reference for domain structure-related applications of LNOI, including guiding wave nonlinear frequency conversion, nonlinear wavefront tailoring, electro-optic modulation, and piezoelectric devices.

  15. Domains in microbial beta-1, 4-glycanases: sequence conservation, function, and enzyme families.

    PubMed Central

    Gilkes, N R; Henrissat, B; Kilburn, D G; Miller, R C; Warren, R A

    1991-01-01

    Several types of domain occur in beta-1, 4-glycanases. The best characterized of these are the catalytic domains and the cellulose-binding domains. The domains may be joined by linker sequences rich in proline or hydroxyamino acids or both. Some of the enzymes contain repeated sequences up to 150 amino acids in length. The enzymes can be grouped into families on the basis of sequence similarities between the catalytic domains. There are sequence similarities between the cellulose-binding domains, of which two types have been identified, and also between some domains of unknown function. The beta-1, 4-glycanases appear to have arisen by the shuffling of a relatively small number of progenitor sequences. PMID:1886523

  16. Frequency Domain Calculations Of Acoustic Propagation

    NASA Technical Reports Server (NTRS)

    Lockard, David P.

    2004-01-01

    Two complex geometry problems are solved using the linearized Euler equations. The impedance mismatch method1 is used to impose the solid surfaces without the need to use a body-fitted grid. The problem is solved in the frequency domain to avoid long run times. Although the harmonic assumption eliminates all time dependence, a pseudo-time term is added to allow conventional iterative methods to be employed. A Jameson type, Runge-Kutta scheme is used to advance the solution in pseudo time. The spatial operator is based on a seven-point, sixth-order finite difference. Constant coefficient, sixth-derivative artificial dissipation is used throughout the domain. A buffer zone technique employing a complex frequency to damp all waves near the boundaries is used to minimize reflections. The results show that the method is capable of capturing the salient features of the scattering, but an excessive number of grid points are required to resolve the phenomena in the vicinity of the solid bodies because the wavelength of the acoustics is relatively short compared with the size of the bodies. Smoothly transitioning into the immersed boundary condition alleviates the difficulties, but a fine mesh is still required.

  17. The Promise of Domain Adaptation

    NASA Astrophysics Data System (ADS)

    Mahabal, Ashish A.; Li, Jingling; Vaijanapurkar, Samarth; Bue, Brian; Miller, Adam; Donalek, Ciro; Djorgovski, Stanislav G.; Drake, Andrew J.; Graham, Matthew; CRTS, iPTF

    2016-01-01

    Most new surveys spend an appreciable time in collecting data on which to train classifiers before they can be used on future observations from the same dataset. The result generating phase can start much earlier if the training could incorporate data accumulated from older surveys enhanced with a small set from the new survey. This is exactly what Domain Adaptation (DA) allows us to do. The main idea behind DAs can be summarized thus: if we have two classes of separable objects in some feature space of a Source survey (S), we can define a hyperplane to separate the two types. In a second Target survey (T), for the same features the hyperplane would be inclined differently. DA methods get the mapping between the two hyperplanes using a small fraction of data from the Target (T) survey and can then be used to predict the classes of the remaining majority of data in T. We discuss the parameters that need to be tuned, the difficulties involved, and ways to improve the results. As we move towards bigger, and deeper surveys, being able to use existing labelled information to conduct classification in future surveys will be more cost-effective and promote time efficiency as well. Starting with the light curve data of 50,000 periodic objects from Catalina Real-Time Transient Survey (CRTS), we have applied domain adaptation techniques such as Geodesic Flow Kernel (GFK) with Random forest classifier and Co-training for domain adaptation (CODA) to the CRTS data which has 35,000 points overlapping with Palomar Transient Factory (PTF), and 12,000 with Lincoln Near-Earth Asteroid Research (LINEAR). The results suggest that domain adaptation is an area worth exploring as the knowledge between these surveys is transferable and the approaches to find the mappings between these surveys can be applied to the remaining data as well as for near future surveys such as CRTS-II, Zwicky Transient Facility (ZTF) and the Large Synoptic Survey Telescope (LSST) to name a few at the optical

  18. Pectin Homogalacturonans: Nanostructural Characterization of Methylesterified Domains

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Functionality of pectic hydrocolloids is largely dependent on the two major domains commonly found in their homogalacturonan (HG) regions, i.e., methylester protected domains (MPDs)and non methylesterified domains (NMDs). MPDs can participate in hydrogen bonding and hydrophobic interactions but unli...

  19. Frequency domain photoacoustic and fluorescence microscopy.

    PubMed

    Langer, Gregor; Buchegger, Bianca; Jacak, Jaroslaw; Klar, Thomas A; Berer, Thomas

    2016-07-01

    We report on simultaneous frequency domain optical-resolution photoacoustic and fluorescence microscopy with sub-µm lateral resolution. With the help of a blood smear, we show that photoacoustic and fluorescence images provide complementary information. Furthermore, we compare theoretically predicted signal-to-noise ratios of sinusoidal modulation in frequency domain with pulsed excitation in time domain. PMID:27446698

  20. Frequency domain photoacoustic and fluorescence microscopy.

    PubMed

    Langer, Gregor; Buchegger, Bianca; Jacak, Jaroslaw; Klar, Thomas A; Berer, Thomas

    2016-07-01

    We report on simultaneous frequency domain optical-resolution photoacoustic and fluorescence microscopy with sub-µm lateral resolution. With the help of a blood smear, we show that photoacoustic and fluorescence images provide complementary information. Furthermore, we compare theoretically predicted signal-to-noise ratios of sinusoidal modulation in frequency domain with pulsed excitation in time domain.

  1. Frequency domain photoacoustic and fluorescence microscopy

    PubMed Central

    Langer, Gregor; Buchegger, Bianca; Jacak, Jaroslaw; Klar, Thomas A.; Berer, Thomas

    2016-01-01

    We report on simultaneous frequency domain optical-resolution photoacoustic and fluorescence microscopy with sub-µm lateral resolution. With the help of a blood smear, we show that photoacoustic and fluorescence images provide complementary information. Furthermore, we compare theoretically predicted signal-to-noise ratios of sinusoidal modulation in frequency domain with pulsed excitation in time domain. PMID:27446698

  2. Children's Experience of Posttraumatic Growth: Distinguishing General from Domain-Specific Correlates.

    PubMed

    Laceulle, Odilia M; Kleber, Rolf J; Alisic, Eva

    2015-01-01

    Although the five domains of posttraumatic growth (new possibilities, relating to others, personal strength, spiritual change and appreciation of life) have been studied extensively in adults, little is known about these domains and their correlates in children. We aimed to examine whether demographic and/or social characteristics are related to children's reports of overall posttraumatic growth and of growth in specific domains. In a general population study, children aged 8-12 years who had been exposed to adverse events (N = 1290) filled out questionnaires on their experiences, demographic characteristics (gender, age, time lag since event), stress reactions, peer support, religiosity and posttraumatic growth. All demographic and social characteristics were related to overall posttraumatic growth, except time lag. Associations varied across the five domains with the strongest effects being found for stress reactions and religiosity. A higher level of stress reactions was related to more growth in all domains (general effect), whereas religious children experienced more spiritual growth than non-religious children without differences on other domains (domain specific effect). Other effects were small, and some did not remain significant after Bonferroni corrections. These findings suggest the presence of both general and domain-specific correlates of child posttraumatic growth. Although effects were generally small, the current findings show the need to differentiate between the domains of posttraumatic growth in both further research and clinical practice. This will allow a better understanding of the mechanisms of posttraumatic growth in children as well as more tailored assessment and intervention.

  3. Children’s Experience of Posttraumatic Growth: Distinguishing General from Domain-Specific Correlates

    PubMed Central

    Laceulle, Odilia M.; Kleber, Rolf J.; Alisic, Eva

    2015-01-01

    Although the five domains of posttraumatic growth (new possibilities, relating to others, personal strength, spiritual change and appreciation of life) have been studied extensively in adults, little is known about these domains and their correlates in children. We aimed to examine whether demographic and/or social characteristics are related to children’s reports of overall posttraumatic growth and of growth in specific domains. In a general population study, children aged 8–12 years who had been exposed to adverse events (N = 1290) filled out questionnaires on their experiences, demographic characteristics (gender, age, time lag since event), stress reactions, peer support, religiosity and posttraumatic growth. All demographic and social characteristics were related to overall posttraumatic growth, except time lag. Associations varied across the five domains with the strongest effects being found for stress reactions and religiosity. A higher level of stress reactions was related to more growth in all domains (general effect), whereas religious children experienced more spiritual growth than non-religious children without differences on other domains (domain specific effect). Other effects were small, and some did not remain significant after Bonferroni corrections. These findings suggest the presence of both general and domain-specific correlates of child posttraumatic growth. Although effects were generally small, the current findings show the need to differentiate between the domains of posttraumatic growth in both further research and clinical practice. This will allow a better understanding of the mechanisms of posttraumatic growth in children as well as more tailored assessment and intervention. PMID:26714193

  4. Structure of a two-CAP-domain protein from the human hookworm parasite Necator americanus

    SciTech Connect

    Asojo, Oluwatoyin A.

    2011-05-01

    The first structure of a two-CAP-domain protein, Na-ASP-1, from the major human hookworm parasite N. americanus refined to a resolution limit of 2.2 Å is presented. Major proteins secreted by the infective larval stage hookworms upon host entry include Ancylostoma secreted proteins (ASPs), which are characterized by one or two CAP (cysteine-rich secretory protein/antigen 5/pathogenesis related-1) domains. The CAP domain has been reported in diverse phylogenetically unrelated proteins, but has no confirmed function. The first structure of a two-CAP-domain protein, Na-ASP-1, from the major human hookworm parasite Necator americanus was refined to a resolution limit of 2.2 Å. The structure was solved by molecular replacement (MR) using Na-ASP-2, a one-CAP-domain ASP, as the search model. The correct MR solution could only be obtained by truncating the polyalanine model of Na-ASP-2 and removing several loops. The structure reveals two CAP domains linked by an extended loop. Overall, the carboxyl-terminal CAP domain is more similar to Na-ASP-2 than to the amino-terminal CAP domain. A large central cavity extends from the amino-terminal CAP domain to the carboxyl-terminal CAP domain, encompassing the putative CAP-binding cavity. The putative CAP-binding cavity is a characteristic cavity in the carboxyl-terminal CAP domain that contains a His and Glu pair. These residues are conserved in all single-CAP-domain proteins, but are absent in the amino-terminal CAP domain. The conserved His residues are oriented such that they appear to be capable of directly coordinating a zinc ion as observed for CAP proteins from reptile venoms. This first structure of a two-CAP-domain ASP can serve as a template for homology modeling of other two-CAP-domain proteins.

  5. From Cognitive-Domain Theory to Assessment Practice

    ERIC Educational Resources Information Center

    Bennett, Randy E.; Deane, Paul; van Rijn, Peter W.

    2016-01-01

    This article exemplifies how assessment design might be grounded in theory, thereby helping to strengthen validity claims. Spanning work across multiple related projects, the article first briefly summarizes an assessment system model for the elementary and secondary levels. Next the article describes how cognitive-domain theory and principles are…

  6. Domain 4: Growth and Development National Standards for Sport Coaches

    ERIC Educational Resources Information Center

    Shimon, Jane; Darden, Gibson

    2004-01-01

    This article, the third in a series of articles from the National Association for Sport and Physical Education (NASPE) sport structures, explains how the following two scenarios relate to Domain 4 Standards: (1) two adolescent boys have different baseball throwing skill levels, even though they have been on the same team for the past four years;…

  7. The Importance of Domain-Specific Expertise in Creativity

    ERIC Educational Resources Information Center

    Baer, John

    2015-01-01

    Although creativity and expertise are related, they are nonetheless very different things. Expertise does not usually require creativity, but creativity generally does require a certain level of expertise. There are similarities in the relationships of both expertise and creativity to domains, however. Research has shown that just as expertise in…

  8. Constructing Librarians' Information Literacy Expertise in the Domain of Nursing

    ERIC Educational Resources Information Center

    Sundin, Olof; Limberg, Louise; Lundh, Anna

    2008-01-01

    This article investigates negotiations of librarians' expertise in relation to information literacy at the micro-level, specifically in the domain of nursing education. A qualitative empirical framework is employed. The study draws on 18 semi-structured interviews, 16 with Swedish nursing students, one with a librarian and one with a nursing…

  9. Repetitive Domain-Referenced Testing Using Computers: the TITA System.

    ERIC Educational Resources Information Center

    Olympia, P. L., Jr.

    The TITA (Totally Interactive Testing and Analysis) System algorithm for the repetitive construction of domain-referenced tests utilizes a compact data bank, is highly portable, is useful in any discipline, requires modest computer hardware, and does not present a security problem. Clusters of related keyphrases, statement phrases, and distractors…

  10. The Motor Domain and its Correlates in Educationally Handicapped Children.

    ERIC Educational Resources Information Center

    Rarick, G. Lawrence; And Others

    This monograph is an account of two related investigations of the motor domain and its correlates in educationally handicapped children. Part I describes an investigation primarily concerned with the identification of the basic components of the motor behavior of educable mentally retarded children through the use of factor analysis techniques.…

  11. Domains of Chronic Stress and Suicidal Behaviors among Inpatient Adolescents

    ERIC Educational Resources Information Center

    Pettit, Jeremy W.; Green, Kelly L.; Grover, Kelly E.; Schatte, Dawnelle J.; Morgan, Sharon T.

    2011-01-01

    Little is known about the role of chronic stress in youth suicidal behaviors. This study examined the relations between specific domains of chronic stress and suicidal behaviors among 131 inpatient youth (M age = 15.02 years) who completed measures of stress, suicidal ideation, suicide attempt, and suicide intent. After controlling for…

  12. Teachers' Domain: Classroom Media Resources from Public Television's WGBH.

    ERIC Educational Resources Information Center

    Blumenthal, Denise

    2003-01-01

    Explains Teachers' Domain, a digital library being developed for the National Science Digital Library (NSDL) by WGBH, the Boston public television station, which includes an online index of archival resources related to K-12 life sciences supported by customized lesson plans, background essays, discussion questions, and correlations to national…

  13. Four Critical Domains of Accountability for School Counselors

    ERIC Educational Resources Information Center

    Bemak, Fred; Willians, Joseph M.; Chung, Rita Chi-Ying

    2015-01-01

    Despite recognition of accountability for school counselors, no clear set of interrelated performance measures exists to guide school counselors in collecting and evaluating data that relates to student academic success. This article outlines four critical domains of accountability for school counselors (i.e., grades, attendance, disciplinary…

  14. One Health Core Competency Domains.

    PubMed

    Frankson, Rebekah; Hueston, William; Christian, Kira; Olson, Debra; Lee, Mary; Valeri, Linda; Hyatt, Raymond; Annelli, Joseph; Rubin, Carol

    2016-01-01

    The emergence of complex global challenges at the convergence of human, animal, and environmental health has catalyzed a movement supporting "One Health" approaches. Despite recognition of the importance of One Health approaches to address these complex challenges, little effort has been directed at identifying the seminal knowledge, skills, and attitudes necessary for individuals to successfully contribute to One Health efforts. Between 2008 and 2011, three groups independently embarked on separate initiatives to identify core competencies for professionals involved with One Health approaches. Core competencies were considered critically important for guiding curriculum development and continuing professional education, as they describe the knowledge, skills, and attitudes required to be effective. A workshop was convened in 2012 to synthesize the various strands of work on One Health competencies. Despite having different mandates, participants, and approaches, all of these initiatives identified similar core competency domains: management; communication and informatics; values and ethics; leadership; teams and collaboration; roles and responsibilities; and systems thinking. These core competency domains have been used to develop new continuing professional education programs for One Health professionals and help university curricula prepare new graduates to be able to contribute more effectively to One Health approaches. PMID:27679794

  15. One Health Core Competency Domains

    PubMed Central

    Frankson, Rebekah; Hueston, William; Christian, Kira; Olson, Debra; Lee, Mary; Valeri, Linda; Hyatt, Raymond; Annelli, Joseph; Rubin, Carol

    2016-01-01

    The emergence of complex global challenges at the convergence of human, animal, and environmental health has catalyzed a movement supporting “One Health” approaches. Despite recognition of the importance of One Health approaches to address these complex challenges, little effort has been directed at identifying the seminal knowledge, skills, and attitudes necessary for individuals to successfully contribute to One Health efforts. Between 2008 and 2011, three groups independently embarked on separate initiatives to identify core competencies for professionals involved with One Health approaches. Core competencies were considered critically important for guiding curriculum development and continuing professional education, as they describe the knowledge, skills, and attitudes required to be effective. A workshop was convened in 2012 to synthesize the various strands of work on One Health competencies. Despite having different mandates, participants, and approaches, all of these initiatives identified similar core competency domains: management; communication and informatics; values and ethics; leadership; teams and collaboration; roles and responsibilities; and systems thinking. These core competency domains have been used to develop new continuing professional education programs for One Health professionals and help university curricula prepare new graduates to be able to contribute more effectively to One Health approaches. PMID:27679794

  16. One Health Core Competency Domains

    PubMed Central

    Frankson, Rebekah; Hueston, William; Christian, Kira; Olson, Debra; Lee, Mary; Valeri, Linda; Hyatt, Raymond; Annelli, Joseph; Rubin, Carol

    2016-01-01

    The emergence of complex global challenges at the convergence of human, animal, and environmental health has catalyzed a movement supporting “One Health” approaches. Despite recognition of the importance of One Health approaches to address these complex challenges, little effort has been directed at identifying the seminal knowledge, skills, and attitudes necessary for individuals to successfully contribute to One Health efforts. Between 2008 and 2011, three groups independently embarked on separate initiatives to identify core competencies for professionals involved with One Health approaches. Core competencies were considered critically important for guiding curriculum development and continuing professional education, as they describe the knowledge, skills, and attitudes required to be effective. A workshop was convened in 2012 to synthesize the various strands of work on One Health competencies. Despite having different mandates, participants, and approaches, all of these initiatives identified similar core competency domains: management; communication and informatics; values and ethics; leadership; teams and collaboration; roles and responsibilities; and systems thinking. These core competency domains have been used to develop new continuing professional education programs for One Health professionals and help university curricula prepare new graduates to be able to contribute more effectively to One Health approaches.

  17. One Health Core Competency Domains.

    PubMed

    Frankson, Rebekah; Hueston, William; Christian, Kira; Olson, Debra; Lee, Mary; Valeri, Linda; Hyatt, Raymond; Annelli, Joseph; Rubin, Carol

    2016-01-01

    The emergence of complex global challenges at the convergence of human, animal, and environmental health has catalyzed a movement supporting "One Health" approaches. Despite recognition of the importance of One Health approaches to address these complex challenges, little effort has been directed at identifying the seminal knowledge, skills, and attitudes necessary for individuals to successfully contribute to One Health efforts. Between 2008 and 2011, three groups independently embarked on separate initiatives to identify core competencies for professionals involved with One Health approaches. Core competencies were considered critically important for guiding curriculum development and continuing professional education, as they describe the knowledge, skills, and attitudes required to be effective. A workshop was convened in 2012 to synthesize the various strands of work on One Health competencies. Despite having different mandates, participants, and approaches, all of these initiatives identified similar core competency domains: management; communication and informatics; values and ethics; leadership; teams and collaboration; roles and responsibilities; and systems thinking. These core competency domains have been used to develop new continuing professional education programs for One Health professionals and help university curricula prepare new graduates to be able to contribute more effectively to One Health approaches.

  18. Research Domain Criteria: toward future psychiatric nosologies.

    PubMed

    Cuthbert, Bruce N

    2015-03-01

    The Research Domain Criteria (RDoC) project was initiated by the National Institute of Mental Health (NIMH) in early 2009 as the implementation of Goal 1.4 of its just-issued strategic plan. In keeping with the NIMH mission, to "transform the understanding and treatment of mental illnesses through basic and clinical research," RDoC was explicitly conceived as a research-related initiative. The statement of the relevant goal in the strategic plan reads: "Develop, for research purposes, new ways of classifying mental disorders based on dimensions of observable behavior and neurobiological measures." Due to the novel approach that RDoC takes to conceptualizing and studying mental disorders, it has received widespread attention, well beyond the borders of the immediate research community. This review discusses the rationale for the experimental framework that RDoC has adopted, and its implications for the nosology of mental disorders in the future.

  19. Research Domain Criteria: toward future psychiatric nosologies.

    PubMed

    Cuthbert, Bruce N

    2015-03-01

    The Research Domain Criteria (RDoC) project was initiated by the National Institute of Mental Health (NIMH) in early 2009 as the implementation of Goal 1.4 of its just-issued strategic plan. In keeping with the NIMH mission, to "transform the understanding and treatment of mental illnesses through basic and clinical research," RDoC was explicitly conceived as a research-related initiative. The statement of the relevant goal in the strategic plan reads: "Develop, for research purposes, new ways of classifying mental disorders based on dimensions of observable behavior and neurobiological measures." Due to the novel approach that RDoC takes to conceptualizing and studying mental disorders, it has received widespread attention, well beyond the borders of the immediate research community. This review discusses the rationale for the experimental framework that RDoC has adopted, and its implications for the nosology of mental disorders in the future. PMID:25987867

  20. Word Domain Disambiguation via Word Sense Disambiguation

    SciTech Connect

    Sanfilippo, Antonio P.; Tratz, Stephen C.; Gregory, Michelle L.

    2006-06-04

    Word subject domains have been widely used to improve the perform-ance of word sense disambiguation al-gorithms. However, comparatively little effort has been devoted so far to the disambiguation of word subject do-mains. The few existing approaches have focused on the development of al-gorithms specific to word domain dis-ambiguation. In this paper we explore an alternative approach where word domain disambiguation is achieved via word sense disambiguation. Our study shows that this approach yields very strong results, suggesting that word domain disambiguation can be ad-dressed in terms of word sense disam-biguation with no need for special purpose algorithms.

  1. GMPLS inter-domain signaling and routing to control LSPs based on per-domain policy

    NASA Astrophysics Data System (ADS)

    Okamoto, S.; Guo, H.; Otani, T.

    2008-11-01

    GMPLS inter-domain network control was investigated by employing BGP-based inter-domain routing and flexible signaling with loose hop expansion. Per-domain based operational policy was successfully applied to the establishment of GMPLS inter-domain LSPs.

  2. Linguistic relativity.

    PubMed

    Wolff, Phillip; Holmes, Kevin J

    2011-05-01

    The central question in research on linguistic relativity, or the Whorfian hypothesis, is whether people who speak different languages think differently. The recent resurgence of research on this question can be attributed, in part, to new insights about the ways in which language might impact thought. We identify seven categories of hypotheses about the possible effects of language on thought across a wide range of domains, including motion, color, spatial relations, number, and false belief understanding. While we do not find support for the idea that language determines the basic categories of thought or that it overwrites preexisting conceptual distinctions, we do find support for the proposal that language can make some distinctions difficult to avoid, as well as for the proposal that language can augment certain types of thinking. Further, we highlight recent evidence suggesting that language may induce a relatively schematic mode of thinking. Although the literature on linguistic relativity remains contentious, there is growing support for the view that language has a profound effect on thought. WIREs Cogni Sci 2011 2 253-265 DOI: 10.1002/wcs.104 For further resources related to this article, please visit the WIREs website.

  3. Domain adaptive boosting method and its applications

    NASA Astrophysics Data System (ADS)

    Geng, Jie; Miao, Zhenjiang

    2015-03-01

    Differences of data distributions widely exist among datasets, i.e., domains. For many pattern recognition, nature language processing, and content-based analysis systems, a decrease in performance caused by the domain differences between the training and testing datasets is still a notable problem. We propose a domain adaptation method called domain adaptive boosting (DAB). It is based on the AdaBoost approach with extensions to cover the domain differences between the source and target domains. Two main stages are contained in this approach: source-domain clustering and source-domain sample selection. By iteratively adding the selected training samples from the source domain, the discrimination model is able to achieve better domain adaptation performance based on a small validation set. The DAB algorithm is suitable for the domains with large scale samples and easy to extend for multisource adaptation. We implement this method on three computer vision systems: the skin detection model in single images, the video concept detection model, and the object classification model. In the experiments, we compare the performances of several commonly used methods and the proposed DAB. Under most situations, the DAB is superior.

  4. Observation of large nematic domains of discotic liquid crystals

    NASA Astrophysics Data System (ADS)

    Shinde, Abhijeet; Wang, Xuezhen; Cheng, Zhengdong

    2015-03-01

    Discotic liquid crystals are commonly found in nature in the form of clay, nacre. They are technologically important in applications such as conductive polymers, semiconductors and photovoltaics. Size and its distribution play an important role in their self-assemblies. Here we observed large nematic domains of discotic liquid crystals grown on a time scale of months. The development of such domains is observed to be faster for nanodisks that relatively smaller in size. The orientation of nanodisks is affected by gravity and inter-particle interactions which are yet to be fully understood.

  5. Domain wall conduction in multiaxial ferroelectrics

    SciTech Connect

    Eliseev, E. A.; Morozovska, A. N.; Svechnikov, S. V.; Maksymovych, Petro; Kalinin, Sergei V

    2012-01-01

    The conductance of domain wall structures consisting of either stripes or cylindrical domains in multiaxial ferroelectric-semiconductors is analyzed. The effects of the flexoelectric coupling, domain size, wall tilt, and curvature on charge accumulation are analyzed using the Landau-Ginsburg Devonshire theory for polarization vector combined with the Poisson equation for charge distributions. The proximity and size effect of the electron and donor accumulation/depletion by thin stripe domains and cylindrical nanodomains are revealed. In contrast to thick domain stripes and wider cylindrical domains, in which the carrier accumulation (and so the static conductivity) sharply increases at the domain walls only, small nanodomains of radii less than 5-10 correlation lengths appeared conducting across the entire cross-section. Implications of such conductive nanosized channels may be promising for nanoelectronics.

  6. Morphology and interaction between lipid domains

    PubMed Central

    Ursell, Tristan S.; Klug, William S.; Phillips, Rob

    2009-01-01

    Cellular membranes are a heterogeneous mix of lipids, proteins and small molecules. Special groupings enriched in saturated lipids and cholesterol form liquid-ordered domains, known as “lipid rafts,” thought to serve as platforms for signaling, trafficking and material transport throughout the secretory pathway. Questions remain as to how the cell maintains small fluid lipid domains, through time, on a length scale consistent with the fact that no large-scale phase separation is observed. Motivated by these examples, we have utilized a combination of mechanical modeling and in vitro experiments to show that membrane morphology plays a key role in maintaining small domain sizes and organizing domains in a model membrane. We demonstrate that lipid domains can adopt a flat or dimpled morphology, where the latter facilitates a repulsive interaction that slows coalescence and helps regulate domain size and tends to laterally organize domains in the membrane. PMID:19620730

  7. On the importance of cognitive profiling: A graphical modelling analysis of domain-specific and domain-general deficits after stroke.

    PubMed

    Massa, M Sofia; Wang, Naxian; Bickerton, Wa-Ling; Demeyere, Nele; Riddoch, M Jane; Humphreys, Glyn W

    2015-10-01

    Cognitive problems following stroke are typically analysed using either short but relatively uninformative general tests or through detailed but time consuming tests of domain specific deficits (e.g., in language, memory, praxis). Here we present an analysis of neuropsychological deficits detected using a screen designed to fall between other screens by being 'broad' (testing multiple cognitive abilities) but 'shallow' (sampling the abilities briefly, to be time efficient) - the BCoS. Assessment using the Birmingham Cognitive Screen (BCoS) enables the relations between 'domain specific' and 'domain general' cognitive deficits to be evaluated as the test generates an overall cognitive profile for individual patients. We analysed data from 287 patients tested at a sub-acute stage of stroke (<3 months). Graphical modelling techniques were used to investigate the associative structure and conditional independence between deficits within and across the domains sampled by BCoS (attention and executive functions, language, memory, praxis and number processing). The patterns of deficit within each domain conformed to existing cognitive models. However, these within-domain patterns underwent substantial change when the whole dataset was modelled, indicating that domain-specific deficits can only be understood in relation to linked changes in domain-general processes. The data point to the importance of using over-arching cognitive screens, measuring domain-general as well as domain-specific processes, in order to account for neuropsychological deficits after stroke. The paper also highlights the utility of using graphical modelling to understand the relations between cognitive components in complex datasets. PMID:26232552

  8. Functional innovation from changes in protein domains and their combinations.

    PubMed

    Lees, Jonathan G; Dawson, Natalie L; Sillitoe, Ian; Orengo, Christine A

    2016-06-01

    Domains are the functional building blocks of proteins. In this work we discuss how domains can contribute to the evolution of new functions. Domains themselves can evolve through various mechanisms, altering their intrinsic function. Domains can also facilitate functional innovations by combining with other domains to make novel proteins. We discuss the mechanisms by which domain and domain combinations support functional innovations. We highlight interesting examples where changes in domain combination promote changes at the domain level. PMID:27309309

  9. Structure and Function of KH Domains

    SciTech Connect

    Valverde, R.; Regan, E

    2008-01-01

    The hnRNP K homology (KH) domain was first identified in the protein human heterogeneous nuclear ribonucleoprotein K (hnRNP K) 14 years ago. Since then, KH domains have been identified as nucleic acid recognition motifs in proteins that perform a wide range of cellular functions. KH domains bind RNA or ssDNA, and are found in proteins associated with transcriptional and translational regulation, along with other cellular processes. Several diseases, e.g. fragile X mental retardation syndrome and paraneoplastic disease, are associated with the loss of function of a particular KH domain. Here we discuss the progress made towards understanding both general and specific features of the molecular recognition of nucleic acids by KH domains. The typical binding surface of KH domains is a cleft that is versatile but that can typically accommodate only four unpaired bases. Van der Waals forces and hydrophobic interactions and, to a lesser extent, electrostatic interactions, contribute to the nucleic acid binding affinity. 'Augmented' KH domains or multiple copies of KH domains within a protein are two strategies that are used to achieve greater affinity and specificity of nucleic acid binding. Isolated KH domains have been seen to crystallize as monomers, dimers and tetramers, but no published data support the formation of noncovalent higher-order oligomers by KH domains in solution. Much attention has been given in the literature to a conserved hydrophobic residue (typically Ile or Leu) that is present in most KH domains. The interest derives from the observation that an individual with this Ile mutated to Asn, in the KH2 domain of fragile X mental retardation protein, exhibits a particularly severe form of the syndrome. The structural effects of this mutation in the fragile X mental retardation protein KH2 domain have recently been reported. We discuss the use of analogous point mutations at this position in other KH domains to dissect both structure and function.

  10. Assimilative domain proficiency and performance in chemistry coursework

    NASA Astrophysics Data System (ADS)

    Byrnes, Scott William

    The assimilation and synthesis of knowledge is essential for students to be successful in chemistry, yet not all students synthesize knowledge as intended. The study used the Learning Preference Checklist to classify students into one of three learning modalities -- visual, auditory, or kinesthetic (VAK). It also used the Kolb Learning Style Inventory (KLSI), which utilizes four learning domains - Converging, Accommodating, Diverging, and Assimilating - to explain the students' maturation process by showing shift from any domain towards the Assimilating domain. A shift approaching this domain was considered as improvement in the assimilation and synthesis of knowledge. This pre-experimental one-group pretest-posttest study was used to test the hypothesis that modifying a high school chemistry curriculum to accentuate a student's learning preference would result in a shift towards the Assimilative domain on the KLSI and if there was a correlation between the improvement in student learning and a shift towards the KLSI Assimilating domain. Forty-two high school students were issued the VAK and provided with differentiated instruction via homologous cooperative learning groups. Pre- and post-KLSI and chemistry concepts tests were administered. T test analyses showed no significant shift towards the Assimilating domain. Further Pearson's r analyses showed no significant correlation between the KLSI and exam scores. This study contributes to social change by providing empirical evidence related to the effectiveness infusing learning styles into the science curriculum and the integration of the KLSI to monitor cognitive development as tools in raising standardized test scores and enhancing academic achievement. Results from the study can also inform future research into learning styles through their incorporation into the science curriculum.

  11. Towards a Domain Specific Software Architecture for Scientific Data Distribution

    NASA Astrophysics Data System (ADS)

    Wilson, A.; Lindholm, D. M.

    2011-12-01

    A reference architecture is a "design that satisfies a clearly distinguished subset of the functional capabilities identified in the reference requirements within the boundaries of certain design and implementation constraints, also identified in reference requirements." [Tracz, 1995] Recognizing the value of a reference architecture, NASA's ESDSWG's Standards Process Group (SPG) is introducing a multi-disciplinary science data systems (SDS) reference architecture in order to provide an implementation neutral, template solution for an architecture to support scientific data systems in general [Burnett, et al, 2011]. This reference architecture describes common features and patterns in scientific data systems, and can thus provide guidelines in building and improving such systems. But, guidelines alone may not be sufficient to actually build a system. A domain specific software architecture (DSSA) is "an assemblage of software components, specialized for a particular type of task (domain), generalized for effective use across that domain, composed in a standardized structure (topology) effective for building successful applications." [Tracz, 1995]. It can be thought of as relatively specific reference architecture. The "DSSA Process" is a software life cycle developed at Carnegie Melon's Software Engineering Institute that is based on the development and use of domain-specific software architectures, components, and tools. The process has four distinct activities: 1) develop a domain specific base/model, 2) populate and maintain the library, 3) build applications, 4) operate and maintain applications [Armitage, 1993]. The DSSA process may provide the missing link between guidelines and actual system construction. In this presentation we focus specifically on the realm of scientific data access and distribution. Assuming the role of domain experts in building data access systems, we report the results of creating a DSSA for scientific data distribution. We describe

  12. Inversion domains in GaN grown on sapphire

    SciTech Connect

    Romano, L.T.; Northrup, J.E.; OKeefe, M.A.

    1996-10-01

    Planar defects observed in GaN films grown on (0001) sapphire have been identified as inversion domain boundaries (IDBs) by a combination of high resolution transmission electron microscopy, multiple dark field imaging, and convergent beam electron diffraction techniques. Films grown by molecular beam epitaxy (MBE), metalorganic vapor deposition (MOCVD), and hydride vapor phase epitaxy (HVPE) were investigated and all were found to contain IDBs. The IDBs in the MBE and HVPE films extended from the interface to the film surface and formed columnar domains that ranged in width from 3 to 20 nm in the MBE films and up to 100 nm in the HVPE films. For the films investigated, the MBE films had the highest density, and the MOCVD films had the lowest density of IDBs. The nucleation of inversion domains (IDs) may result from step-related inhomogeneities of the GaN/sapphire interface. {copyright} {ital 1996 American Institute of Physics.}

  13. Diversity of the DNA replication system in the Archaea domain.

    PubMed

    Sarmiento, Felipe; Long, Feng; Cann, Isaac; Whitman, William B

    2014-01-01

    The precise and timely duplication of the genome is essential for cellular life. It is achieved by DNA replication, a complex process that is conserved among the three domains of life. Even though the cellular structure of archaea closely resembles that of bacteria, the information processing machinery of archaea is evolutionarily more closely related to the eukaryotic system, especially for the proteins involved in the DNA replication process. While the general DNA replication mechanism is conserved among the different domains of life, modifications in functionality and in some of the specialized replication proteins are observed. Indeed, Archaea possess specific features unique to this domain. Moreover, even though the general pattern of the replicative system is the same in all archaea, a great deal of variation exists between specific groups.

  14. Nonlinear dynamics of domain walls with cross-ties

    NASA Astrophysics Data System (ADS)

    Dubovik, M. N.; Zverev, V. V.; Filippov, B. N.

    2016-07-01

    The dynamic behavior of a domain wall with cross-ties is analyzed on the basis of micromagnetic simulation with exact allowance for all main (exchange, magnetoanisotropic, and magnetostatic) interactions in thin magnetically uniaxial ferromagnetic films with planar anisotropy. It is found that the peculiarities of motion of such domain walls are closely related to the behavior of topological defects in the magnetization distribution (generation, motion, and annihilation of vortex-antivortex pairs on the film surface and Bloch points). We observe three different regimes of motion (stationary, periodic, and turbulent regimes), each of which is realized in a certain range of fields oriented along the easy magnetization axis. It is shown that the experimentally observed dynamic bends of the walls with cross-ties are determined by the type of motion of vortices and antivortices. The velocities of domain walls in different regimes are calculated, and the dynamic configurations of the magnetization and existing dynamic transitions between them are investigated.

  15. The structural mechanism of KCNH-channel regulation by the eag domain

    PubMed Central

    Haitin, Yoni; Carlson, Anne E.; Zagotta, William N.

    2013-01-01

    The KCNH voltage-dependent potassium channels (ether-á-go-go, EAG; EAG-related gene, ERG; EAG-like channels, ELK) are important regulators of cellular excitability1-3 and have key roles in diseases such as cardiac long QT syndrome type 2 (LQT2)4, epilepsy5, schizophrenia6 and cancer7. The intracellular domains of KCNH channels are structurally distinct from other voltage-gated channels. The amino-terminal region contains an eag domain, which is comprised of a Per-Arnt-Sim (PAS) domain and a PAS-cap domain8, while the carboxy-terminal region contains a cyclic nucleotide-binding homology domain (CNBHD) which is connected to the pore through a C-linker domain. Many disease-causing mutations localize to these specialized intracellular domains, which underlie the unique gating and regulation of KCNH channels9. It has been suggested that the eag domain may regulate the channel by interacting with either the S4-S5 linker or the CNBHD8,10. Here we present a 2-Å resolution crystal structure of the eag domain-CNBHD complex of the mouse EAG1 (mEAG1) channel. It displays extensive interactions between the eag domain and the CNBHD, indicating that the regulatory mechanism of the eag domain involves primarily the CNBHD. Surprisingly, the structure reveals that a number of LQT2 mutations at homologous positions in hERG, and cancer-associated mutations in EAG channels, localize to the eag domain-CNBHD interface. Furthermore, mutations at the interface produced dramatic effects on channel gating demonstrating the important physiological role of the eag domain-CNBHD interaction. Our structure of the eag domain-CNBHD complex of mEAG1 provides unique insights into the physiological and pathophysiological mechanisms of KCNH channels. PMID:23975098

  16. Structural mapping of the coiled-coil domain of a bacterial condensin and comparative analyses across all domains of life suggest conserved features of SMC proteins.

    PubMed

    Waldman, Vincent M; Stanage, Tyler H; Mims, Alexandra; Norden, Ian S; Oakley, Martha G

    2015-06-01

    The structural maintenance of chromosomes (SMC) proteins form the cores of multisubunit complexes that are required for the segregation and global organization of chromosomes in all domains of life. These proteins share a common domain structure in which N- and C- terminal regions pack against one another to form a globular ATPase domain. This "head" domain is connected to a central, globular, "hinge" or dimerization domain by a long, antiparallel coiled coil. To date, most efforts for structural characterization of SMC proteins have focused on the globular domains. Recently, however, we developed a method to map interstrand interactions in the 50-nm coiled-coil domain of MukB, the divergent SMC protein found in γ-proteobacteria. Here, we apply that technique to map the structure of the Bacillus subtilis SMC (BsSMC) coiled-coil domain. We find that, in contrast to the relatively complicated coiled-coil domain of MukB, the BsSMC domain is nearly continuous, with only two detectable coiled-coil interruptions. Near the middle of the domain is a break in coiled-coil structure in which there are three more residues on the C-terminal strand than on the N-terminal strand. Close to the head domain, there is a second break with a significantly longer insertion on the same strand. These results provide an experience base that allows an informed interpretation of the output of coiled-coil prediction algorithms for this family of proteins. A comparison of such predictions suggests that these coiled-coil deviations are highly conserved across SMC types in a wide variety of organisms, including humans.

  17. Real-time observation of epitaxial graphene domain reorientation

    SciTech Connect

    Thuermer, Konrad; Foster, Michael E.; Bartelt, Norman Charles; Rogge, Paul C.; McCarty, Kevin F.; Dubon, Oscar D.; Bartelt, Norman C.

    2015-04-20

    Graphene films grown by vapour deposition tend to be polycrystalline due to the nucleation and growth of islands with different in-plane orientations. Here, using low-energy electron microscopy, we find that micron-sized graphene islands on Ir(111) rotate to a preferred orientation during thermal annealing. We observe three alignment mechanisms: the simultaneous growth of aligned domains and dissolution of rotated domains, that is, ‘ripening’; domain boundary motion within islands; and continuous lattice rotation of entire domains. By measuring the relative growth velocity of domains during ripening, we estimate that the driving force for alignment is on the order of 0.1 meV per C atom and increases with rotation angle. A simple model of the orientation-dependent energy associated with the moiré corrugation of the graphene sheet due to local variations in the graphene–substrate interaction reproduces the results. This study suggests new strategies for improving the van der Waals epitaxy of 2D materials.

  18. Real-time observation of epitaxial graphene domain reorientation

    DOE PAGES

    Thuermer, Konrad; Foster, Michael E.; Bartelt, Norman Charles; Rogge, Paul C.; Lawrence Berkeley National Lab.; McCarty, Kevin F.; Dubon, Oscar D.; Lawrence Berkeley National Lab.; Bartelt, Norman C.

    2015-04-20

    Graphene films grown by vapour deposition tend to be polycrystalline due to the nucleation and growth of islands with different in-plane orientations. Here, using low-energy electron microscopy, we find that micron-sized graphene islands on Ir(111) rotate to a preferred orientation during thermal annealing. We observe three alignment mechanisms: the simultaneous growth of aligned domains and dissolution of rotated domains, that is, ‘ripening’; domain boundary motion within islands; and continuous lattice rotation of entire domains. By measuring the relative growth velocity of domains during ripening, we estimate that the driving force for alignment is on the order of 0.1 meV permore » C atom and increases with rotation angle. A simple model of the orientation-dependent energy associated with the moiré corrugation of the graphene sheet due to local variations in the graphene–substrate interaction reproduces the results. This study suggests new strategies for improving the van der Waals epitaxy of 2D materials.« less

  19. Domain decomposition approach to flexible multibody dynamics simulation

    NASA Astrophysics Data System (ADS)

    Kwak, JunYoung; Chun, TaeYoung; Shin, SangJoon; Bauchau, Olivier A.

    2014-01-01

    Finite element based formulations for flexible multibody systems are becoming increasingly popular and as the complexity of the configurations to be treated increases, so does the computational cost. It seems natural to investigate the applicability of parallel processing to this type of problems; domain decomposition techniques have been used extensively for this purpose. In this approach, the computational domain is divided into non-overlapping sub-domains, and the continuity of the displacement field across sub-domain boundaries is enforced via the Lagrange multiplier technique. In the finite element literature, this approach is presented as a mathematical algorithm that enables parallel processing. In this paper, the divided system is viewed as a flexible multibody system, and the sub-domains are connected by kinematic constraints. Consequently, all the techniques applicable to the enforcement of constraints in multibody systems become applicable to the present problem. In particular, it is shown that a combination of the localized Lagrange multiplier technique with the augmented Lagrange formulation leads to interesting solution strategies. The proposed algorithm is compared with the well-known FETI approach with regards to convergence and efficiency characteristics. The present algorithm is relatively simple and leads to improved convergence and efficiency characteristics. Finally, implementation on a parallel computer was conducted for the proposed approach.

  20. The Diversity and Evolution of Wolbachia Ankyrin Repeat Domain Genes

    PubMed Central

    Siozios, Stefanos; Ioannidis, Panagiotis; Klasson, Lisa; Andersson, Siv G. E.; Braig, Henk R.; Bourtzis, Kostas

    2013-01-01

    Ankyrin repeat domain-encoding genes are common in the eukaryotic and viral domains of life, but they are rare in bacteria, the exception being a few obligate or facultative intracellular Proteobacteria species. Despite having a reduced genome, the arthropod strains of the alphaproteobacterium Wolbachia contain an unusually high number of ankyrin repeat domain-encoding genes ranging from 23 in wMel to 60 in wPip strain. This group of genes has attracted considerable attention for their astonishing large number as well as for the fact that ankyrin proteins are known to participate in protein-protein interactions, suggesting that they play a critical role in the molecular mechanism that determines host-Wolbachia symbiotic interactions. We present a comparative evolutionary analysis of the wMel-related ankyrin repeat domain-encoding genes present in different Drosophila-Wolbachia associations. Our results show that the ankyrin repeat domain-encoding genes change in size by expansion and contraction mediated by short directly repeated sequences. We provide examples of intra-genic recombination events and show that these genes are likely to be horizontally transferred between strains with the aid of bacteriophages. These results confirm previous findings that the Wolbachia genomes are evolutionary mosaics and illustrate the potential that these bacteria have to generate diversity in proteins potentially involved in the symbiotic interactions. PMID:23390535

  1. Bpur, the Lyme Disease Spirochete's PUR Domain Protein

    PubMed Central

    Jutras, Brandon L.; Chenail, Alicia M.; Carroll, Dustin W.; Miller, M. Clarke; Zhu, Haining; Bowman, Amy; Stevenson, Brian

    2013-01-01

    The PUR domain is a nucleic acid-binding motif found in critical regulatory proteins of higher eukaryotes and in certain species of bacteria. During investigations into mechanisms by which the Lyme disease spirochete controls synthesis of its Erp surface proteins, it was discovered that the borrelial PUR domain protein, Bpur, binds with high affinity to double-stranded DNA adjacent to the erp transcriptional promoter. Bpur was found to enhance the effects of the erp repressor protein, BpaB. Bpur also bound single-stranded DNA and RNA, with relative affinities RNA > double-stranded DNA > single-stranded DNA. Rational site-directed mutagenesis of Bpur identified amino acid residues and domains critical for interactions with nucleic acids, and it revealed that the PUR domain has a distinct mechanism of interaction with each type of nucleic acid ligand. These data shed light on both gene regulation in the Lyme spirochete and functional mechanisms of the widely distributed PUR domain. PMID:23846702

  2. Cooperation of phosphoinositides and BAR domain proteins in endosomal tubulation.

    PubMed

    Shinozaki-Narikawa, Naeko; Kodama, Tatsuhiko; Shibasaki, Yoshikazu

    2006-11-01

    Phosphorylated derivatives of phosphatidylinositol (PtdIns) regulate many intracellular events, including vesicular trafficking and actin remodeling, by recruiting proteins to their sites of function. PtdIns(4,5)-bisphosphate [PI(4,5)P2] and related phosphoinositides are mainly synthesized by type I PtdIns-4-phosphate 5-kinases (PIP5Ks). We found that PIP5K induces endosomal tubules in COS-7 cells. ADP-ribosylation factor (ARF) 6 has been shown to act upstream of PIP5K and regulate endocytic transport and tubulation. ARF GAP with coiled-coil, ankyrin repeat, and pleckstrin homology domains 1 (ACAP1) has guanosine triphosphatase-activating protein (GAP) activity for ARF6. While there were few tubules induced by the expression of ACAP1 alone, numerous endosomal tubules were induced by coexpression of PIP5K and ACAP1. ACAP1 has a pleckstrin homology (PH) domain known to bind phosphoinositide and a Bin/amphiphysin/Rvs (BAR) domain that has been reported to detect membrane curvature. Truncated and point mutations in the ACAP1 BAR and PH domains revealed that both BAR and PH domains are required for tubulation. These results suggest that two ARF6 downstream molecules, PIP5K and ACAP1, function together in endosomal tubulation and that phosphoinositide levels may regulate endosomal dynamics. PMID:17010122

  3. The complex NOD-like receptor repertoire of the coral Acropora digitifera includes novel domain combinations.

    PubMed

    Hamada, Mayuko; Shoguchi, Eiichi; Shinzato, Chuya; Kawashima, Takeshi; Miller, David J; Satoh, Nori

    2013-01-01

    Innate immunity in corals is of special interest not only in the context of self-defense but also in relation to the establishment and collapse of their obligate symbiosis with dinoflagellates of the genus Symbiodinium. In innate immunity system of vertebrates, approximately 20 tripartite nucleotide oligomerization domain (NOD)-like receptor proteins that are defined by the presence of a NAIP, CIIA, HET-E and TP1 (NACHT) domain, a C-terminal leucine-rich repeat (LRR) domain, and one of three types of N-terminal effector domain, are known to function as the primary intracellular pattern recognition molecules. Surveying the coral genome revealed not only a larger number of NACHT- and related domain nucleotide-binding adaptor shared by APAF-1, R proteins, and CED-4 (NB-ARC)-encoding loci (~500) than in other metazoans but also surprising diversity of domain combinations among the coral NACHT/NB-ARC-containing proteins; N-terminal effector domains included the apoptosis-related domains caspase recruitment domain (CARD), death effector domain (DED), and Death, and C-terminal repeat domains included LRRs, tetratricopeptide repeats, ankyrin repeats, and WD40 repeats. Many of the predicted coral proteins that contain a NACHT/NB-ARC domain also contain a glycosyl transferase group 1 domain, a novel domain combination first found in metazoans. Phylogenetic analyses suggest that the NACHT/NB-ARC domain inventories of various metazoan lineages, including corals, are largely products of lineage-specific expansions. Many of the NACHT/NB-ARC loci are organized in pairs or triplets in the Acropora genome, suggesting that the large coral NACHT/NB-ARC repertoire has been generated at least in part by tandem duplication. In addition, shuffling of N-terminal effector domains may have occurred after expansions of specific NACHT/NB-ARC-repeat domain types. These results illustrate the extraordinary complexity of the innate immune repertoire of corals, which may in part reflect adaptive

  4. EuPathDomains: the divergent domain database for eukaryotic pathogens.

    PubMed

    Ghouila, Amel; Terrapon, Nicolas; Gascuel, Olivier; Guerfali, Fatma Z; Laouini, Dhafer; Maréchal, Eric; Bréhélin, Laurent

    2011-06-01

    Eukaryotic pathogens (e.g. Plasmodium, Leishmania, Trypanosomes, etc.) are a major source of morbidity and mortality worldwide. In Africa, one of the most impacted continents, they cause millions of deaths and constitute an immense economic burden. While the genome sequence of several of these organisms is now available, the biological functions of more than half of their proteins are still unknown. This is a serious issue for bringing to the foreground the expected new therapeutic targets. In this context, the identification of protein domains is a key step to improve the functional annotation of the proteins. However, several domains are missed in eukaryotic pathogens because of the high phylogenetic distance of these organisms from the classical eukaryote models. We recently proposed a method, co-occurrence domain detection (CODD), that improves the sensitivity of Pfam domain detection by exploiting the tendency of domains to appear preferentially with a few other favorite domains in a protein. In this paper, we present EuPathDomains (http://www.atgc-montpellier.fr/EuPathDomains/), an extended database of protein domains belonging to ten major eukaryotic human pathogens. EuPathDomains gathers known and new domains detected by CODD, along with the associated confidence measurements and the GO annotations that can be deduced from the new domains. This database significantly extends the Pfam domain coverage of all selected genomes, by proposing new occurrences of domains as well as new domain families that have never been reported before. For example, with a false discovery rate lower than 20%, EuPathDomains increases the number of detected domains by 13% in Toxoplasma gondii genome and up to 28% in Cryptospordium parvum, and the total number of domain families by 10% in Plasmodium falciparum and up to 16% in C. parvum genome. The database can be queried by protein names, domain identifiers, Pfam or Interpro identifiers, or organisms, and should become a valuable

  5. On the Analysis Methods for the Time Domain and Frequency Domain Response of a Buried Objects*

    NASA Astrophysics Data System (ADS)

    Poljak, Dragan; Šesnić, Silvestar; Cvetković, Mario

    2014-05-01

    There has been a continuous interest in the analysis of ground-penetrating radar systems and related applications in civil engineering [1]. Consequently, a deeper insight of scattering phenomena occurring in a lossy half-space, as well as the development of sophisticated numerical methods based on Finite Difference Time Domain (FDTD) method, Finite Element Method (FEM), Boundary Element Method (BEM), Method of Moments (MoM) and various hybrid methods, is required, e.g. [2], [3]. The present paper deals with certain techniques for time and frequency domain analysis, respectively, of buried conducting and dielectric objects. Time domain analysis is related to the assessment of a transient response of a horizontal straight thin wire buried in a lossy half-space using a rigorous antenna theory (AT) approach. The AT approach is based on the space-time integral equation of the Pocklington type (time domain electric field integral equation for thin wires). The influence of the earth-air interface is taken into account via the simplified reflection coefficient arising from the Modified Image Theory (MIT). The obtained results for the transient current induced along the electrode due to the transmitted plane wave excitation are compared to the numerical results calculated via an approximate transmission line (TL) approach and the AT approach based on the space-frequency variant of the Pocklington integro-differential approach, respectively. It is worth noting that the space-frequency Pocklington equation is numerically solved via the Galerkin-Bubnov variant of the Indirect Boundary Element Method (GB-IBEM) and the corresponding transient response is obtained by the aid of inverse fast Fourier transform (IFFT). The results calculated by means of different approaches agree satisfactorily. Frequency domain analysis is related to the assessment of frequency domain response of dielectric sphere using the full wave model based on the set of coupled electric field integral

  6. Domain-Independent Scientific Function Finding

    NASA Astrophysics Data System (ADS)

    Schaffer, Cullen R.

    1990-01-01

    Programs such as Bacon, Abacus, Coper, Kepler and others are designed to find functional relationships of scientific significance in quantitative data without relying on the deep domain knowledge scientists normally bring to bear in analytic work. Whether these systems actually perform as intended is an open question, however. To date, they have been supported only by anecdotal evidence --reports that a desirable answer has been found in one or more selected and often artificial cases. In this dissertation, I thus attempt to develop, not only new approaches to domain -independent scientific function finding, but, equally, a rigorous methodology under which research into such methods can be conducted. A fundamental problem with previous work is that it has investigated scientific data analysis in the abstract --without referring to actual scientific data. By contrast, the work reported here is founded on a collection of 352 real scientific data sets. This empirical base supports a number of strong conclusions. First, while researchers working with artificial data have targeted complex multivariate relations, real data provides powerful evidence that even the simplest bivariate relationships are difficult to identify reliably. Second, despite its ubiquitous presence in previous work, the notion of heuristic search of a potentially explosive space of formulas appears to help very little with the problem of reliably identifying basic bivariate relationships. Instead, third, substantial performance improvement results from viewing function finding as a decision problem, the problem of classifying data sets reliably within a fixed--and quite limited--system of functional categories. This dissertation presents what I believe to be the strongest domain-independent scientific function-finding algorithm currently in existence and, certainly, the only one which has been rigorously demonstrated. At the same time, it suggests fundamental limitations in the power of such

  7. Probing Ferroelectric Domain Engineering in BiFeO3 Thin Films by Second Harmonic Generation.

    PubMed

    Trassin, Morgan; Luca, Gabriele De; Manz, Sebastian; Fiebig, Manfred

    2015-09-01

    An optical probe of the ferroelectric domain distribution and manipulation in BiFeO3 thin films is reported using optical second harmonic generation. A unique relation between the domain distribution and its integral symmetry is established. The ferroelectric signature is even resolved when the film is covered by a top electrode. The effect of voltage-induced ferroelectric switching is imaged.

  8. Design of a Low-Cost Adaptive Question Answering System for Closed Domain Factoid Queries

    ERIC Educational Resources Information Center

    Toh, Huey Ling

    2010-01-01

    Closed domain question answering (QA) systems achieve precision and recall at the cost of complex language processing techniques to parse the answer corpus. We propose a "query-based" model for indexing answers in a closed domain factoid QA system. Further, we use a phrase term inference method for improving the ranking order of related questions.…

  9. Genetic and Environmental Influences on Symptom Domains in Twins and Siblings with Autism

    ERIC Educational Resources Information Center

    Mazefsky, Carla A.; Goin-Kochel, Robin P.; Riley, Brien P.; Maes, Hermine H.

    2008-01-01

    Clarifying the sources of variation among autism symptom domains is important to the identification of homogenous subgroups for molecular genetic studies. This study explored the genetic and environmental bases of nonverbal communication and social interaction, two symptom domains that have also been related to treatment response, in 1294 child…

  10. Conceptualizing and Re-Evaluating Resilience across Levels of Risk, Time, and Domains of Competence

    ERIC Educational Resources Information Center

    Vanderbilt-Adriance, Ella; Shaw, Daniel S.

    2008-01-01

    This article examines potential theoretical constraints on resilience across levels of risk, time, and domain of outcome. Studies of resilience are reviewed as they relate to the prevalence of resilience across levels of risk (e.g., single life events vs. cumulative risk), time, and domains of adjustment. Based on a thorough review of pertinent…

  11. Network Search: A New Way of Seeing the Education Knowledge Domain

    ERIC Educational Resources Information Center

    McFarland, Daniel; Klopfer, Eric

    2010-01-01

    Background: The educational knowledge domain may be understood as a system composed of multiple, co-evolving networks that reflect the form and content of a cultural field. This paper describes the educational knowledge domain as having a community structure (form) based in relations of production (authoring) and consumption (referencing), and a…

  12. Shape of isolated domains in lithium tantalate single crystals at elevated temperatures

    SciTech Connect

    Shur, V. Ya. Akhmatkhanov, A. R.; Baturin, I. S.; Chezganov, D. S.; Lobov, A. I.; Smirnov, M. M.

    2013-12-09

    The shape of isolated domains has been investigated in congruent lithium tantalate (CLT) single crystals at elevated temperatures and analyzed in terms of kinetic approach. The obtained temperature dependence of the growing domain shape in CLT including circular shape at temperatures above 190 °C has been attributed to increase of relative input of isotropic ionic conductivity. The observed nonstop wall motion and independent domain growth after merging in CLT as opposed to stoichiometric lithium tantalate have been attributed to difference in wall orientation. The computer simulation has confirmed applicability of the kinetic approach to the domain shape explanation.

  13. Eukaryotic RNAse H shares a conserved domain with caulimovirus proteins that facilitate translation of polycistronic RNA.

    PubMed Central

    Mushegian, A R; Edskes, H K; Koonin, E V

    1994-01-01

    RNAse H (RNH1 protein) from the trypanosomatid Crithidia fasciculata has a functionally uncharacterized N-terminal domain dispensable for the RNAse H activity. Using computer methods for database search and multiple alignment, we show that the N-terminal domains of RNH1 and its homologue encoded by a cDNA from chicken lens are related to the conserved domain in caulimovirus ORF VI product that facilitates translation of polycistronic virus RNA in plant cells. We hypothesize that the N-terminal domain of eukaryotic RNAse H performs an as yet uncharacterized regulatory function, possibly in mRNA translation or turnover. PMID:7937142

  14. Elastic Membrane Deformations Govern Interleaflet Coupling of Lipid-Ordered Domains

    NASA Astrophysics Data System (ADS)

    Galimzyanov, Timur R.; Molotkovsky, Rodion J.; Bozdaganyan, Marine E.; Cohen, Fredric S.; Pohl, Peter; Akimov, Sergey A.

    2015-08-01

    The mechanism responsible for domain registration in two membrane leaflets has thus far remained enigmatic. Using continuum elasticity theory, we show that minimum line tension is achieved along the rim between thicker (ordered) and thinner (disordered) domains by shifting the rims in opposing leaflets by a few nanometers relative to each other. Increasing surface tension yields an increase in line tension, resulting in larger domains. Because domain registration is driven by lipid deformation energy, it does not require special lipid components or interactions at the membrane midplane.

  15. UXDs-Driven Transferring Method from TRIZ Solution to Domain Solution

    NASA Astrophysics Data System (ADS)

    Ma, Lihui; Cao, Guozhong; Chang, Yunxia; Wei, Zihui; Ma, Kai

    The translation process from TRIZ solutions to domain solutions is an analogy-based process. TRIZ solutions, such as 40 inventive principles and the related cases, are medium-solutions for domain problems. Unexpected discoveries (UXDs) are the key factors to trigger designers to generate new ideas for domain solutions. The Algorithm of UXD resolving based on Means-Ends Analysis(MEA) is studied and an UXDs-driven transferring method from TRIZ solution to domain solution is formed. A case study shows the application of the process.

  16. ELASTIC MEMBRANE DEFORMATIONS GOVERN INTERLEAFLET COUPLING OF LIPID-ORDERED DOMAINS

    PubMed Central

    Galimzyanov, Timur R.; Molotkovsky, Rodion J.; Bozdaganyan, Marine E.; Cohen, Fredric S.; Pohl, Peter; Akimov, Sergey A.

    2016-01-01

    The mechanism responsible for domain registration in two membrane leaflets has thus far remained enigmatic. Using continuum elasticity theory, we show that minimum line tension is achieved along the rim between thicker (ordered) and thinner (disordered) domains by shifting the rims in opposing leaflets by a few nanometers relative to each other. Increasing surface tension yields an increase in line tension, resulting in larger domains. Because domain registration is driven by lipid deformation energy, it does not require special lipid components nor interactions at the membrane midplane. PMID:26340212

  17. Systematic analyses reveal uniqueness and origin of the CFEM domain in fungi.

    PubMed

    Zhang, Zhen-Na; Wu, Qin-Yi; Zhang, Gui-Zhi; Zhu, Yue-Yan; Murphy, Robert W; Liu, Zhen; Zou, Cheng-Gang

    2015-08-10

    CFEM domain commonly occurs in fungal extracellular membrane proteins. To provide insights for understanding putative functions of CFEM, we investigate the evolutionary dynamics of CFEM domains by systematic comparative genomic analyses among diverse animals, plants, and more than 100 fungal species, which are representative across the entire group of fungi. We here show that CFEM domain is unique to fungi. Experiments using tissue culture demonstrate that the CFEM-containing ESTs in some plants originate from endophytic fungi. We also find that CFEM domain does not occur in all fungi. Its single origin dates to the most recent common ancestors of Ascomycota and Basidiomycota, instead of multiple origins. Although the length and architecture of CFEM domains are relatively conserved, the domain-number varies significantly among different fungal species. In general, pathogenic fungi have a larger number of domains compared to other species. Domain-expansion across fungal genomes appears to be driven by domain duplication and gene duplication via recombination. These findings generate a clear evolutionary trajectory of CFEM domains and provide novel insights into the functional exchange of CFEM-containing proteins from cell-surface components to mediators in host-pathogen interactions.

  18. Floret-shaped solid domains on giant fluid lipid vesicles induced by pH

    NASA Astrophysics Data System (ADS)

    Sofou, Stavroula; Bandekar, Amey

    2012-02-01

    Lateral lipid phase separation and domain formation induced by changes in pH is significant in liposome-based drug delivery: environmentally responsive lipid heterogeneities can be tuned to alter collective membrane properties such as drug release and drug carrier reactivity impacting, therefore, the therapeutic outcomes. At the micron-meter scale, fluorescence microscopy on Giant Unilamellar fluid Vesicles (GUVs) shows that lowering pH (from 7.0 to 5.0) promotes the condensation of titratable PS or PA lipids into beautiful floret-shaped solid domains in which lipids are tightly packed via H-bonding and VdWs interactions. Solid domains phenomenologically comprise a circular ``core'' cap beyond which interfacial instabilities emerge resembling leaf-like stripes of almost vanishing Gaussian curvature independent of GUVs' preparation path and in agreement with a general condensation mechanism. Increasing incompressibility of domains is strongly correlated with larger number of thinner stripes per domain, and increasing relative rigidity of domains with smaller core cap areas. Line tension drives domain ripening, however the final domain shape is a result of enhanced incompressibility and rigidity maximized by domain coupling across the bilayer. Introduction of a transmembrane osmotic gradient (hyperosmotic on the outer lipid leaflet) allows the domain condensation process to reach its maximum extent which, however, is limited by the minimal expansivity of the continuous fluid membrane.

  19. Phase transitions and domain structures in multiferroics

    NASA Astrophysics Data System (ADS)

    Vlahos, Eftihia

    2011-12-01

    Thin film ferroelectrics and multiferroics are two important classes of materials interesting both from a scientific and a technological prospective. The volatility of lead and bismuth as well as environmental issues regarding the toxicity of lead are two disadvantages of the most commonly used ferroelectric random access memory (FeRAM) materials such as Pb(Zr,Ti)O3 and SrBi2Ta2O9. Therefore lead-free thin film ferroelectrics are promising substitutes as long as (a) they can be grown on technologically important substrates such as silicon, and (b) their T c and Pr become comparable to that of well established ferroelectrics. On the other hand, the development of functional room temperature ferroelectric ferromagnetic multiferroics could lead to very interesting phenomena such as control of magnetism with electric fields and control of electrical polarization with magnetic fields. This thesis focuses on the understanding of material structure-property relations using nonlinear optical spectroscopy. Nonlinear spectroscopy is an excellent tool for probing the onset of ferroelectricity, and domain dynamics in strained ferroelectrics and multiferroics. Second harmonic generation was used to detect ferroelectricity and the antiferrodistortive phase transition in thin film SrTiO3. Incipient ferroelectric CaTiO3 has been shown to become ferroelectric when strained with a combination of SHG and dielectric measurements. The tensorial nature of the induced nonlinear polarization allows for probing of the BaTiO3 and SrTiO3 polarization contributions in nanoscale BaTiO3/SrTiO3 superlattices. In addition, nonlinear optics was used to demonstrate ferroelectricity in multiferroic EuTiO3. Finally, confocal SHG and Raman microscopy were utilized to visualize polar domains in incipient ferroelectric and ferroelastic CaTiO3.

  20. Imaging Ferroelectric Domains and Domain Walls Using Charge Gradient Microscopy: Role of Screening Charges.

    PubMed

    Tong, Sheng; Jung, Il Woong; Choi, Yoon-Young; Hong, Seungbum; Roelofs, Andreas

    2016-02-23

    Advanced scanning probe microscopies (SPMs) open up the possibilities of the next-generation ferroic devices that utilize both domains and domain walls as active elements. However, current SPMs lack the capability of dynamically monitoring the motion of domains and domain walls in conjunction with the transport of the screening charges that lower the total electrostatic energy of both domains and domain walls. Charge gradient microscopy (CGM) is a strong candidate to overcome these shortcomings because it can map domains and domain walls at high speed and mechanically remove the screening charges. Yet the underlying mechanism of the CGM signals is not fully understood due to the complexity of the electrostatic interactions. Here, we designed a semiconductor-metal CGM tip, which can separate and quantify the ferroelectric domain and domain wall signals by simply changing its scanning direction. Our investigation reveals that the domain wall signals are due to the spatial change of polarization charges, while the domain signals are due to continuous removal and supply of screening charges at the CGM tip. In addition, we observed asymmetric CGM domain currents from the up and down domains, which are originated from the different debonding energies and the amount of the screening charges on positive and negative bound charges. We believe that our findings can help design CGM with high spatial resolution and lead to breakthroughs in information storage and energy-harvesting devices. PMID:26751281

  1. Unsupervised Spatial Event Detection in Targeted Domains with Applications to Civil Unrest Modeling

    PubMed Central

    Zhao, Liang; Chen, Feng; Dai, Jing; Hua, Ting; Lu, Chang-Tien; Ramakrishnan, Naren

    2014-01-01

    Twitter has become a popular data source as a surrogate for monitoring and detecting events. Targeted domains such as crime, election, and social unrest require the creation of algorithms capable of detecting events pertinent to these domains. Due to the unstructured language, short-length messages, dynamics, and heterogeneity typical of Twitter data streams, it is technically difficult and labor-intensive to develop and maintain supervised learning systems. We present a novel unsupervised approach for detecting spatial events in targeted domains and illustrate this approach using one specific domain, viz. civil unrest modeling. Given a targeted domain, we propose a dynamic query expansion algorithm to iteratively expand domain-related terms, and generate a tweet homogeneous graph. An anomaly identification method is utilized to detect spatial events over this graph by jointly maximizing local modularity and spatial scan statistics. Extensive experiments conducted in 10 Latin American countries demonstrate the effectiveness of the proposed approach. PMID:25350136

  2. Transverse field-induced nucleation pad switching modes during domain wall injection

    SciTech Connect

    Bryan, M. T.; Fry, P. W.; Schrefl, T.; Gibbs, M. R. J.; Allwood, D. A.; Im, M.-Y.; Fischer, P.

    2010-03-12

    We have used magnetic transmission X-ray microscopy (M-TXM) to image in-field magnetization configurations of patterned Ni{sub 80}Fe{sub 20} domain wall 'injection pads' and attached planar nanowires. Comparison with micromagnetic simulations suggests that the evolution of magnetic domains in rectangular injection pads depends on the relative orientation of closure domains in the remanent state. The magnetization reversal pathway is also altered by the inclusion of transverse magnetic fields. These different modes explain previous results of domain wall injection into nanowires. Even more striking was the observation of domain walls injecting halfway across the width of wider (>400 nm wide) wires but over wire lengths of several micrometers. These extended Neel walls can interact with adjacent nanowires and cause a switching in the side of the wire undergoing reversal as the domain wall continues to expand.

  3. Pinkbar is an epithelial-specific BAR domain protein that generates planar membrane structures

    SciTech Connect

    Pykäläinen, Anette; Boczkowska, Malgorzata; Zhao, Hongxia; Saarikangas, Juha; Rebowski, Grzegorz; Jansen, Maurice; Hakanen, Janne; Koskela, Essi V.; Peränen, Johan; Vihinen, Helena; Jokitalo, Eija; Salminen, Marjo; Ikonen, Elina; Dominguez, Roberto; Lappalainen, Pekka

    2013-05-29

    Bin/amphipysin/Rvs (BAR)-domain proteins sculpt cellular membranes and have key roles in processes such as endocytosis, cell motility and morphogenesis. BAR domains are divided into three subfamilies: BAR- and F-BAR-domain proteins generate positive membrane curvature and stabilize cellular invaginations, whereas I-BAR-domain proteins induce negative curvature and stabilize protrusions. We show that a previously uncharacterized member of the I-BAR subfamily, Pinkbar, is specifically expressed in intestinal epithelial cells, where it localizes to Rab13-positive vesicles and to the plasma membrane at intercellular junctions. Notably, the BAR domain of Pinkbar does not induce membrane tubulation but promotes the formation of planar membrane sheets. Structural and mutagenesis analyses reveal that the BAR domain of Pinkbar has a relatively flat lipid-binding interface and that it assembles into sheet-like oligomers in crystals and in solution, which may explain its unique membrane-deforming activity.

  4. The formation of a generalized categorization repertoire: effect of training with multiple domains, samples, and comparisons.

    PubMed Central

    Fields, Lanny; Reeve, Kenneth F; Matneja, Priya; Varelas, Antonios; Belanich, James; Fitzer, Adrienne; Shamoun, Kim

    2002-01-01

    The present experiment explored the effects of three variables on the spontaneous categorization of stimuli in perceptually distinct and novel domains. Each of six stimulus domains was created by morphing two images that were the domain endpoints. The endpoints of the domains were male and female faces, two abstract drawings, a car and a truck, two banded-elevation satellite land images, a tree and a cat, and two false-color satellite images. The stimulus variants at each end of a domain defined two potential perceptual classes. Training was conducted in a matching-to-sample format and used stimuli from one or two domains, one or three variants per class as samples, and one or three variants per class as comparisons. The spontaneous categorization of stimuli in the untrained stimulus domains showed the emergence of a generalized categorization repertoire. The proportion of spontaneously categorized stimuli in the new domains was positively related to the number of domains and samples used in training, and was inversely related to the number of comparisons used in training. Differential reaction times demonstrated the discriminability of the stimuli in the emergent classes. This study is among the first to provide an empirical basis for a behavior-analytic model of the development of generalized categorization repertoires in natural settings. PMID:12507005

  5. Pattern orientation in finite domains without boundaries

    NASA Astrophysics Data System (ADS)

    Rapp, Lisa; Bergmann, Fabian; Zimmermann, Walter

    2016-01-01

    We investigate the orientation of nonlinear stripe patterns in finite domains. Motivated by recent experiments, we introduce a control parameter drop from supercritical inside a domain to subcritical outside without boundary conditions at the domain border. As a result, stripes align perpendicularly to shallow control parameter drops. For steeper drops, non-adiabatic effects lead to a surprising orientational transition to parallel stripes with respect to the borders. We demonstrate this effect in terms of the Brusselator model and generic amplitude equations.

  6. Domain decomposition for the SPN solver MINOS

    SciTech Connect

    Jamelot, Erell; Baudron, Anne-Marie; Lautard, Jean-Jacques

    2012-07-01

    In this article we present a domain decomposition method for the mixed SPN equations, discretized with Raviart-Thomas-Nedelec finite elements. This domain decomposition is based on the iterative Schwarz algorithm with Robin interface conditions to handle communications. After having described this method, we give details on how to optimize the convergence. Finally, we give some numerical results computed in a realistic 3D domain. The computations are done with the MINOS solver of the APOLLO3 (R) code. (authors)

  7. Miniature terahertz time-domain spectrometry

    NASA Astrophysics Data System (ADS)

    Schulkin, Brian

    This thesis focuses on the design, development and evaluation of novel concepts which enable the miniaturization of terahertz (THz) time-domain spectrometry. Portable THz spectrometry is applied to research and industrial domains for immediate, short and long term applications in nondestructive evaluation, homeland security, and biomedicine respectively. Due to the previous limitation of THz devices for public uses, in particular, the lack of access to a THz spectrometer, applications of THz science and technology have only recently expanded beyond the laboratory. There is an urgent need for compact, even handheld THz time-domain spectrometry (THz-TDS) platforms which can carry out proven-to-be-useful applications developed and tested in laboratory conditions. There are three major challenges restricting THz-TDS to laboratories. Atmospheric absorption severely limits the propagation distance of the THz beam and confines systems to low-moisture environments. The sample's surface roughness, grain size and geometry severely limit the bandwidth of the measurement. Physical size and weight of THz systems are generally limited by large laser sources and optomechanics. The sensitivity and selectivity of THz-TDS systems are the two most significant parameters used to describe the quality of the system. Sensitivity is directly related to the Signal-to-Noise Ratio (SNR) and dynamic range, which may be improved by either lowering the noise floor or increasing the THz signal. On the other hand, selectivity is far more complex as it is related to the sensitivity, sample preparation, baseline correction, and selection method. Sensitivity is gauged using industrial statistical methods, such as Gauge Repeatability and Reproducibility (GR&R), and can transform a not-so-useful SNR value to an extremely useful measure of the minimum detectable amount of a certain material. It is shown that the GR&R value is inversely proportional to the square root of the number of averaged waveforms

  8. Transform domain steganography with blind source separation

    NASA Astrophysics Data System (ADS)

    Jouny, Ismail

    2015-05-01

    This paper applies blind source separation or independent component analysis for images that may contain mixtures of text, audio, or other images for steganography purposes. The paper focuses on separating mixtures in the transform domain such as Fourier domain or the Wavelet domain. The study addresses the effectiveness of steganography when using linear mixtures of multimedia components and the ability of standard blind sources separation techniques to discern hidden multimedia messages. Mixing in the space, frequency, and wavelet (scale) domains is compared. Effectiveness is measured using mean square error rate between original and recovered images.

  9. Formin homology 2 domains occur in multiple contexts in angiosperms

    PubMed Central

    Cvrčková, Fatima; Novotný, Marian; Pícková, Denisa; Žárský, Viktor

    2004-01-01

    Background Involvement of conservative molecular modules and cellular mechanisms in the widely diversified processes of eukaryotic cell morphogenesis leads to the intriguing question: how do similar proteins contribute to dissimilar morphogenetic outputs. Formins (FH2 proteins) play a central part in the control of actin organization and dynamics, providing a good example of evolutionarily versatile use of a conserved protein domain in the context of a variety of lineage-specific structural and signalling interactions. Results In order to identify possible plant-specific sequence features within the FH2 protein family, we performed a detailed analysis of angiosperm formin-related sequences available in public databases, with particular focus on the complete Arabidopsis genome and the nearly finished rice genome sequence. This has led to revision of the current annotation of half of the 22 Arabidopsis formin-related genes. Comparative analysis of the two plant genomes revealed a good conservation of the previously described two subfamilies of plant formins (Class I and Class II), as well as several subfamilies within them that appear to predate the separation of monocot and dicot plants. Moreover, a number of plant Class II formins share an additional conserved domain, related to the protein phosphatase/tensin/auxilin fold. However, considerable inter-species variability sets limits to generalization of any functional conclusions reached on a single species such as Arabidopsis. Conclusions The plant-specific domain context of the conserved FH2 domain, as well as plant-specific features of the domain itself, may reflect distinct functional requirements in plant cells. The variability of formin structures found in plants far exceeds that known from both fungi and metazoans, suggesting a possible contribution of FH2 proteins in the evolution of the plant type of multicellularity. PMID:15256004

  10. Regularized Laplace-Fourier-Domain Full Waveform Inversion Using a Weighted l 2 Objective Function

    NASA Astrophysics Data System (ADS)

    Jun, Hyunggu; Kwon, Jungmin; Shin, Changsoo; Zhou, Hongbo; Cogan, Mike

    2016-09-01

    Full waveform inversion (FWI) can be applied to obtain an accurate velocity model that contains important geophysical and geological information. FWI suffers from the local minimum problem when the starting model is not sufficiently close to the true model. Therefore, an accurate macroscale velocity model is essential for successful FWI, and Laplace-Fourier-domain FWI is appropriate for obtaining such a velocity model. However, conventional Laplace-Fourier-domain FWI remains an ill-posed and ill-conditioned problem, meaning that small errors in the data can result in large differences in the inverted model. This approach also suffers from certain limitations related to the logarithmic objective function. To overcome the limitations of conventional Laplace-Fourier-domain FWI, we introduce a weighted l 2 objective function, instead of the logarithmic objective function, as the data-domain objective function, and we also introduce two different model-domain regularizations: first-order Tikhonov regularization and prior model regularization. The weighting matrix for the data-domain objective function is constructed to suitably enhance the far-offset information. Tikhonov regularization smoothes the gradient, and prior model regularization allows reliable prior information to be taken into account. Two hyperparameters are obtained through trial and error and used to control the trade-off and achieve an appropriate balance between the data-domain and model-domain gradients. The application of the proposed regularizations facilitates finding a unique solution via FWI, and the weighted l 2 objective function ensures a more reasonable residual, thereby improving the stability of the gradient calculation. Numerical tests performed using the Marmousi synthetic dataset show that the use of the weighted l 2 objective function and the model-domain regularizations significantly improves the Laplace-Fourier-domain FWI. Because the Laplace-Fourier-domain FWI is improved, the

  11. Floret-shaped solid domains on giant fluid lipid vesicles induced by pH.

    PubMed

    Bandekar, Amey; Sofou, Stavroula

    2012-03-01

    Lateral lipid phase separation of titratable PS or PA lipids and their assembly in domains induced by changes in pH are significant in liposome-based drug delivery: environmentally responsive lipid heterogeneities can be tuned to alter collective membrane properties such as permeability (altering drug release) and surface topography (altering drug carrier reactivity) impacting, therefore, the therapeutic outcomes. At the micrometer scale fluorescence microscopy on giant unilamellar fluid vesicles (GUVs) shows that lowering pH (from 7.0 to 5.0) promotes condensation of titratable PS or PA lipids into beautiful floret-shaped domains in which lipids are tightly packed via hydrogen-bonding and van der Waals interactions. The order of lipid packing within domains increases radially toward the domain center. Lowering pH enhances the lipid packing order, and at pH 5.0 domains appear to be entirely in the solid (gel) phase. Domains phenomenologically comprise a circular "core" cap beyond which interfacial instabilities emerge resembling leaf-like stripes. At pH 5.0 stripes are of almost vanishing Gaussian curvature independent of GUVs' preparation path and in agreement with a general condensation mechanism. Increasing incompressibility of domains is strongly correlated with a larger number of thinner stripes per domain and increasing relative rigidity of domains with smaller core cap areas. Line tension drives domain ripening; however, the final domain shape is a result of enhanced incompressibility and rigidity maximized by domain coupling across the bilayer. Introduction of a transmembrane osmotic gradient (hyperosmotic on the outer lipid leaflet) allows the domain condensation process to reach its maximum extent which, however, is limited by the minimal expansivity of the continuous fluid membrane.

  12. Bioconvection in spatially extended domains

    NASA Astrophysics Data System (ADS)

    Karimi, A.; Paul, M. R.

    2013-05-01

    We numerically explore gyrotactic bioconvection in large spatially extended domains of finite depth using parameter values from available experiments with the unicellular alga Chlamydomonas nivalis. We numerically integrate the three-dimensional, time-dependent continuum model of Pedley [J. Fluid Mech.10.1017/S0022112088002393 195, 223 (1988)] using a high-order, parallel, spectral-element approach. We explore the long-time nonlinear patterns and dynamics found for layers with an aspect ratio of 10 over a range of Rayleigh numbers. Our results yield the pattern wavelength and pattern dynamics which we compare with available theory and experimental measurement. There is good agreement for the pattern wavelength at short times between numerics, experiment, and a linear stability analysis. At long times we find that the general sequence of patterns given by the nonlinear evolution of the governing equations correspond qualitatively to what has been described experimentally. However, at long times the patterns in numerics grow to larger wavelengths, in contrast to what is observed in experiment where the wavelength is found to decrease with time.

  13. Optical coherence domain reflectometry guidewire

    DOEpatents

    Colston, Billy W.; Everett, Matthew; Da Silva, Luiz B.; Matthews, Dennis

    2001-01-01

    A guidewire with optical sensing capabilities is based on a multiplexed optical coherence domain reflectometer (OCDR), which allows it to sense location, thickness, and structure of the arterial walls or other intra-cavity regions as it travels through the body during minimally invasive medical procedures. This information will be used both to direct the guidewire through the body by detecting vascular junctions and to evaluate the nearby tissue. The guidewire contains multiple optical fibers which couple light from the proximal to distal end. Light from the fibers at the distal end of the guidewire is directed onto interior cavity walls via small diameter optics such as gradient index lenses and mirrored corner cubes. Both forward viewing and side viewing fibers can be included. The light reflected or scattered from the cavity walls is then collected by the fibers, which are multiplexed at the proximal end to the sample arm of an optical low coherence reflectometer. The guidewire can also be used in nonmedical applications.

  14. Characterization of Two Dinoflagellate Cold Shock Domain Proteins

    PubMed Central

    Beauchemin, Mathieu; Roy, Sougata; Pelletier, Sarah; Averback, Alexandra; Lanthier, Frederic

    2016-01-01

    ABSTRACT Roughly two-thirds of the proteins annotated as transcription factors in dinoflagellate transcriptomes are cold shock domain-containing proteins (CSPs), an uncommon condition in eukaryotic organisms. However, no functional analysis has ever been reported for a dinoflagellate CSP, and so it is not known if they do in fact act as transcription factors. We describe here some of the properties of two CSPs from the dinoflagellate Lingulodinium polyedrum, LpCSP1 and LpCSP2, which contain a glycine-rich C-terminal domain and an N-terminal cold shock domain phylogenetically related to those in bacteria. However, neither of the two LpCSPs act like the bacterial CSP, since they do not functionally complement the Escherichia coli quadruple cold shock domain protein mutant BX04, and cold shock does not induce LpCSP1 and LpCSP2 to detectable levels, based on two-dimensional gel electrophoresis. Both CSPs bind to RNA and single-stranded DNA in a nonspecific manner in electrophoretic mobility shift assays, and both proteins also bind double-stranded DNA nonspecifically, albeit more weakly. These CSPs are thus unlikely to act alone as sequence-specific transcription factors. IMPORTANCE Dinoflagellate transcriptomes contain cold shock domain proteins as the major component of the proteins annotated as transcription factors. We show here that the major family of cold shock domain proteins in the dinoflagellate Lingulodinium do not bind specific sequences, suggesting that transcriptional control is not a predominant mechanism for regulating gene expression in this group of protists. PMID:27303711

  15. Chasing probabilities - Signaling negative and positive prediction errors across domains.

    PubMed

    Meder, David; Madsen, Kristoffer H; Hulme, Oliver; Siebner, Hartwig R

    2016-07-01

    Adaptive actions build on internal probabilistic models of possible outcomes that are tuned according to the errors of their predictions when experiencing an actual outcome. Prediction errors (PEs) inform choice behavior across a diversity of outcome domains and dimensions, yet neuroimaging studies have so far only investigated such signals in singular experimental contexts. It is thus unclear whether the neuroanatomical distribution of PE encoding reported previously pertains to computational features that are invariant with respect to outcome valence, sensory domain, or some combination of the two. We acquired functional MRI data while volunteers performed four probabilistic reversal learning tasks which differed in terms of outcome valence (reward-seeking versus punishment-avoidance) and domain (abstract symbols versus facial expressions) of outcomes. We found that ventral striatum and frontopolar cortex coded increasingly positive PEs, whereas dorsal anterior cingulate cortex (dACC) traced increasingly negative PEs, irrespectively of the outcome dimension. Individual reversal behavior was unaffected by context manipulations and was predicted by activity in dACC and right inferior frontal gyrus (IFG). The stronger the response to negative PEs in these areas, the lower was the tendency to reverse choice behavior in response to negative events, suggesting that these regions enforce a rule-based strategy across outcome dimensions. Outcome valence influenced PE-related activity in left amygdala, IFG, and dorsomedial prefrontal cortex, where activity selectively scaled with increasingly positive PEs in the reward-seeking but not punishment-avoidance context, irrespective of sensory domain. Left amygdala displayed an additional influence of sensory domain. In the context of avoiding punishment, amygdala activity increased with increasingly negative PEs, but only for facial stimuli, indicating an integration of outcome valence and sensory domain during probabilistic

  16. Sequence and structural analysis of BTB domain proteins

    PubMed Central

    Stogios, Peter J; Downs, Gregory S; Jauhal, Jimmy JS; Nandra, Sukhjeen K; Privé, Gilbert G

    2005-01-01

    Background The BTB domain (also known as the POZ domain) is a versatile protein-protein interaction motif that participates in a wide range of cellular functions, including transcriptional regulation, cytoskeleton dynamics, ion channel assembly and gating, and targeting proteins for ubiquitination. Several BTB domain structures have been experimentally determined, revealing a highly conserved core structure. Results We surveyed the protein architecture, genomic distribution and sequence conservation of BTB domain proteins in 17 fully sequenced eukaryotes. The BTB domain is typically found as a single copy in proteins that contain only one or two other types of domain, and this defines the BTB-zinc finger (BTB-ZF), BTB-BACK-kelch (BBK), voltage-gated potassium channel T1 (T1-Kv), MATH-BTB, BTB-NPH3 and BTB-BACK-PHR (BBP) families of proteins, among others. In contrast, the Skp1 and ElonginC proteins consist almost exclusively of the core BTB fold. There are numerous lineage-specific expansions of BTB proteins, as seen by the relatively large number of BTB-ZF and BBK proteins in vertebrates, MATH-BTB proteins in Caenorhabditis elegans, and BTB-NPH3 proteins in Arabidopsis thaliana. Using the structural homology between Skp1 and the PLZF BTB homodimer, we present a model of a BTB-Cul3 SCF-like E3 ubiquitin ligase complex that shows that the BTB dimer or the T1 tetramer is compatible in this complex. Conclusion Despite widely divergent sequences, the BTB fold is structurally well conserved. The fold has adapted to several different modes of self-association and interactions with non-BTB proteins. PMID:16207353

  17. Characterization of Two Dinoflagellate Cold Shock Domain Proteins.

    PubMed

    Beauchemin, Mathieu; Roy, Sougata; Pelletier, Sarah; Averback, Alexandra; Lanthier, Frederic; Morse, David

    2016-01-01

    Roughly two-thirds of the proteins annotated as transcription factors in dinoflagellate transcriptomes are cold shock domain-containing proteins (CSPs), an uncommon condition in eukaryotic organisms. However, no functional analysis has ever been reported for a dinoflagellate CSP, and so it is not known if they do in fact act as transcription factors. We describe here some of the properties of two CSPs from the dinoflagellate Lingulodinium polyedrum, LpCSP1 and LpCSP2, which contain a glycine-rich C-terminal domain and an N-terminal cold shock domain phylogenetically related to those in bacteria. However, neither of the two LpCSPs act like the bacterial CSP, since they do not functionally complement the Escherichia coli quadruple cold shock domain protein mutant BX04, and cold shock does not induce LpCSP1 and LpCSP2 to detectable levels, based on two-dimensional gel electrophoresis. Both CSPs bind to RNA and single-stranded DNA in a nonspecific manner in electrophoretic mobility shift assays, and both proteins also bind double-stranded DNA nonspecifically, albeit more weakly. These CSPs are thus unlikely to act alone as sequence-specific transcription factors. IMPORTANCE Dinoflagellate transcriptomes contain cold shock domain proteins as the major component of the proteins annotated as transcription factors. We show here that the major family of cold shock domain proteins in the dinoflagellate Lingulodinium do not bind specific sequences, suggesting that transcriptional control is not a predominant mechanism for regulating gene expression in this group of protists.

  18. Characterization of Two Dinoflagellate Cold Shock Domain Proteins.

    PubMed

    Beauchemin, Mathieu; Roy, Sougata; Pelletier, Sarah; Averback, Alexandra; Lanthier, Frederic; Morse, David

    2016-01-01

    Roughly two-thirds of the proteins annotated as transcription factors in dinoflagellate transcriptomes are cold shock domain-containing proteins (CSPs), an uncommon condition in eukaryotic organisms. However, no functional analysis has ever been reported for a dinoflagellate CSP, and so it is not known if they do in fact act as transcription factors. We describe here some of the properties of two CSPs from the dinoflagellate Lingulodinium polyedrum, LpCSP1 and LpCSP2, which contain a glycine-rich C-terminal domain and an N-terminal cold shock domain phylogenetically related to those in bacteria. However, neither of the two LpCSPs act like the bacterial CSP, since they do not functionally complement the Escherichia coli quadruple cold shock domain protein mutant BX04, and cold shock does not induce LpCSP1 and LpCSP2 to detectable levels, based on two-dimensional gel electrophoresis. Both CSPs bind to RNA and single-stranded DNA in a nonspecific manner in electrophoretic mobility shift assays, and both proteins also bind double-stranded DNA nonspecifically, albeit more weakly. These CSPs are thus unlikely to act alone as sequence-specific transcription factors. IMPORTANCE Dinoflagellate transcriptomes contain cold shock domain proteins as the major component of the proteins annotated as transcription factors. We show here that the major family of cold shock domain proteins in the dinoflagellate Lingulodinium do not bind specific sequences, suggesting that transcriptional control is not a predominant mechanism for regulating gene expression in this group of protists. PMID:27303711

  19. Time Domain Challenges for Exoplanets

    NASA Astrophysics Data System (ADS)

    Dawson, Rebekah Ilene

    2016-01-01

    Over the past couple decades, thousands of extra-solar planets have been discovered orbiting other stars. Most have been detected and characterized using transit and/or radial velocity time series, and these techniques have undergone huge improvements in instrumental precision. However, the improvements in precision have brought to light new statistical challenges in detecting and characterizing exoplanets in the presence of correlated noise caused by stellar activity (transits and radial velocities) and gaps in the time sampling (radial velocities). These challenges have afflicted many of the most interesting exoplanets, from Earth-like planets to planetary systems whose orbital dynamics place important constraints on how planetary systems form and evolve. In the first part of the talk, I will focus on the problem of correlated noise for characterizing transiting exoplanets using transit timing variations. I will present a comparison of several techniques using wavelets, Gaussian processes, and polynomial splines to account for correlated noise in the likelihood function when inferring planetary parameters. I will also present results on the characteristics of correlated noise that cause planets to be missed by the Kepler and homegrown pipelines despite high nominal signal-to-noise. In the second part of the talk, I will focus on the problem of aliasing caused by gaps in the radial-velocity time series on yearly, daily, and monthly timescales. I will present results on identifying aliases in the Fourier domain by taking advantage of aliasing on multiple timescales and discuss the interplay between aliasing and stellar activity for several habitable-zone "planets" that have recently been called into question as possible spurious signals caused by activity. As we push toward detecting and characterizing lower mass planets, it is essential that astrostatistical advances keep pace with advances in instrumentation.

  20. The Domain of Developmental Psychopathology.

    ERIC Educational Resources Information Center

    Sroufe, L. Alan; Rutter, Michael

    1984-01-01

    Describes how developmental psychopathology differs from related disciplines, including abnormal psychology, psychiatry, clinical child psychology, and developmental psychology. Points out propositions underlying a developmental perspective and discusses implications for research in developmental psychopathology. (Author/RH)

  1. Are Epistemological Beliefs Similar across Domains?

    ERIC Educational Resources Information Center

    Schommer, Marlene; Walker, Kiersten

    1995-01-01

    College students in 2 studies (n=95 and 114) completed an epistemological questionnaire with a specific domain in mind (social sciences or mathematics), read a passage, answered a passage test, and completed another epistemological questionnaire. Results supported the idea that individuals' epistemological beliefs tended to be domain independent.…

  2. Domains of the Florida Performance Measurement System.

    ERIC Educational Resources Information Center

    Florida State Dept. of Education, Tallahassee.

    This monograph sets forth in detail the concepts included in the five domains of teaching as identified by the Florida Coalition for the Development of a Performance Evaluation System. The first domain, planning, includes the concepts: (1) content coverage; (2) utilization of instructional materials; (3) activity structure; (4) goal focusing; and…

  3. The Domain Specificity of Academic Emotional Experiences

    ERIC Educational Resources Information Center

    Goetz, Thomas; Frenzel, Anne C.; Pekrun, Reinhard; Hall, Nathan C.

    2006-01-01

    The authors analyzed the domain specificity of emotions and focused on experiences of enjoyment, anxiety, and boredom in the domains of mathematics, Latin, German, and English. On the basis of assumptions in R. Pekrun's (2000; in press) control-value theory and findings of pilot studies, the authors hypothesized the existence of a largely…

  4. Student Behavior and Attitudes: The Affective Domain.

    ERIC Educational Resources Information Center

    Archer, Patricia F.

    This two-part learning module, designed to acquaint teachers with the affective domain of Bloom's Taxonomy, provides a methodology for identifying the attitudinal and motivational problems of non-traditional students. Part I discusses the cognitive, affective, and psychomotor domains considered in Bloom's Taxonomy and presents possible learning…

  5. Multiple hypothesis tracking for the cyber domain

    NASA Astrophysics Data System (ADS)

    Schwoegler, Stefan; Blackman, Sam; Holsopple, Jared; Hirsch, Michael J.

    2011-09-01

    This paper discusses how methods used for conventional multiple hypothesis tracking (MHT) can be extended to domain-agnostic tracking of entities from non-kinematic constraints such as those imposed by cyber attacks in a potentially dense false alarm background. MHT is widely recognized as the premier method to avoid corrupting tracks with spurious data in the kinematic domain but it has not been extensively applied to other problem domains. The traditional approach is to tightly couple track maintenance (prediction, gating, filtering, probabilistic pruning, and target confirmation) with hypothesis management (clustering, incompatibility maintenance, hypothesis formation, and Nassociation pruning). However, by separating the domain specific track maintenance portion from the domain agnostic hypothesis management piece, we can begin to apply the wealth of knowledge gained from ground and air tracking solutions to the cyber (and other) domains. These realizations led to the creation of Raytheon's Multiple Hypothesis Extensible Tracking Architecture (MHETA). In this paper, we showcase MHETA for the cyber domain, plugging in a well established method, CUBRC's INFormation Engine for Real-time Decision making, (INFERD), for the association portion of the MHT. The result is a CyberMHT. We demonstrate the power of MHETA-INFERD using simulated data. Using metrics from both the tracking and cyber domains, we show that while no tracker is perfect, by applying MHETA-INFERD, advanced nonkinematic tracks can be captured in an automated way, perform better than non-MHT approaches, and decrease analyst response time to cyber threats.

  6. 22 CFR 120.11 - Public domain.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... Public domain. (a) Public domain means information which is published and which is generally accessible... published information; (3) Through second class mailing privileges granted by the U.S. Government; (4) At libraries open to the public or from which the public can obtain documents; (5) Through patents available...

  7. 22 CFR 120.11 - Public domain.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... Public domain. (a) Public domain means information which is published and which is generally accessible... published information; (3) Through second class mailing privileges granted by the U.S. Government; (4) At libraries open to the public or from which the public can obtain documents; (5) Through patents available...

  8. 22 CFR 120.11 - Public domain.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... Public domain. (a) Public domain means information which is published and which is generally accessible... published information; (3) Through second class mailing privileges granted by the U.S. Government; (4) At libraries open to the public or from which the public can obtain documents; (5) Through patents available...

  9. Domain imaging on multiferroic BiFeO{sub 3}(001) by linear and circular dichroism in threshold photoemission

    SciTech Connect

    Sander, Anke; Christl, Maik; Chiang, Cheng-Tien; Alexe, Marin; Widdra, Wolf

    2015-12-14

    We demonstrate ferroelectric domain imaging at BiFeO{sub 3}(001) single crystal surfaces with laser-based threshold photoemission electron microscopy (PEEM). Work function differences and linear dichroism allow for the identification of the eight independent ferroelectric domain configurations in the PEEM images. There, the determined domain structure is consistent with piezoresponse force microscopy of the sample surface and can also be related to the circular dichroic PEEM images. Our results provide a method for efficient mapping of complex ferroelectric domains with laser-excited PEEM and may allow lab-based time-resolved studies of the domain dynamics in the future.

  10. Thermodynamics of heme-induced conformational changes in hemopexin: role of domain-domain interactions.

    PubMed Central

    Wu, M. L.; Morgan, W. T.

    1995-01-01

    Hemopexin is a serum glycoprotein that binds heme with high affinity and delivers heme to the liver cells via receptor-mediated endocytosis. A hinge region connects the two non-disulfide-linked domains of hemopexin, a 35-kDa N-terminal domain (domain I) that binds heme, and a 25-kDa C-terminal domain (domain II). Although domain II does not bind heme, it assumes one structural state in apo-hemopexin and another in heme-hemopexin, and this change is important in facilitating the association of heme-hemopexin with its receptor. In order to elucidate the structure and function of hemopexin, it is important to understand how structural information is transmitted to domain II when domain I binds heme. Here we report a study of the protein-protein interactions between domain I and domain II using analytical ultracentrifugation and isothermal titration calorimetry. Sedimentation equilibrium analysis showed that domain I associates with domain II both in the presence and absence of heme with Kd values of 0.8 microM and 55 microM, respectively. The interaction between heme-domain I and domain II has a calorimetric enthalpy of +11 kcal/mol, a heat capacity (delta Cp) of -720 cal/mol.K, and a calculated entropy of +65 cal/mol.K. By varying the temperature of the centrifugation equilibrium runs, a van't Hoff plot with an apparent change in enthalpy (delta H) of -3.6 kcal/mol and change in entropy (delta S) of +8.1 cal/mol.K for the association of apo-domain I with domain II was obtained.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:7773173

  11. Nonequilibrium Raftlike Membrane Domains under Continuous Recycling

    NASA Astrophysics Data System (ADS)

    Turner, Matthew S.; Sens, Pierre; Socci, Nicholas D.

    2005-10-01

    We present a model for the kinetics of spontaneous membrane domain (raft) assembly that includes the effect of membrane recycling ubiquitous in living cells. We show that domains can have a broad power-law distribution with an average radius that scales with the 1/4 power of the domain lifetime when the line tension at the domain edges is large. For biologically reasonable recycling and diffusion rates, the average domain radius is in the tens of nm range, consistent with observations. This represents one possible link between signaling (involving rafts) and traffic (recycling) in cells. Finally, we present evidence that suggests that the average raft size may be the same for all scale-free recycling schemes.

  12. Investigation of multilayer magnetic domain lattice file

    NASA Technical Reports Server (NTRS)

    Torok, E. J.; Kamin, M.; Tolman, C. H.

    1980-01-01

    The feasibility of the self structured multilayered bubble domain memory as a mass memory medium for satellite applications is examined. Theoretical considerations of multilayer bubble supporting materials are presented, in addition to the experimental evaluation of current accessed circuitry for various memory functions. The design, fabrication, and test of four device designs is described, and a recommended memory storage area configuration is presented. Memory functions which were demonstrated include the current accessed propagation of bubble domains and stripe domains, pinning of stripe domain ends, generation of single and double bubbles, generation of arrays of coexisting strip and bubble domains in a single garnet layer, and demonstration of different values of the strip out field for single and double bubbles indicating adequate margins for data detection. All functions necessary to develop a multilayer self structured bubble memory device were demonstrated in individual experiments.

  13. The SH2 domain interaction landscape

    PubMed Central

    Tinti, Michele; Kiemer, Lars; Costa, Stefano; Miller, Martin; Sacco, Francesca; Olsen, Jesper V.; Carducci, Martina; Paoluzi, Serena; Langone, Francesca; Workman, Christopher T.; Blom, Nikolaj; Machida, Kazuya; Thompson, Christopher M.; Schutkowski, Mike; Brunak, Søren; Mann, Matthias; Mayer, Bruce J.; Castagnoli, Luisa; Cesareni, Gianni

    2014-01-01

    Summary Members of the SH2 domain family modulate signal transduction by binding to short peptides containing phosphorylated tyrosines. Each domain displays a distinct preference for the sequence context of the phosphorylated residue. We have developed a new high-density peptide chip technology that allows probing the affinity of most SH2 domains for a large fraction of the entire complement of tyrosine phosphopeptides in the human proteome. Using this technique we have experimentally identified thousands of putative SH2- peptide interactions for more than 70 different SH2 domains. By integrating this rich data set with orthogonal context-specific information, we have assembled an SH2 mediated probabilistic interaction network, which we make available as a community resource in the PepSpotDB database. A new predicted dynamic interaction between the SH2 domains of the tyrosine phosphatase SHP2 and the phosphorylated tyrosine in the ERK activation loop was validated by experiments in living cells. PMID:23545499

  14. The SH2 domain interaction landscape.

    PubMed

    Tinti, Michele; Kiemer, Lars; Costa, Stefano; Miller, Martin L; Sacco, Francesca; Olsen, Jesper V; Carducci, Martina; Paoluzi, Serena; Langone, Francesca; Workman, Christopher T; Blom, Nikolaj; Machida, Kazuya; Thompson, Christopher M; Schutkowski, Mike; Brunak, Søren; Mann, Matthias; Mayer, Bruce J; Castagnoli, Luisa; Cesareni, Gianni

    2013-04-25

    Members of the SH2 domain family modulate signal transduction by binding to short peptides containing phosphorylated tyrosines. Each domain displays a distinct preference for the sequence context of the phosphorylated residue. We have developed a high-density peptide chip technology that allows for probing of the affinity of most SH2 domains for a large fraction of the entire complement of tyrosine phosphopeptides in the human proteome. Using this technique, we have experimentally identified thousands of putative SH2-peptide interactions for more than 70 different SH2 domains. By integrating this rich data set with orthogonal context-specific information, we have assembled an SH2-mediated probabilistic interaction network, which we make available as a community resource in the PepspotDB database. A predicted dynamic interaction between the SH2 domains of the tyrosine phosphatase SHP2 and the phosphorylated tyrosine in the extracellular signal-regulated kinase activation loop was validated by experiments in living cells.

  15. Using ontology for domain specific information retrieval

    NASA Astrophysics Data System (ADS)

    Shashirekha, H. L.; Murali, S.; Nagabhushan, P.

    2010-02-01

    This paper presents a system for retrieving information from a domain specific document collection made up of data rich unnatural language text documents. Instead of conventional keyword based retrieval, our system makes use of domain ontology to retrieve the information from a collection of documents. The system addresses the problem of representing unnatural language text documents and constructing a classifier model that helps in the efficient retrieval of relevant information. Query to this system may be either the key phrases in terms of concepts or a domain specific unnatural language text document. The classifier used in this system can also be used to assign multiple labels to the previously unseen text document belonging to the same domain. An empirical evaluation of the system is conducted on the domain of text documents describing the classified matrimonial advertisements to determine its performance.

  16. A domain dictionary of trimeric autotransporter adhesins.

    PubMed

    Bassler, Jens; Hernandez Alvarez, Birte; Hartmann, Marcus D; Lupas, Andrei N

    2015-02-01

    Trimeric autotransporter adhesins (TAAs) are modular, highly repetitive outer membrane proteins that mediate adhesion to external surfaces in many Gram-negative bacteria. In recent years, several TAAs have been investigated in considerable detail, also at the structural level. However, in their vast majority, putative TAAs in prokaryotic genomes remain poorly annotated, due to their sequence diversity and changeable domain architecture. In order to achieve an automated annotation of these proteins that is both detailed and accurate we have taken a domain dictionary approach, in which we identify recurrent domains by sequence comparisons, produce bioinformatic descriptors for each domain type, and connect these to structural information where available. We implemented this approach in a web-based platform, daTAA, in 2008 and demonstrated its applicability by reconstructing the complete fiber structure of a TAA conserved in enterobacteria. Here we review current knowledge on the domain structure of TAAs.

  17. Untangling spider silk evolution with spidroin terminal domains

    PubMed Central

    2010-01-01

    Background Spidroins are a unique family of large, structural proteins that make up the bulk of spider silk fibers. Due to the highly variable nature of their repetitive sequences, spidroin evolutionary relationships have principally been determined from their non-repetitive carboxy (C)-terminal domains, though they offer limited character data. The few known spidroin amino (N)-terminal domains have been difficult to obtain, but potentially contain critical phylogenetic information for reconstructing the diversification of spider silks. Here we used silk gland expression data (ESTs) from highly divergent species to evaluate the functional significance and phylogenetic utility of spidroin N-terminal domains. Results We report 11 additional spidroin N-termini found by sequencing ~1,900 silk gland cDNAs from nine spider species that shared a common ancestor > 240 million years ago. In contrast to their hyper-variable repetitive regions, spidroin N-terminal domains have retained striking similarities in sequence identity, predicted secondary structure, and hydrophobicity. Through separate and combined phylogenetic analyses of N-terminal domains and their corresponding C-termini, we find that combined analysis produces the most resolved trees and that N-termini contribute more support and less conflict than the C-termini. These analyses show that paralogs largely group by silk gland type, except for the major ampullate spidroins. Moreover, spidroin structural motifs associated with superior tensile strength arose early in the history of this gene family, whereas a motif conferring greater extensibility convergently evolved in two distantly related paralogs. Conclusions A non-repetitive N-terminal domain appears to be a universal attribute of spidroin proteins, likely retained from the origin of spider silk production. Since this time, spidroin N-termini have maintained several features, consistent with this domain playing a key role in silk assembly. Phylogenetic

  18. [Sex and gender: Two different scientific domains to be clarified].

    PubMed

    Fernández, Juan

    2010-05-01

    Nowadays, the word sex and its related terms (sexual differences, sexual roles and stereotypes), so common not long ago, seems to have been replaced by gender and its related terms (gender differences, gender roles and stereotypes). We can sometimes find both sex and gender sharing the same space in scientific articles, although referring to different domains. In this paper, I try to explain the need for a model that can integrate both of these complex domains of sex and gender, leading to two independent, although complementary, disciplines: Sexology and Genderology. In both cases, I start from a functional standpoint, which will give meaning to both disciplines' specificities, as it is meant to link contributions from different fields of knowledge. This approach can have consequences for research, education, the experience of women, men, and ambiguous individuals, and therapy.

  19. Fourier Phase Domain Steganography: Phase Bin Encoding Via Interpolation

    NASA Astrophysics Data System (ADS)

    Rivas, Edward

    2007-04-01

    In recent years there has been an increased interest in audio steganography and watermarking. This is due primarily to two reasons. First, an acute need to improve our national security capabilities in light of terrorist and criminal activity has driven new ideas and experimentation. Secondly, the explosive proliferation of digital media has forced the music industry to rethink how they will protect their intellectual property. Various techniques have been implemented but the phase domain remains a fertile ground for improvement due to the relative robustness to many types of distortion and immunity to the Human Auditory System. A new method for embedding data in the phase domain of the Discrete Fourier Transform of an audio signal is proposed. Focus is given to robustness and low perceptibility, while maintaining a relatively high capacity rate of up to 172 bits/s.

  20. Domain-Specific Impulsivity in School-Age Children

    PubMed Central

    Tsukayama, Eli; Duckworth, Angela Lee; Kim, Betty

    2013-01-01

    Impulsivity is a salient individual difference in children with well-established predictive validity for life outcomes. The current investigation proposes that impulsive behaviors vary systematically by domain. In a series of studies with ethnically and socioeconomically diverse samples of middle school students, we find that schoolwork-related and interpersonal-related impulsivity, as observed by teachers, parents, and the students themselves, are distinct, moderately correlated behavioral tendencies. Each demonstrates differentiated relationships with dimensions of childhood temperament, Big Five personality factors, and outcomes, such as sociometric popularity, report card grades, and classroom conduct. Implications for theoretical conceptions of impulsivity as well as for practical applications (e.g., domain-specific interventions) are discussed. PMID:24118714